diff --git a/release/3Dmol-min.js b/release/3Dmol-min.js
index 39b97abd7..fc70f88aa 100644
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-this.y=a.elements[13];this.z=a.elements[14];return this},setEulerFromRotationMatrix:function(a,b){var c=a.elements,d=c[0],e=c[4],k=c[8],f=c[5],l=c[9],h=c[6],c=c[10];void 0===b||"XYZ"===b?(this.y=Math.asin($3Dmol.Math.clamp(k,-1,1)),.99999>Math.abs(k)?(this.x=Math.atan2(-l,c),this.z=Math.atan2(-e,d)):(this.x=Math.atan2(h,f),this.z=0)):console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: "+b);return this},clone:function(){return new $3Dmol.Vector3(this.x,this.y,this.z)}};
-$3Dmol.Matrix3=function(a,b,c,d,e,k,f,l,h){this.elements=new Float32Array(9);this.set(void 0!==a?a:1,b||0,c||0,d||0,void 0!==e?e:1,k||0,f||0,l||0,void 0!==h?h:1)};
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-d=this.elements;d[0]=c[10]*c[5]-c[6]*c[9];d[1]=-c[10]*c[1]+c[2]*c[9];d[2]=c[6]*c[1]-c[2]*c[5];d[3]=-c[10]*c[4]+c[6]*c[8];d[4]=c[10]*c[0]-c[2]*c[8];d[5]=-c[6]*c[0]+c[2]*c[4];d[6]=c[9]*c[4]-c[5]*c[8];d[7]=-c[9]*c[0]+c[1]*c[8];d[8]=c[5]*c[0]-c[1]*c[4];c=c[0]*d[0]+c[1]*d[3]+c[2]*d[6];if(0===c){if(b)throw Error("Matrix3.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix3.getInverse(): can't invert matrix, determinant is 0");this.identity();return this}this.multiplyScalar(1/c);return this},
-transpose:function(){var a,b=this.elements;a=b[1];b[1]=b[3];b[3]=a;a=b[2];b[2]=b[6];b[6]=a;a=b[5];b[5]=b[7];b[7]=a;return this},clone:function(){var a=this.elements;return new $3Dmol.Matrix3(a[0],a[3],a[6],a[1],a[4],a[7],a[2],a[5],a[8])}};
-$3Dmol.Matrix4=function(a,b,c,d,e,k,f,l,h,m,q,z,w,v,x,r){var n=this.elements=new Float32Array(16);n[0]=void 0!==a?a:1;n[4]=b||0;n[8]=c||0;n[12]=d||0;n[1]=e||0;n[5]=void 0!==k?k:1;n[9]=f||0;n[13]=l||0;n[2]=h||0;n[6]=m||0;n[10]=void 0!==q?q:1;n[14]=z||0;n[3]=w||0;n[7]=v||0;n[11]=x||0;n[15]=void 0!==r?r:1};
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-this.elements,d=a.x,e=a.y,k=a.z,f=Math.cos(d),d=Math.sin(d),l=Math.cos(e),e=Math.sin(e),h=Math.cos(k),k=Math.sin(k);if(void 0===b||"XYZ"===b){var m=f*h,q=f*k,z=d*h,w=d*k;c[0]=l*h;c[4]=-l*k;c[8]=e;c[1]=q+z*e;c[5]=m-w*e;c[9]=-d*l;c[2]=w-m*e;c[6]=z+q*e;c[10]=f*l}else console.error("Error with matrix4 setRotationFromEuler. Order: "+b);return this},setRotationFromQuaternion:function(a){var b=this.elements,c=a.x,d=a.y,e=a.z,k=a.w,f=c+c,l=d+d,h=e+e;a=c*f;var m=c*l,c=c*h,q=d*l,d=d*h,e=e*h,f=k*f,l=k*l,k=k*
-h;b[0]=1-(q+e);b[4]=m-k;b[8]=c+l;b[1]=m+k;b[5]=1-(a+e);b[9]=d-f;b[2]=c-l;b[6]=d+f;b[10]=1-(a+q);return this},lookAt:function(){var a=new $3Dmol.Vector3,b=new $3Dmol.Vector3,c=new $3Dmol.Vector3;return function(d,e,k){var f=this.elements;c.subVectors(d,e).normalize();0===c.length()&&(c.z=1);a.crossVectors(k,c).normalize();0===a.length()&&(c.x+=1E-4,a.crossVectors(k,c).normalize());b.crossVectors(c,a);f[0]=a.x;f[4]=b.x;f[8]=c.x;f[1]=a.y;f[5]=b.y;f[9]=c.y;f[2]=a.z;f[6]=b.z;f[10]=c.z;return this}}(),
-multiplyMatrices:function(a,b){var c=a.elements,d=b.elements,e=this.elements,k=c[0],f=c[4],l=c[8],h=c[12],m=c[1],q=c[5],z=c[9],w=c[13],v=c[2],x=c[6],r=c[10],n=c[14],t=c[3],u=c[7],y=c[11],c=c[15],F=d[0],B=d[4],C=d[8],s=d[12],p=d[1],A=d[5],E=d[9],H=d[13],G=d[2],D=d[6],I=d[10],L=d[14],M=d[3],N=d[7],J=d[11],d=d[15];e[0]=k*F+f*p+l*G+h*M;e[4]=k*B+f*A+l*D+h*N;e[8]=k*C+f*E+l*I+h*J;e[12]=k*s+f*H+l*L+h*d;e[1]=m*F+q*p+z*G+w*M;e[5]=m*B+q*A+z*D+w*N;e[9]=m*C+q*E+z*I+w*J;e[13]=m*s+q*H+z*L+w*d;e[2]=v*F+x*p+r*G+n*
-M;e[6]=v*B+x*A+r*D+n*N;e[10]=v*C+x*E+r*I+n*J;e[14]=v*s+x*H+r*L+n*d;e[3]=t*F+u*p+y*G+c*M;e[7]=t*B+u*A+y*D+c*N;e[11]=t*C+u*E+y*I+c*J;e[15]=t*s+u*H+y*L+c*d;return this},multiplyScalar:function(a){var b=this.elements;b[0]*=a;b[4]*=a;b[8]*=a;b[12]*=a;b[1]*=a;b[5]*=a;b[9]*=a;b[13]*=a;b[2]*=a;b[6]*=a;b[10]*=a;b[14]*=a;b[3]*=a;b[7]*=a;b[11]*=a;b[15]*=a;return this},transpose:function(){var a=this.elements,b;b=a[1];a[1]=a[4];a[4]=b;b=a[2];a[2]=a[8];a[8]=b;b=a[6];a[6]=a[9];a[9]=b;b=a[3];a[3]=a[12];a[12]=b;
-b=a[7];a[7]=a[13];a[13]=b;b=a[11];a[11]=a[14];a[14]=b;return this},getPosition:function(){var a=new $3Dmol.Vector3;return function(){console.warn("DEPRECATED: Matrix4's .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.");var b=this.elements;return a.set(b[12],b[13],b[14])}}(),setPosition:function(a){var b=this.elements;b[12]=a.x;b[13]=a.y;b[14]=a.z;return this},getInverse:function(a,b){var c=this.elements,d=a.elements,e=d[0],k=d[4],f=d[8],l=d[12],h=d[1],m=d[5],
-q=d[9],z=d[13],w=d[2],v=d[6],x=d[10],r=d[14],n=d[3],t=d[7],u=d[11],y=d[15];c[0]=q*r*t-z*x*t+z*v*u-m*r*u-q*v*y+m*x*y;c[4]=l*x*t-f*r*t-l*v*u+k*r*u+f*v*y-k*x*y;c[8]=f*z*t-l*q*t+l*m*u-k*z*u-f*m*y+k*q*y;c[12]=l*q*v-f*z*v-l*m*x+k*z*x+f*m*r-k*q*r;c[1]=z*x*n-q*r*n-z*w*u+h*r*u+q*w*y-h*x*y;c[5]=f*r*n-l*x*n+l*w*u-e*r*u-f*w*y+e*x*y;c[9]=l*q*n-f*z*n-l*h*u+e*z*u+f*h*y-e*q*y;c[13]=f*z*w-l*q*w+l*h*x-e*z*x-f*h*r+e*q*r;c[2]=m*r*n-z*v*n+z*w*t-h*r*t-m*w*y+h*v*y;c[6]=l*v*n-k*r*n-l*w*t+e*r*t+k*w*y-e*v*y;c[10]=k*z*n-l*
-m*n+l*h*t-e*z*t-k*h*y+e*m*y;c[14]=l*m*w-k*z*w-l*h*v+e*z*v+k*h*r-e*m*r;c[3]=q*v*n-m*x*n-q*w*t+h*x*t+m*w*u-h*v*u;c[7]=k*x*n-f*v*n+f*w*t-e*x*t-k*w*u+e*v*u;c[11]=f*m*n-k*q*n-f*h*t+e*q*t+k*h*u-e*m*u;c[15]=k*q*w-f*m*w+f*h*v-e*q*v-k*h*x+e*m*x;c=d[0]*c[0]+d[1]*c[4]+d[2]*c[8]+d[3]*c[12];if(0===c){if(b)throw Error("Matrix4.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix4.getInverse(): can't invert matrix, determinant is 0");this.identity();return this}this.multiplyScalar(1/c);return this},
-compose:function(){var a=new $3Dmol.Matrix4,b=new $3Dmol.Matrix4;return function(c,d,e){var k=this.elements;a.identity();a.setRotationFromQuaternion(d);b.makeScale(e.x,e.y,e.z);this.multiplyMatrices(a,b);k[12]=c.x;k[13]=c.y;k[14]=c.z;return this}}(),decompose:function(){var a=new $3Dmol.Vector3,b=new $3Dmol.Vector3,c=new $3Dmol.Vector3,d=new $3Dmol.Matrix4;return function(e,k,f){var l=this.elements;a.set(l[0],l[1],l[2]);b.set(l[4],l[5],l[6]);c.set(l[8],l[9],l[10]);e=e instanceof $3Dmol.Vector3?e:
-new $3Dmol.Vector3;k=k instanceof $3Dmol.Quaternion?k:new $3Dmol.Quaternion;f=f instanceof $3Dmol.Vector3?f:new $3Dmol.Vector3;f.x=a.length();f.y=b.length();f.z=c.length();e.x=l[12];e.y=l[13];e.z=l[14];d.copy(this);d.elements[0]/=f.x;d.elements[1]/=f.x;d.elements[2]/=f.x;d.elements[4]/=f.y;d.elements[5]/=f.y;d.elements[6]/=f.y;d.elements[8]/=f.z;d.elements[9]/=f.z;d.elements[10]/=f.z;k.setFromRotationMatrix(d);return[e,k,f]}}(),scale:function(a){var b=this.elements,c=a.x,d=a.y;a=a.z;b[0]*=c;b[4]*=
-d;b[8]*=a;b[1]*=c;b[5]*=d;b[9]*=a;b[2]*=c;b[6]*=d;b[10]*=a;b[3]*=c;b[7]*=d;b[11]*=a;return this},getMaxScaleOnAxis:function(){var a=this.elements;return Math.sqrt(Math.max(a[0]*a[0]+a[1]*a[1]+a[2]*a[2],Math.max(a[4]*a[4]+a[5]*a[5]+a[6]*a[6],a[8]*a[8]+a[9]*a[9]+a[10]*a[10])))},makeFrustum:function(a,b,c,d,e,k){var f=this.elements;f[0]=2*e/(b-a);f[4]=0;f[8]=(b+a)/(b-a);f[12]=0;f[1]=0;f[5]=2*e/(d-c);f[9]=(d+c)/(d-c);f[13]=0;f[2]=0;f[6]=0;f[10]=-(k+e)/(k-e);f[14]=-2*k*e/(k-e);f[3]=0;f[7]=0;f[11]=-1;f[15]=
-0;return this},makePerspective:function(a,b,c,d){a=c*Math.tan($3Dmol.Math.degToRad(.5*a));var e=-a;return this.makeFrustum(e*b,a*b,e,a,c,d)},isEqual:function(a){a=a.elements;var b=this.elements;return b[0]==a[0]&&b[4]==a[4]&&b[8]==a[8]&&b[12]==a[12]&&b[1]==a[1]&&b[5]==a[5]&&b[9]==a[9]&&b[13]==a[13]&&b[2]==a[2]&&b[6]==a[6]&&b[10]==a[10]&&b[14]==a[14]&&b[3]==a[3]&&b[7]==a[7]&&b[11]==a[11]&&b[15]==a[15]?!0:!1},clone:function(){var a=this.elements;return new $3Dmol.Matrix4(a[0],a[4],a[8],a[12],a[1],a[5],
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+d.cssProps[k]||(d.cssProps[k]=nb(l,k));h=d.cssHooks[b]||d.cssHooks[k];if(void 0!==c){if(g=typeof c,"string"===g&&(f=Ac.exec(c))&&(c=(f[1]+1)*f[2]+parseFloat(d.css(a,b)),g="number"),null!=c&&c===c&&("number"!==g||d.cssNumber[k]||(c+="px"),p.clearCloneStyle||""!==c||0!==b.indexOf("background")||(l[b]="inherit"),!(h&&"set"in h)||void 0!==(c=h.set(a,c,e))))try{l[b]=c}catch(n){}}else return h&&"get"in h&&void 0!==(f=h.get(a,!1,e))?f:l[b]}},css:function(a,b,c,e){var f,g;g=d.camelCase(b);b=d.cssProps[g]||
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+d.cssHooks.marginRight=mb(p.reliableMarginRight,function(a,b){if(b)return d.swap(a,{display:"inline-block"},F,[a,"marginRight"])});d.each({margin:"",padding:"",border:"Width"},function(a,b){d.cssHooks[a+b]={expand:function(c){var d=0,f={};for(c="string"===typeof c?c.split(" "):[c];4>d;d++)f[a+M[d]+b]=c[d]||c[d-2]||c[0];return f}};Nb.test(a)||(d.cssHooks[a+b].set=qb)});d.fn.extend({css:function(a,b){return aa(this,function(a,b,f){var g,h={},k=0;if(d.isArray(b)){f=X(a);for(g=b.length;k<g;k++)h[b[k]]=
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+"":"px")},cur:function(){var a=B.propHooks[this.prop];return a&&a.get?a.get(this):B.propHooks._default.get(this)},run:function(a){var b,c=B.propHooks[this.prop];this.pos=this.options.duration?b=d.easing[this.easing](a,this.options.duration*a,0,1,this.options.duration):b=a;this.now=(this.end-this.start)*b+this.start;this.options.step&&this.options.step.call(this.elem,this.now,this);c&&c.set?c.set(this):B.propHooks._default.set(this);return this}};B.prototype.init.prototype=B.prototype;B.propHooks=
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+h.empty.fire()})}));1===a.nodeType&&("height"in b||"width"in b)&&(c.overflow=[m.overflow,m.overflowX,m.overflowY],l=d.css(a,"display"),f="none"===l?d._data(a,"olddisplay")||pa(a.nodeName):l,"inline"===f&&"none"===d.css(a,"float")&&(p.inlineBlockNeedsLayout&&"inline"!==pa(a.nodeName)?m.zoom=1:m.display="inline-block"));c.overflow&&(m.overflow="hidden",p.shrinkWrapBlocks()||n.always(function(){m.overflow=c.overflow[0];m.overflowX=c.overflow[1];m.overflowY=c.overflow[2]}));for(e in b)if(f=b[e],Cc.exec(f)){delete b[e];
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+e||"height"===e?1:0))}],ja={"*":[function(a,b){var c=this.createTween(a,b),e=c.cur(),f=Pb.exec(b),g=f&&f[3]||(d.cssNumber[a]?"":"px"),h=(d.cssNumber[a]||"px"!==g&&+e)&&Pb.exec(d.css(c.elem,a)),k=1,l=20;if(h&&h[3]!==g){g=g||h[3];f=f||[];h=+e||1;do k=k||".5",h/=k,d.style(c.elem,a,h+g);while(k!==(k=c.cur()/e)&&1!==k&&--l)}f&&(h=c.start=+h||+e||0,c.unit=g,c.end=f[1]?h+(f[1]+1)*f[2]:+f[2]);return c}]};d.Animation=d.extend(vb,{tweener:function(a,b){d.isFunction(a)?(b=a,a=["*"]):a=a.split(" ");for(var c,
+e=0,f=a.length;e<f;e++)c=a[e],ja[c]=ja[c]||[],ja[c].unshift(b)},prefilter:function(a,b){b?ca.unshift(a):ca.push(a)}});d.speed=function(a,b,c){var e=a&&"object"===typeof a?d.extend({},a):{complete:c||!c&&b||d.isFunction(a)&&a,duration:a,easing:c&&b||b&&!d.isFunction(b)&&b};e.duration=d.fx.off?0:"number"===typeof e.duration?e.duration:e.duration in d.fx.speeds?d.fx.speeds[e.duration]:d.fx.speeds._default;if(null==e.queue||!0===e.queue)e.queue="fx";e.old=e.complete;e.complete=function(){d.isFunction(e.old)&&
+e.old.call(this);e.queue&&d.dequeue(this,e.queue)};return e};d.fn.extend({fadeTo:function(a,b,c,d){return this.filter(ia).css("opacity",0).show().end().animate({opacity:b},a,c,d)},animate:function(a,b,c,e){var f=d.isEmptyObject(a),g=d.speed(b,c,e);b=function(){var b=vb(this,d.extend({},a),g);(f||d._data(this,"finish"))&&b.stop(!0)};b.finish=b;return f||!1===g.queue?this.each(b):this.queue(g.queue,b)},stop:function(a,b,c){var e=function(a){var b=a.stop;delete a.stop;b(c)};"string"!==typeof a&&(c=b,
+b=a,a=void 0);b&&!1!==a&&this.queue(a||"fx",[]);return this.each(function(){var b=!0,g=null!=a&&a+"queueHooks",h=d.timers,k=d._data(this);if(g)k[g]&&k[g].stop&&e(k[g]);else for(g in k)k[g]&&k[g].stop&&Dc.test(g)&&e(k[g]);for(g=h.length;g--;)h[g].elem!==this||null!=a&&h[g].queue!==a||(h[g].anim.stop(c),b=!1,h.splice(g,1));!b&&c||d.dequeue(this,a)})},finish:function(a){!1!==a&&(a=a||"fx");return this.each(function(){var b,c=d._data(this),e=c[a+"queue"];b=c[a+"queueHooks"];var f=d.timers,g=e?e.length:
+0;c.finish=!0;d.queue(this,a,[]);b&&b.stop&&b.stop.call(this,!0);for(b=f.length;b--;)f[b].elem===this&&f[b].queue===a&&(f[b].anim.stop(!0),f.splice(b,1));for(b=0;b<g;b++)e[b]&&e[b].finish&&e[b].finish.call(this);delete c.finish})}});d.each(["toggle","show","hide"],function(a,b){var c=d.fn[b];d.fn[b]=function(a,d,g){return null==a||"boolean"===typeof a?c.apply(this,arguments):this.animate(ra(b,!0),a,d,g)}});d.each({slideDown:ra("show"),slideUp:ra("hide"),slideToggle:ra("toggle"),fadeIn:{opacity:"show"},
+fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){d.fn[a]=function(a,d,f){return this.animate(b,a,d,f)}});d.timers=[];d.fx.tick=function(){var a,b=d.timers,c=0;for(Y=d.now();c<b.length;c++)a=b[c],a()||b[c]!==a||b.splice(c--,1);b.length||d.fx.stop();Y=void 0};d.fx.timer=function(a){d.timers.push(a);a()?d.fx.start():d.timers.pop()};d.fx.interval=13;d.fx.start=function(){za||(za=setInterval(d.fx.tick,d.fx.interval))};d.fx.stop=function(){clearInterval(za);za=null};d.fx.speeds={slow:600,
+fast:200,_default:400};d.fn.delay=function(a,b){a=d.fx?d.fx.speeds[a]||a:a;return this.queue(b||"fx",function(b,d){var f=setTimeout(b,a);d.stop=function(){clearTimeout(f)}})};(function(){var a,b,c,d,f;b=n.createElement("div");b.setAttribute("className","t");b.innerHTML="  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";d=b.getElementsByTagName("a")[0];c=n.createElement("select");f=c.appendChild(n.createElement("option"));a=b.getElementsByTagName("input")[0];d.style.cssText="top:1px";
+p.getSetAttribute="t"!==b.className;p.style=/top/.test(d.getAttribute("style"));p.hrefNormalized="/a"===d.getAttribute("href");p.checkOn=!!a.value;p.optSelected=f.selected;p.enctype=!!n.createElement("form").enctype;c.disabled=!0;p.optDisabled=!f.disabled;a=n.createElement("input");a.setAttribute("value","");p.input=""===a.getAttribute("value");a.value="t";a.setAttribute("type","radio");p.radioValue="t"===a.value})();var Ec=/\r/g;d.fn.extend({val:function(a){var b,c,e,f=this[0];if(arguments.length)return e=
+d.isFunction(a),this.each(function(c){1===this.nodeType&&(c=e?a.call(this,c,d(this).val()):a,null==c?c="":"number"===typeof c?c+="":d.isArray(c)&&(c=d.map(c,function(a){return null==a?"":a+""})),b=d.valHooks[this.type]||d.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,c,"value")||(this.value=c))});if(f){if((b=d.valHooks[f.type]||d.valHooks[f.nodeName.toLowerCase()])&&"get"in b&&void 0!==(c=b.get(f,"value")))return c;c=f.value;return"string"===typeof c?c.replace(Ec,""):null==
+c?"":c}}});d.extend({valHooks:{option:{get:function(a){var b=d.find.attr(a,"value");return null!=b?b:d.trim(d.text(a))}},select:{get:function(a){for(var b,c=a.options,e=a.selectedIndex,f=(a="select-one"===a.type||0>e)?null:[],g=a?e+1:c.length,h=0>e?g:a?e:0;h<g;h++)if(b=c[h],!(!b.selected&&h!==e||(p.optDisabled?b.disabled:null!==b.getAttribute("disabled"))||b.parentNode.disabled&&d.nodeName(b.parentNode,"optgroup"))){b=d(b).val();if(a)return b;f.push(b)}return f},set:function(a,b){for(var c,e,f=a.options,
+g=d.makeArray(b),h=f.length;h--;)if(e=f[h],0<=d.inArray(d.valHooks.option.get(e),g))try{e.selected=c=!0}catch(k){e.scrollHeight}else e.selected=!1;c||(a.selectedIndex=-1);return f}}}});d.each(["radio","checkbox"],function(){d.valHooks[this]={set:function(a,b){if(d.isArray(b))return a.checked=0<=d.inArray(d(a).val(),b)}};p.checkOn||(d.valHooks[this].get=function(a){return null===a.getAttribute("value")?"on":a.value})});var O,Qb,P=d.expr.attrHandle,Ta=/^(?:checked|selected)$/i,ba=p.getSetAttribute,
+Aa=p.input;d.fn.extend({attr:function(a,b){return aa(this,d.attr,a,b,1<arguments.length)},removeAttr:function(a){return this.each(function(){d.removeAttr(this,a)})}});d.extend({attr:function(a,b,c){var e,f,g=a.nodeType;if(a&&3!==g&&8!==g&&2!==g){if("undefined"===typeof a.getAttribute)return d.prop(a,b,c);1===g&&d.isXMLDoc(a)||(b=b.toLowerCase(),e=d.attrHooks[b]||(d.expr.match.bool.test(b)?Qb:O));if(void 0!==c)if(null===c)d.removeAttr(a,b);else{if(e&&"set"in e&&void 0!==(f=e.set(a,c,b)))return f;a.setAttribute(b,
+c+"");return c}else{if(e&&"get"in e&&null!==(f=e.get(a,b)))return f;f=d.find.attr(a,b);return null==f?void 0:f}}},removeAttr:function(a,b){var c,e,f=0,g=b&&b.match(K);if(g&&1===a.nodeType)for(;c=g[f++];)e=d.propFix[c]||c,d.expr.match.bool.test(c)?Aa&&ba||!Ta.test(c)?a[e]=!1:a[d.camelCase("default-"+c)]=a[e]=!1:d.attr(a,c,""),a.removeAttribute(ba?c:e)},attrHooks:{type:{set:function(a,b){if(!p.radioValue&&"radio"===b&&d.nodeName(a,"input")){var c=a.value;a.setAttribute("type",b);c&&(a.value=c);return b}}}}});
+Qb={set:function(a,b,c){!1===b?d.removeAttr(a,c):Aa&&ba||!Ta.test(c)?a.setAttribute(!ba&&d.propFix[c]||c,c):a[d.camelCase("default-"+c)]=a[c]=!0;return c}};d.each(d.expr.match.bool.source.match(/\w+/g),function(a,b){var c=P[b]||d.find.attr;P[b]=Aa&&ba||!Ta.test(b)?function(a,b,d){var h,k;d||(k=P[b],P[b]=h,h=null!=c(a,b,d)?b.toLowerCase():null,P[b]=k);return h}:function(a,b,c){if(!c)return a[d.camelCase("default-"+b)]?b.toLowerCase():null}});Aa&&ba||(d.attrHooks.value={set:function(a,b,c){if(d.nodeName(a,
+"input"))a.defaultValue=b;else return O&&O.set(a,b,c)}});ba||(O={set:function(a,b,c){var d=a.getAttributeNode(c);d||a.setAttributeNode(d=a.ownerDocument.createAttribute(c));d.value=b+="";if("value"===c||b===a.getAttribute(c))return b}},P.id=P.name=P.coords=function(a,b,c){var d;if(!c)return(d=a.getAttributeNode(b))&&""!==d.value?d.value:null},d.valHooks.button={get:function(a,b){var c=a.getAttributeNode(b);if(c&&c.specified)return c.value},set:O.set},d.attrHooks.contenteditable={set:function(a,b,
+c){O.set(a,""===b?!1:b,c)}},d.each(["width","height"],function(a,b){d.attrHooks[b]={set:function(a,d){if(""===d)return a.setAttribute(b,"auto"),d}}}));p.style||(d.attrHooks.style={get:function(a){return a.style.cssText||void 0},set:function(a,b){return a.style.cssText=b+""}});var Fc=/^(?:input|select|textarea|button|object)$/i,Gc=/^(?:a|area)$/i;d.fn.extend({prop:function(a,b){return aa(this,d.prop,a,b,1<arguments.length)},removeProp:function(a){a=d.propFix[a]||a;return this.each(function(){try{this[a]=
+void 0,delete this[a]}catch(b){}})}});d.extend({propFix:{"for":"htmlFor","class":"className"},prop:function(a,b,c){var e,f,g;g=a.nodeType;if(a&&3!==g&&8!==g&&2!==g){if(g=1!==g||!d.isXMLDoc(a))b=d.propFix[b]||b,f=d.propHooks[b];return void 0!==c?f&&"set"in f&&void 0!==(e=f.set(a,c,b))?e:a[b]=c:f&&"get"in f&&null!==(e=f.get(a,b))?e:a[b]}},propHooks:{tabIndex:{get:function(a){var b=d.find.attr(a,"tabindex");return b?parseInt(b,10):Fc.test(a.nodeName)||Gc.test(a.nodeName)&&a.href?0:-1}}}});p.hrefNormalized||
+d.each(["href","src"],function(a,b){d.propHooks[b]={get:function(a){return a.getAttribute(b,4)}}});p.optSelected||(d.propHooks.selected={get:function(a){if(a=a.parentNode)a.selectedIndex,a.parentNode&&a.parentNode.selectedIndex;return null}});d.each("tabIndex readOnly maxLength cellSpacing cellPadding rowSpan colSpan useMap frameBorder contentEditable".split(" "),function(){d.propFix[this.toLowerCase()]=this});p.enctype||(d.propFix.enctype="encoding");var Ua=/[\t\r\n\f]/g;d.fn.extend({addClass:function(a){var b,
+c,e,f,g,h=0,k=this.length;b="string"===typeof a&&a;if(d.isFunction(a))return this.each(function(b){d(this).addClass(a.call(this,b,this.className))});if(b)for(b=(a||"").match(K)||[];h<k;h++)if(c=this[h],e=1===c.nodeType&&(c.className?(" "+c.className+" ").replace(Ua," "):" ")){for(g=0;f=b[g++];)0>e.indexOf(" "+f+" ")&&(e+=f+" ");e=d.trim(e);c.className!==e&&(c.className=e)}return this},removeClass:function(a){var b,c,e,f,g,h=0,k=this.length;b=0===arguments.length||"string"===typeof a&&a;if(d.isFunction(a))return this.each(function(b){d(this).removeClass(a.call(this,
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+function(c,m){var p=this.strm,s=this.options.chunkSize,b,u,a,y,B;if(this.ended)return!1;u=m===~~m?m:!0===m?g.Z_FINISH:g.Z_NO_FLUSH;"string"===typeof c?p.input=h.binstring2buf(c):"[object ArrayBuffer]"===I.call(c)?p.input=new Uint8Array(c):p.input=c;p.next_in=0;p.avail_in=p.input.length;do{0===p.avail_out&&(p.output=new f.Buf8(s),p.next_out=0,p.avail_out=s);b=x.inflate(p,g.Z_NO_FLUSH);if(b!==g.Z_STREAM_END&&b!==g.Z_OK)return this.onEnd(b),this.ended=!0,!1;if(p.next_out&&(0===p.avail_out||b===g.Z_STREAM_END||
+0===p.avail_in&&(u===g.Z_FINISH||u===g.Z_SYNC_FLUSH)))if("string"===this.options.to)a=h.utf8border(p.output,p.next_out),y=p.next_out-a,B=h.buf2string(p.output,a),p.next_out=y,p.avail_out=s-y,y&&f.arraySet(p.output,p.output,a,y,0),this.onData(B);else this.onData(f.shrinkBuf(p.output,p.next_out))}while(0<p.avail_in&&b!==g.Z_STREAM_END);b===g.Z_STREAM_END&&(u=g.Z_FINISH);if(u===g.Z_FINISH)return b=x.inflateEnd(this.strm),this.onEnd(b),this.ended=!0,b===g.Z_OK;u===g.Z_SYNC_FLUSH&&(this.onEnd(g.Z_OK),
+p.avail_out=0);return!0};E.prototype.onData=function(c){this.chunks.push(c)};E.prototype.onEnd=function(c){c===g.Z_OK&&(this.result="string"===this.options.to?this.chunks.join(""):f.flattenChunks(this.chunks));this.chunks=[];this.err=c;this.msg=this.strm.msg};c.Inflate=E;c.inflate=F;c.inflateRaw=function(c,f){f=f||{};f.raw=!0;return F(c,f)};c.ungzip=F},{"./utils/common":1,"./utils/strings":2,"./zlib/constants":4,"./zlib/gzheader":6,"./zlib/inflate.js":8,"./zlib/messages":10,"./zlib/zstream":11}]},
+{},[])("/lib/inflate.js")});
+$3Dmol=function(b){return b.$3Dmol||{}}(window);"https:"!=document.location.protocol&&$.get("http://3dmol.csb.pitt.edu/track/report.cgi");String.prototype.startsWith||(String.prototype.startsWith=function(b){return 0===this.lastIndexOf(b,0)});String.prototype.endsWith||(String.prototype.endsWith=function(b){return-1!==this.indexOf(b,this.length-b.length)});
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+return c*c+d*d+b*b},applyMatrix4:function(b){var c=this.x,d=this.y,p=this.z;b=b.elements;this.x=b[0]*c+b[4]*d+b[8]*p+b[12];this.y=b[1]*c+b[5]*d+b[9]*p+b[13];this.z=b[2]*c+b[6]*d+b[10]*p+b[14];return this},applyProjection:function(b){var c=this.x,d=this.y,p=this.z;b=b.elements;var y=b[3]*c+b[7]*d+b[11]*p+b[15];this.x=(b[0]*c+b[4]*d+b[8]*p+b[12])/y;this.y=(b[1]*c+b[5]*d+b[9]*p+b[13])/y;this.z=(b[2]*c+b[6]*d+b[10]*p+b[14])/y;return this},applyQuaternion:function(b){var c=this.x,d=this.y,p=this.z,y=b.x,
+A=b.y,q=b.z,B,f,w;B=2*(d*q-p*A);f=2*(p*y-c*q);w=2*(c*A-d*y);this.x=c+b.w*B+(f*q-w*A);this.y=d+b.w*f+(w*y-B*q);this.z=p+b.w*w+(B*A-f*y);return this},negate:function(){return this.multiplyScalar(-1)},dot:function(b){return this.x*b.x+this.y*b.y+this.z*b.z},length:function(){return Math.sqrt(this.x*this.x+this.y*this.y+this.z*this.z)},lengthSq:function(){return this.x*this.x+this.y*this.y+this.z*this.z},normalize:function(){return this.divideScalar(this.length())},cross:function(b){var c=this.x,d=this.y,
+p=this.z;this.x=d*b.z-p*b.y;this.y=p*b.x-c*b.z;this.z=c*b.y-d*b.x;return this},crossVectors:function(b,c){this.x=b.y*c.z-b.z*c.y;this.y=b.z*c.x-b.x*c.z;this.z=b.x*c.y-b.y*c.x;return this},getPositionFromMatrix:function(b){this.x=b.elements[12];this.y=b.elements[13];this.z=b.elements[14];return this},setEulerFromRotationMatrix:function(b,c){var d=b.elements,p=d[0],y=d[4],A=d[8],q=d[5],B=d[9],f=d[6],d=d[10];void 0===c||"XYZ"===c?(this.y=Math.asin($3Dmol.Math.clamp(A,-1,1)),.99999>Math.abs(A)?(this.x=
+Math.atan2(-B,d),this.z=Math.atan2(-y,p)):(this.x=Math.atan2(f,q),this.z=0)):console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: "+c);return this},rotateAboutVector:function(b,c){b.normalize();var d=Math.cos(c),p=Math.sin(c),y=this.clone().multiplyScalar(d),p=b.clone().cross(this).multiplyScalar(p),d=b.clone().multiplyScalar(b.clone().dot(this)).multiplyScalar(1-d),y=y.add(p).add(d);this.x=y.x;this.y=y.y;this.z=y.z;return this},clone:function(){return new $3Dmol.Vector3(this.x,
+this.y,this.z)}};$3Dmol.Matrix3=function(b,c,d,p,y,A,q,B,f){this.elements=new Float32Array(9);this.set(void 0!==b?b:1,c||0,d||0,p||0,void 0!==y?y:1,A||0,q||0,B||0,void 0!==f?f:1)};
+$3Dmol.Matrix3.prototype={constructor:$3Dmol.Matrix3,set:function(b,c,d,p,y,A,q,B,f){var w=this.elements;w[0]=b;w[3]=c;w[6]=d;w[1]=p;w[4]=y;w[7]=A;w[2]=q;w[5]=B;w[8]=f;return this},identity:function(){this.set(1,0,0,0,1,0,0,0,1);return this},copy:function(b){b=b.elements;this.set(b[0],b[3],b[6],b[1],b[4],b[7],b[2],b[5],b[8])},multiplyScalar:function(b){var c=this.elements;c[0]*=b;c[3]*=b;c[6]*=b;c[1]*=b;c[4]*=b;c[7]*=b;c[2]*=b;c[5]*=b;c[8]*=b;return this},getInverse:function(b,c){var d=b.elements,
+p=this.elements;p[0]=d[10]*d[5]-d[6]*d[9];p[1]=-d[10]*d[1]+d[2]*d[9];p[2]=d[6]*d[1]-d[2]*d[5];p[3]=-d[10]*d[4]+d[6]*d[8];p[4]=d[10]*d[0]-d[2]*d[8];p[5]=-d[6]*d[0]+d[2]*d[4];p[6]=d[9]*d[4]-d[5]*d[8];p[7]=-d[9]*d[0]+d[1]*d[8];p[8]=d[5]*d[0]-d[1]*d[4];d=d[0]*p[0]+d[1]*p[3]+d[2]*p[6];if(0===d){if(c)throw Error("Matrix3.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix3.getInverse(): can't invert matrix, determinant is 0");this.identity();return this}this.multiplyScalar(1/d);return this},
+getDeterminant:function(){var b=this.elements;return b[0]*b[4]*b[8]+b[1]*b[5]*b[6]+b[2]*b[3]*b[7]-b[2]*b[4]*b[6]-b[1]*b[3]*b[8]-b[0]*b[5]*b[7]},transpose:function(){var b,c=this.elements;b=c[1];c[1]=c[3];c[3]=b;b=c[2];c[2]=c[6];c[6]=b;b=c[5];c[5]=c[7];c[7]=b;return this},clone:function(){var b=this.elements;return new $3Dmol.Matrix3(b[0],b[3],b[6],b[1],b[4],b[7],b[2],b[5],b[8])}};
+$3Dmol.Matrix4=function(b,c,d,p,y,A,q,B,f,w,h,t,m,e,F,g){var x=this.elements=new Float32Array(16);x[0]=void 0!==b?b:1;x[4]=c||0;x[8]=d||0;x[12]=p||0;x[1]=y||0;x[5]=void 0!==A?A:1;x[9]=q||0;x[13]=B||0;x[2]=f||0;x[6]=w||0;x[10]=void 0!==h?h:1;x[14]=t||0;x[3]=m||0;x[7]=e||0;x[11]=F||0;x[15]=void 0!==g?g:1};
+$3Dmol.Matrix4.prototype={constructor:$3Dmol.Matrix4,set:function(b,c,d,p,y,A,q,B,f,w,h,t,m,e,F,g){var x=this.elements;x[0]=b;x[4]=c;x[8]=d;x[12]=p;x[1]=y;x[5]=A;x[9]=q;x[13]=B;x[2]=f;x[6]=w;x[10]=h;x[14]=t;x[3]=m;x[7]=e;x[11]=F;x[15]=g;return this},identity:function(){this.set(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1);return this},copy:function(b){b=b.elements;this.set(b[0],b[4],b[8],b[12],b[1],b[5],b[9],b[13],b[2],b[6],b[10],b[14],b[3],b[7],b[11],b[15]);return this},matrix3FromTopLeft:function(){var b=this.elements;
+return new $3Dmol.Matrix3(b[0],b[4],b[8],b[1],b[5],b[9],b[2],b[6],b[10])},setRotationFromEuler:function(b,c){var d=this.elements,p=b.x,y=b.y,A=b.z,q=Math.cos(p),p=Math.sin(p),B=Math.cos(y),y=Math.sin(y),f=Math.cos(A),A=Math.sin(A);if(void 0===c||"XYZ"===c){var w=q*f,h=q*A,t=p*f,m=p*A;d[0]=B*f;d[4]=-B*A;d[8]=y;d[1]=h+t*y;d[5]=w-m*y;d[9]=-p*B;d[2]=m-w*y;d[6]=t+h*y;d[10]=q*B}else console.error("Error with matrix4 setRotationFromEuler. Order: "+c);return this},setRotationFromQuaternion:function(b){var c=
+this.elements,d=b.x,p=b.y,y=b.z,A=b.w,q=d+d,B=p+p,f=y+y;b=d*q;var w=d*B,d=d*f,h=p*B,p=p*f,y=y*f,q=A*q,B=A*B,A=A*f;c[0]=1-(h+y);c[4]=w-A;c[8]=d+B;c[1]=w+A;c[5]=1-(b+y);c[9]=p-q;c[2]=d-B;c[6]=p+q;c[10]=1-(b+h);return this},lookAt:function(){var b=new $3Dmol.Vector3,c=new $3Dmol.Vector3,d=new $3Dmol.Vector3;return function(p,y,A){var q=this.elements;d.subVectors(p,y).normalize();0===d.length()&&(d.z=1);b.crossVectors(A,d).normalize();0===b.length()&&(d.x+=1E-4,b.crossVectors(A,d).normalize());c.crossVectors(d,
+b);q[0]=b.x;q[4]=c.x;q[8]=d.x;q[1]=b.y;q[5]=c.y;q[9]=d.y;q[2]=b.z;q[6]=c.z;q[10]=d.z;return this}}(),multiplyMatrices:function(b,c){var d=b.elements,p=c.elements,y=this.elements,A=d[0],q=d[4],B=d[8],f=d[12],w=d[1],h=d[5],t=d[9],m=d[13],e=d[2],F=d[6],g=d[10],x=d[14],u=d[3],s=d[7],l=d[11],d=d[15],E=p[0],M=p[4],C=p[8],G=p[12],z=p[1],H=p[5],L=p[9],N=p[13],J=p[2],I=p[6],K=p[10],O=p[14],Q=p[3],W=p[7],P=p[11],p=p[15];y[0]=A*E+q*z+B*J+f*Q;y[4]=A*M+q*H+B*I+f*W;y[8]=A*C+q*L+B*K+f*P;y[12]=A*G+q*N+B*O+f*p;y[1]=
+w*E+h*z+t*J+m*Q;y[5]=w*M+h*H+t*I+m*W;y[9]=w*C+h*L+t*K+m*P;y[13]=w*G+h*N+t*O+m*p;y[2]=e*E+F*z+g*J+x*Q;y[6]=e*M+F*H+g*I+x*W;y[10]=e*C+F*L+g*K+x*P;y[14]=e*G+F*N+g*O+x*p;y[3]=u*E+s*z+l*J+d*Q;y[7]=u*M+s*H+l*I+d*W;y[11]=u*C+s*L+l*K+d*P;y[15]=u*G+s*N+l*O+d*p;return this},multiplyScalar:function(b){var c=this.elements;c[0]*=b;c[4]*=b;c[8]*=b;c[12]*=b;c[1]*=b;c[5]*=b;c[9]*=b;c[13]*=b;c[2]*=b;c[6]*=b;c[10]*=b;c[14]*=b;c[3]*=b;c[7]*=b;c[11]*=b;c[15]*=b;return this},transpose:function(){var b=this.elements,c;
+c=b[1];b[1]=b[4];b[4]=c;c=b[2];b[2]=b[8];b[8]=c;c=b[6];b[6]=b[9];b[9]=c;c=b[3];b[3]=b[12];b[12]=c;c=b[7];b[7]=b[13];b[13]=c;c=b[11];b[11]=b[14];b[14]=c;return this},getPosition:function(){var b=new $3Dmol.Vector3;return function(){console.warn("DEPRECATED: Matrix4's .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.");var c=this.elements;return b.set(c[12],c[13],c[14])}}(),setPosition:function(b){var c=this.elements;c[12]=b.x;c[13]=b.y;c[14]=b.z;return this},getInverse:function(b,
+c){var d=this.elements,p=b.elements,y=p[0],A=p[4],q=p[8],B=p[12],f=p[1],w=p[5],h=p[9],t=p[13],m=p[2],e=p[6],F=p[10],g=p[14],x=p[3],u=p[7],s=p[11],l=p[15];d[0]=h*g*u-t*F*u+t*e*s-w*g*s-h*e*l+w*F*l;d[4]=B*F*u-q*g*u-B*e*s+A*g*s+q*e*l-A*F*l;d[8]=q*t*u-B*h*u+B*w*s-A*t*s-q*w*l+A*h*l;d[12]=B*h*e-q*t*e-B*w*F+A*t*F+q*w*g-A*h*g;d[1]=t*F*x-h*g*x-t*m*s+f*g*s+h*m*l-f*F*l;d[5]=q*g*x-B*F*x+B*m*s-y*g*s-q*m*l+y*F*l;d[9]=B*h*x-q*t*x-B*f*s+y*t*s+q*f*l-y*h*l;d[13]=q*t*m-B*h*m+B*f*F-y*t*F-q*f*g+y*h*g;d[2]=w*g*x-t*e*x+
+t*m*u-f*g*u-w*m*l+f*e*l;d[6]=B*e*x-A*g*x-B*m*u+y*g*u+A*m*l-y*e*l;d[10]=A*t*x-B*w*x+B*f*u-y*t*u-A*f*l+y*w*l;d[14]=B*w*m-A*t*m-B*f*e+y*t*e+A*f*g-y*w*g;d[3]=h*e*x-w*F*x-h*m*u+f*F*u+w*m*s-f*e*s;d[7]=A*F*x-q*e*x+q*m*u-y*F*u-A*m*s+y*e*s;d[11]=q*w*x-A*h*x-q*f*u+y*h*u+A*f*s-y*w*s;d[15]=A*h*m-q*w*m+q*f*e-y*h*e-A*f*F+y*w*F;d=p[0]*d[0]+p[1]*d[4]+p[2]*d[8]+p[3]*d[12];if(0===d){if(c)throw Error("Matrix4.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix4.getInverse(): can't invert matrix, determinant is 0");
+this.identity();return this}this.multiplyScalar(1/d);return this},isReflected:function(){return 0>this.matrix3FromTopLeft().getDeterminant()},compose:function(){var b=new $3Dmol.Matrix4,c=new $3Dmol.Matrix4;return function(d,p,y){var A=this.elements;b.identity();b.setRotationFromQuaternion(p);c.makeScale(y.x,y.y,y.z);this.multiplyMatrices(b,c);A[12]=d.x;A[13]=d.y;A[14]=d.z;return this}}(),decompose:function(){var b=new $3Dmol.Vector3,c=new $3Dmol.Vector3,d=new $3Dmol.Vector3,p=new $3Dmol.Matrix4;
+return function(y,A,q){var B=this.elements;b.set(B[0],B[1],B[2]);c.set(B[4],B[5],B[6]);d.set(B[8],B[9],B[10]);y=y instanceof $3Dmol.Vector3?y:new $3Dmol.Vector3;A=A instanceof $3Dmol.Quaternion?A:new $3Dmol.Quaternion;q=q instanceof $3Dmol.Vector3?q:new $3Dmol.Vector3;q.x=b.length();q.y=c.length();q.z=d.length();y.x=B[12];y.y=B[13];y.z=B[14];p.copy(this);p.elements[0]/=q.x;p.elements[1]/=q.x;p.elements[2]/=q.x;p.elements[4]/=q.y;p.elements[5]/=q.y;p.elements[6]/=q.y;p.elements[8]/=q.z;p.elements[9]/=
+q.z;p.elements[10]/=q.z;A.setFromRotationMatrix(p);return[y,A,q]}}(),scale:function(b){var c=this.elements,d=b.x,p=b.y;b=b.z;c[0]*=d;c[4]*=p;c[8]*=b;c[1]*=d;c[5]*=p;c[9]*=b;c[2]*=d;c[6]*=p;c[10]*=b;c[3]*=d;c[7]*=p;c[11]*=b;return this},getMaxScaleOnAxis:function(){var b=this.elements;return Math.sqrt(Math.max(b[0]*b[0]+b[1]*b[1]+b[2]*b[2],Math.max(b[4]*b[4]+b[5]*b[5]+b[6]*b[6],b[8]*b[8]+b[9]*b[9]+b[10]*b[10])))},makeFrustum:function(b,c,d,p,y,A){var q=this.elements;q[0]=2*y/(c-b);q[4]=0;q[8]=(c+b)/
+(c-b);q[12]=0;q[1]=0;q[5]=2*y/(p-d);q[9]=(p+d)/(p-d);q[13]=0;q[2]=0;q[6]=0;q[10]=-(A+y)/(A-y);q[14]=-2*A*y/(A-y);q[3]=0;q[7]=0;q[11]=-1;q[15]=0;return this},makePerspective:function(b,c,d,p){b=d*Math.tan($3Dmol.Math.degToRad(.5*b));var y=-b;return this.makeFrustum(y*c,b*c,y,b,d,p)},isEqual:function(b){b=b.elements;var c=this.elements;return c[0]==b[0]&&c[4]==b[4]&&c[8]==b[8]&&c[12]==b[12]&&c[1]==b[1]&&c[5]==b[5]&&c[9]==b[9]&&c[13]==b[13]&&c[2]==b[2]&&c[6]==b[6]&&c[10]==b[10]&&c[14]==b[14]&&c[3]==
+b[3]&&c[7]==b[7]&&c[11]==b[11]&&c[15]==b[15]?!0:!1},clone:function(){var b=this.elements;return new $3Dmol.Matrix4(b[0],b[4],b[8],b[12],b[1],b[5],b[9],b[13],b[2],b[6],b[10],b[14],b[3],b[7],b[11],b[15])},isIdentity:function(){var b=this.elements;return 1==b[0]&&0==b[4]&&0==b[8]&&0==b[12]&&0==b[1]&&1==b[5]&&0==b[9]&&0==b[13]&&0==b[2]&&0==b[6]&&1==b[10]&&0==b[14]&&0==b[3]&&0==b[7]&&0==b[11]&&1==b[15]?!0:!1}};
+$3Dmol.Ray=function(b,c){this.origin=void 0!==b?b:new $3Dmol.Vector3;this.direction=void 0!==c?c:new $3Dmol.Vector3};
+$3Dmol.Ray.prototype={constructor:$3Dmol.Ray,set:function(b,c){this.origin.copy(b);this.direction.copy(c);return this},copy:function(b){this.origin.copy(b.origin);this.direction.copy(b.direction);return this},at:function(b,c){return(c||new $3Dmol.Vector3).copy(this.direction).multiplyScalar(b).add(this.origin)},recast:function(){var b=new $3Dmol.Vector3;return function(c){this.origin.copy(this.at(c,b));return this}}(),closestPointToPoint:function(b,c){var d=c||new $3Dmol.Vector3;d.subVectors(b,this.origin);
+var p=d.dot(this.direction);return d.copy(this.direction).multiplyScalar(p).add(this.origin)},distanceToPoint:function(b){var c=new $3Dmol.Vector3;return function(b){var p=c.subVectors(b,this.origin).dot(this.direction);c.copy(this.direction).multiplyScalar(p).add(this.origin);return c.distanceTo(b)}}(),isIntersectionCylinder:function(){},isIntersectionSphere:function(b){return this.distanceToPoint(b.center)<=b.radius},isIntersectionPlane:function(b){return 0!==b.normal.dot(this.direction)||0===b.distanceToPoint(this.origin)?
+!0:!1},distanceToPlane:function(b){var c=b.normal.dot(this.direction);if(0===c){if(0===b.distanceToPoint(this.origin))return 0}else return-(this.origin.dot(b.normal)+b.constant)/c},intersectPlane:function(b,c){var d=this.distanceToPlane(b);return void 0===d?void 0:this.at(d,c)},applyMatrix4:function(b){this.direction.add(this.origin).applyMatrix4(b);this.origin.applyMatrix4(b);this.direction.sub(this.origin);return this},equals:function(b){return b.origin.equals(this.origin)&&b.direction.equals(this.direction)},
+clone:function(){return(new $3Dmol.Ray).copy(this)}};$3Dmol.Sphere=function(b,c){this.center=void 0!==b?b:new $3Dmol.Vector3;this.radius=void 0!==c?c:0};
+$3Dmol.Sphere.prototype={constructor:$3Dmol.Sphere,set:function(b,c){this.center.copy(b);this.radius=c;return this},copy:function(b){this.center.copy(b.center);this.radius=b.radius;return this},applyMatrix4:function(b){this.center.applyMatrix4(b);this.radius*=b.getMaxScaleOnAxis();return this},translate:function(b){this.center.add(b);return this},equals:function(b){return b.center.equals(this.center)&&b.radius===this.radius},clone:function(){return(new $3Dmol.Sphere).copy(this)}};
+$3Dmol.Cylinder=function(b,c,d){this.c1=void 0!==b?b:new $3Dmol.Vector3;this.c2=void 0!==c?c:new $3Dmol.Vector3;this.direction=(new $3Dmol.Vector3).subVectors(this.c2,this.c1).normalize();this.radius=void 0!==d?d:0};
+$3Dmol.Cylinder.prototype={constructor:$3Dmol.Cylinder,copy:function(b){this.c1.copy(b.c1);this.c2.copy(b.c2);this.direction.copy(b.direction);this.radius=b.radius;return this},lengthSq:function(){var b=new $3Dmol.Vector3;return function(){return b.subVectors(this.c2,this.c1).lengthSq()}}(),applyMatrix4:function(b){this.direction.add(this.c1).applyMatrix4(b);this.c1.applyMatrix4(b);this.c2.applyMatrix4(b);this.direction.sub(this.c1).normalize();this.radius*=b.getMaxScaleOnAxis();return this}};
+$3Dmol.Triangle=function(b,c,d){this.a=void 0!==b?b:new $3Dmol.Vector3;this.b=void 0!==c?c:new $3Dmol.Vector3;this.c=void 0!==d?d:new $3Dmol.Vector3};
+$3Dmol.Triangle.prototype={constructor:$3Dmol.Triangle,copy:function(b){this.a.copy(b.a);this.b.copy(b.b);this.c.copy(b.c);return this},applyMatrix4:function(b){this.a.applyMatrix4(b);this.b.applyMatrix4(b);this.c.applyMatrix4(b);return this},getNormal:function(){var b=new $3Dmol.Vector3;return function(){var c=this.a.clone();c.sub(this.b);b.subVectors(this.c,this.b);c.cross(b);c.normalize();return c}}()};
+$3Dmol.EventDispatcher=function(){var b={};this.addEventListener=function(c,d){void 0===b[c]&&(b[c]=[]);-1===b[c].indexOf(d)&&b[c].push(d)};this.removeEventListener=function(c,d){var p=b[c].indexOf(d);-1!==p&&b[c].splice(p,1)};this.dispatchEvent=function(c){var d=b[c.type];if(void 0!==d){c.target=this;for(var p=0,y=d.length;p<y;p++)d[p].call(this,c)}}};$3Dmol.Color=function(b){return 1<arguments.length?(this.r=arguments[0]||0,this.g=arguments[1]||0,this.b=arguments[2]||0,this):this.set(b)};
+$3Dmol.Color.prototype={constructor:$3Dmol.Color,r:0,g:0,b:0,set:function(b){if(b instanceof $3Dmol.Color)return b.clone();"number"===typeof b?this.setHex(b):"object"===typeof b&&"r"in b&&"g"in b&&"b"in b&&(this.r=b.r,this.g=b.g,this.b=b.b)},setHex:function(b){b=Math.floor(b);this.r=(b>>16&255)/255;this.g=(b>>8&255)/255;this.b=(b&255)/255;return this},getHex:function(){var b=Math.round(255*this.r),c=Math.round(255*this.g),d=Math.round(255*this.b);return b<<16|c<<8|d},clone:function(){return new $3Dmol.Color(this.r,
+this.g,this.b)},copy:function(b){this.r=b.r;this.g=b.g;this.b=b.b;return this},scaled:function(){var b={};b.r=Math.round(255*this.r);b.g=Math.round(255*this.g);b.b=Math.round(255*this.b);b.a=1;return b}};
 $3Dmol.Object3D=function(){this.id=$3Dmol.Object3DIDCount++;this.name="";this.parent=void 0;this.children=[];this.position=new $3Dmol.Vector3;this.rotation=new $3Dmol.Vector3;this.matrix=new $3Dmol.Matrix4;this.matrixWorld=new $3Dmol.Matrix4;this.quaternion=new $3Dmol.Quaternion;this.eulerOrder="XYZ";this.up=new $3Dmol.Vector3(0,1,0);this.scale=new $3Dmol.Vector3(1,1,1);this.rotationAutoUpdate=this.matrixWorldNeedsUpdate=this.matrixAutoUpdate=!0;this.useQuaternion=!1;this.visible=!0};
-$3Dmol.Object3D.prototype={constructor:$3Dmol.Object3D,lookAt:function(a){this.matrix.lookAt(a,this.position,this.up);this.rotationAutoUpdate&&(!0===this.useQuaternion?this.quaternion.copy(this.matrix.decompose()[1]):this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder))},add:function(a){if(a===this)console.error("Can't add $3Dmol.Object3D to itself");else{a.parent=this;this.children.push(a);for(var b=this;void 0!==b.parent;)b=b.parent;void 0!==b&&b instanceof $3Dmol.Scene&&b.__addObject(a)}},
-remove:function(a){var b=this.children.indexOf(a);if(-1!==b){a.parent=void 0;this.children.splice(b,1);for(b=this;void 0!==b.parent;)b=b.parent;void 0!==b&&b instanceof $3Dmol.Scene&&b.__removeObject(a)}},updateMatrix:function(){this.matrix.setPosition(this.position);!1===this.useQuaternion?this.matrix.setRotationFromEuler(this.rotation,this.eulerOrder):this.matrix.setRotationFromQuaternion(this.quaternion);1===this.scale.x&&1===this.scale.y&&1===this.scale.z||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=
-!0},updateMatrixWorld:function(a){!0===this.matrixAutoUpdate&&this.updateMatrix();if(!0===this.matrixWorldNeedsUpdate||!0===a)void 0===this.parent?this.matrixWorld.copy(this.matrix):this.matrixWorld.multiplyMatrices(this.parent.matrixWorld,this.matrix);this.matrixWorldNeedsUpdate=!1;for(a=0;a<this.children.length;a++)this.children[a].updateMatrixWorld(!0)},clone:function(a){void 0===a&&(a=new $3Dmol.Object3D);a.name=this.name;a.up.copy(this.up);a.position.copy(this.position);a.rotation.copy(this.rotation);
-a.eulerOrder=this.eulerOrder;a.scale.copy(this.scale);a.rotationAutoUpdate=this.rotationAutoUpdate;a.matrix.copy(this.matrix);a.matrixWorld.copy(this.matrixWorld);a.quaternion.copy(this.quaternion);a.matrixAutoUpdate=this.matrixAutoUpdate;a.matrixWorldNeedsUpdate=this.matrixWorldNeedsUpdate;a.useQuaternion=this.useQuaternion;a.visible=this.visible;for(var b=0;b<this.children.length;b++)a.add(this.children[b].clone());return a}};$3Dmol.Object3DIDCount=0;
-$3Dmol.Geometry=function(){var a=function(a){this.id=a||0;this.lineArray=this.faceArray=this.normalArray=this.colorArray=this.vertexArray=null;this.lineidx=this.faceidx=this.vertices=0};a.prototype.getNumVertices=function(){return this.vertices};a.prototype.getVertices=function(){return this.vertexArray};a.prototype.getCentroid=function(){for(var a=new $3Dmol.Vector3,b,c,f,l=0;l<this.vertices;++l)b=3*l,c=this.vertexArray[b],f=this.vertexArray[b+1],b=this.vertexArray[b+2],a.x+=c,a.y+=f,a.z+=b;a.divideScalar(this.vertices);
-return a};a.prototype.setNormals=function(){var a=this.faceArray,b=this.vertexArray,c=this.normalArray;if(this.vertices&&this.faceidx)for(var f,l,h,m,q,z,w=0;w<a.length/3;++w)f=3*a[3*w],l=3*a[3*w+1],h=3*a[3*w+2],m=new $3Dmol.Vector3(b[f],b[f+1],b[f+2]),q=new $3Dmol.Vector3(b[l],b[l+1],b[l+2]),z=new $3Dmol.Vector3(b[h],b[h+1],b[h+2]),m.subVectors(m,q),z.subVectors(z,q),z.cross(m),m=z,m.normalize(),c[f]+=m.x,c[l]+=m.x,c[h]+=m.x,c[f+1]+=m.y,c[l+1]+=m.y,c[h+1]+=m.y,c[f+2]+=m.z,c[l+2]+=m.z,c[h+2]+=m.z};
-a.prototype.setLineIndices=function(){if(this.faceidx){var a=this.faceArray,b=this.lineArray=new Uint16Array(2*this.faceidx);this.lineidx=2*this.faceidx;for(var c,f=0;f<this.faceidx/3;++f){c=3*f;lineoffset=2*c;var l=a[c],h=a[c+1];c=a[c+2];b[lineoffset]=l;b[lineoffset+1]=h;b[lineoffset+2]=l;b[lineoffset+3]=c;b[lineoffset+4]=h;b[lineoffset+5]=c}}};a.prototype.truncateArrayBuffers=function(a,b){a=!0===a?!0:!1;var c=this.colorArray,f=this.normalArray,l=this.faceArray,h=this.lineArray;this.vertexArray=
-this.vertexArray.subarray(0,3*this.vertices);this.colorArray=c.subarray(0,3*this.vertices);a?(this.normalArray=f.subarray(0,3*this.vertices),this.faceArray=l.subarray(0,this.faceidx),this.lineArray=0<this.lineidx?h.subarray(0,this.lineidx):new Uint16Array):(this.normalArray=new Float32Array,this.faceArray=new Uint16Array,this.lineArray=new Uint16Array);b&&(this.normalArray&&(this.normalArray=new Float32Array(this.normalArray)),this.faceArray&&(this.faceArray=new Uint16Array(this.faceArray)),this.lineArray&&
-(this.lineArray=new Uint16Array(this.lineArray)),this.vertexArray&&(this.vertexArray=new Float32Array(this.vertexArray)),this.colorArray&&(this.colorArray=new Float32Array(this.colorArray)));this.__inittedArrays=!0};var b=function(b){var c=new a(b.geometryGroups.length);b.geometryGroups.push(c);b.groups=b.geometryGroups.length;c.vertexArray=new Float32Array(196605);c.colorArray=new Float32Array(196605);b.mesh&&(c.normalArray=new Float32Array(196605),c.faceArray=new Uint16Array(393210),c.lineArray=
-new Uint16Array(393210));return c},c=function(a){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.GeometryIDCount++;this.name="";this.hasTangents=!1;this.dynamic=!0;this.mesh=!0===a?!0:!1;this.buffersNeedUpdate=this.colorsNeedUpdate=this.normalsNeedUpdate=this.elementsNeedUpdate=this.verticesNeedUpdate=!1;this.geometryGroups=[];this.groups=0};c.prototype={constructor:c,updateGeoGroup:function(a){var c=0<this.groups?this.geometryGroups[this.groups-1]:null;if(!c||65535<c.vertices+(a||0))c=b(this);return c},
-addGeoGroup:function(){return b(this)},setUpNormals:function(a){a=a||!1;for(var b=0;b<this.groups;b++)this.geometryGroups[b].setNormals(a)},setUpWireframe:function(){for(var a=0;a<this.groups;a++)this.geometryGroups[a].setLineIndices()},initTypedArrays:function(){for(var a=0;a<this.groups;a++){var b=this.geometryGroups[a];!0!==b.__inittedArrays&&b.truncateArrayBuffers(this.mesh,!1)}},dispose:function(){this.dispatchEvent({type:"dispose"})}};return c}();
-Object.defineProperty($3Dmol.Geometry.prototype,"vertices",{get:function(){for(var a=0,b=0;b<this.groups;b++)a+=this.geometryGroups[b].vertices;return a}});$3Dmol.GeometryIDCount=0;
-$3Dmol.Raycaster=function(){var a=function(a,b,c,d){this.ray=new $3Dmol.Ray(a,b);0<this.ray.direction.lengthSq()&&this.ray.direction.normalize();this.near=d||0;this.far=c||Infinity},b=new $3Dmol.Sphere,c=new $3Dmol.Cylinder,d=new $3Dmol.Triangle,e=new $3Dmol.Vector3,k=new $3Dmol.Vector3,f=new $3Dmol.Vector3,l=new $3Dmol.Vector3;new $3Dmol.Ray;new $3Dmol.Vector3;var h=new $3Dmol.Vector3;new $3Dmol.Matrix4;var m=function(a,b){return a.distance-b.distance},q=function(a){return Math.min(Math.max(a,-1),
-1)};a.prototype.precision=1E-4;a.prototype.linePrecision=.2;a.prototype.set=function(a,b){this.ray.set(a,b)};a.prototype.intersectObjects=function(a,w){for(var v=[],x=0,r=w.length;x<r;x++)a:{var n=a,t=w[x],u=v;h.getPositionFromMatrix(n.matrixWorld);if(!0===t.clickable&&void 0!==t.intersectionShape){var y=t.intersectionShape,F=this.linePrecision,F=F*n.matrixWorld.getMaxScaleOnAxis(),F=F*F;if(void 0!==t.boundingSphere&&t.boundingSphere instanceof $3Dmol.Sphere&&(b.copy(t.boundingSphere),b.applyMatrix4(n.matrixWorld),
-!this.ray.isIntersectionSphere(b)))break a;for(var B=void 0,C=void 0,s=void 0,p=void 0,A=s=void 0,E=void 0,H=void 0,G=void 0,D=void 0,I=D=A=p=void 0,B=0,C=y.triangle.length;B<C;B++)y.triangle[B]instanceof $3Dmol.Triangle&&(d.copy(y.triangle[B]),d.applyMatrix4(n.matrixWorld),s=d.getNormal(),p=this.ray.direction.dot(s),0<=p||(e.subVectors(d.a,this.ray.origin),E=s.dot(e)/p,0>E||(k.copy(this.ray.direction).multiplyScalar(E).add(this.ray.origin),k.sub(d.a),f.copy(d.b).sub(d.a),l.copy(d.c).sub(d.a),p=f.dot(l),
-s=f.lengthSq(),A=l.lengthSq(),A=(s*k.dot(l)-p*k.dot(f))/(s*A-p*p),0>A||1<A||(p=(k.dot(f)-A*p)/s,0>p||1<p||1<p+A||u.push({clickable:t,distance:E})))));B=0;for(C=y.cylinder.length;B<C;B++)y.cylinder[B]instanceof $3Dmol.Cylinder&&(c.copy(y.cylinder[B]),c.applyMatrix4(n.matrixWorld),e.subVectors(c.c1,this.ray.origin),s=e.dot(c.direction),A=e.dot(this.ray.direction),p=q(this.ray.direction.dot(c.direction)),G=1-p*p,0!==G&&(D=(p*A-s)/G,I=(A-p*s)/G,k.copy(c.direction).multiplyScalar(D).add(c.c1),f.copy(this.ray.direction).multiplyScalar(I).add(this.ray.origin),
-H=l.subVectors(k,f).lengthSq(),D=c.radius*c.radius,H<=D&&(D=(p*s-A)*(p*s-A)-G*(e.lengthSq()-s*s-D),A=0>=D?E=Math.sqrt(H):E=(A-p*s-Math.sqrt(D))/G,p=p*A-s,0>p||p*p>c.lengthSq()||0>A||u.push({clickable:t,distance:E}))));B=0;for(C=y.line.length;B<C;B+=2)k.copy(y.line[B]),k.applyMatrix4(n.matrixWorld),f.copy(y.line[B+1]),f.applyMatrix4(n.matrixWorld),l.subVectors(f,k),E=l.lengthSq(),l.normalize(),e.subVectors(k,this.ray.origin),lineProj=e.dot(l),A=e.dot(this.ray.direction),p=q(this.ray.direction.dot(l)),
-G=1-p*p,0!==G&&(D=(p*A-lineProj)/G,I=(A-p*lineProj)/G,k.add(l.multiplyScalar(D)),f.copy(this.ray.direction).multiplyScalar(I).add(this.ray.origin),H=l.subVectors(f,k).lengthSq(),H<F&&D*D<E&&u.push({clickable:t,distance:I}));B=0;for(C=y.sphere.length;B<C;B++)if(y.sphere[B]instanceof $3Dmol.Sphere&&(b.copy(y.sphere[B]),b.applyMatrix4(n.matrixWorld),this.ray.isIntersectionSphere(b))){k.subVectors(b.center,this.ray.origin);n=k.dot(this.ray.direction);D=n*n-(k.lengthSq()-b.radius*b.radius);if(0>n)break a;
-E=0>=D?n:n-Math.sqrt(D);u.push({clickable:t,distance:E});break a}}}v.sort(m);return v};return a}();$3Dmol.Projector=function(){new $3Dmol.Matrix4;var a=new $3Dmol.Matrix4;this.projectVector=function(b,c){c.matrixWorldInverse.getInverse(c.matrixWorld);a.multiplyMatrices(c.projectionMatrix,c.matrixWorldInverse);return b.applyProjection(a)};this.unprojectVector=function(b,c){c.projectionMatrixInverse.getInverse(c.projectionMatrix);a.multiplyMatrices(c.matrixWorld,c.projectionMatrixInverse);return b.applyProjection(a)}};
-$3Dmol.Camera=function(a,b,c,d){$3Dmol.Object3D.call(this);this.fov=void 0!==a?a:50;this.aspect=void 0!==b?b:1;this.near=void 0!==c?c:.1;this.far=void 0!==d?d:2E3;this.projectionMatrix=new $3Dmol.Matrix4;this.projectionMatrixInverse=new $3Dmol.Matrix4;this.matrixWorldInverse=new $3Dmol.Matrix4;this.updateProjectionMatrix()};$3Dmol.Camera.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Camera.prototype.lookAt=function(a){this.matrix.lookAt(this.position,a,this.up);this.rotationAutoUpdate&&(!1===this.useQuaternion?this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder):this.quaternion.copy(this.matrix.decompose()[1]))};$3Dmol.Camera.prototype.updateProjectionMatrix=function(){this.projectionMatrix.makePerspective(this.fov,this.aspect,this.near,this.far)};
-$3Dmol.SpritePlugin=function(){function a(a,b){return a.z!==b.z?b.z-a.z:b.id-a.id}var b,c,d,e,k,f,l,h,m,q;this.init=function(a){b=a.context;c=a;d=a.getPrecision();e=new Float32Array(16);k=new Uint16Array(6);a=0;e[a++]=-1;e[a++]=-1;e[a++]=0;e[a++]=0;e[a++]=1;e[a++]=-1;e[a++]=1;e[a++]=0;e[a++]=1;e[a++]=1;e[a++]=1;e[a++]=1;e[a++]=-1;e[a++]=1;e[a++]=0;e[a++]=1;a=0;k[a++]=0;k[a++]=1;k[a++]=2;k[a++]=0;k[a++]=2;k[a++]=3;f=b.createBuffer();l=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,f);b.bufferData(b.ARRAY_BUFFER,
-e,b.STATIC_DRAW);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,l);b.bufferData(b.ELEMENT_ARRAY_BUFFER,k,b.STATIC_DRAW);a=$3Dmol.ShaderLib.sprite;var w=d,v=b.createProgram(),x=b.createShader(b.FRAGMENT_SHADER),r=b.createShader(b.VERTEX_SHADER),w="precision "+w+" float;\n";b.shaderSource(x,w+a.fragmentShader);b.shaderSource(r,w+a.vertexShader);b.compileShader(x);b.compileShader(r);b.getShaderParameter(x,b.COMPILE_STATUS)&&b.getShaderParameter(r,b.COMPILE_STATUS)?(b.attachShader(v,x),b.attachShader(v,r),b.linkProgram(v),
-b.getProgramParameter(v,b.LINK_STATUS)||console.error("Could not initialize shader"),a=v):(console.error(b.getShaderInfoLog(x)),console.error("could not initialize shader"),a=null);h=a;m={};q={};m.position=b.getAttribLocation(h,"position");m.uv=b.getAttribLocation(h,"uv");q.uvOffset=b.getUniformLocation(h,"uvOffset");q.uvScale=b.getUniformLocation(h,"uvScale");q.rotation=b.getUniformLocation(h,"rotation");q.scale=b.getUniformLocation(h,"scale");q.alignment=b.getUniformLocation(h,"alignment");q.color=
-b.getUniformLocation(h,"color");q.map=b.getUniformLocation(h,"map");q.opacity=b.getUniformLocation(h,"opacity");q.useScreenCoordinates=b.getUniformLocation(h,"useScreenCoordinates");q.screenPosition=b.getUniformLocation(h,"screenPosition");q.modelViewMatrix=b.getUniformLocation(h,"modelViewMatrix");q.projectionMatrix=b.getUniformLocation(h,"projectionMatrix");q.fogType=b.getUniformLocation(h,"fogType");q.fogDensity=b.getUniformLocation(h,"fogDensity");q.fogNear=b.getUniformLocation(h,"fogNear");q.fogFar=
-b.getUniformLocation(h,"fogFar");q.fogColor=b.getUniformLocation(h,"fogColor");q.alphaTest=b.getUniformLocation(h,"alphaTest")};this.render=function(d,e,k,x){var r=d.__webglSprites,n=r.length;if(n){var t=m,u=q,y=.5*k,F=.5*x;b.useProgram(h);b.enableVertexAttribArray(t.position);b.enableVertexAttribArray(t.uv);b.disable(b.CULL_FACE);b.enable(b.BLEND);b.bindBuffer(b.ARRAY_BUFFER,f);b.vertexAttribPointer(t.position,2,b.FLOAT,!1,16,0);b.vertexAttribPointer(t.uv,2,b.FLOAT,!1,16,8);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,
-l);b.uniformMatrix4fv(u.projectionMatrix,!1,e.projectionMatrix.elements);b.activeTexture(b.TEXTURE0);b.uniform1i(u.map,0);var B=t=0;(t=d.fog)?(b.uniform3f(u.fogColor,t.color.r,t.color.g,t.color.b),b.uniform1f(u.fogNear,t.near),b.uniform1f(u.fogFar,t.far),b.uniform1i(u.fogType,1),B=t=1):(b.uniform1i(u.fogType,0),B=t=0);var C,s,p,A=[];for(C=0;C<n;C++)s=r[C],p=s.material,s.visible&&0!==p.opacity&&(p.useScreenCoordinates?s.z=-s.position.z:(s._modelViewMatrix.multiplyMatrices(e.matrixWorldInverse,s.matrixWorld),
-s.z=-s._modelViewMatrix.elements[14]));r.sort(a);for(C=0;C<n;C++)s=r[C],p=s.material,s.visible&&0!==p.opacity&&p.map&&p.map.image&&p.map.image.width&&(b.uniform1f(u.alphaTest,p.alphaTest),e=p.map.image.height,A[0]=p.map.image.width*c.devicePixelRatio/k,A[1]=e*c.devicePixelRatio/x,!0===p.useScreenCoordinates?(b.uniform1i(u.useScreenCoordinates,1),b.uniform3f(u.screenPosition,(s.position.x*c.devicePixelRatio-y)/y,(F-s.position.y*c.devicePixelRatio)/F,Math.max(0,Math.min(1,s.position.z)))):(b.uniform1i(u.useScreenCoordinates,
-0),b.uniformMatrix4fv(u.modelViewMatrix,!1,s._modelViewMatrix.elements)),e=d.fog&&p.fog?B:0,t!==e&&(b.uniform1i(u.fogType,e),t=e),e=1/(p.scaleByViewport?x:1),A[0]=A[0]*e*s.scale.x,A[1]=A[1]*e*s.scale.y,b.uniform2f(u.uvScale,p.uvScale.x,p.uvScale.y),b.uniform2f(u.uvOffset,p.uvOffset.x,p.uvOffset.y),b.uniform2f(u.alignment,p.alignment.x,p.alignment.y),b.uniform1f(u.opacity,p.opacity),b.uniform3f(u.color,p.color.r,p.color.g,p.color.b),b.uniform1f(u.rotation,s.rotation),b.uniform2fv(u.scale,A),c.setDepthTest(p.depthTest),
-c.setDepthWrite(p.depthWrite),c.setTexture(p.map,0),b.drawElements(b.TRIANGLES,6,b.UNSIGNED_SHORT,0));b.enable(b.CULL_FACE)}}};$3Dmol.Light=function(a,b){$3Dmol.Object3D.call(this);this.color=new $3Dmol.Color(a);this.position=new $3Dmol.Vector3(0,1,0);this.target=new $3Dmol.Object3D;this.intensity=void 0!==b?b:1;this.onlyShadow=this.castShadow=!1};$3Dmol.Light.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Material=function(){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.MaterialIdCount++;this.name="";this.side=$3Dmol.FrontSide;this.opacity=1;this.transparent=!1;this.depthWrite=this.depthTest=!0;this.polygonOffset=!1;this.alphaTest=this.polygonOffsetUnits=this.polygonOffsetFactor=0;this.needsUpdate=this.visible=!0};
-$3Dmol.Material.prototype.setValues=function(a){if(void 0!==a)for(var b in a){var c=a[b];if(void 0===c)console.warn("$3Dmol.Material: '"+b+"' parameter is undefined.");else if(b in this){var d=this[b];d instanceof $3Dmol.Color&&c instanceof $3Dmol.Color?d.copy(c):d instanceof $3Dmol.Color?d.set(c):d instanceof $3Dmol.Vector3&&c instanceof $3Dmol.Vector3?d.copy(c):this[b]=c}}};
-$3Dmol.Material.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Material);a.name=this.name;a.side=this.side;a.opacity=this.opacity;a.transparent=this.transparent;a.depthTest=this.depthTest;a.depthWrite=this.depthWrite;a.polygonOffset=this.polygonOffset;a.polygonOffsetFactor=this.polygonOffsetFactor;a.polygonOffsetUnits=this.polygonOffsetUnits;a.alphaTest=this.alphaTest;a.overdraw=this.overdraw;a.visible=this.visible;return a};$3Dmol.Material.prototype.dispose=function(){this.dispatchEvent({type:"dispose"})};
-$3Dmol.MaterialIdCount=0;$3Dmol.LineBasicMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.linewidth=1;this.linejoin=this.linecap="round";this.vertexColors=!1;this.fog=!0;this.shaderID="basic";this.setValues(a)};$3Dmol.LineBasicMaterial.prototype=Object.create($3Dmol.Material.prototype);$3Dmol.LineBasicMaterial.prototype.clone=function(){var a=new $3Dmol.LineBasicMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy();return a};
-$3Dmol.MeshLambertMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="lambert";
-this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(a)};$3Dmol.MeshLambertMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.MeshLambertMaterial.prototype.clone=function(a){"undefined"===typeof a&&(a=new $3Dmol.MeshLambertMaterial);$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.ambient.copy(this.ambient);a.emissive.copy(this.emissive);a.wrapAround=this.wrapAround;a.wrapRGB.copy(this.wrapRGB);a.map=this.map;a.lightMap=this.lightMap;a.specularMap=this.specularMap;a.envMap=this.envMap;a.combine=this.combine;a.reflectivity=this.reflectivity;a.refractionRatio=this.refractionRatio;a.fog=this.fog;
-a.shading=this.shading;a.shaderID=this.shaderID;a.vertexColors=this.vertexColors;a.skinning=this.skinning;a.morphTargets=this.morphTargets;a.morphNormals=this.morphNormals;return a};$3Dmol.MeshDoubleLambertMaterial=function(a){$3Dmol.MeshLambertMaterial.call(this,a);this.shaderID="lambertdouble";this.side=$3Dmol.DoubleSide};$3Dmol.MeshDoubleLambertMaterial.prototype=Object.create($3Dmol.MeshLambertMaterial.prototype);
-$3Dmol.MeshDoubleLambertMaterial.prototype.clone=function(){var a=new $3Dmol.MeshDoubleLambertMaterial;$3Dmol.MeshLambertMaterial.prototype.clone.call(this,a);return a};
-$3Dmol.ImposterMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="sphereimposter";
-this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(a)};$3Dmol.ImposterMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.ImposterMaterial.prototype.clone=function(){var a=new $3Dmol.ImposterMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.ambient.copy(this.ambient);a.emissive.copy(this.emissive);a.wrapAround=this.wrapAround;a.wrapRGB.copy(this.wrapRGB);a.map=this.map;a.lightMap=this.lightMap;a.specularMap=this.specularMap;a.envMap=this.envMap;a.combine=this.combine;a.reflectivity=this.reflectivity;a.refractionRatio=this.refractionRatio;a.fog=this.fog;a.shading=this.shading;a.shaderID=
-this.shaderID;a.vertexColors=this.vertexColors;a.skinning=this.skinning;a.morphTargets=this.morphTargets;a.morphNormals=this.morphNormals;return a};
-$3Dmol.SpriteMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.map=new $3Dmol.Texture;this.useScreenCoordinates=!0;this.depthTest=!this.useScreenCoordinates;this.sizeAttenuation=!this.useScreenCoordinates;this.scaleByViewPort=!this.sizeAttenuation;this.alignment=$3Dmol.SpriteAlignment.center.clone();this.fog=!1;this.uvOffset=new $3Dmol.Vector2(0,0);this.uvScale=new $3Dmol.Vector2(1,1);this.setValues(a);a=a||{};void 0===a.depthTest&&(this.depthTest=!this.useScreenCoordinates);
-void 0===a.sizeAttenuation&&(this.sizeAttenuation=!this.useScreenCoordinates);void 0===a.scaleByViewPort&&(this.scaleByViewPort=!this.sizeAttenuation)};$3Dmol.SpriteMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.SpriteMaterial.prototype.clone=function(){var a=new $3Dmol.SpriteMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.map=this.map;a.useScreenCoordinates=useScreenCoordinates;a.sizeAttenuation=this.sizeAttenuation;a.scaleByViewport=this.scaleByViewPort;a.alignment.copy(this.alignment);a.uvOffset.copy(this.uvOffset);return a};$3Dmol.SpriteAlignment={};$3Dmol.SpriteAlignment.topLeft=new $3Dmol.Vector2(1,-1);$3Dmol.SpriteAlignment.topCenter=new $3Dmol.Vector2(0,-1);
+$3Dmol.Object3D.prototype={constructor:$3Dmol.Object3D,lookAt:function(b){this.matrix.lookAt(b,this.position,this.up);this.rotationAutoUpdate&&(!0===this.useQuaternion?this.quaternion.copy(this.matrix.decompose()[1]):this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder))},add:function(b){if(b===this)console.error("Can't add $3Dmol.Object3D to itself");else{b.parent=this;this.children.push(b);for(var c=this;void 0!==c.parent;)c=c.parent;void 0!==c&&c instanceof $3Dmol.Scene&&c.__addObject(b)}},
+remove:function(b){var c=this.children.indexOf(b);if(-1!==c){b.parent=void 0;this.children.splice(c,1);for(c=this;void 0!==c.parent;)c=c.parent;void 0!==c&&c instanceof $3Dmol.Scene&&c.__removeObject(b)}},updateMatrix:function(){this.matrix.setPosition(this.position);!1===this.useQuaternion?this.matrix.setRotationFromEuler(this.rotation,this.eulerOrder):this.matrix.setRotationFromQuaternion(this.quaternion);1===this.scale.x&&1===this.scale.y&&1===this.scale.z||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=
+!0},updateMatrixWorld:function(b){!0===this.matrixAutoUpdate&&this.updateMatrix();if(!0===this.matrixWorldNeedsUpdate||!0===b)void 0===this.parent?this.matrixWorld.copy(this.matrix):this.matrixWorld.multiplyMatrices(this.parent.matrixWorld,this.matrix);this.matrixWorldNeedsUpdate=!1;for(b=0;b<this.children.length;b++)this.children[b].updateMatrixWorld(!0)},clone:function(b){void 0===b&&(b=new $3Dmol.Object3D);b.name=this.name;b.up.copy(this.up);b.position.copy(this.position);b.rotation.copy(this.rotation);
+b.eulerOrder=this.eulerOrder;b.scale.copy(this.scale);b.rotationAutoUpdate=this.rotationAutoUpdate;b.matrix.copy(this.matrix);b.matrixWorld.copy(this.matrixWorld);b.quaternion.copy(this.quaternion);b.matrixAutoUpdate=this.matrixAutoUpdate;b.matrixWorldNeedsUpdate=this.matrixWorldNeedsUpdate;b.useQuaternion=this.useQuaternion;b.visible=this.visible;for(var c=0;c<this.children.length;c++)b.add(this.children[c].clone());return b},setVisible:function(b){this.visible=b;for(var c=0;c<this.children.length;c++)this.children[c].setVisible(b)}};
+$3Dmol.Object3DIDCount=0;
+$3Dmol.Geometry=function(){var b=function(b){this.id=b||0;this.lineArray=this.radiusArray=this.faceArray=this.normalArray=this.colorArray=this.vertexArray=null;this.lineidx=this.faceidx=this.vertices=0};b.prototype.getNumVertices=function(){return this.vertices};b.prototype.getVertices=function(){return this.vertexArray};b.prototype.getCentroid=function(){for(var b=new $3Dmol.Vector3,c,d,q,B=0;B<this.vertices;++B)c=3*B,d=this.vertexArray[c],q=this.vertexArray[c+1],c=this.vertexArray[c+2],b.x+=d,b.y+=
+q,b.z+=c;b.divideScalar(this.vertices);return b};b.prototype.setNormals=function(){var b=this.faceArray,c=this.vertexArray,d=this.normalArray;if(this.vertices&&this.faceidx)for(var q,B,f,w,h,t,m=0;m<b.length/3;++m)q=3*b[3*m],B=3*b[3*m+1],f=3*b[3*m+2],w=new $3Dmol.Vector3(c[q],c[q+1],c[q+2]),h=new $3Dmol.Vector3(c[B],c[B+1],c[B+2]),t=new $3Dmol.Vector3(c[f],c[f+1],c[f+2]),w.subVectors(w,h),t.subVectors(t,h),t.cross(w),w=t,w.normalize(),d[q]+=w.x,d[B]+=w.x,d[f]+=w.x,d[q+1]+=w.y,d[B+1]+=w.y,d[f+1]+=
+w.y,d[q+2]+=w.z,d[B+2]+=w.z,d[f+2]+=w.z};b.prototype.setLineIndices=function(){if(this.faceidx){var b=this.faceArray,c=this.lineArray=new Uint16Array(2*this.faceidx);this.lineidx=2*this.faceidx;for(var d,q=0;q<this.faceidx/3;++q){d=3*q;lineoffset=2*d;var B=b[d],f=b[d+1];d=b[d+2];c[lineoffset]=B;c[lineoffset+1]=f;c[lineoffset+2]=B;c[lineoffset+3]=d;c[lineoffset+4]=f;c[lineoffset+5]=d}}};b.prototype.truncateArrayBuffers=function(b,c){b=!0===b?!0:!1;var d=this.colorArray,q=this.normalArray,B=this.faceArray,
+f=this.lineArray,w=this.radiusArray;this.vertexArray=this.vertexArray.subarray(0,3*this.vertices);this.colorArray=d.subarray(0,3*this.vertices);b?(this.normalArray=q.subarray(0,3*this.vertices),this.faceArray=B.subarray(0,this.faceidx),this.lineArray=0<this.lineidx?f.subarray(0,this.lineidx):new Uint16Array):(this.normalArray=new Float32Array,this.faceArray=new Uint16Array,this.lineArray=new Uint16Array);w&&(this.radiusArray=w.subarray(0,this.vertices));c&&(this.normalArray&&(this.normalArray=new Float32Array(this.normalArray)),
+this.faceArray&&(this.faceArray=new Uint16Array(this.faceArray)),this.lineArray&&(this.lineArray=new Uint16Array(this.lineArray)),this.vertexArray&&(this.vertexArray=new Float32Array(this.vertexArray)),this.colorArray&&(this.colorArray=new Float32Array(this.colorArray)),this.radiusArray&&(this.radiusArray=new Float32Array(this.radiusArray)));this.__inittedArrays=!0};var c=function(c){var d=new b(c.geometryGroups.length);c.geometryGroups.push(d);c.groups=c.geometryGroups.length;d.vertexArray=new Float32Array(196605);
+d.colorArray=new Float32Array(196605);c.mesh&&(d.normalArray=new Float32Array(196605),d.faceArray=new Uint16Array(393210),d.lineArray=new Uint16Array(393210));c.radii&&(d.radiusArray=new Float32Array(65535));d.useOffset=c.offset;return d},d=function(b,c,d){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.GeometryIDCount++;this.name="";this.hasTangents=!1;this.dynamic=!0;this.mesh=!0===b?!0:!1;this.radii=c||!1;this.offset=d||!1;this.buffersNeedUpdate=this.colorsNeedUpdate=this.normalsNeedUpdate=this.elementsNeedUpdate=
+this.verticesNeedUpdate=!1;this.geometryGroups=[];this.groups=0};d.prototype={constructor:d,updateGeoGroup:function(b){var d=0<this.groups?this.geometryGroups[this.groups-1]:null;if(!d||d.vertices+(b||0)>d.vertexArray.length/3)d=c(this);return d},addGeoGroup:function(){return c(this)},setUpNormals:function(b){b=b||!1;for(var c=0;c<this.groups;c++)this.geometryGroups[c].setNormals(b)},setUpWireframe:function(){for(var b=0;b<this.groups;b++)this.geometryGroups[b].setLineIndices()},initTypedArrays:function(){for(var b=
+0;b<this.groups;b++){var c=this.geometryGroups[b];!0!==c.__inittedArrays&&c.truncateArrayBuffers(this.mesh,!1)}},dispose:function(){this.dispatchEvent({type:"dispose"})}};return d}();Object.defineProperty($3Dmol.Geometry.prototype,"vertices",{get:function(){for(var b=0,c=0;c<this.groups;c++)b+=this.geometryGroups[c].vertices;return b}});$3Dmol.GeometryIDCount=0;
+$3Dmol.Raycaster=function(){var b=function(b,c,h,f){this.ray=new $3Dmol.Ray(b,c);0<this.ray.direction.lengthSq()&&this.ray.direction.normalize();this.near=f||0;this.far=h||Infinity},c=new $3Dmol.Sphere,d=new $3Dmol.Cylinder,p=new $3Dmol.Triangle,y=new $3Dmol.Vector3,A=new $3Dmol.Vector3,q=new $3Dmol.Vector3,B=new $3Dmol.Vector3;new $3Dmol.Ray;new $3Dmol.Vector3;var f=new $3Dmol.Vector3;new $3Dmol.Matrix4;var w=function(b,c){return b.distance-c.distance},h=function(b){return Math.min(Math.max(b,-1),
+1)};b.prototype.precision=1E-4;b.prototype.linePrecision=.2;b.prototype.set=function(b,c){this.ray.set(b,c)};b.prototype.intersectObjects=function(b,m){for(var e=[],F=0,g=m.length;F<g;F++)a:{var x=b,u=m[F],s=e;f.getPositionFromMatrix(x.matrixWorld);if(!0===u.clickable&&void 0!==u.intersectionShape){var l=u.intersectionShape,E=this.linePrecision,E=E*x.matrixWorld.getMaxScaleOnAxis(),E=E*E;if(void 0!==u.boundingSphere&&u.boundingSphere instanceof $3Dmol.Sphere&&(c.copy(u.boundingSphere),c.applyMatrix4(x.matrixWorld),
+!this.ray.isIntersectionSphere(c)))break a;for(var M=void 0,C=void 0,G=void 0,z=void 0,H=G=void 0,L=void 0,N=void 0,J=void 0,I=void 0,K=I=H=z=void 0,M=0,C=l.triangle.length;M<C;M++)l.triangle[M]instanceof $3Dmol.Triangle&&(p.copy(l.triangle[M]),p.applyMatrix4(x.matrixWorld),G=p.getNormal(),z=this.ray.direction.dot(G),0<=z||(y.subVectors(p.a,this.ray.origin),L=G.dot(y)/z,0>L||(A.copy(this.ray.direction).multiplyScalar(L).add(this.ray.origin),A.sub(p.a),q.copy(p.b).sub(p.a),B.copy(p.c).sub(p.a),z=q.dot(B),
+G=q.lengthSq(),H=B.lengthSq(),H=(G*A.dot(B)-z*A.dot(q))/(G*H-z*z),0>H||1<H||(z=(A.dot(q)-H*z)/G,0>z||1<z||1<z+H||s.push({clickable:u,distance:L})))));M=0;for(C=l.cylinder.length;M<C;M++)l.cylinder[M]instanceof $3Dmol.Cylinder&&(d.copy(l.cylinder[M]),d.applyMatrix4(x.matrixWorld),y.subVectors(d.c1,this.ray.origin),G=y.dot(d.direction),H=y.dot(this.ray.direction),z=h(this.ray.direction.dot(d.direction)),J=1-z*z,0!==J&&(I=(z*H-G)/J,K=(H-z*G)/J,A.copy(d.direction).multiplyScalar(I).add(d.c1),q.copy(this.ray.direction).multiplyScalar(K).add(this.ray.origin),
+N=B.subVectors(A,q).lengthSq(),I=d.radius*d.radius,N<=I&&(I=(z*G-H)*(z*G-H)-J*(y.lengthSq()-G*G-I),H=0>=I?L=Math.sqrt(N):L=(H-z*G-Math.sqrt(I))/J,z=z*H-G,0>z||z*z>d.lengthSq()||0>H||s.push({clickable:u,distance:L}))));M=0;for(C=l.line.length;M<C;M+=2)A.copy(l.line[M]),A.applyMatrix4(x.matrixWorld),q.copy(l.line[M+1]),q.applyMatrix4(x.matrixWorld),B.subVectors(q,A),L=B.lengthSq(),B.normalize(),y.subVectors(A,this.ray.origin),lineProj=y.dot(B),H=y.dot(this.ray.direction),z=h(this.ray.direction.dot(B)),
+J=1-z*z,0!==J&&(I=(z*H-lineProj)/J,K=(H-z*lineProj)/J,A.add(B.multiplyScalar(I)),q.copy(this.ray.direction).multiplyScalar(K).add(this.ray.origin),N=B.subVectors(q,A).lengthSq(),N<E&&I*I<L&&s.push({clickable:u,distance:K}));M=0;for(C=l.sphere.length;M<C;M++)if(l.sphere[M]instanceof $3Dmol.Sphere&&(c.copy(l.sphere[M]),c.applyMatrix4(x.matrixWorld),this.ray.isIntersectionSphere(c))){A.subVectors(c.center,this.ray.origin);x=A.dot(this.ray.direction);I=x*x-(A.lengthSq()-c.radius*c.radius);if(0>x)break a;
+L=0>=I?x:x-Math.sqrt(I);s.push({clickable:u,distance:L});break a}}}e.sort(w);return e};return b}();$3Dmol.Projector=function(){new $3Dmol.Matrix4;var b=new $3Dmol.Matrix4;this.projectVector=function(c,d){d.matrixWorldInverse.getInverse(d.matrixWorld);b.multiplyMatrices(d.projectionMatrix,d.matrixWorldInverse);return c.applyProjection(b)};this.unprojectVector=function(c,d){d.projectionMatrixInverse.getInverse(d.projectionMatrix);b.multiplyMatrices(d.matrixWorld,d.projectionMatrixInverse);return c.applyProjection(b)}};
+$3Dmol.Camera=function(b,c,d,p){$3Dmol.Object3D.call(this);this.fov=void 0!==b?b:50;this.aspect=void 0!==c?c:1;this.near=void 0!==d?d:.1;this.far=void 0!==p?p:2E3;this.projectionMatrix=new $3Dmol.Matrix4;this.projectionMatrixInverse=new $3Dmol.Matrix4;this.matrixWorldInverse=new $3Dmol.Matrix4;this.updateProjectionMatrix()};$3Dmol.Camera.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Camera.prototype.lookAt=function(b){this.matrix.lookAt(this.position,b,this.up);this.rotationAutoUpdate&&(!1===this.useQuaternion?this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder):this.quaternion.copy(this.matrix.decompose()[1]))};$3Dmol.Camera.prototype.updateProjectionMatrix=function(){this.projectionMatrix.makePerspective(this.fov,this.aspect,this.near,this.far);this.projectionMatrixInverse.getInverse(this.projectionMatrix)};
+$3Dmol.SpritePlugin=function(){function b(b,c){return b.z!==c.z?c.z-b.z:c.id-b.id}var c,d,p,y,A,q,B,f,w,h;this.init=function(b){c=b.context;d=b;p=b.getPrecision();y=new Float32Array(16);A=new Uint16Array(6);b=0;y[b++]=-1;y[b++]=-1;y[b++]=0;y[b++]=0;y[b++]=1;y[b++]=-1;y[b++]=1;y[b++]=0;y[b++]=1;y[b++]=1;y[b++]=1;y[b++]=1;y[b++]=-1;y[b++]=1;y[b++]=0;y[b++]=1;b=0;A[b++]=0;A[b++]=1;A[b++]=2;A[b++]=0;A[b++]=2;A[b++]=3;q=c.createBuffer();B=c.createBuffer();c.bindBuffer(c.ARRAY_BUFFER,q);c.bufferData(c.ARRAY_BUFFER,
+y,c.STATIC_DRAW);c.bindBuffer(c.ELEMENT_ARRAY_BUFFER,B);c.bufferData(c.ELEMENT_ARRAY_BUFFER,A,c.STATIC_DRAW);b=$3Dmol.ShaderLib.sprite;var m=p,e=c.createProgram(),F=c.createShader(c.FRAGMENT_SHADER),g=c.createShader(c.VERTEX_SHADER),m="precision "+m+" float;\n";c.shaderSource(F,m+b.fragmentShader);c.shaderSource(g,m+b.vertexShader);c.compileShader(F);c.compileShader(g);c.getShaderParameter(F,c.COMPILE_STATUS)&&c.getShaderParameter(g,c.COMPILE_STATUS)?(c.attachShader(e,F),c.attachShader(e,g),c.linkProgram(e),
+c.getProgramParameter(e,c.LINK_STATUS)||console.error("Could not initialize shader"),b=e):(console.error(c.getShaderInfoLog(F)),console.error("could not initialize shader"),b=null);f=b;w={};h={};w.position=c.getAttribLocation(f,"position");w.uv=c.getAttribLocation(f,"uv");h.uvOffset=c.getUniformLocation(f,"uvOffset");h.uvScale=c.getUniformLocation(f,"uvScale");h.rotation=c.getUniformLocation(f,"rotation");h.scale=c.getUniformLocation(f,"scale");h.alignment=c.getUniformLocation(f,"alignment");h.color=
+c.getUniformLocation(f,"color");h.map=c.getUniformLocation(f,"map");h.opacity=c.getUniformLocation(f,"opacity");h.useScreenCoordinates=c.getUniformLocation(f,"useScreenCoordinates");h.screenPosition=c.getUniformLocation(f,"screenPosition");h.modelViewMatrix=c.getUniformLocation(f,"modelViewMatrix");h.projectionMatrix=c.getUniformLocation(f,"projectionMatrix");h.fogType=c.getUniformLocation(f,"fogType");h.fogDensity=c.getUniformLocation(f,"fogDensity");h.fogNear=c.getUniformLocation(f,"fogNear");h.fogFar=
+c.getUniformLocation(f,"fogFar");h.fogColor=c.getUniformLocation(f,"fogColor");h.alphaTest=c.getUniformLocation(f,"alphaTest")};this.render=function(t,m,e,F){var g=t.__webglSprites,x=g.length;if(x){var u=w,s=h,l=.5*e,E=.5*F;c.useProgram(f);c.enableVertexAttribArray(u.position);c.enableVertexAttribArray(u.uv);c.disable(c.CULL_FACE);c.enable(c.BLEND);c.bindBuffer(c.ARRAY_BUFFER,q);c.vertexAttribPointer(u.position,2,c.FLOAT,!1,16,0);c.vertexAttribPointer(u.uv,2,c.FLOAT,!1,16,8);c.bindBuffer(c.ELEMENT_ARRAY_BUFFER,
+B);c.uniformMatrix4fv(s.projectionMatrix,!1,m.projectionMatrix.elements);c.activeTexture(c.TEXTURE0);c.uniform1i(s.map,0);var p=u=0;(u=t.fog)?(c.uniform3f(s.fogColor,u.color.r,u.color.g,u.color.b),c.uniform1f(s.fogNear,u.near),c.uniform1f(s.fogFar,u.far),c.uniform1i(s.fogType,1),p=u=1):(c.uniform1i(s.fogType,0),p=u=0);var C,y,z,H=[];for(C=0;C<x;C++)y=g[C],z=y.material,y.visible&&0!==z.opacity&&(z.useScreenCoordinates?y.z=-y.position.z:(y._modelViewMatrix.multiplyMatrices(m.matrixWorldInverse,y.matrixWorld),
+y.z=-y._modelViewMatrix.elements[14]));g.sort(b);for(C=0;C<x;C++)y=g[C],z=y.material,y.visible&&0!==z.opacity&&z.map&&z.map.image&&z.map.image.width&&(c.uniform1f(s.alphaTest,z.alphaTest),m=z.map.image.height,H[0]=z.map.image.width*d.devicePixelRatio/e,H[1]=m*d.devicePixelRatio/F,!0===z.useScreenCoordinates?(c.uniform1i(s.useScreenCoordinates,1),c.uniform3f(s.screenPosition,(y.position.x*d.devicePixelRatio-l)/l,(E-y.position.y*d.devicePixelRatio)/E,Math.max(0,Math.min(1,y.position.z)))):(c.uniform1i(s.useScreenCoordinates,
+0),c.uniformMatrix4fv(s.modelViewMatrix,!1,y._modelViewMatrix.elements)),m=t.fog&&z.fog?p:0,u!==m&&(c.uniform1i(s.fogType,m),u=m),m=1/(z.scaleByViewport?F:1),H[0]=H[0]*m*y.scale.x,H[1]=H[1]*m*y.scale.y,c.uniform2f(s.uvScale,z.uvScale.x,z.uvScale.y),c.uniform2f(s.uvOffset,z.uvOffset.x,z.uvOffset.y),c.uniform2f(s.alignment,z.alignment.x,z.alignment.y),c.uniform1f(s.opacity,z.opacity),c.uniform3f(s.color,z.color.r,z.color.g,z.color.b),c.uniform1f(s.rotation,y.rotation),c.uniform2fv(s.scale,H),d.setDepthTest(z.depthTest),
+d.setDepthWrite(z.depthWrite),d.setTexture(z.map,0),c.drawElements(c.TRIANGLES,6,c.UNSIGNED_SHORT,0));c.enable(c.CULL_FACE)}}};$3Dmol.Light=function(b,c){$3Dmol.Object3D.call(this);this.color=new $3Dmol.Color(b);this.position=new $3Dmol.Vector3(0,1,0);this.target=new $3Dmol.Object3D;this.intensity=void 0!==c?c:1;this.onlyShadow=this.castShadow=!1};$3Dmol.Light.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Material=function(){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.MaterialIdCount++;this.name="";this.side=$3Dmol.FrontSide;this.opacity=1;this.transparent=!1;this.stencilTest=this.depthWrite=this.depthTest=!0;this.polygonOffset=!1;this.alphaTest=this.polygonOffsetUnits=this.polygonOffsetFactor=0;this.needsUpdate=this.visible=!0};
+$3Dmol.Material.prototype.setValues=function(b){if(void 0!==b)for(var c in b){var d=b[c];if(void 0===d)console.warn("$3Dmol.Material: '"+c+"' parameter is undefined.");else if(c in this){var p=this[c];p instanceof $3Dmol.Color&&d instanceof $3Dmol.Color?p.copy(d):p instanceof $3Dmol.Color?p.set(d):p instanceof $3Dmol.Vector3&&d instanceof $3Dmol.Vector3?p.copy(d):this[c]=d}}};
+$3Dmol.Material.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Material);b.name=this.name;b.side=this.side;b.opacity=this.opacity;b.transparent=this.transparent;b.depthTest=this.depthTest;b.depthWrite=this.depthWrite;b.stencilTest=this.stencilTest;b.polygonOffset=this.polygonOffset;b.polygonOffsetFactor=this.polygonOffsetFactor;b.polygonOffsetUnits=this.polygonOffsetUnits;b.alphaTest=this.alphaTest;b.overdraw=this.overdraw;b.visible=this.visible;return b};
+$3Dmol.Material.prototype.dispose=function(){this.dispatchEvent({type:"dispose"})};$3Dmol.MaterialIdCount=0;$3Dmol.LineBasicMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.linewidth=1;this.linejoin=this.linecap="round";this.vertexColors=!1;this.fog=!0;this.shaderID="basic";this.setValues(b)};$3Dmol.LineBasicMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.LineBasicMaterial.prototype.clone=function(){var b=new $3Dmol.LineBasicMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);return b};
+$3Dmol.MeshLambertMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="lambert";
+this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(b)};$3Dmol.MeshLambertMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.MeshLambertMaterial.prototype.clone=function(b){"undefined"===typeof b&&(b=new $3Dmol.MeshLambertMaterial);$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;
+b.shading=this.shading;b.shaderID=this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;return b};$3Dmol.MeshDoubleLambertMaterial=function(b){$3Dmol.MeshLambertMaterial.call(this,b);this.shaderID="lambertdouble";this.side=$3Dmol.DoubleSide};$3Dmol.MeshDoubleLambertMaterial.prototype=Object.create($3Dmol.MeshLambertMaterial.prototype);
+$3Dmol.MeshDoubleLambertMaterial.prototype.clone=function(){var b=new $3Dmol.MeshDoubleLambertMaterial;$3Dmol.MeshLambertMaterial.prototype.clone.call(this,b);return b};$3Dmol.MeshOutlineMaterial=function(b){$3Dmol.Material.call(this);b=b||{};this.fog=!0;this.shaderID="outline";this.wireframe=!1;this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1};$3Dmol.MeshOutlineMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.MeshOutlineMaterial.prototype.clone=function(b){"undefined"===typeof b&&(b=new $3Dmol.MeshOutlineMaterial);$3Dmol.Material.prototype.clone.call(this,b);b.fog=this.fog;b.shaderID=this.shaderID;b.wireframe=this.wireframe;return b};
+$3Dmol.ImposterMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.imposter=!0;this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID=
+null;this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(b)};$3Dmol.ImposterMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.ImposterMaterial.prototype.clone=function(){var b=new $3Dmol.ImposterMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;b.shading=this.shading;b.shaderID=
+this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;return b};$3Dmol.SphereImposterMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="sphereimposter";this.setValues(b)};$3Dmol.SphereImposterMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.SphereImposterMaterial.prototype.clone=function(){var b=new $3Dmol.SphereImposterMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);return b};$3Dmol.SphereImposterOutlineMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="sphereimposteroutline";this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1;this.setValues(b)};$3Dmol.SphereImposterOutlineMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.SphereImposterOutlineMaterial.prototype.clone=function(){var b=new $3Dmol.SphereImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);b.outlineColor=this.outlineColor;b.outlineWidth=this.outlineWidth;b.outlinePushback=this.outlinePushback;return b};$3Dmol.StickImposterMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="stickimposter";this.setValues(b)};$3Dmol.StickImposterMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.StickImposterMaterial.prototype.clone=function(){var b=new $3Dmol.StickImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);return b};$3Dmol.StickImposterOutlineMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="stickimposteroutline";this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1;this.setValues(b)};$3Dmol.StickImposterOutlineMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.StickImposterOutlineMaterial.prototype.clone=function(){var b=new $3Dmol.StickImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);b.outlineColor=this.outlineColor;b.outlineWidth=this.outlineWidth;b.outlinePushback=this.outlinePushback;return b};
+$3Dmol.InstancedMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="instanced";
+this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.sphere=null;this.setValues(b)};$3Dmol.InstancedMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.InstancedMaterial.prototype.clone=function(){var b=new $3Dmol.InstancedMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;b.shading=this.shading;b.shaderID=
+this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;b.sphere=this.sphere;return b};
+$3Dmol.SpriteMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.map=new $3Dmol.Texture;this.useScreenCoordinates=!0;this.depthTest=!this.useScreenCoordinates;this.sizeAttenuation=!this.useScreenCoordinates;this.scaleByViewPort=!this.sizeAttenuation;this.alignment=$3Dmol.SpriteAlignment.center.clone();this.fog=!1;this.uvOffset=new $3Dmol.Vector2(0,0);this.uvScale=new $3Dmol.Vector2(1,1);this.setValues(b);b=b||{};void 0===b.depthTest&&(this.depthTest=!this.useScreenCoordinates);
+void 0===b.sizeAttenuation&&(this.sizeAttenuation=!this.useScreenCoordinates);void 0===b.scaleByViewPort&&(this.scaleByViewPort=!this.sizeAttenuation)};$3Dmol.SpriteMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.SpriteMaterial.prototype.clone=function(){var b=new $3Dmol.SpriteMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.map=this.map;b.useScreenCoordinates=useScreenCoordinates;b.sizeAttenuation=this.sizeAttenuation;b.scaleByViewport=this.scaleByViewPort;b.alignment.copy(this.alignment);b.uvOffset.copy(this.uvOffset);return b};$3Dmol.SpriteAlignment={};$3Dmol.SpriteAlignment.topLeft=new $3Dmol.Vector2(1,-1);$3Dmol.SpriteAlignment.topCenter=new $3Dmol.Vector2(0,-1);
 $3Dmol.SpriteAlignment.topRight=new $3Dmol.Vector2(-1,-1);$3Dmol.SpriteAlignment.centerLeft=new $3Dmol.Vector2(1,0);$3Dmol.SpriteAlignment.center=new $3Dmol.Vector2(0,0);$3Dmol.SpriteAlignment.centerRight=new $3Dmol.Vector2(-1,0);$3Dmol.SpriteAlignment.bottomLeft=new $3Dmol.Vector2(1,1);$3Dmol.SpriteAlignment.bottomCenter=new $3Dmol.Vector2(0,1);$3Dmol.SpriteAlignment.bottomRight=new $3Dmol.Vector2(-1,1);
-$3Dmol.Texture=function(a){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.TextureIdCount++;this.name="";this.image=a;this.mipmaps=[];this.mapping=new $3Dmol.UVMapping;this.wrapT=this.wrapS=$3Dmol.ClampToEdgeWrapping;this.magFilter=$3Dmol.LinearFilter;this.minFilter=$3Dmol.LinearMipMapLinearFilter;this.anisotropy=1;this.format=$3Dmol.RGBAFormat;this.type=$3Dmol.UnsignedByteType;this.offset=new $3Dmol.Vector2(0,0);this.repeat=new $3Dmol.Vector2(1,1);this.generateMipmaps=!0;this.premultiplyAlpha=!1;
+$3Dmol.Texture=function(b){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.TextureIdCount++;this.name="";this.image=b;this.mipmaps=[];this.mapping=new $3Dmol.UVMapping;this.wrapT=this.wrapS=$3Dmol.ClampToEdgeWrapping;this.magFilter=$3Dmol.LinearFilter;this.minFilter=$3Dmol.LinearMipMapLinearFilter;this.anisotropy=1;this.format=$3Dmol.RGBAFormat;this.type=$3Dmol.UnsignedByteType;this.offset=new $3Dmol.Vector2(0,0);this.repeat=new $3Dmol.Vector2(1,1);this.generateMipmaps=!0;this.premultiplyAlpha=!1;
 this.flipY=!0;this.unpackAlignment=4;this.needsUpdate=!1;this.onUpdate=null};
-$3Dmol.Texture.prototype={constructor:$3Dmol.Texture,clone:function(a){void 0===a&&(a=new $3Dmol.Texture);a.image=this.image;a.mipmaps=this.mipmaps.slice(0);a.mapping=this.mapping;a.wrapS=this.wrapS;a.wrapT=this.wrapT;a.magFilter=this.magFilter;a.minFilter=this.minFilter;a.anisotropy=this.anisotropy;a.format=this.format;a.type=this.type;a.offset.copy(this.offset);a.repeat.copy(this.repeat);a.generateMipmaps=this.generateMipmaps;a.premultiplyAlpha=this.premultiplyAlpha;a.flipY=this.flipY;a.unpackAlignment=
-this.unpackAlignment;return a},dispose:function(){this.dispatchEvent({type:"dispose"})}};$3Dmol.TextureIdCount=0;$3Dmol.FrontSide=0;$3Dmol.BackSide=1;$3Dmol.DoubleSide=2;$3Dmol.NoShading=0;$3Dmol.FlatShading=1;$3Dmol.SmoothShading=2;$3Dmol.NoColors=0;$3Dmol.FaceColors=1;$3Dmol.VertexColors=2;$3Dmol.MultiplyOperation=0;$3Dmol.MixOperation=1;$3Dmol.AddOperation=2;$3Dmol.UVMapping=function(){};$3Dmol.ClampToEdgeWrapping=1001;$3Dmol.LinearFilter=1006;$3Dmol.LinearMipMapLinearFilter=1008;
-$3Dmol.UnsignedByteType=1009;$3Dmol.RGBAFormat=1021;$3Dmol.Line=function(a,b,c){$3Dmol.Object3D.call(this);this.geometry=a;this.material=void 0!==b?b:new $3Dmol.LineBasicMaterial({color:16777215*Math.random()});this.type=void 0!==c?c:$3Dmol.LineStrip};$3Dmol.LineStrip=0;$3Dmol.LinePieces=1;$3Dmol.Line.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Line.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Line(this.geometry,this.material,this.type));$3Dmol.Object3D.prototype.clone.call(this,a);return a};$3Dmol.Mesh=function(a,b){$3Dmol.Object3D.call(this);this.geometry=a;this.material=void 0!==b?b:new $3Dmol.MeshBasicMaterial({color:16777215*Math.random(),wireframe:!0})};$3Dmol.Mesh.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Mesh.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Mesh(this.geometry,this.material));$3Dmol.Object3D.prototype.clone.call(this,a);return a};$3Dmol.Sprite=function(a){$3Dmol.Object3D.call(this);this.material=void 0!==a?a:new $3Dmol.SpriteMaterial;this.rotation3d=this.rotation;this.rotation=0};$3Dmol.Sprite.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Sprite.prototype.updateMatrix=function(){this.matrix.setPosition(this.position);this.rotation3d.set(0,0,this.rotation);this.matrix.setRotationFromEuler(this.rotation3d);1===this.scale.x&&1===this.scale.y||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=!0};$3Dmol.Sprite.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Sprite(this.material));$3Dmol.Object3D.prototype.clone.call(this,a);return a};
-$3Dmol.Renderer=function(a){function b(a){J[a]||(g.enableVertexAttribArray(a),J[a]=!0)}function c(a,b){var c;"fragment"===a?c=g.createShader(g.FRAGMENT_SHADER):"vertex"===a&&(c=g.createShader(g.VERTEX_SHADER));g.shaderSource(c,b);g.compileShader(c);return g.getShaderParameter(c,g.COMPILE_STATUS)?c:(console.error(g.getShaderInfoLog(c)),console.error("could not initialize shader"),null)}function d(a,b,c,d,e,f,k,l){var h,n,m;b?(n=a.length-1,l=b=-1):(n=0,b=a.length,l=1);for(var p=n;p!==b;p+=l)if(h=a[p],
-h.render&&(n=h.object,m=h.buffer,h=h[c])){k&&r.setBlending(!0);r.setDepthTest(h.depthTest);r.setDepthWrite(h.depthWrite);var q=h.polygonOffset;null!==q&&(q?g.enable(g.POLYGON_OFFSET_FILL):g.disable(g.POLYGON_OFFSET_FILL));r.setMaterialFaces(h);r.renderBuffer(d,e,f,h,m,n)}}function e(a){return 0===(a&a-1)}function k(a){return a===$3Dmol.UnsignedByteType?g.UNSIGNED_BYTE:a===$3Dmol.RGBAFormat?g.RGBA:0}a=a||{};var f=void 0!==a.canvas?a.canvas:document.createElement("canvas"),l=void 0!==a.precision?a.precision:
-"highp",h=void 0!==a.alpha?a.alpha:!0,m=void 0!==a.premultipliedAlpha?a.premultipliedAlpha:!0,q=void 0!==a.antialias?a.antialias:!1,z=void 0!==a.stencil?a.stencil:!0,w=void 0!==a.preserveDrawingBuffer?a.preserveDrawingBuffer:!1,v=void 0!==a.clearColor?new $3Dmol.Color(a.clearColor):new $3Dmol.Color(0),x=void 0!==a.clearAlpha?a.clearAlpha:0;this.domElement=f;this.context=null;this.devicePixelRatio=void 0!==a.devicePixelRatio?a.devicePixelRatio:void 0!==self.devicePixelRatio?self.devicePixelRatio:1;
-this.autoUpdateScene=this.autoUpdateObjects=this.sortObjects=this.autoClearStencil=this.autoClearDepth=this.autoClearColor=this.autoClear=!0;this.renderPluginsPost=[];this.info={memory:{programs:0,geometries:0,textures:0},render:{calls:0,vertices:0,faces:0,points:0}};var r=this,n=[],t=0,u=null,y=-1,F=null,B=null,C=0,s=-1,p=-1,A=-1,E=-1,H=null,G=0,D=0,I=0,L=0,M=0,N=0,J={},X=new $3Dmol.Matrix4,S=new $3Dmol.Vector3,K=new $3Dmol.Vector3,O=!0,P=[0,0,0],Q=[],R=[],g;try{if(!(g=f.getContext("experimental-webgl",
-{alpha:h,premultipliedAlpha:m,antialias:q,stencil:z,preserveDrawingBuffer:w}))&&!(g=f.getContext("webgl",{alpha:h,premultipliedAlpha:m,antialias:q,stencil:z,preserveDrawingBuffer:w})))throw"Error creating WebGL context.";}catch(Y){console.error(Y)}g.getExtension("EXT_frag_depth");g.clearColor(0,0,0,1);g.clearDepth(1);g.clearStencil(0);g.enable(g.DEPTH_TEST);g.depthFunc(g.LEQUAL);g.frontFace(g.CCW);g.cullFace(g.BACK);g.enable(g.CULL_FACE);g.enable(g.BLEND);g.blendEquation(g.FUNC_ADD);g.blendFunc(g.SRC_ALPHA,
-g.ONE_MINUS_SRC_ALPHA);g.clearColor(v.r,v.g,v.b,x);g.getExtension("EXT_frag_depth");this.context=g;this.getContext=function(){return g};this.getPrecision=function(){return l};this.setClearColorHex=function(a,b){v.setHex(a);x=b;g.clearColor(v.r,v.g,v.b,x)};this.setSize=function(a,b){f.width=a*this.devicePixelRatio;f.height=b*this.devicePixelRatio;f.style.width=a+"px";f.style.height=b+"px";this.setViewport(0,0,f.width,f.height)};this.setViewport=function(a,b,c,d){G=void 0!==a?a:0;D=void 0!==b?b:0;I=
-void 0!==c?c:f.width;L=void 0!==d?d:f.height;g.viewport(G,D,I,L)};this.clear=function(a,b,c){var d=0;if(void 0===a||a)d|=g.COLOR_BUFFER_BIT;if(void 0===b||b)d|=g.DEPTH_BUFFER_BIT;if(void 0===c||c)d|=g.STENCIL_BUFFER_BIT;g.clear(d)};this.clearTarget=function(a,b,c){this.clear(a,b,c)};this.setMaterialFaces=function(a){var b=a.side===$3Dmol.DoubleSide;a=a.side===$3Dmol.BackSide;s!==b&&(b?g.disable(g.CULL_FACE):g.enable(g.CULL_FACE),s=b);p!==a&&(a?g.frontFace(g.CW):g.frontFace(g.CCW),p=a)};this.setDepthTest=
-function(a){A!==a&&(a?g.enable(g.DEPTH_TEST):g.disable(g.DEPTH_TEST),A=a)};this.setDepthWrite=function(a){E!==a&&(g.depthMask(a),E=a)};this.setBlending=function(a){a?(g.enable(g.BLEND),g.blendEquationSeparate(g.FUNC_ADD,g.FUNC_ADD),g.blendFuncSeparate(g.SRC_ALPHA,g.ONE_MINUS_SRC_ALPHA,g.ONE,g.ONE_MINUS_SRC_ALPHA)):g.disable(g.BLEND)};this.addPostPlugin=function(a){a.init(this);this.renderPluginsPost.push(a)};var T=function(a){a=a.target;a.removeEventListener("dispose",T);a.__webglInit=void 0;void 0!==
-a.__webglVertexBuffer&&g.deleteBuffer(a.__webglVertexBuffer);void 0!==a.__webglColorBuffer&&g.deleteBuffer(a.__webglColorBuffer);if(void 0!==a.geometryGroups)for(var b=0,c=a.groups;b<c;b++){var d=a.geometryGroups[b];void 0!==d.__webglVertexBuffer&&g.deleteBuffer(d.__webglVertexBuffer);void 0!==d.__webglColorBuffer&&g.deleteBuffer(d.__webglColorBuffer);void 0!==d.__webglNormalBuffer&&g.deleteBuffer(d.__webglNormalBuffer);void 0!==d.__webglFaceBuffer&&g.deleteBuffer(d.__webglFaceBuffer);void 0!==d.__webglLineBuffer&&
-g.deleteBuffer(d.__webglLineBuffer)}r.info.memory.geometries--},U=function(a){a=a.target;a.removeEventListener("dispose",U);a.image&&a.image.__webglTextureCube?g.deleteTexture(a.image.__webglTextureCube):a.__webglInit&&(a.__webglInit=!1,g.deleteTexture(a.__webglTexture));r.info.memory.textures--},V=function(a){a=a.target;a.removeEventListener("dispose",V);W(a)},W=function(a){var b=a.program;if(void 0!==b){a.program=void 0;var c,d,e=!1;a=0;for(c=n.length;a<c;a++)if(d=n[a],d.program===b){d.usedTimes--;
-0===d.usedTimes&&(e=!0);break}if(!0===e){e=[];a=0;for(c=n.length;a<c;a++)d=n[a],d.program!==b&&e.push(d);n=e;g.deleteProgram(b);r.info.memory.programs--}}};this.initMaterial=function(a,b,d,e){a.addEventListener("dispose",V);if(b=a.shaderID)b=$3Dmol.ShaderLib[b],a.vertexShader=b.vertexShader,a.fragmentShader=b.fragmentShader,a.uniforms=$3Dmol.ShaderUtils.clone(b.uniforms);var f;a:{var k=a.fragmentShader;e=a.vertexShader;d=a.uniforms;var h={wireframe:a.wireframe},m,p;b=[];b.push(k);b.push(e);for(m in h)b.push(m),
-b.push(h[m]);b=b.join();m=0;for(p=n.length;m<p;m++){var q=n[m];if(q.code===b){q.usedTimes++;f=q.program;break a}}m=g.createProgram();q="precision "+l+" float;";p=""+q;h=[h.wireframe?"#define WIREFRAME 1":"",q].join("\n");k=c("fragment",h+k);e=c("vertex",p+e);g.attachShader(m,e);g.attachShader(m,k);g.linkProgram(m);g.getProgramParameter(m,g.LINK_STATUS)||console.error("Could not initialize shader");m.uniforms={};m.attributes={};e="viewMatrix modelViewMatrix projectionMatrix normalMatrix modelMatrix cameraPosition".split(" ");
-for(f in d)e.push(f);for(f=0;f<e.length;f++)d=e[f],m.uniforms[d]=g.getUniformLocation(m,d);e=["position","normal","color","lineDistance"];for(f=0;f<e.length;f++)d=e[f],m.attributes[d]=g.getAttribLocation(m,d);m.id=t++;n.push({program:m,code:b,usedTimes:1});r.info.memory.programs=n.length;f=m}a.program=f};this.renderBuffer=function(a,c,d,e,f,k){if(e.visible){var h;e.needsUpdate&&(e.program&&W(e),r.initMaterial(e,c,d,k),e.needsUpdate=!1);var l=!1,m=e.program,n=m.uniforms;h=e.uniforms;m!=u&&(g.useProgram(m),
-u=m,l=!0);e.id!=y&&(y=e.id,l=!0);a!=B&&(B=a,l=!0);g.uniformMatrix4fv(n.projectionMatrix,!1,a.projectionMatrix.elements);g.uniformMatrix4fv(n.modelViewMatrix,!1,k._modelViewMatrix.elements);g.uniformMatrix3fv(n.normalMatrix,!1,k._normalMatrix.elements);if(l){h.fogColor.value=d.color;h.fogNear.value=d.near;h.fogFar.value=d.far;if(0===e.shaderID.lastIndexOf("lambert",0)){g.uniformMatrix4fv(n.viewMatrix,!1,a.matrixWorldInverse.elements);if(O){var p,q,t=0,w=0,s=0;a=0;for(d=c.length;a<d;a++)if(l=c[a],p=
-l.color,q=l.intensity,l instanceof $3Dmol.Light&&(t++,K.getPositionFromMatrix(l.matrixWorld),S.getPositionFromMatrix(l.target.matrixWorld),K.sub(S),K.normalize(),0!==K.x||0!==K.y||0!==K.z))R[s]=K.x,R[s+1]=K.y,R[s+2]=K.z,Q[s]=p.r*q,Q[s+1]=p.g*q,Q[s+2]=p.b*q,s+=3,w++;P[0]=0;P[1]=0;P[2]=0;O=!1}h.ambientLightColor.value=P;h.directionalLightColor.value=Q;h.directionalLightDirection.value=R;h.ambient.value=e.ambient;h.emissive.value=e.emissive}else"sphereimposter"===e.shaderID&&(g.uniformMatrix4fv(n.viewMatrix,
-!1,a.matrixWorldInverse.elements),g.uniformMatrix3fv(n.normalMatrix,!1,k._normalMatrix.elements));h.opacity.value=e.opacity;h.diffuse.value=e.color;for(var v in h)n[v]&&(c=h[v].type,a=h[v].value,d=n[v],"f"===c?g.uniform1f(d,a):"fv"===c?g.uniform3fv(d,a):"c"===c&&g.uniform3f(d,a.r,a.g,a.b))}h=m.attributes;n=!1;m=16777215*f.id+2*m.id+(e.wireframe?1:0);m!==F&&(F=m,n=!0);if(n){for(var x in J)J[x]&&(g.disableVertexAttribArray(x),J[x]=!1);0<=h.position&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglVertexBuffer),
-b(h.position),g.vertexAttribPointer(h.position,3,g.FLOAT,!1,0,0));0<=h.color&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglColorBuffer),b(h.color),g.vertexAttribPointer(h.color,3,g.FLOAT,!1,0,0));0<=h.normal&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglNormalBuffer),b(h.normal),g.vertexAttribPointer(h.normal,3,g.FLOAT,!1,0,0))}var z;k instanceof $3Dmol.Mesh?(e.wireframe?(k=f.lineidx,e=e.wireframeLinewidth,e!==H&&(g.lineWidth(e),H=e),n&&g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,f.__webglLineBuffer),g.drawElements(g.LINES,
-k,g.UNSIGNED_SHORT,0)):(z=f.faceidx,n&&g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,f.__webglFaceBuffer),g.drawElements(g.TRIANGLES,z,g.UNSIGNED_SHORT,0)),r.info.render.calls++,r.info.render.vertices+=z,r.info.render.faces+=z/3):k instanceof $3Dmol.Line&&(k=f.vertices,f=e.linewidth,f!==H&&(g.lineWidth(f),H=f),g.drawArrays(g.LINES,0,k),r.info.render.calls++)}};this.render=function(a,b,c){if(!1===b instanceof $3Dmol.Camera)console.error("$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.");
-else{var g,e,f,h,k=a.__lights,l=a.fog;y=-1;O=!0;this.autoUpdateScene&&a.updateMatrixWorld();void 0===b.parent&&b.updateMatrixWorld();b.matrixWorldInverse.getInverse(b.matrixWorld);X.multiplyMatrices(b.projectionMatrix,b.matrixWorldInverse);this.autoUpdateObjects&&this.initWebGLObjects(a);r.info.render.calls=0;r.info.render.vertices=0;r.info.render.faces=0;r.info.render.points=0;M=I;N=L;(this.autoClear||c)&&this.clear(this.autoClearColor,this.autoClearDepth,this.autoClearStencil);h=a.__webglObjects;
-c=0;for(g=h.length;c<g;c++)if(e=h[c],f=e.object,e.render=!1,f.visible){f._modelViewMatrix.multiplyMatrices(b.matrixWorldInverse,f.matrixWorld);f._normalMatrix.getInverse(f._modelViewMatrix);f._normalMatrix.transpose();f=e;var m=f.object.material;m.transparent?(f.opaque=null,f.transparent=m,m=m.clone(),m.opacity=0,f.blank=m):(f.opaque=m,f.transparent=null);e.render=!0}this.setBlending(!1);d(a.__webglObjects,!0,"opaque",b,k,l,!1,null);d(a.__webglObjects,!0,"blank",b,k,l,!0,null);d(a.__webglObjects,
-!1,"transparent",b,k,l,!0,null);k=this.renderPluginsPost;F=-1;B=u=null;p=y=s=A=E=-1;if(k.length)for(l=0,c=k.length;l<c;l++)O=!0,k[l].render(a,b,M,N),F=-1,B=u=null,p=y=s=A=E=-1;this.setDepthTest(!0);this.setDepthWrite(!0)}};this.initWebGLObjects=function(a){a.__webglObjects||(a.__webglObjects=[],a.__webglObjectsImmediate=[],a.__webglSprites=[],a.__webglFlares=[]);if(a.__objectsAdded.length){for(;a.__objectsAdded.length;){var b=a.__objectsAdded[0],c=a,d=void 0,e=void 0,f=void 0,h=void 0;if(!b.__webglInit&&
-(b.__webglInit=!0,b._modelViewMatrix=new $3Dmol.Matrix4,b._normalMatrix=new $3Dmol.Matrix3,void 0!==b.geometry&&void 0===b.geometry.__webglInit&&(b.geometry.__webglInit=!0,b.geometry.addEventListener("dispose",T)),b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line))for(f=b.geometry,d=0,e=f.geometryGroups.length;d<e;d++)h=f.geometryGroups[d],h.id=C++,h.__webglVertexBuffer||(b instanceof $3Dmol.Mesh?(h.__webglVertexBuffer=g.createBuffer(),h.__webglNormalBuffer=g.createBuffer(),h.__webglColorBuffer=
-g.createBuffer(),h.__webglFaceBuffer=g.createBuffer(),h.__webglLineBuffer=g.createBuffer(),r.info.memory.geometries++,f.elementsNeedUpdate=!0,f.normalsNeedUpdate=!0):b instanceof $3Dmol.Line&&(h.__webglVertexBuffer=g.createBuffer(),h.__webglColorBuffer=g.createBuffer(),r.info.memory.geometries++),f.verticesNeedUpdate=!0,f.colorsNeedUpdate=!0);if(!b.__webglActive){if(b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line)for(f=b.geometry,d=0,e=f.geometryGroups.length;d<e;d++)h=f.geometryGroups[d],c.__webglObjects.push({buffer:h,
-object:b,opaque:null,transparent:null});else b instanceof $3Dmol.Sprite&&c.__webglSprites.push(b);b.__webglActive=!0}a.__objectsAdded.splice(0,1)}F=-1}for(;a.__objectsRemoved.length;){b=a.__objectsRemoved[0];c=a;if(b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line)for(c=c.__webglObjects,d=b,e=c.length-1;0<=e;--e)c[e].object===d&&c.splice(e,1);else if(b instanceof $3Dmol.Sprite)for(c=c.__webglSprites,d=b,e=c.length-1;0<=e;--e)c[e]===d&&c.splice(e,1);b.__webglActive=!1;a.__objectsRemoved.splice(0,
-1)}b=0;for(c=a.__webglObjects.length;b<c;b++)if(e=a.__webglObjects[b].object,d=e.geometry,h=void 0,e instanceof $3Dmol.Mesh||e instanceof $3Dmol.Line){e=0;for(f=d.geometryGroups.length;e<f;e++)if(h=d.geometryGroups[e],d.verticesNeedUpdate||d.elementsNeedUpdate||d.colorsNeedUpdate||d.normalsNeedUpdate){var k=g.STATIC_DRAW,l=h.vertexArray,m=h.colorArray;g.bindBuffer(g.ARRAY_BUFFER,h.__webglVertexBuffer);g.bufferData(g.ARRAY_BUFFER,l,k);g.bindBuffer(g.ARRAY_BUFFER,h.__webglColorBuffer);g.bufferData(g.ARRAY_BUFFER,
-m,k);void 0!==h.normalArray&&void 0!==h.__webglNormalBuffer&&(l=h.normalArray,g.bindBuffer(g.ARRAY_BUFFER,h.__webglNormalBuffer),g.bufferData(g.ARRAY_BUFFER,l,k));void 0!==h.faceArray&&void 0!==h.__webglFaceBuffer&&(l=h.faceArray,g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,h.__webglFaceBuffer),g.bufferData(g.ELEMENT_ARRAY_BUFFER,l,k));void 0!==h.lineArray&&void 0!==h.__webglLineBuffer&&(l=h.lineArray,g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,h.__webglLineBuffer),g.bufferData(g.ELEMENT_ARRAY_BUFFER,l,k))}d.verticesNeedUpdate=
-!1;d.elementsNeedUpdate=!1;d.normalsNeedUpdate=!1;d.colorsNeedUpdate=!1;d.buffersNeedUpdate=!1}};this.setTexture=function(a,b){if(a.needsUpdate){a.__webglInit||(a.__webglInit=!0,a.addEventListener("dispose",U),a.__webglTexture=g.createTexture(),r.info.memory.textures++);g.activeTexture(g.TEXTURE0+b);g.bindTexture(g.TEXTURE_2D,a.__webglTexture);g.pixelStorei(g.UNPACK_FLIP_Y_WEBGL,a.flipY);g.pixelStorei(g.UNPACK_PREMULTIPLY_ALPHA_WEBGL,a.premultiplyAlpha);g.pixelStorei(g.UNPACK_ALIGNMENT,a.unpackAlignment);
-var c=a.image,c=e(c.width)&&e(c.height),d=k(a.format),f=k(a.type),h=g.TEXTURE_2D;c?(g.texParameteri(h,g.TEXTURE_WRAP_S,k(a.wrapS)),g.texParameteri(h,g.TEXTURE_WRAP_T,k(a.wrapT)),g.texParameteri(h,g.TEXTURE_MAG_FILTER,k(a.magFilter)),g.texParameteri(h,g.TEXTURE_MIN_FILTER,k(a.minFilter))):(g.texParameteri(h,g.TEXTURE_WRAP_S,g.CLAMP_TO_EDGE),g.texParameteri(h,g.TEXTURE_WRAP_T,g.CLAMP_TO_EDGE),g.texParameteri(h,g.TEXTURE_MAG_FILTER,g.LINEAR),g.texParameteri(h,g.TEXTURE_MIN_FILTER,g.LINEAR));var l=a.mipmaps;
-if(0<l.length&&c){for(var m=0,n=l.length;m<n;m++)h=l[m],g.texImage2D(g.TEXTURE_2D,m,d,d,f,h);a.generateMipmaps=!1}else g.texImage2D(g.TEXTURE_2D,0,d,d,f,a.image);a.generateMipmaps&&c&&g.generateMipmap(g.TEXTURE_2D);a.needsUpdate=!1;if(a.onUpdate)a.onUpdate()}else g.activeTexture(g.TEXTURE0+b),g.bindTexture(g.TEXTURE_2D,a.__webglTexture)};this.addPostPlugin(new $3Dmol.SpritePlugin)};
-$3Dmol.Scene=function(){$3Dmol.Object3D.call(this);this.overrideMaterial=this.fog=null;this.matrixAutoUpdate=!1;this.__objects=[];this.__lights=[];this.__objectsAdded=[];this.__objectsRemoved=[]};$3Dmol.Scene.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Scene.prototype.__addObject=function(a){a instanceof $3Dmol.Light?(-1===this.__lights.indexOf(a)&&this.__lights.push(a),a.target&&void 0===a.target.parent&&this.add(a.target)):-1===this.__objects.indexOf(a)&&(this.__objects.push(a),this.__objectsAdded.push(a),-1!==this.__objectsRemoved.indexOf(a)&&this.__objectsRemoved.splice(b,1));for(var b=0;b<a.children.length;b++)this.__addObject(a.children[b])};
-$3Dmol.Scene.prototype.__removeObject=function(a){var b;a instanceof $3Dmol.Light?(b=this.__lights.indexOf(a),-1!==b&&this.__lights.splice(b,1)):(b=this.__objects.indexOf(a),-1!==b&&(this.__objects.splice(b,1),this.__objectsRemoved.push(a),-1!==this.__objectsAdded.indexOf(a)&&this.__objectsAdded.splice(b,1)));for(b=0;b<a.children.length;b++)this.__removeObject(a.children[b])};$3Dmol.Fog=function(a,b,c){this.name="";this.color=new $3Dmol.Color(a);this.near=void 0!==b?b:1;this.far=void 0!==c?c:1E3};
-$3Dmol.Fog.prototype.clone=function(){return new $3Dmol.Fog(this.color.getHex(),this.near,this.far)};$3Dmol.ShaderUtils={clone:function(a){var b,c={};for(b in a){c[b]={};c[b].type=a[b].type;var d=a[b].value;d instanceof $3Dmol.Color?c[b].value=d.clone():"number"===typeof d?c[b].value=d:d instanceof Array?c[b].value=[]:console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform")}return c}};
-$3Dmol.ShaderLib={basic:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 diffuse;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( diffuse, opacity );\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nattribute vec3 position;\nattribute vec3 color;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},sphereimposter:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 diffuse;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvarying vec2 mapping;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    if(lensqr > 2.0)\n       discard;\n    float w = sqrt(2.0 - lensqr);\n    float z = sqrt(sqrt(2.0)-lensqr);\n    gl_FragDepthEXT = -.1*z;\n    gl_FragColor = vec4( w*vColor, 1 );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec4 adjust = projectionMatrix*vec4(normal, 1.0);  adjust.y *= -1.0; adjust.z = 0.0; adjust.w = 0.0;\n    mapping = normal.xy;\n    gl_Position = projPosition+adjust;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},lambert:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 ambient;\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform vec3 ambientLightColor;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},ambient:{type:"c",value:new $3Dmol.Color(1,1,1)},emissive:{type:"c",value:new $3Dmol.Color(1,1,1)},ambientLightColor:{type:"fv",value:[]},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},lambertdouble:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vLightBack;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    if ( gl_FrontFacing )\n       gl_FragColor.xyz *= vLightFront;\n    else\n       gl_FragColor.xyz *= vLightBack;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 ambient;\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform vec3 ambientLightColor;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvarying vec3 vLightBack;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    vLightBack = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;\n    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;\n    vLightBack = vLightBack * diffuse + ambient * ambientLightColor + emissive;\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},ambient:{type:"c",value:new $3Dmol.Color(1,1,1)},emissive:{type:"c",value:new $3Dmol.Color(1,1,1)},ambientLightColor:{type:"fv",value:[]},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},sprite:{fragmentShader:"uniform vec3 color;\nuniform sampler2D map;\nuniform float opacity;\nuniform int fogType;\nuniform vec3 fogColor;\nuniform float fogDensity;\nuniform float fogNear;\nuniform float fogFar;\nuniform float alphaTest;\nvarying vec2 vUV;\nvoid main() {\n    vec4 texture = texture2D(map, vUV);\n    if (texture.a < alphaTest) discard;\n    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);\n    if (fogType > 0) {\n        float depth = gl_FragCoord.z / gl_FragCoord.w;\n        float fogFactor = 0.0;\n        if (fogType == 1) {\n            fogFactor = smoothstep(fogNear, fogFar, depth);\n        }\n        else {\n            const float LOG2 = 1.442695;\n            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);\n            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);\n        }\n        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);\n    }\n}",
+$3Dmol.Texture.prototype={constructor:$3Dmol.Texture,clone:function(b){void 0===b&&(b=new $3Dmol.Texture);b.image=this.image;b.mipmaps=this.mipmaps.slice(0);b.mapping=this.mapping;b.wrapS=this.wrapS;b.wrapT=this.wrapT;b.magFilter=this.magFilter;b.minFilter=this.minFilter;b.anisotropy=this.anisotropy;b.format=this.format;b.type=this.type;b.offset.copy(this.offset);b.repeat.copy(this.repeat);b.generateMipmaps=this.generateMipmaps;b.premultiplyAlpha=this.premultiplyAlpha;b.flipY=this.flipY;b.unpackAlignment=
+this.unpackAlignment;return b},dispose:function(){this.dispatchEvent({type:"dispose"})}};$3Dmol.TextureIdCount=0;$3Dmol.FrontSide=0;$3Dmol.BackSide=1;$3Dmol.DoubleSide=2;$3Dmol.NoShading=0;$3Dmol.FlatShading=1;$3Dmol.SmoothShading=2;$3Dmol.NoColors=0;$3Dmol.FaceColors=1;$3Dmol.VertexColors=2;$3Dmol.MultiplyOperation=0;$3Dmol.MixOperation=1;$3Dmol.AddOperation=2;$3Dmol.UVMapping=function(){};$3Dmol.ClampToEdgeWrapping=1001;$3Dmol.LinearFilter=1006;$3Dmol.LinearMipMapLinearFilter=1008;
+$3Dmol.UnsignedByteType=1009;$3Dmol.RGBAFormat=1021;$3Dmol.Line=function(b,c,d){$3Dmol.Object3D.call(this);this.geometry=b;this.material=void 0!==c?c:new $3Dmol.LineBasicMaterial({color:16777215*Math.random()});this.type=void 0!==d?d:$3Dmol.LineStrip};$3Dmol.LineStrip=0;$3Dmol.LinePieces=1;$3Dmol.Line.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Line.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Line(this.geometry,this.material,this.type));$3Dmol.Object3D.prototype.clone.call(this,b);return b};$3Dmol.Mesh=function(b,c){$3Dmol.Object3D.call(this);this.geometry=b;this.material=void 0!==c?c:new $3Dmol.MeshBasicMaterial({color:16777215*Math.random(),wireframe:!0})};$3Dmol.Mesh.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Mesh.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Mesh(this.geometry,this.material));$3Dmol.Object3D.prototype.clone.call(this,b);return b};$3Dmol.Sprite=function(b){$3Dmol.Object3D.call(this);this.material=void 0!==b?b:new $3Dmol.SpriteMaterial;this.rotation3d=this.rotation;this.rotation=0};$3Dmol.Sprite.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Sprite.prototype.updateMatrix=function(){this.matrix.setPosition(this.position);this.rotation3d.set(0,0,this.rotation);this.matrix.setRotationFromEuler(this.rotation3d);1===this.scale.x&&1===this.scale.y||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=!0};$3Dmol.Sprite.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Sprite(this.material));$3Dmol.Object3D.prototype.clone.call(this,b);return b};
+$3Dmol.Renderer=function(b){function c(b){S[b]||(D.enableVertexAttribArray(b),S[b]=!0)}function d(b,c){var h;"fragment"===b?h=D.createShader(D.FRAGMENT_SHADER):"vertex"===b&&(h=D.createShader(D.VERTEX_SHADER));D.shaderSource(h,c);D.compileShader(h);return D.getShaderParameter(h,D.COMPILE_STATUS)?h:(console.error(D.getShaderInfoLog(h)),console.error("could not initialize shader"),null)}function p(b,c,h,f,e,w,m,d){var q,l,t;c?(l=b.length-1,d=c=-1):(l=0,c=b.length,d=1);for(var s=l;s!==c;s+=d)if(q=b[s],
+q.render&&(l=q.object,t=q.buffer,q=q[h])){m&&x.setBlending(!0);x.setDepthTest(q.depthTest);x.setDepthWrite(q.depthWrite);var N=q.polygonOffset;null!==N&&(N?D.enable(D.POLYGON_OFFSET_FILL):D.disable(D.POLYGON_OFFSET_FILL));N=l._modelViewMatrix.isReflected();x.setMaterialFaces(q,N);x.renderBuffer(f,e,w,q,t,l);g&&("sphereimposter"==q.shaderID?x.renderBuffer(f,e,w,_outlineSphereImposterMaterial,t,l):"stickimposter"==q.shaderID?x.renderBuffer(f,e,w,_outlineStickImposterMaterial,t,l):q.wireframe||"basic"===
+q.shaderID||0===q.opacity||x.renderBuffer(f,e,w,g,t,l))}}function y(b){return 0===(b&b-1)}function A(b){return b===$3Dmol.UnsignedByteType?D.UNSIGNED_BYTE:b===$3Dmol.RGBAFormat?D.RGBA:0}b=b||{};var q=void 0!==b.canvas?b.canvas:document.createElement("canvas"),B=void 0!==b.precision?b.precision:"highp",f=void 0!==b.alpha?b.alpha:!0,w=void 0!==b.premultipliedAlpha?b.premultipliedAlpha:!0,h=void 0!==b.antialias?b.antialias:!1,t=void 0!==b.stencil?b.stencil:!0,m=void 0!==b.preserveDrawingBuffer?b.preserveDrawingBuffer:
+!1,e=void 0!==b.clearColor?new $3Dmol.Color(b.clearColor):new $3Dmol.Color(0),F=void 0!==b.clearAlpha?b.clearAlpha:0,g=void 0!==b.outline?new $3Dmol.MeshOutlineMaterial(b.outline):null;this.domElement=q;this.context=null;this.devicePixelRatio=void 0!==b.devicePixelRatio?b.devicePixelRatio:void 0!==self.devicePixelRatio?self.devicePixelRatio:1;this.autoUpdateScene=this.autoUpdateObjects=this.sortObjects=this.autoClearStencil=this.autoClearDepth=this.autoClearColor=this.autoClear=!0;this.renderPluginsPost=
+[];this.info={memory:{programs:0,geometries:0,textures:0},render:{calls:0,vertices:0,faces:0,points:0}};var x=this,u=[],s=0,l=null,E=-1,M=null,C=null,G=0,z=-1,H=-1,L=-1,N=-1,J=null,I=0,K=0,O=0,Q=0,W=0,P=0,S={},R=new $3Dmol.Matrix4,aa=new $3Dmol.Vector3,V=new $3Dmol.Vector3,Z=!0,ca=[],X=[],D;try{if(!(D=q.getContext("experimental-webgl",{alpha:f,premultipliedAlpha:w,antialias:h,stencil:t,preserveDrawingBuffer:m}))&&!(D=q.getContext("webgl",{alpha:f,premultipliedAlpha:w,antialias:h,stencil:t,preserveDrawingBuffer:m})))throw"Error creating WebGL context.";
+}catch(ba){console.error(ba)}D.clearColor(0,0,0,1);D.clearDepth(1);D.clearStencil(0);D.enable(D.DEPTH_TEST);D.depthFunc(D.LEQUAL);D.frontFace(D.CCW);D.cullFace(D.BACK);D.enable(D.CULL_FACE);D.enable(D.BLEND);D.blendEquation(D.FUNC_ADD);D.blendFunc(D.SRC_ALPHA,D.ONE_MINUS_SRC_ALPHA);D.clearColor(e.r,e.g,e.b,F);this.context=D;var U=D.getExtension("ANGLE_instanced_arrays"),T=D.getExtension("EXT_frag_depth");this.supportedExtensions=function(){return{supportsAIA:Boolean(U),supportsImposters:Boolean(T)}};
+this.getContext=function(){return D};this.getPrecision=function(){return B};this.setClearColorHex=function(b,c){e.setHex(b);F=c;D.clearColor(e.r,e.g,e.b,F)};this.enableOutline=function(b){g=new $3Dmol.MeshOutlineMaterial(b);_outlineSphereImposterMaterial=new $3Dmol.SphereImposterOutlineMaterial(b);_outlineStickImposterMaterial=new $3Dmol.StickImposterOutlineMaterial(b)};this.disableOutline=function(){_outlineStickImposterMaterial=_outlineSphereImposterMaterial=g=null};this.setSize=function(b,c){q.width=
+b*this.devicePixelRatio;q.height=c*this.devicePixelRatio;q.style.width=b+"px";q.style.height=c+"px";this.setViewport(0,0,q.width,q.height)};this.setViewport=function(b,c,h,f){I=void 0!==b?b:0;K=void 0!==c?c:0;O=void 0!==h?h:q.width;Q=void 0!==f?f:q.height;D.viewport(I,K,O,Q)};this.clear=function(b,c,h){var f=0;if(void 0===b||b)f|=D.COLOR_BUFFER_BIT;if(void 0===c||c)f|=D.DEPTH_BUFFER_BIT;if(void 0===h||h)f|=D.STENCIL_BUFFER_BIT;D.clear(f)};this.clearTarget=function(b,c,h){this.clear(b,c,h)};this.setMaterialFaces=
+function(b,c){var h=b.side===$3Dmol.DoubleSide,f=b.side===$3Dmol.BackSide,f=c?!f:f;z!==h&&(h?D.disable(D.CULL_FACE):D.enable(D.CULL_FACE),z=h);H!==f&&(f?D.frontFace(D.CW):D.frontFace(D.CCW),H=f)};this.setDepthTest=function(b){L!==b&&(b?D.enable(D.DEPTH_TEST):D.disable(D.DEPTH_TEST),L=b)};this.setDepthWrite=function(b){N!==b&&(D.depthMask(b),N=b)};this.setBlending=function(b){b?(D.enable(D.BLEND),D.blendEquationSeparate(D.FUNC_ADD,D.FUNC_ADD),D.blendFuncSeparate(D.SRC_ALPHA,D.ONE_MINUS_SRC_ALPHA,D.ONE,
+D.ONE_MINUS_SRC_ALPHA)):D.disable(D.BLEND)};this.addPostPlugin=function(b){b.init(this);this.renderPluginsPost.push(b)};var ea=function(b){b=b.target;b.removeEventListener("dispose",ea);b.__webglInit=void 0;void 0!==b.__webglVertexBuffer&&D.deleteBuffer(b.__webglVertexBuffer);void 0!==b.__webglColorBuffer&&D.deleteBuffer(b.__webglColorBuffer);if(void 0!==b.geometryGroups)for(var c=0,h=b.groups;c<h;c++){var f=b.geometryGroups[c];void 0!==f.__webglVertexBuffer&&D.deleteBuffer(f.__webglVertexBuffer);
+void 0!==f.__webglColorBuffer&&D.deleteBuffer(f.__webglColorBuffer);void 0!==f.__webglNormalBuffer&&D.deleteBuffer(f.__webglNormalBuffer);void 0!==f.__webglFaceBuffer&&D.deleteBuffer(f.__webglFaceBuffer);void 0!==f.__webglLineBuffer&&D.deleteBuffer(f.__webglLineBuffer)}x.info.memory.geometries--},Ba=function(b){b=b.target;b.removeEventListener("dispose",Ba);b.image&&b.image.__webglTextureCube?D.deleteTexture(b.image.__webglTextureCube):b.__webglInit&&(b.__webglInit=!1,D.deleteTexture(b.__webglTexture));
+x.info.memory.textures--},Na=function(b){b=b.target;b.removeEventListener("dispose",Na);Ja(b)},Ja=function(b){var c=b.program;if(void 0!==c){b.program=void 0;var h,f,e=!1;b=0;for(h=u.length;b<h;b++)if(f=u[b],f.program===c){f.usedTimes--;0===f.usedTimes&&(e=!0);break}if(!0===e){e=[];b=0;for(h=u.length;b<h;b++)f=u[b],f.program!==c&&e.push(f);u=e;D.deleteProgram(c);x.info.memory.programs--}}};this.initMaterial=function(b,c,h,f){b.addEventListener("dispose",Na);if(c=b.shaderID)c=$3Dmol.ShaderLib[c],b.vertexShader=
+c.vertexShader,b.fragmentShader=c.fragmentShader,b.uniforms=$3Dmol.ShaderUtils.clone(c.uniforms);var e;a:{var w=b.fragmentShader;f=b.vertexShader;h=b.uniforms;var g={wireframe:b.wireframe,fragdepth:b.imposter},q,m;c=[];c.push(w);c.push(f);for(q in g)c.push(q),c.push(g[q]);c=c.join();q=0;for(m=u.length;q<m;q++){var l=u[q];if(l.code===c){l.usedTimes++;e=l.program;break a}}q=D.createProgram();l="precision "+B+" float;";m=""+l;g=[g.fragdepth?"#extension GL_EXT_frag_depth: enable":"",g.wireframe?"#define WIREFRAME 1":
+"",l].join("\n");w=d("fragment",g+w);f=d("vertex",m+f);D.attachShader(q,f);D.attachShader(q,w);D.linkProgram(q);D.getProgramParameter(q,D.LINK_STATUS)||console.error("Could not initialize shader");q.uniforms={};q.attributes={};f=["viewMatrix","modelViewMatrix","projectionMatrix","normalMatrix"];for(e in h)f.push(e);for(e=0;e<f.length;e++)h=f[e],q.uniforms[h]=D.getUniformLocation(q,h);f="position normal color lineDistance offset radius".split(" ");for(e=0;e<f.length;e++)h=f[e],q.attributes[h]=D.getAttribLocation(q,
+h);q.id=s++;u.push({program:q,code:c,usedTimes:1});x.info.memory.programs=u.length;e=q}b.program=e};this.renderBuffer=function(b,h,f,e,g,w){if(e.visible){var q;e.needsUpdate&&(e.program&&Ja(e),x.initMaterial(e,h,f,w),e.needsUpdate=!1);var m=!1,d=e.program,t=d.uniforms;q=e.uniforms;d!=l&&(D.useProgram(d),l=d,m=!0);e.id!=E&&(E=e.id,m=!0);b!=C&&(C=b,m=!0);D.uniformMatrix4fv(t.projectionMatrix,!1,b.projectionMatrix.elements);D.uniformMatrix4fv(t.modelViewMatrix,!1,w._modelViewMatrix.elements);D.uniformMatrix3fv(t.normalMatrix,
+!1,w._normalMatrix.elements);if(m){q.fogColor.value=f.color;q.fogNear.value=f.near;q.fogFar.value=f.far;if(e.shaderID.startsWith("lambert")||"instanced"===e.shaderID||e.shaderID.endsWith("imposter")){D.uniformMatrix4fv(t.viewMatrix,!1,b.matrixWorldInverse.elements);if(Z){var s,N,B=0,I=0,u=0;b=0;for(f=h.length;b<f;b++)if(m=h[b],s=m.color,N=m.intensity,m instanceof $3Dmol.Light&&(B++,V.getPositionFromMatrix(m.matrixWorld),aa.getPositionFromMatrix(m.target.matrixWorld),V.sub(aa),V.normalize(),0!==V.x||
+0!==V.y||0!==V.z))X[u]=V.x,X[u+1]=V.y,X[u+2]=V.z,ca[u]=s.r*N,ca[u+1]=s.g*N,ca[u+2]=s.b*N,u+=3,I++;Z=!1}q.directionalLightColor.value=ca;q.directionalLightDirection.value=X}else e.shaderID.endsWith("outline")?(q.outlineColor.value=e.outlineColor,q.outlineWidth.value=e.outlineWidth,q.outlinePushback.value=e.outlinePushback):"sphereimposter"===e.shaderID&&(D.uniformMatrix4fv(t.viewMatrix,!1,b.matrixWorldInverse.elements),D.uniformMatrix3fv(t.normalMatrix,!1,w._normalMatrix.elements),q.directionalLightColor.value=
+ca,q.directionalLightDirection.value=X);q.opacity.value=e.opacity;for(var K in q)t[K]&&(h=q[K].type,b=q[K].value,f=t[K],"f"===h?D.uniform1f(f,b):"fv"===h?D.uniform3fv(f,b):"c"===h?D.uniform3f(f,b.r,b.g,b.b):"f4"===h&&D.uniform4f(f,b[0],b[1],b[2],b[3]))}q=d.attributes;t=!1;d=16777215*g.id+2*d.id+(e.wireframe?1:0);d!==M&&(M=d,t=!0);if(t){for(var F in S)S[F]&&(D.disableVertexAttribArray(F),S[F]=!1);0<=q.position&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer),c(q.position),D.vertexAttribPointer(q.position,
+3,D.FLOAT,!1,0,0));0<=q.color&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglColorBuffer),c(q.color),D.vertexAttribPointer(q.color,3,D.FLOAT,!1,0,0));0<=q.normal&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),c(q.normal),D.vertexAttribPointer(q.normal,3,D.FLOAT,!1,0,0));0<=q.offset&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglOffsetBuffer),c(q.offset),D.vertexAttribPointer(q.offset,3,D.FLOAT,!1,0,0));0<=q.radius&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglRadiusBuffer),c(q.radius),D.vertexAttribPointer(q.radius,
+1,D.FLOAT,!1,0,0))}var z;w instanceof $3Dmol.Mesh?("instanced"===e.shaderID?(z=e.sphere.geometryGroups[0],t&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer),D.bufferData(D.ARRAY_BUFFER,z.vertexArray,D.STATIC_DRAW),D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),D.bufferData(D.ARRAY_BUFFER,z.normalArray,D.STATIC_DRAW),D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,z.faceArray,D.STATIC_DRAW)),z=z.faceidx,U.vertexAttribDivisorANGLE(q.offset,1),U.vertexAttribDivisorANGLE(q.radius,
+1),U.vertexAttribDivisorANGLE(q.color,1),U.drawElementsInstancedANGLE(D.TRIANGLES,z,D.UNSIGNED_SHORT,0,g.radiusArray.length),U.vertexAttribDivisorANGLE(q.offset,0),U.vertexAttribDivisorANGLE(q.radius,0),U.vertexAttribDivisorANGLE(q.color,0)):e.wireframe?(w=g.lineidx,e=e.wireframeLinewidth,e!==J&&(D.lineWidth(e),J=e),t&&D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglLineBuffer),D.drawElements(D.LINES,w,D.UNSIGNED_SHORT,0)):(z=g.faceidx,t&&D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.drawElements(D.TRIANGLES,
+z,D.UNSIGNED_SHORT,0)),x.info.render.calls++,x.info.render.vertices+=z,x.info.render.faces+=z/3):w instanceof $3Dmol.Line&&(w=g.vertices,g=e.linewidth,g!==J&&(D.lineWidth(g),J=g),D.drawArrays(D.LINES,0,w),x.info.render.calls++)}};this.render=function(b,c,h){if(!1===c instanceof $3Dmol.Camera)console.error("$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.");else{var f,e,q,g,w=b.__lights,m=b.fog;E=-1;Z=!0;this.autoUpdateScene&&b.updateMatrixWorld();void 0===c.parent&&c.updateMatrixWorld();
+c.matrixWorldInverse.getInverse(c.matrixWorld);R.multiplyMatrices(c.projectionMatrix,c.matrixWorldInverse);this.autoUpdateObjects&&this.initWebGLObjects(b);x.info.render.calls=0;x.info.render.vertices=0;x.info.render.faces=0;x.info.render.points=0;W=O;P=Q;(this.autoClear||h)&&this.clear(this.autoClearColor,this.autoClearDepth,this.autoClearStencil);g=b.__webglObjects;h=0;for(f=g.length;h<f;h++)if(e=g[h],q=e.object,e.render=!1,q.visible){q._modelViewMatrix.multiplyMatrices(c.matrixWorldInverse,q.matrixWorld);
+q._normalMatrix.getInverse(q._modelViewMatrix);q._normalMatrix.transpose();q=e;var t=q.object.material;t.transparent?(q.opaque=null,q.transparent=t,t.wireframe||(t=t.clone(),t.opacity=0,q.blank=t)):(q.opaque=t,q.transparent=null);e.render=!0}this.setBlending(!1);p(b.__webglObjects,!0,"opaque",c,w,m,!1,null);p(b.__webglObjects,!0,"blank",c,w,m,!0,null);p(b.__webglObjects,!1,"transparent",c,w,m,!0,null);w=this.renderPluginsPost;M=-1;C=l=null;H=E=z=L=N=-1;if(w.length)for(m=0,h=w.length;m<h;m++)Z=!0,
+w[m].render(b,c,W,P),M=-1,C=l=null,H=E=z=L=N=-1;this.setDepthTest(!0);this.setDepthWrite(!0)}};this.initWebGLObjects=function(b){b.__webglObjects||(b.__webglObjects=[],b.__webglObjectsImmediate=[],b.__webglSprites=[],b.__webglFlares=[]);if(b.__objectsAdded.length){for(;b.__objectsAdded.length;){var c=b.__objectsAdded[0],h=b,f=void 0,e=void 0,q=void 0,g=void 0;if(!c.__webglInit&&(c.__webglInit=!0,c._modelViewMatrix=new $3Dmol.Matrix4,c._normalMatrix=new $3Dmol.Matrix3,void 0!==c.geometry&&void 0===
+c.geometry.__webglInit&&(c.geometry.__webglInit=!0,c.geometry.addEventListener("dispose",ea)),c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line))for(q=c.geometry,f=0,e=q.geometryGroups.length;f<e;f++)g=q.geometryGroups[f],g.id=G++,g.__webglVertexBuffer||(c instanceof $3Dmol.Mesh?(g.radiusArray&&(g.__webglRadiusBuffer=D.createBuffer()),g.useOffset&&(g.__webglOffsetBuffer=D.createBuffer()),g.__webglVertexBuffer=D.createBuffer(),g.__webglNormalBuffer=D.createBuffer(),g.__webglColorBuffer=D.createBuffer(),
+g.__webglFaceBuffer=D.createBuffer(),g.__webglLineBuffer=D.createBuffer(),x.info.memory.geometries++,q.elementsNeedUpdate=!0,q.normalsNeedUpdate=!0):c instanceof $3Dmol.Line&&(g.__webglVertexBuffer=D.createBuffer(),g.__webglColorBuffer=D.createBuffer(),x.info.memory.geometries++),q.verticesNeedUpdate=!0,q.colorsNeedUpdate=!0);if(!c.__webglActive){if(c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line)for(q=c.geometry,f=0,e=q.geometryGroups.length;f<e;f++)g=q.geometryGroups[f],h.__webglObjects.push({buffer:g,
+object:c,opaque:null,transparent:null});else c instanceof $3Dmol.Sprite&&h.__webglSprites.push(c);c.__webglActive=!0}b.__objectsAdded.splice(0,1)}M=-1}for(;b.__objectsRemoved.length;){c=b.__objectsRemoved[0];h=b;if(c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line)for(h=h.__webglObjects,f=c,e=h.length-1;0<=e;--e)h[e].object===f&&h.splice(e,1);else if(c instanceof $3Dmol.Sprite)for(h=h.__webglSprites,f=c,e=h.length-1;0<=e;--e)h[e]===f&&h.splice(e,1);c.__webglActive=!1;b.__objectsRemoved.splice(0,
+1)}c=0;for(h=b.__webglObjects.length;c<h;c++)if(e=b.__webglObjects[c].object,f=e.geometry,g=void 0,e instanceof $3Dmol.Mesh||e instanceof $3Dmol.Line){e=0;for(q=f.geometryGroups.length;e<q;e++)if(g=f.geometryGroups[e],f.verticesNeedUpdate||f.elementsNeedUpdate||f.colorsNeedUpdate||f.normalsNeedUpdate){var w=D.STATIC_DRAW,m=g.vertexArray,t=g.colorArray;void 0!==g.__webglOffsetBuffer?D.bindBuffer(D.ARRAY_BUFFER,g.__webglOffsetBuffer):D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer);D.bufferData(D.ARRAY_BUFFER,
+m,w);D.bindBuffer(D.ARRAY_BUFFER,g.__webglColorBuffer);D.bufferData(D.ARRAY_BUFFER,t,w);g.normalArray&&void 0!==g.__webglNormalBuffer&&(m=g.normalArray,D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),D.bufferData(D.ARRAY_BUFFER,m,w));g.radiusArray&&void 0!==g.__webglRadiusBuffer&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglRadiusBuffer),D.bufferData(D.ARRAY_BUFFER,g.radiusArray,w));g.faceArray&&void 0!==g.__webglFaceBuffer&&(m=g.faceArray,D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,
+m,w));g.lineArray&&void 0!==g.__webglLineBuffer&&(m=g.lineArray,D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglLineBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,m,w))}f.verticesNeedUpdate=!1;f.elementsNeedUpdate=!1;f.normalsNeedUpdate=!1;f.colorsNeedUpdate=!1;f.buffersNeedUpdate=!1}};this.setTexture=function(b,c){if(b.needsUpdate){b.__webglInit||(b.__webglInit=!0,b.addEventListener("dispose",Ba),b.__webglTexture=D.createTexture(),x.info.memory.textures++);D.activeTexture(D.TEXTURE0+c);D.bindTexture(D.TEXTURE_2D,
+b.__webglTexture);D.pixelStorei(D.UNPACK_FLIP_Y_WEBGL,b.flipY);D.pixelStorei(D.UNPACK_PREMULTIPLY_ALPHA_WEBGL,b.premultiplyAlpha);D.pixelStorei(D.UNPACK_ALIGNMENT,b.unpackAlignment);var h=b.image,h=y(h.width)&&y(h.height),f=A(b.format),e=A(b.type),g=D.TEXTURE_2D;h?(D.texParameteri(g,D.TEXTURE_WRAP_S,A(b.wrapS)),D.texParameteri(g,D.TEXTURE_WRAP_T,A(b.wrapT)),D.texParameteri(g,D.TEXTURE_MAG_FILTER,A(b.magFilter)),D.texParameteri(g,D.TEXTURE_MIN_FILTER,A(b.minFilter))):(D.texParameteri(g,D.TEXTURE_WRAP_S,
+D.CLAMP_TO_EDGE),D.texParameteri(g,D.TEXTURE_WRAP_T,D.CLAMP_TO_EDGE),D.texParameteri(g,D.TEXTURE_MAG_FILTER,D.LINEAR),D.texParameteri(g,D.TEXTURE_MIN_FILTER,D.LINEAR));var q=b.mipmaps;if(0<q.length&&h){for(var w=0,m=q.length;w<m;w++)g=q[w],D.texImage2D(D.TEXTURE_2D,w,f,f,e,g);b.generateMipmaps=!1}else D.texImage2D(D.TEXTURE_2D,0,f,f,e,b.image);b.generateMipmaps&&h&&D.generateMipmap(D.TEXTURE_2D);b.needsUpdate=!1;if(b.onUpdate)b.onUpdate()}else D.activeTexture(D.TEXTURE0+c),D.bindTexture(D.TEXTURE_2D,
+b.__webglTexture)};this.addPostPlugin(new $3Dmol.SpritePlugin)};$3Dmol.Scene=function(){$3Dmol.Object3D.call(this);this.overrideMaterial=this.fog=null;this.matrixAutoUpdate=!1;this.__objects=[];this.__lights=[];this.__objectsAdded=[];this.__objectsRemoved=[]};$3Dmol.Scene.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Scene.prototype.__addObject=function(b){b instanceof $3Dmol.Light?(-1===this.__lights.indexOf(b)&&this.__lights.push(b),b.target&&void 0===b.target.parent&&this.add(b.target)):-1===this.__objects.indexOf(b)&&(this.__objects.push(b),this.__objectsAdded.push(b),-1!==this.__objectsRemoved.indexOf(b)&&this.__objectsRemoved.splice(c,1));for(var c=0;c<b.children.length;c++)this.__addObject(b.children[c])};
+$3Dmol.Scene.prototype.__removeObject=function(b){var c;b instanceof $3Dmol.Light?(c=this.__lights.indexOf(b),-1!==c&&this.__lights.splice(c,1)):(c=this.__objects.indexOf(b),-1!==c&&(this.__objects.splice(c,1),this.__objectsRemoved.push(b),-1!==this.__objectsAdded.indexOf(b)&&this.__objectsAdded.splice(c,1)));for(c=0;c<b.children.length;c++)this.__removeObject(b.children[c])};$3Dmol.Fog=function(b,c,d){this.name="";this.color=new $3Dmol.Color(b);this.near=void 0!==c?c:1;this.far=void 0!==d?d:1E3};
+$3Dmol.Fog.prototype.clone=function(){return new $3Dmol.Fog(this.color.getHex(),this.near,this.far)};$3Dmol.ShaderUtils={clone:function(b){var c,d={};for(c in b){d[c]={};d[c].type=b[c].type;var p=b[c].value;p instanceof $3Dmol.Color?d[c].value=p.clone():"number"===typeof p?d[c].value=p:p instanceof Array?d[c].value=[]:console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform")}return d},stickimposterFragmentShader:"uniform float opacity;\nuniform mat4 projectionMatrix;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLight;\nvarying vec3 vColor;\nvarying vec3 cposition;\nvarying vec3 p1;\nvarying vec3 p2;\nvarying float r;\nvoid main() {\n    vec3 color = abs(vColor);\n    vec3 pos = cposition;\n    vec3 p = pos;\n    vec3 v = normalize(pos);\n    vec3 pa = p1;\n    vec3 va = normalize(p2-p1);\n    vec3 tmp1 = v-(dot(v,va)*va);\n    vec3 deltap = p-pa;\n    float A = dot(tmp1,tmp1);\n    if(A == 0.0) discard;\n    vec3 tmp2 = deltap-(dot(deltap,va)*va);\n    float B = 2.0*dot(tmp1, tmp2);\n    float C = dot(tmp2,tmp2)-r*r;\n    float det = (B*B) - (4.0*A*C);\n    if(det < 0.0) discard;\n    float sqrtDet = sqrt(det);\n    float posT = (-B+sqrtDet)/(2.0*A);\n    float negT = (-B-sqrtDet)/(2.0*A);\n    float intersectionT = min(posT,negT);\n    vec3 qi = p+v*intersectionT;\n    float dotp1 = dot(va,qi-p1);\n    float dotp2 = dot(va,qi-p2);\n    vec3 norm;\n    if( dotp1 < 0.0 || dotp2 > 0.0) {\n       vec3 cp;\n       if( dotp1 < 0.0) {        cp = p1;\n       } else {\n          cp = p2;\n       }\n       vec3 diff = p-cp;\n       A = dot(v,v);\n       B = dot(diff,v)*2.0;\n       C = dot(diff,diff)-r*r;\n       det = (B*B) - (4.0*C);\n       if(det < 0.0) discard;\n       sqrtDet = sqrt(det);\n       posT = (-B+sqrtDet)/(2.0);\n       negT = (-B-sqrtDet)/(2.0);\n       float t = min(posT,negT);\n       qi = p+v*t;\n       norm = normalize(qi-cp);\n    } else {\n       norm = normalize(qi-(dotp1*va + p1));\n    }\n    vec4 clipPos = projectionMatrix * vec4(qi, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    float depth = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    gl_FragDepthEXT = depth;"};
+$3Dmol.ShaderLib={basic:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nattribute vec3 position;\nattribute vec3 color;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},sphereimposter:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform mat4 projectionMatrix;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nuniform float uDepth;\nuniform vec3 directionalLightColor[ 1 ];\nvarying vec3 vColor;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 vLight;\nvarying vec3 center;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    float rsqr = rval*rval;\n    if(lensqr > rsqr)\n       discard;\n    float z = sqrt(rsqr-lensqr);\n    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z);\n    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    vec3 norm = normalize(vec3(mapping.x,mapping.y,z));\n    float dotProduct = dot( norm, vLight );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vec3 vLight = directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_FragColor = vec4(vLight*vColor, opacity*opacity );\n    float fogFactor = smoothstep( fogNear, fogFar, gl_FragDepthEXT/gl_FragCoord.w );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying vec3 vColor;\nvarying float rval;\nvarying vec3 vLight;\nvarying vec3 center;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    center = mvPosition.xyz;\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec4 adjust = projectionMatrix* vec4(normal,0.0); adjust.z = 0.0; adjust.w = 0.0;\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vLight = normalize( lDirection.xyz );\n    mapping = normal.xy;\n    rval = abs(normal.x);\n    gl_Position = projPosition+adjust;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},lambert:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},instanced:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 offset;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nattribute float radius;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position * radius + offset, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},outline:{fragmentShader:"uniform float opacity;\nuniform vec3 outlineColor;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvoid main() {\n    gl_FragColor = vec4( outlineColor, 1 );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform float outlineWidth;\nuniform float outlinePushback;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvoid main() {\n    vec4 norm = modelViewMatrix*vec4(normalize(normal),0.0);\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    mvPosition.xy += norm.xy*outlineWidth;\n    gl_Position = projectionMatrix * mvPosition;\n    mvPosition.z -= outlinePushback;\n    vec4 pushpos = projectionMatrix*mvPosition;\n    gl_Position.z = gl_Position.w*pushpos.z/pushpos.w;\n}",
+uniforms:{opacity:{type:"f",value:1},outlineColor:{type:"c",value:new $3Dmol.Color(0,0,0)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},outlineWidth:{type:"f",value:.1},outlinePushback:{type:"f",value:1}}},sphereimposteroutline:{fragmentShader:"uniform float opacity;\nuniform vec3 outlineColor;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nuniform mat4 projectionMatrix;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 center;\nuniform float outlinePushback;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    float rsqr = rval*rval;\n    if(lensqr > rsqr)\n       discard;\n    float z = sqrt(rsqr-lensqr);\n    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z-outlinePushback);\n    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    gl_FragColor = vec4(outlineColor, 1 );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform float outlineWidth;\nuniform float outlinePushback;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 center;\nvoid main() {\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    center = mvPosition.xyz;\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec2 norm = normal.xy + vec2(sign(normal.x)*outlineWidth,sign(normal.y)*outlineWidth);\n    vec4 adjust = projectionMatrix* vec4(norm,normal.z,0.0); adjust.z = 0.0; adjust.w = 0.0;\n    mapping = norm.xy;\n    rval = abs(norm.x);\n    gl_Position = projPosition+adjust;\n}",
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+p*(e.z+d));var U=s(e),T=0,ea=A*y;G=0;for(ba=E[U];G<ba;G++)for(M=0;M<ba;M++){if(-1!=l[U][T])for(ca=-1;2>ca;ca++)for(X=-1;2>X;X++)for(D=-1;2>D;D++)if(0!==ca&&0!==X&&0!==D)for(z=ca*G,C=D*M,V=0;V<=l[U][T];V++)F=V*X,B=w+z,u=m+F,Z=t+C,0>B||0>u||0>Z||B>=q||u>=A||Z>=y||(Z=B*ea+u*y+Z,f[Z]&1?(x=g[h[Z]],x.serial!=e.serial&&(B=w+z-Math.floor(.5+p*(x.x+b)),u=m+F-Math.floor(.5+p*(x.y+c)),x=t+C-Math.floor(.5+p*(x.z+d)),z*z+F*F+C*C<B*B+u*u+x*x&&(h[Z]=e.serial))):(f[Z]|=1,h[Z]=e.serial));T++}};this.fillvoxelswaals=
+function(b,c){var h,e;h=0;for(e=f.length;h<e;h++)f[h]&=-3;for(h in c)e=b[c[h]],void 0!==e&&this.fillAtomWaals(e,b)};this.fillAtomWaals=function(e,g){var w,m,t,B,u,x,z=0,F,C,G,M,V,Z,ca,X,D,ba,U;w=Math.floor(.5+p*(e.x+b));m=Math.floor(.5+p*(e.y+c));t=Math.floor(.5+p*(e.z+d));var T=s(e),ea=A*y;V=0;for(U=E[T];V<U;V++)for(Z=0;Z<U;Z++){if(-1!=l[T][z])for(X=-1;2>X;X++)for(D=-1;2>D;D++)for(ba=-1;2>ba;ba++)if(0!==X&&0!==D&&0!==ba)for(F=X*V,G=ba*Z,ca=0;ca<=l[T][z];ca++)C=ca*D,B=w+F,u=m+C,M=t+G,0>B||0>u||0>
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+b[d].ix,e=b[d].iy,g=b[d].iz,u=c.get(h,e,g),s=6;18>s;s++)tnv.ix=h+G[s][0],tnv.iy=e+G[s][1],tnv.iz=g+G[s][2],tnv.ix<q&&-1<tnv.ix&&tnv.iy<A&&-1<tnv.iy&&tnv.iz<y&&-1<tnv.iz&&(x=tnv.ix*F+y*tnv.iy+tnv.iz,f[x]&1&&!(f[x]&2)?(c.set(tnv.ix,tnv.iy,g+G[s][2],u),m=tnv.ix-u.ix,l=tnv.iy-u.iy,t=tnv.iz-u.iz,m=m*m+l*l+t*t,w[x]=m,f[x]|=2,f[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):f[x]&1&&f[x]&2&&(m=tnv.ix-u.ix,l=tnv.iy-u.iy,t=tnv.iz-u.iz,m=m*m+l*l+t*t,m<w[x]&&(c.set(tnv.ix,tnv.iy,tnv.iz,u),w[x]=m,f[x]&4||(f[x]|=
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+u.iz,m=m*m+l*l+t*t,m<w[x]&&(c.set(tnv.ix,tnv.iy,tnv.iz,u),w[x]=m,f[x]&4||(f[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return z};this.marchingcubeinit=function(b){for(var c=0,h=f.length;c<h;c++)1==b?f[c]&=-5:4==b?(f[c]&=-3,f[c]&4&&(f[c]|=2),f[c]&=-5):2==b?f[c]&4&&f[c]&2?f[c]&=-5:f[c]&4&&!(f[c]&2)&&(f[c]|=2):3==b&&(f[c]&=-5)};this.marchingcube=function(b){this.marchingcubeinit(b);C=[];M=[];$3Dmol.MarchingCube.march(f,C,M,{smooth:1,nX:q,nY:A,nZ:y});b=A*y;for(var c=0,e=C.length;c<e;c++)C[c].atomid=
+h[C[c].x*b+y*C[c].y+C[c].z];$3Dmol.MarchingCube.laplacianSmooth(1,C,M)}};
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+1]=u.y;J[C+2]=u.z;J[C+3]=u.x;J[C+4]=u.y;J[C+5]=u.z;J[C+6]=s.x;J[C+7]=s.y;J[C+8]=s.z;J[C+9]=s.x;J[C+10]=s.y;J[C+11]=s.z;J[C+12]=l.x;J[C+13]=l.y;J[C+14]=l.z;J[C+15]=l.x;J[C+16]=l.y;J[C+17]=l.z;J[C+18]=E.x;J[C+19]=E.y;J[C+20]=E.z;J[C+21]=E.x;J[C+22]=E.y;J[C+23]=E.z;for(J=0;8>J;++J)I[C+3*J]=y.r,I[C+1+3*J]=y.g,I[C+2+3*J]=y.b;if(0<L)for(C=void 0!==A&&void 0!==z&&A.serial!==z.serial,J=0;4>J;J++)if(I=[w+p[J][0],w+p[J][1],w+p[J][2],w+p[J][3]],s=m.faceidx,K[s]=I[0],K[s+1]=I[1],K[s+2]=I[3],K[s+3]=I[1],K[s+4]=
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+2*z}E=J.faceArray;l=J.vertices;for(A=0;A<z-1;A++)O=[A,A+1,2*z-2-A,2*z-1-A],s=J.faceidx,E[s]=O[0],E[s+1]=O[1],E[s+2]=O[3],E[s+3]=O[1],E[s+4]=O[2],E[s+5]=O[3],J.faceidx+=6;for(A=0;A<z-1;A++)O=[l-1-A,l-2-A,l-2*z+A+1,l-2*z+A],s=J.faceidx,E[s]=O[0],E[s+1]=O[1],E[s+2]=O[3],E[s+3]=O[1],E[s+4]=O[2],E[s+5]=O[3],J.faceidx+=6;w.initTypedArrays();w.setUpNormals();f=new $3Dmol.MeshDoubleLambertMaterial;f.vertexColors=$3Dmol.FaceColors;"number"===typeof t&&0<=t&&1>t&&(f.transparent=!0,f.opacity=t);t=new $3Dmol.Mesh(w,
+f);q.add(t)}else c(q,d[0],d[z-1],f,w,t)}},y=function(b,c){if(b&&c&&b.chain===c.chain){if(b.reschain===c.reschain&&(b.resi===c.resi||b.resi===c.resi-1))return!0;if(b.resi<c.resi){var f=new $3Dmol.Vector3(b.x,b.y,b.z),d=new $3Dmol.Vector3(c.x,c.y,c.z);if(16>f.distanceToSquared(d))return!0}}return!1},A=function(b,c,f,d,h,t,m,e,F){var g,x={ALA:5,ARG:11,ASN:8,ASP:8,CYS:6,GLN:9,GLU:9,GLY:4,HIS:10,ILE:8,LEU:8,LYS:9,MET:8,PHE:11,PRO:7,SER:6,THR:7,TRP:14,TYR:12,VAL:7};if(d&&h&&m){var u=h.sub(d);u.normalize();
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+"default";b.style?b.style!=c&&(console.log("Warning: a cartoon chain's strand-style is ambiguous"),b.style="default"):b.style=c;if("arrow start"===m.ss||"arrow end"===m.ss)m.ss="s";return g}};return function(b,c,f,w){w=parseInt(5*parseFloat(w))||5;var h=fill=!0,t=doNotSmoothen=!1,m=num=w;w=div=w;m=m||5;w=w||5;var e="CA O P OP2 O2P O5' O3' C5' C2' O5* O3* C5* C2* N1 N3".split(" "),F=["DA","DG","A","G"],g=["DT","DC","U","C","T"],x=F.concat(g),u,s,l,E,M,C,G,z,H,L,N,J,I,K,O,Q,W,P=null,S=[],R=[];for(z=
+0;z<m;z++)R[z]=[];var aa=H=!1;z=0;for(z in c)if(E=c[z],"C"===E.elem&&"CA"===E.atom){var V=y(l,E);V&&"s"===E.ss?H=!0:H&&(l&&s&&l.style.cartoon.arrows&&s.style.cartoon.arrows&&(l.ss="arrow end",s.ss="arrow start"),H=!1);V&&"h"===l.ss?(!aa&&E.style.cartoon.tubes&&(E.ss="tube start"),aa=!0):aa&&"tube start"!==l.ss&&(s&&s.style.cartoon.tubes&&(s.ss="tube end"),aa=!1);s=l;l=E}l=void 0;for(z in c)if(E=c[z],void 0!==E&&-1!==$.inArray(E.atom,e))if(H=-1!=$.inArray(E.resn.trim(),x),s=E.style.cartoon,"trace"===
+s.style){if(P||(P=new $3Dmol.Geometry(!0)),"C"===E.elem&&"CA"===E.atom||H&&"P"===E.atom)C=f&&"spectrum"===s.color?f.valueToHex(E.resi,f.range()):$3Dmol.getColorFromStyle(E,s).getHex(),S.push(C),G=$.isNumeric(s.thickness)?s.thickness:.4,y(l,E)&&(C==M?(M=$3Dmol.CC.color(C),$3Dmol.GLDraw.drawCylinder(P,l,E,G,M,2,2)):(s=(new $3Dmol.Vector3).addVectors(l,E).multiplyScalar(.5),M=$3Dmol.CC.color(M),H=$3Dmol.CC.color(C),$3Dmol.GLDraw.drawCylinder(P,l,s,G,M,2,0),$3Dmol.GLDraw.drawCylinder(P,s,E,G,H,0,2))),
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+1),l=E,M=C}else{u||(u=new $3Dmol.Geometry(!0));if(E&&"C"===E.elem&&"CA"===E.atom||H&&("P"===E.atom||0==E.atom.indexOf("O5"))){if(W)if("tube end"===E.ss)W=!1,H=new $3Dmol.Vector3(E.x,E.y,E.z),$3Dmol.GLDraw.drawCylinder(u,Q,H,2,$3Dmol.CC.color(M),1,1),E.ss="h";else continue;if(l&&(!y(l,E)||l.style.cartoon.style!==E.style.cartoon.style||"tube start"===l.ss)){"tube start"===l.ss&&(W=!0,Q=new $3Dmol.Vector3(l.x,l.y,l.z),l.ss="h");O&&(H=I?(new $3Dmol.Vector3).addVectors(l,I).multiplyScalar(.5):new $3Dmol.Vector3(l.x,
+l.y,l.z),$3Dmol.GLDraw.drawCylinder(u,H,O,.4,$3Dmol.CC.color(O.color),0,2),H=A(R,m,!t,I,K,J,l,c,z),S.push(C),H&&S.push(C),O=null);for(z=0;!G&&z<m;z++)d(b,R[z],1,S,w,R.opacity);h&&0<R[0].length&&p(b,R,S,w,G,R.opacity,R.style);null!=u&&0<u.vertices&&(z=new $3Dmol.MeshDoubleLambertMaterial,z.vertexColors=$3Dmol.FaceColors,"number"===typeof R.opacity&&0<=R.opacity&&1>R.opacity&&(z.transparent=!0,z.opacity=R.opacity),u=new $3Dmol.Mesh(u,z),b.add(u),u=null);R=[];for(z=0;z<m;z++)R[z]=[];S=[]}if(void 0===
+l||l.rescode!=E.rescode||l.resi!=E.resi)O&&(H=(new $3Dmol.Vector3).addVectors(l,E).multiplyScalar(.5),C=H.clone().sub(O).multiplyScalar(.02),H.add(C),$3Dmol.GLDraw.drawCylinder(u,H,O,.4,$3Dmol.CC.color(O.color),0,2),O=null),C=f&&"spectrum"===s.color?f.valueToHex(E.resi,f.range()):$3Dmol.getColorFromStyle(E,s).getHex(),S.push(C),G=$.isNumeric(s.thickness)?s.thickness:.4,l=E,L=new $3Dmol.Vector3(l.x,l.y,l.z),L.resi=l.resi,M=C;!0!==E.clickable||void 0!==E.intersectionShape&&void 0!==E.intersectionShape.triangle||
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+g))O=new $3Dmol.Vector3(E.x,E.y,E.z),O.color=$3Dmol.getColorFromStyle(E,s).getHex();N&&L&&N.resi===L.resi&&(H=A(R,m,!t,L,N,J,l,c,z),J=N,N=L=null,S.push(C),H&&S.push(C))}O&&(H=I?(new $3Dmol.Vector3).addVectors(l,I).multiplyScalar(.5):new $3Dmol.Vector3(l.x,l.y,l.z),$3Dmol.GLDraw.drawCylinder(u,H,O,.4,$3Dmol.CC.color(O.color),0,2),H=A(R,m,!t,I,K,J,l,c,z),S.push(C),H&&S.push(C));for(z=0;!G&&z<m;z++)d(b,R[z],1,S,w,R.opacity);h&&0<R[0].length&&p(b,R,S,w,G,R.opacity,R.style);null!=u&&0<u.vertices&&(z=new $3Dmol.MeshDoubleLambertMaterial,
+z.vertexColors=$3Dmol.FaceColors,"number"===typeof R.opacity&&0<=R.opacity&&1>R.opacity&&(z.transparent=!0,z.opacity=R.opacity),u=new $3Dmol.Mesh(u,z),b.add(u));null!=P&&0<P.vertices&&(l=new $3Dmol.MeshDoubleLambertMaterial,l.vertexColors=$3Dmol.FaceColors,"number"===typeof P.opacity&&0<=P.opacity&&1>P.opacity&&(l.transparent=!0,l.opacity=P.opacity,delete P.opacity),P=new $3Dmol.Mesh(P,l),b.add(P))}}();$3Dmol=$3Dmol||{};
+$3Dmol.GLDraw=function(){var b={},c=function(){var b=new $3Dmol.Vector3;return function(c){b.set(c[0],c[1],c[2]);var f=b.x,d=b.y,h=b.z,t=Math.sqrt(f*f+d*d);1E-4>t?(c=0,t=1):(c=-f/t,t=d/t);d=-c*f+t*d;f=Math.sqrt(d*d+h*h);1E-4>f?(h=0,d=1):(h/=f,d/=f);f=new Float32Array(9);f[0]=t;f[1]=c;f[2]=0;f[3]=-c*d;f[4]=t*d;f[5]=h;f[6]=c*h;f[7]=-t*h;f[8]=d;return f}}(),d=function(){var b=[],c=Math.pow(2,4),f,d=Math.pow(2,2),h=c/d,t;b[0]=new $3Dmol.Vector3(-1,0,0);b[h]=new $3Dmol.Vector3(0,0,1);b[2*h]=new $3Dmol.Vector3(1,
+0,0);b[3*h]=new $3Dmol.Vector3(0,0,-1);for(f=3;4>=f;f++){d=Math.pow(2,f-1);h=c/d;for(t=0;t<d-1;t++)b[h/2+t*h]=b[t*h].clone().add(b[(t+1)*h]).normalize();t=d-1;b[h/2+t*h]=b[t*h].clone().add(b[0]).normalize()}return b}(),p={cache:{false:{},true:{}},getVerticesForRadius:function(b,c){if(void 0!==this.cache[c][b])return this.cache[c][b];new $3Dmol.Vector3(0,1,0);for(var f=d.length,w=[],h=[],t,m=0;m<f;m++)w.push(d[m].clone().multiplyScalar(b)),w.push(d[m].clone().multiplyScalar(b)),t=d[m].clone().normalize(),
+h.push(t),h.push(t);var m=[],e=2*Math.PI,F=Math.PI,g,x,u=!1,s=!1;for(x=0;10>=x;x++){var u=0===x||10===x?!0:!1,s=5===x?!0:!1,l=[],E=[];for(g=0;g<=f;g++)if(s){var p=g<f?2*g:0;E.push(p+1);l.push(p)}else{t=g/f;var y=x/10;u&&0!==g?u&&l.push(w.length-1):g<f?(p=new $3Dmol.Vector3,p.x=-b*Math.cos(0+t*e)*Math.sin(0+y*F),p.y=c?0:b*Math.cos(0+y*F),p.z=b*Math.sin(0+t*e)*Math.sin(0+y*F),1E-5>Math.abs(p.x)&&(p.x=0),1E-5>Math.abs(p.y)&&(p.y=0),1E-5>Math.abs(p.z)&&(p.z=0),t=c?new $3Dmol.Vector3(0,Math.cos(0+y*F),
+0):new $3Dmol.Vector3(p.x,p.y,p.z),t.normalize(),w.push(p),h.push(t),l.push(w.length-1)):l.push(w.length-f)}s&&m.push(E);m.push(l)}f={vertices:w,normals:h,verticesRows:m,w:f,h:10};return this.cache[c][b]=f}},y=0;b.drawCylinder=function(b,d,f,w,h,t,m){if(d&&f){y++;var e=t||m,F=!1;1==t&&1==m&&(F=!0);h=h||{r:0,g:0,b:0};var g=[f.x,f.y,f.z];g[0]-=d.x;g[1]-=d.y;g[2]-=d.z;var g=c(g),x=p.getVerticesForRadius(w,F);w=x.w;var F=x.h,u=e?F*w+2:2*w;b=b.updateGeoGroup(u);var s=x.vertices,l=x.normals,x=x.verticesRows,
+E=x[F/2],A=x[F/2+1],C=b.vertices,G,z,H,L,N,J,I=b.vertexArray,K=b.normalArray,O=b.colorArray,Q=b.faceArray;for(H=0;H<w;++H)z=2*H,L=g[0]*s[z].x+g[3]*s[z].y+g[6]*s[z].z,N=g[1]*s[z].x+g[4]*s[z].y+g[7]*s[z].z,J=g[5]*s[z].y+g[8]*s[z].z,G=3*(C+z),z=b.faceidx,I[G]=L+d.x,I[G+1]=N+d.y,I[G+2]=J+d.z,I[G+3]=L+f.x,I[G+4]=N+f.y,I[G+5]=J+f.z,K[G]=L,K[G+3]=L,K[G+1]=N,K[G+4]=N,K[G+2]=J,K[G+5]=J,O[G]=h.r,O[G+3]=h.r,O[G+1]=h.g,O[G+4]=h.g,O[G+2]=h.b,O[G+5]=h.b,Q[z]=A[H]+C,Q[z+1]=A[H+1]+C,Q[z+2]=E[H]+C,Q[z+3]=E[H]+C,Q[z+
+4]=A[H+1]+C,Q[z+5]=E[H+1]+C,b.faceidx+=6;if(e){t=t?F+1:F/2+1;var W,P,S,R,aa,V,Z,ca,X,D,ba,U,T;for(N=m?0:F/2;N<t;N++)if(N!==F/2){var ea=N<=F/2?f:d;for(L=0;L<w;L++)z=b.faceidx,m=x[N][L+1],H=3*(m+C),e=x[N][L],J=3*(e+C),E=x[N+1][L],G=3*(E+C),A=x[N+1][L+1],T=3*(A+C),W=g[0]*s[m].x+g[3]*s[m].y+g[6]*s[m].z,P=g[0]*s[e].x+g[3]*s[e].y+g[6]*s[e].z,S=g[0]*s[E].x+g[3]*s[E].y+g[6]*s[E].z,R=g[0]*s[A].x+g[3]*s[A].y+g[6]*s[A].z,aa=g[1]*s[m].x+g[4]*s[m].y+g[7]*s[m].z,V=g[1]*s[e].x+g[4]*s[e].y+g[7]*s[e].z,Z=g[1]*s[E].x+
+g[4]*s[E].y+g[7]*s[E].z,ca=g[1]*s[A].x+g[4]*s[A].y+g[7]*s[A].z,X=g[5]*s[m].y+g[8]*s[m].z,D=g[5]*s[e].y+g[8]*s[e].z,ba=g[5]*s[E].y+g[8]*s[E].z,U=g[5]*s[A].y+g[8]*s[A].z,I[H]=W+ea.x,I[J]=P+ea.x,I[G]=S+ea.x,I[T]=R+ea.x,I[H+1]=aa+ea.y,I[J+1]=V+ea.y,I[G+1]=Z+ea.y,I[T+1]=ca+ea.y,I[H+2]=X+ea.z,I[J+2]=D+ea.z,I[G+2]=ba+ea.z,I[T+2]=U+ea.z,O[H]=h.r,O[J]=h.r,O[G]=h.r,O[T]=h.r,O[H+1]=h.g,O[J+1]=h.g,O[G+1]=h.g,O[T+1]=h.g,O[H+2]=h.b,O[J+2]=h.b,O[G+2]=h.b,O[T+2]=h.b,W=g[0]*l[m].x+g[3]*l[m].y+g[6]*l[m].z,P=g[0]*l[e].x+
+g[3]*l[e].y+g[6]*l[e].z,S=g[0]*l[E].x+g[3]*l[E].y+g[6]*l[E].z,R=g[0]*l[A].x+g[3]*l[A].y+g[6]*l[A].z,aa=g[1]*l[m].x+g[4]*l[m].y+g[7]*l[m].z,V=g[1]*l[e].x+g[4]*l[e].y+g[7]*l[e].z,Z=g[1]*l[E].x+g[4]*l[E].y+g[7]*l[E].z,ca=g[1]*l[A].x+g[4]*l[A].y+g[7]*l[A].z,X=g[5]*l[m].y+g[8]*l[m].z,D=g[5]*l[e].y+g[8]*l[e].z,ba=g[5]*l[E].y+g[8]*l[E].z,U=g[5]*l[A].y+g[8]*l[A].z,0===N?(K[H]=W,K[G]=S,K[T]=R,K[H+1]=aa,K[G+1]=Z,K[T+1]=ca,K[H+2]=X,K[G+2]=ba,K[T+2]=U,Q[z]=m+C,Q[z+1]=E+C,Q[z+2]=A+C,b.faceidx+=3):N===t-1?(K[H]=
+W,K[J]=P,K[G]=S,K[H+1]=aa,K[J+1]=V,K[G+1]=Z,K[H+2]=X,K[J+2]=D,K[G+2]=ba,Q[z]=m+C,Q[z+1]=e+C,Q[z+2]=E+C,b.faceidx+=3):(K[H]=W,K[J]=P,K[T]=R,K[H+1]=aa,K[J+1]=V,K[T+1]=ca,K[H+2]=X,K[J+2]=D,K[T+2]=U,K[J]=P,K[G]=S,K[T]=R,K[J+1]=V,K[G+1]=Z,K[T+1]=ca,K[J+2]=D,K[G+2]=ba,K[T+2]=U,Q[z]=m+C,Q[z+1]=e+C,Q[z+2]=A+C,Q[z+3]=e+C,Q[z+4]=E+C,Q[z+5]=A+C,b.faceidx+=6)}}b.vertices+=u}};b.drawCone=function(b,p,f,w,h){if(p&&f){h=h||{r:0,g:0,b:0};var t=[f.x,f.y,f.z];t.x-=p.x;t.y-=p.y;t.z-=p.z;var m=c(t),e=d.length;b=b.updateGeoGroup(e+
+2);var F=b.vertices,g,x,u,s=b.vertexArray,l=b.normalArray,E=b.colorArray,y=b.faceArray;g=3*F;t=(new $3Dmol.Vector3(t[0],t[1],t[2])).normalize();s[g]=p.x;s[g+1]=p.y;s[g+2]=p.z;l[g]=-t.x;l[g+1]=-t.y;l[g+2]=-t.z;E[g]=h.r;E[g+1]=h.g;E[g+2]=h.b;s[g+3]=f.x;s[g+4]=f.y;s[g+5]=f.z;l[g+3]=t.x;l[g+4]=t.y;l[g+5]=t.z;E[g+3]=h.r;E[g+4]=h.g;E[g+5]=h.b;g+=6;for(f=0;f<e;++f)u=d[f].clone(),u.multiplyScalar(w),t=m[0]*u.x+m[3]*u.y+m[6]*u.z,x=m[1]*u.x+m[4]*u.y+m[7]*u.z,u=m[5]*u.y+m[8]*u.z,s[g]=t+p.x,s[g+1]=x+p.y,s[g+
+2]=u+p.z,l[g]=t,l[g+1]=x,l[g+2]=u,E[g]=h.r,E[g+1]=h.g,E[g+2]=h.b,g+=3;b.vertices+=e+2;p=b.faceidx;for(f=0;f<e;f++)w=F+2+f,h=F+2+(f+1)%e,y[p]=w,y[p+1]=h,y[p+2]=F,p+=3,y[p]=w,y[p+1]=h,y[p+2]=F+1,p+=3;b.faceidx+=6*e}};var A={cache:{},getVerticesForRadius:function(b){if("undefined"!==typeof this.cache[b])return this.cache[b];var c={vertices:[],verticesRows:[],normals:[]},f=16,d=10;1>b&&(f=10,d=8);var h=2*Math.PI,t=Math.PI,m,e;for(e=0;e<=d;e++){var p=[];for(m=0;m<=f;m++){var g=m/f,x=e/d,u={};u.x=-b*Math.cos(0+
+g*h)*Math.sin(0+x*t);u.y=b*Math.cos(0+x*t);u.z=b*Math.sin(0+g*h)*Math.sin(0+x*t);g=new $3Dmol.Vector3(u.x,u.y,u.z);g.normalize();c.vertices.push(u);c.normals.push(g);p.push(c.vertices.length-1)}c.verticesRows.push(p)}return this.cache[b]=c}};b.drawSphere=function(b,c,f,d){new $3Dmol.Vector3(c.x,c.y,c.z);var h=A.getVerticesForRadius(f),t=h.vertices,m=h.normals;b=b.updateGeoGroup(t.length);for(var e=b.vertices,p=b.vertexArray,g=b.colorArray,x=b.faceArray,u=b.lineArray,s=b.normalArray,l=0,E=t.length;l<
+E;++l){var y=3*(e+l),C=t[l];p[y]=C.x+c.x;p[y+1]=C.y+c.y;p[y+2]=C.z+c.z;g[y]=d.r;g[y+1]=d.g;g[y+2]=d.b}b.vertices+=t.length;h=h.verticesRows;p=h.length-1;for(d=0;d<p;d++)for(g=h[d].length-1,c=0;c<g;c++){var l=b.faceidx,E=b.lineidx,y=h[d][c+1]+e,C=3*y,G=h[d][c]+e,z=3*G,H=h[d+1][c]+e,L=3*H,N=h[d+1][c+1]+e,J=3*N,I=m[y-e],K=m[G-e],O=m[H-e],Q=m[N-e];Math.abs(t[y-e].y)===f?(s[C]=I.x,s[L]=O.x,s[J]=Q.x,s[C+1]=I.y,s[L+1]=O.y,s[J+1]=Q.y,s[C+2]=I.z,s[L+2]=O.z,s[J+2]=Q.z,x[l]=y,x[l+1]=H,x[l+2]=N,u[E]=y,u[E+1]=
+H,u[E+2]=y,u[E+3]=N,u[E+4]=H,u[E+5]=N,b.faceidx+=3,b.lineidx+=6):Math.abs(t[H-e].y)===f?(s[C]=I.x,s[z]=K.x,s[L]=O.x,s[C+1]=I.y,s[z+1]=K.y,s[L+1]=O.y,s[C+2]=I.z,s[z+2]=K.z,s[L+2]=O.z,x[l]=y,x[l+1]=G,x[l+2]=H,u[E]=y,u[E+1]=G,u[E+2]=y,u[E+3]=H,u[E+4]=G,u[E+5]=H,b.faceidx+=3,b.lineidx+=6):(s[C]=I.x,s[z]=K.x,s[J]=Q.x,s[C+1]=I.y,s[z+1]=K.y,s[J+1]=Q.y,s[C+2]=I.z,s[z+2]=K.z,s[J+2]=Q.z,s[z]=K.x,s[L]=O.x,s[J]=Q.x,s[z+1]=K.y,s[L+1]=O.y,s[J+1]=Q.y,s[z+2]=K.z,s[L+2]=O.z,s[J+2]=Q.z,x[l]=y,x[l+1]=G,x[l+2]=N,x[l+
+3]=G,x[l+4]=H,x[l+5]=N,u[E]=y,u[E+1]=G,u[E+2]=y,u[E+3]=N,u[E+4]=G,u[E+5]=H,u[E+6]=H,u[E+7]=N,b.faceidx+=6,b.lineidx+=8)}};return b}();$3Dmol=$3Dmol||{};
+$3Dmol.GLModel=function(){function b(b,q){var B=[],f=[],w=!1,h=null,t=null,m=null,e={},F=new $3Dmol.Matrix4,g,x=$3Dmol.elementColors.defaultColor,u=q?q:$3Dmol.elementColors.defaultColors,s=function(b,c){var h=1.5;"undefined"!=typeof c.radius?h=c.radius:d[b.elem]&&(h=d[b.elem]);"undefined"!=typeof c.scale&&(h*=c.scale);return h},l=function(b,c,h){var e=new $3Dmol.Vector3(b.x,b.y,b.z),f=(new $3Dmol.Vector3(c.x,c.y,c.z)).clone(),g=null;f.sub(e);1===b.bonds.length?1===c.bonds.length?(g=f.clone(),1E-4<
+Math.abs(g.x)?g.y+=1:g.x+=1):(h=(h+1)%c.bonds.length,b=c.bonds[h],b=B[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(e),g=b.clone(),g.cross(f)):(h=(h+1)%b.bonds.length,b=b.bonds[h],b=B[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(e),g=b.clone(),g.cross(f));.01>g.lengthSq()&&(g=f.clone(),1E-4<Math.abs(g.x)?g.y+=1:g.x+=1);g.cross(f);g.normalize();return g},E=function(b,c,h,e,f,g){b[h]=e.x;b[h+1]=e.y;b[h+2]=e.z;c[h]=g.r;c[h+1]=g.g;c[h+2]=g.b;b[h+3]=f.x;b[h+4]=f.y;b[h+5]=f.z;c[h+3]=
+g.r;c[h+4]=g.g;c[h+5]=g.b},M=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=$3Dmol.getColorFromStyle(b,h),h=s(b,h);if(!0===b.clickable&&void 0!==b.intersectionShape){var f=new $3Dmol.Vector3(b.x,b.y,b.z);b.intersectionShape.sphere.push(new $3Dmol.Sphere(f,h))}$3Dmol.GLDraw.drawSphere(c,b,h,e)}}},C=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=s(b,h),h=$3Dmol.getColorFromStyle(b,h),f=c.updateGeoGroup(1),g=f.vertices,d=3*g,m=f.vertexArray,l=f.colorArray,
+t=f.radiusArray;m[d]=b.x;m[d+1]=b.y;m[d+2]=b.z;l=f.colorArray;l[d]=h.r;l[d+1]=h.g;l[d+2]=h.b;t[g]=e;f.vertices+=1}}},G=function(b,c,h,e){b=b.updateGeoGroup(4);for(var f=b.vertices,g=3*f,d=b.vertexArray,m=b.colorArray,l=0;4>l;l++)d[g+3*l]=c.x,d[g+3*l+1]=c.y,d[g+3*l+2]=c.z;c=b.normalArray;m=b.colorArray;for(l=0;4>l;l++)m[g+3*l]=e.r,m[g+3*l+1]=e.g,m[g+3*l+2]=e.b;c[g+0]=-h;c[g+1]=h;c[g+2]=0;c[g+3]=-h;c[g+4]=-h;c[g+5]=0;c[g+6]=h;c[g+7]=-h;c[g+8]=0;c[g+9]=h;c[g+10]=h;c[g+11]=0;b.vertices+=4;h=b.faceArray;
+e=b.faceidx;h[e+0]=f;h[e+1]=f+1;h[e+2]=f+2;h[e+3]=f+2;h[e+4]=f+3;h[e+5]=f;b.faceidx+=6},z=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=s(b,h),h=$3Dmol.getColorFromStyle(b,h);G(c,b,e,h)}}},H=function(b,c,h,e,f,g,d){b=b.updateGeoGroup(4);g=b.vertices;d=b.vertexArray;var m=b.colorArray,l=b.radiusArray,t=b.normalArray,w=f.r,s=f.g;f=f.b;for(var u=3*g,x=0;4>x;x++){d[u]=c.x;t[u]=h.x;m[u]=w;u++;d[u]=c.y;t[u]=h.y;m[u]=s;u++;d[u]=c.z;t[u]=h.z;if(2>x)m[u]=f;else{var q=u,p=-f;0==
+p&&(p=-1E-4);m[q]=p}u++}b.vertices+=4;l[g]=-e;l[g+1]=e;l[g+2]=-e;l[g+3]=e;c=b.faceArray;h=b.faceidx;c[h+0]=g;c[h+1]=g+1;c[h+2]=g+2;c[h+3]=g+2;c[h+4]=g+3;c[h+5]=g;b.faceidx+=6};this.getCrystData=function(){return e.cryst?e.cryst:null};this.getSymmetries=function(){"undefined"==typeof e.symmetries&&(e.symmetries=[F]);return e.symmetries};this.setSymmetries=function(b){e.symmetries="undefined"==typeof b?[F]:b};this.getID=function(){return b};this.getFrames=function(){return f};this.setFrame=function(b){0!=
+f.length&&(B=0<=b&&b<f.length?f[b]:f[f.length-1],h=null)};this.addFrame=function(b){f.push(b)};this.vibrate=function(b,c){var h=[];c=c||1;b=b||10;for(var e=0;e<B.length;e++){var g=new $3Dmol.Vector3(B[e].dx,B[e].dy,B[e].dz);h.push(g)}b--;for(e=1;e<=b;e++){h=[];for(g=0;g<B.length;g++){var d=new $3Dmol.Vector3(B[g].dx,B[g].dy,B[g].dz),m=new $3Dmol.Vector3(B[g].x,B[g].y,B[g].z);d.sub(m);d.multiplyScalar(e*c/b);m.add(d);var d={},l;for(l in B[g])d[l]=B[g][l];d.x=m.x;d.y=m.y;d.z=m.z;h.push(d)}f.push(h)}f.unshift(B)};
+this.setAtomDefaults=function(h){for(var e=0;e<h.length;e++){var f=h[e];f&&(f.style=f.style||c,f.color=f.color||u[f.elem]||x,f.model=b,f.clickable&&(f.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}))}};this.addMolData=function(c,h,d){d=d||{};c=$3Dmol.GLModel.parseMolData(c,h,d);g=!d.duplicateAssemblyAtoms;(h=c.modelData)&&(e=Array.isArray(h)?h[0]:h);if(0==f.length){for(d=0;d<c.length;d++)0!=c[d].length&&f.push(c[d]);f[0]&&(B=f[0])}else if(d.frames)for(d=0;d<c.length;d++)f.push(c[d]);
+else for(d=0;d<c.length;d++)this.addAtoms(c[d]);for(d=0;d<f.length;d++)this.setAtomDefaults(f[d],b)};this.setDontDuplicateAtoms=function(b){g=b};this.setModelData=function(b){e=b};this.atomIsSelected=function(b,c){if("undefined"===typeof c)return!0;var h=!!c.invert,e=!0,f;for(f in c)if("predicate"===f){if(!c.predicate(b)){e=!1;break}}else if("properties"==f&&b[f])for(var g in c.properties){if("undefined"===typeof b.properties[g]){e=!1;break}if(b.properties[g]!=c.properties[g]){e=!1;break}}else if(c.hasOwnProperty(f)&&
+"props"!=f&&"invert"!=f&&"model"!=f&&"byres"!=f&&"expand"!=f&&"within"!=f){if("undefined"===typeof b[f]){e=!1;break}var d=!1;if("bonds"===f){if(d=c[f],d!=b.bonds.length){e=!1;break}}else if($.isArray(c[f])){for(var m=c[f],l=0;l<m.length;l++)if(b[f]==m[l]){d=!0;break}if(!d){e=!1;break}}else if(d=c[f],b[f]!=d){e=!1;break}}return h?!e:e};this.selectedAtoms=function(b,c){var h=[];b=b||{};c||(c=B);for(var e=c.length,f=0;f<e;f++){var g=c[f];g&&this.atomIsSelected(g,b)&&h.push(g)}if(b.hasOwnProperty("expand")){var d;
+var m=parseFloat(b.expand);if(0>=m)d=h;else{f=$3Dmol.getExtent(h);e=[[],[],[]];for(g=0;3>g;g++)e[0][g]=f[0][g]-m,e[1][g]=f[1][g]+m,e[2][g]=f[2][g];m=[];for(g=0;g<B.length;g++){d=B[g].x;var l=B[g].y,t=B[g].z;d>=e[0][0]&&d<=e[1][0]&&l>=e[0][1]&&l<=e[1][1]&&t>=e[0][2]&&t<=e[1][2]&&(d>=f[0][0]&&d<=f[1][0]&&l>=f[0][1]&&l<=f[1][1]&&t>=f[0][2]&&t<=f[1][2]||m.push(B[g]))}d=m}l=h.length;for(f=0;f<d.length;f++)for(e=0;e<l;e++)g=L(d[f],h[e]),m=Math.pow(b.expand,2),g<m&&0<g&&h.push(d[f])}if(b.hasOwnProperty("within")&&
+b.within.hasOwnProperty("sel")&&b.within.hasOwnProperty("distance")){d=this.selectedAtoms(b.within.sel,B);l=[];for(f=0;f<d.length;f++)for(e=0;e<h.length;e++)g=L(d[f],h[e]),m=Math.pow(parseFloat(b.within.distance),2),g<m&&0<g&&l.push(h[e]);h=l}if(b.hasOwnProperty("byres"))for(m={},d=[],l=[],f=0;f<h.length;f++){var g=h[f],t=g.chain,w=g.resi;void 0===m[t]&&(m[t]={});if(g.hasOwnProperty("resi")&&void 0===m[t][w])for(m[t][w]=!0,l.push(g);0<l.length;)if(g=l.pop(),t=g.chain,w=g.resi,void 0===d[g.index])for(d[g.index]=
+!0,e=0;e<g.bonds.length;e++){var s=B[g.bonds[e]];void 0===d[s.index]&&s.hasOwnProperty("resi")&&s.chain==t&&s.resi==w&&(l.push(s),h.push(s))}}return h};var L=function(b,c){var h=c.y-b.y,e=c.z-b.z;return Math.pow(c.x-b.x,2)+Math.pow(h,2)+Math.pow(e,2)};this.addAtoms=function(e){h=null;var f=B.length,g=[],d;for(d=0;d<e.length;d++)"undefined"==typeof e[d].index&&(e[d].index=d),"undefined"==typeof e[d].serial&&(e[d].serial=d),g[e[d].index]=f+d;for(d=0;d<e.length;d++){var f=e[d],m=g[f.index],l=$.extend(!1,
+{},f);l.index=m;l.bonds=[];l.bondOrder=[];l.model=b;l.style=l.style||c;"undefined"==typeof l.color&&(l.color=u[l.elem]||x);for(var m=f.bonds?f.bonds.length:0,t=0;t<m;t++){var w=g[f.bonds[t]];"undefined"!=typeof w&&(l.bonds.push(w),l.bondOrder.push(f.bondOrder?f.bondOrder[t]:1))}B.push(l)}};this.removeAtoms=function(b){h=null;var c=[],e;for(e=0;e<b.length;e++)c[b[e].index]=!0;b=[];for(e=0;e<B.length;e++){var f=B[e];c[f.index]||b.push(f)}B=[];this.addAtoms(b)};this.setStyle=function(b,c,e){"undefined"===
+typeof c&&"undefined"==typeof e&&(c=b,b={});for(var g in b)-1===p.indexOf(g)&&console.log("Unknown selector "+g);for(g in c)-1===y.indexOf(g)&&console.log("Unknown style "+g);var d=!1,m=function(h){for(var f=l.selectedAtoms(b,h),m=0;m<h.length;m++)h[m]&&(h[m].capDrawn=!1);for(m=0;m<f.length;m++)for(g in d=!0,f[m].clickable&&(f[m].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),e||(f[m].style={}),c)if(c.hasOwnProperty(g)){f[m].style[g]=f[m].style[g]||{};for(var t in c[g])f[m].style[g][t]=
+c[g][t]}},l=this;m(B);for(var t=0;t<f.length;t++)m(f[t]);d&&(h=null)};this.setClickable=function(b,c,e){for(var f in b)-1===p.indexOf(f)&&console.log("Unknown selector "+f);c=!!c;if(e&&"function"!=typeof e)console.log("Callback is not a function");else{f=this.selectedAtoms(b,B);var g=f.length;for(b=0;b<g;b++)f[b].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]},f[b].clickable=c,e&&(f[b].callback=e);0<g&&(h=null)}};this.setColorByElement=function(b,c){var e;if(e=null!==h)e=m,e=c&&e?JSON.stringify(c)==
+JSON.stringify(e):c==e;if(!e){m=c;var f=this.selectedAtoms(b,f);0<f.length&&(h=null);for(e=0;e<f.length;e++){var g=f[e];"undefined"!==typeof c[g.elem]&&(g.color=c[g.elem])}}};this.setColorByProperty=function(b,c,e,f){var g=this.selectedAtoms(b,g);m=null;0<g.length&&(h=null);var d;f||(f=e.range());f||(f=$3Dmol.getPropertyRange(g,c));for(b=0;b<g.length;b++)d=g[b],null!=$3Dmol.getAtomProperty(d,c)&&(d.color=e.valueToHex(parseFloat(d.properties[c]),[f[0],f[1]]))};this.setColorByFunction=function(b,c){var e=
+this.selectedAtoms(b,e);m=null;0<e.length&&(h=null);for(i=0;i<e.length;i++)a=e[i],a.color=c(a)};this.toCDObject=function(b){var c={a:[],b:[]};b&&(c.s=[]);for(var h=0;h<B.length;h++){var e={},f=B[h];e.x=f.x;e.y=f.y;e.z=f.z;"C"!=f.elem&&(e.l=f.elem);if(b){for(var g=0;g<c.s.length&&JSON.stringify(f.style)!==JSON.stringify(c.s[g]);)g++;g===c.s.length&&c.s.push(f.style);0!==g&&(e.s=g)}c.a.push(e);for(e=0;e<f.bonds.length;e++){var g=h,d=f.bonds[e];g>=d||(g={b:g,e:d},d=f.bondOrder[e],1!=d&&(g.o=d),c.b.push(g))}}return c};
+this.globj=function(b,c){if(null===h){var f=B,d=c,d=d||{},m=new $3Dmol.Object3D,u=[],x={},q={},p=M,y=null,F=null;d.supportsImposters?(p=z,y=new $3Dmol.Geometry(!0),y.imposter=!0,F=new $3Dmol.Geometry(!0,!0),F.imposter=!0,F.sphereGeometry=y,F.drawnCaps={}):(d.supportsAIA?(p=C,y=new $3Dmol.Geometry(!1,!0,!0),y.instanced=!0):y=new $3Dmol.Geometry(!0),F=new $3Dmol.Geometry(!0));var A,L,ca,X,D={},ba=[Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY];A=0;for(ca=f.length;A<ca;A++){var U=f[A];if(U&&U.style){U.clickable&&
+void 0===U.intersectionShape&&(U.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});X={line:void 0,cross:void 0,stick:void 0,sphere:void 0};for(L in X)X[L]=U.style[L]?U.style[L].opacity?parseFloat(U.style[L].opacity):1:void 0,D[L]?void 0!=X[L]&&D[L]!=X[L]&&(console.log("Warning: "+L+" opacity is ambiguous"),D[L]=1):D[L]=X[L];p(U,y);var T=U,ea=q;if(T.style.cross){var Ba=T.style.cross;if(!Ba.hidden){var Na=Ba.linewidth||1;ea[Na]||(ea[Na]=new $3Dmol.Geometry);var Ja=ea[Na].updateGeoGroup(6),
+La=s(T,Ba),Ia=[[La,0,0],[-La,0,0],[0,La,0],[0,-La,0],[0,0,La],[0,0,-La]],Za=T.clickable;Za&&void 0===T.intersectionShape&&(T.intersectionShape={sphere:[],cylinder:[],line:[]});for(var Ta=$3Dmol.getColorFromStyle(T,Ba),$a=Ja.vertexArray,Ua=Ja.colorArray,xa=0;6>xa;xa++){var Ma=3*Ja.vertices;Ja.vertices++;$a[Ma]=T.x+Ia[xa][0];$a[Ma+1]=T.y+Ia[xa][1];$a[Ma+2]=T.z+Ia[xa][2];Ua[Ma]=Ta.r;Ua[Ma+1]=Ta.g;Ua[Ma+2]=Ta.b;if(Za){var Va=new $3Dmol.Vector3(Ia[xa][0],Ia[xa][1],Ia[xa][2]);Va.multiplyScalar(.1);Va.set(Va.x+
+T.x,Va.y+T.y,Va.z+T.z);T.intersectionShape.line.push(Va)}}}}var fa=U,zb=f,kb=x;if(fa.style.line){var rb=fa.style.line;if(!rb.hidden){var lb=rb.linewidth||1;kb[lb]||(kb[lb]=new $3Dmol.Geometry);for(var ta=kb[lb].updateGeoGroup(6*fa.bonds.length),ja=ta.vertexArray,ka=ta.colorArray,Ea=0;Ea<fa.bonds.length;Ea++){var Oa=zb[fa.bonds[Ea]];if(Oa.style.line&&!(fa.serial>=Oa.serial)){var Ca=new $3Dmol.Vector3(fa.x,fa.y,fa.z),Qa=new $3Dmol.Vector3(Oa.x,Oa.y,Oa.z),fb=Ca.clone().add(Qa).multiplyScalar(.5),sb=
+!1;fa.clickable&&(void 0===fa.intersectionShape&&(fa.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),fa.intersectionShape.line.push(Ca),fa.intersectionShape.line.push(Qa));var pa=$3Dmol.getColorFromStyle(fa,fa.style.line),Fa=$3Dmol.getColorFromStyle(Oa,Oa.style.line);if(fa.bondStyles&&fa.bondStyles[Ea]){var Pa=fa.bondStyles[Ea];if(!Pa.iswire)continue;Pa.radius&&(bondR=Pa.radius);Pa.singleBond&&(sb=!0);"undefined"!=typeof Pa.color1&&(pa=$3Dmol.CC.color(Pa.color1));"undefined"!=typeof Pa.color2&&
+(Fa=$3Dmol.CC.color(Pa.color2))}var la=3*ta.vertices;if(1<fa.bondOrder[Ea]&&4>fa.bondOrder[Ea]&&!sb){var Wa=l(fa,Oa,Ea),Da=Qa.clone();Da.sub(Ca);if(2==fa.bondOrder[Ea])if(Wa.multiplyScalar(.1),p1a=Ca.clone(),p1a.add(Wa),p1b=Ca.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Da),p2b=p1b.clone(),p2b.add(Da),pa==Fa)ta.vertices+=4,E(ja,ka,la,p1a,p2a,pa),E(ja,ka,la+6,p1b,p2b,pa);else{ta.vertices+=8;Da.multiplyScalar(.5);var Ra=p1a.clone();Ra.add(Da);var Sa=p1b.clone();Sa.add(Da);E(ja,ka,la,p1a,Ra,pa);E(ja,
+ka,la+6,Ra,p2a,Fa);E(ja,ka,la+12,p1b,Sa,pa);E(ja,ka,la+18,Sa,p2b,Fa)}else 3==fa.bondOrder[Ea]&&(Wa.multiplyScalar(.1),p1a=Ca.clone(),p1a.add(Wa),p1b=Ca.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Da),p2b=p1b.clone(),p2b.add(Da),pa==Fa?(ta.vertices+=6,E(ja,ka,la,Ca,Qa,pa),E(ja,ka,la+6,p1a,p2a,pa),E(ja,ka,la+12,p1b,p2b,pa)):(ta.vertices+=12,Da.multiplyScalar(.5),Ra=p1a.clone(),Ra.add(Da),Sa=p1b.clone(),Sa.add(Da),E(ja,ka,la,Ca,fb,pa),E(ja,ka,la+6,fb,Qa,Fa),E(ja,ka,la+12,p1a,Ra,pa),E(ja,ka,la+18,Ra,
+p2a,Fa),E(ja,ka,la+24,p1b,Sa,pa),E(ja,ka,la+30,Sa,p2b,Fa)))}else pa==Fa?(ta.vertices+=2,E(ja,ka,la,Ca,Qa,pa)):(ta.vertices+=4,E(ja,ka,la,Ca,fb,pa),E(ja,ka,la+6,fb,Qa,Fa))}}}}var Y=U,Ab=f,ga=F;if(Y.style.stick){var gb=Y.style.stick;if(!gb.hidden){var ab=gb.radius||.25,ua=ab,tb=gb.singleBonds||!1,bb=0,cb=0,ma=$3Dmol.getColorFromStyle(Y,gb),na=void 0,ya=void 0;!Y.capDrawn&&4>Y.bonds.length&&(bb=2);var ia=$3Dmol.GLDraw.drawCylinder;ga.imposter&&(ia=H);for(var oa=0;oa<Y.bonds.length;oa++){var ha=Ab[Y.bonds[oa]];
+if(Y.serial<ha.serial){var ub=ha.style;if(ub.stick){var Ga=$3Dmol.getColorFromStyle(ha,ub.stick),ua=ab,db=tb;if(Y.bondStyles&&Y.bondStyles[oa]){var za=Y.bondStyles[oa];if(za.iswire)continue;za.radius&&(ua=za.radius);za.singleBond&&(db=!0);"undefined"!=typeof za.color1&&(ma=$3Dmol.CC.color(za.color1));"undefined"!=typeof za.color2&&(Ga=$3Dmol.CC.color(za.color2))}var qa=new $3Dmol.Vector3(Y.x,Y.y,Y.z),Aa=new $3Dmol.Vector3(ha.x,ha.y,ha.z);if(1===Y.bondOrder[oa]||db){if(!ha.capDrawn&&4>ha.bonds.length&&
+(cb=2),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5),ia(ga,qa,na,ua,ma,bb,0),ia(ga,na,Aa,ua,Ga,0,cb)):ia(ga,qa,Aa,ua,ma,bb,cb),Y.clickable||ha.clickable){na=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5);if(Y.clickable){var Bb=new $3Dmol.Cylinder(qa,na,ua),Cb=new $3Dmol.Sphere(qa,ua);Y.intersectionShape.cylinder.push(Bb);Y.intersectionShape.sphere.push(Cb)}if(ha.clickable){var Db=new $3Dmol.Cylinder(Aa,na,ua),Eb=new $3Dmol.Sphere(Aa,ua);ha.intersectionShape.cylinder.push(Db);
+ha.intersectionShape.sphere.push(Eb)}}}else if(1<Y.bondOrder[oa]){var Ka=0;mtoCap=0;ua!=ab&&(mtoCap=Ka=2);var Xa=Aa.clone(),Ha=null;Xa.sub(qa);var da,ra,sa,va,wa,Ha=l(Y,ha,oa);if(2==Y.bondOrder[oa]){if(da=ua/2.5,Ha=l(Y,ha,oa),Ha.multiplyScalar(1.5*da),ra=qa.clone(),ra.add(Ha),sa=qa.clone(),sa.sub(Ha),va=ra.clone(),va.add(Xa),wa=sa.clone(),wa.add(Xa),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),ia(ga,ra,na,da,ma,Ka,
+0),ia(ga,na,va,da,Ga,0,mtoCap),ia(ga,sa,ya,da,ma,Ka,0),ia(ga,ya,wa,da,Ga,0,mtoCap)):(ia(ga,ra,va,da,ma,Ka,mtoCap),ia(ga,sa,wa,da,ma,Ka,mtoCap)),Y.clickable||ha.clickable)na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),Y.clickable&&(cylinder1a=new $3Dmol.Cylinder(ra,na,da),cylinder1b=new $3Dmol.Cylinder(sa,ya,da),Y.intersectionShape.cylinder.push(cylinder1a),Y.intersectionShape.cylinder.push(cylinder1b)),ha.clickable&&(cylinder2a=
+new $3Dmol.Cylinder(va,na,da),cylinder2b=new $3Dmol.Cylinder(wa,ya,da),ha.intersectionShape.cylinder.push(cylinder2a),ha.intersectionShape.cylinder.push(cylinder2b))}else 3==Y.bondOrder[oa]&&(da=ua/4,Ha.cross(Xa),Ha.normalize(),Ha.multiplyScalar(3*da),ra=qa.clone(),ra.add(Ha),sa=qa.clone(),sa.sub(Ha),va=ra.clone(),va.add(Xa),wa=sa.clone(),wa.add(Xa),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(qa,
+Aa).multiplyScalar(.5),ia(ga,ra,na,da,ma,Ka,0),ia(ga,na,va,da,Ga,0,mtoCap),ia(ga,qa,mp3,da,ma,bb,0),ia(ga,mp3,Aa,da,Ga,0,cb),ia(ga,sa,ya,da,ma,Ka,0),ia(ga,ya,wa,da,Ga,0,mtoCap)):(ia(ga,ra,va,da,ma,Ka,mtoCap),ia(ga,qa,Aa,da,ma,bb,cb),ia(ga,sa,wa,da,ma,Ka,mtoCap)),Y.clickable||ha.clickable)&&(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5),Y.clickable&&(cylinder1a=
+new $3Dmol.Cylinder(ra.clone(),na.clone(),da),cylinder1b=new $3Dmol.Cylinder(sa.clone(),ya.clone(),da),cylinder1c=new $3Dmol.Cylinder(qa.clone(),mp3.clone(),da),Y.intersectionShape.cylinder.push(cylinder1a),Y.intersectionShape.cylinder.push(cylinder1b),Y.intersectionShape.cylinder.push(cylinder1c)),ha.clickable&&(cylinder2a=new $3Dmol.Cylinder(va.clone(),na.clone(),da),cylinder2b=new $3Dmol.Cylinder(wa.clone(),ya.clone(),da),cylinder2c=new $3Dmol.Cylinder(Aa.clone(),mp3.clone(),da),ha.intersectionShape.cylinder.push(cylinder2a),
+ha.intersectionShape.cylinder.push(cylinder2b),ha.intersectionShape.cylinder.push(cylinder2c)))}}}}for(var mb=!1,nb=0,vb=!1,oa=0;oa<Y.bonds.length;oa++)db=tb,Y.bondStyles&&Y.bondStyles[oa]&&(za=Y.bondStyles[oa],za.singleBond&&(db=!0),za.radius&&za.radius!=ab&&(vb=!0)),(db||1==Y.bondOrder[oa])&&nb++;vb?0<nb&&(mb=!0):0==nb&&0<Y.bonds.length&&(mb=!0);mb&&(ua=ab,ga.imposter?G(ga.sphereGeometry,Y,ua,ma):$3Dmol.GLDraw.drawSphere(ga,Y,ua,ma))}}"undefined"===typeof U.style.cartoon||U.style.cartoon.hidden||
+("spectrum"!==U.style.cartoon.color||"number"!==typeof U.resi||U.hetflag||(U.resi<ba[0]&&(ba[0]=U.resi),U.resi>ba[1]&&(ba[1]=U.resi)),u.push(U))}}if(0<u.length){var wb=null;ba[0]<ba[1]&&(wb=new $3Dmol.Gradient.Sinebow(ba[0],ba[1]));$3Dmol.drawCartoon(m,u,wb)}if(y&&0<y.vertices){y.initTypedArrays();var Ya=null;if(y.imposter)Ya=new $3Dmol.SphereImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});else if(y.instanced){var eb=new $3Dmol.Geometry(!0);$3Dmol.GLDraw.drawSphere(eb,{x:0,y:0,z:0},1,
+new $3Dmol.Color(.5,.5,.5));eb.initTypedArrays();Ya=new $3Dmol.InstancedMaterial({sphereMaterial:new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0}),sphere:eb})}else Ya=new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0});1>D.sphere&&0<=D.sphere&&(Ya.transparent=!0,Ya.opacity=D.sphere);eb=new $3Dmol.Mesh(y,Ya);m.add(eb)}if(0<F.vertices){if(F.imposter){var Fb=new $3Dmol.StickImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});F.initTypedArrays();
+var xb=new $3Dmol.Mesh(F,Fb)}else{var hb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});1>D.stick&&0<=D.stick&&(hb.transparent=!0,hb.opacity=D.stick);F.initTypedArrays();hb.wireframe&&F.setUpWireframe();xb=new $3Dmol.Mesh(F,hb)}m.add(xb)}for(A in x)if(x.hasOwnProperty(A)){var ob=A,pb=new $3Dmol.LineBasicMaterial({linewidth:ob,vertexColors:!0});1>D.line&&0<=D.line&&(pb.transparent=!0,pb.opacity=D.line);x[A].initTypedArrays();var Gb=new $3Dmol.Line(x[A],pb,$3Dmol.LinePieces);
+m.add(Gb)}for(A in q)if(q.hasOwnProperty(A)){var ob=A,qb=new $3Dmol.LineBasicMaterial({linewidth:ob,vertexColors:!0});1>D.cross&&0<=D.cross&&(qb.transparent=!0,qb.opacity=D.cross);q[A].initTypedArrays();var Hb=new $3Dmol.Line(q[A],qb,$3Dmol.LinePieces);m.add(Hb)}if(g&&e.symmetries&&0<e.symmetries.length){var yb=new $3Dmol.Object3D,ib;for(ib=0;ib<e.symmetries.length;ib++){var jb=new $3Dmol.Object3D,jb=m.clone();jb.matrix.copy(e.symmetries[ib]);jb.matrixAutoUpdate=!1;yb.add(jb)}h=yb}else h=m;t&&(b.remove(t),
+t=null);t=h.clone();w&&(t.setVisible(!1),h.setVisible(!1));b.add(t)}};this.removegl=function(b){t&&(void 0!==t.geometry&&t.geometry.dispose(),void 0!==t.material&&t.material.dispose(),b.remove(t),t=null);h=null};this.hide=function(){w=!0;t&&t.setVisible(!1);h&&h.setVisible(!1)};this.show=function(){w=!1;t&&t.setVisible(!0);h&&h.setVisible(!0)};this.addResLabels=function(b,c,h){var e=this.selectedAtoms(b,e);b={};for(var f=0;f<e.length;f++){var g=e[f],d=g.chain,m=g.resn+""+g.resi;b[d]||(b[d]={});b[d][m]||
+(b[d][m]=[]);b[d][m].push(g)}h=$.extend(!0,{},h);for(d in b)if(b.hasOwnProperty(d)){var l=b[d];for(m in l)if(l.hasOwnProperty(m)){for(var e=l[m],t=new $3Dmol.Vector3(0,0,0),f=0;f<e.length;f++)g=e[f],t.x+=g.x,t.y+=g.y,t.z+=g.z;t.divideScalar(e.length);h.position=t;c.addLabel(m,h)}}}}var c={line:{}},d={H:1.2,Li:1.82,LI:1.82,Na:2.27,NA:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,Cl:1.75,BR:1.85,Br:1.85,SE:1.9,Se:1.9,ZN:1.39,Zn:1.39,CU:1.4,Cu:1.4,NI:1.63,Ni:1.63},p="resn x y z color surfaceColor elem hetflag chain resi icode rescode serial atom bonds ss singleBonds bondOrder properties b pdbline clickable callback invert".split(" ").concat("model bonds predicate invert byres expand within".split(" ")),
+y=["line","cross","stick","sphere","cartoon"];b.parseMolData=function(b,c,d){c=c||"";if(!b)return[];if(/\.gz$/.test(c)){c=c.replace(/\.gz$/,"");try{b=pako.inflate(b,{to:"string"})}catch(f){console.log(f)}}"undefined"==typeof $3Dmol.Parsers[c]&&(c=c.split(".").pop(),"undefined"==typeof $3Dmol.Parsers[c]&&(console.log("Unknown format: "+c),c=b.match(/^@<TRIPOS>MOLECULE/gm)?"mol2":b.match(/^HETATM/gm)||b.match(/^ATOM/gm)?"pdb":b.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/gm)?"sdf":"xyz",console.log("Best guess: "+
+c)));return(0,$3Dmol.Parsers[c])(b,d)};b.setAtomDefaults=function(b,d){for(var p=0;p<b.length;p++){var f=b[p];f&&(f.style=f.style||c,f.color=f.color||ElementColors[f.elem]||defaultColor,f.model=d,f.clickable&&(f.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}))}};return b}();
+$3Dmol.GLShape=function(){function b(b){b=b||{};$3Dmol.ShapeIDCount++;this.boundingSphere=new $3Dmol.Sphere;this.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]};p(this,b);var A=[],q=null,B=null,f=new $3Dmol.Geometry(!0),w=new $3Dmol.Geometry(!0);this.updateStyle=function(c){for(var f in c)b[f]=c[f];p(this,b)};this.addCustom=function(b){b.vertexArr=b.vertexArr||[];b.faceArr=b.faceArr||[];b.normalArr=b.normalArr||[];c(this,f,b)};this.addSphere=function(b){b.center=b.center||{x:0,y:0,z:0};
+b.radius=b.radius?$3Dmol.Math.clamp(b.radius,0,Infinity):1.5;b.color=$3Dmol.CC.color(b.color);this.intersectionShape.sphere.push(new $3Dmol.Sphere(b.center,b.radius));$3Dmol.GLDraw.drawSphere(f,b.center,b.radius,b.color);A.push({centroid:new $3Dmol.Vector3(b.center.x,b.center.y,b.center.z)});b=f.updateGeoGroup(0);d(this.boundingSphere,A,b.vertexArray)};this.addCylinder=function(b){b.start=b.start||{};b.end=b.end||{};var c=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0),m=new $3Dmol.Vector3(b.end.x,
+b.end.y||0,b.end.z||0);"undefined"==typeof m.x&&(m.x=3);var e=b.radius||.1,w=$3Dmol.CC.color(b.color);this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(c,m,e));$3Dmol.GLDraw.drawCylinder(f,c,m,e,w,b.fromCap,b.toCap);b=new $3Dmol.Vector3;A.push({centroid:b.addVectors(c,m).multiplyScalar(.5)});c=f.updateGeoGroup(0);d(this.boundingSphere,A,c.vertexArray)};this.addLine=function(b){b.start=b.start||{};b.end=b.end||{};var c=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0),d=new $3Dmol.Vector3(b.end.x,
+b.end.y||0,b.end.z||0);"undefined"==typeof d.x&&(d.x=3);b=f.updateGeoGroup(2);var e=b.vertices,w=3*e,g=b.vertexArray;g[w]=c.x;g[w+1]=c.y;g[w+2]=c.z;g[w+3]=d.x;g[w+4]=d.y;g[w+5]=d.z;b.vertices+=2;c=b.lineArray;d=b.lineidx;c[d]=e;c[d+1]=e+1;b.lineidx+=2};this.addArrow=function(b){b.start=b.start||{};b.end=b.end||{};b.start=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0);if(b.dir instanceof $3Dmol.Vector3&&b.length instanceof number){var c=b.dir.clone().multiplyScalar(b.length).add(start);
+b.end=c}else b.end=new $3Dmol.Vector3(b.end.x,b.end.y||0,b.end.z||0),"undefined"==typeof b.end.x&&(b.end.x=3);b.radius=b.radius||.1;b.radiusRatio=b.radiusRatio||1.618034;b.mid=0<b.mid&&1>b.mid?b.mid:.618034;var m=b.start,e=b.end,w=b.radius,g=b.radiusRatio,x=b.mid;if(m&&e){var c=f.updateGeoGroup(51),u=e.clone();u.sub(m).multiplyScalar(x);var s=m.clone().add(u),x=u.clone().negate();this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(m.clone(),s.clone(),w));this.intersectionShape.sphere.push(new $3Dmol.Sphere(m.clone(),
+w));var l=[];l[0]=u.clone();1E-4<Math.abs(l[0].x)?l[0].y+=1:l[0].x+=1;l[0].cross(u);l[0].normalize();l[0]=l[0];l[4]=l[0].clone();l[4].crossVectors(l[0],u);l[4].normalize();l[8]=l[0].clone().negate();l[12]=l[4].clone().negate();l[2]=l[0].clone().add(l[4]).normalize();l[6]=l[4].clone().add(l[8]).normalize();l[10]=l[8].clone().add(l[12]).normalize();l[14]=l[12].clone().add(l[0]).normalize();l[1]=l[0].clone().add(l[2]).normalize();l[3]=l[2].clone().add(l[4]).normalize();l[5]=l[4].clone().add(l[6]).normalize();
+l[7]=l[6].clone().add(l[8]).normalize();l[9]=l[8].clone().add(l[10]).normalize();l[11]=l[10].clone().add(l[12]).normalize();l[13]=l[12].clone().add(l[14]).normalize();l[15]=l[14].clone().add(l[0]).normalize();var q=c.vertices,p=c.vertexArray,y=c.faceArray,B=c.normalArray,z=c.lineArray,H,L,N;L=0;for(N=l.length;L<N;++L){H=3*(q+3*L);var J=l[L].clone().multiplyScalar(w).add(m),I=l[L].clone().multiplyScalar(w).add(s),K=l[L].clone().multiplyScalar(w*g).add(s);p[H]=J.x;p[H+1]=J.y;p[H+2]=J.z;p[H+3]=I.x;p[H+
+4]=I.y;p[H+5]=I.z;p[H+6]=K.x;p[H+7]=K.y;p[H+8]=K.z;0<L&&(H=new $3Dmol.Vector3(p[H-3],p[H-2],p[H-1]),J=e.clone(),I=s.clone(),K=new $3Dmol.Vector3(K.x,K.y,K.z),this.intersectionShape.triangle.push(new $3Dmol.Triangle(K,J,H)),this.intersectionShape.triangle.push(new $3Dmol.Triangle(H.clone(),I,K.clone())))}c.vertices+=48;H=3*c.vertices;p[H]=m.x;p[H+1]=m.y;p[H+2]=m.z;p[H+3]=s.x;p[H+4]=s.y;p[H+5]=s.z;p[H+6]=e.x;p[H+7]=e.y;p[H+8]=e.z;c.vertices+=3;var O,Q,W,P,S,R,aa,V,Z=c.vertices-3,ca=c.vertices-2,X=c.vertices-
+1,D=3*Z,ba=3*ca,U=3*X;L=0;for(N=l.length-1;L<N;++L)O=q+3*L,m=c.faceidx,e=c.lineidx,w=O,H=3*w,g=O+1,J=3*g,s=O+2,I=3*s,p=O+4,Q=3*p,K=O+5,W=3*K,O+=3,P=3*O,S=R=l[L],aa=V=l[L+1],B[H]=S.x,B[J]=R.x,B[P]=V.x,B[H+1]=S.y,B[J+1]=R.y,B[P+1]=V.y,B[H+2]=S.z,B[J+2]=R.z,B[P+2]=V.z,B[J]=R.x,B[Q]=aa.x,B[P]=V.x,B[J+1]=R.y,B[Q+1]=aa.y,B[P+1]=V.y,B[J+2]=R.z,B[Q+2]=aa.z,B[P+2]=V.z,B[I]=R.x,B[W]=aa.x,B[I+1]=R.y,B[W+1]=aa.y,B[I+2]=R.z,B[W+2]=aa.z,y[m]=w,y[m+1]=g,y[m+2]=O,y[m+3]=g,y[m+4]=p,y[m+5]=O,y[m+6]=w,y[m+7]=O,y[m+
+8]=Z,y[m+9]=s,y[m+10]=ca,y[m+11]=K,y[m+12]=s,y[m+13]=X,y[m+14]=K,z[e]=w,z[e+1]=g,z[e+2]=w,z[e+3]=O,z[e+4]=p,z[e+5]=O,z[e+6]=w,z[e+7]=O,z[e+8]=s,z[e+9]=g,z[e+10]=s,z[e+11]=K,z[e+12]=p,z[e+13]=K,z[e+14]=s,z[e+15]=X,z[e+16]=s,z[e+17]=K,z[e+18]=X,z[e+19]=K,c.faceidx+=15,c.lineidx+=20;q=[q+45,q+46,q+1,q,q+47,q+2];m=c.faceidx;e=c.lineidx;w=q[0];H=3*w;g=q[1];J=3*g;s=q[4];I=3*s;p=q[2];Q=3*p;K=q[5];W=3*K;O=q[3];P=3*O;S=R=l[15];aa=V=l[0];B[H]=S.x;B[J]=R.x;B[P]=V.x;B[H+1]=S.y;B[J+1]=R.y;B[P+1]=V.y;B[H+2]=S.z;
+B[J+2]=R.z;B[P+2]=V.z;B[J]=R.x;B[Q]=aa.x;B[P]=V.x;B[J+1]=R.y;B[Q+1]=aa.y;B[P+1]=V.y;B[J+2]=R.z;B[Q+2]=aa.z;B[P+2]=V.z;B[I]=R.x;B[W]=aa.x;B[I+1]=R.y;B[W+1]=aa.y;B[I+2]=R.z;B[W+2]=aa.z;u.normalize();x.normalize();B[D]=x.x;B[ba]=B[U]=u.x;B[D+1]=x.y;B[ba+1]=B[U+1]=u.y;B[D+2]=x.z;B[ba+2]=B[U+2]=u.z;y[m]=w;y[m+1]=g;y[m+2]=O;y[m+3]=g;y[m+4]=p;y[m+5]=O;y[m+6]=w;y[m+7]=O;y[m+8]=Z;y[m+9]=s;y[m+10]=ca;y[m+11]=K;y[m+12]=s;y[m+13]=X;y[m+14]=K;z[e]=w;z[e+1]=g;z[e+2]=w;z[e+3]=O;z[e+4]=p;z[e+5]=O;z[e+6]=w;z[e+7]=
+O;z[e+8]=s;z[e+9]=g;z[e+10]=s;z[e+11]=K;z[e+12]=p;z[e+13]=K;z[e+14]=s;z[e+15]=X;z[e+16]=s;z[e+17]=K;z[e+18]=X;z[e+19]=K;c.faceidx+=15;c.lineidx+=20}c=new $3Dmol.Vector3;A.push({centroid:c.addVectors(b.start,b.end).multiplyScalar(.5)});b=f.updateGeoGroup(0);d(this.boundingSphere,A,b.vertexArray)};this.addIsosurface=function(b,d){var m=void 0!==d.isoval&&"number"===typeof d.isoval?d.isoval:0,e=d.voxel?!0:!1,w=void 0===d.smoothness?1:d.smoothness,g=b.size.x,x=b.size.y,u=b.size.z,s=new Int16Array(g*x*
+u),l=b.data,q,p;q=0;for(p=s.length;q<p;++q)s[q]=-1;s=new Uint8Array(g*x*u);q=0;for(p=l.length;q<p;++q)0<(0<=m?l[q]-m:m-l[q])&&(s[q]|=2);m=[];q=[];$3Dmol.MarchingCube.march(s,m,q,{fulltable:!0,voxel:e,unitCube:b.unit,origin:b.origin,nX:g,nY:x,nZ:u});e||$3Dmol.MarchingCube.laplacianSmooth(w,m,q);c(this,f,{vertexArr:m,faceArr:q,normalArr:[],clickable:d.clickable});this.updateStyle(d);q=new $3Dmol.Vector3(b.origin.x,b.origin.y,b.origin.z);g=new $3Dmol.Vector3(b.size.x*b.unit.x,b.size.y*b.unit.y,b.size.z*
+b.unit.z);e=new $3Dmol.Vector3(0,0,0);w=q.clone();g=q.clone().add(g);for(q=0;q<m.length;q++)e.add(m[q]),w.max(m[q]),g.min(m[q]);e.divideScalar(m.length);q=e.distanceTo(g);m=e.distanceTo(w);this.boundingSphere.center=e;this.boundingSphere.radius=Math.max(q,m)};this.addVolumetricData=function(b,c,f){b=new $3Dmol.VolumeData(b,c);this.addIsosurface(b,f)};this.globj=function(b){B&&(b.remove(B),B=null);if(!this.hidden){var c=f.updateGeoGroup(0);0<c.vertices&&c.truncateArrayBuffers(!0,!0);f.initTypedArrays();
+if("undefined"!=typeof this.color){(c=this.color)||$3Dmol.CC.color(c);f.colorsNeedUpdate=!0;var d,e,p;c.constructor!==Array&&(d=c.r,e=c.g,p=c.b);for(var g in f.geometryGroups)for(var x=f.geometryGroups[g],u=x.colorArray,s=0,x=x.vertices;s<x;++s)c.constructor===Array&&(p=c[s],d=p.r,e=p.g,p=p.b),u[3*s]=d,u[3*s+1]=e,u[3*s+2]=p}q=new $3Dmol.Object3D;d=null;d=this.side==$3Dmol.DoubleSide?new $3Dmol.MeshDoubleLambertMaterial({wireframe:this.wireframe,side:this.side,transparent:1>this.opacity?!0:!1,opacity:this.opacity,
+wireframeLinewidth:this.linewidth}):new $3Dmol.MeshLambertMaterial({wireframe:this.wireframe,side:this.side,transparent:1>this.opacity?!0:!1,opacity:this.opacity,wireframeLinewidth:this.linewidth});d=new $3Dmol.Mesh(f,d);q.add(d);d=new $3Dmol.LineBasicMaterial({linewidth:this.linewidth,color:this.color});d=new $3Dmol.Line(w,d,$3Dmol.LinePieces);q.add(d);B=q.clone();b.add(B)}};this.removegl=function(b){B&&(void 0!==B.geometry&&B.geometry.dispose(),void 0!==B.material&&B.material.dispose(),b.remove(B),
+B=null);q=null}}var c=function(b,c,q){var p=q.faceArr;0!==q.vertexArr.length&&0!==p.length||console.warn("Error adding custom shape component: No vertices and/or face indices supplied!");p=q.color;"undefined"==typeof p&&(p=b.color);for(var p=$3Dmol.CC.color(p),f=$3Dmol.splitMesh(q),w=0,h=f.length;w<h;w++){var t=b,m=c,e=f[w],F=f[w].colorArr?f[w].colorArr:p,g=q.clickable,x=m.addGeoGroup(),u=e.vertexArr,s=e.normalArr,e=e.faceArr;x.vertices=u.length;x.faceidx=e.length;var l=void 0,E=void 0,M=void 0,C=
+void 0,G=E=void 0,z=void 0,H=x.vertexArray,M=x.colorArray;if(F.constructor!==Array)var L=F.r,N=F.g,C=F.b;G=0;for(z=x.vertices;G<z;++G)l=3*G,E=u[G],H[l]=E.x,H[l+1]=E.y,H[l+2]=E.z,F.constructor===Array&&(E=F[G],L=E.r,N=E.g,C=E.b),M[l]=L,M[l+1]=N,M[l+2]=C;if(g)for(G=0,z=x.faceidx/3;G<z;++G){var l=3*G,M=e[l],C=e[l+1],E=e[l+2],l=new $3Dmol.Vector3,F=new $3Dmol.Vector3,J=new $3Dmol.Vector3;t.intersectionShape.triangle.push(new $3Dmol.Triangle(l.copy(u[M]),F.copy(u[C]),J.copy(u[E])))}if(g){G=new $3Dmol.Vector3(0,
+0,0);for(N=z=0;N<m.geometryGroups.length;N++)G.add(m.geometryGroups[N].getCentroid()),z++;G.divideScalar(z);d(t.boundingSphere,{centroid:G},H)}x.faceArray=new Uint16Array(e);x.truncateArrayBuffers(!0,!0);if(s.length<x.vertices)x.setNormals();else for(t=x.normalArray=new Float32Array(3*x.vertices),m=void 0,G=0,z=x.vertices;G<z;++G)l=3*G,m=s[G],t[l]=m.x,t[l+1]=m.y,t[l+2]=m.z;x.setLineIndices();x.lineidx=x.lineArray.length}},d=function(b,c,d){b.center.set(0,0,0);var p,f;if(0<c.length){p=0;for(f=c.length;p<
+f;++p)b.center.add(c[p].centroid);b.center.divideScalar(c.length)}c=b.radius*b.radius;p=0;for(f=d.length/3;p<f;p++){var w=b.center.distanceToSquared({x:d[3*p],y:d[3*p+1],z:d[3*p+2]});c=Math.max(c,w)}b.radius=Math.sqrt(c)},p=function(b,c){"undefined"!=typeof c.color&&(b.color=c.color||new $3Dmol.Color,c.color instanceof $3Dmol.Color||(b.color=$3Dmol.CC.color(c.color)));b.wireframe=c.wireframe?!0:!1;b.opacity=c.alpha?$3Dmol.Math.clamp(c.alpha,0,1):1;"undefined"!=typeof c.opacity&&(b.opacity=$3Dmol.Math.clamp(c.opacity,
+0,1));b.side=void 0!==c.side?c.side:$3Dmol.DoubleSide;b.linewidth="undefined"==typeof c.linewidth?1:c.linewidth;b.clickable=c.clickable?!0:!1;b.callback="function"===typeof c.callback?c.callback:null;b.hidden=c.hidden};Object.defineProperty(b.prototype,"position",{get:function(){return this.boundingSphere.center}});Object.defineProperty(b.prototype,"x",{get:function(){return this.boundingSphere.center.x}});Object.defineProperty(b.prototype,"y",{get:function(){return this.boundingSphere.center.y}});
+Object.defineProperty(b.prototype,"z",{get:function(){return this.boundingSphere.center.z}});return b}();$3Dmol.ShapeIDCount=0;
+$3Dmol.splitMesh=function(b){if(64E3>b.vertexArr.length)return[b];var c=[{vertexArr:[],normalArr:[],faceArr:[]}];b.colorArr&&(c.colorArr=[]);for(var d=[],p=[],y=0,A=b.faceArr,q=0,B=A.length;q<B;q+=3){for(var f=c[y],w=0;3>w;w++){var h=A[q+w];d[h]!==y&&(d[h]=y,p[h]=f.vertexArr.length,f.vertexArr.push(b.vertexArr[h]),b.normalArr&&b.normalArr[h]&&f.normalArr.push(b.normalArr[h]),b.colorArr&&b.colorArr[h]&&f.colorArr.push(b.colorArr[h]));f.faceArr.push(p[h])}64E3<=f.vertexArr.length&&(c.push({vertexArr:[],
+normalArr:[],faceArr:[]}),b.colorArr&&(c.colorArr=[]),y++)}return c};
+$3Dmol.GLViewer=function(){return function(b,c){function d(b){var c=[];"undefined"===typeof b&&(b={});var f=[],g;if("undefined"===typeof b.model)for(g=0;g<e.length;g++)e[g]&&f.push(e[g]);else f=b.model,$.isArray(f)||(f=[f]);for(g=0;g<f.length;g++)c=c.concat(f[g].selectedAtoms(b));return c}function p(b,c,f,g){var d=[];if("undefined"===typeof c.model)for(h=0;h<e.length;h++)e[h]&&d.push(e[h]);else d=c.model,$.isArray(d)||(d=[d]);for(var h=0;h<d.length;h++)if(d[h])d[h][b](c,f,g)}function y(b){var c=new $3Dmol.MeshLambertMaterial;
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+var Na=this._handleMouseDown=function(b){b.preventDefault();if(J){var c=Ba(b),e=c[0],c=c[1];void 0!==e&&(R=!0,mouseButton=b.which,aa=e,V=c,Z=0,b.originalEvent.targetTouches&&2==b.originalEvent.targetTouches.length&&(Z=ea(b)),W=I.quaternion,X=I.position.z,ca=K.position.clone(),D=O,ba=Q)}},Ja=this._handleMouseScroll=function(b){b.preventDefault();if(J){var c=.85*(150-I.position.z);b.originalEvent.detail?I.position.z+=c*b.originalEvent.detail/10:b.originalEvent.wheelDelta&&(I.position.z-=c*b.originalEvent.wheelDelta/
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+(b=.85*(150-I.position.z),80>b&&(b=80),I.position.z=X+d*b,150<I.position.z&&(I.position.z=149.85)):1==c||2==mouseButton||b.ctrlKey?(b=(f-aa)/s,c=(e-V)/l,f=I.quaternion,e=new $3Dmol.Vector3(0,0,I.position.z),L.projectVector(e,G),e.x+=2*b,e.y-=2*c,L.unprojectVector(e,G),e.z=0,e.applyQuaternion(f),K.position.addVectors(ca,e)):0!==c&&1!=mouseButton||0===h||(b=Math.sin(h*Math.PI)/h,P.x=Math.cos(h*Math.PI),P.y=0,P.z=b*g,P.w=-b*d,I.quaternion=new $3Dmol.Quaternion(1,0,0,0),I.quaternion.multiply(P),I.quaternion.multiply(W));
+T()}}},Ia=function(b){t=b;s=t.width();l=t.height();E=s/l;C.setSize(s,l);t.append(C.domElement);m=$(C.domElement);B||(m.bind("mousedown touchstart",Na),m.bind("DOMMouseScroll mousewheel",Ja),m.bind("mousemove touchmove",La),m.bind("contextmenu",function(b){b.preventDefault()}))};Ia(t);this.setContainer=function(b){"string"===$.type(b)&&(b=$("#"+b));b||(b=t);Ia(b);return this};this.setBackgroundColor=function(b,c){if("undefined"==typeof c)c=1;else if(0>c||1<c)c=1;var e=$3Dmol.CC.color(b);J.fog.color=
+e;f=e.getHex();C.setClearColorHex(e.getHex(),c);T();return this};this.setViewStyle=function(b){if("outline"===b.style){var c={};b.color&&(c.color=$3Dmol.CC.color(b.color));b.width&&(c.width=b.width);C.enableOutline(c)}else C.disableOutline();return this};c.style&&this.setViewStyle(c.style);this.setWidth=function(b){s=b||s;C.setSize(s,l);return this};this.setHeight=function(b){l=b||l;C.setSize(s,l);return this};this.resize=function(){s=t.width();l=t.height();E=s/l;C.setSize(s,l);G.aspect=E;G.updateProjectionMatrix();
+T();return this};$(window).resize(this.resize);this.getModel=function(b){b=b||e.length-1;return e[b]};this.rotate=function(b,c){"undefined"===typeof c&&(c="y");var e=0,f=0,g=0,d=Math.PI*b/180,h=Math.sin(d/2),d=Math.cos(d/2);"x"==c&&(e=h);"y"==c&&(f=h);"z"==c&&(g=h);e=(new $3Dmol.Quaternion(e,f,g,d)).normalize();I.quaternion.multiply(e);T();return this};this.getView=function(){if(!K)return[0,0,0,0,0,0,0,1];var b=K.position,c=I.quaternion;return[b.x,b.y,b.z,I.position.z,c.x,c.y,c.z,c.w]};this.setView=
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+e.setContext();K.add(e.sprite);x.push(e);T();return e};this.addResLabels=function(b,c){p("addResLabels",b,this,c);return this};this.removeLabel=function(b){for(var c=0;c<x.length;c++)if(x[c]==b){x.splice(c,1);b.dispose();K.remove(b.sprite);break}return this};this.removeAllLabels=function(){for(var b=0;b<x.length;b++)K.remove(x[b].sprite);x.splice(0,x.length);return this};this.setLabelStyle=function(b,c){K.remove(b.sprite);b.dispose();b.stylespec=c;b.setContext();K.add(b.sprite);T();return b};this.setLabelText=
+function(b,c){K.remove(b.sprite);b.dispose();b.text=c;b.setContext();K.add(b.sprite);T();return b};this.addShape=function(b){b=b||{};b=new $3Dmol.GLShape(b);b.shapePosition=g.length;g.push(b);return b};this.removeShape=function(b){if(!b)return this;b.removegl(K);for(delete g[b.shapePosition];0<g.length&&"undefined"===typeof g[g.length-1];)g.pop();return this};this.removeAllShapes=function(){for(var b=0;b<g.length;b++)g[b].removegl(K);g.splice(0,g.length);return this};this.addSphere=function(b){b=
+b||{};var c=new $3Dmol.GLShape(b);c.shapePosition=g.length;c.addSphere(b);g.push(c);return c};this.addArrow=function(b){b=b||{};var c=new $3Dmol.GLShape(b);c.shapePosition=g.length;c.addArrow(b);g.push(c);return c};this.addCylinder=function(b){b=b||{};var c=new $3Dmol.GLShape(b);c.shapePosition=g.length;c.addCylinder(b);g.push(c);return c};this.addLine=function(b){b=b||{};b.wireframe=!0;var c=new $3Dmol.GLShape(b);c.shapePosition=g.length;if(b.dashed){b.dashLength=b.dashLength||.5;b.gapLength=b.gapLength||
+.5;b.start=b.start||{};b.end=b.end||{};var e=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0),f=new $3Dmol.Vector3(b.end.x,b.end.y||0,b.end.z||0),d=new $3Dmol.Vector3,h=new $3Dmol.Vector3,m=new $3Dmol.Vector3,l,w,s=e.clone(),t=0;d.subVectors(f,e);l=d.length();d.normalize();h=d.clone();m=d.clone();h.multiplyScalar(b.dashLength);m.multiplyScalar(b.gapLength);d=h.length();for(w=m.length();t<l;){if(t+d>l){b.start=e;b.end=f;c.addLine(b);break}s.addVectors(e,h);b.start=e;b.end=s;c.addLine(b);
+e=s.clone();t+=d;s.addVectors(e,m);e=s.clone();t+=w}}else c.addLine(b);g.push(c);return c};this.addUnitCell=function(b){var c=new $3Dmol.GLShape({wireframe:!0});c.shapePosition=g.length;var e=b.getCrystData();if(e){b=e.a;var f=e.b,d=e.c,h=e.alpha,m=e.beta,e=e.gamma,h=h*Math.PI/180,m=m*Math.PI/180,e=e*Math.PI/180,l;l=Math.cos(m);h=(Math.cos(h)-Math.cos(m)*Math.cos(e))/Math.sin(e);m=Math.sqrt(Math.max(0,1-l*l-h*h));b=new $3Dmol.Matrix4(b,f*Math.cos(e),d*l,0,0,f*Math.sin(e),d*h,0,0,0,d*m,0,0,0,0,1);
+f=[new $3Dmol.Vector3(0,0,0),new $3Dmol.Vector3(1,0,0),new $3Dmol.Vector3(0,1,0),new $3Dmol.Vector3(0,0,1),new $3Dmol.Vector3(1,1,0),new $3Dmol.Vector3(0,1,1),new $3Dmol.Vector3(1,0,1),new $3Dmol.Vector3(1,1,1)];for(d=0;d<f.length;d++)f[d]=f[d].applyMatrix4(b);c.addLine({start:f[0],end:f[1]});c.addLine({start:f[0],end:f[2]});c.addLine({start:f[1],end:f[4]});c.addLine({start:f[2],end:f[4]});c.addLine({start:f[0],end:f[3]});c.addLine({start:f[3],end:f[5]});c.addLine({start:f[2],end:f[5]});c.addLine({start:f[1],
+end:f[6]});c.addLine({start:f[4],end:f[7]});c.addLine({start:f[6],end:f[7]});c.addLine({start:f[3],end:f[6]});c.addLine({start:f[5],end:f[7]})}g.push(c);return c};this.addCustom=function(b){b=b||{};var c=new $3Dmol.GLShape(b);c.shapePosition=g.length;c.addCustom(b);g.push(c);return c};this.addVolumetricData=function(b,c,e){e=e||{};var f=new $3Dmol.GLShape(e);f.shapePosition=g.length;f.addVolumetricData(b,c,e);g.push(f);return f};this.addIsosurface=function(b,c){c=c||{};var e=new $3Dmol.GLShape(c);
+e.shapePosition=g.length;e.addIsosurface(b,c);g.push(e);return e};this.setFrame=function(b){for(var c=0;c<e.length;c++)e[c].setFrame(b);return this};this.getFrames=function(){for(var b=0,c=0;c<e.length;c++)e[c].getFrames().length>b&&(b=e[c].getFrames().length);return b};this.animate=function(b){S=!0;var c=100,e="forward",f=0;b=b||{};b.interval&&(c=b.interval);b.loop&&(e=b.loop);b.reps&&(f=b.reps);var d=this.getFrames(),g=this,h=0,m=1,l=0,w=d*f,s=setInterval(function(){var b=e;"forward"==b?(g.setFrame(h),
+h=(h+m)%d):"backward"==b?(g.setFrame(d-1-h),h=(h+m)%d):(g.setFrame(h),h+=m,m*=0==h%(d-1)?-1:1);g.render();++l!=w&&g.isAnimated()||clearInterval(s)},c);return this};this.stopAnimate=function(){S=!1;return this};this.isAnimated=function(){return S};this.addModel=function(b,c,f){var d=new $3Dmol.GLModel(e.length,q);d.addMolData(b,c,f);e.push(d);return d};this.addModels=function(b,c,f){f=f||{};f.multimodel=!0;f.frames=!0;b=$3Dmol.GLModel.parseMolData(b,c,f);for(c=0;c<b.length;c++){var d=new $3Dmol.GLModel(e.length,
+q);d.setAtomDefaults(b[c]);d.addFrame(b[c]);d.setFrame(0);d.setModelData(b.modelData[c]);d.setDontDuplicateAtoms(!f.duplicateAssemblyAtoms);e.push(d)}return e};this.addModelsAsFrames=function(b,c,f){f=f||{};f.multimodel=!0;f.frames=!0;var d=new $3Dmol.GLModel(e.length,q);d.addMolData(b,c,f);e.push(d);return d};this.addAsOneMolecule=function(b,c,f){f=f||{};f.multimodel=!0;f.onemol=!0;var d=new $3Dmol.GLModel(e.length,q);d.addMolData(b,c,f);e.push(d);return d};this.removeModel=function(b){if(b){b.removegl(K);
+for(delete e[b.getID()];0<e.length&&"undefined"===typeof e[e.length-1];)e.pop();return this}};this.removeAllModels=function(){for(var b=0;b<e.length;b++)e[b].removegl(K);e.splice(0,e.length);return this};this.exportJSON=function(b,c){var f={};f.m=void 0===c?e.map(function(c){return c.toCDObject(b)}):[model[c].toCDObject()];return JSON.stringify(f)};this.createModelFrom=function(b,c){for(var f=new $3Dmol.GLModel(e.length,q),d=0;d<e.length;d++)if(e[d]){var h=e[d].selectedAtoms(b);f.addAtoms(h);c&&e[d].removeAtoms(h)}e.push(f);
+return f};this.setStyle=function(b,c){"undefined"===typeof c&&(c=b,b={});p("setStyle",b,c,!1);return this};this.addStyle=function(b,c){"undefined"===typeof c&&(c=b,b={});p("setStyle",b,c,!0);return this};this.setClickable=function(b,c,f){p("setClickable",b,c,f);return this};this.setColorByProperty=function(b,c,f){p("setColorByProperty",b,c,f);return this};this.setColorByElement=function(b,c){p("setColorByElement",b,c);return this};var Za=function(b,c){for(var f=[],e=0;e<b.length;e++){var d=b[e];"undefined"!=
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+c=h(c);return b.concat(c)};b=h(b);for(var g=0,m=b.length;g<m;g++){var l=d(b[g]);l[0][0]-=6;l[0][1]-=6;l[0][2]-=6;l[1][0]+=6;l[1][1]+=6;l[1][2]+=6;var l=Za(c,l),w=Za(f,b[g]);e.push({extent:b[g],atoms:l,toshow:w})}return e},Ua=function(b,c,f){for(var e=new $3Dmol.Geometry(!0),d=e.updateGeoGroup(0),h=[],g=0,m=b.length;g<m;g++){var l=b[g];l&&("undefined"!=typeof l.surfaceColor?h[g]=l.surfaceColor:l.color&&(h[g]=$3Dmol.CC.color(l.color)))}var w=d.vertexArray,l=c.vertices,g,m;g=0;for(m=l.length;g<m;g++)b=
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+c.length;g<m;g+=3)h=c[g+1],s=c[g+2],b=3*c[g],h*=3,s*=3,t=new $3Dmol.Vector3(l[b],l[b+1],l[b+2]),q=new $3Dmol.Vector3(l[h],l[h+1],l[h+2]),u=new $3Dmol.Vector3(l[s],l[s+1],l[s+2]),u.subVectors(u,q),t.subVectors(t,q),u.cross(t),t=u,t.normalize(),w[b]+=t.x,w[h]+=t.x,w[s]+=t.x,w[b+1]+=t.y,w[h+1]+=t.y,w[s+1]+=t.y,w[b+2]+=t.z,w[h+2]+=t.z,w[s+2]+=t.z;d.faceArray=new Uint16Array(c);f=new $3Dmol.Mesh(e,f);f.doubleSided=!0;return f};this.addMesh=function(b){b={geo:b.geometry,mat:b.material,done:!0,finished:!1};
+var c=U();F[c]=b;return c};var xa=function(b){var c=[];$.each(b,function(b,f){c[b]=$.extend({},f)});return c};this.addSurface=function(b,c,f,g,m){var l=null,w=null;f=xa(d(f));var l=g?xa(d(g)):f,s=!1;for(g=0;g<e.length;g++)if(e[g]){var t=e[g].getSymmetries();if(1<t.length||1==t.length&&!t[0].isIdentity()){s=!0;break}}var q=function(f,e,g){w=m?xa(d(m)):g;var l,s=$3Dmol.getExtent(g,!0),t,q;c.map&&c.map.prop&&(t=c.map.prop,q=c.map.scheme||c.map.gradient||new $3Dmol.Gradient.RWB,(l=q.range())||(l=$3Dmol.getPropertyRange(g,
+t)),c.colorscheme={prop:t,gradient:q});t=0;for(q=e.length;t<q;t++)l=e[t],l.surfaceColor=$3Dmol.getColorFromStyle(l,c);var x=Ta(s),p=$a(s,e,g);if(w&&w.length&&0<w.length){var z=$3Dmol.getExtent(w,!0);p.sort(function(b,c){var f=function(b,c){var f=b.extent,e=f[1][1]-f[0][1],d=f[1][2]-f[0][2],f=f[1][0]-f[0][0]-c[2][0],e=e-c[2][1],d=d-c[2][2];return f*f+e*e+d*d},e=f(b,z),f=f(c,z);return e-f})}var y=[];t=0;for(q=e.length;t<q;t++)l=e[t],y[t]={x:l.x,y:l.y,z:l.z,serial:t,elem:l.elem};if($3Dmol.syncSurface)setTimeout(function ga(c){if(!(c>=
+p.length)){var d;d=b;var g=p[c].extent,l=p[c].atoms,m=p[c].toshow,w=new $3Dmol.ProteinSurface;w.initparm(g,1===d?!1:!0,x);w.fillvoxels(y,l);w.buildboundary();d==$3Dmol.SurfaceType.SES&&(w.fastdistancemap(),w.boundingatom(!1),w.fillvoxelswaals(y,l));w.marchingcube(d);d=w.getFacesAndVertices(m);d=Ua(e,d,u);$3Dmol.mergeGeos(f.geo,d);h.render();setTimeout(ga,1,c+1)}},1,0);else{g=[];0>b&&(b=0);t=0;for(q=4;t<q;t++)s=new Worker($3Dmol.SurfaceWorker),g.push(s),s.postMessage({type:-1,atoms:y,volume:x});var B=
+0,s=function(b){b=$3Dmol.splitMesh({vertexArr:b.data.vertices,faceArr:b.data.faces});for(var c=0,d=b.length;c<d;c++){var g=Ua(e,{vertices:b[c].vertexArr,faces:b[c].faceArr},u);$3Dmol.mergeGeos(f.geo,g);h.render()}B++;B==p.length&&(f.done=!0)};q=function(b){console.log(b.message+" ("+b.filename+":"+b.lineno+")")};for(t=0;t<p.length;t++)l=g[t%g.length],l.onmessage=s,l.onerror=q,l.postMessage({type:b,expandedExtent:p[t].extent,extendedAtoms:p[t].atoms,atomsToShow:p[t].toshow})}};c=c||{};var u=y(c),t=
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+f[g];b(l)}else for(g=0,h=f.length;g<h;g++)for(var l=f[g],m=0,w=b.length;m<w;m++){var t=b[m];if(t.props)for(var s in t.props)if(t.props.hasOwnProperty(s)){var q;a:{q=l;var u=t;"undefined"===typeof u&&(u={});var x=[],p=void 0;if("undefined"===typeof u.model)for(p=0;p<e.length;p++)e[p]&&x.push(e[p]);else x=u.model,$.isArray(x)||(x=[x]);for(p=0;p<x.length;p++)if(x[p].atomIsSelected(q,u)){q=!0;break a}q=!1}q&&(l.properties||(l.properties={}),l.properties[s]=t.props[s])}}return this};this.linkViewer=function(b){M.push(b);
+return this};try{"function"===typeof A&&A(this)}catch(Ma){console.log("error with glviewer callback: "+Ma)}}}();$3Dmol.glmolViewer=$3Dmol.GLViewer;$3Dmol=$3Dmol||{};$3Dmol.Gradient=function(b,c){};$3Dmol.Gradient.valueToHex=function(b,c){};$3Dmol.Gradient.range=function(){};
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+typeof c?[b,c]:null}};
+$3Dmol.Gradient.ROYGB=function(b,c){var d=1;"undefined"==typeof c&&$.isArray(b)&&2<=b.length&&(c=b[1],b=b[0]);c<b&&(d=-1,b*=-1,c*=-1);this.valueToHex=function(p,y){var A,q;p*=d;y?(A=y[0],q=y[1]):(A=b,q=c);if("undefined"==typeof p)return 16777215;p<A&&(p=A);p>q&&(p=q);var B=(A+q)/2,f=(A+B)/2,w=(B+q)/2;p<f?(A=Math.floor(255*Math.sqrt((p-A)/(f-A))),A=256*A+16711680):p<B?(A=Math.floor(255*Math.sqrt(1-(p-f)/(B-f))),A=65536*A+65280):p<w?(A=Math.floor(255*Math.sqrt((p-B)/(w-B))),A=65280+1*A):(A=Math.floor(255*
+Math.sqrt(1-(p-w)/(q-w))),A=256*A+255);return A};this.range=function(){return"undefined"!=typeof b&&"undefined"!=typeof c?[b,c]:null}};
+$3Dmol.Gradient.Sinebow=function(b,c){var d=1;"undefined"==typeof c&&$.isArray(b)&&2<=b.length&&(c=b[1],b=b[0]);c<b&&(d=-1,b*=-1,c*=-1);this.valueToHex=function(p,y){var A,q;p*=d;y?(A=y[0],q=y[1]):(A=b,q=c);if("undefined"==typeof p)return 16777215;p<A&&(p=A);p>q&&(p=q);var B=(p-A)/(q-A)*5/6+.5;A=Math.sin(Math.PI*B);A*=255*A;q=Math.sin(Math.PI*(B+1/3));q*=255*q;B=Math.sin(Math.PI*(B+2/3));return 65536*Math.floor(A)+256*Math.floor(255*B*B)+1*Math.floor(q)};this.range=function(){return"undefined"!=typeof b&&
+"undefined"!=typeof c?[b,c]:null}};$3Dmol.LabelCount=0;$3Dmol.Label=function(b,c){this.id=$3Dmol.LabelCount++;this.stylespec=c||{};this.canvas=document.createElement("canvas");this.canvas.width=134;this.canvas.height=35;this.context=this.canvas.getContext("2d");this.sprite=new $3Dmol.Sprite;this.text=b};
+$3Dmol.Label.prototype={constructor:$3Dmol.Label,getStyle:function(){return this.stylespec},setContext:function(){var b=function(b,d,p){"undefined"!=typeof b&&(p=b instanceof $3Dmol.Color?b.scaled():$3Dmol.CC.color(b).scaled());"undefined"!=typeof d&&(p.a=parseFloat(d));return p};return function(){var c=this.stylespec,d="undefined"==typeof c.useScreen?!1:c.useScreen,p=c.showBackground;if("0"===p||"false"===p)p=!1;"undefined"==typeof p&&(p=!0);var y=c.font?c.font:"sans-serif",A=parseInt(c.fontSize)?
+parseInt(c.fontSize):18,q=b(c.fontColor,c.fontOpacity,{r:255,g:255,b:255,a:1}),B=c.padding?c.padding:4,f=c.borderThickness?c.borderThickness:0,w=b(c.backgroundColor,c.backgroundOpacity,{r:0,g:0,b:0,a:1}),h=b(c.borderColor,c.borderOpacity,w),t=c.position?c.position:{x:-10,y:1,z:1},m=void 0!==c.inFront?c.inFront:!0;if("false"===m||"0"===m)m=!1;var e=c.alignment||$3Dmol.SpriteAlignment.topLeft,F="";c.bold&&(F="bold ");this.context.font=F+A+"px  "+y;var g=this.context.measureText(this.text).width;p||
+(f=0);var x=g+2.5*f+2*B,u=1.25*A+2*f+2*B;if(c.backgroundImage){var F=c.backgroundImage,s=c.backgroundWidth?c.backgroundWidth:F.width,l=c.backgroundHeight?c.backgroundHeight:F.height;s>x&&(x=s);l>u&&(u=l)}this.canvas.width=x;this.canvas.height=u;this.context.clearRect(0,0,this.canvas.width,this.canvas.height);F="";c.bold&&(F="bold ");this.context.font=F+A+"px  "+y;this.context.fillStyle="rgba("+w.r+","+w.g+","+w.b+","+w.a+")";this.context.strokeStyle="rgba("+h.r+","+h.g+","+h.b+","+h.a+")";this.context.lineWidth=
+f;p&&(p=this.context,w=y=f,x-=2*f,u-=2*f,h=0<f,p.beginPath(),p.moveTo(y+6,w),p.lineTo(y+x-6,w),p.quadraticCurveTo(y+x,w,y+x,w+6),p.lineTo(y+x,w+u-6),p.quadraticCurveTo(y+x,w+u,y+x-6,w+u),p.lineTo(y+6,w+u),p.quadraticCurveTo(y,w+u,y,w+u-6),p.lineTo(y,w+6),p.quadraticCurveTo(y,w,y+6,w),p.closePath(),p.fill(),h&&p.stroke());c.backgroundImage&&(F=c.backgroundImage,s=c.backgroundWidth?c.backgroundWidth:F.width,l=c.backgroundHeight?c.backgroundHeight:F.height,this.context.drawImage(F,0,0,s,l));this.context.fillStyle=
+"rgba("+q.r+","+q.g+","+q.b+","+q.a+")";this.context.fillText(this.text,f+B,A+f+B,g);c=new $3Dmol.Texture(this.canvas);c.needsUpdate=!0;this.sprite.material=new $3Dmol.SpriteMaterial({map:c,useScreenCoordinates:d,alignment:e,depthTest:!m});this.sprite.scale.set(1,1,1);this.sprite.position.set(t.x,t.y,t.z)}}(),dispose:function(){void 0!==this.sprite.material.map&&this.sprite.material.map.dispose();void 0!==this.sprite.material&&this.sprite.material.dispose()}};$3Dmol=$3Dmol||{};
+$3Dmol.MarchingCubeInitializer=function(){var b={march:function(b,q,B,f){var w=!!f.fulltable,h=f.hasOwnProperty("origin")&&f.origin.hasOwnProperty("x")?f.origin:{x:0,y:0,z:0},t=!!f.voxel,m=f.nX||0,e=f.nY||0,F=f.nZ||0,g=f.scale||1,x=null,x=f.unitCube?f.unitCube:{x:g,y:g,z:g},u=new Int32Array(m*e*F);f=0;for(g=u.length;f<g;++f)u[f]=-1;var g=function(b,c,f,d,g,l){var m={x:h.x,y:h.y,z:h.z},w=g;d&1<<g||!(d&1<<l)||(w=l);w&1&&f++;w&2&&c++;w&4&&b++;m.x+=x.x*b;m.y+=x.y*c;m.z+=x.z*f;b=(e*b+c)*F+f;if(t)return q.push(m),
+q.length-1;0>u[b]&&(u[b]=q.length,q.push(m));return u[b]},s=new Int32Array(12),l=w?p:c,w=w?y:d;for(f=0;f<m-1;++f)for(var E=0;E<e-1;++E)for(var M=0;M<F-1;++M){for(var C=0,G=0;8>G;++G)C|=!!(b[(e*(f+((G&4)>>2))+E+((G&2)>>1))*F+M+(G&1)]&2)<<G;if(0!==C&&255!==C){var z=l[C];if(0!==z)for(G=w[C],z&1&&(s[0]=g(f,E,M,C,0,1)),z&2&&(s[1]=g(f,E,M,C,1,3)),z&4&&(s[2]=g(f,E,M,C,3,2)),z&8&&(s[3]=g(f,E,M,C,2,0)),z&16&&(s[4]=g(f,E,M,C,4,5)),z&32&&(s[5]=g(f,E,M,C,5,7)),z&64&&(s[6]=g(f,E,M,C,7,6)),z&128&&(s[7]=g(f,E,M,
+C,6,4)),z&256&&(s[8]=g(f,E,M,C,0,4)),z&512&&(s[9]=g(f,E,M,C,1,5)),z&1024&&(s[10]=g(f,E,M,C,3,7)),z&2048&&(s[11]=g(f,E,M,C,2,6)),C=0;C<G.length;C+=3){var z=s[G[C]],H=s[G[C+1]],L=s[G[C+2]];t&&3<=C&&(q.push(q[z]),z=q.length-1,q.push(q[H]),H=q.length-1,q.push(q[L]),L=q.length-1);B.push(z);B.push(H);B.push(L)}}}},laplacianSmooth:function(b,c,d){var f=Array(c.length),w,h,t,m;w=0;for(h=c.length;w<h;w++)f[w]={x:0,y:0,z:0};var e=Array(20),p;for(w=0;20>w;w++)e[w]=Array(c.length);w=0;for(h=c.length;w<h;w++)e[0][w]=
+0;w=0;for(h=d.length/3;w<h;w++){var g=3*w,x=3*w+1,u=3*w+2;p=!0;t=0;for(m=e[0][d[g]];t<m;t++)if(d[x]==e[t+1][d[g]]){p=!1;break}p&&(e[0][d[g]]++,e[e[0][d[g]]][d[g]]=d[x]);p=!0;t=0;for(m=e[0][d[g]];t<m;t++)if(d[u]==e[t+1][d[g]]){p=!1;break}p&&(e[0][d[g]]++,e[e[0][d[g]]][d[g]]=d[u]);p=!0;t=0;for(m=e[0][d[x]];t<m;t++)if(d[g]==e[t+1][d[x]]){p=!1;break}p&&(e[0][d[x]]++,e[e[0][d[x]]][d[x]]=d[g]);p=!0;t=0;for(m=e[0][d[x]];t<m;t++)if(d[u]==e[t+1][d[x]]){p=!1;break}p&&(e[0][d[x]]++,e[e[0][d[x]]][d[x]]=d[u]);
+p=!0;for(t=0;t<e[0][d[u]];t++)if(d[g]==e[t+1][d[u]]){p=!1;break}p&&(e[0][d[u]]++,e[e[0][d[u]]][d[u]]=d[g]);p=!0;t=0;for(m=e[0][d[u]];t<m;t++)if(d[x]==e[t+1][d[u]]){p=!1;break}p&&(e[0][d[u]]++,e[e[0][d[u]]][d[u]]=d[x])}for(d=0;d<b;d++){w=0;for(h=c.length;w<h;w++)if(3>e[0][w])f[w].x=c[w].x,f[w].y=c[w].y,f[w].z=c[w].z;else if(3==e[0][w]||4==e[0][w]){f[w].x=0;f[w].y=0;t=f[w].z=0;for(m=e[0][w];t<m;t++)f[w].x+=c[e[t+1][w]].x,f[w].y+=c[e[t+1][w]].y,f[w].z+=c[e[t+1][w]].z;f[w].x+=.5*c[w].x;f[w].y+=.5*c[w].y;
+f[w].z+=.5*c[w].z;f[w].x/=.5+e[0][w];f[w].y/=.5+e[0][w];f[w].z/=.5+e[0][w]}else{f[w].x=0;f[w].y=0;t=f[w].z=0;for(m=e[0][w];t<m;t++)f[w].x+=c[e[t+1][w]].x,f[w].y+=c[e[t+1][w]].y,f[w].z+=c[e[t+1][w]].z;f[w].x+=1*c[w].x;f[w].y+=1*c[w].y;f[w].z+=1*c[w].z;f[w].x/=1+e[0][w];f[w].y/=1+e[0][w];f[w].z/=1+e[0][w]}w=0;for(h=c.length;w<h;w++)c[w].x=f[w].x,c[w].y=f[w].y,c[w].z=f[w].z}},edgeTable:[0,0,0,0,0,0,0,2816,0,0,0,1792,0,3328,3584,3840,0,0,0,138,0,21,0,134,0,0,0,652,0,2067,3865,3600,0,0,0,42,0,0,0,294,
 0,0,21,28,0,3875,1049,3360,0,168,162,170,0,645,2475,2210,0,687,293,172,4010,3747,3497,3232,0,0,0,0,0,69,0,900,0,0,0,1792,138,131,1608,1920,0,81,0,2074,84,85,84,86,0,81,0,3676,330,1105,1881,1616,0,0,0,42,0,69,0,502,0,0,21,3580,138,2035,1273,1520,2816,104,2337,106,840,581,367,102,2816,3695,3429,3180,1898,1635,1385,1120,0,0,0,0,0,0,0,3910,0,0,69,588,42,2083,41,2880,0,0,0,1722,0,2293,4095,3830,0,255,757,764,2538,2291,3065,2800,0,0,81,338,0,3925,1119,3414,84,855,85,340,2130,2899,89,2384,1792,712,194,1162,
-4036,3781,3535,3270,708,719,197,204,3018,2755,2505,2240,0,0,0,0,168,420,168,1958,162,162,676,2988,170,163,680,928,3328,3096,3328,3642,52,53,1855,1590,2340,2111,2869,2620,298,51,825,560,3584,3584,3090,3482,1668,1941,1183,1430,146,2975,2069,2460,154,915,153,400,3840,3592,3329,3082,1796,1541,1295,1030,2818,2575,2309,2060,778,515,265,0]},q=new Uint32Array(u.edgeTable),C=u.triTable=[[],[],[],[],[],[],[],[11,9,8],[],[],[],[8,10,9],[],[10,8,11],[9,11,10],[8,10,9,8,11,10],[],[],[],[1,7,3],[],[4,2,0],[],[2,
+4036,3781,3535,3270,708,719,197,204,3018,2755,2505,2240,0,0,0,0,168,420,168,1958,162,162,676,2988,170,163,680,928,3328,3096,3328,3642,52,53,1855,1590,2340,2111,2869,2620,298,51,825,560,3584,3584,3090,3482,1668,1941,1183,1430,146,2975,2069,2460,154,915,153,400,3840,3592,3329,3082,1796,1541,1295,1030,2818,2575,2309,2060,778,515,265,0]},c=new Uint32Array(b.edgeTable),d=b.triTable=[[],[],[],[],[],[],[],[11,9,8],[],[],[],[8,10,9],[],[10,8,11],[9,11,10],[8,10,9,8,11,10],[],[],[],[1,7,3],[],[4,2,0],[],[2,
 1,7],[],[],[],[2,7,3,2,9,7],[],[1,4,11,1,0,4],[3,8,0,11,9,4,11,10,9],[4,11,9,11,10,9],[],[],[],[5,3,1],[],[],[],[2,5,8,2,1,5],[],[],[2,4,0],[3,2,4],[],[0,9,1,8,10,5,8,11,10],[3,4,0,3,10,4],[5,8,10,8,11,10],[],[3,5,7],[7,1,5],[1,7,3,1,5,7],[],[9,2,0,9,7,2],[0,3,8,1,7,11,1,5,7],[11,1,7,1,5,7],[],[9,1,0,5,3,2,5,7,3],[8,2,5,8,0,2],[2,5,3,5,7,3],[3,9,1,3,8,9,7,11,10,7,10,5],[9,1,0,10,7,11,10,5,7],[3,8,0,7,10,5,7,11,10],[11,5,7,11,10,5],[],[],[],[],[],[0,6,2],[],[7,2,9,7,9,8],[],[],[],[8,10,9],[7,1,3],
 [7,1,0],[6,9,3,6,10,9],[7,10,8,10,9,8],[],[6,0,4],[],[11,1,4,11,3,1],[2,4,6],[2,0,4,2,4,6],[2,4,6],[1,4,2,4,6,2],[],[6,0,4],[],[2,11,3,6,9,4,6,10,9],[8,6,1,8,1,3],[10,0,6,0,4,6],[8,0,3,9,6,10,9,4,6],[10,4,6,10,9,4],[],[],[],[5,3,1],[],[0,6,2],[],[7,4,8,5,2,1,5,6,2],[],[],[2,4,0],[7,4,8,2,11,3,10,5,6],[7,1,3],[5,6,10,0,9,1,8,7,4],[5,6,10,7,0,3,7,4,0],[10,5,6,4,8,7],[9,11,8],[3,5,6],[0,5,11,0,11,8],[6,3,5,3,1,5],[3,9,6,3,8,9],[9,6,0,6,2,0],[0,3,8,2,5,6,2,1,5],[1,6,2,1,5,6],[9,11,8],[1,0,9,6,10,5,11,
 3,2],[6,10,5,2,8,0,2,11,8],[3,2,11,10,5,6],[10,5,6,9,3,8,9,1,3],[0,9,1,5,6,10],[8,0,3,10,5,6],[10,5,6],[],[],[],[],[],[],[],[1,10,2,9,11,6,9,8,11],[],[],[6,0,2],[3,6,9,3,2,6],[3,5,1],[0,5,1,0,11,5],[0,3,5],[6,9,11,9,8,11],[],[],[],[4,5,9,7,1,10,7,3,1],[],[11,6,7,2,4,5,2,0,4],[11,6,7,8,0,3,1,10,2,9,4,5],[6,7,11,1,10,2,9,4,5],[],[4,1,0,4,5,1,6,7,3,6,3,2],[9,4,5,0,6,7,0,2,6],[4,5,9,6,3,2,6,7,3],[6,7,11,5,3,8,5,1,3],[6,7,11,4,1,0,4,5,1],[4,5,9,3,8,0,11,6,7],[9,4,5,7,11,6],[],[],[0,6,4],[8,6,4,8,1,6],
 [],[0,10,2,0,9,10,4,8,11,4,11,6],[10,2,1,6,0,3,6,4,0],[10,2,1,11,4,8,11,6,4],[4,2,6],[1,0,9,2,4,8,2,6,4],[2,4,0,2,6,4],[8,2,4,2,6,4],[11,4,1,11,6,4],[0,9,1,4,11,6,4,8,11],[3,6,0,6,4,0],[8,6,4,8,11,6],[10,8,9],[6,3,9,6,7,3],[6,7,1],[10,7,1,7,3,1],[7,11,6,8,10,2,8,9,10],[11,6,7,10,0,9,10,2,0],[2,1,10,7,11,6,8,0,3],[1,10,2,6,7,11],[7,2,6,7,9,2],[1,0,9,3,6,7,3,2,6],[7,0,6,0,2,6],[2,7,3,2,6,7],[7,11,6,3,9,1,3,8,9],[9,1,0,11,6,7],[0,3,8,11,6,7],[11,6,7],[],[],[],[],[5,3,7],[8,5,2,8,7,5],[5,3,7],[1,10,2,
 5,8,7,5,9,8],[1,7,5],[1,7,5],[9,2,7,9,7,5],[11,3,2,8,5,9,8,7,5],[1,3,7,1,7,5],[0,7,1,7,5,1],[9,3,5,3,7,5],[9,7,5,9,8,7],[8,10,11],[3,4,10,3,10,11],[8,10,11],[5,9,4,1,11,3,1,10,11],[2,4,5],[5,2,4,2,0,4],[0,3,8,5,9,4,10,2,1],[2,1,10,9,4,5],[2,8,5,2,11,8],[3,2,11,1,4,5,1,0,4],[9,4,5,8,2,11,8,0,2],[11,3,2,9,4,5],[8,5,3,5,1,3],[5,0,4,5,1,0],[3,8,0,4,5,9],[9,4,5],[11,9,10],[11,9,10],[1,11,4,1,10,11],[8,7,4,11,1,10,11,3,1],[2,7,9,2,9,10],[4,8,7,0,10,2,0,9,10],[2,1,10,0,7,4,0,3,7],[10,2,1,8,7,4],[1,7,4],
-[3,2,11,4,8,7,9,1,0],[11,4,2,4,0,2],[2,11,3,7,4,8],[4,1,7,1,3,7],[1,0,9,8,7,4],[3,4,0,3,7,4],[8,7,4],[8,9,10,8,10,11],[3,9,11,9,10,11],[0,10,8,10,11,8],[10,3,1,10,11,3],[2,8,10,8,9,10],[9,2,0,9,10,2],[8,0,3,1,10,2],[10,2,1],[1,11,9,11,8,9],[11,3,2,0,9,1],[11,0,2,11,8,0],[11,3,2],[8,1,3,8,9,1],[9,1,0],[8,0,3],[]],A=[0,265,515,778,2060,2309,2575,2822,1030,1295,1541,1804,3082,3331,3593,3840,400,153,915,666,2460,2197,2975,2710,1430,1183,1941,1692,3482,3219,3993,3728,560,825,51,314,2620,2869,2111,2358,
+[3,2,11,4,8,7,9,1,0],[11,4,2,4,0,2],[2,11,3,7,4,8],[4,1,7,1,3,7],[1,0,9,8,7,4],[3,4,0,3,7,4],[8,7,4],[8,9,10,8,10,11],[3,9,11,9,10,11],[0,10,8,10,11,8],[10,3,1,10,11,3],[2,8,10,8,9,10],[9,2,0,9,10,2],[8,0,3,1,10,2],[10,2,1],[1,11,9,11,8,9],[11,3,2,0,9,1],[11,0,2,11,8,0],[11,3,2],[8,1,3,8,9,1],[9,1,0],[8,0,3],[]],p=[0,265,515,778,2060,2309,2575,2822,1030,1295,1541,1804,3082,3331,3593,3840,400,153,915,666,2460,2197,2975,2710,1430,1183,1941,1692,3482,3219,3993,3728,560,825,51,314,2620,2869,2111,2358,
 1590,1855,1077,1340,3642,3891,3129,3376,928,681,419,170,2988,2725,2479,2214,1958,1711,1445,1196,4010,3747,3497,3232,2240,2505,2755,3018,204,453,719,966,3270,3535,3781,4044,1226,1475,1737,1984,2384,2137,2899,2650,348,85,863,598,3414,3167,3925,3676,1370,1107,1881,1616,2800,3065,2291,2554,764,1013,255,502,3830,4095,3317,3580,1786,2035,1273,1520,2912,2665,2403,2154,876,613,367,102,3942,3695,3429,3180,1898,1635,1385,1120,1120,1385,1635,1898,3180,3429,3695,3942,102,367,613,876,2154,2403,2665,2912,1520,
 1273,2035,1786,3580,3317,4095,3830,502,255,1013,764,2554,2291,3065,2800,1616,1881,1107,1370,3676,3925,3167,3414,598,863,85,348,2650,2899,2137,2384,1984,1737,1475,1226,4044,3781,3535,3270,966,719,453,204,3018,2755,2505,2240,3232,3497,3747,4010,1196,1445,1711,1958,2214,2479,2725,2988,170,419,681,928,3376,3129,3891,3642,1340,1077,1855,1590,2358,2111,2869,2620,314,51,825,560,3728,3993,3219,3482,1692,1941,1183,1430,2710,2975,2197,2460,666,915,153,400,3840,3593,3331,3082,1804,1541,1295,1030,2822,2575,2309,
-2060,778,515,265,0],w=[[],[8,3,0],[9,0,1],[8,3,1,8,1,9],[11,2,3],[11,2,0,11,0,8],[11,2,3,0,1,9],[2,1,11,1,9,11,11,9,8],[10,1,2],[8,3,0,1,2,10],[9,0,2,9,2,10],[3,2,8,2,10,8,8,10,9],[10,1,3,10,3,11],[1,0,10,0,8,10,10,8,11],[0,3,9,3,11,9,9,11,10],[8,10,9,8,11,10],[8,4,7],[3,0,4,3,4,7],[1,9,0,8,4,7],[9,4,1,4,7,1,1,7,3],[2,3,11,7,8,4],[7,11,4,11,2,4,4,2,0],[3,11,2,4,7,8,9,0,1],[2,7,11,2,1,7,1,4,7,1,9,4],[10,1,2,8,4,7],[2,10,1,0,4,7,0,7,3],[4,7,8,0,2,10,0,10,9],[2,7,3,2,9,7,7,9,4,2,10,9],[8,4,7,11,10,1,
+2060,778,515,265,0],y=[[],[8,3,0],[9,0,1],[8,3,1,8,1,9],[11,2,3],[11,2,0,11,0,8],[11,2,3,0,1,9],[2,1,11,1,9,11,11,9,8],[10,1,2],[8,3,0,1,2,10],[9,0,2,9,2,10],[3,2,8,2,10,8,8,10,9],[10,1,3,10,3,11],[1,0,10,0,8,10,10,8,11],[0,3,9,3,11,9,9,11,10],[8,10,9,8,11,10],[8,4,7],[3,0,4,3,4,7],[1,9,0,8,4,7],[9,4,1,4,7,1,1,7,3],[2,3,11,7,8,4],[7,11,4,11,2,4,4,2,0],[3,11,2,4,7,8,9,0,1],[2,7,11,2,1,7,1,4,7,1,9,4],[10,1,2,8,4,7],[2,10,1,0,4,7,0,7,3],[4,7,8,0,2,10,0,10,9],[2,7,3,2,9,7,7,9,4,2,10,9],[8,4,7,11,10,1,
 11,1,3],[11,4,7,1,4,11,1,11,10,1,0,4],[3,8,0,7,11,4,11,9,4,11,10,9],[7,11,4,4,11,9,11,10,9],[9,5,4],[3,0,8,4,9,5],[5,4,0,5,0,1],[4,8,5,8,3,5,5,3,1],[11,2,3,9,5,4],[9,5,4,8,11,2,8,2,0],[3,11,2,1,5,4,1,4,0],[8,5,4,2,5,8,2,8,11,2,1,5],[2,10,1,9,5,4],[0,8,3,5,4,9,10,1,2],[10,5,2,5,4,2,2,4,0],[3,4,8,3,2,4,2,5,4,2,10,5],[5,4,9,1,3,11,1,11,10],[0,9,1,4,8,5,8,10,5,8,11,10],[3,4,0,3,10,4,4,10,5,3,11,10],[4,8,5,5,8,10,8,11,10],[9,5,7,9,7,8],[0,9,3,9,5,3,3,5,7],[8,0,7,0,1,7,7,1,5],[1,7,3,1,5,7],[11,2,3,8,9,
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 9],[6,10,7,10,1,7,7,1,3],[6,10,1,6,1,7,7,1,0,7,0,8],[9,0,3,6,9,3,6,10,9,6,3,7],[6,10,7,7,10,8,10,9,8],[8,4,6,8,6,11],[11,3,6,3,0,6,6,0,4],[0,1,9,4,6,11,4,11,8],[1,9,4,11,1,4,11,3,1,11,4,6],[3,8,2,8,4,2,2,4,6],[2,0,4,2,4,6],[1,9,0,3,8,2,2,8,4,2,4,6],[9,4,1,1,4,2,4,6,2],[10,1,2,11,8,4,11,4,6],[10,1,2,11,3,6,6,3,0,6,0,4],[0,2,10,0,10,9,4,11,8,4,6,11],[2,11,3,6,9,4,6,10,9],[8,4,6,8,6,1,6,10,1,8,1,3],[1,0,10,10,0,6,0,4,6],[8,0,3,9,6,10,9,4,6],[10,4,6,10,9,4],[9,5,4,7,6,11],[4,9,5,3,0,8,11,7,6],[6,11,7,
@@ -349,200 +621,54 @@ c[h].z+=.5*g[h].z;c[h].x/=.5+l[0][h];c[h].y/=.5+l[0][h];c[h].z/=.5+l[0][h]}else{
 2,1,11,4,8,11,6,4],[9,1,4,1,2,4,4,2,6],[1,0,9,3,2,8,2,4,8,2,6,4],[2,4,0,2,6,4],[3,2,8,8,2,4,2,6,4],[1,4,9,11,4,1,11,1,3,11,6,4],[0,9,1,4,11,6,4,8,11],[11,6,3,3,6,0,6,4,0],[8,6,4,8,11,6],[6,7,10,7,8,10,10,8,9],[9,3,0,6,3,9,6,9,10,6,7,3],[6,1,10,6,7,1,7,0,1,7,8,0],[6,7,10,10,7,1,7,3,1],[7,11,6,3,8,2,8,10,2,8,9,10],[11,6,7,10,0,9,10,2,0],[2,1,10,7,11,6,8,0,3],[1,10,2,6,7,11],[7,2,6,7,9,2,2,9,1,7,8,9],[1,0,9,3,6,7,3,2,6],[8,0,7,7,0,6,0,2,6],[2,7,3,2,6,7],[7,11,6,3,9,1,3,8,9],[9,1,0,11,6,7],[0,3,8,11,
 6,7],[11,6,7],[11,7,5,11,5,10],[3,0,8,7,5,10,7,10,11],[9,0,1,10,11,7,10,7,5],[3,1,9,3,9,8,7,10,11,7,5,10],[10,2,5,2,3,5,5,3,7],[5,10,2,8,5,2,8,7,5,8,2,0],[9,0,1,10,2,5,5,2,3,5,3,7],[1,10,2,5,8,7,5,9,8],[2,11,1,11,7,1,1,7,5],[0,8,3,2,11,1,1,11,7,1,7,5],[9,0,2,9,2,7,2,11,7,9,7,5],[11,3,2,8,5,9,8,7,5],[1,3,7,1,7,5],[8,7,0,0,7,1,7,5,1],[0,3,9,9,3,5,3,7,5],[9,7,5,9,8,7],[4,5,8,5,10,8,8,10,11],[3,0,4,3,4,10,4,5,10,3,10,11],[0,1,9,4,5,8,8,5,10,8,10,11],[5,9,4,1,11,3,1,10,11],[3,8,4,3,4,2,2,4,5,2,5,10],[10,
 2,5,5,2,4,2,0,4],[0,3,8,5,9,4,10,2,1],[2,1,10,9,4,5],[8,4,5,2,8,5,2,11,8,2,5,1],[3,2,11,1,4,5,1,0,4],[9,4,5,8,2,11,8,0,2],[11,3,2,9,4,5],[4,5,8,8,5,3,5,1,3],[5,0,4,5,1,0],[3,8,0,4,5,9],[9,4,5],[7,4,11,4,9,11,11,9,10],[3,0,8,7,4,11,11,4,9,11,9,10],[11,7,4,1,11,4,1,10,11,1,4,0],[8,7,4,11,1,10,11,3,1],[2,3,7,2,7,9,7,4,9,2,9,10],[4,8,7,0,10,2,0,9,10],[2,1,10,0,7,4,0,3,7],[10,2,1,8,7,4],[2,11,7,2,7,1,1,7,4,1,4,9],[3,2,11,4,8,7,9,1,0],[7,4,11,11,4,2,4,0,2],[2,11,3,7,4,8],[9,1,4,4,1,7,1,3,7],[1,0,9,8,7,
-4],[3,4,0,3,7,4],[8,7,4],[8,9,10,8,10,11],[0,9,3,3,9,11,9,10,11],[1,10,0,0,10,8,10,11,8],[10,3,1,10,11,3],[3,8,2,2,8,10,8,9,10],[9,2,0,9,10,2],[8,0,3,1,10,2],[10,2,1],[2,11,1,1,11,9,11,8,9],[11,3,2,0,9,1],[11,0,2,11,8,0],[11,3,2],[8,1,3,8,9,1],[9,1,0],[8,0,3],[]];return u}();"undefined"===typeof console&&(console={log:function(){}});
-$3Dmol.ProteinSurface=function(){var u=0,q=0,C=0,A=2,w=0,B=0,g=0,a=0,c=null,h=null,m=null,b=0,f=0,l=0,d=0,e=0,p=0,z={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},t=function(c){return c.elem&&"undefined"!=typeof z[c.elem]?c.elem:"X"},n={},s={},x,E,y=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,
--1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];this.getFacesAndVertices=function(b){var a=
-{},d,e;d=0;for(e=b.length;d<e;d++)a[b[d]]=!0;b=E;d=0;for(e=b.length;d<e;d++)b[d].x=b[d].x/A-u,b[d].y=b[d].y/A-q,b[d].z=b[d].z/A-C;var g=[];d=0;for(e=x.length;d<e;d+=3){var l=x[d],t=x[d+1],s=x[d+2],n=b[t].atomid,f=b[s].atomid,y=b[l].atomid;n<y&&(y=n);f<y&&(y=f);a[y]&&l!==t&&t!==s&&l!==s&&(g.push(l),g.push(t),g.push(s))}m=h=c=null;return{vertices:b,faces:g}};this.initparm=function(t,s,n){1E6<n&&(A=1);n=1/A*5.5;b=t[0][0];d=t[1][0];f=t[0][1];e=t[1][1];l=t[0][2];p=t[1][2];s?(b-=1.4+n,f-=1.4+n,l-=1.4+n,
-d+=1.4+n,e+=1.4+n,p+=1.4+n):(b-=n,f-=n,l-=n,d+=n,e+=n,p+=n);b=Math.floor(b*A)/A;f=Math.floor(f*A)/A;l=Math.floor(l*A)/A;d=Math.ceil(d*A)/A;e=Math.ceil(e*A)/A;p=Math.ceil(p*A)/A;u=-b;q=-f;C=-l;g=Math.ceil(A*(d-b))+1;B=Math.ceil(A*(e-f))+1;w=Math.ceil(A*(p-l))+1;this.boundingatom(s);a=1.4*A;c=new Uint8Array(g*B*w);h=new Float64Array(g*B*w);m=new Int32Array(g*B*w);console.log("Box size: ",g,B,w,c.length)};this.boundingatom=function(c){var b=[],a,d;flagradius=c;for(var m in z)if(z.hasOwnProperty(m))for(d=
-z[m],b[m]=c?(d+1.4)*A+.5:d*A+.5,d=b[m]*b[m],s[m]=Math.floor(b[m])+1,n[m]=new Int32Array(s[m]*s[m]),j=indx=0;j<s[m];j++)for(k=0;k<s[m];k++)a=j*j+k*k,a>d?n[m][indx]=-1:(a=Math.sqrt(d-a),n[m][indx]=Math.floor(a)),indx++};this.fillvoxels=function(b,a){var d,e;d=0;for(e=c.length;d<e;d++)c[d]=0,h[d]=-1,m[d]=-1;for(d in a)e=b[a[d]],void 0!==e&&this.fillAtom(e,b);d=0;for(e=c.length;d<e;d++)c[d]&1&&(c[d]|=2)};this.fillAtom=function(b,d){var a,e,l,h,f,y,E,p,x,z,H,N,U,P,Q,W,R;a=Math.floor(.5+A*(b.x+u));e=Math.floor(.5+
-A*(b.y+q));l=Math.floor(.5+A*(b.z+C));var X=t(b),L=0,ea=B*w;z=0;for(R=s[X];z<R;z++)for(H=0;H<R;H++){if(-1!=n[X][L])for(P=-1;2>P;P++)for(Q=-1;2>Q;Q++)for(W=-1;2>W;W++)if(0!==P&&0!==Q&&0!==W)for(E=P*z,x=W*H,N=0;N<=n[X][L];N++)p=N*Q,h=a+E,f=e+p,U=l+x,0>h||0>f||0>U||h>=g||f>=B||U>=w||(U=h*ea+f*w+U,c[U]&1?(y=d[m[U]],y.serial!=b.serial&&(h=a+E-Math.floor(.5+A*(y.x+u)),f=e+p-Math.floor(.5+A*(y.y+q)),y=l+x-Math.floor(.5+A*(y.z+C)),E*E+p*p+x*x<h*h+f*f+y*y&&(m[U]=b.serial))):(c[U]|=1,m[U]=b.serial));L++}};
-this.fillvoxelswaals=function(b,d){var a,m;a=0;for(m=c.length;a<m;a++)c[a]&=-3;for(a in d)m=b[d[a]],void 0!==m&&this.fillAtomWaals(m,b)};this.fillAtomWaals=function(b,a){var d,e,l,h,f,y,E=0,p,x,z,H,N,U,P,Q,W,R,X;d=Math.floor(.5+A*(b.x+u));e=Math.floor(.5+A*(b.y+q));l=Math.floor(.5+A*(b.z+C));var L=t(b),ea=B*w;N=0;for(X=s[L];N<X;N++)for(U=0;U<X;U++){if(-1!=n[L][E])for(Q=-1;2>Q;Q++)for(W=-1;2>W;W++)for(R=-1;2>R;R++)if(0!==Q&&0!==W&&0!==R)for(p=Q*N,z=R*U,P=0;P<=n[L][E];P++)x=P*W,h=d+p,f=e+x,H=l+z,0>
-h||0>f||0>H||h>=g||f>=B||H>=w||(H=h*ea+f*w+H,c[H]&2?(y=a[m[H]],y.serial!=b.serial&&(h=d+p-Math.floor(.5+A*(y.x+u)),f=e+x-Math.floor(.5+A*(y.y+q)),y=l+z-Math.floor(.5+A*(y.z+C)),p*p+x*x+z*z<h*h+f*f+y*y&&(m[H]=b.serial))):(c[H]|=2,m[H]=b.serial));E++}};this.buildboundary=function(){var b=B*w;for(i=0;i<g;i++)for(j=0;j<w;j++)for(k=0;k<B;k++){var a=i*b+k*w+j;if(c[a]&1)for(var d=0;26>d;){var m=i+y[d][0],e=j+y[d][2],h=k+y[d][1];if(-1<m&&m<g&&-1<h&&h<B&&-1<e&&e<w&&!(c[m*b+h*w+e]&1)){c[a]|=4;break}else d++}}};
-var H=function(c,b,d){var a=new Int32Array(c*b*d*3);this.set=function(c,m,e,g){c=3*((c*b+m)*d+e);a[c]=g.ix;a[c+1]=g.iy;a[c+2]=g.iz};this.get=function(c,m,e){c=3*((c*b+m)*d+e);return{ix:a[c],iy:a[c+1],iz:a[c+2]}}};this.fastdistancemap=function(){var b,d,m,e=new H(g,B,w),l=B*w,t=a*a,n=[];m=[];var f;for(b=0;b<g;b++)for(d=0;d<B;d++)for(m=0;m<w;m++)if(f=b*l+d*w+m,c[f]&=-3,c[f]&1&&c[f]&4){var s={ix:b,iy:d,iz:m};e.set(b,d,m,s);n.push(s);h[f]=0;c[f]|=2;c[f]&=-5}do for(m=this.fastoneshell(n,e),n=[],b=0,d=
-m.length;b<d;b++)f=l*m[b].ix+w*m[b].iy+m[b].iz,c[f]&=-5,h[f]<=1.0404*t&&n.push({ix:m[b].ix,iy:m[b].iy,iz:m[b].iz});while(0!==n.length);b=A-.5;0>b&&(b=0);t-=.5/(.1+b);for(b=0;b<g;b++)for(d=0;d<B;d++)for(m=0;m<w;m++)f=b*l+d*w+m,c[f]&=-5,c[f]&1&&(!(c[f]&2)||c[f]&2&&h[f]>=t)&&(c[f]|=4)};this.fastoneshell=function(b,d){var a,m,e,f,l,t,n,s,E,p,x,z=[];if(0===b.length)return z;tnv={ix:-1,iy:-1,iz:-1};var H=B*w;n=0;for(E=b.length;n<E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=0;6>s;s++)tnv.ix=
-a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));n=0;for(E=b.length;n<
-E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=6;18>s;s++)tnv.ix=a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,
-c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));n=0;for(E=b.length;n<E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=18;26>s;s++)tnv.ix=a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-
-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return z};this.marchingcubeinit=function(b){for(var d=0,a=c.length;d<a;d++)1==b?c[d]&=-5:4==b?(c[d]&=-3,c[d]&4&&(c[d]|=2),c[d]&=-5):2==b?c[d]&4&&c[d]&2?c[d]&=-5:c[d]&4&&!(c[d]&2)&&(c[d]|=2):3==b&&(c[d]&=-5)};this.marchingcube=function(b){this.marchingcubeinit(b);E=[];x=[];$3Dmol.MarchingCube.march(c,E,x,{smooth:1,nX:g,nY:B,nZ:w});b=B*w;for(var d=0,a=E.length;d<
-a;d++)E[d].atomid=m[E[d].x*b+w*E[d].y+E[d].z];$3Dmol.MarchingCube.laplacianSmooth(1,E,x)}};$3Dmol=function(u){return u.$3Dmol||{}}(window);$.get("http://3dmol.csb.pitt.edu/track/report.cgi");$3Dmol.createViewer=function(u,q){"string"===$.type(u)&&(u=$("#"+u));if(u){q=q||{};try{return new $3Dmol.GLViewer(u,q)}catch(C){throw"error creating viewer: "+C;}}};$3Dmol.viewers={};
-$3Dmol.download=function(u,q,C,A){var w="",B=q.addModel();if("pdb:"===u.substr(0,4)){w="pdb";u=u.substr(4).toUpperCase();if(!u.match(/^[1-9][A-Za-z0-9]{3}$/)){alert("Wrong PDB ID");return}uri="http://www.rcsb.org/pdb/files/"+u+".pdb"}else if("cid:"==u.substr(0,4)){w="sdf";u=u.substr(4);if(!u.match(/^[1-9]+$/)){alert("Wrong Compound ID");return}uri="http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+u+"/SDF?record_type=3d"}$.get(uri,function(g){B.addMolData(g,w,C);q.zoomTo();q.render();A&&A(B)});
-return B};$3Dmol.SurfaceType={VDW:1,MS:2,SAS:3,SES:4};$3Dmol.mergeGeos=function(u,q){var C=q.geometry;void 0!==C&&u.geometryGroups.push(C.geometryGroups[0])};$3Dmol.multiLineString=function(u){return u.toString().replace(/^[^\/]+\/\*!?/,"").replace(/\*\/[^\/]+$/,"")};$3Dmol.syncSurface=!1;if(0<=window.navigator.userAgent.indexOf("MSIE ")||0<=window.navigator.userAgent.indexOf("Trident/"))$3Dmol.syncSurface=!0;
-$3Dmol.specStringToObject=function(u){if("object"===typeof u||"undefined"===typeof u||null==u)return u;var q={};u=u.split(";");for(var C=0;C<u.length;C++){var A=u[C].split(":"),w=A[0],B={};if(A=A[1])if(A=A.replace(/~/g,"="),-1!==A.indexOf("="))for(var A=A.split(","),g=0;g<A.length;g++){var a=A[g].split("=",2);B[a[0]]=a[1]}else B=-1!==A.indexOf(",")?A.split(","):A;q[w]=B}return q};
-$3Dmol.getExtent=function(u,q){var C,A,w,B,g,a,c,h,m,b,f=!q;C=A=w=9999;B=g=a=-9999;c=h=m=b=0;if(0===u.length)return[[0,0,0],[0,0,0],[0,0,0]];for(var l=0;l<u.length;l++){var d=u[l];if(void 0!==d&&(b++,c+=d.x,h+=d.y,m+=d.z,C=C<d.x?C:d.x,A=A<d.y?A:d.y,w=w<d.z?w:d.z,B=B>d.x?B:d.x,g=g>d.y?g:d.y,a=a>d.z?a:d.z,d.symmetries&&f))for(var e=0;e<d.symmetries.length;e++)b++,c+=d.symmetries[e].x,h+=d.symmetries[e].y,m+=d.symmetries[e].z,C=C<d.symmetries[e].x?C:d.symmetries[e].x,A=A<d.symmetries[e].y?A:d.symmetries[e].y,
-w=w<d.symmetries[e].z?w:d.symmetries[e].z,B=B>d.symmetries[e].x?B:d.symmetries[e].x,g=g>d.symmetries[e].y?g:d.symmetries[e].y,a=a>d.symmetries[e].z?a:d.symmetries[e].z}return[[C,A,w],[B,g,a],[c/b,h/b,m/b]]};$3Dmol.workerString='self.onmessage=function(oEvent){var obj=oEvent.data,type=obj.type;if(0>type)self.atomData=obj.atoms,self.volume=obj.volume,self.ps=new ProteinSurface;else{var ps=self.ps;ps.initparm(obj.expandedExtent,1==type?!1:!0,self.volume),ps.fillvoxels(self.atomData,obj.extendedAtoms),ps.buildboundary(),(4===type||2===type)&&(ps.fastdistancemap(),ps.boundingatom(!1),ps.fillvoxelswaals(self.atomData,obj.extendedAtoms)),ps.marchingcube(type);var VandF=ps.getFacesAndVertices(obj.atomsToShow);self.postMessage(VandF)}};var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}};var ISDONE=2,ProteinSurface=function (){var faces,verts,origextent,INOUT=1,ISDONE=2,ISBOUND=4,ptranx=0,ptrany=0,ptranz=0,probeRadius=1.4,defaultScaleFactor=2,scaleFactor=defaultScaleFactor,pHeight=0,pWidth=0,pLength=0,cutRadius=0,vpBits=null,vpDistance=null,vpAtomID=null,pminx=0,pminy=0,pminz=0,pmaxx=0,pmaxy=0,pmaxz=0,vdwRadii={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},getVDWIndex=function(atom){return atom.elem&&"undefined"!=typeof vdwRadii[atom.elem]?atom.elem:"X"},depty={},widxz={},nb=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,-1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];this.getFacesAndVertices=function(atomlist){var i,il,atomsToShow={};for(i=0,il=atomlist.length;il>i;i++)atomsToShow[atomlist[i]]=!0;var vertices=verts;for(i=0,il=vertices.length;il>i;i++)vertices[i].x=vertices[i].x/scaleFactor-ptranx,vertices[i].y=vertices[i].y/scaleFactor-ptrany,vertices[i].z=vertices[i].z/scaleFactor-ptranz;var finalfaces=[];for(i=0,il=faces.length;il>i;i+=3){var fa=faces[i],fb=faces[i+1],fc=faces[i+2],a=vertices[fa].atomid,b=vertices[fb].atomid,c=vertices[fc].atomid,which=a;if(which>b&&(which=b),which>c&&(which=c),atomsToShow[which]){{vertices[faces[i]],vertices[faces[i+1]],vertices[faces[i+2]]}fa!==fb&&fb!==fc&&fa!==fc&&(finalfaces.push(fa),finalfaces.push(fb),finalfaces.push(fc))}}return vpBits=null,vpDistance=null,vpAtomID=null,{vertices:vertices,faces:finalfaces}},this.initparm=function(extent,btype,volume){volume>1e6&&(scaleFactor=defaultScaleFactor/2);var margin=1/scaleFactor*5.5;origextent=extent,pminx=extent[0][0],pmaxx=extent[1][0],pminy=extent[0][1],pmaxy=extent[1][1],pminz=extent[0][2],pmaxz=extent[1][2],btype?(pminx-=probeRadius+margin,pminy-=probeRadius+margin,pminz-=probeRadius+margin,pmaxx+=probeRadius+margin,pmaxy+=probeRadius+margin,pmaxz+=probeRadius+margin):(pminx-=margin,pminy-=margin,pminz-=margin,pmaxx+=margin,pmaxy+=margin,pmaxz+=margin),pminx=Math.floor(pminx*scaleFactor)/scaleFactor,pminy=Math.floor(pminy*scaleFactor)/scaleFactor,pminz=Math.floor(pminz*scaleFactor)/scaleFactor,pmaxx=Math.ceil(pmaxx*scaleFactor)/scaleFactor,pmaxy=Math.ceil(pmaxy*scaleFactor)/scaleFactor,pmaxz=Math.ceil(pmaxz*scaleFactor)/scaleFactor,ptranx=-pminx,ptrany=-pminy,ptranz=-pminz,pLength=Math.ceil(scaleFactor*(pmaxx-pminx))+1,pWidth=Math.ceil(scaleFactor*(pmaxy-pminy))+1,pHeight=Math.ceil(scaleFactor*(pmaxz-pminz))+1,this.boundingatom(btype),cutRadius=probeRadius*scaleFactor,vpBits=new Uint8Array(pLength*pWidth*pHeight),vpDistance=new Float64Array(pLength*pWidth*pHeight),vpAtomID=new Int32Array(pLength*pWidth*pHeight)},this.boundingatom=function(btype){var txz,tdept,sradius,tradius=[];flagradius=btype;for(var i in vdwRadii)if(vdwRadii.hasOwnProperty(i)){var r=vdwRadii[i];for(tradius[i]=btype?(r+probeRadius)*scaleFactor+.5:r*scaleFactor+.5,sradius=tradius[i]*tradius[i],widxz[i]=Math.floor(tradius[i])+1,depty[i]=new Int32Array(widxz[i]*widxz[i]),indx=0,j=0;j<widxz[i];j++)for(k=0;k<widxz[i];k++)txz=j*j+k*k,txz>sradius?depty[i][indx]=-1:(tdept=Math.sqrt(sradius-txz),depty[i][indx]=Math.floor(tdept)),indx++}},this.fillvoxels=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]=0,vpDistance[i]=-1,vpAtomID[i]=-1;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtom(atom,atoms)}for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&INOUT&&(vpBits[i]|=ISDONE)},this.fillAtom=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,i,j,k,si,sj,sk,ii,jj,kk,n;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),nind=0,pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&INOUT){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=INOUT,vpAtomID[index]=atom.serial}nind++}},this.fillvoxelswaals=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&=~ISDONE;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtomWaals(atom,atoms)}},this.fillAtomWaals=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,si,sj,sk,i,j,k,ii,jj,kk,n,nind=0;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&ISDONE){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=ISDONE,vpAtomID[index]=atom.serial}nind++}},this.buildboundary=function(){var pWH=pWidth*pHeight;for(i=0;pLength>i;i++)for(j=0;pHeight>j;j++)for(k=0;pWidth>k;k++){var index=i*pWH+k*pHeight+j;if(vpBits[index]&INOUT)for(var ii=0;26>ii;){var ti=i+nb[ii][0],tj=j+nb[ii][2],tk=k+nb[ii][1];if(ti>-1&&pLength>ti&&tk>-1&&pWidth>tk&&tj>-1&&pHeight>tj&&!(vpBits[ti*pWH+tk*pHeight+tj]&INOUT)){vpBits[index]|=ISBOUND;break}ii++}}};var PointGrid=function(length,width,height){var data=new Int32Array(length*width*height*3);this.set=function(x,y,z,pt){var index=3*((x*width+y)*height+z);data[index]=pt.ix,data[index+1]=pt.iy,data[index+2]=pt.iz},this.get=function(x,y,z){var index=3*((x*width+y)*height+z);return{ix:data[index],iy:data[index+1],iz:data[index+2]}}};this.fastdistancemap=function(){var i,j,k,n,index,boundPoint=new PointGrid(pLength,pWidth,pHeight),pWH=pWidth*pHeight,cutRSq=cutRadius*cutRadius,inarray=[],outarray=[];for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)if(index=i*pWH+j*pHeight+k,vpBits[index]&=~ISDONE,vpBits[index]&INOUT&&vpBits[index]&ISBOUND){var triple={ix:i,iy:j,iz:k};boundPoint.set(i,j,k,triple),inarray.push(triple),vpDistance[index]=0,vpBits[index]|=ISDONE,vpBits[index]&=~ISBOUND}do for(outarray=this.fastoneshell(inarray,boundPoint),inarray=[],i=0,n=outarray.length;n>i;i++)index=pWH*outarray[i].ix+pHeight*outarray[i].iy+outarray[i].iz,vpBits[index]&=~ISBOUND,vpDistance[index]<=1.0404*cutRSq&&inarray.push({ix:outarray[i].ix,iy:outarray[i].iy,iz:outarray[i].iz});while(0!==inarray.length);inarray=[],outarray=[],boundPoint=null;var cutsf=scaleFactor-.5;0>cutsf&&(cutsf=0);var cutoff=cutRSq-.5/(.1+cutsf);for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)index=i*pWH+j*pHeight+k,vpBits[index]&=~ISBOUND,vpBits[index]&INOUT&&(!(vpBits[index]&ISDONE)||vpBits[index]&ISDONE&&vpDistance[index]>=cutoff)&&(vpBits[index]|=ISBOUND)},this.fastoneshell=function(inarray,boundPoint){var tx,ty,tz,dx,dy,dz,i,j,n,square,bp,index,outarray=[];if(0===inarray.length)return outarray;tnv={ix:-1,iy:-1,iz:-1};var pWH=pWidth*pHeight;for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=0;6>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=6;18>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=18;26>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return outarray},this.marchingcubeinit=function(stype){for(var i=0,lim=vpBits.length;lim>i;i++)1==stype?vpBits[i]&=~ISBOUND:4==stype?(vpBits[i]&=~ISDONE,vpBits[i]&ISBOUND&&(vpBits[i]|=ISDONE),vpBits[i]&=~ISBOUND):2==stype?vpBits[i]&ISBOUND&&vpBits[i]&ISDONE?vpBits[i]&=~ISBOUND:vpBits[i]&ISBOUND&&!(vpBits[i]&ISDONE)&&(vpBits[i]|=ISDONE):3==stype&&(vpBits[i]&=~ISBOUND)};this.marchingcube=function(stype){this.marchingcubeinit(stype),verts=[],faces=[],march(vpBits,verts,faces,{smooth:1,nX:pLength,nY:pWidth,nZ:pHeight});for(var pWH=pWidth*pHeight,i=0,vlen=verts.length;vlen>i;i++)verts[i].atomid=vpAtomID[verts[i].x*pWH+pHeight*verts[i].y+verts[i].z];laplacianSmooth(1,verts,faces)}},march=function (data,verts,faces,spec){var i,il,fulltable=!!spec.fulltable,origin=spec.hasOwnProperty("origin")&&spec.origin.hasOwnProperty("x")?spec.origin:{x:0,y:0,z:0},voxel=!!spec.voxel,nX=spec.nX||0,nY=spec.nY||0,nZ=spec.nZ||0,scale=spec.scale||1,unitCube=new Vector3(1,1,1).multiplyScalar(scale),vertnums=new Int32Array(nX*nY*nZ);for(i=0,il=vertnums.length;il>i;++i)vertnums[i]=-1;var getVertex=function(i,j,k,code,p1,p2){var pt=new Vector3;pt.copy(origin);var val1=!!(code&1<<p1),val2=!!(code&1<<p2),p=p1;!val1&&val2&&(p=p2),1&p&&k++,2&p&&j++,4&p&&i++,pt.x+=unitCube.x*i,pt.y+=unitCube.y*j,pt.z+=unitCube.z*k;var index=(nY*i+j)*nZ+k;return voxel?(verts.push(pt),verts.length-1):(vertnums[index]<0&&(vertnums[index]=verts.length,verts.push(pt)),vertnums[index])},intersects=new Int32Array(12),etable=fulltable?edgeTable2:edgeTable,tritable=fulltable?triTable2:triTable;for(i=0;nX-1>i;++i)for(var j=0;nY-1>j;++j)for(var k=0;nZ-1>k;++k){for(var code=0,p=0;8>p;++p){var index=(nY*(i+((4&p)>>2))+j+((2&p)>>1))*nZ+k+(1&p),val=!!(data[index]&ISDONE);code|=val<<p}if(0!==code&&255!==code){var ecode=etable[code];if(0!==ecode){var ttable=tritable[code];1&ecode&&(intersects[0]=getVertex(i,j,k,code,0,1)),2&ecode&&(intersects[1]=getVertex(i,j,k,code,1,3)),4&ecode&&(intersects[2]=getVertex(i,j,k,code,3,2)),8&ecode&&(intersects[3]=getVertex(i,j,k,code,2,0)),16&ecode&&(intersects[4]=getVertex(i,j,k,code,4,5)),32&ecode&&(intersects[5]=getVertex(i,j,k,code,5,7)),64&ecode&&(intersects[6]=getVertex(i,j,k,code,7,6)),128&ecode&&(intersects[7]=getVertex(i,j,k,code,6,4)),256&ecode&&(intersects[8]=getVertex(i,j,k,code,0,4)),512&ecode&&(intersects[9]=getVertex(i,j,k,code,1,5)),1024&ecode&&(intersects[10]=getVertex(i,j,k,code,3,7)),2048&ecode&&(intersects[11]=getVertex(i,j,k,code,2,6));for(var t=0;t<ttable.length;t+=3){var a=intersects[ttable[t]],b=intersects[ttable[t+1]],c=intersects[ttable[t+2]];voxel&&t>=3&&(verts.push(verts[a]),a=verts.length-1,verts.push(verts[b]),b=verts.length-1,verts.push(verts[c]),c=verts.length-1),faces.push(a),faces.push(b),faces.push(c)}}}}},laplacianSmooth=function (numiter,verts,faces){var i,il,j,jl,k,tps=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)tps[i]={x:0,y:0,z:0};var flagvert,vertdeg=new Array(20);for(i=0;20>i;i++)vertdeg[i]=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)vertdeg[0][i]=0;for(i=0,il=faces.length/3;il>i;i++){var 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-E,y,H,I,F,G;y=0;for(H=B.length;y<H;y++){s=$3Dmol.CC.color(a[Math.round((y-1)/c)]);b.push(l=B[y]);b.push(l);b.push(d=g[y]);b.push(d);y<H-1&&(t=B[y+1].clone().sub(B[y]),f=g[y].clone().sub(B[y]).cross(t).normalize().multiplyScalar(h));b.push(e=B[y].clone().add(f));b.push(e);b.push(p=g[y].clone().add(f));b.push(p);void 0!==l.atom&&(x=l.atom);G=m.updateGeoGroup(8);I=G.vertexArray;F=G.colorArray;var q=G.faceArray;t=G.vertices;n=3*t;I[n]=l.x;I[n+1]=l.y;I[n+2]=l.z;I[n+3]=l.x;I[n+4]=l.y;I[n+5]=l.z;I[n+6]=
-d.x;I[n+7]=d.y;I[n+8]=d.z;I[n+9]=d.x;I[n+10]=d.y;I[n+11]=d.z;I[n+12]=e.x;I[n+13]=e.y;I[n+14]=e.z;I[n+15]=e.x;I[n+16]=e.y;I[n+17]=e.z;I[n+18]=p.x;I[n+19]=p.y;I[n+20]=p.z;I[n+21]=p.x;I[n+22]=p.y;I[n+23]=p.z;for(I=0;8>I;++I)F[n+3*I]=s.r,F[n+1+3*I]=s.g,F[n+2+3*I]=s.b;if(0<y)for(n=void 0!==E&&void 0!==x&&E.serial!==x.serial,I=0;4>I;I++)if(F=[t+z[I][0],t+z[I][1],t+z[I][2],t+z[I][3]],d=G.faceidx,q[d]=F[0],q[d+1]=F[1],q[d+2]=F[3],q[d+3]=F[1],q[d+4]=F[2],q[d+5]=F[3],G.faceidx+=6,x.clickable||E.clickable){p=
-b[F[3]].clone();d=b[F[0]].clone();var A=b[F[2]].clone();e=b[F[1]].clone();p.atom=b[F[3]].atom||null;A.atom=b[F[2]].atom||null;d.atom=b[F[0]].atom||null;e.atom=b[F[1]].atom||null;if(n){var D=p.clone().add(d).multiplyScalar(.5),C=A.clone().add(e).multiplyScalar(.5),K=p.clone().add(e).multiplyScalar(.5);0===I%2?(E.clickable&&(F=new $3Dmol.Triangle(D,K,p),l=new $3Dmol.Triangle(C,A,K),p=new $3Dmol.Triangle(K,A,p),E.intersectionShape.triangle.push(F),E.intersectionShape.triangle.push(l),E.intersectionShape.triangle.push(p)),
-x.clickable&&(F=new $3Dmol.Triangle(d,e,K),l=new $3Dmol.Triangle(e,C,K),p=new $3Dmol.Triangle(d,K,D),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l),x.intersectionShape.triangle.push(p))):(x.clickable&&(F=new $3Dmol.Triangle(D,K,p),l=new $3Dmol.Triangle(C,A,K),p=new $3Dmol.Triangle(K,A,p),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l),x.intersectionShape.triangle.push(p)),E.clickable&&(F=new $3Dmol.Triangle(d,e,K),l=new $3Dmol.Triangle(e,C,K),p=
-new $3Dmol.Triangle(d,K,D),E.intersectionShape.triangle.push(F),E.intersectionShape.triangle.push(l),E.intersectionShape.triangle.push(p)))}else x.clickable&&(F=new $3Dmol.Triangle(d,e,p),l=new $3Dmol.Triangle(e,A,p),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l))}G.vertices+=8;E=x}a=b.length-8;G=m.updateGeoGroup(8);I=G.vertexArray;F=G.colorArray;q=G.faceArray;t=G.vertices;n=3*t;d=G.faceidx;for(y=0;4>y;y++)b.push(b[2*y]),b.push(b[a+2*y]),c=b[2*y],g=b[a+2*y],I[n+6*y]=c.x,
-I[n+1+6*y]=c.y,I[n+2+6*y]=c.z,I[n+3+6*y]=g.x,I[n+4+6*y]=g.y,I[n+5+6*y]=g.z,F[n+6*y]=s.r,F[n+1+6*y]=s.g,F[n+2+6*y]=s.b,F[n+3+6*y]=s.r,F[n+4+6*y]=s.g,F[n+5+6*y]=s.b;F=[t,t+2,t+6,t+4];l=[t+1,t+5,t+7,t+3];q[d]=F[0];q[d+1]=F[1];q[d+2]=F[3];q[d+3]=F[1];q[d+4]=F[2];q[d+5]=F[3];q[d+6]=l[0];q[d+7]=l[1];q[d+8]=l[3];q[d+9]=l[1];q[d+10]=l[2];q[d+11]=l[3];G.faceidx+=12;G.vertices+=8;m.initTypedArrays();m.setUpNormals();a=new $3Dmol.MeshLambertMaterial;a.vertexColors=$3Dmol.FaceColors;a.side=$3Dmol.DoubleSide;
-a=new $3Dmol.Mesh(m,a)}else{m=B;b=g;y=c;s=new $3Dmol.Geometry(!0);c=0;for(t=m.length;c<t;c++){B=$3Dmol.CC.color(a[Math.round((c-1)/y)]);geoGroup=s.updateGeoGroup(2);z=geoGroup.vertexArray;h=geoGroup.colorArray;G=geoGroup.faceArray;q=geoGroup.vertices;g=3*q;z[g]=m[c].x;z[g+1]=m[c].y;z[g+2]=m[c].z;z[g+3]=b[c].x;z[g+4]=b[c].y;z[g+5]=b[c].z;for(z=0;6>z;++z)h[g+3*z]=B.r,h[g+1+3*z]=B.g,h[g+2+3*z]=B.b;0<c&&(q=[q,q+1,q-1,q-2],g=geoGroup.faceidx,G[g]=q[0],G[g+1]=q[1],G[g+2]=q[3],G[g+3]=q[1],G[g+4]=q[2],G[g+
-5]=q[3],geoGroup.faceidx+=6);geoGroup.vertices+=2}s.initTypedArrays();s.setUpNormals();a=new $3Dmol.MeshLambertMaterial;a.vertexColors=$3Dmol.FaceColors;a.side=$3Dmol.DoubleSide;a=new $3Dmol.Mesh(s,a)}w.add(a)}},C=function(w,B,g,a,c){0!==B.length&&(c=void 0===c?5:c,a=new $3Dmol.Geometry,u(B,c),B=new $3Dmol.LineBasicMaterial({linewidth:g}),B.vertexColors=!0,B=new $3Dmol.Line(a,B),B.type=$3Dmol.LineStrip,w.add(B))},A=function(w,B,g,a,c,h,m){var b;c.sub(a);c.normalize();c.multiplyScalar("c"===m.ss?"P"===
-m.atom?.8:.3:1.3);null!=h&&0>c.dot(h)&&c.negate();for(h=0;h<B;h++)b=-1+2*h/(B-1),b=new $3Dmol.Vector3(a.x+b*c.x,a.y+b*c.y,a.z+b*c.z),b.atom=m,g&&"s"===m.ss&&(b.smoothen=!0),w[h].push(b)};return function(w,B,g,a){var c,h,m;c=2;h=5;m=!1;var b="CA O P OP2 O5' O3' C5' C2' N1 N3".split(" "),f=[" DA"," DG","  A","  G"],l=[" DT"," DC","  U","  C"],d,e,p,z,t,n,s,x,E,y,H,I,F,G,u=null,S=[],D=[];for(s=0;s<c;s++)D[s]=[];for(s in B)if(p=B[s],void 0!==p&&-1!==$.inArray(p.atom,b)&&!p.hetflag)if(d=p.style.cartoon,
-"trace"===d.style){if(u||(u=new $3Dmol.Geometry(!0)),"CA"===p.atom||"P"===p.atom)t=a?a.valueToHex(p.resi,a.range()):$3Dmol.getColorFromStyle(p,d).getHex(),S.push(t),n=$.isNumeric(d.thickness)?d.thickness:.4,e&&e.chain===p.chain&&e.resi+1===p.resi&&(t==z?(z=$3Dmol.CC.color(t),$3Dmol.GLDraw.drawCylinder(u,e,p,n,z,!0,!0)):(d=(new $3Dmol.Vector3).addVectors(e,p).multiplyScalar(.5),z=$3Dmol.CC.color(z),F=$3Dmol.CC.color(t),$3Dmol.GLDraw.drawCylinder(u,e,d,n,z,!0,!1),$3Dmol.GLDraw.drawCylinder(u,d,p,n,
-F,!1,!0))),e=p,z=t}else{if("CA"===p.atom||"P"===p.atom||"O5'"===p.atom){if(void 0!=e&&(e.chain!=p.chain||e.resi!==p.resi&&e.resi+1!==p.resi||e.reschain!=p.reschain)){G&&(F=H?(new $3Dmol.Vector3).addVectors(e,H).multiplyScalar(.5):new $3Dmol.Vector3(e.x,e.y,e.z),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),A(D,c,!m,H,I,y,e),S.push(t),G=null);for(s=0;!n&&s<c;s++)C(w,D[s],1,S,h);q(w,D[0],D[c-1],S,h,n);D=[];for(s=0;s<c;s++)D[s]=[];S=[]}if(void 0===e||e.resi!=p.resi)G&&(F=(new $3Dmol.Vector3).addVectors(e,
-p).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),G=null),t=a?a.valueToHex(p.resi,a.range()):$3Dmol.getColorFromStyle(p,d).getHex(),S.push(t),n=$.isNumeric(d.thickness)?d.thickness:.4,e=p,x=new $3Dmol.Vector3(e.x,e.y,e.z),x.resi=e.resi,z=t;!0!==p.clickable||void 0!==p.intersectionShape&&void 0!==p.intersectionShape.triangle||(p.intersectionShape={sphere:null,cylinder:[],line:[],triangle:[]})}else if("O"===p.atom&&"CA"===e.atom||"OP2"===p.atom&&"P"===e.atom||
-"C5'"===p.atom&&"O5'"===e.atom)E=new $3Dmol.Vector3(p.x,p.y,p.z),E.resi=p.resi,"OP2"===p.atom&&(I=new $3Dmol.Vector3(p.x,p.y,p.z));else if("O3'"===p.atom)H=new $3Dmol.Vector3(p.x,p.y,p.z);else if("N1"===p.atom&&-1!=$.inArray(p.resn,f)||"N3"===p.atom&&-1!=$.inArray(p.resn,l))G=new $3Dmol.Vector3(p.x,p.y,p.z),G.color=$3Dmol.getColorFromStyle(p,d).getHex();E&&x&&E.resi===x.resi&&(A(D,c,!m,x,E,y,e),y=E,E=x=null)}G&&(F=H?(new $3Dmol.Vector3).addVectors(e,H).multiplyScalar(.5):new $3Dmol.Vector3(e.x,e.y,
-e.z),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),A(D,c,!m,H,I,y,e),S.push(t));for(s=0;!n&&s<c;s++)C(w,D[s],1,S,h);q(w,D[0],D[c-1],S,h,n);u&&(B=new $3Dmol.MeshLambertMaterial,B.vertexColors=$3Dmol.FaceColors,B.side=$3Dmol.DoubleSide,u=new $3Dmol.Mesh(u,B),w.add(u))}}();$3Dmol=$3Dmol||{};
-$3Dmol.GLDraw=function(){var u={},q=function(){var g=new $3Dmol.Vector3;return function(a){g.set(a[0],a[1],a[2]);var c=g.x,h=g.y,m=g.z,b=Math.sqrt(c*c+h*h);1E-4>b?(a=0,b=1):(a=-c/b,b=h/b);h=-a*c+b*h;c=Math.sqrt(h*h+m*m);1E-4>c?(m=0,h=1):(m/=c,h/=c);c=new Float32Array(9);c[0]=b;c[1]=a;c[2]=0;c[3]=-a*h;c[4]=b*h;c[5]=m;c[6]=a*m;c[7]=-b*m;c[8]=h;return c}}(),C=function(){var g=[],a=Math.pow(2,4),c,h=Math.pow(2,2),m=a/h,b;g[0]=new $3Dmol.Vector3(-1,0,0);g[m]=new $3Dmol.Vector3(0,0,1);g[2*m]=new $3Dmol.Vector3(1,
-0,0);g[3*m]=new $3Dmol.Vector3(0,0,-1);for(c=3;4>=c;c++){h=Math.pow(2,c-1);m=a/h;for(b=0;b<h-1;b++)g[m/2+b*m]=g[b*m].clone().add(g[(b+1)*m]).normalize();b=h-1;g[m/2+b*m]=g[b*m].clone().add(g[0]).normalize()}return g}(),A={cache:{},getVerticesForRadius:function(g){if(void 0!==this.cache[g])return this.cache[g];new $3Dmol.Vector3(0,1,0);for(var a=C.length,c=[],h=[],m,b=0;b<a;b++)c.push(C[b].clone().multiplyScalar(g)),c.push(C[b].clone().multiplyScalar(g)),m=C[b].clone().normalize(),h.push(m),h.push(m);
-var b=[],f=2*Math.PI,l=Math.PI,d,e,p=!1,z=!1;for(e=0;10>=e;e++){var p=0===e||10===e?!0:!1,z=5===e?!0:!1,t=[],n=[];for(d=0;d<=a;d++)if(z){var s=d<a?2*d:0;n.push(s+1);t.push(s)}else{m=d/a;var x=e/10;p&&0!==d?p&&t.push(c.length-1):d<a?(s=new $3Dmol.Vector3,s.x=-g*Math.cos(0+m*f)*Math.sin(0+x*l),s.y=g*Math.cos(0+x*l),s.z=g*Math.sin(0+m*f)*Math.sin(0+x*l),1E-5>Math.abs(s.x)&&(s.x=0),1E-5>Math.abs(s.y)&&(s.y=0),1E-5>Math.abs(s.z)&&(s.z=0),m=new $3Dmol.Vector3(s.x,s.y,s.z),m.normalize(),c.push(s),h.push(m),
-t.push(c.length-1)):t.push(c.length-a)}z&&b.push(n);b.push(t)}a={vertices:c,normals:h,verticesRows:b,w:a,h:10};return this.cache[g]=a}},w=0;u.drawCylinder=function(g,a,c,h,m,b,f){if(a&&c){w++;var l=b||f;m=m||{r:0,g:0,b:0};var d=[c.x,c.y,c.z];d[0]-=a.x;d[1]-=a.y;d[2]-=a.z;var d=q(d),e=A.getVerticesForRadius(h);h=e.w;var p=e.h,z=l?p*h+2:2*h;g=g.updateGeoGroup(z);var t=e.vertices,n=e.normals,e=e.verticesRows,s=e[p/2],x=e[p/2+1],E=g.vertices,y,H,I,B,G,u,C=g.vertexArray,D=g.normalArray,J=g.colorArray,
-K=g.faceArray;for(I=0;I<h;++I)H=2*I,B=d[0]*t[H].x+d[3]*t[H].y+d[6]*t[H].z,G=d[1]*t[H].x+d[4]*t[H].y+d[7]*t[H].z,u=d[5]*t[H].y+d[8]*t[H].z,y=3*(E+H),H=g.faceidx,C[y]=B+a.x,C[y+1]=G+a.y,C[y+2]=u+a.z,C[y+3]=B+c.x,C[y+4]=G+c.y,C[y+5]=u+c.z,D[y]=B,D[y+3]=B,D[y+1]=G,D[y+4]=G,D[y+2]=u,D[y+5]=u,J[y]=m.r,J[y+3]=m.r,J[y+1]=m.g,J[y+4]=m.g,J[y+2]=m.b,J[y+5]=m.b,K[H]=x[I]+E,K[H+1]=x[I+1]+E,K[H+2]=s[I]+E,K[H+3]=s[I]+E,K[H+4]=x[I+1]+E,K[H+5]=s[I+1]+E,g.faceidx+=6;if(l){b=b?p+1:p/2+1;var ca,V,da,T,Z,N,U,P,Q,W,R,
-X,L;for(G=f?0:p/2;G<b;G++)if(G!==p/2){var ea=G<=p/2?c:a;for(B=0;B<h;B++)H=g.faceidx,f=e[G][B+1],I=3*(f+E),l=e[G][B],u=3*(l+E),s=e[G+1][B],y=3*(s+E),x=e[G+1][B+1],L=3*(x+E),ca=d[0]*t[f].x+d[3]*t[f].y+d[6]*t[f].z,V=d[0]*t[l].x+d[3]*t[l].y+d[6]*t[l].z,da=d[0]*t[s].x+d[3]*t[s].y+d[6]*t[s].z,T=d[0]*t[x].x+d[3]*t[x].y+d[6]*t[x].z,Z=d[1]*t[f].x+d[4]*t[f].y+d[7]*t[f].z,N=d[1]*t[l].x+d[4]*t[l].y+d[7]*t[l].z,U=d[1]*t[s].x+d[4]*t[s].y+d[7]*t[s].z,P=d[1]*t[x].x+d[4]*t[x].y+d[7]*t[x].z,Q=d[5]*t[f].y+d[8]*t[f].z,
-W=d[5]*t[l].y+d[8]*t[l].z,R=d[5]*t[s].y+d[8]*t[s].z,X=d[5]*t[x].y+d[8]*t[x].z,C[I]=ca+ea.x,C[u]=V+ea.x,C[y]=da+ea.x,C[L]=T+ea.x,C[I+1]=Z+ea.y,C[u+1]=N+ea.y,C[y+1]=U+ea.y,C[L+1]=P+ea.y,C[I+2]=Q+ea.z,C[u+2]=W+ea.z,C[y+2]=R+ea.z,C[L+2]=X+ea.z,J[I]=m.r,J[u]=m.r,J[y]=m.r,J[L]=m.r,J[I+1]=m.g,J[u+1]=m.g,J[y+1]=m.g,J[L+1]=m.g,J[I+2]=m.b,J[u+2]=m.b,J[y+2]=m.b,J[L+2]=m.b,ca=d[0]*n[f].x+d[3]*n[f].y+d[6]*n[f].z,V=d[0]*n[l].x+d[3]*n[l].y+d[6]*n[l].z,da=d[0]*n[s].x+d[3]*n[s].y+d[6]*n[s].z,T=d[0]*n[x].x+d[3]*n[x].y+
-d[6]*n[x].z,Z=d[1]*n[f].x+d[4]*n[f].y+d[7]*n[f].z,N=d[1]*n[l].x+d[4]*n[l].y+d[7]*n[l].z,U=d[1]*n[s].x+d[4]*n[s].y+d[7]*n[s].z,P=d[1]*n[x].x+d[4]*n[x].y+d[7]*n[x].z,Q=d[5]*n[f].y+d[8]*n[f].z,W=d[5]*n[l].y+d[8]*n[l].z,R=d[5]*n[s].y+d[8]*n[s].z,X=d[5]*n[x].y+d[8]*n[x].z,0===G?(D[I]=ca,D[y]=da,D[L]=T,D[I+1]=Z,D[y+1]=U,D[L+1]=P,D[I+2]=Q,D[y+2]=R,D[L+2]=X,K[H]=f+E,K[H+1]=s+E,K[H+2]=x+E,g.faceidx+=3):G===b-1?(D[I]=ca,D[u]=V,D[y]=da,D[I+1]=Z,D[u+1]=N,D[y+1]=U,D[I+2]=Q,D[u+2]=W,D[y+2]=R,K[H]=f+E,K[H+1]=l+
-E,K[H+2]=s+E,g.faceidx+=3):(D[I]=ca,D[u]=V,D[L]=T,D[I+1]=Z,D[u+1]=N,D[L+1]=P,D[I+2]=Q,D[u+2]=W,D[L+2]=X,D[u]=V,D[y]=da,D[L]=T,D[u+1]=N,D[y+1]=U,D[L+1]=P,D[u+2]=W,D[y+2]=R,D[L+2]=X,K[H]=f+E,K[H+1]=l+E,K[H+2]=x+E,K[H+3]=l+E,K[H+4]=s+E,K[H+5]=x+E,g.faceidx+=6)}}g.vertices+=z}};u.drawCone=function(g,a,c,h,m){if(a&&c){m=m||{r:0,g:0,b:0};var b=[c.x,c.y,c.z];b.x-=a.x;b.y-=a.y;b.z-=a.z;var f=q(b),l=C.length;g=g.updateGeoGroup(l+2);var d=g.vertices,e,p,z,t=g.vertexArray,n=g.normalArray,s=g.colorArray,x=g.faceArray;
-e=3*d;b=(new $3Dmol.Vector3(b[0],b[1],b[2])).normalize();t[e]=a.x;t[e+1]=a.y;t[e+2]=a.z;n[e]=-b.x;n[e+1]=-b.y;n[e+2]=-b.z;s[e]=m.r;s[e+1]=m.g;s[e+2]=m.b;t[e+3]=c.x;t[e+4]=c.y;t[e+5]=c.z;n[e+3]=b.x;n[e+4]=b.y;n[e+5]=b.z;s[e+3]=m.r;s[e+4]=m.g;s[e+5]=m.b;e+=6;for(c=0;c<l;++c)z=C[c].clone(),z.multiplyScalar(h),b=f[0]*z.x+f[3]*z.y+f[6]*z.z,p=f[1]*z.x+f[4]*z.y+f[7]*z.z,z=f[5]*z.y+f[8]*z.z,t[e]=b+a.x,t[e+1]=p+a.y,t[e+2]=z+a.z,n[e]=b,n[e+1]=p,n[e+2]=z,s[e]=m.r,s[e+1]=m.g,s[e+2]=m.b,e+=3;g.vertices+=l+2;a=
-g.faceidx;for(c=0;c<l;c++)h=d+2+c,m=d+2+(c+1)%l,x[a]=h,x[a+1]=m,x[a+2]=d,a+=3,x[a]=h,x[a+1]=m,x[a+2]=d+1,a+=3;g.faceidx+=6*l}};var B={cache:{},getVerticesForRadius:function(g){if("undefined"!==typeof this.cache[g])return this.cache[g];var a={vertices:[],verticesRows:[],normals:[]},c=16,h=10;1>g&&(c=10,h=8);var m=2*Math.PI,b=Math.PI,f,l;for(l=0;l<=h;l++){var d=[];for(f=0;f<=c;f++){var e=f/c,p=l/h,z={};z.x=-g*Math.cos(0+e*m)*Math.sin(0+p*b);z.y=g*Math.cos(0+p*b);z.z=g*Math.sin(0+e*m)*Math.sin(0+p*b);
-e=new $3Dmol.Vector3(z.x,z.y,z.z);e.normalize();a.vertices.push(z);a.normals.push(e);d.push(a.vertices.length-1)}a.verticesRows.push(d)}return this.cache[g]=a}};u.drawSphere=function(g,a,c,h){new $3Dmol.Vector3(a.x,a.y,a.z);var m=B.getVerticesForRadius(c),b=m.vertices,f=m.normals;g=g.updateGeoGroup(b.length);for(var l=g.vertices,d=g.vertexArray,e=g.colorArray,p=g.faceArray,z=g.lineArray,t=g.normalArray,n=0,s=b.length;n<s;++n){var x=3*(l+n),E=b[n];d[x]=E.x+a.x;d[x+1]=E.y+a.y;d[x+2]=E.z+a.z;e[x]=h.r;
-e[x+1]=h.g;e[x+2]=h.b}g.vertices+=b.length;m=m.verticesRows;d=m.length-1;for(h=0;h<d;h++)for(e=m[h].length-1,a=0;a<e;a++){var n=g.faceidx,s=g.lineidx,x=m[h][a+1]+l,E=3*x,y=m[h][a]+l,H=3*y,w=m[h+1][a]+l,q=3*w,u=m[h+1][a+1]+l,A=3*u,C=f[x-l],D=f[y-l],J=f[w-l],K=f[u-l];Math.abs(b[x-l].y)===c?(t[E]=C.x,t[q]=J.x,t[A]=K.x,t[E+1]=C.y,t[q+1]=J.y,t[A+1]=K.y,t[E+2]=C.z,t[q+2]=J.z,t[A+2]=K.z,p[n]=x,p[n+1]=w,p[n+2]=u,z[s]=x,z[s+1]=w,z[s+2]=x,z[s+3]=u,z[s+4]=w,z[s+5]=u,g.faceidx+=3,g.lineidx+=6):Math.abs(b[w-l].y)===
-c?(t[E]=C.x,t[H]=D.x,t[q]=J.x,t[E+1]=C.y,t[H+1]=D.y,t[q+1]=J.y,t[E+2]=C.z,t[H+2]=D.z,t[q+2]=J.z,p[n]=x,p[n+1]=y,p[n+2]=w,z[s]=x,z[s+1]=y,z[s+2]=x,z[s+3]=w,z[s+4]=y,z[s+5]=w,g.faceidx+=3,g.lineidx+=6):(t[E]=C.x,t[H]=D.x,t[A]=K.x,t[E+1]=C.y,t[H+1]=D.y,t[A+1]=K.y,t[E+2]=C.z,t[H+2]=D.z,t[A+2]=K.z,t[H]=D.x,t[q]=J.x,t[A]=K.x,t[H+1]=D.y,t[q+1]=J.y,t[A+1]=K.y,t[H+2]=D.z,t[q+2]=J.z,t[A+2]=K.z,p[n]=x,p[n+1]=y,p[n+2]=u,p[n+3]=y,p[n+4]=w,p[n+5]=u,z[s]=x,z[s+1]=y,z[s+2]=x,z[s+3]=u,z[s+4]=y,z[s+5]=w,z[s+6]=w,z[s+
-7]=u,g.faceidx+=6,g.lineidx+=8)}};return u}();$3Dmol=$3Dmol||{};
-$3Dmol.GLModel=function(){var u={line:{}},q={H:1.2,Li:1.82,LI:1.82,Na:2.27,NA:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,Cl:1.75,BR:1.85,Br:1.85,SE:1.9,Se:1.9,ZN:1.39,Zn:1.39,CU:1.4,Cu:1.4,NI:1.63,Ni:1.63};return function(C,A){var w=[],B=null,g=null,a=null,c=[],h=new $3Dmol.Matrix4;h.identity();var m,b,f=$3Dmol.elementColors.defaultColor,l=A?A:$3Dmol.elementColors.defaultColors,d=function(b,c){var d=1.5;"undefined"!=typeof c.radius?d=c.radius:q[b.elem]&&(d=q[b.elem]);"undefined"!=
-typeof c.scale&&(d*=c.scale);return d},e=function(b,c,d){var a=new $3Dmol.Vector3(b.x,b.y,b.z),m=(new $3Dmol.Vector3(c.x,c.y,c.z)).clone(),e=null;m.sub(a);1===b.bonds.length?1===c.bonds.length?(e=m.clone(),1E-4<Math.abs(e.x)?e.y+=1:e.x+=1):(d=(d+1)%c.bonds.length,b=c.bonds[d],b=w[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(a),e=b.clone(),e.cross(m)):(d=(d+1)%b.bonds.length,b=b.bonds[d],b=w[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(a),e=b.clone(),e.cross(m));.01>e.lengthSq()&&
-(e=m.clone(),1E-4<Math.abs(e.x)?e.y+=1:e.x+=1);e.cross(m);e.normalize();return e},p=function(b,c,d,a,m,e){b[d]=a.x;b[d+1]=a.y;b[d+2]=a.z;c[d]=e.r;c[d+1]=e.g;c[d+2]=e.b;b[d+3]=m.x;b[d+4]=m.y;b[d+5]=m.z;c[d+3]=e.r;c[d+4]=e.g;c[d+5]=e.b};this.getSymmetries=function(){return 0<c.length?c:[h]};this.setSymmetries=function(b){c="undefined"==typeof b?[h]:b};this.getID=function(){return C};this.addMolData=function(d,a,e){e=e||{};a=a||"";if(d)for("undefined"==typeof $3Dmol.Parsers[a]&&(a=a.split(".").pop(),
-typeof("undefined"==$3Dmol.Parsers[a])&&(console.log("Unknown format: "+a),a=d.match(/^@<TRIPOS>MOLECULE/)?"mol2":d.match(/^HETATM/)||d.match(/^ATOM/)?"pdb":d.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/)?"sdf":"xyz",console.log("Best guess: "+a))),(0,$3Dmol.Parsers[a])(w,d,e,c),m=!e.doAssembly,b=!e.duplicateAssemblyAtoms,d=w,a=0;a<d.length;a++)if(e=d[a])e.style=e.style||u,e.color=e.color||l[e.elem]||f,e.model=C,e.clickable&&(e.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]})};this.atomIsSelected=
-function(b,c){if("undefined"===typeof c)return!0;var d=!!c.invert,a=!0,e;for(e in c)if("predicate"===e){if(!c.predicate(b)){a=!1;break}}else if(c.hasOwnProperty(e)&&"props"!=e&&"invert"!=e&&"model"!=e&&"byres"!=e&&"expand"!=e&&"within"!=e){if("undefined"===typeof b[e]){a=!1;break}var m=!1;if("bonds"===e){if(m=c[e],m!=b.bonds.length){a=!1;break}}else if($.isArray(c[e])){for(var f=c[e],l=0;l<f.length;l++)if(b[e]==f[l]){m=!0;break}if(!m){a=!1;break}}else if(m=c[e],b[e]!=m){a=!1;break}}return d?!a:a};
-this.selectedAtoms=function(b,c){var d=[];c||(c=w);for(var a=c.length,e=0;e<a;e++){var m=c[e];m&&this.atomIsSelected(m,b)&&d.push(m)}if(b.hasOwnProperty("expand")){for(var m=b.expand,e=$3Dmol.getExtent(d),a=[[],[],[]],f=0;3>f;f++)a[0][f]=e[0][f]-m,a[1][f]=e[1][f]+m,a[2][f]=e[2][f];m=[];for(f=0;f<w.length;f++){var l=w[f].x,g=w[f].y,h=w[f].z;(l>=a[0][0]&&l<e[0][0]||l>e[1][0]&&l<=a[1][0])&&(g>=a[0][1]&&g<e[0][1]||g>e[1][1]&&g<=a[1][1])&&(h>=a[0][2]&&h<e[0][2]||h>e[1][2]&&h<=a[1][2])&&m.push(w[f])}g=
-d.length;for(e=0;e<m.length;e++)for(a=0;a<g;a++)f=z(m[e],d[a]),l=Math.pow(b.expand,2),f<l&&0<f&&d.push(m[e])}if(b.hasOwnProperty("within")&&b.within.hasOwnProperty("sel")&&b.within.hasOwnProperty("distance")){m=this.selectedAtoms(b.within.sel,w);g=[];for(e=0;e<m.length;e++)for(a=0;a<d.length;a++)f=z(m[e],d[a]),l=Math.pow(b.within.distance,2),f<l&&0<f&&g.push(d[a]);d=g}if(b.hasOwnProperty("byres"))for(f={},l=[],g=[],e=0;e<d.length;e++){var m=d[e],h=m.chain,p=m.resi;void 0===f[h]&&(f[h]={});if(m.hasOwnProperty("resi")&&
-void 0===f[h][p])for(f[h][p]=!0,g.push(m);0<g.length;)if(m=g.pop(),h=m.chain,p=m.resi,void 0===l[m.index])for(l[m.index]=!0,a=0;a<m.bonds.length;a++){var B=w[m.bonds[a]];void 0===l[B.index]&&B.hasOwnProperty("resi")&&B.chain==h&&B.resi==p&&(g.push(B),d.push(B))}}return d};var z=function(b,c){var d=c.y-b.y,a=c.z-b.z;return Math.pow(c.x-b.x,2)+Math.pow(d,2)+Math.pow(a,2)};this.addAtoms=function(b){B=null;var c=w.length,d=[],a;for(a=0;a<b.length;a++)d[b[a].index]=c+a;for(a=0;a<b.length;a++){var c=b[a],
-e=d[c.index],m=$.extend(!1,{},c);m.index=e;m.bonds=[];m.bondOrder=[];for(e=0;e<c.bonds.length;e++){var f=d[c.bonds[e]];"undefined"!=typeof f&&(m.bonds.push(f),m.bondOrder.push(c.bondOrder[e]))}w.push(m)}};this.removeAtoms=function(b){B=null;var c=[],d;for(d=0;d<b.length;d++)c[b[d].index]=!0;b=[];for(d=0;d<w.length;d++){var a=w[d];c[a.index]||b.push(a)}w=[];this.addAtoms(b)};this.setStyle=function(b,c,d){c=$.extend(!0,{},c);var a=!1;b=this.selectedAtoms(b,w);for(var e=0;e<w.length;e++)w[e]&&(w[e].capDrawn=
-!1);for(e=0;e<b.length;e++){a=!0;"undefined"!=typeof c.clickable&&(b[e].clickable=c.clickable);"undefined"!=typeof c.callback&&(b[e].callback=c.callback);b[e].clickable&&(b[e].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});d||(b[e].style={});for(var m in c)c.hasOwnProperty(m)&&(b[e].style[m]=c[m])}a&&(B=null)};this.setColorByElement=function(b,c){var d;if(d=null!==B)d=a,d=c&&d?JSON.stringify(c)==JSON.stringify(d):c==d;if(!d){a=c;var e=this.selectedAtoms(b,e);0<e.length&&(B=null);for(d=
-0;d<e.length;d++){var m=e[d];"undefined"!==typeof c[m.elem]&&(m.color=c[m.elem])}}};this.setColorByProperty=function(b,c,d){var e=this.selectedAtoms(b,e);a=null;0<e.length&&(B=null);b=Number.POSITIVE_INFINITY;var m=Number.NEGATIVE_INFINITY,f,l;for(f=0;f<e.length;f++)l=e[f],l.properties&&void 0!==typeof l.properties[c]&&(l=parseFloat(l.properties[c]),l<b&&(b=l),l>m&&(m=l));for(f=0;f<e.length;f++)if(l=e[f],l.properties&&void 0!==typeof l.properties[c]){var g=d.valueToHex(parseFloat(l.properties[c]),
-[b,m]);l.color=g}};this.globj=function(a){if(null===B){var f=w,l=new $3Dmol.Object3D,h=[],z={},y={},q=new $3Dmol.Geometry(!0),u=new $3Dmol.Geometry(!0),A=new $3Dmol.Geometry(!0),C=new $3Dmol.Geometry(!0),M,S,D=[Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY];M=0;for(S=f.length;M<S;M++){var J=f[M];if(J&&J.style){J.clickable&&void 0===J.intersectionShape&&(J.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});var K=J,ca=q;if(K.style.sphere){var V=K.style.sphere;if(!V.hidden){var da=$3Dmol.getColorFromStyle(K,
-V),T=d(K,V);if(!0===K.clickable&&void 0!==K.intersectionShape){var Z=new $3Dmol.Vector3(K.x,K.y,K.z);K.intersectionShape.sphere.push(new $3Dmol.Sphere(Z,T))}$3Dmol.GLDraw.drawSphere(ca,K,T,da)}}var N=J,U=u;if(N.style.spherei){var P=N.style.spherei;if(!P.hidden){for(var Q=d(N,P),W=$3Dmol.getColorFromStyle(N,P),R=U.updateGeoGroup(4),X=R.vertices,L=3*X,ea=R.vertexArray,Ma=R.colorArray,ra=0;4>ra;ra++)ea[L+3*ra]=N.x,ea[L+3*ra+1]=N.y,ea[L+3*ra+2]=N.z;for(var ta=R.normalArray,Ma=R.colorArray,ra=0;4>ra;ra++)Ma[L+
-3*ra]=W.r,Ma[L+3*ra+1]=W.g,Ma[L+3*ra+2]=W.b;ta[L+0]=-Q;ta[L+1]=-Q;ta[L+2]=0;ta[L+3]=-Q;ta[L+4]=Q;ta[L+5]=0;ta[L+6]=Q;ta[L+7]=Q;ta[L+8]=0;ta[L+9]=Q;ta[L+10]=-Q;ta[L+11]=0;R.vertices+=4;var Pa=R.faceArray,Qa=R.faceidx;Pa[Qa+0]=X;Pa[Qa+1]=X+1;Pa[Qa+2]=X+2;Pa[Qa+3]=X+2;Pa[Qa+4]=X+3;Pa[Qa+5]=X;R.faceidx+=6}}var ua=J,hb=y;if(ua.style.cross){var cb=ua.style.cross;if(!cb.hidden){var ib=cb.linewidth||1;hb[ib]||(hb[ib]=new $3Dmol.Geometry);var db=hb[ib].updateGeoGroup(6),Ra=d(ua,cb),Sa=[[Ra,0,0],[-Ra,0,0],
-[0,Ra,0],[0,-Ra,0],[0,0,Ra],[0,0,-Ra]],rb=ua.clickable;rb&&void 0===ua.intersectionShape&&(ua.intersectionShape={sphere:[],cylinder:[],line:[]});for(var jb=$3Dmol.getColorFromStyle(ua,cb),kb=db.vertexArray,lb=db.colorArray,Ia=0;6>Ia;Ia++){var Ta=3*db.vertices;db.vertices++;kb[Ta]=ua.x+Sa[Ia][0];kb[Ta+1]=ua.y+Sa[Ia][1];kb[Ta+2]=ua.z+Sa[Ia][2];lb[Ta]=jb.r;lb[Ta+1]=jb.g;lb[Ta+2]=jb.b;if(rb){var Ua=new $3Dmol.Vector3(Sa[Ia][0],Sa[Ia][1],Sa[Ia][2]);Ua.multiplyScalar(.1);Ua.set(Ua.x+ua.x,Ua.y+ua.y,Ua.z+
-ua.z);ua.intersectionShape.line.push(Ua)}}}}var ba=J,zb=f,mb=z;if(ba.style.line){var sb=ba.style.line;if(!sb.hidden){var nb=sb.linewidth||1;mb[nb]||(mb[nb]=new $3Dmol.Geometry);for(var sa=mb[nb].updateGeoGroup(2*ba.bonds.length),ga=sa.vertexArray,ha=sa.colorArray,Da=0;Da<ba.bonds.length;Da++){var ya=zb[ba.bonds[Da]];if(ya.style.line&&!(ba.serial>=ya.serial)){var za=new $3Dmol.Vector3(ba.x,ba.y,ba.z),Ja=new $3Dmol.Vector3(ya.x,ya.y,ya.z),Va=za.clone().add(Ja).multiplyScalar(.5),tb=!1;ba.clickable&&
-(void 0===ba.intersectionShape&&(ba.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),ba.intersectionShape.line.push(za),ba.intersectionShape.line.push(Ja));ya.clickable&&(void 0===ya.intersectionShape&&(ya.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),ya.intersectionShape.line.push(Ja),ya.intersectionShape.line.push(za));var oa=$3Dmol.getColorFromStyle(ba,ba.style.line),Ea=$3Dmol.getColorFromStyle(ya,ya.style.line);if(ba.bondStyles&&ba.bondStyles[Da]){var Ka=ba.bondStyles[Da];
-if(!Ka.iswire)continue;Ka.radius&&(bondR=Ka.radius);Ka.singleBond&&(tb=!0);"undefined"!=typeof Ka.color1&&(oa=$3Dmol.CC.color(Ka.color1));"undefined"!=typeof Ka.color2&&(Ea=$3Dmol.CC.color(Ka.color2))}var ia=3*sa.vertices;if(1<ba.bondOrder[Da]&&4>ba.bondOrder[Da]&&!tb){var Wa=e(ba,ya,Da),Ca=Ja.clone();Ca.sub(za);if(2==ba.bondOrder[Da])if(Wa.multiplyScalar(.1),p1a=za.clone(),p1a.add(Wa),p1b=za.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Ca),p2b=p1b.clone(),p2b.add(Ca),oa==Ea)sa.vertices+=4,p(ga,ha,
-ia,p1a,p2a,oa),p(ga,ha,ia+6,p1b,p2b,oa);else{sa.vertices+=8;Ca.multiplyScalar(.5);var Na=p1a.clone();Na.add(Ca);var Oa=p1b.clone();Oa.add(Ca);p(ga,ha,ia,p1a,Na,oa);p(ga,ha,ia+6,Na,p2a,Ea);p(ga,ha,ia+12,p1b,Oa,oa);p(ga,ha,ia+18,Oa,p2b,Ea)}else 3==ba.bondOrder[Da]&&(Wa.multiplyScalar(.1),p1a=za.clone(),p1a.add(Wa),p1b=za.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Ca),p2b=p1b.clone(),p2b.add(Ca),oa==Ea?(sa.vertices+=6,p(ga,ha,ia,za,Ja,oa),p(ga,ha,ia+6,p1a,p2a,oa),p(ga,ha,ia+12,p1b,p2b,oa)):(sa.vertices+=
-12,Ca.multiplyScalar(.5),Na=p1a.clone(),Na.add(Ca),Oa=p1b.clone(),Oa.add(Ca),p(ga,ha,ia,za,Va,oa),p(ga,ha,ia+6,Va,Ja,Ea),p(ga,ha,ia+12,p1a,Na,oa),p(ga,ha,ia+18,Na,p2a,Ea),p(ga,ha,ia+24,p1b,Oa,oa),p(ga,ha,ia+30,Oa,p2b,Ea)))}else oa==Ea?(sa.vertices+=2,p(ga,ha,ia,za,Ja,oa)):(sa.vertices+=4,p(ga,ha,ia,za,Va,oa),p(ga,ha,ia+6,Va,Ja,Ea))}}}}var O=J,Ab=f,fa=A;if(O.style.stick){var eb=O.style.stick;if(!eb.hidden){var Ya=eb.radius||.25,ja=Ya,ub=eb.singleBonds||!1,Za=!1,$a=!1,ma=$3Dmol.getColorFromStyle(O,
-eb),ka=void 0,Aa=void 0;!O.capDrawn&&4>O.bonds.length&&(Za=!0);for(var na=0;na<O.bonds.length;na++){var aa=Ab[O.bonds[na]];if(O.serial<aa.serial){var vb=aa.style;if(vb.stick){var Fa=$3Dmol.getColorFromStyle(aa,vb.stick),ja=Ya,ab=ub;if(O.bondStyles&&O.bondStyles[na]){var Ba=O.bondStyles[na];if(Ba.iswire)continue;Ba.radius&&(ja=Ba.radius);Ba.singleBond&&(ab=!0);"undefined"!=typeof Ba.color1&&(ma=$3Dmol.CC.color(Ba.color1));"undefined"!=typeof Ba.color2&&(Fa=$3Dmol.CC.color(Ba.color2))}var la=new $3Dmol.Vector3(O.x,
-O.y,O.z),va=new $3Dmol.Vector3(aa.x,aa.y,aa.z);if(1===O.bondOrder[na]||ab){if(!aa.capDrawn&&4>aa.bonds.length&&($a=!0),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,la,ka,ja,ma,Za,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,va,ja,Fa,!1,$a)):$3Dmol.GLDraw.drawCylinder(fa,la,va,ja,ma,Za,$a),O.clickable||aa.clickable){ka=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5);if(O.clickable){var Bb=new $3Dmol.Cylinder(la,ka,ja),La=new $3Dmol.Sphere(la,
-ja);O.intersectionShape.cylinder.push(Bb);O.intersectionShape.sphere.push(La)}if(aa.clickable){var Cb=new $3Dmol.Cylinder(va,ka,ja),Db=new $3Dmol.Sphere(va,ja);aa.intersectionShape.cylinder.push(Cb);aa.intersectionShape.sphere.push(Db)}}}else if(1<O.bondOrder[na]){var Ha=!1;mtoCap=!1;ja!=Ya&&(mtoCap=Ha=!0);var Xa=va.clone(),Ga=null;Xa.sub(la);var Y,pa,qa,wa,xa,Ga=e(O,aa,na);if(2==O.bondOrder[na]){if(Y=ja/2.5,Ga=e(O,aa,na),Ga.multiplyScalar(1.5*Y),pa=la.clone(),pa.add(Ga),qa=la.clone(),qa.sub(Ga),
-wa=pa.clone(),wa.add(Xa),xa=qa.clone(),xa.add(Xa),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,pa,ka,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,wa,Y,Fa,!1,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,qa,Aa,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,Aa,xa,Y,Fa,!1,mtoCap)):($3Dmol.GLDraw.drawCylinder(fa,pa,wa,Y,ma,Ha,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,qa,xa,Y,ma,Ha,mtoCap)),O.clickable||aa.clickable)ka=
-(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),O.clickable&&(cylinder1a=new $3Dmol.Cylinder(pa,ka,Y),cylinder1b=new $3Dmol.Cylinder(qa,Aa,Y),O.intersectionShape.cylinder.push(cylinder1a),O.intersectionShape.cylinder.push(cylinder1b),La=new $3Dmol.Sphere(la,ja),O.intersectionShape.sphere.push(La)),aa.clickable&&(cylinder2a=new $3Dmol.Cylinder(wa,ka,Y),cylinder2b=new $3Dmol.Cylinder(xa,Aa,Y),aa.intersectionShape.cylinder.push(cylinder2a),
-aa.intersectionShape.cylinder.push(cylinder2b),new $3Dmol.Sphere(va,ja),aa.intersectionShape.sphere.push(La))}else 3==O.bondOrder[na]&&(Y=ja/4,Ga.cross(Xa),Ga.normalize(),Ga.multiplyScalar(3*Y),pa=la.clone(),pa.add(Ga),qa=la.clone(),qa.sub(Ga),wa=pa.clone(),wa.add(Xa),xa=qa.clone(),xa.add(Xa),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,
-pa,ka,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,wa,Y,Fa,!1,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,la,mp3,Y,ma,Za,!1),$3Dmol.GLDraw.drawCylinder(fa,mp3,va,Y,Fa,!1,$a),$3Dmol.GLDraw.drawCylinder(fa,qa,Aa,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,Aa,xa,Y,Fa,!1,mtoCap)):($3Dmol.GLDraw.drawCylinder(fa,pa,wa,Y,ma,Ha,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,la,va,Y,ma,Za,$a),$3Dmol.GLDraw.drawCylinder(fa,qa,xa,Y,ma,Ha,mtoCap)),O.clickable||aa.clickable)&&(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),
-Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),O.clickable&&(cylinder1a=new $3Dmol.Cylinder(pa.clone(),ka.clone(),Y),cylinder1b=new $3Dmol.Cylinder(qa.clone(),Aa.clone(),Y),cylinder1c=new $3Dmol.Cylinder(la.clone(),mp3.clone(),Y),O.intersectionShape.cylinder.push(cylinder1a),O.intersectionShape.cylinder.push(cylinder1b),O.intersectionShape.cylinder.push(cylinder1c),La=new $3Dmol.Sphere(la,ja),O.intersectionShape.sphere.push(La)),
-aa.clickable&&(cylinder2a=new $3Dmol.Cylinder(wa.clone(),ka.clone(),Y),cylinder2b=new $3Dmol.Cylinder(xa.clone(),Aa.clone(),Y),cylinder2c=new $3Dmol.Cylinder(va.clone(),mp3.clone(),Y),aa.intersectionShape.cylinder.push(cylinder2a),aa.intersectionShape.cylinder.push(cylinder2b),aa.intersectionShape.cylinder.push(cylinder2c),La=new $3Dmol.Sphere(va,ja),aa.intersectionShape.sphere.push(La)))}}}}for(var ob=!1,pb=0,wb=!1,na=0;na<O.bonds.length;na++)ab=ub,O.bondStyles&&O.bondStyles[na]&&(Ba=O.bondStyles[na],
-Ba.singleBond&&(ab=!0),Ba.radius&&Ba.radius!=Ya&&(wb=!0)),(ab||1==O.bondOrder[na])&&pb++;wb?0<pb&&(ob=!0):0==pb&&0<O.bonds.length&&(ob=!0);ob&&(ja=Ya,$3Dmol.GLDraw.drawSphere(fa,O,ja,ma))}}"undefined"===typeof J.style.cartoon||J.style.cartoon.hidden||("spectrum"===J.style.cartoon.color&&"number"===typeof J.resi&&(J.resi<D[0]&&(D[0]=J.resi),J.resi>D[1]&&(D[1]=J.resi)),h.push(J))}}if(0<h.length){var xb=null;D[0]<D[1]&&(xb=new $3Dmol.Gradient.Sinebow(D[0],D[1]));$3Dmol.drawCartoon(l,h,C,xb);for(M=0;M<
-l.children.length;M++);}if(0<q.vertices){var Eb=new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0});q.initTypedArrays();var Fb=new $3Dmol.Mesh(q,Eb);l.add(Fb)}if(0<u.vertices){var Gb=new $3Dmol.ImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});u.initTypedArrays();var Hb=new $3Dmol.Mesh(u,Gb);console.log("spherei geometry "+u.vertices.length);l.add(Hb)}if(0<A.vertices){var bb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});A.initTypedArrays();
-bb.wireframe&&A.setUpWireframe();var Ib=new $3Dmol.Mesh(A,bb);l.add(Ib)}if(0<C.vertices){bb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});C.initTypedArrays();bb.wireframe&&C.setUpWireframe();var Jb=new $3Dmol.Mesh(C,bb);l.add(Jb)}for(M in z)if(z.hasOwnProperty(M)){var qb=M,Kb=new $3Dmol.LineBasicMaterial({linewidth:qb,vertexColors:!0});z[M].initTypedArrays();var Lb=new $3Dmol.Line(z[M],Kb,$3Dmol.LinePieces);l.add(Lb)}for(M in y)if(y.hasOwnProperty(M)){var qb=M,Mb=new $3Dmol.LineBasicMaterial({linewidth:qb,
-vertexColors:!0});y[M].initTypedArrays();var Nb=new $3Dmol.Line(y[M],Mb,$3Dmol.LinePieces);l.add(Nb)}if(b&&!m){var yb=new $3Dmol.Object3D,fb;for(fb=0;fb<c.length;fb++){var gb=new $3Dmol.Object3D,gb=l.clone();gb.matrix.copy(c[fb]);gb.matrixAutoUpdate=!1;yb.add(gb)}l=yb}B=l;g&&(a.remove(g),g=null);g=B.clone();a.add(g)}};this.removegl=function(b){g&&(void 0!==g.geometry&&g.geometry.dispose(),void 0!==g.material&&g.material.dispose(),b.remove(g),g=null);B=null};this.addResLabels=function(b,c,d){var e=
-this.selectedAtoms(b,e);b={};for(var a=0;a<e.length;a++){var m=e[a],f=m.chain,l=m.resn+""+m.resi;b[f]||(b[f]={});b[f][l]||(b[f][l]=[]);b[f][l].push(m)}d=$.extend(!0,{},d);for(f in b)if(b.hasOwnProperty(f)){var g=b[f];for(l in g)if(g.hasOwnProperty(l)){for(var e=g[l],h=new $3Dmol.Vector3(0,0,0),a=0;a<e.length;a++)m=e[a],h.x+=m.x,h.y+=m.y,h.z+=m.z;h.divideScalar(e.length);d.position=h;c.addLabel(l,d)}}}}}();
-$3Dmol.GLShape=function(){function u(w){w=w||{};$3Dmol.ShapeIDCount++;this.boundingSphere=new $3Dmol.Sphere;this.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]};A(this,w);var B=[],g=null,a=null,c=new $3Dmol.Geometry(!0),h=new $3Dmol.Geometry(!0);this.updateStyle=function(c){for(var b in c)w[b]=c[b];A(this,w)};this.addCustom=function(a){a.vertexArr=a.vertexArr||[];a.faceArr=a.faceArr||[];a.normalArr=a.normalArr||[];a.lineArr=a.lineArr||[];var b=c.addGeoGroup();q(this,b,a);b.truncateArrayBuffers(!0,
-!0);for(a=0;a<b.colorArray.length/3;++a)b.colorArray[3*a]=this.color.r,b.colorArray[3*a+1]=this.color.g,b.colorArray[3*a+2]=this.color.b;B.push({id:b.id,geoGroup:b,centroid:b.getCentroid()});C(this.boundingSphere,B,b.vertexArray)};this.addSphere=function(a){a.center=a.center||{x:0,y:0,z:0};a.radius=a.radius?$3Dmol.Math.clamp(a.radius,0,Infinity):1.5;a.color=$3Dmol.CC.color(a.color);this.intersectionShape.sphere.push(new $3Dmol.Sphere(a.center,a.radius));var b=c.addGeoGroup();$3Dmol.GLDraw.drawSphere(c,
-a.center,a.radius,a.color);b.truncateArrayBuffers(!0,!0);B.push({id:b.id,geoGroup:b,centroid:new $3Dmol.Vector3(a.center.x,a.center.y,a.center.z)});C(this.boundingSphere,B,b.vertexArray)};this.addCylinder=function(a){a.start=a.start||{};a.end=a.end||{};var b=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0),f=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0);"undefined"==typeof f.x&&(f.x=3);var l=a.radius||.1,d=$3Dmol.CC.color(a.color);this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(b,
-f,l));var e=c.addGeoGroup();$3Dmol.GLDraw.drawCylinder(c,b,f,l,d,a.fromCap,a.toCap);e.truncateArrayBuffers(!0,!0);a=new $3Dmol.Vector3;B.push({id:e.id,geoGroup:e,centroid:a.addVectors(b,f).multiplyScalar(.5)});C(this.boundingSphere,B,e.vertexArray)};this.addLine=function(a){a.start=a.start||{};a.end=a.end||{};var b=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0),f=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0);"undefined"==typeof f.x&&(f.x=3);a=c.addGeoGroup();var l=a.vertices,d=3*l,
-e=a.vertexArray;e[d]=b.x;e[d+1]=b.y;e[d+2]=b.z;e[d+3]=f.x;e[d+4]=f.y;e[d+5]=f.z;a.vertices+=2;b=a.lineArray;f=a.lineidx;b[f]=l;b[f+1]=l+1;a.lineidx+=2;a.truncateArrayBuffers(!0,!0)};this.addArrow=function(a){a.start=a.start||{};a.end=a.end||{};a.start=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0);if(a.dir instanceof $3Dmol.Vector3&&a.length instanceof number){var b=a.dir.clone().multiplyScalar(a.length).add(start);a.end=b}else a.end=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0),"undefined"==
-typeof a.end.x&&(a.end.x=3);a.radius=a.radius||.1;a.radiusRatio=a.radiusRatio||1.618034;a.mid=0<a.mid&&1>a.mid?a.mid:.618034;b=c.addGeoGroup();var f=a.start,l=a.end,d=a.radius,e=a.radiusRatio,g=a.mid;if(f&&l){var h=l.clone();h.sub(f).multiplyScalar(g);var t=f.clone().add(h),g=h.clone().negate();this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(f.clone(),t.clone(),d));this.intersectionShape.sphere.push(new $3Dmol.Sphere(f.clone(),d));var n=[];n[0]=h.clone();1E-4<Math.abs(n[0].x)?n[0].y+=1:n[0].x+=
-1;n[0].cross(h);n[0].normalize();n[0]=n[0];n[4]=n[0].clone();n[4].crossVectors(n[0],h);n[4].normalize();n[8]=n[0].clone().negate();n[12]=n[4].clone().negate();n[2]=n[0].clone().add(n[4]).normalize();n[6]=n[4].clone().add(n[8]).normalize();n[10]=n[8].clone().add(n[12]).normalize();n[14]=n[12].clone().add(n[0]).normalize();n[1]=n[0].clone().add(n[2]).normalize();n[3]=n[2].clone().add(n[4]).normalize();n[5]=n[4].clone().add(n[6]).normalize();n[7]=n[6].clone().add(n[8]).normalize();n[9]=n[8].clone().add(n[10]).normalize();
-n[11]=n[10].clone().add(n[12]).normalize();n[13]=n[12].clone().add(n[14]).normalize();n[15]=n[14].clone().add(n[0]).normalize();var s=b.vertices,x=b.vertexArray,w=b.faceArray,y=b.normalArray,q=b.lineArray,u,A,G;A=0;for(G=n.length;A<G;++A){u=3*(s+3*A);var M=n[A].clone().multiplyScalar(d).add(f),S=n[A].clone().multiplyScalar(d).add(t),D=n[A].clone().multiplyScalar(d*e).add(t);x[u]=M.x;x[u+1]=M.y;x[u+2]=M.z;x[u+3]=S.x;x[u+4]=S.y;x[u+5]=S.z;x[u+6]=D.x;x[u+7]=D.y;x[u+8]=D.z;0<A&&(u=new $3Dmol.Vector3(x[u-
-3],x[u-2],x[u-1]),M=l.clone(),S=t.clone(),D=new $3Dmol.Vector3(D.x,D.y,D.z),this.intersectionShape.triangle.push(new $3Dmol.Triangle(D,M,u)),this.intersectionShape.triangle.push(new $3Dmol.Triangle(u.clone(),S,D.clone())))}b.vertices+=48;u=3*b.vertices;x[u]=f.x;x[u+1]=f.y;x[u+2]=f.z;x[u+3]=t.x;x[u+4]=t.y;x[u+5]=t.z;x[u+6]=l.x;x[u+7]=l.y;x[u+8]=l.z;b.vertices+=3;var J,K,ca,V,da,T,Z,N,U=b.vertices-3,P=b.vertices-2,Q=b.vertices-1,W=3*U,R=3*P,X=3*Q;A=0;for(G=n.length-1;A<G;++A)J=s+3*A,f=b.faceidx,l=b.lineidx,
-d=J,u=3*d,e=J+1,M=3*e,t=J+2,S=3*t,x=J+4,K=3*x,D=J+5,ca=3*D,J+=3,V=3*J,da=T=n[A],Z=N=n[A+1],y[u]=da.x,y[M]=T.x,y[V]=N.x,y[u+1]=da.y,y[M+1]=T.y,y[V+1]=N.y,y[u+2]=da.z,y[M+2]=T.z,y[V+2]=N.z,y[M]=T.x,y[K]=Z.x,y[V]=N.x,y[M+1]=T.y,y[K+1]=Z.y,y[V+1]=N.y,y[M+2]=T.z,y[K+2]=Z.z,y[V+2]=N.z,y[S]=T.x,y[ca]=Z.x,y[S+1]=T.y,y[ca+1]=Z.y,y[S+2]=T.z,y[ca+2]=Z.z,w[f]=d,w[f+1]=e,w[f+2]=J,w[f+3]=e,w[f+4]=x,w[f+5]=J,w[f+6]=d,w[f+7]=J,w[f+8]=U,w[f+9]=t,w[f+10]=P,w[f+11]=D,w[f+12]=t,w[f+13]=Q,w[f+14]=D,q[l]=d,q[l+1]=e,q[l+
-2]=d,q[l+3]=J,q[l+4]=x,q[l+5]=J,q[l+6]=d,q[l+7]=J,q[l+8]=t,q[l+9]=e,q[l+10]=t,q[l+11]=D,q[l+12]=x,q[l+13]=D,q[l+14]=t,q[l+15]=Q,q[l+16]=t,q[l+17]=D,q[l+18]=Q,q[l+19]=D,b.faceidx+=15,b.lineidx+=20;s=[s+45,s+46,s+1,s,s+47,s+2];f=b.faceidx;l=b.lineidx;d=s[0];u=3*d;e=s[1];M=3*e;t=s[4];S=3*t;x=s[2];K=3*x;D=s[5];ca=3*D;J=s[3];V=3*J;da=T=n[15];Z=N=n[0];y[u]=da.x;y[M]=T.x;y[V]=N.x;y[u+1]=da.y;y[M+1]=T.y;y[V+1]=N.y;y[u+2]=da.z;y[M+2]=T.z;y[V+2]=N.z;y[M]=T.x;y[K]=Z.x;y[V]=N.x;y[M+1]=T.y;y[K+1]=Z.y;y[V+1]=N.y;
-y[M+2]=T.z;y[K+2]=Z.z;y[V+2]=N.z;y[S]=T.x;y[ca]=Z.x;y[S+1]=T.y;y[ca+1]=Z.y;y[S+2]=T.z;y[ca+2]=Z.z;h.normalize();g.normalize();y[W]=g.x;y[R]=y[X]=h.x;y[W+1]=g.y;y[R+1]=y[X+1]=h.y;y[W+2]=g.z;y[R+2]=y[X+2]=h.z;w[f]=d;w[f+1]=e;w[f+2]=J;w[f+3]=e;w[f+4]=x;w[f+5]=J;w[f+6]=d;w[f+7]=J;w[f+8]=U;w[f+9]=t;w[f+10]=P;w[f+11]=D;w[f+12]=t;w[f+13]=Q;w[f+14]=D;q[l]=d;q[l+1]=e;q[l+2]=d;q[l+3]=J;q[l+4]=x;q[l+5]=J;q[l+6]=d;q[l+7]=J;q[l+8]=t;q[l+9]=e;q[l+10]=t;q[l+11]=D;q[l+12]=x;q[l+13]=D;q[l+14]=t;q[l+15]=Q;q[l+16]=
-t;q[l+17]=D;q[l+18]=Q;q[l+19]=D;b.faceidx+=15;b.lineidx+=20}b.truncateArrayBuffers(!0,!0);h=new $3Dmol.Vector3;B.push({id:b.id,geoGroup:b,centroid:h.addVectors(a.start,a.end).multiplyScalar(.5)});C(this.boundingSphere,B,b.vertexArray)};this.addVolumetricData=function(a,b,f){var l=void 0!==f.isoval&&"number"===typeof f.isoval?f.isoval:0,d=f.voxel?!0:!1,e=c.addGeoGroup();switch(b){case "cube":var h=a.replace(/^\s+/,"").split(/[\n\r]+/);if(!(6>h.length)){var g=h[2].replace(/^\s+/,"").replace(/\s+/g,
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-$3Dmol.Gradient.Sinebow=function(u,q){this.valueToHex=function(C,A){var w,B;A?(w=A[0],B=A[1]):(w=u,B=q);if("undefined"==typeof C)return 16777215;C<w&&(C=w);C>B&&(C=B);var g=(C-w)/(B-w)*5/6+.5;w=Math.sin(Math.PI*g);w*=255*w;B=Math.sin(Math.PI*(g+1/3));B*=255*B;g=Math.sin(Math.PI*(g+2/3));return 65536*Math.floor(w)+256*Math.floor(255*g*g)+1*Math.floor(B)};this.jmolID=function(){return"sinebow"};this.range=function(){return"undefined"!=typeof u&&"undefined"!=typeof q?[u,q]:null}};$3Dmol.LabelCount=0;
-$3Dmol.Label=function(u,q){this.id=$3Dmol.LabelCount++;this.stylespec=q||{};this.canvas=document.createElement("canvas");this.canvas.width=134;this.canvas.height=35;this.context=this.canvas.getContext("2d");this.sprite=new $3Dmol.Sprite;this.text=u};
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-$3Dmol.Parsers=function(){var u={},q=function(g){var a=g.slice(0),c,h;c=0;for(h=g.length;c<h;c++)g[c].index||(g[c].index=c);a.sort(function(a,b){return a.z-b.z});c=0;for(h=a.length;c<h;c++){var m=a[c];for(g=c+1;g<h;g++){var b=a[g];if(1.9<b.z-m.z)break;B(m,b)&&-1==m.bonds.indexOf(b.index)&&(m.bonds.push(b.index),m.bondOrder.push(1),b.bonds.push(m.index),b.bondOrder.push(1))}}},C=function(g){var a=[],c=[],h,m;h=0;for(m=g.length;h<m;h++){var b=g[h];b.index=h;b.hetflag?c.push(b):a.push(b)}q(c);a.sort(function(a,
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-a.elem)?!0:2.78<c?!1:!0};u.pdb=u.PDB=u.pdbqt=u.PDBQT=function(g,a,c,h){var m=!c.keepH,b=!c.noSecondaryStructure,f=!c.doAssembly,l=!c.duplicateAssemblyAtoms,d=[];c=g.length;var e,p=[],q=[],t=!1,n=[];a=a.split("\n");var s,x,u;for(s=0;s<a.length;s++){u=a[s].replace(/^\s*/,"");e=u.substr(0,6);var y;if("ATOM  "==e||"HETATM"==e){var A,B,F,G,M,S,D,J,K;e=u.substr(16,1);if(" "==e||"A"==e)if(J=parseInt(u.substr(6,5)),e=u.substr(12,4).replace(/ /g,""),x=u.substr(17,3),y=u.substr(21,1),A=parseInt(u.substr(22,
-4)),B=u.substr(26,1),F=parseFloat(u.substr(30,8)),G=parseFloat(u.substr(38,8)),M=parseFloat(u.substr(46,8)),K=parseFloat(u.substr(60,8)),D=u.substr(76,2).replace(/ /g,""),""===D&&(D=u.substr(12,2).replace(/ /g,"")),"H"!=D&&"HH"!=D&&"HD"!=D||!m)S="H"==u[0]?!0:!1,n[J]=g.length,g.push({resn:x,x:F,y:G,z:M,elem:D,hetflag:S,chain:y,resi:A,icode:B,rescode:A+(" "!=B?"^"+B:""),serial:J,atom:e,bonds:[],ss:"c",bondOrder:[],properties:{},b:K,pdbline:u})}else if("SHEET "==e)t=!0,e=u.substr(21,1),x=parseInt(u.substr(22,
-4)),y=u.substr(32,1),u=parseInt(u.substr(33,4)),p.push([e,x,y,u]);else if("CONECT"==e)for(e=parseInt(u.substr(6,5)),e=g[n[e]],x=0;4>x;x++)y=parseInt(u.substr([11,16,21,26][x],5)),A=g[n[y]],void 0!==e&&void 0!==A&&(y=n[y],e.bonds[e.bonds.length-1]!=y&&(e.bonds.push(y),e.bondOrder.push(1)));else if("HELIX "==e)t=!0,e=u.substr(19,1),x=parseInt(u.substr(21,4)),y=u.substr(31,1),u=parseInt(u.substr(33,4)),q.push([e,x,y,u]);else if(!f&&"REMARK"==e&&"BIOMT"==u.substr(13,5)){x=new $3Dmol.Matrix4;for(e=1;3>=
-e;e++)if(u=a[s].replace(/^\s*/,""),parseInt(u.substr(18,1))==e)x.elements[e-1]=parseFloat(u.substr(23,10)),x.elements[e-1+4]=parseFloat(u.substr(33,10)),x.elements[e-1+8]=parseFloat(u.substr(43,10)),x.elements[e-1+12]=parseFloat(u.substr(53)),s++;else for(;"BIOMT"==u.substr(13,5);)s++,u=a[s].replace(/^\s*/,"");x.elements[3]=0;x.elements[7]=0;x.elements[11]=0;x.elements[15]=1;d.push(x);h.push(x);s--}}(new Date).getTime();C(g);n=f=g.length;if(l)for(l=0;l<g.length;l++){d=[];for(m=0;m<h.length;m++)h[m].isIdentity()||
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-x:t,y:n,z:s,elem:A,hetflag:hetflag,chain:e,resi:p,serial:l,atom:h,bonds:[],ss:"c",bondOrder:[],properties:{charge:u,partialCharge:u,radius:q},pdbline:f})}else if("CONECT"==h)for(h=parseInt(f.substr(6,5)),l=g[m[h]],h=0;4>h;h++)d=parseInt(f.substr([11,16,21,26][h],5)),e=g[m[d]],void 0!==l&&void 0!==e&&(l.bonds.push(m[d]),l.bondOrder.push(1));C(g);c&&w(g);return!0};return u}();$3Dmol=$3Dmol||{};
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+$3Dmol.Parsers=function(){var b={},c=function(b){for(var c=0,d=b.length;c<d;c++)b[c].index||(b[c].index=c);for(var d={},t=0;t<b.length;t++){var c=b[t],m=Math.floor(c.x/4.95),e=Math.floor(c.y/4.95),p=Math.floor(c.z/4.95);d[m]||(d[m]={});d[m][e]||(d[m][e]={});d[m][e][p]||(d[m][e][p]=[]);d[m][e][p].push(c)}b=[{x:0,y:0,z:1},{x:0,y:1,z:-1},{x:0,y:1,z:0},{x:0,y:1,z:1},{x:1,y:-1,z:-1},{x:1,y:-1,z:0},{x:1,y:-1,z:1},{x:1,y:0,z:-1},{x:1,y:0,z:0},{x:1,y:0,z:1},{x:1,y:1,z:-1},{x:1,y:1,z:0},{x:1,y:1,z:1}];for(m in d)for(e in m=
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+s.bondOrder.push(1),y.bonds.push(s.index),y.bondOrder.push(1))}}},d=function(b){var d=[],h=[],t,m;t=0;for(m=b.length;t<m;t++){var e=b[t];e.index=t;e.hetflag?h.push(e):d.push(e)}c(h);d.sort(function(b,c){return b.chain!=c.chain?b.chain<c.chain?-1:1:b.resi-c.resi});var h=b=-1,p;t=0;for(m=d.length;t<m;t++){e=d[t];e.resi!==b&&(b=e.resi,p||h++,p=!1);e.reschain=h;for(var g=t+1;g<d.length;g++){var x=d[g];if(x.chain!=e.chain)break;if(1<x.resi-e.resi)break;q(e,x)&&(-1===e.bonds.indexOf(x.index)&&(e.bonds.push(x.index),
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+parseFloat(H.substr(25,8)),J=parseFloat(H.substr(34,6)),I=parseFloat(H.substr(41,6)),H=parseFloat(H.substr(48,6)),g[g.length-1].cryst={a:u,b:z,c:N,alpha:J,beta:I,gamma:H});else{z=new $3Dmol.Matrix4;for(N=1;3>=N;N++)if(H=C[G].replace(/^\s*/,""),parseInt(H.substr(18,1))==N)z.elements[N-1]=parseFloat(H.substr(23,10)),z.elements[N-1+4]=parseFloat(H.substr(33,10)),z.elements[N-1+8]=parseFloat(H.substr(43,10)),z.elements[N-1+12]=parseFloat(H.substr(53)),G++;else for(;"BIOMT"==H.substr(13,5);)G++,H=C[G].replace(/^\s*/,
+"");z.elements[3]=0;z.elements[7]=0;z.elements[11]=0;z.elements[15]=1;g[g.length-1].symmetries.push(z);G--}}(new Date).getTime();for(N=0;N<h.length;N++){d(h[N]);e||B(g[g.length-1].symmetries,q,h[N]);if(m||!E)(new Date).getTime(),y(h[N]);for(G=x;G<h[N].length;G++)if(u=h[N][G],void 0!==u){for(z=0;z<s.length;z++)u.chain!=s[z][0]||u.resi<s[z][1]||u.resi>s[z][3]||(u.ss="s",u.resi==s[z][1]&&(u.ssbegin=!0),u.resi==s[z][3]&&(u.ssend=!0));for(z=0;z<l.length;z++)u.chain!=l[z][0]||u.resi<l[z][1]||u.resi>l[z][3]||
+(u.ss="h",u.resi==l[z][1]?u.ssbegin=!0:u.resi==l[z][3]&&(u.ssend=!0))}}return h};b.pqr=b.PQR=function(b,c){var h=[[]],p,m=!c.noSecondaryStructure,e=[],q=b.split(/\r?\n|\r/),g,x;for(g=0;g<q.length;g++)if(x=q[g].replace(/^\s*/,""),p=x.substr(0,6),0==p.indexOf("END"))if(c.multimodel)c.onemol||h.push([]);else break;else if("ATOM  "==p||"HETATM"==p){var u=parseInt(x.substr(6,5));p=x.substr(12,4).replace(/ /g,"");var s=x.substr(17,3),l=x.substr(21,1),A=parseInt(x.substr(22,4)),B=x.substr(30).trim().split(/\s+/),
+C=parseFloat(B[0]),G=parseFloat(B[1]),z=parseFloat(B[2]),H=parseFloat(B[3]),B=parseFloat(B[4]),L=p[0];1<p.length&&p[1].toUpperCase()!=p[1]&&(L=p.substr(0,2));hetflag="H"==x[0]?!0:!1;e[u]=h[h.length-1].length;h[h.length-1].push({resn:s,x:C,y:G,z:z,elem:L,hetflag:hetflag,chain:l,resi:A,serial:u,atom:p,bonds:[],ss:"c",bondOrder:[],properties:{charge:H,partialCharge:H,radius:B},pdbline:x})}else if("CONECT"==p)for(p=parseInt(x.substr(6,5)),u=h[h.length-1][e[p]],p=0;4>p;p++)s=parseInt(x.substr([11,16,21,
+26][p],5)),l=h[h.length-1][e[s]],void 0!==u&&void 0!==l&&(u.bonds.push(e[s]),u.bondOrder.push(1));for(g=0;g<h.length;g++)d(h[g]),m&&y(h[g]);return h};return b}();$3Dmol=$3Dmol||{};
 $3Dmol.partialCharges={"ALA:N":-.15,"ALA:CA":.1,"ALA:CB":0,"ALA:C":.6,"ALA:O":-.55,"ARG:N":-.15,"ARG:CA":.1,"ARG:CB":0,"ARG:CG":0,"ARG:CD":.1,"ARG:NE":-.1,"ARG:CZ":.5,"ARG:NH1":.25,"ARG:NH2":.25,"ARG:C":.6,"ARG:O":-.55,"ASN:N":-.15,"ASN:CA":.1,"ASN:CB":0,"ASN:CG":.55,"ASN:OD1":-.55,"ASN:ND2":0,"ASN:C":.6,"ASN:O":-.55,"ASP:N":-.15,"ASP:CA":.1,"ASP:CB":0,"ASP:CG":.14,"ASP:OD1":-.57,"ASP:OD2":-.57,"ASP:C":.6,"ASP:O":-.55,"CYS:N":-.15,"CYS:CA":.1,"CYS:CB":.19,"CYS:SG":-.19,"CYS:C":.6,"CYS:O":-.55,"GLN:N":-.15,
 "GLN:CA":.1,"GLN:CB":0,"GLN:CG":0,"GLN:CD":.55,"GLN:OE1":-.55,"GLN:NE2":0,"GLN:C":.6,"GLN:O":-.55,"GLU:N":-.15,"GLU:CA":.1,"GLU:CB":0,"GLU:CG":0,"GLU:CD":.14,"GLU:OE1":-.57,"GLU:OE2":-.57,"GLU:C":.6,"GLU:O":-.55,"GLY:N":-.15,"GLY:CA":.1,"GLY:C":.6,"GLY:O":-.55,"HIS:N":-.15,"HIS:CA":.1,"HIS:CB":0,"HIS:CG":.1,"HIS:ND1":-.1,"HIS:CD2":.1,"HIS:NE2":-.4,"HIS:CE1":.3,"HIS:C":.6,"HIS:O":-.55,"ILE:N":-.15,"ILE:CA":.1,"ILE:CB":0,"ILE:CG2":0,"ILE:CG1":0,"ILE:CD":0,"ILE:C":.6,"ILE:O":-.55,"LEU:N":-.15,"LEU:CA":.1,
 "LEU:CB":0,"LEU:CG":0,"LEU:CD1":0,"LEU:CD2":0,"LEU:C":.6,"LEU:O":-.55,"LYS:N":-.15,"LYS:CA":.1,"LYS:CB":0,"LYS:CG":0,"LYS:CD":0,"LYS:CE":.25,"LYS:NZ":.75,"LYS:C":.6,"LYS:O":-.55,"MET:N":-.15,"MET:CA":.1,"MET:CB":0,"MET:CG":.06,"MET:SD":-.12,"MET:CE":.06,"MET:C":.6,"MET:O":-.55,"PHE:N":-.15,"PHE:CA":.1,"PHE:CB":0,"PHE:CG":0,"PHE:CD1":0,"PHE:CD2":0,"PHE:CE1":0,"PHE:CE2":0,"PHE:CZ":0,"PHE:C":.6,"PHE:O":-.55,"PRO:N":-.25,"PRO:CD":.1,"PRO:CA":.1,"PRO:CB":0,"PRO:CG":0,"PRO:C":.6,"PRO:O":-.55,"SER:N":-.15,
 "SER:CA":.1,"SER:CB":.25,"SER:OG":-.25,"SER:C":.6,"SER:O":-.55,"THR:N":-.15,"THR:CA":.1,"THR:CB":.25,"THR:OG1":-.25,"THR:CG2":0,"THR:C":.6,"THR:O":-.55,"TRP:N":-.15,"TRP:CA":.1,"TRP:CB":0,"TRP:CG":-.03,"TRP:CD2":.1,"TRP:CE2":-.04,"TRP:CE3":-.03,"TRP:CD1":.06,"TRP:NE1":-.06,"TRP:CZ2":0,"TRP:CZ3":0,"TRP:CH2":0,"TRP:C":.6,"TRP:O":-.55,"TYR:N":-.15,"TYR:CA":.1,"TYR:CB":0,"TYR:CG":0,"TYR:CD1":0,"TYR:CE1":0,"TYR:CD2":0,"TYR:CE2":0,"TYR:CZ":.25,"TYR:OH":-.25,"TYR:C":.6,"TYR:O":-.55,"VAL:N":-.15,"VAL:CA":.1,
-"VAL:CB":0,"VAL:CG1":0,"VAL:CG2":0,"VAL:C":.6,"VAL:O":-.55};$3Dmol.applyPartialCharges=function(u,q){q&&"undefined"!==typeof u.partialCharge||u.resn&&u.atom&&(u.properties.partialCharge=$3Dmol.partialCharges[u.resn+":"+u.atom])};(function(){});
+"VAL:CB":0,"VAL:CG1":0,"VAL:CG2":0,"VAL:C":.6,"VAL:O":-.55};$3Dmol.applyPartialCharges=function(b,c){c&&"undefined"!==typeof b.partialCharge||b.resn&&b.atom&&(b.properties.partialCharge=$3Dmol.partialCharges[b.resn+":"+b.atom])};(function(){});$3Dmol.VolumeData=function(b,c){this.unit={x:1,y:1,z:1};this.origin={x:0,y:0,z:0};this.size={x:0,y:0,z:0};this.data=new Float32Array([]);c=c.toLowerCase();if(this[c])this[c](b)};
+$3Dmol.VolumeData.prototype.getVal=function(b,c,d){b-=this.origin.x;c-=this.origin.y;d-=this.origin.z;b/=this.unit.x;c/=this.unit.y;d/=this.unit.z;b=Math.round(b);c=Math.round(c);d=Math.round(d);return 0>b||b>=this.size.x||0>c||c>=this.size.y||0>d||d>=this.size.z?0:this.data[b*this.size.y*this.size.z+c*this.size.z+d]};
+$3Dmol.VolumeData.prototype.cube=function(b){b=b.replace(/^\s+/,"").split(/[\n\r]+/);if(!(6>b.length)){var c=b[2].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),d=parseFloat(c[0]),p=Math.abs(d),y=this.origin=new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3])),c=b[3].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),A=0<c[0]?.529177:1;y.multiplyScalar(A);var y=Math.abs(c[0]),q=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A),c=b[4].replace(/^\s+/,
+"").replace(/\s+/g," ").split(" "),B=Math.abs(c[0]),f=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A),c=b[5].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),w=Math.abs(c[0]),c=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A);this.size={x:y,y:B,z:w};this.unit=new $3Dmol.Vector3(q.x,f.y,c.z);0==q.y&&0==q.z&&0==f.x&&0==f.z&&0==c.x&&0==c.y||console.log("Warning: Cube file is not axis aligned.  This isn't going to look right.");
+c=6;0>d&&c++;b=b.splice(p+c).join(" ");b=b.replace(/^\s+/,"");b=b.split(/[\s\r]+/);this.data=new Float32Array(b)}};
+$3Dmol.VolumeData.prototype.ccp4=function(b){var c,d,p,y,A,q,B,f,w,h,t,m,e,F,g,x=new Int32Array(b,0,56);m=new Float32Array(b,0,56);c=x[0];d=x[1];p=x[2];y=x[4];A=x[5];q=x[6];B=Math.abs(x[7]);f=Math.abs(x[8]);w=Math.abs(x[9]);h=m[10];t=m[11];m=m[12];xVox=h/c;yVox=t/d;zVox=m/p;switch(x[16]){case 1:e=y;g=F=0;break;case 2:F=y;g=e=0;break;case 3:g=y,F=e=0}switch(x[17]){case 1:e=A;g=F=0;break;case 2:F=A;g=e=0;break;case 3:g=A,F=e=0}switch(x[18]){case 1:e=q;g=F=0;break;case 2:F=q;g=e=0;break;case 3:g=q,F=
+e=0}this.origin=new $3Dmol.Vector3(e,F,g);c=x[23];this.size={x:B,y:f,z:w};this.unit=new $3Dmol.Vector3(xVox,yVox,zVox);new Int8Array(b);this.data=new Float32Array(b,1024+c)};
+$3Dmol.workerString=function(){self.onmessage=function(b){b=b.data;var c=b.type;if(0>c)self.atomData=b.atoms,self.volume=b.volume,self.ps=new ProteinSurface;else{var d=self.ps;d.initparm(b.expandedExtent,1==c?!1:!0,self.volume);d.fillvoxels(self.atomData,b.extendedAtoms);d.buildboundary();if(4===c||2===c)d.fastdistancemap(),d.boundingatom(!1),d.fillvoxelswaals(self.atomData,b.extendedAtoms);d.marchingcube(c);b=d.getFacesAndVertices(b.atomsToShow);self.postMessage(b)}}}.toString().replace(/(^.*?\{|\}$)/g,
+"");$3Dmol.workerString+="; var ProteinSurface="+$3Dmol.ProteinSurface.toString().replace(/\$3Dmol.MarchingCube./g,"MarchingCube.");$3Dmol.workerString+=",MarchingCube=("+$3Dmol.MarchingCubeInitializer.toString()+")();";$3Dmol.SurfaceWorker=window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type:"text/javascript"}));$3Dmol.workerString=$3Dmol.workerString;$3Dmol.SurfaceWorker=$3Dmol.SurfaceWorker;
diff --git a/release/3Dmol-nojquery-min.js b/release/3Dmol-nojquery-min.js
index d438763d2..8566c0aab 100644
--- a/release/3Dmol-nojquery-min.js
+++ b/release/3Dmol-nojquery-min.js
@@ -1,164 +1,430 @@
-var $3Dmol=$3Dmol||{};$3Dmol.Math={clamp:function(a,b,c){return Math.min(Math.max(a,b),c)},degToRad:function(){var a=Math.PI/180;return function(b){return b*a}}()};$3Dmol.Quaternion=function(a,b,c,d){this.x=a||0;this.y=b||0;this.z=c||0;this.w=void 0!==d?d:1};
-$3Dmol.Quaternion.prototype={constructor:$3Dmol.Quaternion,set:function(a,b,c,d){this.x=a;this.y=b;this.z=c;this.w=d;return this},copy:function(a){this.x=a.x;this.y=a.y;this.z=a.z;this.w=a.w;return this},conjugate:function(){this.x*=-1;this.y*=-1;this.z*=-1;return this},inverse:function(){return this.conjugate().normalize()},length:function(){return Math.sqrt(this.x*this.x+this.y*this.y+this.z*this.z+this.w*this.w)},normalize:function(){var a=this.length();0===a?(this.z=this.y=this.x=0,this.w=1):
-(a=1/a,this.x*=a,this.y*=a,this.z*=a,this.w*=a);return this},multiply:function(a){return this.multiplyQuaternions(this,a)},multiplyQuaternions:function(a,b){var c=a.x,d=a.y,e=a.z,k=a.w,f=b.x,l=b.y,h=b.z,m=b.w;this.x=c*m+k*f+d*h-e*l;this.y=d*m+k*l+e*f-c*h;this.z=e*m+k*h+c*l-d*f;this.w=k*m-c*f-d*l-e*h}};$3Dmol.Vector2=function(a,b){this.x=a||0;this.y=b||0};
-$3Dmol.Vector2.prototype={constructor:$3Dmol.Vector2,set:function(a,b){this.x=a;this.y=b;return this},subVectors:function(a,b){this.x=a.x-b.x;this.y=a.y-b.y;return this},copy:function(a){this.x=a.x;this.y=a.y;return this},clone:function(){return new $3Dmol.Vector2(this.x,this.y)}};$3Dmol.Vector3=function(a,b,c){this.x=a||0;this.y=b||0;this.z=c||0};
-$3Dmol.Vector3.prototype={constructor:$3Dmol.Vector3,set:function(a,b,c){this.x=a;this.y=b;this.z=c;return this},copy:function(a){this.x=a.x;this.y=a.y;this.z=a.z;return this},add:function(a){this.x+=a.x;this.y+=a.y;this.z+=a.z;return this},addVectors:function(a,b){this.x=a.x+b.x;this.y=a.y+b.y;this.z=a.z+b.z;return this},sub:function(a){this.x-=a.x;this.y-=a.y;this.z-=a.z;return this},subVectors:function(a,b){this.x=a.x-b.x;this.y=a.y-b.y;this.z=a.z-b.z;return this},multiplyScalar:function(a){this.x*=
-a;this.y*=a;this.z*=a;return this},divideScalar:function(a){0!==a?(this.x/=a,this.y/=a,this.z/=a):this.z=this.y=this.x=0;return this},distanceTo:function(a){return Math.sqrt(this.distanceToSquared(a))},distanceToSquared:function(a){var b=this.x-a.x,c=this.y-a.y;a=this.z-a.z;return b*b+c*c+a*a},applyMatrix4:function(a){var b=this.x,c=this.y,d=this.z;a=a.elements;this.x=a[0]*b+a[4]*c+a[8]*d+a[12];this.y=a[1]*b+a[5]*c+a[9]*d+a[13];this.z=a[2]*b+a[6]*c+a[10]*d+a[14];return this},applyProjection:function(a){var b=
-this.x,c=this.y,d=this.z;a=a.elements;var e=a[3]*b+a[7]*c+a[11]*d+a[15];this.x=(a[0]*b+a[4]*c+a[8]*d+a[12])/e;this.y=(a[1]*b+a[5]*c+a[9]*d+a[13])/e;this.z=(a[2]*b+a[6]*c+a[10]*d+a[14])/e;return this},applyQuaternion:function(a){var b=this.x,c=this.y,d=this.z,e=a.x,k=a.y,f=a.z,l,h,m;l=2*(c*f-d*k);h=2*(d*e-b*f);m=2*(b*k-c*e);this.x=b+a.w*l+(h*f-m*k);this.y=c+a.w*h+(m*e-l*f);this.z=d+a.w*m+(l*k-h*e);return this},negate:function(){return this.multiplyScalar(-1)},dot:function(a){return this.x*a.x+this.y*
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-this.y=a.elements[13];this.z=a.elements[14];return this},setEulerFromRotationMatrix:function(a,b){var c=a.elements,d=c[0],e=c[4],k=c[8],f=c[5],l=c[9],h=c[6],c=c[10];void 0===b||"XYZ"===b?(this.y=Math.asin($3Dmol.Math.clamp(k,-1,1)),.99999>Math.abs(k)?(this.x=Math.atan2(-l,c),this.z=Math.atan2(-e,d)):(this.x=Math.atan2(h,f),this.z=0)):console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: "+b);return this},clone:function(){return new $3Dmol.Vector3(this.x,this.y,this.z)}};
-$3Dmol.Matrix3=function(a,b,c,d,e,k,f,l,h){this.elements=new Float32Array(9);this.set(void 0!==a?a:1,b||0,c||0,d||0,void 0!==e?e:1,k||0,f||0,l||0,void 0!==h?h:1)};
-$3Dmol.Matrix3.prototype={constructor:$3Dmol.Matrix3,set:function(a,b,c,d,e,k,f,l,h){var m=this.elements;m[0]=a;m[3]=b;m[6]=c;m[1]=d;m[4]=e;m[7]=k;m[2]=f;m[5]=l;m[8]=h;return this},identity:function(){this.set(1,0,0,0,1,0,0,0,1);return this},copy:function(a){a=a.elements;this.set(a[0],a[3],a[6],a[1],a[4],a[7],a[2],a[5],a[8])},multiplyScalar:function(a){var b=this.elements;b[0]*=a;b[3]*=a;b[6]*=a;b[1]*=a;b[4]*=a;b[7]*=a;b[2]*=a;b[5]*=a;b[8]*=a;return this},getInverse:function(a,b){var c=a.elements,
-d=this.elements;d[0]=c[10]*c[5]-c[6]*c[9];d[1]=-c[10]*c[1]+c[2]*c[9];d[2]=c[6]*c[1]-c[2]*c[5];d[3]=-c[10]*c[4]+c[6]*c[8];d[4]=c[10]*c[0]-c[2]*c[8];d[5]=-c[6]*c[0]+c[2]*c[4];d[6]=c[9]*c[4]-c[5]*c[8];d[7]=-c[9]*c[0]+c[1]*c[8];d[8]=c[5]*c[0]-c[1]*c[4];c=c[0]*d[0]+c[1]*d[3]+c[2]*d[6];if(0===c){if(b)throw Error("Matrix3.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix3.getInverse(): can't invert matrix, determinant is 0");this.identity();return this}this.multiplyScalar(1/c);return this},
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+c)b[m++]=65533,h+=c-1;else{for(t&=2===c?31:3===c?15:7;1<c&&h<s;)t=t<<6|f[h++]&63,c--;1<c?b[m++]=65533:65536>t?b[m++]=t:(t-=65536,b[m++]=55296|t>>10&1023,b[m++]=56320|t&1023)}return F(b,m)};c.utf8border=function(f,h){var g;h=h||f.length;h>f.length&&(h=f.length);for(g=h-1;0<=g&&128===(f[g]&192);)g--;return 0>g||0===g?h:g+y[f[g]]>h?g:h}},{"./common":1}],3:[function(p,u,c){u.exports=function(c,p,f,h){var g=c&65535|0;c=c>>>16&65535|0;for(var m=0;0!==f;){m=2E3<f?2E3:f;f-=m;do g=g+p[h++]|0,c=c+g|0;while(--m);
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+-1;return 0}function h(b){var c;if(!b||!b.state)return-2;c=b.state;c.wsize=0;c.whave=0;c.wnext=0;return f(b)}function g(b,c){var a,f;if(!b||!b.state)return-2;f=b.state;0>c?(a=0,c=-c):(a=(c>>4)+1,48>c&&(c&=15));if(c&&(8>c||15<c))return-2;null!==f.window&&f.wbits!==c&&(f.window=null);f.wrap=a;f.wbits=c;return h(b)}function m(b,c){var a;if(!b)return-2;a=new x;b.state=a;a.window=null;a=g(b,c);0!==a&&(b.state=null);return a}var y=p("../utils/common"),B=p("./adler32"),I=p("./crc32"),E=p("./inffast"),M=
+p("./inftrees"),t=!0,C,s;c.inflateReset=h;c.inflateReset2=g;c.inflateResetKeep=f;c.inflateInit=function(b){return m(b,15)};c.inflateInit2=m;c.inflate=function(b,c){var a,f,h,g,m,k,n,d,e,p,z,l,r,u;l=0;var w,G,x,N,J,H=new y.Buf8(4),R=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];if(!b||!b.state||!b.output||!b.input&&0!==b.avail_in)return-2;a=b.state;12===a.mode&&(a.mode=13);m=b.next_out;h=b.output;n=b.avail_out;g=b.next_in;f=b.input;k=b.avail_in;d=a.hold;e=a.bits;p=k;z=n;J=0;a:for(;;)switch(a.mode){case 1:if(0===
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+d+=f[g++]<<e;e+=8}b.adler=a.check=F(d);e=d=0;a.mode=11;case 11:if(0===a.havedict)return b.next_out=m,b.avail_out=n,b.next_in=g,b.avail_in=k,a.hold=d,a.bits=e,2;b.adler=a.check=1;a.mode=12;case 12:if(5===c||6===c)break a;case 13:if(a.last){d>>>=e&7;e-=e&7;a.mode=27;break}for(;3>e;){if(0===k)break a;k--;d+=f[g++]<<e;e+=8}a.last=d&1;d>>>=1;e-=1;switch(d&3){case 0:a.mode=14;break;case 1:l=a;if(t){r=void 0;C=new y.Buf32(512);s=new y.Buf32(32);for(r=0;144>r;)l.lens[r++]=8;for(;256>r;)l.lens[r++]=9;for(;280>
+r;)l.lens[r++]=7;for(;288>r;)l.lens[r++]=8;M(1,l.lens,0,288,C,0,l.work,{bits:9});for(r=0;32>r;)l.lens[r++]=5;M(2,l.lens,0,32,s,0,l.work,{bits:5});t=!1}l.lencode=C;l.lenbits=9;l.distcode=s;l.distbits=5;a.mode=20;if(6===c){d>>>=2;e-=2;break a}break;case 2:a.mode=17;break;case 3:b.msg="invalid block type",a.mode=30}d>>>=2;e-=2;break;case 14:d>>>=e&7;for(e-=e&7;32>e;){if(0===k)break a;k--;d+=f[g++]<<e;e+=8}if((d&65535)!==(d>>>16^65535)){b.msg="invalid stored block lengths";a.mode=30;break}a.length=d&
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+k--;d+=f[g++]<<e;e+=8}a.lens[R[a.have++]]=d&7;d>>>=3;e-=3}for(;19>a.have;)a.lens[R[a.have++]]=0;a.lencode=a.lendyn;a.lenbits=7;l={bits:a.lenbits};J=M(0,a.lens,0,19,a.lencode,0,a.work,l);a.lenbits=l.bits;if(J){b.msg="invalid code lengths set";a.mode=30;break}a.have=0;a.mode=19;case 19:for(;a.have<a.nlen+a.ndist;){for(;;){l=a.lencode[d&(1<<a.lenbits)-1];w=l>>>24;G=l>>>16&255;x=l&65535;if(w<=e)break;if(0===k)break a;k--;d+=f[g++]<<e;e+=8}if(16>x)d>>>=w,e-=w,a.lens[a.have++]=x;else{if(16===x){for(l=w+
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+if(0===a.lens[256]){b.msg="invalid code -- missing end-of-block";a.mode=30;break}a.lenbits=9;l={bits:a.lenbits};J=M(1,a.lens,0,a.nlen,a.lencode,0,a.work,l);a.lenbits=l.bits;if(J){b.msg="invalid literal/lengths set";a.mode=30;break}a.distbits=6;a.distcode=a.distdyn;l={bits:a.distbits};J=M(2,a.lens,a.nlen,a.ndist,a.distcode,0,a.work,l);a.distbits=l.bits;if(J){b.msg="invalid distances set";a.mode=30;break}a.mode=20;if(6===c)break a;case 20:a.mode=21;case 21:if(6<=k&&258<=n){b.next_out=m;b.avail_out=
+n;b.next_in=g;b.avail_in=k;a.hold=d;a.bits=e;E(b,z);m=b.next_out;h=b.output;n=b.avail_out;g=b.next_in;f=b.input;k=b.avail_in;d=a.hold;e=a.bits;12===a.mode&&(a.back=-1);break}for(a.back=0;;){l=a.lencode[d&(1<<a.lenbits)-1];w=l>>>24;G=l>>>16&255;x=l&65535;if(w<=e)break;if(0===k)break a;k--;d+=f[g++]<<e;e+=8}if(G&&0===(G&240)){r=w;u=G;for(N=x;;){l=a.lencode[N+((d&(1<<r+u)-1)>>r)];w=l>>>24;G=l>>>16&255;x=l&65535;if(r+w<=e)break;if(0===k)break a;k--;d+=f[g++]<<e;e+=8}d>>>=r;e-=r;a.back+=r}d>>>=w;e-=w;
+a.back+=w;a.length=x;if(0===G){a.mode=26;break}if(G&32){a.back=-1;a.mode=12;break}if(G&64){b.msg="invalid literal/length code";a.mode=30;break}a.extra=G&15;a.mode=22;case 22:if(a.extra){for(l=a.extra;e<l;){if(0===k)break a;k--;d+=f[g++]<<e;e+=8}a.length+=d&(1<<a.extra)-1;d>>>=a.extra;e-=a.extra;a.back+=a.extra}a.was=a.length;a.mode=23;case 23:for(;;){l=a.distcode[d&(1<<a.distbits)-1];w=l>>>24;G=l>>>16&255;x=l&65535;if(w<=e)break;if(0===k)break a;k--;d+=f[g++]<<e;e+=8}if(0===(G&240)){r=w;u=G;for(N=
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+n)break a;l=z-n;if(a.offset>l){l=a.offset-l;if(l>a.whave&&a.sane){b.msg="invalid distance too far back";a.mode=30;break}l>a.wnext?(l-=a.wnext,r=a.wsize-l):r=a.wnext-l;l>a.length&&(l=a.length);u=a.window}else u=h,r=m-a.offset,l=a.length;l>n&&(l=n);n-=l;a.length-=l;do h[m++]=u[r++];while(--l);0===a.length&&(a.mode=21);break;case 26:if(0===n)break a;h[m++]=a.length;n--;a.mode=21;break;case 27:if(a.wrap){for(;32>e;){if(0===k)break a;k--;d|=f[g++]<<e;e+=8}z-=n;b.total_out+=z;a.total+=z;z&&(b.adler=a.check=
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+z;a.wrap&&z&&(b.adler=a.check=a.flags?I(a.check,h,z,b.next_out-z):B(a.check,h,z,b.next_out-z));b.data_type=a.bits+(a.last?64:0)+(12===a.mode?128:0)+(20===a.mode||15===a.mode?256:0);(0===p&&0===z||4===c)&&0===J&&(J=-5);return J};c.inflateEnd=function(b){if(!b||!b.state)return-2;var c=b.state;c.window&&(c.window=null);b.state=null;return 0};c.inflateGetHeader=function(b,c){var a;if(!b||!b.state)return-2;a=b.state;if(0===(a.wrap&2))return-2;a.head=c;c.done=!1;return 0};c.inflateInfo="pako inflate (from Nodeca project)"},
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+0;this.output=null;this.total_out=this.avail_out=this.next_out=0;this.msg="";this.state=null;this.data_type=2;this.adler=0}},{}],"/lib/inflate.js":[function(p,u,c){function F(c,f){var g=new E(f);g.push(c,!0);if(g.err)throw g.msg;return g.result}var x=p("./zlib/inflate.js"),f=p("./utils/common"),h=p("./utils/strings"),g=p("./zlib/constants"),m=p("./zlib/messages"),y=p("./zlib/zstream"),B=p("./zlib/gzheader"),I=Object.prototype.toString,E=function(c){var h=this.options=f.assign({chunkSize:16384,windowBits:0,
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+0===p.avail_in&&(u===g.Z_FINISH||u===g.Z_SYNC_FLUSH)))if("string"===this.options.to)a=h.utf8border(p.output,p.next_out),y=p.next_out-a,B=h.buf2string(p.output,a),p.next_out=y,p.avail_out=s-y,y&&f.arraySet(p.output,p.output,a,y,0),this.onData(B);else this.onData(f.shrinkBuf(p.output,p.next_out))}while(0<p.avail_in&&b!==g.Z_STREAM_END);b===g.Z_STREAM_END&&(u=g.Z_FINISH);if(u===g.Z_FINISH)return b=x.inflateEnd(this.strm),this.onEnd(b),this.ended=!0,b===g.Z_OK;u===g.Z_SYNC_FLUSH&&(this.onEnd(g.Z_OK),
+p.avail_out=0);return!0};E.prototype.onData=function(c){this.chunks.push(c)};E.prototype.onEnd=function(c){c===g.Z_OK&&(this.result="string"===this.options.to?this.chunks.join(""):f.flattenChunks(this.chunks));this.chunks=[];this.err=c;this.msg=this.strm.msg};c.Inflate=E;c.inflate=F;c.inflateRaw=function(c,f){f=f||{};f.raw=!0;return F(c,f)};c.ungzip=F},{"./utils/common":1,"./utils/strings":2,"./zlib/constants":4,"./zlib/gzheader":6,"./zlib/inflate.js":8,"./zlib/messages":10,"./zlib/zstream":11}]},
+{},[])("/lib/inflate.js")});
+$3Dmol=function(b){return b.$3Dmol||{}}(window);"https:"!=document.location.protocol&&$.get("http://3dmol.csb.pitt.edu/track/report.cgi");String.prototype.startsWith||(String.prototype.startsWith=function(b){return 0===this.lastIndexOf(b,0)});String.prototype.endsWith||(String.prototype.endsWith=function(b){return-1!==this.indexOf(b,this.length-b.length)});
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+Math.atan2(-B,d),this.z=Math.atan2(-y,p)):(this.x=Math.atan2(f,q),this.z=0)):console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: "+c);return this},rotateAboutVector:function(b,c){b.normalize();var d=Math.cos(c),p=Math.sin(c),y=this.clone().multiplyScalar(d),p=b.clone().cross(this).multiplyScalar(p),d=b.clone().multiplyScalar(b.clone().dot(this)).multiplyScalar(1-d),y=y.add(p).add(d);this.x=y.x;this.y=y.y;this.z=y.z;return this},clone:function(){return new $3Dmol.Vector3(this.x,
+this.y,this.z)}};$3Dmol.Matrix3=function(b,c,d,p,y,A,q,B,f){this.elements=new Float32Array(9);this.set(void 0!==b?b:1,c||0,d||0,p||0,void 0!==y?y:1,A||0,q||0,B||0,void 0!==f?f:1)};
+$3Dmol.Matrix3.prototype={constructor:$3Dmol.Matrix3,set:function(b,c,d,p,y,A,q,B,f){var w=this.elements;w[0]=b;w[3]=c;w[6]=d;w[1]=p;w[4]=y;w[7]=A;w[2]=q;w[5]=B;w[8]=f;return this},identity:function(){this.set(1,0,0,0,1,0,0,0,1);return this},copy:function(b){b=b.elements;this.set(b[0],b[3],b[6],b[1],b[4],b[7],b[2],b[5],b[8])},multiplyScalar:function(b){var c=this.elements;c[0]*=b;c[3]*=b;c[6]*=b;c[1]*=b;c[4]*=b;c[7]*=b;c[2]*=b;c[5]*=b;c[8]*=b;return this},getInverse:function(b,c){var d=b.elements,
+p=this.elements;p[0]=d[10]*d[5]-d[6]*d[9];p[1]=-d[10]*d[1]+d[2]*d[9];p[2]=d[6]*d[1]-d[2]*d[5];p[3]=-d[10]*d[4]+d[6]*d[8];p[4]=d[10]*d[0]-d[2]*d[8];p[5]=-d[6]*d[0]+d[2]*d[4];p[6]=d[9]*d[4]-d[5]*d[8];p[7]=-d[9]*d[0]+d[1]*d[8];p[8]=d[5]*d[0]-d[1]*d[4];d=d[0]*p[0]+d[1]*p[3]+d[2]*p[6];if(0===d){if(c)throw Error("Matrix3.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix3.getInverse(): can't invert matrix, determinant is 0");this.identity();return this}this.multiplyScalar(1/d);return this},
+getDeterminant:function(){var b=this.elements;return b[0]*b[4]*b[8]+b[1]*b[5]*b[6]+b[2]*b[3]*b[7]-b[2]*b[4]*b[6]-b[1]*b[3]*b[8]-b[0]*b[5]*b[7]},transpose:function(){var b,c=this.elements;b=c[1];c[1]=c[3];c[3]=b;b=c[2];c[2]=c[6];c[6]=b;b=c[5];c[5]=c[7];c[7]=b;return this},clone:function(){var b=this.elements;return new $3Dmol.Matrix3(b[0],b[3],b[6],b[1],b[4],b[7],b[2],b[5],b[8])}};
+$3Dmol.Matrix4=function(b,c,d,p,y,A,q,B,f,w,h,t,m,e,F,g){var x=this.elements=new Float32Array(16);x[0]=void 0!==b?b:1;x[4]=c||0;x[8]=d||0;x[12]=p||0;x[1]=y||0;x[5]=void 0!==A?A:1;x[9]=q||0;x[13]=B||0;x[2]=f||0;x[6]=w||0;x[10]=void 0!==h?h:1;x[14]=t||0;x[3]=m||0;x[7]=e||0;x[11]=F||0;x[15]=void 0!==g?g:1};
+$3Dmol.Matrix4.prototype={constructor:$3Dmol.Matrix4,set:function(b,c,d,p,y,A,q,B,f,w,h,t,m,e,F,g){var x=this.elements;x[0]=b;x[4]=c;x[8]=d;x[12]=p;x[1]=y;x[5]=A;x[9]=q;x[13]=B;x[2]=f;x[6]=w;x[10]=h;x[14]=t;x[3]=m;x[7]=e;x[11]=F;x[15]=g;return this},identity:function(){this.set(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1);return this},copy:function(b){b=b.elements;this.set(b[0],b[4],b[8],b[12],b[1],b[5],b[9],b[13],b[2],b[6],b[10],b[14],b[3],b[7],b[11],b[15]);return this},matrix3FromTopLeft:function(){var b=this.elements;
+return new $3Dmol.Matrix3(b[0],b[4],b[8],b[1],b[5],b[9],b[2],b[6],b[10])},setRotationFromEuler:function(b,c){var d=this.elements,p=b.x,y=b.y,A=b.z,q=Math.cos(p),p=Math.sin(p),B=Math.cos(y),y=Math.sin(y),f=Math.cos(A),A=Math.sin(A);if(void 0===c||"XYZ"===c){var w=q*f,h=q*A,t=p*f,m=p*A;d[0]=B*f;d[4]=-B*A;d[8]=y;d[1]=h+t*y;d[5]=w-m*y;d[9]=-p*B;d[2]=m-w*y;d[6]=t+h*y;d[10]=q*B}else console.error("Error with matrix4 setRotationFromEuler. Order: "+c);return this},setRotationFromQuaternion:function(b){var c=
+this.elements,d=b.x,p=b.y,y=b.z,A=b.w,q=d+d,B=p+p,f=y+y;b=d*q;var w=d*B,d=d*f,h=p*B,p=p*f,y=y*f,q=A*q,B=A*B,A=A*f;c[0]=1-(h+y);c[4]=w-A;c[8]=d+B;c[1]=w+A;c[5]=1-(b+y);c[9]=p-q;c[2]=d-B;c[6]=p+q;c[10]=1-(b+h);return this},lookAt:function(){var b=new $3Dmol.Vector3,c=new $3Dmol.Vector3,d=new $3Dmol.Vector3;return function(p,y,A){var q=this.elements;d.subVectors(p,y).normalize();0===d.length()&&(d.z=1);b.crossVectors(A,d).normalize();0===b.length()&&(d.x+=1E-4,b.crossVectors(A,d).normalize());c.crossVectors(d,
+b);q[0]=b.x;q[4]=c.x;q[8]=d.x;q[1]=b.y;q[5]=c.y;q[9]=d.y;q[2]=b.z;q[6]=c.z;q[10]=d.z;return this}}(),multiplyMatrices:function(b,c){var d=b.elements,p=c.elements,y=this.elements,A=d[0],q=d[4],B=d[8],f=d[12],w=d[1],h=d[5],t=d[9],m=d[13],e=d[2],F=d[6],g=d[10],x=d[14],u=d[3],s=d[7],l=d[11],d=d[15],E=p[0],M=p[4],C=p[8],G=p[12],z=p[1],H=p[5],L=p[9],N=p[13],J=p[2],I=p[6],K=p[10],O=p[14],Q=p[3],W=p[7],P=p[11],p=p[15];y[0]=A*E+q*z+B*J+f*Q;y[4]=A*M+q*H+B*I+f*W;y[8]=A*C+q*L+B*K+f*P;y[12]=A*G+q*N+B*O+f*p;y[1]=
+w*E+h*z+t*J+m*Q;y[5]=w*M+h*H+t*I+m*W;y[9]=w*C+h*L+t*K+m*P;y[13]=w*G+h*N+t*O+m*p;y[2]=e*E+F*z+g*J+x*Q;y[6]=e*M+F*H+g*I+x*W;y[10]=e*C+F*L+g*K+x*P;y[14]=e*G+F*N+g*O+x*p;y[3]=u*E+s*z+l*J+d*Q;y[7]=u*M+s*H+l*I+d*W;y[11]=u*C+s*L+l*K+d*P;y[15]=u*G+s*N+l*O+d*p;return this},multiplyScalar:function(b){var c=this.elements;c[0]*=b;c[4]*=b;c[8]*=b;c[12]*=b;c[1]*=b;c[5]*=b;c[9]*=b;c[13]*=b;c[2]*=b;c[6]*=b;c[10]*=b;c[14]*=b;c[3]*=b;c[7]*=b;c[11]*=b;c[15]*=b;return this},transpose:function(){var b=this.elements,c;
+c=b[1];b[1]=b[4];b[4]=c;c=b[2];b[2]=b[8];b[8]=c;c=b[6];b[6]=b[9];b[9]=c;c=b[3];b[3]=b[12];b[12]=c;c=b[7];b[7]=b[13];b[13]=c;c=b[11];b[11]=b[14];b[14]=c;return this},getPosition:function(){var b=new $3Dmol.Vector3;return function(){console.warn("DEPRECATED: Matrix4's .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.");var c=this.elements;return b.set(c[12],c[13],c[14])}}(),setPosition:function(b){var c=this.elements;c[12]=b.x;c[13]=b.y;c[14]=b.z;return this},getInverse:function(b,
+c){var d=this.elements,p=b.elements,y=p[0],A=p[4],q=p[8],B=p[12],f=p[1],w=p[5],h=p[9],t=p[13],m=p[2],e=p[6],F=p[10],g=p[14],x=p[3],u=p[7],s=p[11],l=p[15];d[0]=h*g*u-t*F*u+t*e*s-w*g*s-h*e*l+w*F*l;d[4]=B*F*u-q*g*u-B*e*s+A*g*s+q*e*l-A*F*l;d[8]=q*t*u-B*h*u+B*w*s-A*t*s-q*w*l+A*h*l;d[12]=B*h*e-q*t*e-B*w*F+A*t*F+q*w*g-A*h*g;d[1]=t*F*x-h*g*x-t*m*s+f*g*s+h*m*l-f*F*l;d[5]=q*g*x-B*F*x+B*m*s-y*g*s-q*m*l+y*F*l;d[9]=B*h*x-q*t*x-B*f*s+y*t*s+q*f*l-y*h*l;d[13]=q*t*m-B*h*m+B*f*F-y*t*F-q*f*g+y*h*g;d[2]=w*g*x-t*e*x+
+t*m*u-f*g*u-w*m*l+f*e*l;d[6]=B*e*x-A*g*x-B*m*u+y*g*u+A*m*l-y*e*l;d[10]=A*t*x-B*w*x+B*f*u-y*t*u-A*f*l+y*w*l;d[14]=B*w*m-A*t*m-B*f*e+y*t*e+A*f*g-y*w*g;d[3]=h*e*x-w*F*x-h*m*u+f*F*u+w*m*s-f*e*s;d[7]=A*F*x-q*e*x+q*m*u-y*F*u-A*m*s+y*e*s;d[11]=q*w*x-A*h*x-q*f*u+y*h*u+A*f*s-y*w*s;d[15]=A*h*m-q*w*m+q*f*e-y*h*e-A*f*F+y*w*F;d=p[0]*d[0]+p[1]*d[4]+p[2]*d[8]+p[3]*d[12];if(0===d){if(c)throw Error("Matrix4.getInverse(): can't invert matrix, determinant is 0");console.warn("Matrix4.getInverse(): can't invert matrix, determinant is 0");
+this.identity();return this}this.multiplyScalar(1/d);return this},isReflected:function(){return 0>this.matrix3FromTopLeft().getDeterminant()},compose:function(){var b=new $3Dmol.Matrix4,c=new $3Dmol.Matrix4;return function(d,p,y){var A=this.elements;b.identity();b.setRotationFromQuaternion(p);c.makeScale(y.x,y.y,y.z);this.multiplyMatrices(b,c);A[12]=d.x;A[13]=d.y;A[14]=d.z;return this}}(),decompose:function(){var b=new $3Dmol.Vector3,c=new $3Dmol.Vector3,d=new $3Dmol.Vector3,p=new $3Dmol.Matrix4;
+return function(y,A,q){var B=this.elements;b.set(B[0],B[1],B[2]);c.set(B[4],B[5],B[6]);d.set(B[8],B[9],B[10]);y=y instanceof $3Dmol.Vector3?y:new $3Dmol.Vector3;A=A instanceof $3Dmol.Quaternion?A:new $3Dmol.Quaternion;q=q instanceof $3Dmol.Vector3?q:new $3Dmol.Vector3;q.x=b.length();q.y=c.length();q.z=d.length();y.x=B[12];y.y=B[13];y.z=B[14];p.copy(this);p.elements[0]/=q.x;p.elements[1]/=q.x;p.elements[2]/=q.x;p.elements[4]/=q.y;p.elements[5]/=q.y;p.elements[6]/=q.y;p.elements[8]/=q.z;p.elements[9]/=
+q.z;p.elements[10]/=q.z;A.setFromRotationMatrix(p);return[y,A,q]}}(),scale:function(b){var c=this.elements,d=b.x,p=b.y;b=b.z;c[0]*=d;c[4]*=p;c[8]*=b;c[1]*=d;c[5]*=p;c[9]*=b;c[2]*=d;c[6]*=p;c[10]*=b;c[3]*=d;c[7]*=p;c[11]*=b;return this},getMaxScaleOnAxis:function(){var b=this.elements;return Math.sqrt(Math.max(b[0]*b[0]+b[1]*b[1]+b[2]*b[2],Math.max(b[4]*b[4]+b[5]*b[5]+b[6]*b[6],b[8]*b[8]+b[9]*b[9]+b[10]*b[10])))},makeFrustum:function(b,c,d,p,y,A){var q=this.elements;q[0]=2*y/(c-b);q[4]=0;q[8]=(c+b)/
+(c-b);q[12]=0;q[1]=0;q[5]=2*y/(p-d);q[9]=(p+d)/(p-d);q[13]=0;q[2]=0;q[6]=0;q[10]=-(A+y)/(A-y);q[14]=-2*A*y/(A-y);q[3]=0;q[7]=0;q[11]=-1;q[15]=0;return this},makePerspective:function(b,c,d,p){b=d*Math.tan($3Dmol.Math.degToRad(.5*b));var y=-b;return this.makeFrustum(y*c,b*c,y,b,d,p)},isEqual:function(b){b=b.elements;var c=this.elements;return c[0]==b[0]&&c[4]==b[4]&&c[8]==b[8]&&c[12]==b[12]&&c[1]==b[1]&&c[5]==b[5]&&c[9]==b[9]&&c[13]==b[13]&&c[2]==b[2]&&c[6]==b[6]&&c[10]==b[10]&&c[14]==b[14]&&c[3]==
+b[3]&&c[7]==b[7]&&c[11]==b[11]&&c[15]==b[15]?!0:!1},clone:function(){var b=this.elements;return new $3Dmol.Matrix4(b[0],b[4],b[8],b[12],b[1],b[5],b[9],b[13],b[2],b[6],b[10],b[14],b[3],b[7],b[11],b[15])},isIdentity:function(){var b=this.elements;return 1==b[0]&&0==b[4]&&0==b[8]&&0==b[12]&&0==b[1]&&1==b[5]&&0==b[9]&&0==b[13]&&0==b[2]&&0==b[6]&&1==b[10]&&0==b[14]&&0==b[3]&&0==b[7]&&0==b[11]&&1==b[15]?!0:!1}};
+$3Dmol.Ray=function(b,c){this.origin=void 0!==b?b:new $3Dmol.Vector3;this.direction=void 0!==c?c:new $3Dmol.Vector3};
+$3Dmol.Ray.prototype={constructor:$3Dmol.Ray,set:function(b,c){this.origin.copy(b);this.direction.copy(c);return this},copy:function(b){this.origin.copy(b.origin);this.direction.copy(b.direction);return this},at:function(b,c){return(c||new $3Dmol.Vector3).copy(this.direction).multiplyScalar(b).add(this.origin)},recast:function(){var b=new $3Dmol.Vector3;return function(c){this.origin.copy(this.at(c,b));return this}}(),closestPointToPoint:function(b,c){var d=c||new $3Dmol.Vector3;d.subVectors(b,this.origin);
+var p=d.dot(this.direction);return d.copy(this.direction).multiplyScalar(p).add(this.origin)},distanceToPoint:function(b){var c=new $3Dmol.Vector3;return function(b){var p=c.subVectors(b,this.origin).dot(this.direction);c.copy(this.direction).multiplyScalar(p).add(this.origin);return c.distanceTo(b)}}(),isIntersectionCylinder:function(){},isIntersectionSphere:function(b){return this.distanceToPoint(b.center)<=b.radius},isIntersectionPlane:function(b){return 0!==b.normal.dot(this.direction)||0===b.distanceToPoint(this.origin)?
+!0:!1},distanceToPlane:function(b){var c=b.normal.dot(this.direction);if(0===c){if(0===b.distanceToPoint(this.origin))return 0}else return-(this.origin.dot(b.normal)+b.constant)/c},intersectPlane:function(b,c){var d=this.distanceToPlane(b);return void 0===d?void 0:this.at(d,c)},applyMatrix4:function(b){this.direction.add(this.origin).applyMatrix4(b);this.origin.applyMatrix4(b);this.direction.sub(this.origin);return this},equals:function(b){return b.origin.equals(this.origin)&&b.direction.equals(this.direction)},
+clone:function(){return(new $3Dmol.Ray).copy(this)}};$3Dmol.Sphere=function(b,c){this.center=void 0!==b?b:new $3Dmol.Vector3;this.radius=void 0!==c?c:0};
+$3Dmol.Sphere.prototype={constructor:$3Dmol.Sphere,set:function(b,c){this.center.copy(b);this.radius=c;return this},copy:function(b){this.center.copy(b.center);this.radius=b.radius;return this},applyMatrix4:function(b){this.center.applyMatrix4(b);this.radius*=b.getMaxScaleOnAxis();return this},translate:function(b){this.center.add(b);return this},equals:function(b){return b.center.equals(this.center)&&b.radius===this.radius},clone:function(){return(new $3Dmol.Sphere).copy(this)}};
+$3Dmol.Cylinder=function(b,c,d){this.c1=void 0!==b?b:new $3Dmol.Vector3;this.c2=void 0!==c?c:new $3Dmol.Vector3;this.direction=(new $3Dmol.Vector3).subVectors(this.c2,this.c1).normalize();this.radius=void 0!==d?d:0};
+$3Dmol.Cylinder.prototype={constructor:$3Dmol.Cylinder,copy:function(b){this.c1.copy(b.c1);this.c2.copy(b.c2);this.direction.copy(b.direction);this.radius=b.radius;return this},lengthSq:function(){var b=new $3Dmol.Vector3;return function(){return b.subVectors(this.c2,this.c1).lengthSq()}}(),applyMatrix4:function(b){this.direction.add(this.c1).applyMatrix4(b);this.c1.applyMatrix4(b);this.c2.applyMatrix4(b);this.direction.sub(this.c1).normalize();this.radius*=b.getMaxScaleOnAxis();return this}};
+$3Dmol.Triangle=function(b,c,d){this.a=void 0!==b?b:new $3Dmol.Vector3;this.b=void 0!==c?c:new $3Dmol.Vector3;this.c=void 0!==d?d:new $3Dmol.Vector3};
+$3Dmol.Triangle.prototype={constructor:$3Dmol.Triangle,copy:function(b){this.a.copy(b.a);this.b.copy(b.b);this.c.copy(b.c);return this},applyMatrix4:function(b){this.a.applyMatrix4(b);this.b.applyMatrix4(b);this.c.applyMatrix4(b);return this},getNormal:function(){var b=new $3Dmol.Vector3;return function(){var c=this.a.clone();c.sub(this.b);b.subVectors(this.c,this.b);c.cross(b);c.normalize();return c}}()};
+$3Dmol.EventDispatcher=function(){var b={};this.addEventListener=function(c,d){void 0===b[c]&&(b[c]=[]);-1===b[c].indexOf(d)&&b[c].push(d)};this.removeEventListener=function(c,d){var p=b[c].indexOf(d);-1!==p&&b[c].splice(p,1)};this.dispatchEvent=function(c){var d=b[c.type];if(void 0!==d){c.target=this;for(var p=0,y=d.length;p<y;p++)d[p].call(this,c)}}};$3Dmol.Color=function(b){return 1<arguments.length?(this.r=arguments[0]||0,this.g=arguments[1]||0,this.b=arguments[2]||0,this):this.set(b)};
+$3Dmol.Color.prototype={constructor:$3Dmol.Color,r:0,g:0,b:0,set:function(b){if(b instanceof $3Dmol.Color)return b.clone();"number"===typeof b?this.setHex(b):"object"===typeof b&&"r"in b&&"g"in b&&"b"in b&&(this.r=b.r,this.g=b.g,this.b=b.b)},setHex:function(b){b=Math.floor(b);this.r=(b>>16&255)/255;this.g=(b>>8&255)/255;this.b=(b&255)/255;return this},getHex:function(){var b=Math.round(255*this.r),c=Math.round(255*this.g),d=Math.round(255*this.b);return b<<16|c<<8|d},clone:function(){return new $3Dmol.Color(this.r,
+this.g,this.b)},copy:function(b){this.r=b.r;this.g=b.g;this.b=b.b;return this},scaled:function(){var b={};b.r=Math.round(255*this.r);b.g=Math.round(255*this.g);b.b=Math.round(255*this.b);b.a=1;return b}};
 $3Dmol.Object3D=function(){this.id=$3Dmol.Object3DIDCount++;this.name="";this.parent=void 0;this.children=[];this.position=new $3Dmol.Vector3;this.rotation=new $3Dmol.Vector3;this.matrix=new $3Dmol.Matrix4;this.matrixWorld=new $3Dmol.Matrix4;this.quaternion=new $3Dmol.Quaternion;this.eulerOrder="XYZ";this.up=new $3Dmol.Vector3(0,1,0);this.scale=new $3Dmol.Vector3(1,1,1);this.rotationAutoUpdate=this.matrixWorldNeedsUpdate=this.matrixAutoUpdate=!0;this.useQuaternion=!1;this.visible=!0};
-$3Dmol.Object3D.prototype={constructor:$3Dmol.Object3D,lookAt:function(a){this.matrix.lookAt(a,this.position,this.up);this.rotationAutoUpdate&&(!0===this.useQuaternion?this.quaternion.copy(this.matrix.decompose()[1]):this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder))},add:function(a){if(a===this)console.error("Can't add $3Dmol.Object3D to itself");else{a.parent=this;this.children.push(a);for(var b=this;void 0!==b.parent;)b=b.parent;void 0!==b&&b instanceof $3Dmol.Scene&&b.__addObject(a)}},
-remove:function(a){var b=this.children.indexOf(a);if(-1!==b){a.parent=void 0;this.children.splice(b,1);for(b=this;void 0!==b.parent;)b=b.parent;void 0!==b&&b instanceof $3Dmol.Scene&&b.__removeObject(a)}},updateMatrix:function(){this.matrix.setPosition(this.position);!1===this.useQuaternion?this.matrix.setRotationFromEuler(this.rotation,this.eulerOrder):this.matrix.setRotationFromQuaternion(this.quaternion);1===this.scale.x&&1===this.scale.y&&1===this.scale.z||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=
-!0},updateMatrixWorld:function(a){!0===this.matrixAutoUpdate&&this.updateMatrix();if(!0===this.matrixWorldNeedsUpdate||!0===a)void 0===this.parent?this.matrixWorld.copy(this.matrix):this.matrixWorld.multiplyMatrices(this.parent.matrixWorld,this.matrix);this.matrixWorldNeedsUpdate=!1;for(a=0;a<this.children.length;a++)this.children[a].updateMatrixWorld(!0)},clone:function(a){void 0===a&&(a=new $3Dmol.Object3D);a.name=this.name;a.up.copy(this.up);a.position.copy(this.position);a.rotation.copy(this.rotation);
-a.eulerOrder=this.eulerOrder;a.scale.copy(this.scale);a.rotationAutoUpdate=this.rotationAutoUpdate;a.matrix.copy(this.matrix);a.matrixWorld.copy(this.matrixWorld);a.quaternion.copy(this.quaternion);a.matrixAutoUpdate=this.matrixAutoUpdate;a.matrixWorldNeedsUpdate=this.matrixWorldNeedsUpdate;a.useQuaternion=this.useQuaternion;a.visible=this.visible;for(var b=0;b<this.children.length;b++)a.add(this.children[b].clone());return a}};$3Dmol.Object3DIDCount=0;
-$3Dmol.Geometry=function(){var a=function(a){this.id=a||0;this.lineArray=this.faceArray=this.normalArray=this.colorArray=this.vertexArray=null;this.lineidx=this.faceidx=this.vertices=0};a.prototype.getNumVertices=function(){return this.vertices};a.prototype.getVertices=function(){return this.vertexArray};a.prototype.getCentroid=function(){for(var a=new $3Dmol.Vector3,b,c,f,l=0;l<this.vertices;++l)b=3*l,c=this.vertexArray[b],f=this.vertexArray[b+1],b=this.vertexArray[b+2],a.x+=c,a.y+=f,a.z+=b;a.divideScalar(this.vertices);
-return a};a.prototype.setNormals=function(){var a=this.faceArray,b=this.vertexArray,c=this.normalArray;if(this.vertices&&this.faceidx)for(var f,l,h,m,q,z,w=0;w<a.length/3;++w)f=3*a[3*w],l=3*a[3*w+1],h=3*a[3*w+2],m=new $3Dmol.Vector3(b[f],b[f+1],b[f+2]),q=new $3Dmol.Vector3(b[l],b[l+1],b[l+2]),z=new $3Dmol.Vector3(b[h],b[h+1],b[h+2]),m.subVectors(m,q),z.subVectors(z,q),z.cross(m),m=z,m.normalize(),c[f]+=m.x,c[l]+=m.x,c[h]+=m.x,c[f+1]+=m.y,c[l+1]+=m.y,c[h+1]+=m.y,c[f+2]+=m.z,c[l+2]+=m.z,c[h+2]+=m.z};
-a.prototype.setLineIndices=function(){if(this.faceidx){var a=this.faceArray,b=this.lineArray=new Uint16Array(2*this.faceidx);this.lineidx=2*this.faceidx;for(var c,f=0;f<this.faceidx/3;++f){c=3*f;lineoffset=2*c;var l=a[c],h=a[c+1];c=a[c+2];b[lineoffset]=l;b[lineoffset+1]=h;b[lineoffset+2]=l;b[lineoffset+3]=c;b[lineoffset+4]=h;b[lineoffset+5]=c}}};a.prototype.truncateArrayBuffers=function(a,b){a=!0===a?!0:!1;var c=this.colorArray,f=this.normalArray,l=this.faceArray,h=this.lineArray;this.vertexArray=
-this.vertexArray.subarray(0,3*this.vertices);this.colorArray=c.subarray(0,3*this.vertices);a?(this.normalArray=f.subarray(0,3*this.vertices),this.faceArray=l.subarray(0,this.faceidx),this.lineArray=0<this.lineidx?h.subarray(0,this.lineidx):new Uint16Array):(this.normalArray=new Float32Array,this.faceArray=new Uint16Array,this.lineArray=new Uint16Array);b&&(this.normalArray&&(this.normalArray=new Float32Array(this.normalArray)),this.faceArray&&(this.faceArray=new Uint16Array(this.faceArray)),this.lineArray&&
-(this.lineArray=new Uint16Array(this.lineArray)),this.vertexArray&&(this.vertexArray=new Float32Array(this.vertexArray)),this.colorArray&&(this.colorArray=new Float32Array(this.colorArray)));this.__inittedArrays=!0};var b=function(b){var c=new a(b.geometryGroups.length);b.geometryGroups.push(c);b.groups=b.geometryGroups.length;c.vertexArray=new Float32Array(196605);c.colorArray=new Float32Array(196605);b.mesh&&(c.normalArray=new Float32Array(196605),c.faceArray=new Uint16Array(393210),c.lineArray=
-new Uint16Array(393210));return c},c=function(a){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.GeometryIDCount++;this.name="";this.hasTangents=!1;this.dynamic=!0;this.mesh=!0===a?!0:!1;this.buffersNeedUpdate=this.colorsNeedUpdate=this.normalsNeedUpdate=this.elementsNeedUpdate=this.verticesNeedUpdate=!1;this.geometryGroups=[];this.groups=0};c.prototype={constructor:c,updateGeoGroup:function(a){var c=0<this.groups?this.geometryGroups[this.groups-1]:null;if(!c||65535<c.vertices+(a||0))c=b(this);return c},
-addGeoGroup:function(){return b(this)},setUpNormals:function(a){a=a||!1;for(var b=0;b<this.groups;b++)this.geometryGroups[b].setNormals(a)},setUpWireframe:function(){for(var a=0;a<this.groups;a++)this.geometryGroups[a].setLineIndices()},initTypedArrays:function(){for(var a=0;a<this.groups;a++){var b=this.geometryGroups[a];!0!==b.__inittedArrays&&b.truncateArrayBuffers(this.mesh,!1)}},dispose:function(){this.dispatchEvent({type:"dispose"})}};return c}();
-Object.defineProperty($3Dmol.Geometry.prototype,"vertices",{get:function(){for(var a=0,b=0;b<this.groups;b++)a+=this.geometryGroups[b].vertices;return a}});$3Dmol.GeometryIDCount=0;
-$3Dmol.Raycaster=function(){var a=function(a,b,c,d){this.ray=new $3Dmol.Ray(a,b);0<this.ray.direction.lengthSq()&&this.ray.direction.normalize();this.near=d||0;this.far=c||Infinity},b=new $3Dmol.Sphere,c=new $3Dmol.Cylinder,d=new $3Dmol.Triangle,e=new $3Dmol.Vector3,k=new $3Dmol.Vector3,f=new $3Dmol.Vector3,l=new $3Dmol.Vector3;new $3Dmol.Ray;new $3Dmol.Vector3;var h=new $3Dmol.Vector3;new $3Dmol.Matrix4;var m=function(a,b){return a.distance-b.distance},q=function(a){return Math.min(Math.max(a,-1),
-1)};a.prototype.precision=1E-4;a.prototype.linePrecision=.2;a.prototype.set=function(a,b){this.ray.set(a,b)};a.prototype.intersectObjects=function(a,w){for(var v=[],x=0,r=w.length;x<r;x++)a:{var n=a,t=w[x],u=v;h.getPositionFromMatrix(n.matrixWorld);if(!0===t.clickable&&void 0!==t.intersectionShape){var y=t.intersectionShape,F=this.linePrecision,F=F*n.matrixWorld.getMaxScaleOnAxis(),F=F*F;if(void 0!==t.boundingSphere&&t.boundingSphere instanceof $3Dmol.Sphere&&(b.copy(t.boundingSphere),b.applyMatrix4(n.matrixWorld),
-!this.ray.isIntersectionSphere(b)))break a;for(var B=void 0,C=void 0,s=void 0,p=void 0,A=s=void 0,E=void 0,H=void 0,G=void 0,D=void 0,I=D=A=p=void 0,B=0,C=y.triangle.length;B<C;B++)y.triangle[B]instanceof $3Dmol.Triangle&&(d.copy(y.triangle[B]),d.applyMatrix4(n.matrixWorld),s=d.getNormal(),p=this.ray.direction.dot(s),0<=p||(e.subVectors(d.a,this.ray.origin),E=s.dot(e)/p,0>E||(k.copy(this.ray.direction).multiplyScalar(E).add(this.ray.origin),k.sub(d.a),f.copy(d.b).sub(d.a),l.copy(d.c).sub(d.a),p=f.dot(l),
-s=f.lengthSq(),A=l.lengthSq(),A=(s*k.dot(l)-p*k.dot(f))/(s*A-p*p),0>A||1<A||(p=(k.dot(f)-A*p)/s,0>p||1<p||1<p+A||u.push({clickable:t,distance:E})))));B=0;for(C=y.cylinder.length;B<C;B++)y.cylinder[B]instanceof $3Dmol.Cylinder&&(c.copy(y.cylinder[B]),c.applyMatrix4(n.matrixWorld),e.subVectors(c.c1,this.ray.origin),s=e.dot(c.direction),A=e.dot(this.ray.direction),p=q(this.ray.direction.dot(c.direction)),G=1-p*p,0!==G&&(D=(p*A-s)/G,I=(A-p*s)/G,k.copy(c.direction).multiplyScalar(D).add(c.c1),f.copy(this.ray.direction).multiplyScalar(I).add(this.ray.origin),
-H=l.subVectors(k,f).lengthSq(),D=c.radius*c.radius,H<=D&&(D=(p*s-A)*(p*s-A)-G*(e.lengthSq()-s*s-D),A=0>=D?E=Math.sqrt(H):E=(A-p*s-Math.sqrt(D))/G,p=p*A-s,0>p||p*p>c.lengthSq()||0>A||u.push({clickable:t,distance:E}))));B=0;for(C=y.line.length;B<C;B+=2)k.copy(y.line[B]),k.applyMatrix4(n.matrixWorld),f.copy(y.line[B+1]),f.applyMatrix4(n.matrixWorld),l.subVectors(f,k),E=l.lengthSq(),l.normalize(),e.subVectors(k,this.ray.origin),lineProj=e.dot(l),A=e.dot(this.ray.direction),p=q(this.ray.direction.dot(l)),
-G=1-p*p,0!==G&&(D=(p*A-lineProj)/G,I=(A-p*lineProj)/G,k.add(l.multiplyScalar(D)),f.copy(this.ray.direction).multiplyScalar(I).add(this.ray.origin),H=l.subVectors(f,k).lengthSq(),H<F&&D*D<E&&u.push({clickable:t,distance:I}));B=0;for(C=y.sphere.length;B<C;B++)if(y.sphere[B]instanceof $3Dmol.Sphere&&(b.copy(y.sphere[B]),b.applyMatrix4(n.matrixWorld),this.ray.isIntersectionSphere(b))){k.subVectors(b.center,this.ray.origin);n=k.dot(this.ray.direction);D=n*n-(k.lengthSq()-b.radius*b.radius);if(0>n)break a;
-E=0>=D?n:n-Math.sqrt(D);u.push({clickable:t,distance:E});break a}}}v.sort(m);return v};return a}();$3Dmol.Projector=function(){new $3Dmol.Matrix4;var a=new $3Dmol.Matrix4;this.projectVector=function(b,c){c.matrixWorldInverse.getInverse(c.matrixWorld);a.multiplyMatrices(c.projectionMatrix,c.matrixWorldInverse);return b.applyProjection(a)};this.unprojectVector=function(b,c){c.projectionMatrixInverse.getInverse(c.projectionMatrix);a.multiplyMatrices(c.matrixWorld,c.projectionMatrixInverse);return b.applyProjection(a)}};
-$3Dmol.Camera=function(a,b,c,d){$3Dmol.Object3D.call(this);this.fov=void 0!==a?a:50;this.aspect=void 0!==b?b:1;this.near=void 0!==c?c:.1;this.far=void 0!==d?d:2E3;this.projectionMatrix=new $3Dmol.Matrix4;this.projectionMatrixInverse=new $3Dmol.Matrix4;this.matrixWorldInverse=new $3Dmol.Matrix4;this.updateProjectionMatrix()};$3Dmol.Camera.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Camera.prototype.lookAt=function(a){this.matrix.lookAt(this.position,a,this.up);this.rotationAutoUpdate&&(!1===this.useQuaternion?this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder):this.quaternion.copy(this.matrix.decompose()[1]))};$3Dmol.Camera.prototype.updateProjectionMatrix=function(){this.projectionMatrix.makePerspective(this.fov,this.aspect,this.near,this.far)};
-$3Dmol.SpritePlugin=function(){function a(a,b){return a.z!==b.z?b.z-a.z:b.id-a.id}var b,c,d,e,k,f,l,h,m,q;this.init=function(a){b=a.context;c=a;d=a.getPrecision();e=new Float32Array(16);k=new Uint16Array(6);a=0;e[a++]=-1;e[a++]=-1;e[a++]=0;e[a++]=0;e[a++]=1;e[a++]=-1;e[a++]=1;e[a++]=0;e[a++]=1;e[a++]=1;e[a++]=1;e[a++]=1;e[a++]=-1;e[a++]=1;e[a++]=0;e[a++]=1;a=0;k[a++]=0;k[a++]=1;k[a++]=2;k[a++]=0;k[a++]=2;k[a++]=3;f=b.createBuffer();l=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,f);b.bufferData(b.ARRAY_BUFFER,
-e,b.STATIC_DRAW);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,l);b.bufferData(b.ELEMENT_ARRAY_BUFFER,k,b.STATIC_DRAW);a=$3Dmol.ShaderLib.sprite;var w=d,v=b.createProgram(),x=b.createShader(b.FRAGMENT_SHADER),r=b.createShader(b.VERTEX_SHADER),w="precision "+w+" float;\n";b.shaderSource(x,w+a.fragmentShader);b.shaderSource(r,w+a.vertexShader);b.compileShader(x);b.compileShader(r);b.getShaderParameter(x,b.COMPILE_STATUS)&&b.getShaderParameter(r,b.COMPILE_STATUS)?(b.attachShader(v,x),b.attachShader(v,r),b.linkProgram(v),
-b.getProgramParameter(v,b.LINK_STATUS)||console.error("Could not initialize shader"),a=v):(console.error(b.getShaderInfoLog(x)),console.error("could not initialize shader"),a=null);h=a;m={};q={};m.position=b.getAttribLocation(h,"position");m.uv=b.getAttribLocation(h,"uv");q.uvOffset=b.getUniformLocation(h,"uvOffset");q.uvScale=b.getUniformLocation(h,"uvScale");q.rotation=b.getUniformLocation(h,"rotation");q.scale=b.getUniformLocation(h,"scale");q.alignment=b.getUniformLocation(h,"alignment");q.color=
-b.getUniformLocation(h,"color");q.map=b.getUniformLocation(h,"map");q.opacity=b.getUniformLocation(h,"opacity");q.useScreenCoordinates=b.getUniformLocation(h,"useScreenCoordinates");q.screenPosition=b.getUniformLocation(h,"screenPosition");q.modelViewMatrix=b.getUniformLocation(h,"modelViewMatrix");q.projectionMatrix=b.getUniformLocation(h,"projectionMatrix");q.fogType=b.getUniformLocation(h,"fogType");q.fogDensity=b.getUniformLocation(h,"fogDensity");q.fogNear=b.getUniformLocation(h,"fogNear");q.fogFar=
-b.getUniformLocation(h,"fogFar");q.fogColor=b.getUniformLocation(h,"fogColor");q.alphaTest=b.getUniformLocation(h,"alphaTest")};this.render=function(d,e,k,x){var r=d.__webglSprites,n=r.length;if(n){var t=m,u=q,y=.5*k,F=.5*x;b.useProgram(h);b.enableVertexAttribArray(t.position);b.enableVertexAttribArray(t.uv);b.disable(b.CULL_FACE);b.enable(b.BLEND);b.bindBuffer(b.ARRAY_BUFFER,f);b.vertexAttribPointer(t.position,2,b.FLOAT,!1,16,0);b.vertexAttribPointer(t.uv,2,b.FLOAT,!1,16,8);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,
-l);b.uniformMatrix4fv(u.projectionMatrix,!1,e.projectionMatrix.elements);b.activeTexture(b.TEXTURE0);b.uniform1i(u.map,0);var B=t=0;(t=d.fog)?(b.uniform3f(u.fogColor,t.color.r,t.color.g,t.color.b),b.uniform1f(u.fogNear,t.near),b.uniform1f(u.fogFar,t.far),b.uniform1i(u.fogType,1),B=t=1):(b.uniform1i(u.fogType,0),B=t=0);var C,s,p,A=[];for(C=0;C<n;C++)s=r[C],p=s.material,s.visible&&0!==p.opacity&&(p.useScreenCoordinates?s.z=-s.position.z:(s._modelViewMatrix.multiplyMatrices(e.matrixWorldInverse,s.matrixWorld),
-s.z=-s._modelViewMatrix.elements[14]));r.sort(a);for(C=0;C<n;C++)s=r[C],p=s.material,s.visible&&0!==p.opacity&&p.map&&p.map.image&&p.map.image.width&&(b.uniform1f(u.alphaTest,p.alphaTest),e=p.map.image.height,A[0]=p.map.image.width*c.devicePixelRatio/k,A[1]=e*c.devicePixelRatio/x,!0===p.useScreenCoordinates?(b.uniform1i(u.useScreenCoordinates,1),b.uniform3f(u.screenPosition,(s.position.x*c.devicePixelRatio-y)/y,(F-s.position.y*c.devicePixelRatio)/F,Math.max(0,Math.min(1,s.position.z)))):(b.uniform1i(u.useScreenCoordinates,
-0),b.uniformMatrix4fv(u.modelViewMatrix,!1,s._modelViewMatrix.elements)),e=d.fog&&p.fog?B:0,t!==e&&(b.uniform1i(u.fogType,e),t=e),e=1/(p.scaleByViewport?x:1),A[0]=A[0]*e*s.scale.x,A[1]=A[1]*e*s.scale.y,b.uniform2f(u.uvScale,p.uvScale.x,p.uvScale.y),b.uniform2f(u.uvOffset,p.uvOffset.x,p.uvOffset.y),b.uniform2f(u.alignment,p.alignment.x,p.alignment.y),b.uniform1f(u.opacity,p.opacity),b.uniform3f(u.color,p.color.r,p.color.g,p.color.b),b.uniform1f(u.rotation,s.rotation),b.uniform2fv(u.scale,A),c.setDepthTest(p.depthTest),
-c.setDepthWrite(p.depthWrite),c.setTexture(p.map,0),b.drawElements(b.TRIANGLES,6,b.UNSIGNED_SHORT,0));b.enable(b.CULL_FACE)}}};$3Dmol.Light=function(a,b){$3Dmol.Object3D.call(this);this.color=new $3Dmol.Color(a);this.position=new $3Dmol.Vector3(0,1,0);this.target=new $3Dmol.Object3D;this.intensity=void 0!==b?b:1;this.onlyShadow=this.castShadow=!1};$3Dmol.Light.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Material=function(){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.MaterialIdCount++;this.name="";this.side=$3Dmol.FrontSide;this.opacity=1;this.transparent=!1;this.depthWrite=this.depthTest=!0;this.polygonOffset=!1;this.alphaTest=this.polygonOffsetUnits=this.polygonOffsetFactor=0;this.needsUpdate=this.visible=!0};
-$3Dmol.Material.prototype.setValues=function(a){if(void 0!==a)for(var b in a){var c=a[b];if(void 0===c)console.warn("$3Dmol.Material: '"+b+"' parameter is undefined.");else if(b in this){var d=this[b];d instanceof $3Dmol.Color&&c instanceof $3Dmol.Color?d.copy(c):d instanceof $3Dmol.Color?d.set(c):d instanceof $3Dmol.Vector3&&c instanceof $3Dmol.Vector3?d.copy(c):this[b]=c}}};
-$3Dmol.Material.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Material);a.name=this.name;a.side=this.side;a.opacity=this.opacity;a.transparent=this.transparent;a.depthTest=this.depthTest;a.depthWrite=this.depthWrite;a.polygonOffset=this.polygonOffset;a.polygonOffsetFactor=this.polygonOffsetFactor;a.polygonOffsetUnits=this.polygonOffsetUnits;a.alphaTest=this.alphaTest;a.overdraw=this.overdraw;a.visible=this.visible;return a};$3Dmol.Material.prototype.dispose=function(){this.dispatchEvent({type:"dispose"})};
-$3Dmol.MaterialIdCount=0;$3Dmol.LineBasicMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.linewidth=1;this.linejoin=this.linecap="round";this.vertexColors=!1;this.fog=!0;this.shaderID="basic";this.setValues(a)};$3Dmol.LineBasicMaterial.prototype=Object.create($3Dmol.Material.prototype);$3Dmol.LineBasicMaterial.prototype.clone=function(){var a=new $3Dmol.LineBasicMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy();return a};
-$3Dmol.MeshLambertMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="lambert";
-this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(a)};$3Dmol.MeshLambertMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.MeshLambertMaterial.prototype.clone=function(a){"undefined"===typeof a&&(a=new $3Dmol.MeshLambertMaterial);$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.ambient.copy(this.ambient);a.emissive.copy(this.emissive);a.wrapAround=this.wrapAround;a.wrapRGB.copy(this.wrapRGB);a.map=this.map;a.lightMap=this.lightMap;a.specularMap=this.specularMap;a.envMap=this.envMap;a.combine=this.combine;a.reflectivity=this.reflectivity;a.refractionRatio=this.refractionRatio;a.fog=this.fog;
-a.shading=this.shading;a.shaderID=this.shaderID;a.vertexColors=this.vertexColors;a.skinning=this.skinning;a.morphTargets=this.morphTargets;a.morphNormals=this.morphNormals;return a};$3Dmol.MeshDoubleLambertMaterial=function(a){$3Dmol.MeshLambertMaterial.call(this,a);this.shaderID="lambertdouble";this.side=$3Dmol.DoubleSide};$3Dmol.MeshDoubleLambertMaterial.prototype=Object.create($3Dmol.MeshLambertMaterial.prototype);
-$3Dmol.MeshDoubleLambertMaterial.prototype.clone=function(){var a=new $3Dmol.MeshDoubleLambertMaterial;$3Dmol.MeshLambertMaterial.prototype.clone.call(this,a);return a};
-$3Dmol.ImposterMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="sphereimposter";
-this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(a)};$3Dmol.ImposterMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.ImposterMaterial.prototype.clone=function(){var a=new $3Dmol.ImposterMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.ambient.copy(this.ambient);a.emissive.copy(this.emissive);a.wrapAround=this.wrapAround;a.wrapRGB.copy(this.wrapRGB);a.map=this.map;a.lightMap=this.lightMap;a.specularMap=this.specularMap;a.envMap=this.envMap;a.combine=this.combine;a.reflectivity=this.reflectivity;a.refractionRatio=this.refractionRatio;a.fog=this.fog;a.shading=this.shading;a.shaderID=
-this.shaderID;a.vertexColors=this.vertexColors;a.skinning=this.skinning;a.morphTargets=this.morphTargets;a.morphNormals=this.morphNormals;return a};
-$3Dmol.SpriteMaterial=function(a){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.map=new $3Dmol.Texture;this.useScreenCoordinates=!0;this.depthTest=!this.useScreenCoordinates;this.sizeAttenuation=!this.useScreenCoordinates;this.scaleByViewPort=!this.sizeAttenuation;this.alignment=$3Dmol.SpriteAlignment.center.clone();this.fog=!1;this.uvOffset=new $3Dmol.Vector2(0,0);this.uvScale=new $3Dmol.Vector2(1,1);this.setValues(a);a=a||{};void 0===a.depthTest&&(this.depthTest=!this.useScreenCoordinates);
-void 0===a.sizeAttenuation&&(this.sizeAttenuation=!this.useScreenCoordinates);void 0===a.scaleByViewPort&&(this.scaleByViewPort=!this.sizeAttenuation)};$3Dmol.SpriteMaterial.prototype=Object.create($3Dmol.Material.prototype);
-$3Dmol.SpriteMaterial.prototype.clone=function(){var a=new $3Dmol.SpriteMaterial;$3Dmol.Material.prototype.clone.call(this,a);a.color.copy(this.color);a.map=this.map;a.useScreenCoordinates=useScreenCoordinates;a.sizeAttenuation=this.sizeAttenuation;a.scaleByViewport=this.scaleByViewPort;a.alignment.copy(this.alignment);a.uvOffset.copy(this.uvOffset);return a};$3Dmol.SpriteAlignment={};$3Dmol.SpriteAlignment.topLeft=new $3Dmol.Vector2(1,-1);$3Dmol.SpriteAlignment.topCenter=new $3Dmol.Vector2(0,-1);
+$3Dmol.Object3D.prototype={constructor:$3Dmol.Object3D,lookAt:function(b){this.matrix.lookAt(b,this.position,this.up);this.rotationAutoUpdate&&(!0===this.useQuaternion?this.quaternion.copy(this.matrix.decompose()[1]):this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder))},add:function(b){if(b===this)console.error("Can't add $3Dmol.Object3D to itself");else{b.parent=this;this.children.push(b);for(var c=this;void 0!==c.parent;)c=c.parent;void 0!==c&&c instanceof $3Dmol.Scene&&c.__addObject(b)}},
+remove:function(b){var c=this.children.indexOf(b);if(-1!==c){b.parent=void 0;this.children.splice(c,1);for(c=this;void 0!==c.parent;)c=c.parent;void 0!==c&&c instanceof $3Dmol.Scene&&c.__removeObject(b)}},updateMatrix:function(){this.matrix.setPosition(this.position);!1===this.useQuaternion?this.matrix.setRotationFromEuler(this.rotation,this.eulerOrder):this.matrix.setRotationFromQuaternion(this.quaternion);1===this.scale.x&&1===this.scale.y&&1===this.scale.z||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=
+!0},updateMatrixWorld:function(b){!0===this.matrixAutoUpdate&&this.updateMatrix();if(!0===this.matrixWorldNeedsUpdate||!0===b)void 0===this.parent?this.matrixWorld.copy(this.matrix):this.matrixWorld.multiplyMatrices(this.parent.matrixWorld,this.matrix);this.matrixWorldNeedsUpdate=!1;for(b=0;b<this.children.length;b++)this.children[b].updateMatrixWorld(!0)},clone:function(b){void 0===b&&(b=new $3Dmol.Object3D);b.name=this.name;b.up.copy(this.up);b.position.copy(this.position);b.rotation.copy(this.rotation);
+b.eulerOrder=this.eulerOrder;b.scale.copy(this.scale);b.rotationAutoUpdate=this.rotationAutoUpdate;b.matrix.copy(this.matrix);b.matrixWorld.copy(this.matrixWorld);b.quaternion.copy(this.quaternion);b.matrixAutoUpdate=this.matrixAutoUpdate;b.matrixWorldNeedsUpdate=this.matrixWorldNeedsUpdate;b.useQuaternion=this.useQuaternion;b.visible=this.visible;for(var c=0;c<this.children.length;c++)b.add(this.children[c].clone());return b},setVisible:function(b){this.visible=b;for(var c=0;c<this.children.length;c++)this.children[c].setVisible(b)}};
+$3Dmol.Object3DIDCount=0;
+$3Dmol.Geometry=function(){var b=function(b){this.id=b||0;this.lineArray=this.radiusArray=this.faceArray=this.normalArray=this.colorArray=this.vertexArray=null;this.lineidx=this.faceidx=this.vertices=0};b.prototype.getNumVertices=function(){return this.vertices};b.prototype.getVertices=function(){return this.vertexArray};b.prototype.getCentroid=function(){for(var b=new $3Dmol.Vector3,c,d,q,B=0;B<this.vertices;++B)c=3*B,d=this.vertexArray[c],q=this.vertexArray[c+1],c=this.vertexArray[c+2],b.x+=d,b.y+=
+q,b.z+=c;b.divideScalar(this.vertices);return b};b.prototype.setNormals=function(){var b=this.faceArray,c=this.vertexArray,d=this.normalArray;if(this.vertices&&this.faceidx)for(var q,B,f,w,h,t,m=0;m<b.length/3;++m)q=3*b[3*m],B=3*b[3*m+1],f=3*b[3*m+2],w=new $3Dmol.Vector3(c[q],c[q+1],c[q+2]),h=new $3Dmol.Vector3(c[B],c[B+1],c[B+2]),t=new $3Dmol.Vector3(c[f],c[f+1],c[f+2]),w.subVectors(w,h),t.subVectors(t,h),t.cross(w),w=t,w.normalize(),d[q]+=w.x,d[B]+=w.x,d[f]+=w.x,d[q+1]+=w.y,d[B+1]+=w.y,d[f+1]+=
+w.y,d[q+2]+=w.z,d[B+2]+=w.z,d[f+2]+=w.z};b.prototype.setLineIndices=function(){if(this.faceidx){var b=this.faceArray,c=this.lineArray=new Uint16Array(2*this.faceidx);this.lineidx=2*this.faceidx;for(var d,q=0;q<this.faceidx/3;++q){d=3*q;lineoffset=2*d;var B=b[d],f=b[d+1];d=b[d+2];c[lineoffset]=B;c[lineoffset+1]=f;c[lineoffset+2]=B;c[lineoffset+3]=d;c[lineoffset+4]=f;c[lineoffset+5]=d}}};b.prototype.truncateArrayBuffers=function(b,c){b=!0===b?!0:!1;var d=this.colorArray,q=this.normalArray,B=this.faceArray,
+f=this.lineArray,w=this.radiusArray;this.vertexArray=this.vertexArray.subarray(0,3*this.vertices);this.colorArray=d.subarray(0,3*this.vertices);b?(this.normalArray=q.subarray(0,3*this.vertices),this.faceArray=B.subarray(0,this.faceidx),this.lineArray=0<this.lineidx?f.subarray(0,this.lineidx):new Uint16Array):(this.normalArray=new Float32Array,this.faceArray=new Uint16Array,this.lineArray=new Uint16Array);w&&(this.radiusArray=w.subarray(0,this.vertices));c&&(this.normalArray&&(this.normalArray=new Float32Array(this.normalArray)),
+this.faceArray&&(this.faceArray=new Uint16Array(this.faceArray)),this.lineArray&&(this.lineArray=new Uint16Array(this.lineArray)),this.vertexArray&&(this.vertexArray=new Float32Array(this.vertexArray)),this.colorArray&&(this.colorArray=new Float32Array(this.colorArray)),this.radiusArray&&(this.radiusArray=new Float32Array(this.radiusArray)));this.__inittedArrays=!0};var c=function(c){var d=new b(c.geometryGroups.length);c.geometryGroups.push(d);c.groups=c.geometryGroups.length;d.vertexArray=new Float32Array(196605);
+d.colorArray=new Float32Array(196605);c.mesh&&(d.normalArray=new Float32Array(196605),d.faceArray=new Uint16Array(393210),d.lineArray=new Uint16Array(393210));c.radii&&(d.radiusArray=new Float32Array(65535));d.useOffset=c.offset;return d},d=function(b,c,d){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.GeometryIDCount++;this.name="";this.hasTangents=!1;this.dynamic=!0;this.mesh=!0===b?!0:!1;this.radii=c||!1;this.offset=d||!1;this.buffersNeedUpdate=this.colorsNeedUpdate=this.normalsNeedUpdate=this.elementsNeedUpdate=
+this.verticesNeedUpdate=!1;this.geometryGroups=[];this.groups=0};d.prototype={constructor:d,updateGeoGroup:function(b){var d=0<this.groups?this.geometryGroups[this.groups-1]:null;if(!d||d.vertices+(b||0)>d.vertexArray.length/3)d=c(this);return d},addGeoGroup:function(){return c(this)},setUpNormals:function(b){b=b||!1;for(var c=0;c<this.groups;c++)this.geometryGroups[c].setNormals(b)},setUpWireframe:function(){for(var b=0;b<this.groups;b++)this.geometryGroups[b].setLineIndices()},initTypedArrays:function(){for(var b=
+0;b<this.groups;b++){var c=this.geometryGroups[b];!0!==c.__inittedArrays&&c.truncateArrayBuffers(this.mesh,!1)}},dispose:function(){this.dispatchEvent({type:"dispose"})}};return d}();Object.defineProperty($3Dmol.Geometry.prototype,"vertices",{get:function(){for(var b=0,c=0;c<this.groups;c++)b+=this.geometryGroups[c].vertices;return b}});$3Dmol.GeometryIDCount=0;
+$3Dmol.Raycaster=function(){var b=function(b,c,h,f){this.ray=new $3Dmol.Ray(b,c);0<this.ray.direction.lengthSq()&&this.ray.direction.normalize();this.near=f||0;this.far=h||Infinity},c=new $3Dmol.Sphere,d=new $3Dmol.Cylinder,p=new $3Dmol.Triangle,y=new $3Dmol.Vector3,A=new $3Dmol.Vector3,q=new $3Dmol.Vector3,B=new $3Dmol.Vector3;new $3Dmol.Ray;new $3Dmol.Vector3;var f=new $3Dmol.Vector3;new $3Dmol.Matrix4;var w=function(b,c){return b.distance-c.distance},h=function(b){return Math.min(Math.max(b,-1),
+1)};b.prototype.precision=1E-4;b.prototype.linePrecision=.2;b.prototype.set=function(b,c){this.ray.set(b,c)};b.prototype.intersectObjects=function(b,m){for(var e=[],F=0,g=m.length;F<g;F++)a:{var x=b,u=m[F],s=e;f.getPositionFromMatrix(x.matrixWorld);if(!0===u.clickable&&void 0!==u.intersectionShape){var l=u.intersectionShape,E=this.linePrecision,E=E*x.matrixWorld.getMaxScaleOnAxis(),E=E*E;if(void 0!==u.boundingSphere&&u.boundingSphere instanceof $3Dmol.Sphere&&(c.copy(u.boundingSphere),c.applyMatrix4(x.matrixWorld),
+!this.ray.isIntersectionSphere(c)))break a;for(var M=void 0,C=void 0,G=void 0,z=void 0,H=G=void 0,L=void 0,N=void 0,J=void 0,I=void 0,K=I=H=z=void 0,M=0,C=l.triangle.length;M<C;M++)l.triangle[M]instanceof $3Dmol.Triangle&&(p.copy(l.triangle[M]),p.applyMatrix4(x.matrixWorld),G=p.getNormal(),z=this.ray.direction.dot(G),0<=z||(y.subVectors(p.a,this.ray.origin),L=G.dot(y)/z,0>L||(A.copy(this.ray.direction).multiplyScalar(L).add(this.ray.origin),A.sub(p.a),q.copy(p.b).sub(p.a),B.copy(p.c).sub(p.a),z=q.dot(B),
+G=q.lengthSq(),H=B.lengthSq(),H=(G*A.dot(B)-z*A.dot(q))/(G*H-z*z),0>H||1<H||(z=(A.dot(q)-H*z)/G,0>z||1<z||1<z+H||s.push({clickable:u,distance:L})))));M=0;for(C=l.cylinder.length;M<C;M++)l.cylinder[M]instanceof $3Dmol.Cylinder&&(d.copy(l.cylinder[M]),d.applyMatrix4(x.matrixWorld),y.subVectors(d.c1,this.ray.origin),G=y.dot(d.direction),H=y.dot(this.ray.direction),z=h(this.ray.direction.dot(d.direction)),J=1-z*z,0!==J&&(I=(z*H-G)/J,K=(H-z*G)/J,A.copy(d.direction).multiplyScalar(I).add(d.c1),q.copy(this.ray.direction).multiplyScalar(K).add(this.ray.origin),
+N=B.subVectors(A,q).lengthSq(),I=d.radius*d.radius,N<=I&&(I=(z*G-H)*(z*G-H)-J*(y.lengthSq()-G*G-I),H=0>=I?L=Math.sqrt(N):L=(H-z*G-Math.sqrt(I))/J,z=z*H-G,0>z||z*z>d.lengthSq()||0>H||s.push({clickable:u,distance:L}))));M=0;for(C=l.line.length;M<C;M+=2)A.copy(l.line[M]),A.applyMatrix4(x.matrixWorld),q.copy(l.line[M+1]),q.applyMatrix4(x.matrixWorld),B.subVectors(q,A),L=B.lengthSq(),B.normalize(),y.subVectors(A,this.ray.origin),lineProj=y.dot(B),H=y.dot(this.ray.direction),z=h(this.ray.direction.dot(B)),
+J=1-z*z,0!==J&&(I=(z*H-lineProj)/J,K=(H-z*lineProj)/J,A.add(B.multiplyScalar(I)),q.copy(this.ray.direction).multiplyScalar(K).add(this.ray.origin),N=B.subVectors(q,A).lengthSq(),N<E&&I*I<L&&s.push({clickable:u,distance:K}));M=0;for(C=l.sphere.length;M<C;M++)if(l.sphere[M]instanceof $3Dmol.Sphere&&(c.copy(l.sphere[M]),c.applyMatrix4(x.matrixWorld),this.ray.isIntersectionSphere(c))){A.subVectors(c.center,this.ray.origin);x=A.dot(this.ray.direction);I=x*x-(A.lengthSq()-c.radius*c.radius);if(0>x)break a;
+L=0>=I?x:x-Math.sqrt(I);s.push({clickable:u,distance:L});break a}}}e.sort(w);return e};return b}();$3Dmol.Projector=function(){new $3Dmol.Matrix4;var b=new $3Dmol.Matrix4;this.projectVector=function(c,d){d.matrixWorldInverse.getInverse(d.matrixWorld);b.multiplyMatrices(d.projectionMatrix,d.matrixWorldInverse);return c.applyProjection(b)};this.unprojectVector=function(c,d){d.projectionMatrixInverse.getInverse(d.projectionMatrix);b.multiplyMatrices(d.matrixWorld,d.projectionMatrixInverse);return c.applyProjection(b)}};
+$3Dmol.Camera=function(b,c,d,p){$3Dmol.Object3D.call(this);this.fov=void 0!==b?b:50;this.aspect=void 0!==c?c:1;this.near=void 0!==d?d:.1;this.far=void 0!==p?p:2E3;this.projectionMatrix=new $3Dmol.Matrix4;this.projectionMatrixInverse=new $3Dmol.Matrix4;this.matrixWorldInverse=new $3Dmol.Matrix4;this.updateProjectionMatrix()};$3Dmol.Camera.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Camera.prototype.lookAt=function(b){this.matrix.lookAt(this.position,b,this.up);this.rotationAutoUpdate&&(!1===this.useQuaternion?this.rotation.setEulerFromRotationMatrix(this.matrix,this.eulerOrder):this.quaternion.copy(this.matrix.decompose()[1]))};$3Dmol.Camera.prototype.updateProjectionMatrix=function(){this.projectionMatrix.makePerspective(this.fov,this.aspect,this.near,this.far);this.projectionMatrixInverse.getInverse(this.projectionMatrix)};
+$3Dmol.SpritePlugin=function(){function b(b,c){return b.z!==c.z?c.z-b.z:c.id-b.id}var c,d,p,y,A,q,B,f,w,h;this.init=function(b){c=b.context;d=b;p=b.getPrecision();y=new Float32Array(16);A=new Uint16Array(6);b=0;y[b++]=-1;y[b++]=-1;y[b++]=0;y[b++]=0;y[b++]=1;y[b++]=-1;y[b++]=1;y[b++]=0;y[b++]=1;y[b++]=1;y[b++]=1;y[b++]=1;y[b++]=-1;y[b++]=1;y[b++]=0;y[b++]=1;b=0;A[b++]=0;A[b++]=1;A[b++]=2;A[b++]=0;A[b++]=2;A[b++]=3;q=c.createBuffer();B=c.createBuffer();c.bindBuffer(c.ARRAY_BUFFER,q);c.bufferData(c.ARRAY_BUFFER,
+y,c.STATIC_DRAW);c.bindBuffer(c.ELEMENT_ARRAY_BUFFER,B);c.bufferData(c.ELEMENT_ARRAY_BUFFER,A,c.STATIC_DRAW);b=$3Dmol.ShaderLib.sprite;var m=p,e=c.createProgram(),F=c.createShader(c.FRAGMENT_SHADER),g=c.createShader(c.VERTEX_SHADER),m="precision "+m+" float;\n";c.shaderSource(F,m+b.fragmentShader);c.shaderSource(g,m+b.vertexShader);c.compileShader(F);c.compileShader(g);c.getShaderParameter(F,c.COMPILE_STATUS)&&c.getShaderParameter(g,c.COMPILE_STATUS)?(c.attachShader(e,F),c.attachShader(e,g),c.linkProgram(e),
+c.getProgramParameter(e,c.LINK_STATUS)||console.error("Could not initialize shader"),b=e):(console.error(c.getShaderInfoLog(F)),console.error("could not initialize shader"),b=null);f=b;w={};h={};w.position=c.getAttribLocation(f,"position");w.uv=c.getAttribLocation(f,"uv");h.uvOffset=c.getUniformLocation(f,"uvOffset");h.uvScale=c.getUniformLocation(f,"uvScale");h.rotation=c.getUniformLocation(f,"rotation");h.scale=c.getUniformLocation(f,"scale");h.alignment=c.getUniformLocation(f,"alignment");h.color=
+c.getUniformLocation(f,"color");h.map=c.getUniformLocation(f,"map");h.opacity=c.getUniformLocation(f,"opacity");h.useScreenCoordinates=c.getUniformLocation(f,"useScreenCoordinates");h.screenPosition=c.getUniformLocation(f,"screenPosition");h.modelViewMatrix=c.getUniformLocation(f,"modelViewMatrix");h.projectionMatrix=c.getUniformLocation(f,"projectionMatrix");h.fogType=c.getUniformLocation(f,"fogType");h.fogDensity=c.getUniformLocation(f,"fogDensity");h.fogNear=c.getUniformLocation(f,"fogNear");h.fogFar=
+c.getUniformLocation(f,"fogFar");h.fogColor=c.getUniformLocation(f,"fogColor");h.alphaTest=c.getUniformLocation(f,"alphaTest")};this.render=function(t,m,e,F){var g=t.__webglSprites,x=g.length;if(x){var u=w,s=h,l=.5*e,E=.5*F;c.useProgram(f);c.enableVertexAttribArray(u.position);c.enableVertexAttribArray(u.uv);c.disable(c.CULL_FACE);c.enable(c.BLEND);c.bindBuffer(c.ARRAY_BUFFER,q);c.vertexAttribPointer(u.position,2,c.FLOAT,!1,16,0);c.vertexAttribPointer(u.uv,2,c.FLOAT,!1,16,8);c.bindBuffer(c.ELEMENT_ARRAY_BUFFER,
+B);c.uniformMatrix4fv(s.projectionMatrix,!1,m.projectionMatrix.elements);c.activeTexture(c.TEXTURE0);c.uniform1i(s.map,0);var p=u=0;(u=t.fog)?(c.uniform3f(s.fogColor,u.color.r,u.color.g,u.color.b),c.uniform1f(s.fogNear,u.near),c.uniform1f(s.fogFar,u.far),c.uniform1i(s.fogType,1),p=u=1):(c.uniform1i(s.fogType,0),p=u=0);var C,y,z,H=[];for(C=0;C<x;C++)y=g[C],z=y.material,y.visible&&0!==z.opacity&&(z.useScreenCoordinates?y.z=-y.position.z:(y._modelViewMatrix.multiplyMatrices(m.matrixWorldInverse,y.matrixWorld),
+y.z=-y._modelViewMatrix.elements[14]));g.sort(b);for(C=0;C<x;C++)y=g[C],z=y.material,y.visible&&0!==z.opacity&&z.map&&z.map.image&&z.map.image.width&&(c.uniform1f(s.alphaTest,z.alphaTest),m=z.map.image.height,H[0]=z.map.image.width*d.devicePixelRatio/e,H[1]=m*d.devicePixelRatio/F,!0===z.useScreenCoordinates?(c.uniform1i(s.useScreenCoordinates,1),c.uniform3f(s.screenPosition,(y.position.x*d.devicePixelRatio-l)/l,(E-y.position.y*d.devicePixelRatio)/E,Math.max(0,Math.min(1,y.position.z)))):(c.uniform1i(s.useScreenCoordinates,
+0),c.uniformMatrix4fv(s.modelViewMatrix,!1,y._modelViewMatrix.elements)),m=t.fog&&z.fog?p:0,u!==m&&(c.uniform1i(s.fogType,m),u=m),m=1/(z.scaleByViewport?F:1),H[0]=H[0]*m*y.scale.x,H[1]=H[1]*m*y.scale.y,c.uniform2f(s.uvScale,z.uvScale.x,z.uvScale.y),c.uniform2f(s.uvOffset,z.uvOffset.x,z.uvOffset.y),c.uniform2f(s.alignment,z.alignment.x,z.alignment.y),c.uniform1f(s.opacity,z.opacity),c.uniform3f(s.color,z.color.r,z.color.g,z.color.b),c.uniform1f(s.rotation,y.rotation),c.uniform2fv(s.scale,H),d.setDepthTest(z.depthTest),
+d.setDepthWrite(z.depthWrite),d.setTexture(z.map,0),c.drawElements(c.TRIANGLES,6,c.UNSIGNED_SHORT,0));c.enable(c.CULL_FACE)}}};$3Dmol.Light=function(b,c){$3Dmol.Object3D.call(this);this.color=new $3Dmol.Color(b);this.position=new $3Dmol.Vector3(0,1,0);this.target=new $3Dmol.Object3D;this.intensity=void 0!==c?c:1;this.onlyShadow=this.castShadow=!1};$3Dmol.Light.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Material=function(){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.MaterialIdCount++;this.name="";this.side=$3Dmol.FrontSide;this.opacity=1;this.transparent=!1;this.stencilTest=this.depthWrite=this.depthTest=!0;this.polygonOffset=!1;this.alphaTest=this.polygonOffsetUnits=this.polygonOffsetFactor=0;this.needsUpdate=this.visible=!0};
+$3Dmol.Material.prototype.setValues=function(b){if(void 0!==b)for(var c in b){var d=b[c];if(void 0===d)console.warn("$3Dmol.Material: '"+c+"' parameter is undefined.");else if(c in this){var p=this[c];p instanceof $3Dmol.Color&&d instanceof $3Dmol.Color?p.copy(d):p instanceof $3Dmol.Color?p.set(d):p instanceof $3Dmol.Vector3&&d instanceof $3Dmol.Vector3?p.copy(d):this[c]=d}}};
+$3Dmol.Material.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Material);b.name=this.name;b.side=this.side;b.opacity=this.opacity;b.transparent=this.transparent;b.depthTest=this.depthTest;b.depthWrite=this.depthWrite;b.stencilTest=this.stencilTest;b.polygonOffset=this.polygonOffset;b.polygonOffsetFactor=this.polygonOffsetFactor;b.polygonOffsetUnits=this.polygonOffsetUnits;b.alphaTest=this.alphaTest;b.overdraw=this.overdraw;b.visible=this.visible;return b};
+$3Dmol.Material.prototype.dispose=function(){this.dispatchEvent({type:"dispose"})};$3Dmol.MaterialIdCount=0;$3Dmol.LineBasicMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.linewidth=1;this.linejoin=this.linecap="round";this.vertexColors=!1;this.fog=!0;this.shaderID="basic";this.setValues(b)};$3Dmol.LineBasicMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.LineBasicMaterial.prototype.clone=function(){var b=new $3Dmol.LineBasicMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);return b};
+$3Dmol.MeshLambertMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="lambert";
+this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(b)};$3Dmol.MeshLambertMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.MeshLambertMaterial.prototype.clone=function(b){"undefined"===typeof b&&(b=new $3Dmol.MeshLambertMaterial);$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;
+b.shading=this.shading;b.shaderID=this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;return b};$3Dmol.MeshDoubleLambertMaterial=function(b){$3Dmol.MeshLambertMaterial.call(this,b);this.shaderID="lambertdouble";this.side=$3Dmol.DoubleSide};$3Dmol.MeshDoubleLambertMaterial.prototype=Object.create($3Dmol.MeshLambertMaterial.prototype);
+$3Dmol.MeshDoubleLambertMaterial.prototype.clone=function(){var b=new $3Dmol.MeshDoubleLambertMaterial;$3Dmol.MeshLambertMaterial.prototype.clone.call(this,b);return b};$3Dmol.MeshOutlineMaterial=function(b){$3Dmol.Material.call(this);b=b||{};this.fog=!0;this.shaderID="outline";this.wireframe=!1;this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1};$3Dmol.MeshOutlineMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.MeshOutlineMaterial.prototype.clone=function(b){"undefined"===typeof b&&(b=new $3Dmol.MeshOutlineMaterial);$3Dmol.Material.prototype.clone.call(this,b);b.fog=this.fog;b.shaderID=this.shaderID;b.wireframe=this.wireframe;return b};
+$3Dmol.ImposterMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.imposter=!0;this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID=
+null;this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.setValues(b)};$3Dmol.ImposterMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.ImposterMaterial.prototype.clone=function(){var b=new $3Dmol.ImposterMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;b.shading=this.shading;b.shaderID=
+this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;return b};$3Dmol.SphereImposterMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="sphereimposter";this.setValues(b)};$3Dmol.SphereImposterMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.SphereImposterMaterial.prototype.clone=function(){var b=new $3Dmol.SphereImposterMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);return b};$3Dmol.SphereImposterOutlineMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="sphereimposteroutline";this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1;this.setValues(b)};$3Dmol.SphereImposterOutlineMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.SphereImposterOutlineMaterial.prototype.clone=function(){var b=new $3Dmol.SphereImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);b.outlineColor=this.outlineColor;b.outlineWidth=this.outlineWidth;b.outlinePushback=this.outlinePushback;return b};$3Dmol.StickImposterMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="stickimposter";this.setValues(b)};$3Dmol.StickImposterMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.StickImposterMaterial.prototype.clone=function(){var b=new $3Dmol.StickImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);return b};$3Dmol.StickImposterOutlineMaterial=function(b){$3Dmol.ImposterMaterial.call(this);this.shaderID="stickimposteroutline";this.outlineColor=b.color||new $3Dmol.Color(0,0,0);this.outlineWidth=b.width||.1;this.outlinePushback=b.pushback||1;this.setValues(b)};$3Dmol.StickImposterOutlineMaterial.prototype=Object.create($3Dmol.ImposterMaterial.prototype);
+$3Dmol.StickImposterOutlineMaterial.prototype.clone=function(){var b=new $3Dmol.StickImposterOutlineMaterial;$3Dmol.ImposterMaterial.prototype.clone.call(this,b);b.outlineColor=this.outlineColor;b.outlineWidth=this.outlineWidth;b.outlinePushback=this.outlinePushback;return b};
+$3Dmol.InstancedMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.ambient=new $3Dmol.Color(1048575);this.emissive=new $3Dmol.Color(0);this.wrapAround=!1;this.wrapRGB=new $3Dmol.Vector3(1,1,1);this.envMap=this.specularMap=this.lightMap=this.map=null;this.reflectivity=1;this.refractionRatio=.98;this.fog=!0;this.wireframe=!1;this.wireframeLinewidth=1;this.wireframeLinejoin=this.wireframeLinecap="round";this.shading=$3Dmol.SmoothShading;this.shaderID="instanced";
+this.vertexColors=$3Dmol.NoColors;this.skinning=!1;this.sphere=null;this.setValues(b)};$3Dmol.InstancedMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.InstancedMaterial.prototype.clone=function(){var b=new $3Dmol.InstancedMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.ambient.copy(this.ambient);b.emissive.copy(this.emissive);b.wrapAround=this.wrapAround;b.wrapRGB.copy(this.wrapRGB);b.map=this.map;b.lightMap=this.lightMap;b.specularMap=this.specularMap;b.envMap=this.envMap;b.combine=this.combine;b.reflectivity=this.reflectivity;b.refractionRatio=this.refractionRatio;b.fog=this.fog;b.shading=this.shading;b.shaderID=
+this.shaderID;b.vertexColors=this.vertexColors;b.skinning=this.skinning;b.morphTargets=this.morphTargets;b.morphNormals=this.morphNormals;b.sphere=this.sphere;return b};
+$3Dmol.SpriteMaterial=function(b){$3Dmol.Material.call(this);this.color=new $3Dmol.Color(16777215);this.map=new $3Dmol.Texture;this.useScreenCoordinates=!0;this.depthTest=!this.useScreenCoordinates;this.sizeAttenuation=!this.useScreenCoordinates;this.scaleByViewPort=!this.sizeAttenuation;this.alignment=$3Dmol.SpriteAlignment.center.clone();this.fog=!1;this.uvOffset=new $3Dmol.Vector2(0,0);this.uvScale=new $3Dmol.Vector2(1,1);this.setValues(b);b=b||{};void 0===b.depthTest&&(this.depthTest=!this.useScreenCoordinates);
+void 0===b.sizeAttenuation&&(this.sizeAttenuation=!this.useScreenCoordinates);void 0===b.scaleByViewPort&&(this.scaleByViewPort=!this.sizeAttenuation)};$3Dmol.SpriteMaterial.prototype=Object.create($3Dmol.Material.prototype);
+$3Dmol.SpriteMaterial.prototype.clone=function(){var b=new $3Dmol.SpriteMaterial;$3Dmol.Material.prototype.clone.call(this,b);b.color.copy(this.color);b.map=this.map;b.useScreenCoordinates=useScreenCoordinates;b.sizeAttenuation=this.sizeAttenuation;b.scaleByViewport=this.scaleByViewPort;b.alignment.copy(this.alignment);b.uvOffset.copy(this.uvOffset);return b};$3Dmol.SpriteAlignment={};$3Dmol.SpriteAlignment.topLeft=new $3Dmol.Vector2(1,-1);$3Dmol.SpriteAlignment.topCenter=new $3Dmol.Vector2(0,-1);
 $3Dmol.SpriteAlignment.topRight=new $3Dmol.Vector2(-1,-1);$3Dmol.SpriteAlignment.centerLeft=new $3Dmol.Vector2(1,0);$3Dmol.SpriteAlignment.center=new $3Dmol.Vector2(0,0);$3Dmol.SpriteAlignment.centerRight=new $3Dmol.Vector2(-1,0);$3Dmol.SpriteAlignment.bottomLeft=new $3Dmol.Vector2(1,1);$3Dmol.SpriteAlignment.bottomCenter=new $3Dmol.Vector2(0,1);$3Dmol.SpriteAlignment.bottomRight=new $3Dmol.Vector2(-1,1);
-$3Dmol.Texture=function(a){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.TextureIdCount++;this.name="";this.image=a;this.mipmaps=[];this.mapping=new $3Dmol.UVMapping;this.wrapT=this.wrapS=$3Dmol.ClampToEdgeWrapping;this.magFilter=$3Dmol.LinearFilter;this.minFilter=$3Dmol.LinearMipMapLinearFilter;this.anisotropy=1;this.format=$3Dmol.RGBAFormat;this.type=$3Dmol.UnsignedByteType;this.offset=new $3Dmol.Vector2(0,0);this.repeat=new $3Dmol.Vector2(1,1);this.generateMipmaps=!0;this.premultiplyAlpha=!1;
+$3Dmol.Texture=function(b){$3Dmol.EventDispatcher.call(this);this.id=$3Dmol.TextureIdCount++;this.name="";this.image=b;this.mipmaps=[];this.mapping=new $3Dmol.UVMapping;this.wrapT=this.wrapS=$3Dmol.ClampToEdgeWrapping;this.magFilter=$3Dmol.LinearFilter;this.minFilter=$3Dmol.LinearMipMapLinearFilter;this.anisotropy=1;this.format=$3Dmol.RGBAFormat;this.type=$3Dmol.UnsignedByteType;this.offset=new $3Dmol.Vector2(0,0);this.repeat=new $3Dmol.Vector2(1,1);this.generateMipmaps=!0;this.premultiplyAlpha=!1;
 this.flipY=!0;this.unpackAlignment=4;this.needsUpdate=!1;this.onUpdate=null};
-$3Dmol.Texture.prototype={constructor:$3Dmol.Texture,clone:function(a){void 0===a&&(a=new $3Dmol.Texture);a.image=this.image;a.mipmaps=this.mipmaps.slice(0);a.mapping=this.mapping;a.wrapS=this.wrapS;a.wrapT=this.wrapT;a.magFilter=this.magFilter;a.minFilter=this.minFilter;a.anisotropy=this.anisotropy;a.format=this.format;a.type=this.type;a.offset.copy(this.offset);a.repeat.copy(this.repeat);a.generateMipmaps=this.generateMipmaps;a.premultiplyAlpha=this.premultiplyAlpha;a.flipY=this.flipY;a.unpackAlignment=
-this.unpackAlignment;return a},dispose:function(){this.dispatchEvent({type:"dispose"})}};$3Dmol.TextureIdCount=0;$3Dmol.FrontSide=0;$3Dmol.BackSide=1;$3Dmol.DoubleSide=2;$3Dmol.NoShading=0;$3Dmol.FlatShading=1;$3Dmol.SmoothShading=2;$3Dmol.NoColors=0;$3Dmol.FaceColors=1;$3Dmol.VertexColors=2;$3Dmol.MultiplyOperation=0;$3Dmol.MixOperation=1;$3Dmol.AddOperation=2;$3Dmol.UVMapping=function(){};$3Dmol.ClampToEdgeWrapping=1001;$3Dmol.LinearFilter=1006;$3Dmol.LinearMipMapLinearFilter=1008;
-$3Dmol.UnsignedByteType=1009;$3Dmol.RGBAFormat=1021;$3Dmol.Line=function(a,b,c){$3Dmol.Object3D.call(this);this.geometry=a;this.material=void 0!==b?b:new $3Dmol.LineBasicMaterial({color:16777215*Math.random()});this.type=void 0!==c?c:$3Dmol.LineStrip};$3Dmol.LineStrip=0;$3Dmol.LinePieces=1;$3Dmol.Line.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Line.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Line(this.geometry,this.material,this.type));$3Dmol.Object3D.prototype.clone.call(this,a);return a};$3Dmol.Mesh=function(a,b){$3Dmol.Object3D.call(this);this.geometry=a;this.material=void 0!==b?b:new $3Dmol.MeshBasicMaterial({color:16777215*Math.random(),wireframe:!0})};$3Dmol.Mesh.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Mesh.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Mesh(this.geometry,this.material));$3Dmol.Object3D.prototype.clone.call(this,a);return a};$3Dmol.Sprite=function(a){$3Dmol.Object3D.call(this);this.material=void 0!==a?a:new $3Dmol.SpriteMaterial;this.rotation3d=this.rotation;this.rotation=0};$3Dmol.Sprite.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Sprite.prototype.updateMatrix=function(){this.matrix.setPosition(this.position);this.rotation3d.set(0,0,this.rotation);this.matrix.setRotationFromEuler(this.rotation3d);1===this.scale.x&&1===this.scale.y||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=!0};$3Dmol.Sprite.prototype.clone=function(a){void 0===a&&(a=new $3Dmol.Sprite(this.material));$3Dmol.Object3D.prototype.clone.call(this,a);return a};
-$3Dmol.Renderer=function(a){function b(a){J[a]||(g.enableVertexAttribArray(a),J[a]=!0)}function c(a,b){var c;"fragment"===a?c=g.createShader(g.FRAGMENT_SHADER):"vertex"===a&&(c=g.createShader(g.VERTEX_SHADER));g.shaderSource(c,b);g.compileShader(c);return g.getShaderParameter(c,g.COMPILE_STATUS)?c:(console.error(g.getShaderInfoLog(c)),console.error("could not initialize shader"),null)}function d(a,b,c,d,e,f,k,l){var h,n,m;b?(n=a.length-1,l=b=-1):(n=0,b=a.length,l=1);for(var p=n;p!==b;p+=l)if(h=a[p],
-h.render&&(n=h.object,m=h.buffer,h=h[c])){k&&r.setBlending(!0);r.setDepthTest(h.depthTest);r.setDepthWrite(h.depthWrite);var q=h.polygonOffset;null!==q&&(q?g.enable(g.POLYGON_OFFSET_FILL):g.disable(g.POLYGON_OFFSET_FILL));r.setMaterialFaces(h);r.renderBuffer(d,e,f,h,m,n)}}function e(a){return 0===(a&a-1)}function k(a){return a===$3Dmol.UnsignedByteType?g.UNSIGNED_BYTE:a===$3Dmol.RGBAFormat?g.RGBA:0}a=a||{};var f=void 0!==a.canvas?a.canvas:document.createElement("canvas"),l=void 0!==a.precision?a.precision:
-"highp",h=void 0!==a.alpha?a.alpha:!0,m=void 0!==a.premultipliedAlpha?a.premultipliedAlpha:!0,q=void 0!==a.antialias?a.antialias:!1,z=void 0!==a.stencil?a.stencil:!0,w=void 0!==a.preserveDrawingBuffer?a.preserveDrawingBuffer:!1,v=void 0!==a.clearColor?new $3Dmol.Color(a.clearColor):new $3Dmol.Color(0),x=void 0!==a.clearAlpha?a.clearAlpha:0;this.domElement=f;this.context=null;this.devicePixelRatio=void 0!==a.devicePixelRatio?a.devicePixelRatio:void 0!==self.devicePixelRatio?self.devicePixelRatio:1;
-this.autoUpdateScene=this.autoUpdateObjects=this.sortObjects=this.autoClearStencil=this.autoClearDepth=this.autoClearColor=this.autoClear=!0;this.renderPluginsPost=[];this.info={memory:{programs:0,geometries:0,textures:0},render:{calls:0,vertices:0,faces:0,points:0}};var r=this,n=[],t=0,u=null,y=-1,F=null,B=null,C=0,s=-1,p=-1,A=-1,E=-1,H=null,G=0,D=0,I=0,L=0,M=0,N=0,J={},X=new $3Dmol.Matrix4,S=new $3Dmol.Vector3,K=new $3Dmol.Vector3,O=!0,P=[0,0,0],Q=[],R=[],g;try{if(!(g=f.getContext("experimental-webgl",
-{alpha:h,premultipliedAlpha:m,antialias:q,stencil:z,preserveDrawingBuffer:w}))&&!(g=f.getContext("webgl",{alpha:h,premultipliedAlpha:m,antialias:q,stencil:z,preserveDrawingBuffer:w})))throw"Error creating WebGL context.";}catch(Y){console.error(Y)}g.getExtension("EXT_frag_depth");g.clearColor(0,0,0,1);g.clearDepth(1);g.clearStencil(0);g.enable(g.DEPTH_TEST);g.depthFunc(g.LEQUAL);g.frontFace(g.CCW);g.cullFace(g.BACK);g.enable(g.CULL_FACE);g.enable(g.BLEND);g.blendEquation(g.FUNC_ADD);g.blendFunc(g.SRC_ALPHA,
-g.ONE_MINUS_SRC_ALPHA);g.clearColor(v.r,v.g,v.b,x);g.getExtension("EXT_frag_depth");this.context=g;this.getContext=function(){return g};this.getPrecision=function(){return l};this.setClearColorHex=function(a,b){v.setHex(a);x=b;g.clearColor(v.r,v.g,v.b,x)};this.setSize=function(a,b){f.width=a*this.devicePixelRatio;f.height=b*this.devicePixelRatio;f.style.width=a+"px";f.style.height=b+"px";this.setViewport(0,0,f.width,f.height)};this.setViewport=function(a,b,c,d){G=void 0!==a?a:0;D=void 0!==b?b:0;I=
-void 0!==c?c:f.width;L=void 0!==d?d:f.height;g.viewport(G,D,I,L)};this.clear=function(a,b,c){var d=0;if(void 0===a||a)d|=g.COLOR_BUFFER_BIT;if(void 0===b||b)d|=g.DEPTH_BUFFER_BIT;if(void 0===c||c)d|=g.STENCIL_BUFFER_BIT;g.clear(d)};this.clearTarget=function(a,b,c){this.clear(a,b,c)};this.setMaterialFaces=function(a){var b=a.side===$3Dmol.DoubleSide;a=a.side===$3Dmol.BackSide;s!==b&&(b?g.disable(g.CULL_FACE):g.enable(g.CULL_FACE),s=b);p!==a&&(a?g.frontFace(g.CW):g.frontFace(g.CCW),p=a)};this.setDepthTest=
-function(a){A!==a&&(a?g.enable(g.DEPTH_TEST):g.disable(g.DEPTH_TEST),A=a)};this.setDepthWrite=function(a){E!==a&&(g.depthMask(a),E=a)};this.setBlending=function(a){a?(g.enable(g.BLEND),g.blendEquationSeparate(g.FUNC_ADD,g.FUNC_ADD),g.blendFuncSeparate(g.SRC_ALPHA,g.ONE_MINUS_SRC_ALPHA,g.ONE,g.ONE_MINUS_SRC_ALPHA)):g.disable(g.BLEND)};this.addPostPlugin=function(a){a.init(this);this.renderPluginsPost.push(a)};var T=function(a){a=a.target;a.removeEventListener("dispose",T);a.__webglInit=void 0;void 0!==
-a.__webglVertexBuffer&&g.deleteBuffer(a.__webglVertexBuffer);void 0!==a.__webglColorBuffer&&g.deleteBuffer(a.__webglColorBuffer);if(void 0!==a.geometryGroups)for(var b=0,c=a.groups;b<c;b++){var d=a.geometryGroups[b];void 0!==d.__webglVertexBuffer&&g.deleteBuffer(d.__webglVertexBuffer);void 0!==d.__webglColorBuffer&&g.deleteBuffer(d.__webglColorBuffer);void 0!==d.__webglNormalBuffer&&g.deleteBuffer(d.__webglNormalBuffer);void 0!==d.__webglFaceBuffer&&g.deleteBuffer(d.__webglFaceBuffer);void 0!==d.__webglLineBuffer&&
-g.deleteBuffer(d.__webglLineBuffer)}r.info.memory.geometries--},U=function(a){a=a.target;a.removeEventListener("dispose",U);a.image&&a.image.__webglTextureCube?g.deleteTexture(a.image.__webglTextureCube):a.__webglInit&&(a.__webglInit=!1,g.deleteTexture(a.__webglTexture));r.info.memory.textures--},V=function(a){a=a.target;a.removeEventListener("dispose",V);W(a)},W=function(a){var b=a.program;if(void 0!==b){a.program=void 0;var c,d,e=!1;a=0;for(c=n.length;a<c;a++)if(d=n[a],d.program===b){d.usedTimes--;
-0===d.usedTimes&&(e=!0);break}if(!0===e){e=[];a=0;for(c=n.length;a<c;a++)d=n[a],d.program!==b&&e.push(d);n=e;g.deleteProgram(b);r.info.memory.programs--}}};this.initMaterial=function(a,b,d,e){a.addEventListener("dispose",V);if(b=a.shaderID)b=$3Dmol.ShaderLib[b],a.vertexShader=b.vertexShader,a.fragmentShader=b.fragmentShader,a.uniforms=$3Dmol.ShaderUtils.clone(b.uniforms);var f;a:{var k=a.fragmentShader;e=a.vertexShader;d=a.uniforms;var h={wireframe:a.wireframe},m,p;b=[];b.push(k);b.push(e);for(m in h)b.push(m),
-b.push(h[m]);b=b.join();m=0;for(p=n.length;m<p;m++){var q=n[m];if(q.code===b){q.usedTimes++;f=q.program;break a}}m=g.createProgram();q="precision "+l+" float;";p=""+q;h=[h.wireframe?"#define WIREFRAME 1":"",q].join("\n");k=c("fragment",h+k);e=c("vertex",p+e);g.attachShader(m,e);g.attachShader(m,k);g.linkProgram(m);g.getProgramParameter(m,g.LINK_STATUS)||console.error("Could not initialize shader");m.uniforms={};m.attributes={};e="viewMatrix modelViewMatrix projectionMatrix normalMatrix modelMatrix cameraPosition".split(" ");
-for(f in d)e.push(f);for(f=0;f<e.length;f++)d=e[f],m.uniforms[d]=g.getUniformLocation(m,d);e=["position","normal","color","lineDistance"];for(f=0;f<e.length;f++)d=e[f],m.attributes[d]=g.getAttribLocation(m,d);m.id=t++;n.push({program:m,code:b,usedTimes:1});r.info.memory.programs=n.length;f=m}a.program=f};this.renderBuffer=function(a,c,d,e,f,k){if(e.visible){var h;e.needsUpdate&&(e.program&&W(e),r.initMaterial(e,c,d,k),e.needsUpdate=!1);var l=!1,m=e.program,n=m.uniforms;h=e.uniforms;m!=u&&(g.useProgram(m),
-u=m,l=!0);e.id!=y&&(y=e.id,l=!0);a!=B&&(B=a,l=!0);g.uniformMatrix4fv(n.projectionMatrix,!1,a.projectionMatrix.elements);g.uniformMatrix4fv(n.modelViewMatrix,!1,k._modelViewMatrix.elements);g.uniformMatrix3fv(n.normalMatrix,!1,k._normalMatrix.elements);if(l){h.fogColor.value=d.color;h.fogNear.value=d.near;h.fogFar.value=d.far;if(0===e.shaderID.lastIndexOf("lambert",0)){g.uniformMatrix4fv(n.viewMatrix,!1,a.matrixWorldInverse.elements);if(O){var p,q,t=0,w=0,s=0;a=0;for(d=c.length;a<d;a++)if(l=c[a],p=
-l.color,q=l.intensity,l instanceof $3Dmol.Light&&(t++,K.getPositionFromMatrix(l.matrixWorld),S.getPositionFromMatrix(l.target.matrixWorld),K.sub(S),K.normalize(),0!==K.x||0!==K.y||0!==K.z))R[s]=K.x,R[s+1]=K.y,R[s+2]=K.z,Q[s]=p.r*q,Q[s+1]=p.g*q,Q[s+2]=p.b*q,s+=3,w++;P[0]=0;P[1]=0;P[2]=0;O=!1}h.ambientLightColor.value=P;h.directionalLightColor.value=Q;h.directionalLightDirection.value=R;h.ambient.value=e.ambient;h.emissive.value=e.emissive}else"sphereimposter"===e.shaderID&&(g.uniformMatrix4fv(n.viewMatrix,
-!1,a.matrixWorldInverse.elements),g.uniformMatrix3fv(n.normalMatrix,!1,k._normalMatrix.elements));h.opacity.value=e.opacity;h.diffuse.value=e.color;for(var v in h)n[v]&&(c=h[v].type,a=h[v].value,d=n[v],"f"===c?g.uniform1f(d,a):"fv"===c?g.uniform3fv(d,a):"c"===c&&g.uniform3f(d,a.r,a.g,a.b))}h=m.attributes;n=!1;m=16777215*f.id+2*m.id+(e.wireframe?1:0);m!==F&&(F=m,n=!0);if(n){for(var x in J)J[x]&&(g.disableVertexAttribArray(x),J[x]=!1);0<=h.position&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglVertexBuffer),
-b(h.position),g.vertexAttribPointer(h.position,3,g.FLOAT,!1,0,0));0<=h.color&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglColorBuffer),b(h.color),g.vertexAttribPointer(h.color,3,g.FLOAT,!1,0,0));0<=h.normal&&(g.bindBuffer(g.ARRAY_BUFFER,f.__webglNormalBuffer),b(h.normal),g.vertexAttribPointer(h.normal,3,g.FLOAT,!1,0,0))}var z;k instanceof $3Dmol.Mesh?(e.wireframe?(k=f.lineidx,e=e.wireframeLinewidth,e!==H&&(g.lineWidth(e),H=e),n&&g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,f.__webglLineBuffer),g.drawElements(g.LINES,
-k,g.UNSIGNED_SHORT,0)):(z=f.faceidx,n&&g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,f.__webglFaceBuffer),g.drawElements(g.TRIANGLES,z,g.UNSIGNED_SHORT,0)),r.info.render.calls++,r.info.render.vertices+=z,r.info.render.faces+=z/3):k instanceof $3Dmol.Line&&(k=f.vertices,f=e.linewidth,f!==H&&(g.lineWidth(f),H=f),g.drawArrays(g.LINES,0,k),r.info.render.calls++)}};this.render=function(a,b,c){if(!1===b instanceof $3Dmol.Camera)console.error("$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.");
-else{var g,e,f,h,k=a.__lights,l=a.fog;y=-1;O=!0;this.autoUpdateScene&&a.updateMatrixWorld();void 0===b.parent&&b.updateMatrixWorld();b.matrixWorldInverse.getInverse(b.matrixWorld);X.multiplyMatrices(b.projectionMatrix,b.matrixWorldInverse);this.autoUpdateObjects&&this.initWebGLObjects(a);r.info.render.calls=0;r.info.render.vertices=0;r.info.render.faces=0;r.info.render.points=0;M=I;N=L;(this.autoClear||c)&&this.clear(this.autoClearColor,this.autoClearDepth,this.autoClearStencil);h=a.__webglObjects;
-c=0;for(g=h.length;c<g;c++)if(e=h[c],f=e.object,e.render=!1,f.visible){f._modelViewMatrix.multiplyMatrices(b.matrixWorldInverse,f.matrixWorld);f._normalMatrix.getInverse(f._modelViewMatrix);f._normalMatrix.transpose();f=e;var m=f.object.material;m.transparent?(f.opaque=null,f.transparent=m,m=m.clone(),m.opacity=0,f.blank=m):(f.opaque=m,f.transparent=null);e.render=!0}this.setBlending(!1);d(a.__webglObjects,!0,"opaque",b,k,l,!1,null);d(a.__webglObjects,!0,"blank",b,k,l,!0,null);d(a.__webglObjects,
-!1,"transparent",b,k,l,!0,null);k=this.renderPluginsPost;F=-1;B=u=null;p=y=s=A=E=-1;if(k.length)for(l=0,c=k.length;l<c;l++)O=!0,k[l].render(a,b,M,N),F=-1,B=u=null,p=y=s=A=E=-1;this.setDepthTest(!0);this.setDepthWrite(!0)}};this.initWebGLObjects=function(a){a.__webglObjects||(a.__webglObjects=[],a.__webglObjectsImmediate=[],a.__webglSprites=[],a.__webglFlares=[]);if(a.__objectsAdded.length){for(;a.__objectsAdded.length;){var b=a.__objectsAdded[0],c=a,d=void 0,e=void 0,f=void 0,h=void 0;if(!b.__webglInit&&
-(b.__webglInit=!0,b._modelViewMatrix=new $3Dmol.Matrix4,b._normalMatrix=new $3Dmol.Matrix3,void 0!==b.geometry&&void 0===b.geometry.__webglInit&&(b.geometry.__webglInit=!0,b.geometry.addEventListener("dispose",T)),b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line))for(f=b.geometry,d=0,e=f.geometryGroups.length;d<e;d++)h=f.geometryGroups[d],h.id=C++,h.__webglVertexBuffer||(b instanceof $3Dmol.Mesh?(h.__webglVertexBuffer=g.createBuffer(),h.__webglNormalBuffer=g.createBuffer(),h.__webglColorBuffer=
-g.createBuffer(),h.__webglFaceBuffer=g.createBuffer(),h.__webglLineBuffer=g.createBuffer(),r.info.memory.geometries++,f.elementsNeedUpdate=!0,f.normalsNeedUpdate=!0):b instanceof $3Dmol.Line&&(h.__webglVertexBuffer=g.createBuffer(),h.__webglColorBuffer=g.createBuffer(),r.info.memory.geometries++),f.verticesNeedUpdate=!0,f.colorsNeedUpdate=!0);if(!b.__webglActive){if(b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line)for(f=b.geometry,d=0,e=f.geometryGroups.length;d<e;d++)h=f.geometryGroups[d],c.__webglObjects.push({buffer:h,
-object:b,opaque:null,transparent:null});else b instanceof $3Dmol.Sprite&&c.__webglSprites.push(b);b.__webglActive=!0}a.__objectsAdded.splice(0,1)}F=-1}for(;a.__objectsRemoved.length;){b=a.__objectsRemoved[0];c=a;if(b instanceof $3Dmol.Mesh||b instanceof $3Dmol.Line)for(c=c.__webglObjects,d=b,e=c.length-1;0<=e;--e)c[e].object===d&&c.splice(e,1);else if(b instanceof $3Dmol.Sprite)for(c=c.__webglSprites,d=b,e=c.length-1;0<=e;--e)c[e]===d&&c.splice(e,1);b.__webglActive=!1;a.__objectsRemoved.splice(0,
-1)}b=0;for(c=a.__webglObjects.length;b<c;b++)if(e=a.__webglObjects[b].object,d=e.geometry,h=void 0,e instanceof $3Dmol.Mesh||e instanceof $3Dmol.Line){e=0;for(f=d.geometryGroups.length;e<f;e++)if(h=d.geometryGroups[e],d.verticesNeedUpdate||d.elementsNeedUpdate||d.colorsNeedUpdate||d.normalsNeedUpdate){var k=g.STATIC_DRAW,l=h.vertexArray,m=h.colorArray;g.bindBuffer(g.ARRAY_BUFFER,h.__webglVertexBuffer);g.bufferData(g.ARRAY_BUFFER,l,k);g.bindBuffer(g.ARRAY_BUFFER,h.__webglColorBuffer);g.bufferData(g.ARRAY_BUFFER,
-m,k);void 0!==h.normalArray&&void 0!==h.__webglNormalBuffer&&(l=h.normalArray,g.bindBuffer(g.ARRAY_BUFFER,h.__webglNormalBuffer),g.bufferData(g.ARRAY_BUFFER,l,k));void 0!==h.faceArray&&void 0!==h.__webglFaceBuffer&&(l=h.faceArray,g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,h.__webglFaceBuffer),g.bufferData(g.ELEMENT_ARRAY_BUFFER,l,k));void 0!==h.lineArray&&void 0!==h.__webglLineBuffer&&(l=h.lineArray,g.bindBuffer(g.ELEMENT_ARRAY_BUFFER,h.__webglLineBuffer),g.bufferData(g.ELEMENT_ARRAY_BUFFER,l,k))}d.verticesNeedUpdate=
-!1;d.elementsNeedUpdate=!1;d.normalsNeedUpdate=!1;d.colorsNeedUpdate=!1;d.buffersNeedUpdate=!1}};this.setTexture=function(a,b){if(a.needsUpdate){a.__webglInit||(a.__webglInit=!0,a.addEventListener("dispose",U),a.__webglTexture=g.createTexture(),r.info.memory.textures++);g.activeTexture(g.TEXTURE0+b);g.bindTexture(g.TEXTURE_2D,a.__webglTexture);g.pixelStorei(g.UNPACK_FLIP_Y_WEBGL,a.flipY);g.pixelStorei(g.UNPACK_PREMULTIPLY_ALPHA_WEBGL,a.premultiplyAlpha);g.pixelStorei(g.UNPACK_ALIGNMENT,a.unpackAlignment);
-var c=a.image,c=e(c.width)&&e(c.height),d=k(a.format),f=k(a.type),h=g.TEXTURE_2D;c?(g.texParameteri(h,g.TEXTURE_WRAP_S,k(a.wrapS)),g.texParameteri(h,g.TEXTURE_WRAP_T,k(a.wrapT)),g.texParameteri(h,g.TEXTURE_MAG_FILTER,k(a.magFilter)),g.texParameteri(h,g.TEXTURE_MIN_FILTER,k(a.minFilter))):(g.texParameteri(h,g.TEXTURE_WRAP_S,g.CLAMP_TO_EDGE),g.texParameteri(h,g.TEXTURE_WRAP_T,g.CLAMP_TO_EDGE),g.texParameteri(h,g.TEXTURE_MAG_FILTER,g.LINEAR),g.texParameteri(h,g.TEXTURE_MIN_FILTER,g.LINEAR));var l=a.mipmaps;
-if(0<l.length&&c){for(var m=0,n=l.length;m<n;m++)h=l[m],g.texImage2D(g.TEXTURE_2D,m,d,d,f,h);a.generateMipmaps=!1}else g.texImage2D(g.TEXTURE_2D,0,d,d,f,a.image);a.generateMipmaps&&c&&g.generateMipmap(g.TEXTURE_2D);a.needsUpdate=!1;if(a.onUpdate)a.onUpdate()}else g.activeTexture(g.TEXTURE0+b),g.bindTexture(g.TEXTURE_2D,a.__webglTexture)};this.addPostPlugin(new $3Dmol.SpritePlugin)};
-$3Dmol.Scene=function(){$3Dmol.Object3D.call(this);this.overrideMaterial=this.fog=null;this.matrixAutoUpdate=!1;this.__objects=[];this.__lights=[];this.__objectsAdded=[];this.__objectsRemoved=[]};$3Dmol.Scene.prototype=Object.create($3Dmol.Object3D.prototype);
-$3Dmol.Scene.prototype.__addObject=function(a){a instanceof $3Dmol.Light?(-1===this.__lights.indexOf(a)&&this.__lights.push(a),a.target&&void 0===a.target.parent&&this.add(a.target)):-1===this.__objects.indexOf(a)&&(this.__objects.push(a),this.__objectsAdded.push(a),-1!==this.__objectsRemoved.indexOf(a)&&this.__objectsRemoved.splice(b,1));for(var b=0;b<a.children.length;b++)this.__addObject(a.children[b])};
-$3Dmol.Scene.prototype.__removeObject=function(a){var b;a instanceof $3Dmol.Light?(b=this.__lights.indexOf(a),-1!==b&&this.__lights.splice(b,1)):(b=this.__objects.indexOf(a),-1!==b&&(this.__objects.splice(b,1),this.__objectsRemoved.push(a),-1!==this.__objectsAdded.indexOf(a)&&this.__objectsAdded.splice(b,1)));for(b=0;b<a.children.length;b++)this.__removeObject(a.children[b])};$3Dmol.Fog=function(a,b,c){this.name="";this.color=new $3Dmol.Color(a);this.near=void 0!==b?b:1;this.far=void 0!==c?c:1E3};
-$3Dmol.Fog.prototype.clone=function(){return new $3Dmol.Fog(this.color.getHex(),this.near,this.far)};$3Dmol.ShaderUtils={clone:function(a){var b,c={};for(b in a){c[b]={};c[b].type=a[b].type;var d=a[b].value;d instanceof $3Dmol.Color?c[b].value=d.clone():"number"===typeof d?c[b].value=d:d instanceof Array?c[b].value=[]:console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform")}return c}};
-$3Dmol.ShaderLib={basic:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 diffuse;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( diffuse, opacity );\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nattribute vec3 position;\nattribute vec3 color;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},sphereimposter:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 diffuse;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvarying vec2 mapping;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    if(lensqr > 2.0)\n       discard;\n    float w = sqrt(2.0 - lensqr);\n    float z = sqrt(sqrt(2.0)-lensqr);\n    gl_FragDepthEXT = -.1*z;\n    gl_FragColor = vec4( w*vColor, 1 );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec4 adjust = projectionMatrix*vec4(normal, 1.0);  adjust.y *= -1.0; adjust.z = 0.0; adjust.w = 0.0;\n    mapping = normal.xy;\n    gl_Position = projPosition+adjust;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},lambert:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 ambient;\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform vec3 ambientLightColor;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},ambient:{type:"c",value:new $3Dmol.Color(1,1,1)},emissive:{type:"c",value:new $3Dmol.Color(1,1,1)},ambientLightColor:{type:"fv",value:[]},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},lambertdouble:{fragmentShader:"uniform mat4 viewMatrix;\nuniform vec3 cameraPosition;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vLightBack;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    if ( gl_FrontFacing )\n       gl_FragColor.xyz *= vLightFront;\n    else\n       gl_FragColor.xyz *= vLightBack;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
-vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 cameraPosition;\nuniform vec3 ambient;\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform vec3 ambientLightColor;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvarying vec3 vLightBack;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    vLightBack = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;\n    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;\n    vLightBack = vLightBack * diffuse + ambient * ambientLightColor + emissive;\n    gl_Position = projectionMatrix * mvPosition;\n}",
-uniforms:{opacity:{type:"f",value:1},diffuse:{type:"c",value:new $3Dmol.Color(1,1,1)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},ambient:{type:"c",value:new $3Dmol.Color(1,1,1)},emissive:{type:"c",value:new $3Dmol.Color(1,1,1)},ambientLightColor:{type:"fv",value:[]},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},sprite:{fragmentShader:"uniform vec3 color;\nuniform sampler2D map;\nuniform float opacity;\nuniform int fogType;\nuniform vec3 fogColor;\nuniform float fogDensity;\nuniform float fogNear;\nuniform float fogFar;\nuniform float alphaTest;\nvarying vec2 vUV;\nvoid main() {\n    vec4 texture = texture2D(map, vUV);\n    if (texture.a < alphaTest) discard;\n    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);\n    if (fogType > 0) {\n        float depth = gl_FragCoord.z / gl_FragCoord.w;\n        float fogFactor = 0.0;\n        if (fogType == 1) {\n            fogFactor = smoothstep(fogNear, fogFar, depth);\n        }\n        else {\n            const float LOG2 = 1.442695;\n            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);\n            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);\n        }\n        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);\n    }\n}",
+$3Dmol.Texture.prototype={constructor:$3Dmol.Texture,clone:function(b){void 0===b&&(b=new $3Dmol.Texture);b.image=this.image;b.mipmaps=this.mipmaps.slice(0);b.mapping=this.mapping;b.wrapS=this.wrapS;b.wrapT=this.wrapT;b.magFilter=this.magFilter;b.minFilter=this.minFilter;b.anisotropy=this.anisotropy;b.format=this.format;b.type=this.type;b.offset.copy(this.offset);b.repeat.copy(this.repeat);b.generateMipmaps=this.generateMipmaps;b.premultiplyAlpha=this.premultiplyAlpha;b.flipY=this.flipY;b.unpackAlignment=
+this.unpackAlignment;return b},dispose:function(){this.dispatchEvent({type:"dispose"})}};$3Dmol.TextureIdCount=0;$3Dmol.FrontSide=0;$3Dmol.BackSide=1;$3Dmol.DoubleSide=2;$3Dmol.NoShading=0;$3Dmol.FlatShading=1;$3Dmol.SmoothShading=2;$3Dmol.NoColors=0;$3Dmol.FaceColors=1;$3Dmol.VertexColors=2;$3Dmol.MultiplyOperation=0;$3Dmol.MixOperation=1;$3Dmol.AddOperation=2;$3Dmol.UVMapping=function(){};$3Dmol.ClampToEdgeWrapping=1001;$3Dmol.LinearFilter=1006;$3Dmol.LinearMipMapLinearFilter=1008;
+$3Dmol.UnsignedByteType=1009;$3Dmol.RGBAFormat=1021;$3Dmol.Line=function(b,c,d){$3Dmol.Object3D.call(this);this.geometry=b;this.material=void 0!==c?c:new $3Dmol.LineBasicMaterial({color:16777215*Math.random()});this.type=void 0!==d?d:$3Dmol.LineStrip};$3Dmol.LineStrip=0;$3Dmol.LinePieces=1;$3Dmol.Line.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Line.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Line(this.geometry,this.material,this.type));$3Dmol.Object3D.prototype.clone.call(this,b);return b};$3Dmol.Mesh=function(b,c){$3Dmol.Object3D.call(this);this.geometry=b;this.material=void 0!==c?c:new $3Dmol.MeshBasicMaterial({color:16777215*Math.random(),wireframe:!0})};$3Dmol.Mesh.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Mesh.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Mesh(this.geometry,this.material));$3Dmol.Object3D.prototype.clone.call(this,b);return b};$3Dmol.Sprite=function(b){$3Dmol.Object3D.call(this);this.material=void 0!==b?b:new $3Dmol.SpriteMaterial;this.rotation3d=this.rotation;this.rotation=0};$3Dmol.Sprite.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Sprite.prototype.updateMatrix=function(){this.matrix.setPosition(this.position);this.rotation3d.set(0,0,this.rotation);this.matrix.setRotationFromEuler(this.rotation3d);1===this.scale.x&&1===this.scale.y||this.matrix.scale(this.scale);this.matrixWorldNeedsUpdate=!0};$3Dmol.Sprite.prototype.clone=function(b){void 0===b&&(b=new $3Dmol.Sprite(this.material));$3Dmol.Object3D.prototype.clone.call(this,b);return b};
+$3Dmol.Renderer=function(b){function c(b){S[b]||(D.enableVertexAttribArray(b),S[b]=!0)}function d(b,c){var h;"fragment"===b?h=D.createShader(D.FRAGMENT_SHADER):"vertex"===b&&(h=D.createShader(D.VERTEX_SHADER));D.shaderSource(h,c);D.compileShader(h);return D.getShaderParameter(h,D.COMPILE_STATUS)?h:(console.error(D.getShaderInfoLog(h)),console.error("could not initialize shader"),null)}function p(b,c,h,f,e,w,m,d){var q,l,t;c?(l=b.length-1,d=c=-1):(l=0,c=b.length,d=1);for(var s=l;s!==c;s+=d)if(q=b[s],
+q.render&&(l=q.object,t=q.buffer,q=q[h])){m&&x.setBlending(!0);x.setDepthTest(q.depthTest);x.setDepthWrite(q.depthWrite);var N=q.polygonOffset;null!==N&&(N?D.enable(D.POLYGON_OFFSET_FILL):D.disable(D.POLYGON_OFFSET_FILL));N=l._modelViewMatrix.isReflected();x.setMaterialFaces(q,N);x.renderBuffer(f,e,w,q,t,l);g&&("sphereimposter"==q.shaderID?x.renderBuffer(f,e,w,_outlineSphereImposterMaterial,t,l):"stickimposter"==q.shaderID?x.renderBuffer(f,e,w,_outlineStickImposterMaterial,t,l):q.wireframe||"basic"===
+q.shaderID||0===q.opacity||x.renderBuffer(f,e,w,g,t,l))}}function y(b){return 0===(b&b-1)}function A(b){return b===$3Dmol.UnsignedByteType?D.UNSIGNED_BYTE:b===$3Dmol.RGBAFormat?D.RGBA:0}b=b||{};var q=void 0!==b.canvas?b.canvas:document.createElement("canvas"),B=void 0!==b.precision?b.precision:"highp",f=void 0!==b.alpha?b.alpha:!0,w=void 0!==b.premultipliedAlpha?b.premultipliedAlpha:!0,h=void 0!==b.antialias?b.antialias:!1,t=void 0!==b.stencil?b.stencil:!0,m=void 0!==b.preserveDrawingBuffer?b.preserveDrawingBuffer:
+!1,e=void 0!==b.clearColor?new $3Dmol.Color(b.clearColor):new $3Dmol.Color(0),F=void 0!==b.clearAlpha?b.clearAlpha:0,g=void 0!==b.outline?new $3Dmol.MeshOutlineMaterial(b.outline):null;this.domElement=q;this.context=null;this.devicePixelRatio=void 0!==b.devicePixelRatio?b.devicePixelRatio:void 0!==self.devicePixelRatio?self.devicePixelRatio:1;this.autoUpdateScene=this.autoUpdateObjects=this.sortObjects=this.autoClearStencil=this.autoClearDepth=this.autoClearColor=this.autoClear=!0;this.renderPluginsPost=
+[];this.info={memory:{programs:0,geometries:0,textures:0},render:{calls:0,vertices:0,faces:0,points:0}};var x=this,u=[],s=0,l=null,E=-1,M=null,C=null,G=0,z=-1,H=-1,L=-1,N=-1,J=null,I=0,K=0,O=0,Q=0,W=0,P=0,S={},R=new $3Dmol.Matrix4,aa=new $3Dmol.Vector3,V=new $3Dmol.Vector3,Z=!0,ca=[],X=[],D;try{if(!(D=q.getContext("experimental-webgl",{alpha:f,premultipliedAlpha:w,antialias:h,stencil:t,preserveDrawingBuffer:m}))&&!(D=q.getContext("webgl",{alpha:f,premultipliedAlpha:w,antialias:h,stencil:t,preserveDrawingBuffer:m})))throw"Error creating WebGL context.";
+}catch(ba){console.error(ba)}D.clearColor(0,0,0,1);D.clearDepth(1);D.clearStencil(0);D.enable(D.DEPTH_TEST);D.depthFunc(D.LEQUAL);D.frontFace(D.CCW);D.cullFace(D.BACK);D.enable(D.CULL_FACE);D.enable(D.BLEND);D.blendEquation(D.FUNC_ADD);D.blendFunc(D.SRC_ALPHA,D.ONE_MINUS_SRC_ALPHA);D.clearColor(e.r,e.g,e.b,F);this.context=D;var U=D.getExtension("ANGLE_instanced_arrays"),T=D.getExtension("EXT_frag_depth");this.supportedExtensions=function(){return{supportsAIA:Boolean(U),supportsImposters:Boolean(T)}};
+this.getContext=function(){return D};this.getPrecision=function(){return B};this.setClearColorHex=function(b,c){e.setHex(b);F=c;D.clearColor(e.r,e.g,e.b,F)};this.enableOutline=function(b){g=new $3Dmol.MeshOutlineMaterial(b);_outlineSphereImposterMaterial=new $3Dmol.SphereImposterOutlineMaterial(b);_outlineStickImposterMaterial=new $3Dmol.StickImposterOutlineMaterial(b)};this.disableOutline=function(){_outlineStickImposterMaterial=_outlineSphereImposterMaterial=g=null};this.setSize=function(b,c){q.width=
+b*this.devicePixelRatio;q.height=c*this.devicePixelRatio;q.style.width=b+"px";q.style.height=c+"px";this.setViewport(0,0,q.width,q.height)};this.setViewport=function(b,c,h,f){I=void 0!==b?b:0;K=void 0!==c?c:0;O=void 0!==h?h:q.width;Q=void 0!==f?f:q.height;D.viewport(I,K,O,Q)};this.clear=function(b,c,h){var f=0;if(void 0===b||b)f|=D.COLOR_BUFFER_BIT;if(void 0===c||c)f|=D.DEPTH_BUFFER_BIT;if(void 0===h||h)f|=D.STENCIL_BUFFER_BIT;D.clear(f)};this.clearTarget=function(b,c,h){this.clear(b,c,h)};this.setMaterialFaces=
+function(b,c){var h=b.side===$3Dmol.DoubleSide,f=b.side===$3Dmol.BackSide,f=c?!f:f;z!==h&&(h?D.disable(D.CULL_FACE):D.enable(D.CULL_FACE),z=h);H!==f&&(f?D.frontFace(D.CW):D.frontFace(D.CCW),H=f)};this.setDepthTest=function(b){L!==b&&(b?D.enable(D.DEPTH_TEST):D.disable(D.DEPTH_TEST),L=b)};this.setDepthWrite=function(b){N!==b&&(D.depthMask(b),N=b)};this.setBlending=function(b){b?(D.enable(D.BLEND),D.blendEquationSeparate(D.FUNC_ADD,D.FUNC_ADD),D.blendFuncSeparate(D.SRC_ALPHA,D.ONE_MINUS_SRC_ALPHA,D.ONE,
+D.ONE_MINUS_SRC_ALPHA)):D.disable(D.BLEND)};this.addPostPlugin=function(b){b.init(this);this.renderPluginsPost.push(b)};var ea=function(b){b=b.target;b.removeEventListener("dispose",ea);b.__webglInit=void 0;void 0!==b.__webglVertexBuffer&&D.deleteBuffer(b.__webglVertexBuffer);void 0!==b.__webglColorBuffer&&D.deleteBuffer(b.__webglColorBuffer);if(void 0!==b.geometryGroups)for(var c=0,h=b.groups;c<h;c++){var f=b.geometryGroups[c];void 0!==f.__webglVertexBuffer&&D.deleteBuffer(f.__webglVertexBuffer);
+void 0!==f.__webglColorBuffer&&D.deleteBuffer(f.__webglColorBuffer);void 0!==f.__webglNormalBuffer&&D.deleteBuffer(f.__webglNormalBuffer);void 0!==f.__webglFaceBuffer&&D.deleteBuffer(f.__webglFaceBuffer);void 0!==f.__webglLineBuffer&&D.deleteBuffer(f.__webglLineBuffer)}x.info.memory.geometries--},Ba=function(b){b=b.target;b.removeEventListener("dispose",Ba);b.image&&b.image.__webglTextureCube?D.deleteTexture(b.image.__webglTextureCube):b.__webglInit&&(b.__webglInit=!1,D.deleteTexture(b.__webglTexture));
+x.info.memory.textures--},Na=function(b){b=b.target;b.removeEventListener("dispose",Na);Ja(b)},Ja=function(b){var c=b.program;if(void 0!==c){b.program=void 0;var h,f,e=!1;b=0;for(h=u.length;b<h;b++)if(f=u[b],f.program===c){f.usedTimes--;0===f.usedTimes&&(e=!0);break}if(!0===e){e=[];b=0;for(h=u.length;b<h;b++)f=u[b],f.program!==c&&e.push(f);u=e;D.deleteProgram(c);x.info.memory.programs--}}};this.initMaterial=function(b,c,h,f){b.addEventListener("dispose",Na);if(c=b.shaderID)c=$3Dmol.ShaderLib[c],b.vertexShader=
+c.vertexShader,b.fragmentShader=c.fragmentShader,b.uniforms=$3Dmol.ShaderUtils.clone(c.uniforms);var e;a:{var w=b.fragmentShader;f=b.vertexShader;h=b.uniforms;var g={wireframe:b.wireframe,fragdepth:b.imposter},q,m;c=[];c.push(w);c.push(f);for(q in g)c.push(q),c.push(g[q]);c=c.join();q=0;for(m=u.length;q<m;q++){var l=u[q];if(l.code===c){l.usedTimes++;e=l.program;break a}}q=D.createProgram();l="precision "+B+" float;";m=""+l;g=[g.fragdepth?"#extension GL_EXT_frag_depth: enable":"",g.wireframe?"#define WIREFRAME 1":
+"",l].join("\n");w=d("fragment",g+w);f=d("vertex",m+f);D.attachShader(q,f);D.attachShader(q,w);D.linkProgram(q);D.getProgramParameter(q,D.LINK_STATUS)||console.error("Could not initialize shader");q.uniforms={};q.attributes={};f=["viewMatrix","modelViewMatrix","projectionMatrix","normalMatrix"];for(e in h)f.push(e);for(e=0;e<f.length;e++)h=f[e],q.uniforms[h]=D.getUniformLocation(q,h);f="position normal color lineDistance offset radius".split(" ");for(e=0;e<f.length;e++)h=f[e],q.attributes[h]=D.getAttribLocation(q,
+h);q.id=s++;u.push({program:q,code:c,usedTimes:1});x.info.memory.programs=u.length;e=q}b.program=e};this.renderBuffer=function(b,h,f,e,g,w){if(e.visible){var q;e.needsUpdate&&(e.program&&Ja(e),x.initMaterial(e,h,f,w),e.needsUpdate=!1);var m=!1,d=e.program,t=d.uniforms;q=e.uniforms;d!=l&&(D.useProgram(d),l=d,m=!0);e.id!=E&&(E=e.id,m=!0);b!=C&&(C=b,m=!0);D.uniformMatrix4fv(t.projectionMatrix,!1,b.projectionMatrix.elements);D.uniformMatrix4fv(t.modelViewMatrix,!1,w._modelViewMatrix.elements);D.uniformMatrix3fv(t.normalMatrix,
+!1,w._normalMatrix.elements);if(m){q.fogColor.value=f.color;q.fogNear.value=f.near;q.fogFar.value=f.far;if(e.shaderID.startsWith("lambert")||"instanced"===e.shaderID||e.shaderID.endsWith("imposter")){D.uniformMatrix4fv(t.viewMatrix,!1,b.matrixWorldInverse.elements);if(Z){var s,N,B=0,I=0,u=0;b=0;for(f=h.length;b<f;b++)if(m=h[b],s=m.color,N=m.intensity,m instanceof $3Dmol.Light&&(B++,V.getPositionFromMatrix(m.matrixWorld),aa.getPositionFromMatrix(m.target.matrixWorld),V.sub(aa),V.normalize(),0!==V.x||
+0!==V.y||0!==V.z))X[u]=V.x,X[u+1]=V.y,X[u+2]=V.z,ca[u]=s.r*N,ca[u+1]=s.g*N,ca[u+2]=s.b*N,u+=3,I++;Z=!1}q.directionalLightColor.value=ca;q.directionalLightDirection.value=X}else e.shaderID.endsWith("outline")?(q.outlineColor.value=e.outlineColor,q.outlineWidth.value=e.outlineWidth,q.outlinePushback.value=e.outlinePushback):"sphereimposter"===e.shaderID&&(D.uniformMatrix4fv(t.viewMatrix,!1,b.matrixWorldInverse.elements),D.uniformMatrix3fv(t.normalMatrix,!1,w._normalMatrix.elements),q.directionalLightColor.value=
+ca,q.directionalLightDirection.value=X);q.opacity.value=e.opacity;for(var K in q)t[K]&&(h=q[K].type,b=q[K].value,f=t[K],"f"===h?D.uniform1f(f,b):"fv"===h?D.uniform3fv(f,b):"c"===h?D.uniform3f(f,b.r,b.g,b.b):"f4"===h&&D.uniform4f(f,b[0],b[1],b[2],b[3]))}q=d.attributes;t=!1;d=16777215*g.id+2*d.id+(e.wireframe?1:0);d!==M&&(M=d,t=!0);if(t){for(var F in S)S[F]&&(D.disableVertexAttribArray(F),S[F]=!1);0<=q.position&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer),c(q.position),D.vertexAttribPointer(q.position,
+3,D.FLOAT,!1,0,0));0<=q.color&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglColorBuffer),c(q.color),D.vertexAttribPointer(q.color,3,D.FLOAT,!1,0,0));0<=q.normal&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),c(q.normal),D.vertexAttribPointer(q.normal,3,D.FLOAT,!1,0,0));0<=q.offset&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglOffsetBuffer),c(q.offset),D.vertexAttribPointer(q.offset,3,D.FLOAT,!1,0,0));0<=q.radius&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglRadiusBuffer),c(q.radius),D.vertexAttribPointer(q.radius,
+1,D.FLOAT,!1,0,0))}var z;w instanceof $3Dmol.Mesh?("instanced"===e.shaderID?(z=e.sphere.geometryGroups[0],t&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer),D.bufferData(D.ARRAY_BUFFER,z.vertexArray,D.STATIC_DRAW),D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),D.bufferData(D.ARRAY_BUFFER,z.normalArray,D.STATIC_DRAW),D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,z.faceArray,D.STATIC_DRAW)),z=z.faceidx,U.vertexAttribDivisorANGLE(q.offset,1),U.vertexAttribDivisorANGLE(q.radius,
+1),U.vertexAttribDivisorANGLE(q.color,1),U.drawElementsInstancedANGLE(D.TRIANGLES,z,D.UNSIGNED_SHORT,0,g.radiusArray.length),U.vertexAttribDivisorANGLE(q.offset,0),U.vertexAttribDivisorANGLE(q.radius,0),U.vertexAttribDivisorANGLE(q.color,0)):e.wireframe?(w=g.lineidx,e=e.wireframeLinewidth,e!==J&&(D.lineWidth(e),J=e),t&&D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglLineBuffer),D.drawElements(D.LINES,w,D.UNSIGNED_SHORT,0)):(z=g.faceidx,t&&D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.drawElements(D.TRIANGLES,
+z,D.UNSIGNED_SHORT,0)),x.info.render.calls++,x.info.render.vertices+=z,x.info.render.faces+=z/3):w instanceof $3Dmol.Line&&(w=g.vertices,g=e.linewidth,g!==J&&(D.lineWidth(g),J=g),D.drawArrays(D.LINES,0,w),x.info.render.calls++)}};this.render=function(b,c,h){if(!1===c instanceof $3Dmol.Camera)console.error("$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.");else{var f,e,q,g,w=b.__lights,m=b.fog;E=-1;Z=!0;this.autoUpdateScene&&b.updateMatrixWorld();void 0===c.parent&&c.updateMatrixWorld();
+c.matrixWorldInverse.getInverse(c.matrixWorld);R.multiplyMatrices(c.projectionMatrix,c.matrixWorldInverse);this.autoUpdateObjects&&this.initWebGLObjects(b);x.info.render.calls=0;x.info.render.vertices=0;x.info.render.faces=0;x.info.render.points=0;W=O;P=Q;(this.autoClear||h)&&this.clear(this.autoClearColor,this.autoClearDepth,this.autoClearStencil);g=b.__webglObjects;h=0;for(f=g.length;h<f;h++)if(e=g[h],q=e.object,e.render=!1,q.visible){q._modelViewMatrix.multiplyMatrices(c.matrixWorldInverse,q.matrixWorld);
+q._normalMatrix.getInverse(q._modelViewMatrix);q._normalMatrix.transpose();q=e;var t=q.object.material;t.transparent?(q.opaque=null,q.transparent=t,t.wireframe||(t=t.clone(),t.opacity=0,q.blank=t)):(q.opaque=t,q.transparent=null);e.render=!0}this.setBlending(!1);p(b.__webglObjects,!0,"opaque",c,w,m,!1,null);p(b.__webglObjects,!0,"blank",c,w,m,!0,null);p(b.__webglObjects,!1,"transparent",c,w,m,!0,null);w=this.renderPluginsPost;M=-1;C=l=null;H=E=z=L=N=-1;if(w.length)for(m=0,h=w.length;m<h;m++)Z=!0,
+w[m].render(b,c,W,P),M=-1,C=l=null,H=E=z=L=N=-1;this.setDepthTest(!0);this.setDepthWrite(!0)}};this.initWebGLObjects=function(b){b.__webglObjects||(b.__webglObjects=[],b.__webglObjectsImmediate=[],b.__webglSprites=[],b.__webglFlares=[]);if(b.__objectsAdded.length){for(;b.__objectsAdded.length;){var c=b.__objectsAdded[0],h=b,f=void 0,e=void 0,q=void 0,g=void 0;if(!c.__webglInit&&(c.__webglInit=!0,c._modelViewMatrix=new $3Dmol.Matrix4,c._normalMatrix=new $3Dmol.Matrix3,void 0!==c.geometry&&void 0===
+c.geometry.__webglInit&&(c.geometry.__webglInit=!0,c.geometry.addEventListener("dispose",ea)),c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line))for(q=c.geometry,f=0,e=q.geometryGroups.length;f<e;f++)g=q.geometryGroups[f],g.id=G++,g.__webglVertexBuffer||(c instanceof $3Dmol.Mesh?(g.radiusArray&&(g.__webglRadiusBuffer=D.createBuffer()),g.useOffset&&(g.__webglOffsetBuffer=D.createBuffer()),g.__webglVertexBuffer=D.createBuffer(),g.__webglNormalBuffer=D.createBuffer(),g.__webglColorBuffer=D.createBuffer(),
+g.__webglFaceBuffer=D.createBuffer(),g.__webglLineBuffer=D.createBuffer(),x.info.memory.geometries++,q.elementsNeedUpdate=!0,q.normalsNeedUpdate=!0):c instanceof $3Dmol.Line&&(g.__webglVertexBuffer=D.createBuffer(),g.__webglColorBuffer=D.createBuffer(),x.info.memory.geometries++),q.verticesNeedUpdate=!0,q.colorsNeedUpdate=!0);if(!c.__webglActive){if(c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line)for(q=c.geometry,f=0,e=q.geometryGroups.length;f<e;f++)g=q.geometryGroups[f],h.__webglObjects.push({buffer:g,
+object:c,opaque:null,transparent:null});else c instanceof $3Dmol.Sprite&&h.__webglSprites.push(c);c.__webglActive=!0}b.__objectsAdded.splice(0,1)}M=-1}for(;b.__objectsRemoved.length;){c=b.__objectsRemoved[0];h=b;if(c instanceof $3Dmol.Mesh||c instanceof $3Dmol.Line)for(h=h.__webglObjects,f=c,e=h.length-1;0<=e;--e)h[e].object===f&&h.splice(e,1);else if(c instanceof $3Dmol.Sprite)for(h=h.__webglSprites,f=c,e=h.length-1;0<=e;--e)h[e]===f&&h.splice(e,1);c.__webglActive=!1;b.__objectsRemoved.splice(0,
+1)}c=0;for(h=b.__webglObjects.length;c<h;c++)if(e=b.__webglObjects[c].object,f=e.geometry,g=void 0,e instanceof $3Dmol.Mesh||e instanceof $3Dmol.Line){e=0;for(q=f.geometryGroups.length;e<q;e++)if(g=f.geometryGroups[e],f.verticesNeedUpdate||f.elementsNeedUpdate||f.colorsNeedUpdate||f.normalsNeedUpdate){var w=D.STATIC_DRAW,m=g.vertexArray,t=g.colorArray;void 0!==g.__webglOffsetBuffer?D.bindBuffer(D.ARRAY_BUFFER,g.__webglOffsetBuffer):D.bindBuffer(D.ARRAY_BUFFER,g.__webglVertexBuffer);D.bufferData(D.ARRAY_BUFFER,
+m,w);D.bindBuffer(D.ARRAY_BUFFER,g.__webglColorBuffer);D.bufferData(D.ARRAY_BUFFER,t,w);g.normalArray&&void 0!==g.__webglNormalBuffer&&(m=g.normalArray,D.bindBuffer(D.ARRAY_BUFFER,g.__webglNormalBuffer),D.bufferData(D.ARRAY_BUFFER,m,w));g.radiusArray&&void 0!==g.__webglRadiusBuffer&&(D.bindBuffer(D.ARRAY_BUFFER,g.__webglRadiusBuffer),D.bufferData(D.ARRAY_BUFFER,g.radiusArray,w));g.faceArray&&void 0!==g.__webglFaceBuffer&&(m=g.faceArray,D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglFaceBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,
+m,w));g.lineArray&&void 0!==g.__webglLineBuffer&&(m=g.lineArray,D.bindBuffer(D.ELEMENT_ARRAY_BUFFER,g.__webglLineBuffer),D.bufferData(D.ELEMENT_ARRAY_BUFFER,m,w))}f.verticesNeedUpdate=!1;f.elementsNeedUpdate=!1;f.normalsNeedUpdate=!1;f.colorsNeedUpdate=!1;f.buffersNeedUpdate=!1}};this.setTexture=function(b,c){if(b.needsUpdate){b.__webglInit||(b.__webglInit=!0,b.addEventListener("dispose",Ba),b.__webglTexture=D.createTexture(),x.info.memory.textures++);D.activeTexture(D.TEXTURE0+c);D.bindTexture(D.TEXTURE_2D,
+b.__webglTexture);D.pixelStorei(D.UNPACK_FLIP_Y_WEBGL,b.flipY);D.pixelStorei(D.UNPACK_PREMULTIPLY_ALPHA_WEBGL,b.premultiplyAlpha);D.pixelStorei(D.UNPACK_ALIGNMENT,b.unpackAlignment);var h=b.image,h=y(h.width)&&y(h.height),f=A(b.format),e=A(b.type),g=D.TEXTURE_2D;h?(D.texParameteri(g,D.TEXTURE_WRAP_S,A(b.wrapS)),D.texParameteri(g,D.TEXTURE_WRAP_T,A(b.wrapT)),D.texParameteri(g,D.TEXTURE_MAG_FILTER,A(b.magFilter)),D.texParameteri(g,D.TEXTURE_MIN_FILTER,A(b.minFilter))):(D.texParameteri(g,D.TEXTURE_WRAP_S,
+D.CLAMP_TO_EDGE),D.texParameteri(g,D.TEXTURE_WRAP_T,D.CLAMP_TO_EDGE),D.texParameteri(g,D.TEXTURE_MAG_FILTER,D.LINEAR),D.texParameteri(g,D.TEXTURE_MIN_FILTER,D.LINEAR));var q=b.mipmaps;if(0<q.length&&h){for(var w=0,m=q.length;w<m;w++)g=q[w],D.texImage2D(D.TEXTURE_2D,w,f,f,e,g);b.generateMipmaps=!1}else D.texImage2D(D.TEXTURE_2D,0,f,f,e,b.image);b.generateMipmaps&&h&&D.generateMipmap(D.TEXTURE_2D);b.needsUpdate=!1;if(b.onUpdate)b.onUpdate()}else D.activeTexture(D.TEXTURE0+c),D.bindTexture(D.TEXTURE_2D,
+b.__webglTexture)};this.addPostPlugin(new $3Dmol.SpritePlugin)};$3Dmol.Scene=function(){$3Dmol.Object3D.call(this);this.overrideMaterial=this.fog=null;this.matrixAutoUpdate=!1;this.__objects=[];this.__lights=[];this.__objectsAdded=[];this.__objectsRemoved=[]};$3Dmol.Scene.prototype=Object.create($3Dmol.Object3D.prototype);
+$3Dmol.Scene.prototype.__addObject=function(b){b instanceof $3Dmol.Light?(-1===this.__lights.indexOf(b)&&this.__lights.push(b),b.target&&void 0===b.target.parent&&this.add(b.target)):-1===this.__objects.indexOf(b)&&(this.__objects.push(b),this.__objectsAdded.push(b),-1!==this.__objectsRemoved.indexOf(b)&&this.__objectsRemoved.splice(c,1));for(var c=0;c<b.children.length;c++)this.__addObject(b.children[c])};
+$3Dmol.Scene.prototype.__removeObject=function(b){var c;b instanceof $3Dmol.Light?(c=this.__lights.indexOf(b),-1!==c&&this.__lights.splice(c,1)):(c=this.__objects.indexOf(b),-1!==c&&(this.__objects.splice(c,1),this.__objectsRemoved.push(b),-1!==this.__objectsAdded.indexOf(b)&&this.__objectsAdded.splice(c,1)));for(c=0;c<b.children.length;c++)this.__removeObject(b.children[c])};$3Dmol.Fog=function(b,c,d){this.name="";this.color=new $3Dmol.Color(b);this.near=void 0!==c?c:1;this.far=void 0!==d?d:1E3};
+$3Dmol.Fog.prototype.clone=function(){return new $3Dmol.Fog(this.color.getHex(),this.near,this.far)};$3Dmol.ShaderUtils={clone:function(b){var c,d={};for(c in b){d[c]={};d[c].type=b[c].type;var p=b[c].value;p instanceof $3Dmol.Color?d[c].value=p.clone():"number"===typeof p?d[c].value=p:p instanceof Array?d[c].value=[]:console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform")}return d},stickimposterFragmentShader:"uniform float opacity;\nuniform mat4 projectionMatrix;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLight;\nvarying vec3 vColor;\nvarying vec3 cposition;\nvarying vec3 p1;\nvarying vec3 p2;\nvarying float r;\nvoid main() {\n    vec3 color = abs(vColor);\n    vec3 pos = cposition;\n    vec3 p = pos;\n    vec3 v = normalize(pos);\n    vec3 pa = p1;\n    vec3 va = normalize(p2-p1);\n    vec3 tmp1 = v-(dot(v,va)*va);\n    vec3 deltap = p-pa;\n    float A = dot(tmp1,tmp1);\n    if(A == 0.0) discard;\n    vec3 tmp2 = deltap-(dot(deltap,va)*va);\n    float B = 2.0*dot(tmp1, tmp2);\n    float C = dot(tmp2,tmp2)-r*r;\n    float det = (B*B) - (4.0*A*C);\n    if(det < 0.0) discard;\n    float sqrtDet = sqrt(det);\n    float posT = (-B+sqrtDet)/(2.0*A);\n    float negT = (-B-sqrtDet)/(2.0*A);\n    float intersectionT = min(posT,negT);\n    vec3 qi = p+v*intersectionT;\n    float dotp1 = dot(va,qi-p1);\n    float dotp2 = dot(va,qi-p2);\n    vec3 norm;\n    if( dotp1 < 0.0 || dotp2 > 0.0) {\n       vec3 cp;\n       if( dotp1 < 0.0) {        cp = p1;\n       } else {\n          cp = p2;\n       }\n       vec3 diff = p-cp;\n       A = dot(v,v);\n       B = dot(diff,v)*2.0;\n       C = dot(diff,diff)-r*r;\n       det = (B*B) - (4.0*C);\n       if(det < 0.0) discard;\n       sqrtDet = sqrt(det);\n       posT = (-B+sqrtDet)/(2.0);\n       negT = (-B-sqrtDet)/(2.0);\n       float t = min(posT,negT);\n       qi = p+v*t;\n       norm = normalize(qi-cp);\n    } else {\n       norm = normalize(qi-(dotp1*va + p1));\n    }\n    vec4 clipPos = projectionMatrix * vec4(qi, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    float depth = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    gl_FragDepthEXT = depth;"};
+$3Dmol.ShaderLib={basic:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nattribute vec3 position;\nattribute vec3 color;\nvarying vec3 vColor;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3}}},sphereimposter:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform mat4 projectionMatrix;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nuniform float uDepth;\nuniform vec3 directionalLightColor[ 1 ];\nvarying vec3 vColor;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 vLight;\nvarying vec3 center;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    float rsqr = rval*rval;\n    if(lensqr > rsqr)\n       discard;\n    float z = sqrt(rsqr-lensqr);\n    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z);\n    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    vec3 norm = normalize(vec3(mapping.x,mapping.y,z));\n    float dotProduct = dot( norm, vLight );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vec3 vLight = directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_FragColor = vec4(vLight*vColor, opacity*opacity );\n    float fogFactor = smoothstep( fogNear, fogFar, gl_FragDepthEXT/gl_FragCoord.w );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying vec3 vColor;\nvarying float rval;\nvarying vec3 vLight;\nvarying vec3 center;\nvoid main() {\n    vColor = color;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    center = mvPosition.xyz;\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec4 adjust = projectionMatrix* vec4(normal,0.0); adjust.z = 0.0; adjust.w = 0.0;\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vLight = normalize( lDirection.xyz );\n    mapping = normal.xy;\n    rval = abs(normal.x);\n    gl_Position = projPosition+adjust;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},lambert:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},instanced:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    gl_FragColor.xyz *= vLightFront;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 offset;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nattribute float radius;\nvarying vec3 vColor;\nvarying vec3 vLightFront;\nvoid main() {\n    vColor = color;\n    vec3 objectNormal = normal;\n    vec3 transformedNormal = normalMatrix * objectNormal;\n    vec4 mvPosition = modelViewMatrix * vec4( position * radius + offset, 1.0 );\n    vLightFront = vec3( 0.0 );\n    transformedNormal = normalize( transformedNormal );\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vec3 dirVector = normalize( lDirection.xyz );\n    float dotProduct = dot( transformedNormal, dirVector );\n    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );\n    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;\n    gl_Position = projectionMatrix * mvPosition;\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},outline:{fragmentShader:"uniform float opacity;\nuniform vec3 outlineColor;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvoid main() {\n    gl_FragColor = vec4( outlineColor, 1 );\n}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform float outlineWidth;\nuniform float outlinePushback;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvoid main() {\n    vec4 norm = modelViewMatrix*vec4(normalize(normal),0.0);\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    mvPosition.xy += norm.xy*outlineWidth;\n    gl_Position = projectionMatrix * mvPosition;\n    mvPosition.z -= outlinePushback;\n    vec4 pushpos = projectionMatrix*mvPosition;\n    gl_Position.z = gl_Position.w*pushpos.z/pushpos.w;\n}",
+uniforms:{opacity:{type:"f",value:1},outlineColor:{type:"c",value:new $3Dmol.Color(0,0,0)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},outlineWidth:{type:"f",value:.1},outlinePushback:{type:"f",value:1}}},sphereimposteroutline:{fragmentShader:"uniform float opacity;\nuniform vec3 outlineColor;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nuniform mat4 projectionMatrix;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 center;\nuniform float outlinePushback;\nvoid main() {\n    float lensqr = dot(mapping,mapping);\n    float rsqr = rval*rval;\n    if(lensqr > rsqr)\n       discard;\n    float z = sqrt(rsqr-lensqr);\n    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z-outlinePushback);\n    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);\n    float ndcDepth = clipPos.z / clipPos.w;\n    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;\n    gl_FragColor = vec4(outlineColor, 1 );\n}",
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform float outlineWidth;\nuniform float outlinePushback;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nvarying vec2 mapping;\nvarying float rval;\nvarying vec3 center;\nvoid main() {\n    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n    center = mvPosition.xyz;\n    vec4 projPosition = projectionMatrix * mvPosition;\n    vec2 norm = normal.xy + vec2(sign(normal.x)*outlineWidth,sign(normal.y)*outlineWidth);\n    vec4 adjust = projectionMatrix* vec4(norm,normal.z,0.0); adjust.z = 0.0; adjust.w = 0.0;\n    mapping = norm.xy;\n    rval = abs(norm.x);\n    gl_Position = projPosition+adjust;\n}",
+uniforms:{opacity:{type:"f",value:1},outlineColor:{type:"c",value:new $3Dmol.Color(0,0,0)},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},outlineWidth:{type:"f",value:.1},outlinePushback:{type:"f",value:1}}},stickimposter:{fragmentShader:[$3Dmol.ShaderUtils.stickimposterFragmentShader,"    float dotProduct = dot( norm, vLight );\n    vec3 light = vec3( max( dotProduct, 0.0 ) );\n    gl_FragColor = vec4(light*color, opacity*opacity );\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}"].join("\n"),
+vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nattribute float radius;\nvarying vec3 vColor;\nvarying vec3 vLight;\nvarying vec3 cposition;\nvarying vec3 p1;\nvarying vec3 p2;\nvarying float r;\nvoid main() {\n    vColor = color; vColor.z = abs(vColor.z);\n    r = abs(radius);\n    vec4 to = modelViewMatrix*vec4(normal, 1.0);\n    vec4 pt = modelViewMatrix*vec4(position, 1.0);\n    vec4 mvPosition = pt;\n    p1 = pt.xyz; p2 = to.xyz;\n    vec3 norm = to.xyz-pt.xyz;\n    float mult = 1.1;\n    if(length(p1) > length(p2)) {\n       mvPosition = to;\n    }\n    vec3 n = normalize(mvPosition.xyz);\n    if(color.z >= 0.0) {\n       vec3 pnorm = normalize(p1);\n       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);\n       mvPosition.xyz = p1+t*pnorm;\n    } else {\n       vec3 pnorm = normalize(p2);\n       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);\n       mvPosition.xyz = p2+t*pnorm;\n       mult *= -1.0;\n    }\n    vec3 cr = normalize(cross(mvPosition.xyz,norm))*radius;\n    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*radius;\n    mvPosition.xy +=  mult*(cr + doublecr).xy;\n    cposition = mvPosition.xyz;\n    gl_Position = projectionMatrix * mvPosition;\n    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );\n    vLight = normalize( lDirection.xyz )*directionalLightColor[0];\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},directionalLightColor:{type:"fv",value:[]},directionalLightDirection:{type:"fv",value:[]}}},stickimposteroutline:{fragmentShader:$3Dmol.ShaderUtils.stickimposterFragmentShader+"gl_FragColor = vec4(color,1.0);}",vertexShader:"uniform mat4 modelViewMatrix;\nuniform mat4 projectionMatrix;\nuniform mat4 viewMatrix;\nuniform mat3 normalMatrix;\nuniform vec3 directionalLightColor[ 1 ];\nuniform vec3 directionalLightDirection[ 1 ];\nuniform vec3 outlineColor;\nuniform float outlineWidth;\nuniform float outlinePushback;\nattribute vec3 position;\nattribute vec3 normal;\nattribute vec3 color;\nattribute float radius;\nvarying vec3 vColor;\nvarying vec3 vLight;\nvarying vec3 cposition;\nvarying vec3 p1;\nvarying vec3 p2;\nvarying float r;\nvoid main() {\n    vColor = outlineColor;\n    float rad = radius+sign(radius)*outlineWidth;\n    r = abs(rad);\n    vec4 to = modelViewMatrix*vec4(normal, 1.0);\n    vec4 pt = modelViewMatrix*vec4(position, 1.0);\n    to.xyz += normalize(to.xyz)*outlinePushback;\n    pt.xyz += normalize(pt.xyz)*outlinePushback;\n    vec4 mvPosition = pt;\n    p1 = pt.xyz; p2 = to.xyz;\n    vec3 norm = to.xyz-pt.xyz;\n    float mult = 1.1;\n    if(length(p1) > length(p2)) {\n       mvPosition = to;\n    }\n    vec3 n = normalize(mvPosition.xyz);\n    if(color.z >= 0.0) {\n       vec3 pnorm = normalize(p1);\n       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);\n       mvPosition.xyz = p1+t*pnorm;\n    } else {\n       vec3 pnorm = normalize(p2);\n       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);\n       mvPosition.xyz = p2+t*pnorm;\n       mult *= -1.0;\n    }\n    vec3 cr = normalize(cross(mvPosition.xyz,norm))*rad;\n    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*rad;\n    mvPosition.xy +=  mult*(cr + doublecr).xy;\n    cposition = mvPosition.xyz;\n    gl_Position = projectionMatrix * mvPosition;\n    vLight = vec3(1.0,1.0,1.0);\n}",
+uniforms:{opacity:{type:"f",value:1},fogColor:{type:"c",value:new $3Dmol.Color(1,1,1)},fogNear:{type:"f",value:1},fogFar:{type:"f",value:2E3},outlineColor:{type:"c",value:new $3Dmol.Color(0,0,0)},outlineWidth:{type:"f",value:.1},outlinePushback:{type:"f",value:1}}},lambertdouble:{fragmentShader:"uniform mat4 viewMatrix;\nuniform float opacity;\nuniform vec3 fogColor;\nuniform float fogNear;\nuniform float fogFar;\nvarying vec3 vLightFront;\nvarying vec3 vLightBack;\nvarying vec3 vColor;\nvoid main() {\n    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );\n    #ifndef WIREFRAME\n    if ( gl_FrontFacing )\n       gl_FragColor.xyz *= vLightFront;\n    else\n       gl_FragColor.xyz *= vLightBack;\n    #endif\n    gl_FragColor = gl_FragColor * vec4( vColor, opacity );\n    float depth = gl_FragCoord.z / gl_FragCoord.w;\n    float fogFactor = smoothstep( fogNear, fogFar, depth );\n    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );\n}",
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+0;4>L;L++)g.push(g[2*L]),g.push(g[f+2*L]),h=g[2*L],z=g[f+2*L],J[C+6*L]=h.x,J[C+1+6*L]=h.y,J[C+2+6*L]=h.z,J[C+3+6*L]=z.x,J[C+4+6*L]=z.y,J[C+5+6*L]=z.z,I[C+6*L]=y.r,I[C+1+6*L]=y.g,I[C+2+6*L]=y.b,I[C+3+6*L]=y.r,I[C+4+6*L]=y.g,I[C+5+6*L]=y.b;I=[w,w+2,w+6,w+4];u=[w+1,w+5,w+7,w+3];K[s]=I[0];K[s+1]=I[1];K[s+2]=I[3];K[s+3]=I[1];K[s+4]=I[2];K[s+5]=I[3];K[s+6]=u[0];K[s+7]=u[1];K[s+8]=u[3];K[s+9]=u[1];K[s+10]=u[2];K[s+11]=u[3];m.faceidx+=12;m.vertices+=8;d.initTypedArrays();d.setUpNormals();f=new $3Dmol.MeshDoubleLambertMaterial;
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+C+1-2*z,C-2*z];N[2*z-1]=[C,C+1-2*z,C+1-4*z,C-2*z];J=w.updateGeoGroup(2*z*x);for(A=0;A<x;A++){C=Math.round(A*(f.length-1)/x);s=$3Dmol.CC.color(f[C]);I=g;u=L;g=[];L=[];l=[];void 0!==d[0][A].atom&&(F=d[0][A].atom,"oval"===y?e=m:"rectangle"===y?e=K:"parabola"===y&&(e=p));e||(e=K);for(C=0;C<z;C++)E=A<x-1?d[C][A+1].clone().sub(d[C][A]):d[C][A-1].clone().sub(d[C][A]).negate(),O=C<z-1?d[C+1][A].clone().sub(d[C][A]):d[C-1][A].clone().sub(d[C][A]).negate(),l[C]=O.cross(E).normalize().multiplyScalar(h*e[C]);
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+2*z}E=J.faceArray;l=J.vertices;for(A=0;A<z-1;A++)O=[A,A+1,2*z-2-A,2*z-1-A],s=J.faceidx,E[s]=O[0],E[s+1]=O[1],E[s+2]=O[3],E[s+3]=O[1],E[s+4]=O[2],E[s+5]=O[3],J.faceidx+=6;for(A=0;A<z-1;A++)O=[l-1-A,l-2-A,l-2*z+A+1,l-2*z+A],s=J.faceidx,E[s]=O[0],E[s+1]=O[1],E[s+2]=O[3],E[s+3]=O[1],E[s+4]=O[2],E[s+5]=O[3],J.faceidx+=6;w.initTypedArrays();w.setUpNormals();f=new $3Dmol.MeshDoubleLambertMaterial;f.vertexColors=$3Dmol.FaceColors;"number"===typeof t&&0<=t&&1>t&&(f.transparent=!0,f.opacity=t);t=new $3Dmol.Mesh(w,
+f);q.add(t)}else c(q,d[0],d[z-1],f,w,t)}},y=function(b,c){if(b&&c&&b.chain===c.chain){if(b.reschain===c.reschain&&(b.resi===c.resi||b.resi===c.resi-1))return!0;if(b.resi<c.resi){var f=new $3Dmol.Vector3(b.x,b.y,b.z),d=new $3Dmol.Vector3(c.x,c.y,c.z);if(16>f.distanceToSquared(d))return!0}}return!1},A=function(b,c,f,d,h,t,m,e,F){var g,x={ALA:5,ARG:11,ASN:8,ASP:8,CYS:6,GLN:9,GLU:9,GLY:4,HIS:10,ILE:8,LEU:8,LYS:9,MET:8,PHE:11,PRO:7,SER:6,THR:7,TRP:14,TYR:12,VAL:7};if(d&&h&&m){var u=h.sub(d);u.normalize();
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+"default";b.style?b.style!=c&&(console.log("Warning: a cartoon chain's strand-style is ambiguous"),b.style="default"):b.style=c;if("arrow start"===m.ss||"arrow end"===m.ss)m.ss="s";return g}};return function(b,c,f,w){w=parseInt(5*parseFloat(w))||5;var h=fill=!0,t=doNotSmoothen=!1,m=num=w;w=div=w;m=m||5;w=w||5;var e="CA O P OP2 O2P O5' O3' C5' C2' O5* O3* C5* C2* N1 N3".split(" "),F=["DA","DG","A","G"],g=["DT","DC","U","C","T"],x=F.concat(g),u,s,l,E,M,C,G,z,H,L,N,J,I,K,O,Q,W,P=null,S=[],R=[];for(z=
+0;z<m;z++)R[z]=[];var aa=H=!1;z=0;for(z in c)if(E=c[z],"C"===E.elem&&"CA"===E.atom){var V=y(l,E);V&&"s"===E.ss?H=!0:H&&(l&&s&&l.style.cartoon.arrows&&s.style.cartoon.arrows&&(l.ss="arrow end",s.ss="arrow start"),H=!1);V&&"h"===l.ss?(!aa&&E.style.cartoon.tubes&&(E.ss="tube start"),aa=!0):aa&&"tube start"!==l.ss&&(s&&s.style.cartoon.tubes&&(s.ss="tube end"),aa=!1);s=l;l=E}l=void 0;for(z in c)if(E=c[z],void 0!==E&&-1!==$.inArray(E.atom,e))if(H=-1!=$.inArray(E.resn.trim(),x),s=E.style.cartoon,"trace"===
+s.style){if(P||(P=new $3Dmol.Geometry(!0)),"C"===E.elem&&"CA"===E.atom||H&&"P"===E.atom)C=f&&"spectrum"===s.color?f.valueToHex(E.resi,f.range()):$3Dmol.getColorFromStyle(E,s).getHex(),S.push(C),G=$.isNumeric(s.thickness)?s.thickness:.4,y(l,E)&&(C==M?(M=$3Dmol.CC.color(C),$3Dmol.GLDraw.drawCylinder(P,l,E,G,M,2,2)):(s=(new $3Dmol.Vector3).addVectors(l,E).multiplyScalar(.5),M=$3Dmol.CC.color(M),H=$3Dmol.CC.color(C),$3Dmol.GLDraw.drawCylinder(P,l,s,G,M,2,0),$3Dmol.GLDraw.drawCylinder(P,s,E,G,H,0,2))),
+l&&P&&(l.style.cartoon&&"trace"!=l.style.cartoon.style||l.chain!=E.chain)?(l=new $3Dmol.MeshDoubleLambertMaterial,l.vertexColors=$3Dmol.FaceColors,"number"===typeof P.opacity&&0<=P.opacity&&1>P.opacity&&(l.transparent=!0,l.opacity=P.opacity,delete P.opacity),P=new $3Dmol.Mesh(P,l),b.add(P),P=null):l&&(P.opacity&&l.style.cartoon.opacity?P.opacity!=l.style.cartoon.opacity&&(console.log("Warning: a trace-style chain's opacity is ambiguous"),P.opacity=1):P.opacity=parseFloat(l.style.cartoon.opacity)||
+1),l=E,M=C}else{u||(u=new $3Dmol.Geometry(!0));if(E&&"C"===E.elem&&"CA"===E.atom||H&&("P"===E.atom||0==E.atom.indexOf("O5"))){if(W)if("tube end"===E.ss)W=!1,H=new $3Dmol.Vector3(E.x,E.y,E.z),$3Dmol.GLDraw.drawCylinder(u,Q,H,2,$3Dmol.CC.color(M),1,1),E.ss="h";else continue;if(l&&(!y(l,E)||l.style.cartoon.style!==E.style.cartoon.style||"tube start"===l.ss)){"tube start"===l.ss&&(W=!0,Q=new $3Dmol.Vector3(l.x,l.y,l.z),l.ss="h");O&&(H=I?(new $3Dmol.Vector3).addVectors(l,I).multiplyScalar(.5):new $3Dmol.Vector3(l.x,
+l.y,l.z),$3Dmol.GLDraw.drawCylinder(u,H,O,.4,$3Dmol.CC.color(O.color),0,2),H=A(R,m,!t,I,K,J,l,c,z),S.push(C),H&&S.push(C),O=null);for(z=0;!G&&z<m;z++)d(b,R[z],1,S,w,R.opacity);h&&0<R[0].length&&p(b,R,S,w,G,R.opacity,R.style);null!=u&&0<u.vertices&&(z=new $3Dmol.MeshDoubleLambertMaterial,z.vertexColors=$3Dmol.FaceColors,"number"===typeof R.opacity&&0<=R.opacity&&1>R.opacity&&(z.transparent=!0,z.opacity=R.opacity),u=new $3Dmol.Mesh(u,z),b.add(u),u=null);R=[];for(z=0;z<m;z++)R[z]=[];S=[]}if(void 0===
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+g))O=new $3Dmol.Vector3(E.x,E.y,E.z),O.color=$3Dmol.getColorFromStyle(E,s).getHex();N&&L&&N.resi===L.resi&&(H=A(R,m,!t,L,N,J,l,c,z),J=N,N=L=null,S.push(C),H&&S.push(C))}O&&(H=I?(new $3Dmol.Vector3).addVectors(l,I).multiplyScalar(.5):new $3Dmol.Vector3(l.x,l.y,l.z),$3Dmol.GLDraw.drawCylinder(u,H,O,.4,$3Dmol.CC.color(O.color),0,2),H=A(R,m,!t,I,K,J,l,c,z),S.push(C),H&&S.push(C));for(z=0;!G&&z<m;z++)d(b,R[z],1,S,w,R.opacity);h&&0<R[0].length&&p(b,R,S,w,G,R.opacity,R.style);null!=u&&0<u.vertices&&(z=new $3Dmol.MeshDoubleLambertMaterial,
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+E=x[F/2],A=x[F/2+1],C=b.vertices,G,z,H,L,N,J,I=b.vertexArray,K=b.normalArray,O=b.colorArray,Q=b.faceArray;for(H=0;H<w;++H)z=2*H,L=g[0]*s[z].x+g[3]*s[z].y+g[6]*s[z].z,N=g[1]*s[z].x+g[4]*s[z].y+g[7]*s[z].z,J=g[5]*s[z].y+g[8]*s[z].z,G=3*(C+z),z=b.faceidx,I[G]=L+d.x,I[G+1]=N+d.y,I[G+2]=J+d.z,I[G+3]=L+f.x,I[G+4]=N+f.y,I[G+5]=J+f.z,K[G]=L,K[G+3]=L,K[G+1]=N,K[G+4]=N,K[G+2]=J,K[G+5]=J,O[G]=h.r,O[G+3]=h.r,O[G+1]=h.g,O[G+4]=h.g,O[G+2]=h.b,O[G+5]=h.b,Q[z]=A[H]+C,Q[z+1]=A[H+1]+C,Q[z+2]=E[H]+C,Q[z+3]=E[H]+C,Q[z+
+4]=A[H+1]+C,Q[z+5]=E[H+1]+C,b.faceidx+=6;if(e){t=t?F+1:F/2+1;var W,P,S,R,aa,V,Z,ca,X,D,ba,U,T;for(N=m?0:F/2;N<t;N++)if(N!==F/2){var ea=N<=F/2?f:d;for(L=0;L<w;L++)z=b.faceidx,m=x[N][L+1],H=3*(m+C),e=x[N][L],J=3*(e+C),E=x[N+1][L],G=3*(E+C),A=x[N+1][L+1],T=3*(A+C),W=g[0]*s[m].x+g[3]*s[m].y+g[6]*s[m].z,P=g[0]*s[e].x+g[3]*s[e].y+g[6]*s[e].z,S=g[0]*s[E].x+g[3]*s[E].y+g[6]*s[E].z,R=g[0]*s[A].x+g[3]*s[A].y+g[6]*s[A].z,aa=g[1]*s[m].x+g[4]*s[m].y+g[7]*s[m].z,V=g[1]*s[e].x+g[4]*s[e].y+g[7]*s[e].z,Z=g[1]*s[E].x+
+g[4]*s[E].y+g[7]*s[E].z,ca=g[1]*s[A].x+g[4]*s[A].y+g[7]*s[A].z,X=g[5]*s[m].y+g[8]*s[m].z,D=g[5]*s[e].y+g[8]*s[e].z,ba=g[5]*s[E].y+g[8]*s[E].z,U=g[5]*s[A].y+g[8]*s[A].z,I[H]=W+ea.x,I[J]=P+ea.x,I[G]=S+ea.x,I[T]=R+ea.x,I[H+1]=aa+ea.y,I[J+1]=V+ea.y,I[G+1]=Z+ea.y,I[T+1]=ca+ea.y,I[H+2]=X+ea.z,I[J+2]=D+ea.z,I[G+2]=ba+ea.z,I[T+2]=U+ea.z,O[H]=h.r,O[J]=h.r,O[G]=h.r,O[T]=h.r,O[H+1]=h.g,O[J+1]=h.g,O[G+1]=h.g,O[T+1]=h.g,O[H+2]=h.b,O[J+2]=h.b,O[G+2]=h.b,O[T+2]=h.b,W=g[0]*l[m].x+g[3]*l[m].y+g[6]*l[m].z,P=g[0]*l[e].x+
+g[3]*l[e].y+g[6]*l[e].z,S=g[0]*l[E].x+g[3]*l[E].y+g[6]*l[E].z,R=g[0]*l[A].x+g[3]*l[A].y+g[6]*l[A].z,aa=g[1]*l[m].x+g[4]*l[m].y+g[7]*l[m].z,V=g[1]*l[e].x+g[4]*l[e].y+g[7]*l[e].z,Z=g[1]*l[E].x+g[4]*l[E].y+g[7]*l[E].z,ca=g[1]*l[A].x+g[4]*l[A].y+g[7]*l[A].z,X=g[5]*l[m].y+g[8]*l[m].z,D=g[5]*l[e].y+g[8]*l[e].z,ba=g[5]*l[E].y+g[8]*l[E].z,U=g[5]*l[A].y+g[8]*l[A].z,0===N?(K[H]=W,K[G]=S,K[T]=R,K[H+1]=aa,K[G+1]=Z,K[T+1]=ca,K[H+2]=X,K[G+2]=ba,K[T+2]=U,Q[z]=m+C,Q[z+1]=E+C,Q[z+2]=A+C,b.faceidx+=3):N===t-1?(K[H]=
+W,K[J]=P,K[G]=S,K[H+1]=aa,K[J+1]=V,K[G+1]=Z,K[H+2]=X,K[J+2]=D,K[G+2]=ba,Q[z]=m+C,Q[z+1]=e+C,Q[z+2]=E+C,b.faceidx+=3):(K[H]=W,K[J]=P,K[T]=R,K[H+1]=aa,K[J+1]=V,K[T+1]=ca,K[H+2]=X,K[J+2]=D,K[T+2]=U,K[J]=P,K[G]=S,K[T]=R,K[J+1]=V,K[G+1]=Z,K[T+1]=ca,K[J+2]=D,K[G+2]=ba,K[T+2]=U,Q[z]=m+C,Q[z+1]=e+C,Q[z+2]=A+C,Q[z+3]=e+C,Q[z+4]=E+C,Q[z+5]=A+C,b.faceidx+=6)}}b.vertices+=u}};b.drawCone=function(b,p,f,w,h){if(p&&f){h=h||{r:0,g:0,b:0};var t=[f.x,f.y,f.z];t.x-=p.x;t.y-=p.y;t.z-=p.z;var m=c(t),e=d.length;b=b.updateGeoGroup(e+
+2);var F=b.vertices,g,x,u,s=b.vertexArray,l=b.normalArray,E=b.colorArray,y=b.faceArray;g=3*F;t=(new $3Dmol.Vector3(t[0],t[1],t[2])).normalize();s[g]=p.x;s[g+1]=p.y;s[g+2]=p.z;l[g]=-t.x;l[g+1]=-t.y;l[g+2]=-t.z;E[g]=h.r;E[g+1]=h.g;E[g+2]=h.b;s[g+3]=f.x;s[g+4]=f.y;s[g+5]=f.z;l[g+3]=t.x;l[g+4]=t.y;l[g+5]=t.z;E[g+3]=h.r;E[g+4]=h.g;E[g+5]=h.b;g+=6;for(f=0;f<e;++f)u=d[f].clone(),u.multiplyScalar(w),t=m[0]*u.x+m[3]*u.y+m[6]*u.z,x=m[1]*u.x+m[4]*u.y+m[7]*u.z,u=m[5]*u.y+m[8]*u.z,s[g]=t+p.x,s[g+1]=x+p.y,s[g+
+2]=u+p.z,l[g]=t,l[g+1]=x,l[g+2]=u,E[g]=h.r,E[g+1]=h.g,E[g+2]=h.b,g+=3;b.vertices+=e+2;p=b.faceidx;for(f=0;f<e;f++)w=F+2+f,h=F+2+(f+1)%e,y[p]=w,y[p+1]=h,y[p+2]=F,p+=3,y[p]=w,y[p+1]=h,y[p+2]=F+1,p+=3;b.faceidx+=6*e}};var A={cache:{},getVerticesForRadius:function(b){if("undefined"!==typeof this.cache[b])return this.cache[b];var c={vertices:[],verticesRows:[],normals:[]},f=16,d=10;1>b&&(f=10,d=8);var h=2*Math.PI,t=Math.PI,m,e;for(e=0;e<=d;e++){var p=[];for(m=0;m<=f;m++){var g=m/f,x=e/d,u={};u.x=-b*Math.cos(0+
+g*h)*Math.sin(0+x*t);u.y=b*Math.cos(0+x*t);u.z=b*Math.sin(0+g*h)*Math.sin(0+x*t);g=new $3Dmol.Vector3(u.x,u.y,u.z);g.normalize();c.vertices.push(u);c.normals.push(g);p.push(c.vertices.length-1)}c.verticesRows.push(p)}return this.cache[b]=c}};b.drawSphere=function(b,c,f,d){new $3Dmol.Vector3(c.x,c.y,c.z);var h=A.getVerticesForRadius(f),t=h.vertices,m=h.normals;b=b.updateGeoGroup(t.length);for(var e=b.vertices,p=b.vertexArray,g=b.colorArray,x=b.faceArray,u=b.lineArray,s=b.normalArray,l=0,E=t.length;l<
+E;++l){var y=3*(e+l),C=t[l];p[y]=C.x+c.x;p[y+1]=C.y+c.y;p[y+2]=C.z+c.z;g[y]=d.r;g[y+1]=d.g;g[y+2]=d.b}b.vertices+=t.length;h=h.verticesRows;p=h.length-1;for(d=0;d<p;d++)for(g=h[d].length-1,c=0;c<g;c++){var l=b.faceidx,E=b.lineidx,y=h[d][c+1]+e,C=3*y,G=h[d][c]+e,z=3*G,H=h[d+1][c]+e,L=3*H,N=h[d+1][c+1]+e,J=3*N,I=m[y-e],K=m[G-e],O=m[H-e],Q=m[N-e];Math.abs(t[y-e].y)===f?(s[C]=I.x,s[L]=O.x,s[J]=Q.x,s[C+1]=I.y,s[L+1]=O.y,s[J+1]=Q.y,s[C+2]=I.z,s[L+2]=O.z,s[J+2]=Q.z,x[l]=y,x[l+1]=H,x[l+2]=N,u[E]=y,u[E+1]=
+H,u[E+2]=y,u[E+3]=N,u[E+4]=H,u[E+5]=N,b.faceidx+=3,b.lineidx+=6):Math.abs(t[H-e].y)===f?(s[C]=I.x,s[z]=K.x,s[L]=O.x,s[C+1]=I.y,s[z+1]=K.y,s[L+1]=O.y,s[C+2]=I.z,s[z+2]=K.z,s[L+2]=O.z,x[l]=y,x[l+1]=G,x[l+2]=H,u[E]=y,u[E+1]=G,u[E+2]=y,u[E+3]=H,u[E+4]=G,u[E+5]=H,b.faceidx+=3,b.lineidx+=6):(s[C]=I.x,s[z]=K.x,s[J]=Q.x,s[C+1]=I.y,s[z+1]=K.y,s[J+1]=Q.y,s[C+2]=I.z,s[z+2]=K.z,s[J+2]=Q.z,s[z]=K.x,s[L]=O.x,s[J]=Q.x,s[z+1]=K.y,s[L+1]=O.y,s[J+1]=Q.y,s[z+2]=K.z,s[L+2]=O.z,s[J+2]=Q.z,x[l]=y,x[l+1]=G,x[l+2]=N,x[l+
+3]=G,x[l+4]=H,x[l+5]=N,u[E]=y,u[E+1]=G,u[E+2]=y,u[E+3]=N,u[E+4]=G,u[E+5]=H,u[E+6]=H,u[E+7]=N,b.faceidx+=6,b.lineidx+=8)}};return b}();$3Dmol=$3Dmol||{};
+$3Dmol.GLModel=function(){function b(b,q){var B=[],f=[],w=!1,h=null,t=null,m=null,e={},F=new $3Dmol.Matrix4,g,x=$3Dmol.elementColors.defaultColor,u=q?q:$3Dmol.elementColors.defaultColors,s=function(b,c){var h=1.5;"undefined"!=typeof c.radius?h=c.radius:d[b.elem]&&(h=d[b.elem]);"undefined"!=typeof c.scale&&(h*=c.scale);return h},l=function(b,c,h){var e=new $3Dmol.Vector3(b.x,b.y,b.z),f=(new $3Dmol.Vector3(c.x,c.y,c.z)).clone(),g=null;f.sub(e);1===b.bonds.length?1===c.bonds.length?(g=f.clone(),1E-4<
+Math.abs(g.x)?g.y+=1:g.x+=1):(h=(h+1)%c.bonds.length,b=c.bonds[h],b=B[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(e),g=b.clone(),g.cross(f)):(h=(h+1)%b.bonds.length,b=b.bonds[h],b=B[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(e),g=b.clone(),g.cross(f));.01>g.lengthSq()&&(g=f.clone(),1E-4<Math.abs(g.x)?g.y+=1:g.x+=1);g.cross(f);g.normalize();return g},E=function(b,c,h,e,f,g){b[h]=e.x;b[h+1]=e.y;b[h+2]=e.z;c[h]=g.r;c[h+1]=g.g;c[h+2]=g.b;b[h+3]=f.x;b[h+4]=f.y;b[h+5]=f.z;c[h+3]=
+g.r;c[h+4]=g.g;c[h+5]=g.b},M=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=$3Dmol.getColorFromStyle(b,h),h=s(b,h);if(!0===b.clickable&&void 0!==b.intersectionShape){var f=new $3Dmol.Vector3(b.x,b.y,b.z);b.intersectionShape.sphere.push(new $3Dmol.Sphere(f,h))}$3Dmol.GLDraw.drawSphere(c,b,h,e)}}},C=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=s(b,h),h=$3Dmol.getColorFromStyle(b,h),f=c.updateGeoGroup(1),g=f.vertices,d=3*g,m=f.vertexArray,l=f.colorArray,
+t=f.radiusArray;m[d]=b.x;m[d+1]=b.y;m[d+2]=b.z;l=f.colorArray;l[d]=h.r;l[d+1]=h.g;l[d+2]=h.b;t[g]=e;f.vertices+=1}}},G=function(b,c,h,e){b=b.updateGeoGroup(4);for(var f=b.vertices,g=3*f,d=b.vertexArray,m=b.colorArray,l=0;4>l;l++)d[g+3*l]=c.x,d[g+3*l+1]=c.y,d[g+3*l+2]=c.z;c=b.normalArray;m=b.colorArray;for(l=0;4>l;l++)m[g+3*l]=e.r,m[g+3*l+1]=e.g,m[g+3*l+2]=e.b;c[g+0]=-h;c[g+1]=h;c[g+2]=0;c[g+3]=-h;c[g+4]=-h;c[g+5]=0;c[g+6]=h;c[g+7]=-h;c[g+8]=0;c[g+9]=h;c[g+10]=h;c[g+11]=0;b.vertices+=4;h=b.faceArray;
+e=b.faceidx;h[e+0]=f;h[e+1]=f+1;h[e+2]=f+2;h[e+3]=f+2;h[e+4]=f+3;h[e+5]=f;b.faceidx+=6},z=function(b,c){if(b.style.sphere){var h=b.style.sphere;if(!h.hidden){var e=s(b,h),h=$3Dmol.getColorFromStyle(b,h);G(c,b,e,h)}}},H=function(b,c,h,e,f,g,d){b=b.updateGeoGroup(4);g=b.vertices;d=b.vertexArray;var m=b.colorArray,l=b.radiusArray,t=b.normalArray,w=f.r,s=f.g;f=f.b;for(var u=3*g,x=0;4>x;x++){d[u]=c.x;t[u]=h.x;m[u]=w;u++;d[u]=c.y;t[u]=h.y;m[u]=s;u++;d[u]=c.z;t[u]=h.z;if(2>x)m[u]=f;else{var q=u,p=-f;0==
+p&&(p=-1E-4);m[q]=p}u++}b.vertices+=4;l[g]=-e;l[g+1]=e;l[g+2]=-e;l[g+3]=e;c=b.faceArray;h=b.faceidx;c[h+0]=g;c[h+1]=g+1;c[h+2]=g+2;c[h+3]=g+2;c[h+4]=g+3;c[h+5]=g;b.faceidx+=6};this.getCrystData=function(){return e.cryst?e.cryst:null};this.getSymmetries=function(){"undefined"==typeof e.symmetries&&(e.symmetries=[F]);return e.symmetries};this.setSymmetries=function(b){e.symmetries="undefined"==typeof b?[F]:b};this.getID=function(){return b};this.getFrames=function(){return f};this.setFrame=function(b){0!=
+f.length&&(B=0<=b&&b<f.length?f[b]:f[f.length-1],h=null)};this.addFrame=function(b){f.push(b)};this.vibrate=function(b,c){var h=[];c=c||1;b=b||10;for(var e=0;e<B.length;e++){var g=new $3Dmol.Vector3(B[e].dx,B[e].dy,B[e].dz);h.push(g)}b--;for(e=1;e<=b;e++){h=[];for(g=0;g<B.length;g++){var d=new $3Dmol.Vector3(B[g].dx,B[g].dy,B[g].dz),m=new $3Dmol.Vector3(B[g].x,B[g].y,B[g].z);d.sub(m);d.multiplyScalar(e*c/b);m.add(d);var d={},l;for(l in B[g])d[l]=B[g][l];d.x=m.x;d.y=m.y;d.z=m.z;h.push(d)}f.push(h)}f.unshift(B)};
+this.setAtomDefaults=function(h){for(var e=0;e<h.length;e++){var f=h[e];f&&(f.style=f.style||c,f.color=f.color||u[f.elem]||x,f.model=b,f.clickable&&(f.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}))}};this.addMolData=function(c,h,d){d=d||{};c=$3Dmol.GLModel.parseMolData(c,h,d);g=!d.duplicateAssemblyAtoms;(h=c.modelData)&&(e=Array.isArray(h)?h[0]:h);if(0==f.length){for(d=0;d<c.length;d++)0!=c[d].length&&f.push(c[d]);f[0]&&(B=f[0])}else if(d.frames)for(d=0;d<c.length;d++)f.push(c[d]);
+else for(d=0;d<c.length;d++)this.addAtoms(c[d]);for(d=0;d<f.length;d++)this.setAtomDefaults(f[d],b)};this.setDontDuplicateAtoms=function(b){g=b};this.setModelData=function(b){e=b};this.atomIsSelected=function(b,c){if("undefined"===typeof c)return!0;var h=!!c.invert,e=!0,f;for(f in c)if("predicate"===f){if(!c.predicate(b)){e=!1;break}}else if("properties"==f&&b[f])for(var g in c.properties){if("undefined"===typeof b.properties[g]){e=!1;break}if(b.properties[g]!=c.properties[g]){e=!1;break}}else if(c.hasOwnProperty(f)&&
+"props"!=f&&"invert"!=f&&"model"!=f&&"byres"!=f&&"expand"!=f&&"within"!=f){if("undefined"===typeof b[f]){e=!1;break}var d=!1;if("bonds"===f){if(d=c[f],d!=b.bonds.length){e=!1;break}}else if($.isArray(c[f])){for(var m=c[f],l=0;l<m.length;l++)if(b[f]==m[l]){d=!0;break}if(!d){e=!1;break}}else if(d=c[f],b[f]!=d){e=!1;break}}return h?!e:e};this.selectedAtoms=function(b,c){var h=[];b=b||{};c||(c=B);for(var e=c.length,f=0;f<e;f++){var g=c[f];g&&this.atomIsSelected(g,b)&&h.push(g)}if(b.hasOwnProperty("expand")){var d;
+var m=parseFloat(b.expand);if(0>=m)d=h;else{f=$3Dmol.getExtent(h);e=[[],[],[]];for(g=0;3>g;g++)e[0][g]=f[0][g]-m,e[1][g]=f[1][g]+m,e[2][g]=f[2][g];m=[];for(g=0;g<B.length;g++){d=B[g].x;var l=B[g].y,t=B[g].z;d>=e[0][0]&&d<=e[1][0]&&l>=e[0][1]&&l<=e[1][1]&&t>=e[0][2]&&t<=e[1][2]&&(d>=f[0][0]&&d<=f[1][0]&&l>=f[0][1]&&l<=f[1][1]&&t>=f[0][2]&&t<=f[1][2]||m.push(B[g]))}d=m}l=h.length;for(f=0;f<d.length;f++)for(e=0;e<l;e++)g=L(d[f],h[e]),m=Math.pow(b.expand,2),g<m&&0<g&&h.push(d[f])}if(b.hasOwnProperty("within")&&
+b.within.hasOwnProperty("sel")&&b.within.hasOwnProperty("distance")){d=this.selectedAtoms(b.within.sel,B);l=[];for(f=0;f<d.length;f++)for(e=0;e<h.length;e++)g=L(d[f],h[e]),m=Math.pow(parseFloat(b.within.distance),2),g<m&&0<g&&l.push(h[e]);h=l}if(b.hasOwnProperty("byres"))for(m={},d=[],l=[],f=0;f<h.length;f++){var g=h[f],t=g.chain,w=g.resi;void 0===m[t]&&(m[t]={});if(g.hasOwnProperty("resi")&&void 0===m[t][w])for(m[t][w]=!0,l.push(g);0<l.length;)if(g=l.pop(),t=g.chain,w=g.resi,void 0===d[g.index])for(d[g.index]=
+!0,e=0;e<g.bonds.length;e++){var s=B[g.bonds[e]];void 0===d[s.index]&&s.hasOwnProperty("resi")&&s.chain==t&&s.resi==w&&(l.push(s),h.push(s))}}return h};var L=function(b,c){var h=c.y-b.y,e=c.z-b.z;return Math.pow(c.x-b.x,2)+Math.pow(h,2)+Math.pow(e,2)};this.addAtoms=function(e){h=null;var f=B.length,g=[],d;for(d=0;d<e.length;d++)"undefined"==typeof e[d].index&&(e[d].index=d),"undefined"==typeof e[d].serial&&(e[d].serial=d),g[e[d].index]=f+d;for(d=0;d<e.length;d++){var f=e[d],m=g[f.index],l=$.extend(!1,
+{},f);l.index=m;l.bonds=[];l.bondOrder=[];l.model=b;l.style=l.style||c;"undefined"==typeof l.color&&(l.color=u[l.elem]||x);for(var m=f.bonds?f.bonds.length:0,t=0;t<m;t++){var w=g[f.bonds[t]];"undefined"!=typeof w&&(l.bonds.push(w),l.bondOrder.push(f.bondOrder?f.bondOrder[t]:1))}B.push(l)}};this.removeAtoms=function(b){h=null;var c=[],e;for(e=0;e<b.length;e++)c[b[e].index]=!0;b=[];for(e=0;e<B.length;e++){var f=B[e];c[f.index]||b.push(f)}B=[];this.addAtoms(b)};this.setStyle=function(b,c,e){"undefined"===
+typeof c&&"undefined"==typeof e&&(c=b,b={});for(var g in b)-1===p.indexOf(g)&&console.log("Unknown selector "+g);for(g in c)-1===y.indexOf(g)&&console.log("Unknown style "+g);var d=!1,m=function(h){for(var f=l.selectedAtoms(b,h),m=0;m<h.length;m++)h[m]&&(h[m].capDrawn=!1);for(m=0;m<f.length;m++)for(g in d=!0,f[m].clickable&&(f[m].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),e||(f[m].style={}),c)if(c.hasOwnProperty(g)){f[m].style[g]=f[m].style[g]||{};for(var t in c[g])f[m].style[g][t]=
+c[g][t]}},l=this;m(B);for(var t=0;t<f.length;t++)m(f[t]);d&&(h=null)};this.setClickable=function(b,c,e){for(var f in b)-1===p.indexOf(f)&&console.log("Unknown selector "+f);c=!!c;if(e&&"function"!=typeof e)console.log("Callback is not a function");else{f=this.selectedAtoms(b,B);var g=f.length;for(b=0;b<g;b++)f[b].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]},f[b].clickable=c,e&&(f[b].callback=e);0<g&&(h=null)}};this.setColorByElement=function(b,c){var e;if(e=null!==h)e=m,e=c&&e?JSON.stringify(c)==
+JSON.stringify(e):c==e;if(!e){m=c;var f=this.selectedAtoms(b,f);0<f.length&&(h=null);for(e=0;e<f.length;e++){var g=f[e];"undefined"!==typeof c[g.elem]&&(g.color=c[g.elem])}}};this.setColorByProperty=function(b,c,e,f){var g=this.selectedAtoms(b,g);m=null;0<g.length&&(h=null);var d;f||(f=e.range());f||(f=$3Dmol.getPropertyRange(g,c));for(b=0;b<g.length;b++)d=g[b],null!=$3Dmol.getAtomProperty(d,c)&&(d.color=e.valueToHex(parseFloat(d.properties[c]),[f[0],f[1]]))};this.setColorByFunction=function(b,c){var e=
+this.selectedAtoms(b,e);m=null;0<e.length&&(h=null);for(i=0;i<e.length;i++)a=e[i],a.color=c(a)};this.toCDObject=function(b){var c={a:[],b:[]};b&&(c.s=[]);for(var h=0;h<B.length;h++){var e={},f=B[h];e.x=f.x;e.y=f.y;e.z=f.z;"C"!=f.elem&&(e.l=f.elem);if(b){for(var g=0;g<c.s.length&&JSON.stringify(f.style)!==JSON.stringify(c.s[g]);)g++;g===c.s.length&&c.s.push(f.style);0!==g&&(e.s=g)}c.a.push(e);for(e=0;e<f.bonds.length;e++){var g=h,d=f.bonds[e];g>=d||(g={b:g,e:d},d=f.bondOrder[e],1!=d&&(g.o=d),c.b.push(g))}}return c};
+this.globj=function(b,c){if(null===h){var f=B,d=c,d=d||{},m=new $3Dmol.Object3D,u=[],x={},q={},p=M,y=null,F=null;d.supportsImposters?(p=z,y=new $3Dmol.Geometry(!0),y.imposter=!0,F=new $3Dmol.Geometry(!0,!0),F.imposter=!0,F.sphereGeometry=y,F.drawnCaps={}):(d.supportsAIA?(p=C,y=new $3Dmol.Geometry(!1,!0,!0),y.instanced=!0):y=new $3Dmol.Geometry(!0),F=new $3Dmol.Geometry(!0));var A,L,ca,X,D={},ba=[Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY];A=0;for(ca=f.length;A<ca;A++){var U=f[A];if(U&&U.style){U.clickable&&
+void 0===U.intersectionShape&&(U.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});X={line:void 0,cross:void 0,stick:void 0,sphere:void 0};for(L in X)X[L]=U.style[L]?U.style[L].opacity?parseFloat(U.style[L].opacity):1:void 0,D[L]?void 0!=X[L]&&D[L]!=X[L]&&(console.log("Warning: "+L+" opacity is ambiguous"),D[L]=1):D[L]=X[L];p(U,y);var T=U,ea=q;if(T.style.cross){var Ba=T.style.cross;if(!Ba.hidden){var Na=Ba.linewidth||1;ea[Na]||(ea[Na]=new $3Dmol.Geometry);var Ja=ea[Na].updateGeoGroup(6),
+La=s(T,Ba),Ia=[[La,0,0],[-La,0,0],[0,La,0],[0,-La,0],[0,0,La],[0,0,-La]],Za=T.clickable;Za&&void 0===T.intersectionShape&&(T.intersectionShape={sphere:[],cylinder:[],line:[]});for(var Ta=$3Dmol.getColorFromStyle(T,Ba),$a=Ja.vertexArray,Ua=Ja.colorArray,xa=0;6>xa;xa++){var Ma=3*Ja.vertices;Ja.vertices++;$a[Ma]=T.x+Ia[xa][0];$a[Ma+1]=T.y+Ia[xa][1];$a[Ma+2]=T.z+Ia[xa][2];Ua[Ma]=Ta.r;Ua[Ma+1]=Ta.g;Ua[Ma+2]=Ta.b;if(Za){var Va=new $3Dmol.Vector3(Ia[xa][0],Ia[xa][1],Ia[xa][2]);Va.multiplyScalar(.1);Va.set(Va.x+
+T.x,Va.y+T.y,Va.z+T.z);T.intersectionShape.line.push(Va)}}}}var fa=U,zb=f,kb=x;if(fa.style.line){var rb=fa.style.line;if(!rb.hidden){var lb=rb.linewidth||1;kb[lb]||(kb[lb]=new $3Dmol.Geometry);for(var ta=kb[lb].updateGeoGroup(6*fa.bonds.length),ja=ta.vertexArray,ka=ta.colorArray,Ea=0;Ea<fa.bonds.length;Ea++){var Oa=zb[fa.bonds[Ea]];if(Oa.style.line&&!(fa.serial>=Oa.serial)){var Ca=new $3Dmol.Vector3(fa.x,fa.y,fa.z),Qa=new $3Dmol.Vector3(Oa.x,Oa.y,Oa.z),fb=Ca.clone().add(Qa).multiplyScalar(.5),sb=
+!1;fa.clickable&&(void 0===fa.intersectionShape&&(fa.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),fa.intersectionShape.line.push(Ca),fa.intersectionShape.line.push(Qa));var pa=$3Dmol.getColorFromStyle(fa,fa.style.line),Fa=$3Dmol.getColorFromStyle(Oa,Oa.style.line);if(fa.bondStyles&&fa.bondStyles[Ea]){var Pa=fa.bondStyles[Ea];if(!Pa.iswire)continue;Pa.radius&&(bondR=Pa.radius);Pa.singleBond&&(sb=!0);"undefined"!=typeof Pa.color1&&(pa=$3Dmol.CC.color(Pa.color1));"undefined"!=typeof Pa.color2&&
+(Fa=$3Dmol.CC.color(Pa.color2))}var la=3*ta.vertices;if(1<fa.bondOrder[Ea]&&4>fa.bondOrder[Ea]&&!sb){var Wa=l(fa,Oa,Ea),Da=Qa.clone();Da.sub(Ca);if(2==fa.bondOrder[Ea])if(Wa.multiplyScalar(.1),p1a=Ca.clone(),p1a.add(Wa),p1b=Ca.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Da),p2b=p1b.clone(),p2b.add(Da),pa==Fa)ta.vertices+=4,E(ja,ka,la,p1a,p2a,pa),E(ja,ka,la+6,p1b,p2b,pa);else{ta.vertices+=8;Da.multiplyScalar(.5);var Ra=p1a.clone();Ra.add(Da);var Sa=p1b.clone();Sa.add(Da);E(ja,ka,la,p1a,Ra,pa);E(ja,
+ka,la+6,Ra,p2a,Fa);E(ja,ka,la+12,p1b,Sa,pa);E(ja,ka,la+18,Sa,p2b,Fa)}else 3==fa.bondOrder[Ea]&&(Wa.multiplyScalar(.1),p1a=Ca.clone(),p1a.add(Wa),p1b=Ca.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Da),p2b=p1b.clone(),p2b.add(Da),pa==Fa?(ta.vertices+=6,E(ja,ka,la,Ca,Qa,pa),E(ja,ka,la+6,p1a,p2a,pa),E(ja,ka,la+12,p1b,p2b,pa)):(ta.vertices+=12,Da.multiplyScalar(.5),Ra=p1a.clone(),Ra.add(Da),Sa=p1b.clone(),Sa.add(Da),E(ja,ka,la,Ca,fb,pa),E(ja,ka,la+6,fb,Qa,Fa),E(ja,ka,la+12,p1a,Ra,pa),E(ja,ka,la+18,Ra,
+p2a,Fa),E(ja,ka,la+24,p1b,Sa,pa),E(ja,ka,la+30,Sa,p2b,Fa)))}else pa==Fa?(ta.vertices+=2,E(ja,ka,la,Ca,Qa,pa)):(ta.vertices+=4,E(ja,ka,la,Ca,fb,pa),E(ja,ka,la+6,fb,Qa,Fa))}}}}var Y=U,Ab=f,ga=F;if(Y.style.stick){var gb=Y.style.stick;if(!gb.hidden){var ab=gb.radius||.25,ua=ab,tb=gb.singleBonds||!1,bb=0,cb=0,ma=$3Dmol.getColorFromStyle(Y,gb),na=void 0,ya=void 0;!Y.capDrawn&&4>Y.bonds.length&&(bb=2);var ia=$3Dmol.GLDraw.drawCylinder;ga.imposter&&(ia=H);for(var oa=0;oa<Y.bonds.length;oa++){var ha=Ab[Y.bonds[oa]];
+if(Y.serial<ha.serial){var ub=ha.style;if(ub.stick){var Ga=$3Dmol.getColorFromStyle(ha,ub.stick),ua=ab,db=tb;if(Y.bondStyles&&Y.bondStyles[oa]){var za=Y.bondStyles[oa];if(za.iswire)continue;za.radius&&(ua=za.radius);za.singleBond&&(db=!0);"undefined"!=typeof za.color1&&(ma=$3Dmol.CC.color(za.color1));"undefined"!=typeof za.color2&&(Ga=$3Dmol.CC.color(za.color2))}var qa=new $3Dmol.Vector3(Y.x,Y.y,Y.z),Aa=new $3Dmol.Vector3(ha.x,ha.y,ha.z);if(1===Y.bondOrder[oa]||db){if(!ha.capDrawn&&4>ha.bonds.length&&
+(cb=2),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5),ia(ga,qa,na,ua,ma,bb,0),ia(ga,na,Aa,ua,Ga,0,cb)):ia(ga,qa,Aa,ua,ma,bb,cb),Y.clickable||ha.clickable){na=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5);if(Y.clickable){var Bb=new $3Dmol.Cylinder(qa,na,ua),Cb=new $3Dmol.Sphere(qa,ua);Y.intersectionShape.cylinder.push(Bb);Y.intersectionShape.sphere.push(Cb)}if(ha.clickable){var Db=new $3Dmol.Cylinder(Aa,na,ua),Eb=new $3Dmol.Sphere(Aa,ua);ha.intersectionShape.cylinder.push(Db);
+ha.intersectionShape.sphere.push(Eb)}}}else if(1<Y.bondOrder[oa]){var Ka=0;mtoCap=0;ua!=ab&&(mtoCap=Ka=2);var Xa=Aa.clone(),Ha=null;Xa.sub(qa);var da,ra,sa,va,wa,Ha=l(Y,ha,oa);if(2==Y.bondOrder[oa]){if(da=ua/2.5,Ha=l(Y,ha,oa),Ha.multiplyScalar(1.5*da),ra=qa.clone(),ra.add(Ha),sa=qa.clone(),sa.sub(Ha),va=ra.clone(),va.add(Xa),wa=sa.clone(),wa.add(Xa),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),ia(ga,ra,na,da,ma,Ka,
+0),ia(ga,na,va,da,Ga,0,mtoCap),ia(ga,sa,ya,da,ma,Ka,0),ia(ga,ya,wa,da,Ga,0,mtoCap)):(ia(ga,ra,va,da,ma,Ka,mtoCap),ia(ga,sa,wa,da,ma,Ka,mtoCap)),Y.clickable||ha.clickable)na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),Y.clickable&&(cylinder1a=new $3Dmol.Cylinder(ra,na,da),cylinder1b=new $3Dmol.Cylinder(sa,ya,da),Y.intersectionShape.cylinder.push(cylinder1a),Y.intersectionShape.cylinder.push(cylinder1b)),ha.clickable&&(cylinder2a=
+new $3Dmol.Cylinder(va,na,da),cylinder2b=new $3Dmol.Cylinder(wa,ya,da),ha.intersectionShape.cylinder.push(cylinder2a),ha.intersectionShape.cylinder.push(cylinder2b))}else 3==Y.bondOrder[oa]&&(da=ua/4,Ha.cross(Xa),Ha.normalize(),Ha.multiplyScalar(3*da),ra=qa.clone(),ra.add(Ha),sa=qa.clone(),sa.sub(Ha),va=ra.clone(),va.add(Xa),wa=sa.clone(),wa.add(Xa),ma!=Ga?(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(qa,
+Aa).multiplyScalar(.5),ia(ga,ra,na,da,ma,Ka,0),ia(ga,na,va,da,Ga,0,mtoCap),ia(ga,qa,mp3,da,ma,bb,0),ia(ga,mp3,Aa,da,Ga,0,cb),ia(ga,sa,ya,da,ma,Ka,0),ia(ga,ya,wa,da,Ga,0,mtoCap)):(ia(ga,ra,va,da,ma,Ka,mtoCap),ia(ga,qa,Aa,da,ma,bb,cb),ia(ga,sa,wa,da,ma,Ka,mtoCap)),Y.clickable||ha.clickable)&&(na=(new $3Dmol.Vector3).addVectors(ra,va).multiplyScalar(.5),ya=(new $3Dmol.Vector3).addVectors(sa,wa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(qa,Aa).multiplyScalar(.5),Y.clickable&&(cylinder1a=
+new $3Dmol.Cylinder(ra.clone(),na.clone(),da),cylinder1b=new $3Dmol.Cylinder(sa.clone(),ya.clone(),da),cylinder1c=new $3Dmol.Cylinder(qa.clone(),mp3.clone(),da),Y.intersectionShape.cylinder.push(cylinder1a),Y.intersectionShape.cylinder.push(cylinder1b),Y.intersectionShape.cylinder.push(cylinder1c)),ha.clickable&&(cylinder2a=new $3Dmol.Cylinder(va.clone(),na.clone(),da),cylinder2b=new $3Dmol.Cylinder(wa.clone(),ya.clone(),da),cylinder2c=new $3Dmol.Cylinder(Aa.clone(),mp3.clone(),da),ha.intersectionShape.cylinder.push(cylinder2a),
+ha.intersectionShape.cylinder.push(cylinder2b),ha.intersectionShape.cylinder.push(cylinder2c)))}}}}for(var mb=!1,nb=0,vb=!1,oa=0;oa<Y.bonds.length;oa++)db=tb,Y.bondStyles&&Y.bondStyles[oa]&&(za=Y.bondStyles[oa],za.singleBond&&(db=!0),za.radius&&za.radius!=ab&&(vb=!0)),(db||1==Y.bondOrder[oa])&&nb++;vb?0<nb&&(mb=!0):0==nb&&0<Y.bonds.length&&(mb=!0);mb&&(ua=ab,ga.imposter?G(ga.sphereGeometry,Y,ua,ma):$3Dmol.GLDraw.drawSphere(ga,Y,ua,ma))}}"undefined"===typeof U.style.cartoon||U.style.cartoon.hidden||
+("spectrum"!==U.style.cartoon.color||"number"!==typeof U.resi||U.hetflag||(U.resi<ba[0]&&(ba[0]=U.resi),U.resi>ba[1]&&(ba[1]=U.resi)),u.push(U))}}if(0<u.length){var wb=null;ba[0]<ba[1]&&(wb=new $3Dmol.Gradient.Sinebow(ba[0],ba[1]));$3Dmol.drawCartoon(m,u,wb)}if(y&&0<y.vertices){y.initTypedArrays();var Ya=null;if(y.imposter)Ya=new $3Dmol.SphereImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});else if(y.instanced){var eb=new $3Dmol.Geometry(!0);$3Dmol.GLDraw.drawSphere(eb,{x:0,y:0,z:0},1,
+new $3Dmol.Color(.5,.5,.5));eb.initTypedArrays();Ya=new $3Dmol.InstancedMaterial({sphereMaterial:new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0}),sphere:eb})}else Ya=new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0});1>D.sphere&&0<=D.sphere&&(Ya.transparent=!0,Ya.opacity=D.sphere);eb=new $3Dmol.Mesh(y,Ya);m.add(eb)}if(0<F.vertices){if(F.imposter){var Fb=new $3Dmol.StickImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});F.initTypedArrays();
+var xb=new $3Dmol.Mesh(F,Fb)}else{var hb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});1>D.stick&&0<=D.stick&&(hb.transparent=!0,hb.opacity=D.stick);F.initTypedArrays();hb.wireframe&&F.setUpWireframe();xb=new $3Dmol.Mesh(F,hb)}m.add(xb)}for(A in x)if(x.hasOwnProperty(A)){var ob=A,pb=new $3Dmol.LineBasicMaterial({linewidth:ob,vertexColors:!0});1>D.line&&0<=D.line&&(pb.transparent=!0,pb.opacity=D.line);x[A].initTypedArrays();var Gb=new $3Dmol.Line(x[A],pb,$3Dmol.LinePieces);
+m.add(Gb)}for(A in q)if(q.hasOwnProperty(A)){var ob=A,qb=new $3Dmol.LineBasicMaterial({linewidth:ob,vertexColors:!0});1>D.cross&&0<=D.cross&&(qb.transparent=!0,qb.opacity=D.cross);q[A].initTypedArrays();var Hb=new $3Dmol.Line(q[A],qb,$3Dmol.LinePieces);m.add(Hb)}if(g&&e.symmetries&&0<e.symmetries.length){var yb=new $3Dmol.Object3D,ib;for(ib=0;ib<e.symmetries.length;ib++){var jb=new $3Dmol.Object3D,jb=m.clone();jb.matrix.copy(e.symmetries[ib]);jb.matrixAutoUpdate=!1;yb.add(jb)}h=yb}else h=m;t&&(b.remove(t),
+t=null);t=h.clone();w&&(t.setVisible(!1),h.setVisible(!1));b.add(t)}};this.removegl=function(b){t&&(void 0!==t.geometry&&t.geometry.dispose(),void 0!==t.material&&t.material.dispose(),b.remove(t),t=null);h=null};this.hide=function(){w=!0;t&&t.setVisible(!1);h&&h.setVisible(!1)};this.show=function(){w=!1;t&&t.setVisible(!0);h&&h.setVisible(!0)};this.addResLabels=function(b,c,h){var e=this.selectedAtoms(b,e);b={};for(var f=0;f<e.length;f++){var g=e[f],d=g.chain,m=g.resn+""+g.resi;b[d]||(b[d]={});b[d][m]||
+(b[d][m]=[]);b[d][m].push(g)}h=$.extend(!0,{},h);for(d in b)if(b.hasOwnProperty(d)){var l=b[d];for(m in l)if(l.hasOwnProperty(m)){for(var e=l[m],t=new $3Dmol.Vector3(0,0,0),f=0;f<e.length;f++)g=e[f],t.x+=g.x,t.y+=g.y,t.z+=g.z;t.divideScalar(e.length);h.position=t;c.addLabel(m,h)}}}}var c={line:{}},d={H:1.2,Li:1.82,LI:1.82,Na:2.27,NA:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,Cl:1.75,BR:1.85,Br:1.85,SE:1.9,Se:1.9,ZN:1.39,Zn:1.39,CU:1.4,Cu:1.4,NI:1.63,Ni:1.63},p="resn x y z color surfaceColor elem hetflag chain resi icode rescode serial atom bonds ss singleBonds bondOrder properties b pdbline clickable callback invert".split(" ").concat("model bonds predicate invert byres expand within".split(" ")),
+y=["line","cross","stick","sphere","cartoon"];b.parseMolData=function(b,c,d){c=c||"";if(!b)return[];if(/\.gz$/.test(c)){c=c.replace(/\.gz$/,"");try{b=pako.inflate(b,{to:"string"})}catch(f){console.log(f)}}"undefined"==typeof $3Dmol.Parsers[c]&&(c=c.split(".").pop(),"undefined"==typeof $3Dmol.Parsers[c]&&(console.log("Unknown format: "+c),c=b.match(/^@<TRIPOS>MOLECULE/gm)?"mol2":b.match(/^HETATM/gm)||b.match(/^ATOM/gm)?"pdb":b.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/gm)?"sdf":"xyz",console.log("Best guess: "+
+c)));return(0,$3Dmol.Parsers[c])(b,d)};b.setAtomDefaults=function(b,d){for(var p=0;p<b.length;p++){var f=b[p];f&&(f.style=f.style||c,f.color=f.color||ElementColors[f.elem]||defaultColor,f.model=d,f.clickable&&(f.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}))}};return b}();
+$3Dmol.GLShape=function(){function b(b){b=b||{};$3Dmol.ShapeIDCount++;this.boundingSphere=new $3Dmol.Sphere;this.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]};p(this,b);var A=[],q=null,B=null,f=new $3Dmol.Geometry(!0),w=new $3Dmol.Geometry(!0);this.updateStyle=function(c){for(var f in c)b[f]=c[f];p(this,b)};this.addCustom=function(b){b.vertexArr=b.vertexArr||[];b.faceArr=b.faceArr||[];b.normalArr=b.normalArr||[];c(this,f,b)};this.addSphere=function(b){b.center=b.center||{x:0,y:0,z:0};
+b.radius=b.radius?$3Dmol.Math.clamp(b.radius,0,Infinity):1.5;b.color=$3Dmol.CC.color(b.color);this.intersectionShape.sphere.push(new $3Dmol.Sphere(b.center,b.radius));$3Dmol.GLDraw.drawSphere(f,b.center,b.radius,b.color);A.push({centroid:new $3Dmol.Vector3(b.center.x,b.center.y,b.center.z)});b=f.updateGeoGroup(0);d(this.boundingSphere,A,b.vertexArray)};this.addCylinder=function(b){b.start=b.start||{};b.end=b.end||{};var c=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0),m=new $3Dmol.Vector3(b.end.x,
+b.end.y||0,b.end.z||0);"undefined"==typeof m.x&&(m.x=3);var e=b.radius||.1,w=$3Dmol.CC.color(b.color);this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(c,m,e));$3Dmol.GLDraw.drawCylinder(f,c,m,e,w,b.fromCap,b.toCap);b=new $3Dmol.Vector3;A.push({centroid:b.addVectors(c,m).multiplyScalar(.5)});c=f.updateGeoGroup(0);d(this.boundingSphere,A,c.vertexArray)};this.addLine=function(b){b.start=b.start||{};b.end=b.end||{};var c=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0),d=new $3Dmol.Vector3(b.end.x,
+b.end.y||0,b.end.z||0);"undefined"==typeof d.x&&(d.x=3);b=f.updateGeoGroup(2);var e=b.vertices,w=3*e,g=b.vertexArray;g[w]=c.x;g[w+1]=c.y;g[w+2]=c.z;g[w+3]=d.x;g[w+4]=d.y;g[w+5]=d.z;b.vertices+=2;c=b.lineArray;d=b.lineidx;c[d]=e;c[d+1]=e+1;b.lineidx+=2};this.addArrow=function(b){b.start=b.start||{};b.end=b.end||{};b.start=new $3Dmol.Vector3(b.start.x||0,b.start.y||0,b.start.z||0);if(b.dir instanceof $3Dmol.Vector3&&b.length instanceof number){var c=b.dir.clone().multiplyScalar(b.length).add(start);
+b.end=c}else b.end=new $3Dmol.Vector3(b.end.x,b.end.y||0,b.end.z||0),"undefined"==typeof b.end.x&&(b.end.x=3);b.radius=b.radius||.1;b.radiusRatio=b.radiusRatio||1.618034;b.mid=0<b.mid&&1>b.mid?b.mid:.618034;var m=b.start,e=b.end,w=b.radius,g=b.radiusRatio,x=b.mid;if(m&&e){var c=f.updateGeoGroup(51),u=e.clone();u.sub(m).multiplyScalar(x);var s=m.clone().add(u),x=u.clone().negate();this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(m.clone(),s.clone(),w));this.intersectionShape.sphere.push(new $3Dmol.Sphere(m.clone(),
+w));var l=[];l[0]=u.clone();1E-4<Math.abs(l[0].x)?l[0].y+=1:l[0].x+=1;l[0].cross(u);l[0].normalize();l[0]=l[0];l[4]=l[0].clone();l[4].crossVectors(l[0],u);l[4].normalize();l[8]=l[0].clone().negate();l[12]=l[4].clone().negate();l[2]=l[0].clone().add(l[4]).normalize();l[6]=l[4].clone().add(l[8]).normalize();l[10]=l[8].clone().add(l[12]).normalize();l[14]=l[12].clone().add(l[0]).normalize();l[1]=l[0].clone().add(l[2]).normalize();l[3]=l[2].clone().add(l[4]).normalize();l[5]=l[4].clone().add(l[6]).normalize();
+l[7]=l[6].clone().add(l[8]).normalize();l[9]=l[8].clone().add(l[10]).normalize();l[11]=l[10].clone().add(l[12]).normalize();l[13]=l[12].clone().add(l[14]).normalize();l[15]=l[14].clone().add(l[0]).normalize();var q=c.vertices,p=c.vertexArray,y=c.faceArray,B=c.normalArray,z=c.lineArray,H,L,N;L=0;for(N=l.length;L<N;++L){H=3*(q+3*L);var J=l[L].clone().multiplyScalar(w).add(m),I=l[L].clone().multiplyScalar(w).add(s),K=l[L].clone().multiplyScalar(w*g).add(s);p[H]=J.x;p[H+1]=J.y;p[H+2]=J.z;p[H+3]=I.x;p[H+
+4]=I.y;p[H+5]=I.z;p[H+6]=K.x;p[H+7]=K.y;p[H+8]=K.z;0<L&&(H=new $3Dmol.Vector3(p[H-3],p[H-2],p[H-1]),J=e.clone(),I=s.clone(),K=new $3Dmol.Vector3(K.x,K.y,K.z),this.intersectionShape.triangle.push(new $3Dmol.Triangle(K,J,H)),this.intersectionShape.triangle.push(new $3Dmol.Triangle(H.clone(),I,K.clone())))}c.vertices+=48;H=3*c.vertices;p[H]=m.x;p[H+1]=m.y;p[H+2]=m.z;p[H+3]=s.x;p[H+4]=s.y;p[H+5]=s.z;p[H+6]=e.x;p[H+7]=e.y;p[H+8]=e.z;c.vertices+=3;var O,Q,W,P,S,R,aa,V,Z=c.vertices-3,ca=c.vertices-2,X=c.vertices-
+1,D=3*Z,ba=3*ca,U=3*X;L=0;for(N=l.length-1;L<N;++L)O=q+3*L,m=c.faceidx,e=c.lineidx,w=O,H=3*w,g=O+1,J=3*g,s=O+2,I=3*s,p=O+4,Q=3*p,K=O+5,W=3*K,O+=3,P=3*O,S=R=l[L],aa=V=l[L+1],B[H]=S.x,B[J]=R.x,B[P]=V.x,B[H+1]=S.y,B[J+1]=R.y,B[P+1]=V.y,B[H+2]=S.z,B[J+2]=R.z,B[P+2]=V.z,B[J]=R.x,B[Q]=aa.x,B[P]=V.x,B[J+1]=R.y,B[Q+1]=aa.y,B[P+1]=V.y,B[J+2]=R.z,B[Q+2]=aa.z,B[P+2]=V.z,B[I]=R.x,B[W]=aa.x,B[I+1]=R.y,B[W+1]=aa.y,B[I+2]=R.z,B[W+2]=aa.z,y[m]=w,y[m+1]=g,y[m+2]=O,y[m+3]=g,y[m+4]=p,y[m+5]=O,y[m+6]=w,y[m+7]=O,y[m+
+8]=Z,y[m+9]=s,y[m+10]=ca,y[m+11]=K,y[m+12]=s,y[m+13]=X,y[m+14]=K,z[e]=w,z[e+1]=g,z[e+2]=w,z[e+3]=O,z[e+4]=p,z[e+5]=O,z[e+6]=w,z[e+7]=O,z[e+8]=s,z[e+9]=g,z[e+10]=s,z[e+11]=K,z[e+12]=p,z[e+13]=K,z[e+14]=s,z[e+15]=X,z[e+16]=s,z[e+17]=K,z[e+18]=X,z[e+19]=K,c.faceidx+=15,c.lineidx+=20;q=[q+45,q+46,q+1,q,q+47,q+2];m=c.faceidx;e=c.lineidx;w=q[0];H=3*w;g=q[1];J=3*g;s=q[4];I=3*s;p=q[2];Q=3*p;K=q[5];W=3*K;O=q[3];P=3*O;S=R=l[15];aa=V=l[0];B[H]=S.x;B[J]=R.x;B[P]=V.x;B[H+1]=S.y;B[J+1]=R.y;B[P+1]=V.y;B[H+2]=S.z;
+B[J+2]=R.z;B[P+2]=V.z;B[J]=R.x;B[Q]=aa.x;B[P]=V.x;B[J+1]=R.y;B[Q+1]=aa.y;B[P+1]=V.y;B[J+2]=R.z;B[Q+2]=aa.z;B[P+2]=V.z;B[I]=R.x;B[W]=aa.x;B[I+1]=R.y;B[W+1]=aa.y;B[I+2]=R.z;B[W+2]=aa.z;u.normalize();x.normalize();B[D]=x.x;B[ba]=B[U]=u.x;B[D+1]=x.y;B[ba+1]=B[U+1]=u.y;B[D+2]=x.z;B[ba+2]=B[U+2]=u.z;y[m]=w;y[m+1]=g;y[m+2]=O;y[m+3]=g;y[m+4]=p;y[m+5]=O;y[m+6]=w;y[m+7]=O;y[m+8]=Z;y[m+9]=s;y[m+10]=ca;y[m+11]=K;y[m+12]=s;y[m+13]=X;y[m+14]=K;z[e]=w;z[e+1]=g;z[e+2]=w;z[e+3]=O;z[e+4]=p;z[e+5]=O;z[e+6]=w;z[e+7]=
+O;z[e+8]=s;z[e+9]=g;z[e+10]=s;z[e+11]=K;z[e+12]=p;z[e+13]=K;z[e+14]=s;z[e+15]=X;z[e+16]=s;z[e+17]=K;z[e+18]=X;z[e+19]=K;c.faceidx+=15;c.lineidx+=20}c=new $3Dmol.Vector3;A.push({centroid:c.addVectors(b.start,b.end).multiplyScalar(.5)});b=f.updateGeoGroup(0);d(this.boundingSphere,A,b.vertexArray)};this.addIsosurface=function(b,d){var m=void 0!==d.isoval&&"number"===typeof d.isoval?d.isoval:0,e=d.voxel?!0:!1,w=void 0===d.smoothness?1:d.smoothness,g=b.size.x,x=b.size.y,u=b.size.z,s=new Int16Array(g*x*
+u),l=b.data,q,p;q=0;for(p=s.length;q<p;++q)s[q]=-1;s=new Uint8Array(g*x*u);q=0;for(p=l.length;q<p;++q)0<(0<=m?l[q]-m:m-l[q])&&(s[q]|=2);m=[];q=[];$3Dmol.MarchingCube.march(s,m,q,{fulltable:!0,voxel:e,unitCube:b.unit,origin:b.origin,nX:g,nY:x,nZ:u});e||$3Dmol.MarchingCube.laplacianSmooth(w,m,q);c(this,f,{vertexArr:m,faceArr:q,normalArr:[],clickable:d.clickable});this.updateStyle(d);q=new $3Dmol.Vector3(b.origin.x,b.origin.y,b.origin.z);g=new $3Dmol.Vector3(b.size.x*b.unit.x,b.size.y*b.unit.y,b.size.z*
+b.unit.z);e=new $3Dmol.Vector3(0,0,0);w=q.clone();g=q.clone().add(g);for(q=0;q<m.length;q++)e.add(m[q]),w.max(m[q]),g.min(m[q]);e.divideScalar(m.length);q=e.distanceTo(g);m=e.distanceTo(w);this.boundingSphere.center=e;this.boundingSphere.radius=Math.max(q,m)};this.addVolumetricData=function(b,c,f){b=new $3Dmol.VolumeData(b,c);this.addIsosurface(b,f)};this.globj=function(b){B&&(b.remove(B),B=null);if(!this.hidden){var c=f.updateGeoGroup(0);0<c.vertices&&c.truncateArrayBuffers(!0,!0);f.initTypedArrays();
+if("undefined"!=typeof this.color){(c=this.color)||$3Dmol.CC.color(c);f.colorsNeedUpdate=!0;var d,e,p;c.constructor!==Array&&(d=c.r,e=c.g,p=c.b);for(var g in f.geometryGroups)for(var x=f.geometryGroups[g],u=x.colorArray,s=0,x=x.vertices;s<x;++s)c.constructor===Array&&(p=c[s],d=p.r,e=p.g,p=p.b),u[3*s]=d,u[3*s+1]=e,u[3*s+2]=p}q=new $3Dmol.Object3D;d=null;d=this.side==$3Dmol.DoubleSide?new $3Dmol.MeshDoubleLambertMaterial({wireframe:this.wireframe,side:this.side,transparent:1>this.opacity?!0:!1,opacity:this.opacity,
+wireframeLinewidth:this.linewidth}):new $3Dmol.MeshLambertMaterial({wireframe:this.wireframe,side:this.side,transparent:1>this.opacity?!0:!1,opacity:this.opacity,wireframeLinewidth:this.linewidth});d=new $3Dmol.Mesh(f,d);q.add(d);d=new $3Dmol.LineBasicMaterial({linewidth:this.linewidth,color:this.color});d=new $3Dmol.Line(w,d,$3Dmol.LinePieces);q.add(d);B=q.clone();b.add(B)}};this.removegl=function(b){B&&(void 0!==B.geometry&&B.geometry.dispose(),void 0!==B.material&&B.material.dispose(),b.remove(B),
+B=null);q=null}}var c=function(b,c,q){var p=q.faceArr;0!==q.vertexArr.length&&0!==p.length||console.warn("Error adding custom shape component: No vertices and/or face indices supplied!");p=q.color;"undefined"==typeof p&&(p=b.color);for(var p=$3Dmol.CC.color(p),f=$3Dmol.splitMesh(q),w=0,h=f.length;w<h;w++){var t=b,m=c,e=f[w],F=f[w].colorArr?f[w].colorArr:p,g=q.clickable,x=m.addGeoGroup(),u=e.vertexArr,s=e.normalArr,e=e.faceArr;x.vertices=u.length;x.faceidx=e.length;var l=void 0,E=void 0,M=void 0,C=
+void 0,G=E=void 0,z=void 0,H=x.vertexArray,M=x.colorArray;if(F.constructor!==Array)var L=F.r,N=F.g,C=F.b;G=0;for(z=x.vertices;G<z;++G)l=3*G,E=u[G],H[l]=E.x,H[l+1]=E.y,H[l+2]=E.z,F.constructor===Array&&(E=F[G],L=E.r,N=E.g,C=E.b),M[l]=L,M[l+1]=N,M[l+2]=C;if(g)for(G=0,z=x.faceidx/3;G<z;++G){var l=3*G,M=e[l],C=e[l+1],E=e[l+2],l=new $3Dmol.Vector3,F=new $3Dmol.Vector3,J=new $3Dmol.Vector3;t.intersectionShape.triangle.push(new $3Dmol.Triangle(l.copy(u[M]),F.copy(u[C]),J.copy(u[E])))}if(g){G=new $3Dmol.Vector3(0,
+0,0);for(N=z=0;N<m.geometryGroups.length;N++)G.add(m.geometryGroups[N].getCentroid()),z++;G.divideScalar(z);d(t.boundingSphere,{centroid:G},H)}x.faceArray=new Uint16Array(e);x.truncateArrayBuffers(!0,!0);if(s.length<x.vertices)x.setNormals();else for(t=x.normalArray=new Float32Array(3*x.vertices),m=void 0,G=0,z=x.vertices;G<z;++G)l=3*G,m=s[G],t[l]=m.x,t[l+1]=m.y,t[l+2]=m.z;x.setLineIndices();x.lineidx=x.lineArray.length}},d=function(b,c,d){b.center.set(0,0,0);var p,f;if(0<c.length){p=0;for(f=c.length;p<
+f;++p)b.center.add(c[p].centroid);b.center.divideScalar(c.length)}c=b.radius*b.radius;p=0;for(f=d.length/3;p<f;p++){var w=b.center.distanceToSquared({x:d[3*p],y:d[3*p+1],z:d[3*p+2]});c=Math.max(c,w)}b.radius=Math.sqrt(c)},p=function(b,c){"undefined"!=typeof c.color&&(b.color=c.color||new $3Dmol.Color,c.color instanceof $3Dmol.Color||(b.color=$3Dmol.CC.color(c.color)));b.wireframe=c.wireframe?!0:!1;b.opacity=c.alpha?$3Dmol.Math.clamp(c.alpha,0,1):1;"undefined"!=typeof c.opacity&&(b.opacity=$3Dmol.Math.clamp(c.opacity,
+0,1));b.side=void 0!==c.side?c.side:$3Dmol.DoubleSide;b.linewidth="undefined"==typeof c.linewidth?1:c.linewidth;b.clickable=c.clickable?!0:!1;b.callback="function"===typeof c.callback?c.callback:null;b.hidden=c.hidden};Object.defineProperty(b.prototype,"position",{get:function(){return this.boundingSphere.center}});Object.defineProperty(b.prototype,"x",{get:function(){return this.boundingSphere.center.x}});Object.defineProperty(b.prototype,"y",{get:function(){return this.boundingSphere.center.y}});
+Object.defineProperty(b.prototype,"z",{get:function(){return this.boundingSphere.center.z}});return b}();$3Dmol.ShapeIDCount=0;
+$3Dmol.splitMesh=function(b){if(64E3>b.vertexArr.length)return[b];var c=[{vertexArr:[],normalArr:[],faceArr:[]}];b.colorArr&&(c.colorArr=[]);for(var d=[],p=[],y=0,A=b.faceArr,q=0,B=A.length;q<B;q+=3){for(var f=c[y],w=0;3>w;w++){var h=A[q+w];d[h]!==y&&(d[h]=y,p[h]=f.vertexArr.length,f.vertexArr.push(b.vertexArr[h]),b.normalArr&&b.normalArr[h]&&f.normalArr.push(b.normalArr[h]),b.colorArr&&b.colorArr[h]&&f.colorArr.push(b.colorArr[h]));f.faceArr.push(p[h])}64E3<=f.vertexArr.length&&(c.push({vertexArr:[],
+normalArr:[],faceArr:[]}),b.colorArr&&(c.colorArr=[]),y++)}return c};
+$3Dmol.GLViewer=function(){return function(b,c){function d(b){var c=[];"undefined"===typeof b&&(b={});var f=[],g;if("undefined"===typeof b.model)for(g=0;g<e.length;g++)e[g]&&f.push(e[g]);else f=b.model,$.isArray(f)||(f=[f]);for(g=0;g<f.length;g++)c=c.concat(f[g].selectedAtoms(b));return c}function p(b,c,f,g){var d=[];if("undefined"===typeof c.model)for(h=0;h<e.length;h++)e[h]&&d.push(e[h]);else d=c.model,$.isArray(d)||(d=[d]);for(var h=0;h<d.length;h++)if(d[h])d[h][b](c,f,g)}function y(b){var c=new $3Dmol.MeshLambertMaterial;
+c.vertexColors=$3Dmol.VertexColors;for(var e in b)"color"!==e&&"map"!==e&&b.hasOwnProperty(e)&&(c[e]=b[e]);void 0!==b.opacity&&(c.transparent=1===b.opacity?!1:!0);return c}c=c||{};var A=c.callback,q=c.defaultcolors;q||(q=$3Dmol.elementColors.defaultColors);var B=c.nomouse,f=0;void 0!=typeof c.backgroundColor&&(f=$3Dmol.CC.color(c.backgroundColor).getHex());var w=0;void 0!=typeof c.camerax&&(w=parseFloat(c.camerax));var h=this,t=b,m=null,e=[],F={},g=[],x=[],u=[],s=t.width(),l=t.height(),E=s/l,M=[],
+C=new $3Dmol.Renderer({antialias:!0,preserveDrawingBuffer:!0,premultipliedAlpha:!1});C.domElement.style.width="100%";C.domElement.style.height="100%";C.domElement.style.padding="0";C.domElement.style.position="absolute";C.domElement.style.top="0px";C.domElement.style.left="0px";C.domElement.style.zIndex="0";var G=new $3Dmol.Camera(20,E,1,800);G.position=new $3Dmol.Vector3(w,0,150);var z=new $3Dmol.Vector3;G.lookAt(z);var H=new $3Dmol.Raycaster(new $3Dmol.Vector3(0,0,0),new $3Dmol.Vector3(0,0,0)),
+L=new $3Dmol.Projector,N=new $3Dmol.Vector3(0,0,0),J=null,I=null,K=null,O=-50,Q=50,W=new $3Dmol.Quaternion(0,0,0,1),P=new $3Dmol.Quaternion(0,0,0,1),S=!1,R=!1,aa=0,V=0,Z=0,ca=0,X=0,D=0,ba=0,U=function(){var b=0;for(i in F)F.hasOwnProperty(i)&&i>b&&(b=i);return b+1},T=function(b){if(J){var c=G.position.z-I.position.z;1>c&&(c=1);G.near=c+O;1>G.near&&(G.near=1);G.far=c+Q;G.near+1>G.far&&(G.far=G.near+1);G instanceof $3Dmol.Camera?G.fov=20:(G.right=c*Math.tan(Math.PI/180*20),G.left=-G.right,G.top=G.right/
+E,G.bottom=-G.top);G.updateProjectionMatrix();J.fog.near=G.near+.4*(G.far-G.near);J.fog.far=G.far;C.render(J,G);if(!b&&0<M.length)for(b=h.getView(),c=0;c<M.length;c++)M[c].setView(b,!0)}};(function(){J=new $3Dmol.Scene;J.fog=new $3Dmol.Fog(f,100,200);K=new $3Dmol.Object3D;I=new $3Dmol.Object3D;I.useQuaternion=!0;I.quaternion=new $3Dmol.Quaternion(0,0,0,1);I.add(K);J.add(I);var b=new $3Dmol.Light(16777215);b.position=(new $3Dmol.Vector3(.2,.2,1)).normalize();b.intensity=1;J.add(b)})();C.setClearColorHex(f,
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+var c=U();F[c]=b;return c};var xa=function(b){var c=[];$.each(b,function(b,f){c[b]=$.extend({},f)});return c};this.addSurface=function(b,c,f,g,m){var l=null,w=null;f=xa(d(f));var l=g?xa(d(g)):f,s=!1;for(g=0;g<e.length;g++)if(e[g]){var t=e[g].getSymmetries();if(1<t.length||1==t.length&&!t[0].isIdentity()){s=!0;break}}var q=function(f,e,g){w=m?xa(d(m)):g;var l,s=$3Dmol.getExtent(g,!0),t,q;c.map&&c.map.prop&&(t=c.map.prop,q=c.map.scheme||c.map.gradient||new $3Dmol.Gradient.RWB,(l=q.range())||(l=$3Dmol.getPropertyRange(g,
+t)),c.colorscheme={prop:t,gradient:q});t=0;for(q=e.length;t<q;t++)l=e[t],l.surfaceColor=$3Dmol.getColorFromStyle(l,c);var x=Ta(s),p=$a(s,e,g);if(w&&w.length&&0<w.length){var z=$3Dmol.getExtent(w,!0);p.sort(function(b,c){var f=function(b,c){var f=b.extent,e=f[1][1]-f[0][1],d=f[1][2]-f[0][2],f=f[1][0]-f[0][0]-c[2][0],e=e-c[2][1],d=d-c[2][2];return f*f+e*e+d*d},e=f(b,z),f=f(c,z);return e-f})}var y=[];t=0;for(q=e.length;t<q;t++)l=e[t],y[t]={x:l.x,y:l.y,z:l.z,serial:t,elem:l.elem};if($3Dmol.syncSurface)setTimeout(function ga(c){if(!(c>=
+p.length)){var d;d=b;var g=p[c].extent,l=p[c].atoms,m=p[c].toshow,w=new $3Dmol.ProteinSurface;w.initparm(g,1===d?!1:!0,x);w.fillvoxels(y,l);w.buildboundary();d==$3Dmol.SurfaceType.SES&&(w.fastdistancemap(),w.boundingatom(!1),w.fillvoxelswaals(y,l));w.marchingcube(d);d=w.getFacesAndVertices(m);d=Ua(e,d,u);$3Dmol.mergeGeos(f.geo,d);h.render();setTimeout(ga,1,c+1)}},1,0);else{g=[];0>b&&(b=0);t=0;for(q=4;t<q;t++)s=new Worker($3Dmol.SurfaceWorker),g.push(s),s.postMessage({type:-1,atoms:y,volume:x});var B=
+0,s=function(b){b=$3Dmol.splitMesh({vertexArr:b.data.vertices,faceArr:b.data.faces});for(var c=0,d=b.length;c<d;c++){var g=Ua(e,{vertices:b[c].vertexArr,faces:b[c].faceArr},u);$3Dmol.mergeGeos(f.geo,g);h.render()}B++;B==p.length&&(f.done=!0)};q=function(b){console.log(b.message+" ("+b.filename+":"+b.lineno+")")};for(t=0;t<p.length;t++)l=g[t%g.length],l.onmessage=s,l.onerror=q,l.postMessage({type:b,expandedExtent:p[t].extent,extendedAtoms:p[t].atoms,atomsToShow:p[t].toshow})}};c=c||{};var u=y(c),t=
+[];if(s){var s={},x={};for(g=0;g<e.length;g++)s[g]=[],x[g]=[];for(g=0;g<l.length;g++)s[l[g].model].push(l[g]);for(g=0;g<f.length;g++)x[f[g].model].push(f[g]);for(g=0;g<e.length;g++)t.push({geo:new $3Dmol.Geometry(!0),mat:u,done:!1,finished:!1,symmetries:e[g].getSymmetries()}),q(t[g],s[g],x[g])}else t.push({geo:new $3Dmol.Geometry(!0),mat:u,done:!1,finished:!1,symmetries:[new $3Dmol.Matrix4]}),q(t[t.length-1],l,f);l=U();F[l]=t;return l};this.setSurfaceMaterialStyle=function(b,c){if(F[b]){surfArr=F[b];
+for(var f=0;f<surfArr.length;f++)surfArr[f].mat=y(c),surfArr[f].mat.side=$3Dmol.FrontSide,surfArr[f].finished=!1}return this};this.removeSurface=function(b){for(var c=F[b],f=0;f<c.length;f++)c[f]&&c[f].lastGL&&(void 0!==c[f].geo&&c[f].geo.dispose(),void 0!==c[f].mat&&c[f].mat.dispose(),K.remove(c[f].lastGL));delete F[b];T();return this};this.removeAllSurfaces=function(){for(n in F)if(F.hasOwnProperty(n)){for(var b=F[n],c=0;c<b.length;c++)b[c]&&b[c].lastGL&&(void 0!==b[c].geo&&b[c].geo.dispose(),void 0!==
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+f[g];b(l)}else for(g=0,h=f.length;g<h;g++)for(var l=f[g],m=0,w=b.length;m<w;m++){var t=b[m];if(t.props)for(var s in t.props)if(t.props.hasOwnProperty(s)){var q;a:{q=l;var u=t;"undefined"===typeof u&&(u={});var x=[],p=void 0;if("undefined"===typeof u.model)for(p=0;p<e.length;p++)e[p]&&x.push(e[p]);else x=u.model,$.isArray(x)||(x=[x]);for(p=0;p<x.length;p++)if(x[p].atomIsSelected(q,u)){q=!0;break a}q=!1}q&&(l.properties||(l.properties={}),l.properties[s]=t.props[s])}}return this};this.linkViewer=function(b){M.push(b);
+return this};try{"function"===typeof A&&A(this)}catch(Ma){console.log("error with glviewer callback: "+Ma)}}}();$3Dmol.glmolViewer=$3Dmol.GLViewer;$3Dmol=$3Dmol||{};$3Dmol.Gradient=function(b,c){};$3Dmol.Gradient.valueToHex=function(b,c){};$3Dmol.Gradient.range=function(){};
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+typeof c?[b,c]:null}};
+$3Dmol.Gradient.ROYGB=function(b,c){var d=1;"undefined"==typeof c&&$.isArray(b)&&2<=b.length&&(c=b[1],b=b[0]);c<b&&(d=-1,b*=-1,c*=-1);this.valueToHex=function(p,y){var A,q;p*=d;y?(A=y[0],q=y[1]):(A=b,q=c);if("undefined"==typeof p)return 16777215;p<A&&(p=A);p>q&&(p=q);var B=(A+q)/2,f=(A+B)/2,w=(B+q)/2;p<f?(A=Math.floor(255*Math.sqrt((p-A)/(f-A))),A=256*A+16711680):p<B?(A=Math.floor(255*Math.sqrt(1-(p-f)/(B-f))),A=65536*A+65280):p<w?(A=Math.floor(255*Math.sqrt((p-B)/(w-B))),A=65280+1*A):(A=Math.floor(255*
+Math.sqrt(1-(p-w)/(q-w))),A=256*A+255);return A};this.range=function(){return"undefined"!=typeof b&&"undefined"!=typeof c?[b,c]:null}};
+$3Dmol.Gradient.Sinebow=function(b,c){var d=1;"undefined"==typeof c&&$.isArray(b)&&2<=b.length&&(c=b[1],b=b[0]);c<b&&(d=-1,b*=-1,c*=-1);this.valueToHex=function(p,y){var A,q;p*=d;y?(A=y[0],q=y[1]):(A=b,q=c);if("undefined"==typeof p)return 16777215;p<A&&(p=A);p>q&&(p=q);var B=(p-A)/(q-A)*5/6+.5;A=Math.sin(Math.PI*B);A*=255*A;q=Math.sin(Math.PI*(B+1/3));q*=255*q;B=Math.sin(Math.PI*(B+2/3));return 65536*Math.floor(A)+256*Math.floor(255*B*B)+1*Math.floor(q)};this.range=function(){return"undefined"!=typeof b&&
+"undefined"!=typeof c?[b,c]:null}};$3Dmol.LabelCount=0;$3Dmol.Label=function(b,c){this.id=$3Dmol.LabelCount++;this.stylespec=c||{};this.canvas=document.createElement("canvas");this.canvas.width=134;this.canvas.height=35;this.context=this.canvas.getContext("2d");this.sprite=new $3Dmol.Sprite;this.text=b};
+$3Dmol.Label.prototype={constructor:$3Dmol.Label,getStyle:function(){return this.stylespec},setContext:function(){var b=function(b,d,p){"undefined"!=typeof b&&(p=b instanceof $3Dmol.Color?b.scaled():$3Dmol.CC.color(b).scaled());"undefined"!=typeof d&&(p.a=parseFloat(d));return p};return function(){var c=this.stylespec,d="undefined"==typeof c.useScreen?!1:c.useScreen,p=c.showBackground;if("0"===p||"false"===p)p=!1;"undefined"==typeof p&&(p=!0);var y=c.font?c.font:"sans-serif",A=parseInt(c.fontSize)?
+parseInt(c.fontSize):18,q=b(c.fontColor,c.fontOpacity,{r:255,g:255,b:255,a:1}),B=c.padding?c.padding:4,f=c.borderThickness?c.borderThickness:0,w=b(c.backgroundColor,c.backgroundOpacity,{r:0,g:0,b:0,a:1}),h=b(c.borderColor,c.borderOpacity,w),t=c.position?c.position:{x:-10,y:1,z:1},m=void 0!==c.inFront?c.inFront:!0;if("false"===m||"0"===m)m=!1;var e=c.alignment||$3Dmol.SpriteAlignment.topLeft,F="";c.bold&&(F="bold ");this.context.font=F+A+"px  "+y;var g=this.context.measureText(this.text).width;p||
+(f=0);var x=g+2.5*f+2*B,u=1.25*A+2*f+2*B;if(c.backgroundImage){var F=c.backgroundImage,s=c.backgroundWidth?c.backgroundWidth:F.width,l=c.backgroundHeight?c.backgroundHeight:F.height;s>x&&(x=s);l>u&&(u=l)}this.canvas.width=x;this.canvas.height=u;this.context.clearRect(0,0,this.canvas.width,this.canvas.height);F="";c.bold&&(F="bold ");this.context.font=F+A+"px  "+y;this.context.fillStyle="rgba("+w.r+","+w.g+","+w.b+","+w.a+")";this.context.strokeStyle="rgba("+h.r+","+h.g+","+h.b+","+h.a+")";this.context.lineWidth=
+f;p&&(p=this.context,w=y=f,x-=2*f,u-=2*f,h=0<f,p.beginPath(),p.moveTo(y+6,w),p.lineTo(y+x-6,w),p.quadraticCurveTo(y+x,w,y+x,w+6),p.lineTo(y+x,w+u-6),p.quadraticCurveTo(y+x,w+u,y+x-6,w+u),p.lineTo(y+6,w+u),p.quadraticCurveTo(y,w+u,y,w+u-6),p.lineTo(y,w+6),p.quadraticCurveTo(y,w,y+6,w),p.closePath(),p.fill(),h&&p.stroke());c.backgroundImage&&(F=c.backgroundImage,s=c.backgroundWidth?c.backgroundWidth:F.width,l=c.backgroundHeight?c.backgroundHeight:F.height,this.context.drawImage(F,0,0,s,l));this.context.fillStyle=
+"rgba("+q.r+","+q.g+","+q.b+","+q.a+")";this.context.fillText(this.text,f+B,A+f+B,g);c=new $3Dmol.Texture(this.canvas);c.needsUpdate=!0;this.sprite.material=new $3Dmol.SpriteMaterial({map:c,useScreenCoordinates:d,alignment:e,depthTest:!m});this.sprite.scale.set(1,1,1);this.sprite.position.set(t.x,t.y,t.z)}}(),dispose:function(){void 0!==this.sprite.material.map&&this.sprite.material.map.dispose();void 0!==this.sprite.material&&this.sprite.material.dispose()}};$3Dmol=$3Dmol||{};
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+q.length-1;0>u[b]&&(u[b]=q.length,q.push(m));return u[b]},s=new Int32Array(12),l=w?p:c,w=w?y:d;for(f=0;f<m-1;++f)for(var E=0;E<e-1;++E)for(var M=0;M<F-1;++M){for(var C=0,G=0;8>G;++G)C|=!!(b[(e*(f+((G&4)>>2))+E+((G&2)>>1))*F+M+(G&1)]&2)<<G;if(0!==C&&255!==C){var z=l[C];if(0!==z)for(G=w[C],z&1&&(s[0]=g(f,E,M,C,0,1)),z&2&&(s[1]=g(f,E,M,C,1,3)),z&4&&(s[2]=g(f,E,M,C,3,2)),z&8&&(s[3]=g(f,E,M,C,2,0)),z&16&&(s[4]=g(f,E,M,C,4,5)),z&32&&(s[5]=g(f,E,M,C,5,7)),z&64&&(s[6]=g(f,E,M,C,7,6)),z&128&&(s[7]=g(f,E,M,
+C,6,4)),z&256&&(s[8]=g(f,E,M,C,0,4)),z&512&&(s[9]=g(f,E,M,C,1,5)),z&1024&&(s[10]=g(f,E,M,C,3,7)),z&2048&&(s[11]=g(f,E,M,C,2,6)),C=0;C<G.length;C+=3){var z=s[G[C]],H=s[G[C+1]],L=s[G[C+2]];t&&3<=C&&(q.push(q[z]),z=q.length-1,q.push(q[H]),H=q.length-1,q.push(q[L]),L=q.length-1);B.push(z);B.push(H);B.push(L)}}}},laplacianSmooth:function(b,c,d){var f=Array(c.length),w,h,t,m;w=0;for(h=c.length;w<h;w++)f[w]={x:0,y:0,z:0};var e=Array(20),p;for(w=0;20>w;w++)e[w]=Array(c.length);w=0;for(h=c.length;w<h;w++)e[0][w]=
+0;w=0;for(h=d.length/3;w<h;w++){var g=3*w,x=3*w+1,u=3*w+2;p=!0;t=0;for(m=e[0][d[g]];t<m;t++)if(d[x]==e[t+1][d[g]]){p=!1;break}p&&(e[0][d[g]]++,e[e[0][d[g]]][d[g]]=d[x]);p=!0;t=0;for(m=e[0][d[g]];t<m;t++)if(d[u]==e[t+1][d[g]]){p=!1;break}p&&(e[0][d[g]]++,e[e[0][d[g]]][d[g]]=d[u]);p=!0;t=0;for(m=e[0][d[x]];t<m;t++)if(d[g]==e[t+1][d[x]]){p=!1;break}p&&(e[0][d[x]]++,e[e[0][d[x]]][d[x]]=d[g]);p=!0;t=0;for(m=e[0][d[x]];t<m;t++)if(d[u]==e[t+1][d[x]]){p=!1;break}p&&(e[0][d[x]]++,e[e[0][d[x]]][d[x]]=d[u]);
+p=!0;for(t=0;t<e[0][d[u]];t++)if(d[g]==e[t+1][d[u]]){p=!1;break}p&&(e[0][d[u]]++,e[e[0][d[u]]][d[u]]=d[g]);p=!0;t=0;for(m=e[0][d[u]];t<m;t++)if(d[x]==e[t+1][d[u]]){p=!1;break}p&&(e[0][d[u]]++,e[e[0][d[u]]][d[u]]=d[x])}for(d=0;d<b;d++){w=0;for(h=c.length;w<h;w++)if(3>e[0][w])f[w].x=c[w].x,f[w].y=c[w].y,f[w].z=c[w].z;else if(3==e[0][w]||4==e[0][w]){f[w].x=0;f[w].y=0;t=f[w].z=0;for(m=e[0][w];t<m;t++)f[w].x+=c[e[t+1][w]].x,f[w].y+=c[e[t+1][w]].y,f[w].z+=c[e[t+1][w]].z;f[w].x+=.5*c[w].x;f[w].y+=.5*c[w].y;
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-$3Dmol.ProteinSurface=function(){var u=0,q=0,C=0,A=2,w=0,B=0,g=0,a=0,c=null,h=null,m=null,b=0,f=0,l=0,d=0,e=0,p=0,z={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},t=function(c){return c.elem&&"undefined"!=typeof z[c.elem]?c.elem:"X"},n={},s={},x,E,y=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,
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-{},d,e;d=0;for(e=b.length;d<e;d++)a[b[d]]=!0;b=E;d=0;for(e=b.length;d<e;d++)b[d].x=b[d].x/A-u,b[d].y=b[d].y/A-q,b[d].z=b[d].z/A-C;var g=[];d=0;for(e=x.length;d<e;d+=3){var l=x[d],t=x[d+1],s=x[d+2],n=b[t].atomid,f=b[s].atomid,y=b[l].atomid;n<y&&(y=n);f<y&&(y=f);a[y]&&l!==t&&t!==s&&l!==s&&(g.push(l),g.push(t),g.push(s))}m=h=c=null;return{vertices:b,faces:g}};this.initparm=function(t,s,n){1E6<n&&(A=1);n=1/A*5.5;b=t[0][0];d=t[1][0];f=t[0][1];e=t[1][1];l=t[0][2];p=t[1][2];s?(b-=1.4+n,f-=1.4+n,l-=1.4+n,
-d+=1.4+n,e+=1.4+n,p+=1.4+n):(b-=n,f-=n,l-=n,d+=n,e+=n,p+=n);b=Math.floor(b*A)/A;f=Math.floor(f*A)/A;l=Math.floor(l*A)/A;d=Math.ceil(d*A)/A;e=Math.ceil(e*A)/A;p=Math.ceil(p*A)/A;u=-b;q=-f;C=-l;g=Math.ceil(A*(d-b))+1;B=Math.ceil(A*(e-f))+1;w=Math.ceil(A*(p-l))+1;this.boundingatom(s);a=1.4*A;c=new Uint8Array(g*B*w);h=new Float64Array(g*B*w);m=new Int32Array(g*B*w);console.log("Box size: ",g,B,w,c.length)};this.boundingatom=function(c){var b=[],a,d;flagradius=c;for(var m in z)if(z.hasOwnProperty(m))for(d=
-z[m],b[m]=c?(d+1.4)*A+.5:d*A+.5,d=b[m]*b[m],s[m]=Math.floor(b[m])+1,n[m]=new Int32Array(s[m]*s[m]),j=indx=0;j<s[m];j++)for(k=0;k<s[m];k++)a=j*j+k*k,a>d?n[m][indx]=-1:(a=Math.sqrt(d-a),n[m][indx]=Math.floor(a)),indx++};this.fillvoxels=function(b,a){var d,e;d=0;for(e=c.length;d<e;d++)c[d]=0,h[d]=-1,m[d]=-1;for(d in a)e=b[a[d]],void 0!==e&&this.fillAtom(e,b);d=0;for(e=c.length;d<e;d++)c[d]&1&&(c[d]|=2)};this.fillAtom=function(b,d){var a,e,l,h,f,y,E,p,x,z,H,N,U,P,Q,W,R;a=Math.floor(.5+A*(b.x+u));e=Math.floor(.5+
-A*(b.y+q));l=Math.floor(.5+A*(b.z+C));var X=t(b),L=0,ea=B*w;z=0;for(R=s[X];z<R;z++)for(H=0;H<R;H++){if(-1!=n[X][L])for(P=-1;2>P;P++)for(Q=-1;2>Q;Q++)for(W=-1;2>W;W++)if(0!==P&&0!==Q&&0!==W)for(E=P*z,x=W*H,N=0;N<=n[X][L];N++)p=N*Q,h=a+E,f=e+p,U=l+x,0>h||0>f||0>U||h>=g||f>=B||U>=w||(U=h*ea+f*w+U,c[U]&1?(y=d[m[U]],y.serial!=b.serial&&(h=a+E-Math.floor(.5+A*(y.x+u)),f=e+p-Math.floor(.5+A*(y.y+q)),y=l+x-Math.floor(.5+A*(y.z+C)),E*E+p*p+x*x<h*h+f*f+y*y&&(m[U]=b.serial))):(c[U]|=1,m[U]=b.serial));L++}};
-this.fillvoxelswaals=function(b,d){var a,m;a=0;for(m=c.length;a<m;a++)c[a]&=-3;for(a in d)m=b[d[a]],void 0!==m&&this.fillAtomWaals(m,b)};this.fillAtomWaals=function(b,a){var d,e,l,h,f,y,E=0,p,x,z,H,N,U,P,Q,W,R,X;d=Math.floor(.5+A*(b.x+u));e=Math.floor(.5+A*(b.y+q));l=Math.floor(.5+A*(b.z+C));var L=t(b),ea=B*w;N=0;for(X=s[L];N<X;N++)for(U=0;U<X;U++){if(-1!=n[L][E])for(Q=-1;2>Q;Q++)for(W=-1;2>W;W++)for(R=-1;2>R;R++)if(0!==Q&&0!==W&&0!==R)for(p=Q*N,z=R*U,P=0;P<=n[L][E];P++)x=P*W,h=d+p,f=e+x,H=l+z,0>
-h||0>f||0>H||h>=g||f>=B||H>=w||(H=h*ea+f*w+H,c[H]&2?(y=a[m[H]],y.serial!=b.serial&&(h=d+p-Math.floor(.5+A*(y.x+u)),f=e+x-Math.floor(.5+A*(y.y+q)),y=l+z-Math.floor(.5+A*(y.z+C)),p*p+x*x+z*z<h*h+f*f+y*y&&(m[H]=b.serial))):(c[H]|=2,m[H]=b.serial));E++}};this.buildboundary=function(){var b=B*w;for(i=0;i<g;i++)for(j=0;j<w;j++)for(k=0;k<B;k++){var a=i*b+k*w+j;if(c[a]&1)for(var d=0;26>d;){var m=i+y[d][0],e=j+y[d][2],h=k+y[d][1];if(-1<m&&m<g&&-1<h&&h<B&&-1<e&&e<w&&!(c[m*b+h*w+e]&1)){c[a]|=4;break}else d++}}};
-var H=function(c,b,d){var a=new Int32Array(c*b*d*3);this.set=function(c,m,e,g){c=3*((c*b+m)*d+e);a[c]=g.ix;a[c+1]=g.iy;a[c+2]=g.iz};this.get=function(c,m,e){c=3*((c*b+m)*d+e);return{ix:a[c],iy:a[c+1],iz:a[c+2]}}};this.fastdistancemap=function(){var b,d,m,e=new H(g,B,w),l=B*w,t=a*a,n=[];m=[];var f;for(b=0;b<g;b++)for(d=0;d<B;d++)for(m=0;m<w;m++)if(f=b*l+d*w+m,c[f]&=-3,c[f]&1&&c[f]&4){var s={ix:b,iy:d,iz:m};e.set(b,d,m,s);n.push(s);h[f]=0;c[f]|=2;c[f]&=-5}do for(m=this.fastoneshell(n,e),n=[],b=0,d=
-m.length;b<d;b++)f=l*m[b].ix+w*m[b].iy+m[b].iz,c[f]&=-5,h[f]<=1.0404*t&&n.push({ix:m[b].ix,iy:m[b].iy,iz:m[b].iz});while(0!==n.length);b=A-.5;0>b&&(b=0);t-=.5/(.1+b);for(b=0;b<g;b++)for(d=0;d<B;d++)for(m=0;m<w;m++)f=b*l+d*w+m,c[f]&=-5,c[f]&1&&(!(c[f]&2)||c[f]&2&&h[f]>=t)&&(c[f]|=4)};this.fastoneshell=function(b,d){var a,m,e,f,l,t,n,s,E,p,x,z=[];if(0===b.length)return z;tnv={ix:-1,iy:-1,iz:-1};var H=B*w;n=0;for(E=b.length;n<E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=0;6>s;s++)tnv.ix=
-a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));n=0;for(E=b.length;n<
-E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=6;18>s;s++)tnv.ix=a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,
-c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));n=0;for(E=b.length;n<E;n++)for(a=b[n].ix,m=b[n].iy,e=b[n].iz,p=d.get(a,m,e),s=18;26>s;s++)tnv.ix=a+y[s][0],tnv.iy=m+y[s][1],tnv.iz=e+y[s][2],tnv.ix<g&&-1<tnv.ix&&tnv.iy<B&&-1<tnv.iy&&tnv.iz<w&&-1<tnv.iz&&(x=tnv.ix*H+w*tnv.iy+tnv.iz,c[x]&1&&!(c[x]&2)?(d.set(tnv.ix,tnv.iy,e+y[s][2],p),f=tnv.ix-p.ix,l=tnv.iy-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,h[x]=f,c[x]|=2,c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):c[x]&1&&c[x]&2&&(f=tnv.ix-p.ix,l=tnv.iy-
-p.iy,t=tnv.iz-p.iz,f=f*f+l*l+t*t,f<h[x]&&(d.set(tnv.ix,tnv.iy,tnv.iz,p),h[x]=f,c[x]&4||(c[x]|=4,z.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return z};this.marchingcubeinit=function(b){for(var d=0,a=c.length;d<a;d++)1==b?c[d]&=-5:4==b?(c[d]&=-3,c[d]&4&&(c[d]|=2),c[d]&=-5):2==b?c[d]&4&&c[d]&2?c[d]&=-5:c[d]&4&&!(c[d]&2)&&(c[d]|=2):3==b&&(c[d]&=-5)};this.marchingcube=function(b){this.marchingcubeinit(b);E=[];x=[];$3Dmol.MarchingCube.march(c,E,x,{smooth:1,nX:g,nY:B,nZ:w});b=B*w;for(var d=0,a=E.length;d<
-a;d++)E[d].atomid=m[E[d].x*b+w*E[d].y+E[d].z];$3Dmol.MarchingCube.laplacianSmooth(1,E,x)}};$3Dmol=function(u){return u.$3Dmol||{}}(window);$.get("http://3dmol.csb.pitt.edu/track/report.cgi");$3Dmol.createViewer=function(u,q){"string"===$.type(u)&&(u=$("#"+u));if(u){q=q||{};try{return new $3Dmol.GLViewer(u,q)}catch(C){throw"error creating viewer: "+C;}}};$3Dmol.viewers={};
-$3Dmol.download=function(u,q,C,A){var w="",B=q.addModel();if("pdb:"===u.substr(0,4)){w="pdb";u=u.substr(4).toUpperCase();if(!u.match(/^[1-9][A-Za-z0-9]{3}$/)){alert("Wrong PDB ID");return}uri="http://www.rcsb.org/pdb/files/"+u+".pdb"}else if("cid:"==u.substr(0,4)){w="sdf";u=u.substr(4);if(!u.match(/^[1-9]+$/)){alert("Wrong Compound ID");return}uri="http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+u+"/SDF?record_type=3d"}$.get(uri,function(g){B.addMolData(g,w,C);q.zoomTo();q.render();A&&A(B)});
-return B};$3Dmol.SurfaceType={VDW:1,MS:2,SAS:3,SES:4};$3Dmol.mergeGeos=function(u,q){var C=q.geometry;void 0!==C&&u.geometryGroups.push(C.geometryGroups[0])};$3Dmol.multiLineString=function(u){return u.toString().replace(/^[^\/]+\/\*!?/,"").replace(/\*\/[^\/]+$/,"")};$3Dmol.syncSurface=!1;if(0<=window.navigator.userAgent.indexOf("MSIE ")||0<=window.navigator.userAgent.indexOf("Trident/"))$3Dmol.syncSurface=!0;
-$3Dmol.specStringToObject=function(u){if("object"===typeof u||"undefined"===typeof u||null==u)return u;var q={};u=u.split(";");for(var C=0;C<u.length;C++){var A=u[C].split(":"),w=A[0],B={};if(A=A[1])if(A=A.replace(/~/g,"="),-1!==A.indexOf("="))for(var A=A.split(","),g=0;g<A.length;g++){var a=A[g].split("=",2);B[a[0]]=a[1]}else B=-1!==A.indexOf(",")?A.split(","):A;q[w]=B}return q};
-$3Dmol.getExtent=function(u,q){var C,A,w,B,g,a,c,h,m,b,f=!q;C=A=w=9999;B=g=a=-9999;c=h=m=b=0;if(0===u.length)return[[0,0,0],[0,0,0],[0,0,0]];for(var l=0;l<u.length;l++){var d=u[l];if(void 0!==d&&(b++,c+=d.x,h+=d.y,m+=d.z,C=C<d.x?C:d.x,A=A<d.y?A:d.y,w=w<d.z?w:d.z,B=B>d.x?B:d.x,g=g>d.y?g:d.y,a=a>d.z?a:d.z,d.symmetries&&f))for(var e=0;e<d.symmetries.length;e++)b++,c+=d.symmetries[e].x,h+=d.symmetries[e].y,m+=d.symmetries[e].z,C=C<d.symmetries[e].x?C:d.symmetries[e].x,A=A<d.symmetries[e].y?A:d.symmetries[e].y,
-w=w<d.symmetries[e].z?w:d.symmetries[e].z,B=B>d.symmetries[e].x?B:d.symmetries[e].x,g=g>d.symmetries[e].y?g:d.symmetries[e].y,a=a>d.symmetries[e].z?a:d.symmetries[e].z}return[[C,A,w],[B,g,a],[c/b,h/b,m/b]]};$3Dmol.workerString='self.onmessage=function(oEvent){var obj=oEvent.data,type=obj.type;if(0>type)self.atomData=obj.atoms,self.volume=obj.volume,self.ps=new ProteinSurface;else{var ps=self.ps;ps.initparm(obj.expandedExtent,1==type?!1:!0,self.volume),ps.fillvoxels(self.atomData,obj.extendedAtoms),ps.buildboundary(),(4===type||2===type)&&(ps.fastdistancemap(),ps.boundingatom(!1),ps.fillvoxelswaals(self.atomData,obj.extendedAtoms)),ps.marchingcube(type);var VandF=ps.getFacesAndVertices(obj.atomsToShow);self.postMessage(VandF)}};var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}};var ISDONE=2,ProteinSurface=function (){var faces,verts,origextent,INOUT=1,ISDONE=2,ISBOUND=4,ptranx=0,ptrany=0,ptranz=0,probeRadius=1.4,defaultScaleFactor=2,scaleFactor=defaultScaleFactor,pHeight=0,pWidth=0,pLength=0,cutRadius=0,vpBits=null,vpDistance=null,vpAtomID=null,pminx=0,pminy=0,pminz=0,pmaxx=0,pmaxy=0,pmaxz=0,vdwRadii={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},getVDWIndex=function(atom){return atom.elem&&"undefined"!=typeof vdwRadii[atom.elem]?atom.elem:"X"},depty={},widxz={},nb=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,-1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];this.getFacesAndVertices=function(atomlist){var i,il,atomsToShow={};for(i=0,il=atomlist.length;il>i;i++)atomsToShow[atomlist[i]]=!0;var vertices=verts;for(i=0,il=vertices.length;il>i;i++)vertices[i].x=vertices[i].x/scaleFactor-ptranx,vertices[i].y=vertices[i].y/scaleFactor-ptrany,vertices[i].z=vertices[i].z/scaleFactor-ptranz;var finalfaces=[];for(i=0,il=faces.length;il>i;i+=3){var fa=faces[i],fb=faces[i+1],fc=faces[i+2],a=vertices[fa].atomid,b=vertices[fb].atomid,c=vertices[fc].atomid,which=a;if(which>b&&(which=b),which>c&&(which=c),atomsToShow[which]){{vertices[faces[i]],vertices[faces[i+1]],vertices[faces[i+2]]}fa!==fb&&fb!==fc&&fa!==fc&&(finalfaces.push(fa),finalfaces.push(fb),finalfaces.push(fc))}}return vpBits=null,vpDistance=null,vpAtomID=null,{vertices:vertices,faces:finalfaces}},this.initparm=function(extent,btype,volume){volume>1e6&&(scaleFactor=defaultScaleFactor/2);var margin=1/scaleFactor*5.5;origextent=extent,pminx=extent[0][0],pmaxx=extent[1][0],pminy=extent[0][1],pmaxy=extent[1][1],pminz=extent[0][2],pmaxz=extent[1][2],btype?(pminx-=probeRadius+margin,pminy-=probeRadius+margin,pminz-=probeRadius+margin,pmaxx+=probeRadius+margin,pmaxy+=probeRadius+margin,pmaxz+=probeRadius+margin):(pminx-=margin,pminy-=margin,pminz-=margin,pmaxx+=margin,pmaxy+=margin,pmaxz+=margin),pminx=Math.floor(pminx*scaleFactor)/scaleFactor,pminy=Math.floor(pminy*scaleFactor)/scaleFactor,pminz=Math.floor(pminz*scaleFactor)/scaleFactor,pmaxx=Math.ceil(pmaxx*scaleFactor)/scaleFactor,pmaxy=Math.ceil(pmaxy*scaleFactor)/scaleFactor,pmaxz=Math.ceil(pmaxz*scaleFactor)/scaleFactor,ptranx=-pminx,ptrany=-pminy,ptranz=-pminz,pLength=Math.ceil(scaleFactor*(pmaxx-pminx))+1,pWidth=Math.ceil(scaleFactor*(pmaxy-pminy))+1,pHeight=Math.ceil(scaleFactor*(pmaxz-pminz))+1,this.boundingatom(btype),cutRadius=probeRadius*scaleFactor,vpBits=new Uint8Array(pLength*pWidth*pHeight),vpDistance=new Float64Array(pLength*pWidth*pHeight),vpAtomID=new Int32Array(pLength*pWidth*pHeight)},this.boundingatom=function(btype){var txz,tdept,sradius,tradius=[];flagradius=btype;for(var i in vdwRadii)if(vdwRadii.hasOwnProperty(i)){var r=vdwRadii[i];for(tradius[i]=btype?(r+probeRadius)*scaleFactor+.5:r*scaleFactor+.5,sradius=tradius[i]*tradius[i],widxz[i]=Math.floor(tradius[i])+1,depty[i]=new Int32Array(widxz[i]*widxz[i]),indx=0,j=0;j<widxz[i];j++)for(k=0;k<widxz[i];k++)txz=j*j+k*k,txz>sradius?depty[i][indx]=-1:(tdept=Math.sqrt(sradius-txz),depty[i][indx]=Math.floor(tdept)),indx++}},this.fillvoxels=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]=0,vpDistance[i]=-1,vpAtomID[i]=-1;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtom(atom,atoms)}for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&INOUT&&(vpBits[i]|=ISDONE)},this.fillAtom=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,i,j,k,si,sj,sk,ii,jj,kk,n;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),nind=0,pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&INOUT){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=INOUT,vpAtomID[index]=atom.serial}nind++}},this.fillvoxelswaals=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&=~ISDONE;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtomWaals(atom,atoms)}},this.fillAtomWaals=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,si,sj,sk,i,j,k,ii,jj,kk,n,nind=0;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&ISDONE){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=ISDONE,vpAtomID[index]=atom.serial}nind++}},this.buildboundary=function(){var pWH=pWidth*pHeight;for(i=0;pLength>i;i++)for(j=0;pHeight>j;j++)for(k=0;pWidth>k;k++){var index=i*pWH+k*pHeight+j;if(vpBits[index]&INOUT)for(var ii=0;26>ii;){var ti=i+nb[ii][0],tj=j+nb[ii][2],tk=k+nb[ii][1];if(ti>-1&&pLength>ti&&tk>-1&&pWidth>tk&&tj>-1&&pHeight>tj&&!(vpBits[ti*pWH+tk*pHeight+tj]&INOUT)){vpBits[index]|=ISBOUND;break}ii++}}};var PointGrid=function(length,width,height){var data=new Int32Array(length*width*height*3);this.set=function(x,y,z,pt){var index=3*((x*width+y)*height+z);data[index]=pt.ix,data[index+1]=pt.iy,data[index+2]=pt.iz},this.get=function(x,y,z){var index=3*((x*width+y)*height+z);return{ix:data[index],iy:data[index+1],iz:data[index+2]}}};this.fastdistancemap=function(){var i,j,k,n,index,boundPoint=new PointGrid(pLength,pWidth,pHeight),pWH=pWidth*pHeight,cutRSq=cutRadius*cutRadius,inarray=[],outarray=[];for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)if(index=i*pWH+j*pHeight+k,vpBits[index]&=~ISDONE,vpBits[index]&INOUT&&vpBits[index]&ISBOUND){var triple={ix:i,iy:j,iz:k};boundPoint.set(i,j,k,triple),inarray.push(triple),vpDistance[index]=0,vpBits[index]|=ISDONE,vpBits[index]&=~ISBOUND}do for(outarray=this.fastoneshell(inarray,boundPoint),inarray=[],i=0,n=outarray.length;n>i;i++)index=pWH*outarray[i].ix+pHeight*outarray[i].iy+outarray[i].iz,vpBits[index]&=~ISBOUND,vpDistance[index]<=1.0404*cutRSq&&inarray.push({ix:outarray[i].ix,iy:outarray[i].iy,iz:outarray[i].iz});while(0!==inarray.length);inarray=[],outarray=[],boundPoint=null;var cutsf=scaleFactor-.5;0>cutsf&&(cutsf=0);var cutoff=cutRSq-.5/(.1+cutsf);for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)index=i*pWH+j*pHeight+k,vpBits[index]&=~ISBOUND,vpBits[index]&INOUT&&(!(vpBits[index]&ISDONE)||vpBits[index]&ISDONE&&vpDistance[index]>=cutoff)&&(vpBits[index]|=ISBOUND)},this.fastoneshell=function(inarray,boundPoint){var tx,ty,tz,dx,dy,dz,i,j,n,square,bp,index,outarray=[];if(0===inarray.length)return outarray;tnv={ix:-1,iy:-1,iz:-1};var pWH=pWidth*pHeight;for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=0;6>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=6;18>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=18;26>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return outarray},this.marchingcubeinit=function(stype){for(var i=0,lim=vpBits.length;lim>i;i++)1==stype?vpBits[i]&=~ISBOUND:4==stype?(vpBits[i]&=~ISDONE,vpBits[i]&ISBOUND&&(vpBits[i]|=ISDONE),vpBits[i]&=~ISBOUND):2==stype?vpBits[i]&ISBOUND&&vpBits[i]&ISDONE?vpBits[i]&=~ISBOUND:vpBits[i]&ISBOUND&&!(vpBits[i]&ISDONE)&&(vpBits[i]|=ISDONE):3==stype&&(vpBits[i]&=~ISBOUND)};this.marchingcube=function(stype){this.marchingcubeinit(stype),verts=[],faces=[],march(vpBits,verts,faces,{smooth:1,nX:pLength,nY:pWidth,nZ:pHeight});for(var pWH=pWidth*pHeight,i=0,vlen=verts.length;vlen>i;i++)verts[i].atomid=vpAtomID[verts[i].x*pWH+pHeight*verts[i].y+verts[i].z];laplacianSmooth(1,verts,faces)}},march=function (data,verts,faces,spec){var i,il,fulltable=!!spec.fulltable,origin=spec.hasOwnProperty("origin")&&spec.origin.hasOwnProperty("x")?spec.origin:{x:0,y:0,z:0},voxel=!!spec.voxel,nX=spec.nX||0,nY=spec.nY||0,nZ=spec.nZ||0,scale=spec.scale||1,unitCube=new Vector3(1,1,1).multiplyScalar(scale),vertnums=new Int32Array(nX*nY*nZ);for(i=0,il=vertnums.length;il>i;++i)vertnums[i]=-1;var getVertex=function(i,j,k,code,p1,p2){var pt=new Vector3;pt.copy(origin);var val1=!!(code&1<<p1),val2=!!(code&1<<p2),p=p1;!val1&&val2&&(p=p2),1&p&&k++,2&p&&j++,4&p&&i++,pt.x+=unitCube.x*i,pt.y+=unitCube.y*j,pt.z+=unitCube.z*k;var index=(nY*i+j)*nZ+k;return voxel?(verts.push(pt),verts.length-1):(vertnums[index]<0&&(vertnums[index]=verts.length,verts.push(pt)),vertnums[index])},intersects=new Int32Array(12),etable=fulltable?edgeTable2:edgeTable,tritable=fulltable?triTable2:triTable;for(i=0;nX-1>i;++i)for(var j=0;nY-1>j;++j)for(var k=0;nZ-1>k;++k){for(var code=0,p=0;8>p;++p){var index=(nY*(i+((4&p)>>2))+j+((2&p)>>1))*nZ+k+(1&p),val=!!(data[index]&ISDONE);code|=val<<p}if(0!==code&&255!==code){var ecode=etable[code];if(0!==ecode){var ttable=tritable[code];1&ecode&&(intersects[0]=getVertex(i,j,k,code,0,1)),2&ecode&&(intersects[1]=getVertex(i,j,k,code,1,3)),4&ecode&&(intersects[2]=getVertex(i,j,k,code,3,2)),8&ecode&&(intersects[3]=getVertex(i,j,k,code,2,0)),16&ecode&&(intersects[4]=getVertex(i,j,k,code,4,5)),32&ecode&&(intersects[5]=getVertex(i,j,k,code,5,7)),64&ecode&&(intersects[6]=getVertex(i,j,k,code,7,6)),128&ecode&&(intersects[7]=getVertex(i,j,k,code,6,4)),256&ecode&&(intersects[8]=getVertex(i,j,k,code,0,4)),512&ecode&&(intersects[9]=getVertex(i,j,k,code,1,5)),1024&ecode&&(intersects[10]=getVertex(i,j,k,code,3,7)),2048&ecode&&(intersects[11]=getVertex(i,j,k,code,2,6));for(var t=0;t<ttable.length;t+=3){var a=intersects[ttable[t]],b=intersects[ttable[t+1]],c=intersects[ttable[t+2]];voxel&&t>=3&&(verts.push(verts[a]),a=verts.length-1,verts.push(verts[b]),b=verts.length-1,verts.push(verts[c]),c=verts.length-1),faces.push(a),faces.push(b),faces.push(c)}}}}},laplacianSmooth=function (numiter,verts,faces){var i,il,j,jl,k,tps=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)tps[i]={x:0,y:0,z:0};var flagvert,vertdeg=new Array(20);for(i=0;20>i;i++)vertdeg[i]=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)vertdeg[0][i]=0;for(i=0,il=faces.length/3;il>i;i++){var aoffset=3*i,boffset=3*i+1,coffset=3*i+2;for(flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[boffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[coffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[aoffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[coffset]),flagvert=!0,j=0;j<vertdeg[0][faces[coffset]];j++)if(faces[aoffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[coffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[boffset])}var wt=1,wt2=.5;for(k=0;numiter>k;k++){for(i=0,il=verts.length;il>i;i++)if(vertdeg[0][i]<3)tps[i].x=verts[i].x,tps[i].y=verts[i].y,tps[i].z=verts[i].z;else if(3==vertdeg[0][i]||4==vertdeg[0][i]){for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt2*verts[i].x,tps[i].y+=wt2*verts[i].y,tps[i].z+=wt2*verts[i].z,tps[i].x/=wt2+vertdeg[0][i],tps[i].y/=wt2+vertdeg[0][i],tps[i].z/=wt2+vertdeg[0][i]}else{for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt*verts[i].x,tps[i].y+=wt*verts[i].y,tps[i].z+=wt*verts[i].z,tps[i].x/=wt+vertdeg[0][i],tps[i].y/=wt+vertdeg[0][i],tps[i].z/=wt+vertdeg[0][i]}for(i=0,il=verts.length;il>i;i++)verts[i].x=tps[i].x,verts[i].y=tps[i].y,verts[i].z=tps[i].z}},edgeTable=new 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-b[F[3]].clone();d=b[F[0]].clone();var A=b[F[2]].clone();e=b[F[1]].clone();p.atom=b[F[3]].atom||null;A.atom=b[F[2]].atom||null;d.atom=b[F[0]].atom||null;e.atom=b[F[1]].atom||null;if(n){var D=p.clone().add(d).multiplyScalar(.5),C=A.clone().add(e).multiplyScalar(.5),K=p.clone().add(e).multiplyScalar(.5);0===I%2?(E.clickable&&(F=new $3Dmol.Triangle(D,K,p),l=new $3Dmol.Triangle(C,A,K),p=new $3Dmol.Triangle(K,A,p),E.intersectionShape.triangle.push(F),E.intersectionShape.triangle.push(l),E.intersectionShape.triangle.push(p)),
-x.clickable&&(F=new $3Dmol.Triangle(d,e,K),l=new $3Dmol.Triangle(e,C,K),p=new $3Dmol.Triangle(d,K,D),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l),x.intersectionShape.triangle.push(p))):(x.clickable&&(F=new $3Dmol.Triangle(D,K,p),l=new $3Dmol.Triangle(C,A,K),p=new $3Dmol.Triangle(K,A,p),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l),x.intersectionShape.triangle.push(p)),E.clickable&&(F=new $3Dmol.Triangle(d,e,K),l=new $3Dmol.Triangle(e,C,K),p=
-new $3Dmol.Triangle(d,K,D),E.intersectionShape.triangle.push(F),E.intersectionShape.triangle.push(l),E.intersectionShape.triangle.push(p)))}else x.clickable&&(F=new $3Dmol.Triangle(d,e,p),l=new $3Dmol.Triangle(e,A,p),x.intersectionShape.triangle.push(F),x.intersectionShape.triangle.push(l))}G.vertices+=8;E=x}a=b.length-8;G=m.updateGeoGroup(8);I=G.vertexArray;F=G.colorArray;q=G.faceArray;t=G.vertices;n=3*t;d=G.faceidx;for(y=0;4>y;y++)b.push(b[2*y]),b.push(b[a+2*y]),c=b[2*y],g=b[a+2*y],I[n+6*y]=c.x,
-I[n+1+6*y]=c.y,I[n+2+6*y]=c.z,I[n+3+6*y]=g.x,I[n+4+6*y]=g.y,I[n+5+6*y]=g.z,F[n+6*y]=s.r,F[n+1+6*y]=s.g,F[n+2+6*y]=s.b,F[n+3+6*y]=s.r,F[n+4+6*y]=s.g,F[n+5+6*y]=s.b;F=[t,t+2,t+6,t+4];l=[t+1,t+5,t+7,t+3];q[d]=F[0];q[d+1]=F[1];q[d+2]=F[3];q[d+3]=F[1];q[d+4]=F[2];q[d+5]=F[3];q[d+6]=l[0];q[d+7]=l[1];q[d+8]=l[3];q[d+9]=l[1];q[d+10]=l[2];q[d+11]=l[3];G.faceidx+=12;G.vertices+=8;m.initTypedArrays();m.setUpNormals();a=new $3Dmol.MeshLambertMaterial;a.vertexColors=$3Dmol.FaceColors;a.side=$3Dmol.DoubleSide;
-a=new $3Dmol.Mesh(m,a)}else{m=B;b=g;y=c;s=new $3Dmol.Geometry(!0);c=0;for(t=m.length;c<t;c++){B=$3Dmol.CC.color(a[Math.round((c-1)/y)]);geoGroup=s.updateGeoGroup(2);z=geoGroup.vertexArray;h=geoGroup.colorArray;G=geoGroup.faceArray;q=geoGroup.vertices;g=3*q;z[g]=m[c].x;z[g+1]=m[c].y;z[g+2]=m[c].z;z[g+3]=b[c].x;z[g+4]=b[c].y;z[g+5]=b[c].z;for(z=0;6>z;++z)h[g+3*z]=B.r,h[g+1+3*z]=B.g,h[g+2+3*z]=B.b;0<c&&(q=[q,q+1,q-1,q-2],g=geoGroup.faceidx,G[g]=q[0],G[g+1]=q[1],G[g+2]=q[3],G[g+3]=q[1],G[g+4]=q[2],G[g+
-5]=q[3],geoGroup.faceidx+=6);geoGroup.vertices+=2}s.initTypedArrays();s.setUpNormals();a=new $3Dmol.MeshLambertMaterial;a.vertexColors=$3Dmol.FaceColors;a.side=$3Dmol.DoubleSide;a=new $3Dmol.Mesh(s,a)}w.add(a)}},C=function(w,B,g,a,c){0!==B.length&&(c=void 0===c?5:c,a=new $3Dmol.Geometry,u(B,c),B=new $3Dmol.LineBasicMaterial({linewidth:g}),B.vertexColors=!0,B=new $3Dmol.Line(a,B),B.type=$3Dmol.LineStrip,w.add(B))},A=function(w,B,g,a,c,h,m){var b;c.sub(a);c.normalize();c.multiplyScalar("c"===m.ss?"P"===
-m.atom?.8:.3:1.3);null!=h&&0>c.dot(h)&&c.negate();for(h=0;h<B;h++)b=-1+2*h/(B-1),b=new $3Dmol.Vector3(a.x+b*c.x,a.y+b*c.y,a.z+b*c.z),b.atom=m,g&&"s"===m.ss&&(b.smoothen=!0),w[h].push(b)};return function(w,B,g,a){var c,h,m;c=2;h=5;m=!1;var b="CA O P OP2 O5' O3' C5' C2' N1 N3".split(" "),f=[" DA"," DG","  A","  G"],l=[" DT"," DC","  U","  C"],d,e,p,z,t,n,s,x,E,y,H,I,F,G,u=null,S=[],D=[];for(s=0;s<c;s++)D[s]=[];for(s in B)if(p=B[s],void 0!==p&&-1!==$.inArray(p.atom,b)&&!p.hetflag)if(d=p.style.cartoon,
-"trace"===d.style){if(u||(u=new $3Dmol.Geometry(!0)),"CA"===p.atom||"P"===p.atom)t=a?a.valueToHex(p.resi,a.range()):$3Dmol.getColorFromStyle(p,d).getHex(),S.push(t),n=$.isNumeric(d.thickness)?d.thickness:.4,e&&e.chain===p.chain&&e.resi+1===p.resi&&(t==z?(z=$3Dmol.CC.color(t),$3Dmol.GLDraw.drawCylinder(u,e,p,n,z,!0,!0)):(d=(new $3Dmol.Vector3).addVectors(e,p).multiplyScalar(.5),z=$3Dmol.CC.color(z),F=$3Dmol.CC.color(t),$3Dmol.GLDraw.drawCylinder(u,e,d,n,z,!0,!1),$3Dmol.GLDraw.drawCylinder(u,d,p,n,
-F,!1,!0))),e=p,z=t}else{if("CA"===p.atom||"P"===p.atom||"O5'"===p.atom){if(void 0!=e&&(e.chain!=p.chain||e.resi!==p.resi&&e.resi+1!==p.resi||e.reschain!=p.reschain)){G&&(F=H?(new $3Dmol.Vector3).addVectors(e,H).multiplyScalar(.5):new $3Dmol.Vector3(e.x,e.y,e.z),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),A(D,c,!m,H,I,y,e),S.push(t),G=null);for(s=0;!n&&s<c;s++)C(w,D[s],1,S,h);q(w,D[0],D[c-1],S,h,n);D=[];for(s=0;s<c;s++)D[s]=[];S=[]}if(void 0===e||e.resi!=p.resi)G&&(F=(new $3Dmol.Vector3).addVectors(e,
-p).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),G=null),t=a?a.valueToHex(p.resi,a.range()):$3Dmol.getColorFromStyle(p,d).getHex(),S.push(t),n=$.isNumeric(d.thickness)?d.thickness:.4,e=p,x=new $3Dmol.Vector3(e.x,e.y,e.z),x.resi=e.resi,z=t;!0!==p.clickable||void 0!==p.intersectionShape&&void 0!==p.intersectionShape.triangle||(p.intersectionShape={sphere:null,cylinder:[],line:[],triangle:[]})}else if("O"===p.atom&&"CA"===e.atom||"OP2"===p.atom&&"P"===e.atom||
-"C5'"===p.atom&&"O5'"===e.atom)E=new $3Dmol.Vector3(p.x,p.y,p.z),E.resi=p.resi,"OP2"===p.atom&&(I=new $3Dmol.Vector3(p.x,p.y,p.z));else if("O3'"===p.atom)H=new $3Dmol.Vector3(p.x,p.y,p.z);else if("N1"===p.atom&&-1!=$.inArray(p.resn,f)||"N3"===p.atom&&-1!=$.inArray(p.resn,l))G=new $3Dmol.Vector3(p.x,p.y,p.z),G.color=$3Dmol.getColorFromStyle(p,d).getHex();E&&x&&E.resi===x.resi&&(A(D,c,!m,x,E,y,e),y=E,E=x=null)}G&&(F=H?(new $3Dmol.Vector3).addVectors(e,H).multiplyScalar(.5):new $3Dmol.Vector3(e.x,e.y,
-e.z),$3Dmol.GLDraw.drawCylinder(g,F,G,.4,$3Dmol.CC.color(G.color),!1,!0),A(D,c,!m,H,I,y,e),S.push(t));for(s=0;!n&&s<c;s++)C(w,D[s],1,S,h);q(w,D[0],D[c-1],S,h,n);u&&(B=new $3Dmol.MeshLambertMaterial,B.vertexColors=$3Dmol.FaceColors,B.side=$3Dmol.DoubleSide,u=new $3Dmol.Mesh(u,B),w.add(u))}}();$3Dmol=$3Dmol||{};
-$3Dmol.GLDraw=function(){var u={},q=function(){var g=new $3Dmol.Vector3;return function(a){g.set(a[0],a[1],a[2]);var c=g.x,h=g.y,m=g.z,b=Math.sqrt(c*c+h*h);1E-4>b?(a=0,b=1):(a=-c/b,b=h/b);h=-a*c+b*h;c=Math.sqrt(h*h+m*m);1E-4>c?(m=0,h=1):(m/=c,h/=c);c=new Float32Array(9);c[0]=b;c[1]=a;c[2]=0;c[3]=-a*h;c[4]=b*h;c[5]=m;c[6]=a*m;c[7]=-b*m;c[8]=h;return c}}(),C=function(){var g=[],a=Math.pow(2,4),c,h=Math.pow(2,2),m=a/h,b;g[0]=new $3Dmol.Vector3(-1,0,0);g[m]=new $3Dmol.Vector3(0,0,1);g[2*m]=new $3Dmol.Vector3(1,
-0,0);g[3*m]=new $3Dmol.Vector3(0,0,-1);for(c=3;4>=c;c++){h=Math.pow(2,c-1);m=a/h;for(b=0;b<h-1;b++)g[m/2+b*m]=g[b*m].clone().add(g[(b+1)*m]).normalize();b=h-1;g[m/2+b*m]=g[b*m].clone().add(g[0]).normalize()}return g}(),A={cache:{},getVerticesForRadius:function(g){if(void 0!==this.cache[g])return this.cache[g];new $3Dmol.Vector3(0,1,0);for(var a=C.length,c=[],h=[],m,b=0;b<a;b++)c.push(C[b].clone().multiplyScalar(g)),c.push(C[b].clone().multiplyScalar(g)),m=C[b].clone().normalize(),h.push(m),h.push(m);
-var b=[],f=2*Math.PI,l=Math.PI,d,e,p=!1,z=!1;for(e=0;10>=e;e++){var p=0===e||10===e?!0:!1,z=5===e?!0:!1,t=[],n=[];for(d=0;d<=a;d++)if(z){var s=d<a?2*d:0;n.push(s+1);t.push(s)}else{m=d/a;var x=e/10;p&&0!==d?p&&t.push(c.length-1):d<a?(s=new $3Dmol.Vector3,s.x=-g*Math.cos(0+m*f)*Math.sin(0+x*l),s.y=g*Math.cos(0+x*l),s.z=g*Math.sin(0+m*f)*Math.sin(0+x*l),1E-5>Math.abs(s.x)&&(s.x=0),1E-5>Math.abs(s.y)&&(s.y=0),1E-5>Math.abs(s.z)&&(s.z=0),m=new $3Dmol.Vector3(s.x,s.y,s.z),m.normalize(),c.push(s),h.push(m),
-t.push(c.length-1)):t.push(c.length-a)}z&&b.push(n);b.push(t)}a={vertices:c,normals:h,verticesRows:b,w:a,h:10};return this.cache[g]=a}},w=0;u.drawCylinder=function(g,a,c,h,m,b,f){if(a&&c){w++;var l=b||f;m=m||{r:0,g:0,b:0};var d=[c.x,c.y,c.z];d[0]-=a.x;d[1]-=a.y;d[2]-=a.z;var d=q(d),e=A.getVerticesForRadius(h);h=e.w;var p=e.h,z=l?p*h+2:2*h;g=g.updateGeoGroup(z);var t=e.vertices,n=e.normals,e=e.verticesRows,s=e[p/2],x=e[p/2+1],E=g.vertices,y,H,I,B,G,u,C=g.vertexArray,D=g.normalArray,J=g.colorArray,
-K=g.faceArray;for(I=0;I<h;++I)H=2*I,B=d[0]*t[H].x+d[3]*t[H].y+d[6]*t[H].z,G=d[1]*t[H].x+d[4]*t[H].y+d[7]*t[H].z,u=d[5]*t[H].y+d[8]*t[H].z,y=3*(E+H),H=g.faceidx,C[y]=B+a.x,C[y+1]=G+a.y,C[y+2]=u+a.z,C[y+3]=B+c.x,C[y+4]=G+c.y,C[y+5]=u+c.z,D[y]=B,D[y+3]=B,D[y+1]=G,D[y+4]=G,D[y+2]=u,D[y+5]=u,J[y]=m.r,J[y+3]=m.r,J[y+1]=m.g,J[y+4]=m.g,J[y+2]=m.b,J[y+5]=m.b,K[H]=x[I]+E,K[H+1]=x[I+1]+E,K[H+2]=s[I]+E,K[H+3]=s[I]+E,K[H+4]=x[I+1]+E,K[H+5]=s[I+1]+E,g.faceidx+=6;if(l){b=b?p+1:p/2+1;var ca,V,da,T,Z,N,U,P,Q,W,R,
-X,L;for(G=f?0:p/2;G<b;G++)if(G!==p/2){var ea=G<=p/2?c:a;for(B=0;B<h;B++)H=g.faceidx,f=e[G][B+1],I=3*(f+E),l=e[G][B],u=3*(l+E),s=e[G+1][B],y=3*(s+E),x=e[G+1][B+1],L=3*(x+E),ca=d[0]*t[f].x+d[3]*t[f].y+d[6]*t[f].z,V=d[0]*t[l].x+d[3]*t[l].y+d[6]*t[l].z,da=d[0]*t[s].x+d[3]*t[s].y+d[6]*t[s].z,T=d[0]*t[x].x+d[3]*t[x].y+d[6]*t[x].z,Z=d[1]*t[f].x+d[4]*t[f].y+d[7]*t[f].z,N=d[1]*t[l].x+d[4]*t[l].y+d[7]*t[l].z,U=d[1]*t[s].x+d[4]*t[s].y+d[7]*t[s].z,P=d[1]*t[x].x+d[4]*t[x].y+d[7]*t[x].z,Q=d[5]*t[f].y+d[8]*t[f].z,
-W=d[5]*t[l].y+d[8]*t[l].z,R=d[5]*t[s].y+d[8]*t[s].z,X=d[5]*t[x].y+d[8]*t[x].z,C[I]=ca+ea.x,C[u]=V+ea.x,C[y]=da+ea.x,C[L]=T+ea.x,C[I+1]=Z+ea.y,C[u+1]=N+ea.y,C[y+1]=U+ea.y,C[L+1]=P+ea.y,C[I+2]=Q+ea.z,C[u+2]=W+ea.z,C[y+2]=R+ea.z,C[L+2]=X+ea.z,J[I]=m.r,J[u]=m.r,J[y]=m.r,J[L]=m.r,J[I+1]=m.g,J[u+1]=m.g,J[y+1]=m.g,J[L+1]=m.g,J[I+2]=m.b,J[u+2]=m.b,J[y+2]=m.b,J[L+2]=m.b,ca=d[0]*n[f].x+d[3]*n[f].y+d[6]*n[f].z,V=d[0]*n[l].x+d[3]*n[l].y+d[6]*n[l].z,da=d[0]*n[s].x+d[3]*n[s].y+d[6]*n[s].z,T=d[0]*n[x].x+d[3]*n[x].y+
-d[6]*n[x].z,Z=d[1]*n[f].x+d[4]*n[f].y+d[7]*n[f].z,N=d[1]*n[l].x+d[4]*n[l].y+d[7]*n[l].z,U=d[1]*n[s].x+d[4]*n[s].y+d[7]*n[s].z,P=d[1]*n[x].x+d[4]*n[x].y+d[7]*n[x].z,Q=d[5]*n[f].y+d[8]*n[f].z,W=d[5]*n[l].y+d[8]*n[l].z,R=d[5]*n[s].y+d[8]*n[s].z,X=d[5]*n[x].y+d[8]*n[x].z,0===G?(D[I]=ca,D[y]=da,D[L]=T,D[I+1]=Z,D[y+1]=U,D[L+1]=P,D[I+2]=Q,D[y+2]=R,D[L+2]=X,K[H]=f+E,K[H+1]=s+E,K[H+2]=x+E,g.faceidx+=3):G===b-1?(D[I]=ca,D[u]=V,D[y]=da,D[I+1]=Z,D[u+1]=N,D[y+1]=U,D[I+2]=Q,D[u+2]=W,D[y+2]=R,K[H]=f+E,K[H+1]=l+
-E,K[H+2]=s+E,g.faceidx+=3):(D[I]=ca,D[u]=V,D[L]=T,D[I+1]=Z,D[u+1]=N,D[L+1]=P,D[I+2]=Q,D[u+2]=W,D[L+2]=X,D[u]=V,D[y]=da,D[L]=T,D[u+1]=N,D[y+1]=U,D[L+1]=P,D[u+2]=W,D[y+2]=R,D[L+2]=X,K[H]=f+E,K[H+1]=l+E,K[H+2]=x+E,K[H+3]=l+E,K[H+4]=s+E,K[H+5]=x+E,g.faceidx+=6)}}g.vertices+=z}};u.drawCone=function(g,a,c,h,m){if(a&&c){m=m||{r:0,g:0,b:0};var b=[c.x,c.y,c.z];b.x-=a.x;b.y-=a.y;b.z-=a.z;var f=q(b),l=C.length;g=g.updateGeoGroup(l+2);var d=g.vertices,e,p,z,t=g.vertexArray,n=g.normalArray,s=g.colorArray,x=g.faceArray;
-e=3*d;b=(new $3Dmol.Vector3(b[0],b[1],b[2])).normalize();t[e]=a.x;t[e+1]=a.y;t[e+2]=a.z;n[e]=-b.x;n[e+1]=-b.y;n[e+2]=-b.z;s[e]=m.r;s[e+1]=m.g;s[e+2]=m.b;t[e+3]=c.x;t[e+4]=c.y;t[e+5]=c.z;n[e+3]=b.x;n[e+4]=b.y;n[e+5]=b.z;s[e+3]=m.r;s[e+4]=m.g;s[e+5]=m.b;e+=6;for(c=0;c<l;++c)z=C[c].clone(),z.multiplyScalar(h),b=f[0]*z.x+f[3]*z.y+f[6]*z.z,p=f[1]*z.x+f[4]*z.y+f[7]*z.z,z=f[5]*z.y+f[8]*z.z,t[e]=b+a.x,t[e+1]=p+a.y,t[e+2]=z+a.z,n[e]=b,n[e+1]=p,n[e+2]=z,s[e]=m.r,s[e+1]=m.g,s[e+2]=m.b,e+=3;g.vertices+=l+2;a=
-g.faceidx;for(c=0;c<l;c++)h=d+2+c,m=d+2+(c+1)%l,x[a]=h,x[a+1]=m,x[a+2]=d,a+=3,x[a]=h,x[a+1]=m,x[a+2]=d+1,a+=3;g.faceidx+=6*l}};var B={cache:{},getVerticesForRadius:function(g){if("undefined"!==typeof this.cache[g])return this.cache[g];var a={vertices:[],verticesRows:[],normals:[]},c=16,h=10;1>g&&(c=10,h=8);var m=2*Math.PI,b=Math.PI,f,l;for(l=0;l<=h;l++){var d=[];for(f=0;f<=c;f++){var e=f/c,p=l/h,z={};z.x=-g*Math.cos(0+e*m)*Math.sin(0+p*b);z.y=g*Math.cos(0+p*b);z.z=g*Math.sin(0+e*m)*Math.sin(0+p*b);
-e=new $3Dmol.Vector3(z.x,z.y,z.z);e.normalize();a.vertices.push(z);a.normals.push(e);d.push(a.vertices.length-1)}a.verticesRows.push(d)}return this.cache[g]=a}};u.drawSphere=function(g,a,c,h){new $3Dmol.Vector3(a.x,a.y,a.z);var m=B.getVerticesForRadius(c),b=m.vertices,f=m.normals;g=g.updateGeoGroup(b.length);for(var l=g.vertices,d=g.vertexArray,e=g.colorArray,p=g.faceArray,z=g.lineArray,t=g.normalArray,n=0,s=b.length;n<s;++n){var x=3*(l+n),E=b[n];d[x]=E.x+a.x;d[x+1]=E.y+a.y;d[x+2]=E.z+a.z;e[x]=h.r;
-e[x+1]=h.g;e[x+2]=h.b}g.vertices+=b.length;m=m.verticesRows;d=m.length-1;for(h=0;h<d;h++)for(e=m[h].length-1,a=0;a<e;a++){var n=g.faceidx,s=g.lineidx,x=m[h][a+1]+l,E=3*x,y=m[h][a]+l,H=3*y,w=m[h+1][a]+l,q=3*w,u=m[h+1][a+1]+l,A=3*u,C=f[x-l],D=f[y-l],J=f[w-l],K=f[u-l];Math.abs(b[x-l].y)===c?(t[E]=C.x,t[q]=J.x,t[A]=K.x,t[E+1]=C.y,t[q+1]=J.y,t[A+1]=K.y,t[E+2]=C.z,t[q+2]=J.z,t[A+2]=K.z,p[n]=x,p[n+1]=w,p[n+2]=u,z[s]=x,z[s+1]=w,z[s+2]=x,z[s+3]=u,z[s+4]=w,z[s+5]=u,g.faceidx+=3,g.lineidx+=6):Math.abs(b[w-l].y)===
-c?(t[E]=C.x,t[H]=D.x,t[q]=J.x,t[E+1]=C.y,t[H+1]=D.y,t[q+1]=J.y,t[E+2]=C.z,t[H+2]=D.z,t[q+2]=J.z,p[n]=x,p[n+1]=y,p[n+2]=w,z[s]=x,z[s+1]=y,z[s+2]=x,z[s+3]=w,z[s+4]=y,z[s+5]=w,g.faceidx+=3,g.lineidx+=6):(t[E]=C.x,t[H]=D.x,t[A]=K.x,t[E+1]=C.y,t[H+1]=D.y,t[A+1]=K.y,t[E+2]=C.z,t[H+2]=D.z,t[A+2]=K.z,t[H]=D.x,t[q]=J.x,t[A]=K.x,t[H+1]=D.y,t[q+1]=J.y,t[A+1]=K.y,t[H+2]=D.z,t[q+2]=J.z,t[A+2]=K.z,p[n]=x,p[n+1]=y,p[n+2]=u,p[n+3]=y,p[n+4]=w,p[n+5]=u,z[s]=x,z[s+1]=y,z[s+2]=x,z[s+3]=u,z[s+4]=y,z[s+5]=w,z[s+6]=w,z[s+
-7]=u,g.faceidx+=6,g.lineidx+=8)}};return u}();$3Dmol=$3Dmol||{};
-$3Dmol.GLModel=function(){var u={line:{}},q={H:1.2,Li:1.82,LI:1.82,Na:2.27,NA:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,Cl:1.75,BR:1.85,Br:1.85,SE:1.9,Se:1.9,ZN:1.39,Zn:1.39,CU:1.4,Cu:1.4,NI:1.63,Ni:1.63};return function(C,A){var w=[],B=null,g=null,a=null,c=[],h=new $3Dmol.Matrix4;h.identity();var m,b,f=$3Dmol.elementColors.defaultColor,l=A?A:$3Dmol.elementColors.defaultColors,d=function(b,c){var d=1.5;"undefined"!=typeof c.radius?d=c.radius:q[b.elem]&&(d=q[b.elem]);"undefined"!=
-typeof c.scale&&(d*=c.scale);return d},e=function(b,c,d){var a=new $3Dmol.Vector3(b.x,b.y,b.z),m=(new $3Dmol.Vector3(c.x,c.y,c.z)).clone(),e=null;m.sub(a);1===b.bonds.length?1===c.bonds.length?(e=m.clone(),1E-4<Math.abs(e.x)?e.y+=1:e.x+=1):(d=(d+1)%c.bonds.length,b=c.bonds[d],b=w[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(a),e=b.clone(),e.cross(m)):(d=(d+1)%b.bonds.length,b=b.bonds[d],b=w[b],b=new $3Dmol.Vector3(b.x,b.y,b.z),b=b.clone(),b.sub(a),e=b.clone(),e.cross(m));.01>e.lengthSq()&&
-(e=m.clone(),1E-4<Math.abs(e.x)?e.y+=1:e.x+=1);e.cross(m);e.normalize();return e},p=function(b,c,d,a,m,e){b[d]=a.x;b[d+1]=a.y;b[d+2]=a.z;c[d]=e.r;c[d+1]=e.g;c[d+2]=e.b;b[d+3]=m.x;b[d+4]=m.y;b[d+5]=m.z;c[d+3]=e.r;c[d+4]=e.g;c[d+5]=e.b};this.getSymmetries=function(){return 0<c.length?c:[h]};this.setSymmetries=function(b){c="undefined"==typeof b?[h]:b};this.getID=function(){return C};this.addMolData=function(d,a,e){e=e||{};a=a||"";if(d)for("undefined"==typeof $3Dmol.Parsers[a]&&(a=a.split(".").pop(),
-typeof("undefined"==$3Dmol.Parsers[a])&&(console.log("Unknown format: "+a),a=d.match(/^@<TRIPOS>MOLECULE/)?"mol2":d.match(/^HETATM/)||d.match(/^ATOM/)?"pdb":d.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/)?"sdf":"xyz",console.log("Best guess: "+a))),(0,$3Dmol.Parsers[a])(w,d,e,c),m=!e.doAssembly,b=!e.duplicateAssemblyAtoms,d=w,a=0;a<d.length;a++)if(e=d[a])e.style=e.style||u,e.color=e.color||l[e.elem]||f,e.model=C,e.clickable&&(e.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]})};this.atomIsSelected=
-function(b,c){if("undefined"===typeof c)return!0;var d=!!c.invert,a=!0,e;for(e in c)if("predicate"===e){if(!c.predicate(b)){a=!1;break}}else if(c.hasOwnProperty(e)&&"props"!=e&&"invert"!=e&&"model"!=e&&"byres"!=e&&"expand"!=e&&"within"!=e){if("undefined"===typeof b[e]){a=!1;break}var m=!1;if("bonds"===e){if(m=c[e],m!=b.bonds.length){a=!1;break}}else if($.isArray(c[e])){for(var f=c[e],l=0;l<f.length;l++)if(b[e]==f[l]){m=!0;break}if(!m){a=!1;break}}else if(m=c[e],b[e]!=m){a=!1;break}}return d?!a:a};
-this.selectedAtoms=function(b,c){var d=[];c||(c=w);for(var a=c.length,e=0;e<a;e++){var m=c[e];m&&this.atomIsSelected(m,b)&&d.push(m)}if(b.hasOwnProperty("expand")){for(var m=b.expand,e=$3Dmol.getExtent(d),a=[[],[],[]],f=0;3>f;f++)a[0][f]=e[0][f]-m,a[1][f]=e[1][f]+m,a[2][f]=e[2][f];m=[];for(f=0;f<w.length;f++){var l=w[f].x,g=w[f].y,h=w[f].z;(l>=a[0][0]&&l<e[0][0]||l>e[1][0]&&l<=a[1][0])&&(g>=a[0][1]&&g<e[0][1]||g>e[1][1]&&g<=a[1][1])&&(h>=a[0][2]&&h<e[0][2]||h>e[1][2]&&h<=a[1][2])&&m.push(w[f])}g=
-d.length;for(e=0;e<m.length;e++)for(a=0;a<g;a++)f=z(m[e],d[a]),l=Math.pow(b.expand,2),f<l&&0<f&&d.push(m[e])}if(b.hasOwnProperty("within")&&b.within.hasOwnProperty("sel")&&b.within.hasOwnProperty("distance")){m=this.selectedAtoms(b.within.sel,w);g=[];for(e=0;e<m.length;e++)for(a=0;a<d.length;a++)f=z(m[e],d[a]),l=Math.pow(b.within.distance,2),f<l&&0<f&&g.push(d[a]);d=g}if(b.hasOwnProperty("byres"))for(f={},l=[],g=[],e=0;e<d.length;e++){var m=d[e],h=m.chain,p=m.resi;void 0===f[h]&&(f[h]={});if(m.hasOwnProperty("resi")&&
-void 0===f[h][p])for(f[h][p]=!0,g.push(m);0<g.length;)if(m=g.pop(),h=m.chain,p=m.resi,void 0===l[m.index])for(l[m.index]=!0,a=0;a<m.bonds.length;a++){var B=w[m.bonds[a]];void 0===l[B.index]&&B.hasOwnProperty("resi")&&B.chain==h&&B.resi==p&&(g.push(B),d.push(B))}}return d};var z=function(b,c){var d=c.y-b.y,a=c.z-b.z;return Math.pow(c.x-b.x,2)+Math.pow(d,2)+Math.pow(a,2)};this.addAtoms=function(b){B=null;var c=w.length,d=[],a;for(a=0;a<b.length;a++)d[b[a].index]=c+a;for(a=0;a<b.length;a++){var c=b[a],
-e=d[c.index],m=$.extend(!1,{},c);m.index=e;m.bonds=[];m.bondOrder=[];for(e=0;e<c.bonds.length;e++){var f=d[c.bonds[e]];"undefined"!=typeof f&&(m.bonds.push(f),m.bondOrder.push(c.bondOrder[e]))}w.push(m)}};this.removeAtoms=function(b){B=null;var c=[],d;for(d=0;d<b.length;d++)c[b[d].index]=!0;b=[];for(d=0;d<w.length;d++){var a=w[d];c[a.index]||b.push(a)}w=[];this.addAtoms(b)};this.setStyle=function(b,c,d){c=$.extend(!0,{},c);var a=!1;b=this.selectedAtoms(b,w);for(var e=0;e<w.length;e++)w[e]&&(w[e].capDrawn=
-!1);for(e=0;e<b.length;e++){a=!0;"undefined"!=typeof c.clickable&&(b[e].clickable=c.clickable);"undefined"!=typeof c.callback&&(b[e].callback=c.callback);b[e].clickable&&(b[e].intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});d||(b[e].style={});for(var m in c)c.hasOwnProperty(m)&&(b[e].style[m]=c[m])}a&&(B=null)};this.setColorByElement=function(b,c){var d;if(d=null!==B)d=a,d=c&&d?JSON.stringify(c)==JSON.stringify(d):c==d;if(!d){a=c;var e=this.selectedAtoms(b,e);0<e.length&&(B=null);for(d=
-0;d<e.length;d++){var m=e[d];"undefined"!==typeof c[m.elem]&&(m.color=c[m.elem])}}};this.setColorByProperty=function(b,c,d){var e=this.selectedAtoms(b,e);a=null;0<e.length&&(B=null);b=Number.POSITIVE_INFINITY;var m=Number.NEGATIVE_INFINITY,f,l;for(f=0;f<e.length;f++)l=e[f],l.properties&&void 0!==typeof l.properties[c]&&(l=parseFloat(l.properties[c]),l<b&&(b=l),l>m&&(m=l));for(f=0;f<e.length;f++)if(l=e[f],l.properties&&void 0!==typeof l.properties[c]){var g=d.valueToHex(parseFloat(l.properties[c]),
-[b,m]);l.color=g}};this.globj=function(a){if(null===B){var f=w,l=new $3Dmol.Object3D,h=[],z={},y={},q=new $3Dmol.Geometry(!0),u=new $3Dmol.Geometry(!0),A=new $3Dmol.Geometry(!0),C=new $3Dmol.Geometry(!0),M,S,D=[Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY];M=0;for(S=f.length;M<S;M++){var J=f[M];if(J&&J.style){J.clickable&&void 0===J.intersectionShape&&(J.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]});var K=J,ca=q;if(K.style.sphere){var V=K.style.sphere;if(!V.hidden){var da=$3Dmol.getColorFromStyle(K,
-V),T=d(K,V);if(!0===K.clickable&&void 0!==K.intersectionShape){var Z=new $3Dmol.Vector3(K.x,K.y,K.z);K.intersectionShape.sphere.push(new $3Dmol.Sphere(Z,T))}$3Dmol.GLDraw.drawSphere(ca,K,T,da)}}var N=J,U=u;if(N.style.spherei){var P=N.style.spherei;if(!P.hidden){for(var Q=d(N,P),W=$3Dmol.getColorFromStyle(N,P),R=U.updateGeoGroup(4),X=R.vertices,L=3*X,ea=R.vertexArray,Ma=R.colorArray,ra=0;4>ra;ra++)ea[L+3*ra]=N.x,ea[L+3*ra+1]=N.y,ea[L+3*ra+2]=N.z;for(var ta=R.normalArray,Ma=R.colorArray,ra=0;4>ra;ra++)Ma[L+
-3*ra]=W.r,Ma[L+3*ra+1]=W.g,Ma[L+3*ra+2]=W.b;ta[L+0]=-Q;ta[L+1]=-Q;ta[L+2]=0;ta[L+3]=-Q;ta[L+4]=Q;ta[L+5]=0;ta[L+6]=Q;ta[L+7]=Q;ta[L+8]=0;ta[L+9]=Q;ta[L+10]=-Q;ta[L+11]=0;R.vertices+=4;var Pa=R.faceArray,Qa=R.faceidx;Pa[Qa+0]=X;Pa[Qa+1]=X+1;Pa[Qa+2]=X+2;Pa[Qa+3]=X+2;Pa[Qa+4]=X+3;Pa[Qa+5]=X;R.faceidx+=6}}var ua=J,hb=y;if(ua.style.cross){var cb=ua.style.cross;if(!cb.hidden){var ib=cb.linewidth||1;hb[ib]||(hb[ib]=new $3Dmol.Geometry);var db=hb[ib].updateGeoGroup(6),Ra=d(ua,cb),Sa=[[Ra,0,0],[-Ra,0,0],
-[0,Ra,0],[0,-Ra,0],[0,0,Ra],[0,0,-Ra]],rb=ua.clickable;rb&&void 0===ua.intersectionShape&&(ua.intersectionShape={sphere:[],cylinder:[],line:[]});for(var jb=$3Dmol.getColorFromStyle(ua,cb),kb=db.vertexArray,lb=db.colorArray,Ia=0;6>Ia;Ia++){var Ta=3*db.vertices;db.vertices++;kb[Ta]=ua.x+Sa[Ia][0];kb[Ta+1]=ua.y+Sa[Ia][1];kb[Ta+2]=ua.z+Sa[Ia][2];lb[Ta]=jb.r;lb[Ta+1]=jb.g;lb[Ta+2]=jb.b;if(rb){var Ua=new $3Dmol.Vector3(Sa[Ia][0],Sa[Ia][1],Sa[Ia][2]);Ua.multiplyScalar(.1);Ua.set(Ua.x+ua.x,Ua.y+ua.y,Ua.z+
-ua.z);ua.intersectionShape.line.push(Ua)}}}}var ba=J,zb=f,mb=z;if(ba.style.line){var sb=ba.style.line;if(!sb.hidden){var nb=sb.linewidth||1;mb[nb]||(mb[nb]=new $3Dmol.Geometry);for(var sa=mb[nb].updateGeoGroup(2*ba.bonds.length),ga=sa.vertexArray,ha=sa.colorArray,Da=0;Da<ba.bonds.length;Da++){var ya=zb[ba.bonds[Da]];if(ya.style.line&&!(ba.serial>=ya.serial)){var za=new $3Dmol.Vector3(ba.x,ba.y,ba.z),Ja=new $3Dmol.Vector3(ya.x,ya.y,ya.z),Va=za.clone().add(Ja).multiplyScalar(.5),tb=!1;ba.clickable&&
-(void 0===ba.intersectionShape&&(ba.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),ba.intersectionShape.line.push(za),ba.intersectionShape.line.push(Ja));ya.clickable&&(void 0===ya.intersectionShape&&(ya.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]}),ya.intersectionShape.line.push(Ja),ya.intersectionShape.line.push(za));var oa=$3Dmol.getColorFromStyle(ba,ba.style.line),Ea=$3Dmol.getColorFromStyle(ya,ya.style.line);if(ba.bondStyles&&ba.bondStyles[Da]){var Ka=ba.bondStyles[Da];
-if(!Ka.iswire)continue;Ka.radius&&(bondR=Ka.radius);Ka.singleBond&&(tb=!0);"undefined"!=typeof Ka.color1&&(oa=$3Dmol.CC.color(Ka.color1));"undefined"!=typeof Ka.color2&&(Ea=$3Dmol.CC.color(Ka.color2))}var ia=3*sa.vertices;if(1<ba.bondOrder[Da]&&4>ba.bondOrder[Da]&&!tb){var Wa=e(ba,ya,Da),Ca=Ja.clone();Ca.sub(za);if(2==ba.bondOrder[Da])if(Wa.multiplyScalar(.1),p1a=za.clone(),p1a.add(Wa),p1b=za.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Ca),p2b=p1b.clone(),p2b.add(Ca),oa==Ea)sa.vertices+=4,p(ga,ha,
-ia,p1a,p2a,oa),p(ga,ha,ia+6,p1b,p2b,oa);else{sa.vertices+=8;Ca.multiplyScalar(.5);var Na=p1a.clone();Na.add(Ca);var Oa=p1b.clone();Oa.add(Ca);p(ga,ha,ia,p1a,Na,oa);p(ga,ha,ia+6,Na,p2a,Ea);p(ga,ha,ia+12,p1b,Oa,oa);p(ga,ha,ia+18,Oa,p2b,Ea)}else 3==ba.bondOrder[Da]&&(Wa.multiplyScalar(.1),p1a=za.clone(),p1a.add(Wa),p1b=za.clone(),p1b.sub(Wa),p2a=p1a.clone(),p2a.add(Ca),p2b=p1b.clone(),p2b.add(Ca),oa==Ea?(sa.vertices+=6,p(ga,ha,ia,za,Ja,oa),p(ga,ha,ia+6,p1a,p2a,oa),p(ga,ha,ia+12,p1b,p2b,oa)):(sa.vertices+=
-12,Ca.multiplyScalar(.5),Na=p1a.clone(),Na.add(Ca),Oa=p1b.clone(),Oa.add(Ca),p(ga,ha,ia,za,Va,oa),p(ga,ha,ia+6,Va,Ja,Ea),p(ga,ha,ia+12,p1a,Na,oa),p(ga,ha,ia+18,Na,p2a,Ea),p(ga,ha,ia+24,p1b,Oa,oa),p(ga,ha,ia+30,Oa,p2b,Ea)))}else oa==Ea?(sa.vertices+=2,p(ga,ha,ia,za,Ja,oa)):(sa.vertices+=4,p(ga,ha,ia,za,Va,oa),p(ga,ha,ia+6,Va,Ja,Ea))}}}}var O=J,Ab=f,fa=A;if(O.style.stick){var eb=O.style.stick;if(!eb.hidden){var Ya=eb.radius||.25,ja=Ya,ub=eb.singleBonds||!1,Za=!1,$a=!1,ma=$3Dmol.getColorFromStyle(O,
-eb),ka=void 0,Aa=void 0;!O.capDrawn&&4>O.bonds.length&&(Za=!0);for(var na=0;na<O.bonds.length;na++){var aa=Ab[O.bonds[na]];if(O.serial<aa.serial){var vb=aa.style;if(vb.stick){var Fa=$3Dmol.getColorFromStyle(aa,vb.stick),ja=Ya,ab=ub;if(O.bondStyles&&O.bondStyles[na]){var Ba=O.bondStyles[na];if(Ba.iswire)continue;Ba.radius&&(ja=Ba.radius);Ba.singleBond&&(ab=!0);"undefined"!=typeof Ba.color1&&(ma=$3Dmol.CC.color(Ba.color1));"undefined"!=typeof Ba.color2&&(Fa=$3Dmol.CC.color(Ba.color2))}var la=new $3Dmol.Vector3(O.x,
-O.y,O.z),va=new $3Dmol.Vector3(aa.x,aa.y,aa.z);if(1===O.bondOrder[na]||ab){if(!aa.capDrawn&&4>aa.bonds.length&&($a=!0),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,la,ka,ja,ma,Za,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,va,ja,Fa,!1,$a)):$3Dmol.GLDraw.drawCylinder(fa,la,va,ja,ma,Za,$a),O.clickable||aa.clickable){ka=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5);if(O.clickable){var Bb=new $3Dmol.Cylinder(la,ka,ja),La=new $3Dmol.Sphere(la,
-ja);O.intersectionShape.cylinder.push(Bb);O.intersectionShape.sphere.push(La)}if(aa.clickable){var Cb=new $3Dmol.Cylinder(va,ka,ja),Db=new $3Dmol.Sphere(va,ja);aa.intersectionShape.cylinder.push(Cb);aa.intersectionShape.sphere.push(Db)}}}else if(1<O.bondOrder[na]){var Ha=!1;mtoCap=!1;ja!=Ya&&(mtoCap=Ha=!0);var Xa=va.clone(),Ga=null;Xa.sub(la);var Y,pa,qa,wa,xa,Ga=e(O,aa,na);if(2==O.bondOrder[na]){if(Y=ja/2.5,Ga=e(O,aa,na),Ga.multiplyScalar(1.5*Y),pa=la.clone(),pa.add(Ga),qa=la.clone(),qa.sub(Ga),
-wa=pa.clone(),wa.add(Xa),xa=qa.clone(),xa.add(Xa),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,pa,ka,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,wa,Y,Fa,!1,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,qa,Aa,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,Aa,xa,Y,Fa,!1,mtoCap)):($3Dmol.GLDraw.drawCylinder(fa,pa,wa,Y,ma,Ha,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,qa,xa,Y,ma,Ha,mtoCap)),O.clickable||aa.clickable)ka=
-(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),O.clickable&&(cylinder1a=new $3Dmol.Cylinder(pa,ka,Y),cylinder1b=new $3Dmol.Cylinder(qa,Aa,Y),O.intersectionShape.cylinder.push(cylinder1a),O.intersectionShape.cylinder.push(cylinder1b),La=new $3Dmol.Sphere(la,ja),O.intersectionShape.sphere.push(La)),aa.clickable&&(cylinder2a=new $3Dmol.Cylinder(wa,ka,Y),cylinder2b=new $3Dmol.Cylinder(xa,Aa,Y),aa.intersectionShape.cylinder.push(cylinder2a),
-aa.intersectionShape.cylinder.push(cylinder2b),new $3Dmol.Sphere(va,ja),aa.intersectionShape.sphere.push(La))}else 3==O.bondOrder[na]&&(Y=ja/4,Ga.cross(Xa),Ga.normalize(),Ga.multiplyScalar(3*Y),pa=la.clone(),pa.add(Ga),qa=la.clone(),qa.sub(Ga),wa=pa.clone(),wa.add(Xa),xa=qa.clone(),xa.add(Xa),ma!=Fa?(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),$3Dmol.GLDraw.drawCylinder(fa,
-pa,ka,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,ka,wa,Y,Fa,!1,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,la,mp3,Y,ma,Za,!1),$3Dmol.GLDraw.drawCylinder(fa,mp3,va,Y,Fa,!1,$a),$3Dmol.GLDraw.drawCylinder(fa,qa,Aa,Y,ma,Ha,!1),$3Dmol.GLDraw.drawCylinder(fa,Aa,xa,Y,Fa,!1,mtoCap)):($3Dmol.GLDraw.drawCylinder(fa,pa,wa,Y,ma,Ha,mtoCap),$3Dmol.GLDraw.drawCylinder(fa,la,va,Y,ma,Za,$a),$3Dmol.GLDraw.drawCylinder(fa,qa,xa,Y,ma,Ha,mtoCap)),O.clickable||aa.clickable)&&(ka=(new $3Dmol.Vector3).addVectors(pa,wa).multiplyScalar(.5),
-Aa=(new $3Dmol.Vector3).addVectors(qa,xa).multiplyScalar(.5),mp3=(new $3Dmol.Vector3).addVectors(la,va).multiplyScalar(.5),O.clickable&&(cylinder1a=new $3Dmol.Cylinder(pa.clone(),ka.clone(),Y),cylinder1b=new $3Dmol.Cylinder(qa.clone(),Aa.clone(),Y),cylinder1c=new $3Dmol.Cylinder(la.clone(),mp3.clone(),Y),O.intersectionShape.cylinder.push(cylinder1a),O.intersectionShape.cylinder.push(cylinder1b),O.intersectionShape.cylinder.push(cylinder1c),La=new $3Dmol.Sphere(la,ja),O.intersectionShape.sphere.push(La)),
-aa.clickable&&(cylinder2a=new $3Dmol.Cylinder(wa.clone(),ka.clone(),Y),cylinder2b=new $3Dmol.Cylinder(xa.clone(),Aa.clone(),Y),cylinder2c=new $3Dmol.Cylinder(va.clone(),mp3.clone(),Y),aa.intersectionShape.cylinder.push(cylinder2a),aa.intersectionShape.cylinder.push(cylinder2b),aa.intersectionShape.cylinder.push(cylinder2c),La=new $3Dmol.Sphere(va,ja),aa.intersectionShape.sphere.push(La)))}}}}for(var ob=!1,pb=0,wb=!1,na=0;na<O.bonds.length;na++)ab=ub,O.bondStyles&&O.bondStyles[na]&&(Ba=O.bondStyles[na],
-Ba.singleBond&&(ab=!0),Ba.radius&&Ba.radius!=Ya&&(wb=!0)),(ab||1==O.bondOrder[na])&&pb++;wb?0<pb&&(ob=!0):0==pb&&0<O.bonds.length&&(ob=!0);ob&&(ja=Ya,$3Dmol.GLDraw.drawSphere(fa,O,ja,ma))}}"undefined"===typeof J.style.cartoon||J.style.cartoon.hidden||("spectrum"===J.style.cartoon.color&&"number"===typeof J.resi&&(J.resi<D[0]&&(D[0]=J.resi),J.resi>D[1]&&(D[1]=J.resi)),h.push(J))}}if(0<h.length){var xb=null;D[0]<D[1]&&(xb=new $3Dmol.Gradient.Sinebow(D[0],D[1]));$3Dmol.drawCartoon(l,h,C,xb);for(M=0;M<
-l.children.length;M++);}if(0<q.vertices){var Eb=new $3Dmol.MeshLambertMaterial({ambient:0,vertexColors:!0,reflectivity:0});q.initTypedArrays();var Fb=new $3Dmol.Mesh(q,Eb);l.add(Fb)}if(0<u.vertices){var Gb=new $3Dmol.ImposterMaterial({ambient:0,vertexColors:!0,reflectivity:0});u.initTypedArrays();var Hb=new $3Dmol.Mesh(u,Gb);console.log("spherei geometry "+u.vertices.length);l.add(Hb)}if(0<A.vertices){var bb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});A.initTypedArrays();
-bb.wireframe&&A.setUpWireframe();var Ib=new $3Dmol.Mesh(A,bb);l.add(Ib)}if(0<C.vertices){bb=new $3Dmol.MeshLambertMaterial({vertexColors:!0,ambient:0,reflectivity:0});C.initTypedArrays();bb.wireframe&&C.setUpWireframe();var Jb=new $3Dmol.Mesh(C,bb);l.add(Jb)}for(M in z)if(z.hasOwnProperty(M)){var qb=M,Kb=new $3Dmol.LineBasicMaterial({linewidth:qb,vertexColors:!0});z[M].initTypedArrays();var Lb=new $3Dmol.Line(z[M],Kb,$3Dmol.LinePieces);l.add(Lb)}for(M in y)if(y.hasOwnProperty(M)){var qb=M,Mb=new $3Dmol.LineBasicMaterial({linewidth:qb,
-vertexColors:!0});y[M].initTypedArrays();var Nb=new $3Dmol.Line(y[M],Mb,$3Dmol.LinePieces);l.add(Nb)}if(b&&!m){var yb=new $3Dmol.Object3D,fb;for(fb=0;fb<c.length;fb++){var gb=new $3Dmol.Object3D,gb=l.clone();gb.matrix.copy(c[fb]);gb.matrixAutoUpdate=!1;yb.add(gb)}l=yb}B=l;g&&(a.remove(g),g=null);g=B.clone();a.add(g)}};this.removegl=function(b){g&&(void 0!==g.geometry&&g.geometry.dispose(),void 0!==g.material&&g.material.dispose(),b.remove(g),g=null);B=null};this.addResLabels=function(b,c,d){var e=
-this.selectedAtoms(b,e);b={};for(var a=0;a<e.length;a++){var m=e[a],f=m.chain,l=m.resn+""+m.resi;b[f]||(b[f]={});b[f][l]||(b[f][l]=[]);b[f][l].push(m)}d=$.extend(!0,{},d);for(f in b)if(b.hasOwnProperty(f)){var g=b[f];for(l in g)if(g.hasOwnProperty(l)){for(var e=g[l],h=new $3Dmol.Vector3(0,0,0),a=0;a<e.length;a++)m=e[a],h.x+=m.x,h.y+=m.y,h.z+=m.z;h.divideScalar(e.length);d.position=h;c.addLabel(l,d)}}}}}();
-$3Dmol.GLShape=function(){function u(w){w=w||{};$3Dmol.ShapeIDCount++;this.boundingSphere=new $3Dmol.Sphere;this.intersectionShape={sphere:[],cylinder:[],line:[],triangle:[]};A(this,w);var B=[],g=null,a=null,c=new $3Dmol.Geometry(!0),h=new $3Dmol.Geometry(!0);this.updateStyle=function(c){for(var b in c)w[b]=c[b];A(this,w)};this.addCustom=function(a){a.vertexArr=a.vertexArr||[];a.faceArr=a.faceArr||[];a.normalArr=a.normalArr||[];a.lineArr=a.lineArr||[];var b=c.addGeoGroup();q(this,b,a);b.truncateArrayBuffers(!0,
-!0);for(a=0;a<b.colorArray.length/3;++a)b.colorArray[3*a]=this.color.r,b.colorArray[3*a+1]=this.color.g,b.colorArray[3*a+2]=this.color.b;B.push({id:b.id,geoGroup:b,centroid:b.getCentroid()});C(this.boundingSphere,B,b.vertexArray)};this.addSphere=function(a){a.center=a.center||{x:0,y:0,z:0};a.radius=a.radius?$3Dmol.Math.clamp(a.radius,0,Infinity):1.5;a.color=$3Dmol.CC.color(a.color);this.intersectionShape.sphere.push(new $3Dmol.Sphere(a.center,a.radius));var b=c.addGeoGroup();$3Dmol.GLDraw.drawSphere(c,
-a.center,a.radius,a.color);b.truncateArrayBuffers(!0,!0);B.push({id:b.id,geoGroup:b,centroid:new $3Dmol.Vector3(a.center.x,a.center.y,a.center.z)});C(this.boundingSphere,B,b.vertexArray)};this.addCylinder=function(a){a.start=a.start||{};a.end=a.end||{};var b=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0),f=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0);"undefined"==typeof f.x&&(f.x=3);var l=a.radius||.1,d=$3Dmol.CC.color(a.color);this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(b,
-f,l));var e=c.addGeoGroup();$3Dmol.GLDraw.drawCylinder(c,b,f,l,d,a.fromCap,a.toCap);e.truncateArrayBuffers(!0,!0);a=new $3Dmol.Vector3;B.push({id:e.id,geoGroup:e,centroid:a.addVectors(b,f).multiplyScalar(.5)});C(this.boundingSphere,B,e.vertexArray)};this.addLine=function(a){a.start=a.start||{};a.end=a.end||{};var b=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0),f=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0);"undefined"==typeof f.x&&(f.x=3);a=c.addGeoGroup();var l=a.vertices,d=3*l,
-e=a.vertexArray;e[d]=b.x;e[d+1]=b.y;e[d+2]=b.z;e[d+3]=f.x;e[d+4]=f.y;e[d+5]=f.z;a.vertices+=2;b=a.lineArray;f=a.lineidx;b[f]=l;b[f+1]=l+1;a.lineidx+=2;a.truncateArrayBuffers(!0,!0)};this.addArrow=function(a){a.start=a.start||{};a.end=a.end||{};a.start=new $3Dmol.Vector3(a.start.x||0,a.start.y||0,a.start.z||0);if(a.dir instanceof $3Dmol.Vector3&&a.length instanceof number){var b=a.dir.clone().multiplyScalar(a.length).add(start);a.end=b}else a.end=new $3Dmol.Vector3(a.end.x,a.end.y||0,a.end.z||0),"undefined"==
-typeof a.end.x&&(a.end.x=3);a.radius=a.radius||.1;a.radiusRatio=a.radiusRatio||1.618034;a.mid=0<a.mid&&1>a.mid?a.mid:.618034;b=c.addGeoGroup();var f=a.start,l=a.end,d=a.radius,e=a.radiusRatio,g=a.mid;if(f&&l){var h=l.clone();h.sub(f).multiplyScalar(g);var t=f.clone().add(h),g=h.clone().negate();this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(f.clone(),t.clone(),d));this.intersectionShape.sphere.push(new $3Dmol.Sphere(f.clone(),d));var n=[];n[0]=h.clone();1E-4<Math.abs(n[0].x)?n[0].y+=1:n[0].x+=
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-n[11]=n[10].clone().add(n[12]).normalize();n[13]=n[12].clone().add(n[14]).normalize();n[15]=n[14].clone().add(n[0]).normalize();var s=b.vertices,x=b.vertexArray,w=b.faceArray,y=b.normalArray,q=b.lineArray,u,A,G;A=0;for(G=n.length;A<G;++A){u=3*(s+3*A);var M=n[A].clone().multiplyScalar(d).add(f),S=n[A].clone().multiplyScalar(d).add(t),D=n[A].clone().multiplyScalar(d*e).add(t);x[u]=M.x;x[u+1]=M.y;x[u+2]=M.z;x[u+3]=S.x;x[u+4]=S.y;x[u+5]=S.z;x[u+6]=D.x;x[u+7]=D.y;x[u+8]=D.z;0<A&&(u=new $3Dmol.Vector3(x[u-
-3],x[u-2],x[u-1]),M=l.clone(),S=t.clone(),D=new $3Dmol.Vector3(D.x,D.y,D.z),this.intersectionShape.triangle.push(new $3Dmol.Triangle(D,M,u)),this.intersectionShape.triangle.push(new $3Dmol.Triangle(u.clone(),S,D.clone())))}b.vertices+=48;u=3*b.vertices;x[u]=f.x;x[u+1]=f.y;x[u+2]=f.z;x[u+3]=t.x;x[u+4]=t.y;x[u+5]=t.z;x[u+6]=l.x;x[u+7]=l.y;x[u+8]=l.z;b.vertices+=3;var J,K,ca,V,da,T,Z,N,U=b.vertices-3,P=b.vertices-2,Q=b.vertices-1,W=3*U,R=3*P,X=3*Q;A=0;for(G=n.length-1;A<G;++A)J=s+3*A,f=b.faceidx,l=b.lineidx,
-d=J,u=3*d,e=J+1,M=3*e,t=J+2,S=3*t,x=J+4,K=3*x,D=J+5,ca=3*D,J+=3,V=3*J,da=T=n[A],Z=N=n[A+1],y[u]=da.x,y[M]=T.x,y[V]=N.x,y[u+1]=da.y,y[M+1]=T.y,y[V+1]=N.y,y[u+2]=da.z,y[M+2]=T.z,y[V+2]=N.z,y[M]=T.x,y[K]=Z.x,y[V]=N.x,y[M+1]=T.y,y[K+1]=Z.y,y[V+1]=N.y,y[M+2]=T.z,y[K+2]=Z.z,y[V+2]=N.z,y[S]=T.x,y[ca]=Z.x,y[S+1]=T.y,y[ca+1]=Z.y,y[S+2]=T.z,y[ca+2]=Z.z,w[f]=d,w[f+1]=e,w[f+2]=J,w[f+3]=e,w[f+4]=x,w[f+5]=J,w[f+6]=d,w[f+7]=J,w[f+8]=U,w[f+9]=t,w[f+10]=P,w[f+11]=D,w[f+12]=t,w[f+13]=Q,w[f+14]=D,q[l]=d,q[l+1]=e,q[l+
-2]=d,q[l+3]=J,q[l+4]=x,q[l+5]=J,q[l+6]=d,q[l+7]=J,q[l+8]=t,q[l+9]=e,q[l+10]=t,q[l+11]=D,q[l+12]=x,q[l+13]=D,q[l+14]=t,q[l+15]=Q,q[l+16]=t,q[l+17]=D,q[l+18]=Q,q[l+19]=D,b.faceidx+=15,b.lineidx+=20;s=[s+45,s+46,s+1,s,s+47,s+2];f=b.faceidx;l=b.lineidx;d=s[0];u=3*d;e=s[1];M=3*e;t=s[4];S=3*t;x=s[2];K=3*x;D=s[5];ca=3*D;J=s[3];V=3*J;da=T=n[15];Z=N=n[0];y[u]=da.x;y[M]=T.x;y[V]=N.x;y[u+1]=da.y;y[M+1]=T.y;y[V+1]=N.y;y[u+2]=da.z;y[M+2]=T.z;y[V+2]=N.z;y[M]=T.x;y[K]=Z.x;y[V]=N.x;y[M+1]=T.y;y[K+1]=Z.y;y[V+1]=N.y;
-y[M+2]=T.z;y[K+2]=Z.z;y[V+2]=N.z;y[S]=T.x;y[ca]=Z.x;y[S+1]=T.y;y[ca+1]=Z.y;y[S+2]=T.z;y[ca+2]=Z.z;h.normalize();g.normalize();y[W]=g.x;y[R]=y[X]=h.x;y[W+1]=g.y;y[R+1]=y[X+1]=h.y;y[W+2]=g.z;y[R+2]=y[X+2]=h.z;w[f]=d;w[f+1]=e;w[f+2]=J;w[f+3]=e;w[f+4]=x;w[f+5]=J;w[f+6]=d;w[f+7]=J;w[f+8]=U;w[f+9]=t;w[f+10]=P;w[f+11]=D;w[f+12]=t;w[f+13]=Q;w[f+14]=D;q[l]=d;q[l+1]=e;q[l+2]=d;q[l+3]=J;q[l+4]=x;q[l+5]=J;q[l+6]=d;q[l+7]=J;q[l+8]=t;q[l+9]=e;q[l+10]=t;q[l+11]=D;q[l+12]=x;q[l+13]=D;q[l+14]=t;q[l+15]=Q;q[l+16]=
-t;q[l+17]=D;q[l+18]=Q;q[l+19]=D;b.faceidx+=15;b.lineidx+=20}b.truncateArrayBuffers(!0,!0);h=new $3Dmol.Vector3;B.push({id:b.id,geoGroup:b,centroid:h.addVectors(a.start,a.end).multiplyScalar(.5)});C(this.boundingSphere,B,b.vertexArray)};this.addVolumetricData=function(a,b,f){var l=void 0!==f.isoval&&"number"===typeof f.isoval?f.isoval:0,d=f.voxel?!0:!1,e=c.addGeoGroup();switch(b){case "cube":var h=a.replace(/^\s+/,"").split(/[\n\r]+/);if(!(6>h.length)){var g=h[2].replace(/^\s+/,"").replace(/\s+/g,
-" ").split(" "),t=Math.abs(parseFloat(g[0]));a=new $3Dmol.Vector3(parseFloat(g[1]),parseFloat(g[2]),parseFloat(g[3]));var g=h[3].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),n=0<parseFloat(g[0])?.529177:1;a.multiplyScalar(n);b=Math.abs(g[0]);var s=(new $3Dmol.Vector3(parseFloat(g[1]),parseFloat(g[2]),parseFloat(g[3]))).multiplyScalar(n),g=h[4].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),w=Math.abs(g[0]);(new $3Dmol.Vector3(parseFloat(g[1]),parseFloat(g[2]),parseFloat(g[3]))).multiplyScalar(n);
-var g=h[5].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),u=Math.abs(g[0]);(new $3Dmol.Vector3(parseFloat(g[1]),parseFloat(g[2]),parseFloat(g[3]))).multiplyScalar(n);h=new Float32Array(h.splice(t+7).join(" ").replace(/^\s+/,"").split(/[\s\r]+/));g=new Int16Array(b*w*u);t=0;for(n=g.length;t<n;++t)g[t]=-1;g=new Uint8Array(b*w*u);t=0;for(n=h.length;t<n;++t)0<(0<=l?h[t]-l:l-h[t])&&(g[t]|=2);l=[];h=[];$3Dmol.MarchingCube.march(g,l,h,{fulltable:!0,voxel:d,scale:s.length(),origin:a,nX:b,nY:w,nZ:u});d||
-$3Dmol.MarchingCube.laplacianSmooth(10,l,h);q(this,e,{vertexArr:l,faceArr:h,normalArr:[],lineArr:[]})}}B.push({id:e.id,geoGroup:e,centroid:e.getCentroid()});this.updateStyle(f);C(this.boundingSphere,B,e.vertexArray)};this.globj=function(m){c.initTypedArrays();var b=this.color,b=b||$3Dmol.CC.color(b);c.colorsNeedUpdate=!0;for(var f in c.geometryGroups)for(var l=c.geometryGroups[f],d=l.colorArray,e=0,l=l.vertices;e<l;++e)d[3*e]=b.r,d[3*e+1]=b.g,d[3*e+2]=b.b;g=new $3Dmol.Object3D;f=new $3Dmol.MeshLambertMaterial({wireframe:this.wireframe,
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-n.buildboundary();e==$3Dmol.SurfaceType.SES&&(n.fastdistancemap(),n.boundingatom(!1),n.fillvoxelswaals(z,g));g=new Date;console.log("buildboundaryetc "+(g-f)+"  "+(g-l)+"ms");n.marchingcube(e);e=n.getFacesAndVertices(h);e=Ma(d,e,t);$3Dmol.mergeGeos(b.geo,e);m.render();setTimeout(Va,1,c+1)}},1,0);else{e=[];0>a&&(a=0);n=0;for(p=4;n<p;n++)f=new Worker($3Dmol.SurfaceWorker),e.push(f),f.postMessage({type:-1,atoms:z,volume:x});var A=0;p=function(a){a=Ma(d,a.data,t);$3Dmol.mergeGeos(b.geo,a);m.render();
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-{});var q=[],t=void 0;if("undefined"===typeof s.model)for(t=0;t<b.length;t++)b[t]&&q.push(b[t]);else q=s.model,$.isArray(q)||(q=[q]);for(t=0;t<q.length;t++)if(q[t].atomIsSelected(p,s)){p=!0;break a}p=!1}p&&(g.properties||(g.properties={}),g.properties[n]=m.props[n])}}};try{"function"===typeof g&&g(this)}catch(ta){console.log("error with glviewer callback: "+ta)}}}();$3Dmol.glmolViewer=$3Dmol.GLViewer;$3Dmol=$3Dmol||{};$3Dmol.Gradient=function(u,q){};$3Dmol.Gradient.valueToHex=function(u,q){};
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-$3Dmol.Gradient.Sinebow=function(u,q){this.valueToHex=function(C,A){var w,B;A?(w=A[0],B=A[1]):(w=u,B=q);if("undefined"==typeof C)return 16777215;C<w&&(C=w);C>B&&(C=B);var g=(C-w)/(B-w)*5/6+.5;w=Math.sin(Math.PI*g);w*=255*w;B=Math.sin(Math.PI*(g+1/3));B*=255*B;g=Math.sin(Math.PI*(g+2/3));return 65536*Math.floor(w)+256*Math.floor(255*g*g)+1*Math.floor(B)};this.jmolID=function(){return"sinebow"};this.range=function(){return"undefined"!=typeof u&&"undefined"!=typeof q?[u,q]:null}};$3Dmol.LabelCount=0;
-$3Dmol.Label=function(u,q){this.id=$3Dmol.LabelCount++;this.stylespec=q||{};this.canvas=document.createElement("canvas");this.canvas.width=134;this.canvas.height=35;this.context=this.canvas.getContext("2d");this.sprite=new $3Dmol.Sprite;this.text=u};
-$3Dmol.Label.prototype={constructor:$3Dmol.Label,getStyle:function(){return this.stylespec},setContext:function(){var u=function(q,u,A){"undefined"!=typeof q&&(A=q instanceof $3Dmol.Color?q.scaled():$3Dmol.CC.color(q).scaled());"undefined"!=typeof u&&(A.a=parseFloat(u));return A};return function(){var q=this.stylespec,C="undefined"==typeof q.useScreen?!1:q.useScreen,A=q.showBackground;if("0"===A||"false"===A)A=!1;"undefined"==typeof A&&(A=!0);var w=q.font?q.font:"sans-serif",B=parseInt(q.fontSize)?
-parseInt(q.fontSize):18,g=u(q.fontColor,q.fontOpacity,{r:255,g:255,b:255,a:1}),a=q.padding?q.padding:4,c=q.borderThickness?q.borderThickness:0,h=u(q.backgroundColor,q.backgroundOpacity,{r:0,g:0,b:0,a:1}),m=u(q.borderColor,q.borderOpacity,h),b=q.position?q.position:{x:-10,y:1,z:1},f=void 0!==q.inFront?q.inFront:!0;if("false"===f||"0"===f)f=!1;var l=q.alignment||$3Dmol.SpriteAlignment.topLeft,d="";q.bold&&(d="bold ");this.context.font=d+B+"px  "+w;var e=this.context.measureText(this.text).width;A||
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-$3Dmol.Parsers=function(){var u={},q=function(g){var a=g.slice(0),c,h;c=0;for(h=g.length;c<h;c++)g[c].index||(g[c].index=c);a.sort(function(a,b){return a.z-b.z});c=0;for(h=a.length;c<h;c++){var m=a[c];for(g=c+1;g<h;g++){var b=a[g];if(1.9<b.z-m.z)break;B(m,b)&&-1==m.bonds.indexOf(b.index)&&(m.bonds.push(b.index),m.bondOrder.push(1),b.bonds.push(m.index),b.bondOrder.push(1))}}},C=function(g){var a=[],c=[],h,m;h=0;for(m=g.length;h<m;h++){var b=g[h];b.index=h;b.hetflag?c.push(b):a.push(b)}q(c);a.sort(function(a,
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-e;e++)if(u=a[s].replace(/^\s*/,""),parseInt(u.substr(18,1))==e)x.elements[e-1]=parseFloat(u.substr(23,10)),x.elements[e-1+4]=parseFloat(u.substr(33,10)),x.elements[e-1+8]=parseFloat(u.substr(43,10)),x.elements[e-1+12]=parseFloat(u.substr(53)),s++;else for(;"BIOMT"==u.substr(13,5);)s++,u=a[s].replace(/^\s*/,"");x.elements[3]=0;x.elements[7]=0;x.elements[11]=0;x.elements[15]=1;d.push(x);h.push(x);s--}}(new Date).getTime();C(g);n=f=g.length;if(l)for(l=0;l<g.length;l++){d=[];for(m=0;m<h.length;m++)h[m].isIdentity()||
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+1],e=c[m][d+1],q=c[m][d],"h"==t&&t==e&&q!=t&&(c[m][d]=t);d=0;for(t=b.length;d<t;d++)e=b[d],isFinite(e.hbondDistanceSq)&&"h"!=c[e.chain][e.resi]&&"h"!=e.ss&&(c[e.chain][e.resi]="maybesheet");d=0;for(t=b.length;d<t;d++)if(e=b[d],isFinite(e.hbondDistanceSq)&&"maybesheet"==c[e.chain][e.resi]){q=e.hbondOther;var g=c[q.chain][q.resi];if("maybesheet"==g||"s"==g)c[e.chain][e.resi]="s",c[q.chain][q.resi]="s"}for(m in c){for(d=1;d<c[m].length-1;d++)t=c[m][d-1],e=c[m][d+1],q=c[m][d],"s"==t&&t==e&&q!=t&&(c[m][d]=
+t);for(d=0;d<c[m].length;d++)q=c[m][d],"h"!=q&&"s"!=q||c[m][d-1]==q||c[m][d+1]==q||delete c[m][d]}d=0;for(t=b.length;d<t;d++)e=b[d],q=c[e.chain][e.resi],"undefined"!=typeof q&&"maybesheet"!=q&&(e.ss=q,c[e.chain][e.resi-1]!=q&&(e.ssbegin=!0),c[e.chain][e.resi+1]!=q&&(e.ssend=!0))};b.cube=b.CUBE=function(b,d){var h=[[]],t=b.replace(/^\s+/,"").split(/\n\r|\r+/);if(6>t.length)return h;for(var m=t[2].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),e=Math.abs(parseFloat(m[0])),m=t[3].replace(/^\s+/,"").replace(/\s+/g,
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+"");z.elements[3]=0;z.elements[7]=0;z.elements[11]=0;z.elements[15]=1;g[g.length-1].symmetries.push(z);G--}}(new Date).getTime();for(N=0;N<h.length;N++){d(h[N]);e||B(g[g.length-1].symmetries,q,h[N]);if(m||!E)(new Date).getTime(),y(h[N]);for(G=x;G<h[N].length;G++)if(u=h[N][G],void 0!==u){for(z=0;z<s.length;z++)u.chain!=s[z][0]||u.resi<s[z][1]||u.resi>s[z][3]||(u.ss="s",u.resi==s[z][1]&&(u.ssbegin=!0),u.resi==s[z][3]&&(u.ssend=!0));for(z=0;z<l.length;z++)u.chain!=l[z][0]||u.resi<l[z][1]||u.resi>l[z][3]||
+(u.ss="h",u.resi==l[z][1]?u.ssbegin=!0:u.resi==l[z][3]&&(u.ssend=!0))}}return h};b.pqr=b.PQR=function(b,c){var h=[[]],p,m=!c.noSecondaryStructure,e=[],q=b.split(/\r?\n|\r/),g,x;for(g=0;g<q.length;g++)if(x=q[g].replace(/^\s*/,""),p=x.substr(0,6),0==p.indexOf("END"))if(c.multimodel)c.onemol||h.push([]);else break;else if("ATOM  "==p||"HETATM"==p){var u=parseInt(x.substr(6,5));p=x.substr(12,4).replace(/ /g,"");var s=x.substr(17,3),l=x.substr(21,1),A=parseInt(x.substr(22,4)),B=x.substr(30).trim().split(/\s+/),
+C=parseFloat(B[0]),G=parseFloat(B[1]),z=parseFloat(B[2]),H=parseFloat(B[3]),B=parseFloat(B[4]),L=p[0];1<p.length&&p[1].toUpperCase()!=p[1]&&(L=p.substr(0,2));hetflag="H"==x[0]?!0:!1;e[u]=h[h.length-1].length;h[h.length-1].push({resn:s,x:C,y:G,z:z,elem:L,hetflag:hetflag,chain:l,resi:A,serial:u,atom:p,bonds:[],ss:"c",bondOrder:[],properties:{charge:H,partialCharge:H,radius:B},pdbline:x})}else if("CONECT"==p)for(p=parseInt(x.substr(6,5)),u=h[h.length-1][e[p]],p=0;4>p;p++)s=parseInt(x.substr([11,16,21,
+26][p],5)),l=h[h.length-1][e[s]],void 0!==u&&void 0!==l&&(u.bonds.push(e[s]),u.bondOrder.push(1));for(g=0;g<h.length;g++)d(h[g]),m&&y(h[g]);return h};return b}();$3Dmol=$3Dmol||{};
 $3Dmol.partialCharges={"ALA:N":-.15,"ALA:CA":.1,"ALA:CB":0,"ALA:C":.6,"ALA:O":-.55,"ARG:N":-.15,"ARG:CA":.1,"ARG:CB":0,"ARG:CG":0,"ARG:CD":.1,"ARG:NE":-.1,"ARG:CZ":.5,"ARG:NH1":.25,"ARG:NH2":.25,"ARG:C":.6,"ARG:O":-.55,"ASN:N":-.15,"ASN:CA":.1,"ASN:CB":0,"ASN:CG":.55,"ASN:OD1":-.55,"ASN:ND2":0,"ASN:C":.6,"ASN:O":-.55,"ASP:N":-.15,"ASP:CA":.1,"ASP:CB":0,"ASP:CG":.14,"ASP:OD1":-.57,"ASP:OD2":-.57,"ASP:C":.6,"ASP:O":-.55,"CYS:N":-.15,"CYS:CA":.1,"CYS:CB":.19,"CYS:SG":-.19,"CYS:C":.6,"CYS:O":-.55,"GLN:N":-.15,
 "GLN:CA":.1,"GLN:CB":0,"GLN:CG":0,"GLN:CD":.55,"GLN:OE1":-.55,"GLN:NE2":0,"GLN:C":.6,"GLN:O":-.55,"GLU:N":-.15,"GLU:CA":.1,"GLU:CB":0,"GLU:CG":0,"GLU:CD":.14,"GLU:OE1":-.57,"GLU:OE2":-.57,"GLU:C":.6,"GLU:O":-.55,"GLY:N":-.15,"GLY:CA":.1,"GLY:C":.6,"GLY:O":-.55,"HIS:N":-.15,"HIS:CA":.1,"HIS:CB":0,"HIS:CG":.1,"HIS:ND1":-.1,"HIS:CD2":.1,"HIS:NE2":-.4,"HIS:CE1":.3,"HIS:C":.6,"HIS:O":-.55,"ILE:N":-.15,"ILE:CA":.1,"ILE:CB":0,"ILE:CG2":0,"ILE:CG1":0,"ILE:CD":0,"ILE:C":.6,"ILE:O":-.55,"LEU:N":-.15,"LEU:CA":.1,
 "LEU:CB":0,"LEU:CG":0,"LEU:CD1":0,"LEU:CD2":0,"LEU:C":.6,"LEU:O":-.55,"LYS:N":-.15,"LYS:CA":.1,"LYS:CB":0,"LYS:CG":0,"LYS:CD":0,"LYS:CE":.25,"LYS:NZ":.75,"LYS:C":.6,"LYS:O":-.55,"MET:N":-.15,"MET:CA":.1,"MET:CB":0,"MET:CG":.06,"MET:SD":-.12,"MET:CE":.06,"MET:C":.6,"MET:O":-.55,"PHE:N":-.15,"PHE:CA":.1,"PHE:CB":0,"PHE:CG":0,"PHE:CD1":0,"PHE:CD2":0,"PHE:CE1":0,"PHE:CE2":0,"PHE:CZ":0,"PHE:C":.6,"PHE:O":-.55,"PRO:N":-.25,"PRO:CD":.1,"PRO:CA":.1,"PRO:CB":0,"PRO:CG":0,"PRO:C":.6,"PRO:O":-.55,"SER:N":-.15,
 "SER:CA":.1,"SER:CB":.25,"SER:OG":-.25,"SER:C":.6,"SER:O":-.55,"THR:N":-.15,"THR:CA":.1,"THR:CB":.25,"THR:OG1":-.25,"THR:CG2":0,"THR:C":.6,"THR:O":-.55,"TRP:N":-.15,"TRP:CA":.1,"TRP:CB":0,"TRP:CG":-.03,"TRP:CD2":.1,"TRP:CE2":-.04,"TRP:CE3":-.03,"TRP:CD1":.06,"TRP:NE1":-.06,"TRP:CZ2":0,"TRP:CZ3":0,"TRP:CH2":0,"TRP:C":.6,"TRP:O":-.55,"TYR:N":-.15,"TYR:CA":.1,"TYR:CB":0,"TYR:CG":0,"TYR:CD1":0,"TYR:CE1":0,"TYR:CD2":0,"TYR:CE2":0,"TYR:CZ":.25,"TYR:OH":-.25,"TYR:C":.6,"TYR:O":-.55,"VAL:N":-.15,"VAL:CA":.1,
-"VAL:CB":0,"VAL:CG1":0,"VAL:CG2":0,"VAL:C":.6,"VAL:O":-.55};$3Dmol.applyPartialCharges=function(u,q){q&&"undefined"!==typeof u.partialCharge||u.resn&&u.atom&&(u.properties.partialCharge=$3Dmol.partialCharges[u.resn+":"+u.atom])};(function(){});
+"VAL:CB":0,"VAL:CG1":0,"VAL:CG2":0,"VAL:C":.6,"VAL:O":-.55};$3Dmol.applyPartialCharges=function(b,c){c&&"undefined"!==typeof b.partialCharge||b.resn&&b.atom&&(b.properties.partialCharge=$3Dmol.partialCharges[b.resn+":"+b.atom])};(function(){});$3Dmol.VolumeData=function(b,c){this.unit={x:1,y:1,z:1};this.origin={x:0,y:0,z:0};this.size={x:0,y:0,z:0};this.data=new Float32Array([]);c=c.toLowerCase();if(this[c])this[c](b)};
+$3Dmol.VolumeData.prototype.getVal=function(b,c,d){b-=this.origin.x;c-=this.origin.y;d-=this.origin.z;b/=this.unit.x;c/=this.unit.y;d/=this.unit.z;b=Math.round(b);c=Math.round(c);d=Math.round(d);return 0>b||b>=this.size.x||0>c||c>=this.size.y||0>d||d>=this.size.z?0:this.data[b*this.size.y*this.size.z+c*this.size.z+d]};
+$3Dmol.VolumeData.prototype.cube=function(b){b=b.replace(/^\s+/,"").split(/[\n\r]+/);if(!(6>b.length)){var c=b[2].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),d=parseFloat(c[0]),p=Math.abs(d),y=this.origin=new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3])),c=b[3].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),A=0<c[0]?.529177:1;y.multiplyScalar(A);var y=Math.abs(c[0]),q=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A),c=b[4].replace(/^\s+/,
+"").replace(/\s+/g," ").split(" "),B=Math.abs(c[0]),f=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A),c=b[5].replace(/^\s+/,"").replace(/\s+/g," ").split(" "),w=Math.abs(c[0]),c=(new $3Dmol.Vector3(parseFloat(c[1]),parseFloat(c[2]),parseFloat(c[3]))).multiplyScalar(A);this.size={x:y,y:B,z:w};this.unit=new $3Dmol.Vector3(q.x,f.y,c.z);0==q.y&&0==q.z&&0==f.x&&0==f.z&&0==c.x&&0==c.y||console.log("Warning: Cube file is not axis aligned.  This isn't going to look right.");
+c=6;0>d&&c++;b=b.splice(p+c).join(" ");b=b.replace(/^\s+/,"");b=b.split(/[\s\r]+/);this.data=new Float32Array(b)}};
+$3Dmol.VolumeData.prototype.ccp4=function(b){var c,d,p,y,A,q,B,f,w,h,t,m,e,F,g,x=new Int32Array(b,0,56);m=new Float32Array(b,0,56);c=x[0];d=x[1];p=x[2];y=x[4];A=x[5];q=x[6];B=Math.abs(x[7]);f=Math.abs(x[8]);w=Math.abs(x[9]);h=m[10];t=m[11];m=m[12];xVox=h/c;yVox=t/d;zVox=m/p;switch(x[16]){case 1:e=y;g=F=0;break;case 2:F=y;g=e=0;break;case 3:g=y,F=e=0}switch(x[17]){case 1:e=A;g=F=0;break;case 2:F=A;g=e=0;break;case 3:g=A,F=e=0}switch(x[18]){case 1:e=q;g=F=0;break;case 2:F=q;g=e=0;break;case 3:g=q,F=
+e=0}this.origin=new $3Dmol.Vector3(e,F,g);c=x[23];this.size={x:B,y:f,z:w};this.unit=new $3Dmol.Vector3(xVox,yVox,zVox);new Int8Array(b);this.data=new Float32Array(b,1024+c)};
+$3Dmol.workerString=function(){self.onmessage=function(b){b=b.data;var c=b.type;if(0>c)self.atomData=b.atoms,self.volume=b.volume,self.ps=new ProteinSurface;else{var d=self.ps;d.initparm(b.expandedExtent,1==c?!1:!0,self.volume);d.fillvoxels(self.atomData,b.extendedAtoms);d.buildboundary();if(4===c||2===c)d.fastdistancemap(),d.boundingatom(!1),d.fillvoxelswaals(self.atomData,b.extendedAtoms);d.marchingcube(c);b=d.getFacesAndVertices(b.atomsToShow);self.postMessage(b)}}}.toString().replace(/(^.*?\{|\}$)/g,
+"");$3Dmol.workerString+="; var ProteinSurface="+$3Dmol.ProteinSurface.toString().replace(/\$3Dmol.MarchingCube./g,"MarchingCube.");$3Dmol.workerString+=",MarchingCube=("+$3Dmol.MarchingCubeInitializer.toString()+")();";$3Dmol.SurfaceWorker=window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type:"text/javascript"}));$3Dmol.workerString=$3Dmol.workerString;$3Dmol.SurfaceWorker=$3Dmol.SurfaceWorker;
diff --git a/release/3Dmol-nojquery.js b/release/3Dmol-nojquery.js
index e56273ac4..290ce79ec 100644
--- a/release/3Dmol-nojquery.js
+++ b/release/3Dmol-nojquery.js
@@ -1,14424 +1,20226 @@
-/*
-* math-like functionality
-* quaternion, vector, matrix
-*/
+/* pako 0.2.7 nodeca/pako */(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.pako = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
+'use strict';
 
-var $3Dmol = $3Dmol || {};
-$3Dmol.Math = {
 
-    clamp : function(x, min, max) {
-        return Math.min( Math.max( x, min ), max );
-    },
+var TYPED_OK =  (typeof Uint8Array !== 'undefined') &&
+                (typeof Uint16Array !== 'undefined') &&
+                (typeof Int32Array !== 'undefined');
 
-    degToRad : function() {
-       var degreeToRadiansFactor = Math.PI / 180;
-       
-       return function(deg) {
-           return deg * degreeToRadiansFactor;
-       };
-    
-    }()
-    
-};
 
+exports.assign = function (obj /*from1, from2, from3, ...*/) {
+  var sources = Array.prototype.slice.call(arguments, 1);
+  while (sources.length) {
+    var source = sources.shift();
+    if (!source) { continue; }
 
-// Quaternion
-/** @constructor */
-$3Dmol.Quaternion = function(x, y, z, w) {
+    if (typeof source !== 'object') {
+      throw new TypeError(source + 'must be non-object');
+    }
 
-    this.x = x || 0;
-    this.y = y || 0;
-    this.z = z || 0;
-    this.w = (w !== undefined) ? w : 1;
+    for (var p in source) {
+      if (source.hasOwnProperty(p)) {
+        obj[p] = source[p];
+      }
+    }
+  }
 
+  return obj;
 };
 
-$3Dmol.Quaternion.prototype = {
 
-    constructor : $3Dmol.Quaternion,
+// reduce buffer size, avoiding mem copy
+exports.shrinkBuf = function (buf, size) {
+  if (buf.length === size) { return buf; }
+  if (buf.subarray) { return buf.subarray(0, size); }
+  buf.length = size;
+  return buf;
+};
 
-    set : function(x, y, z, w) {
-        
-        this.x = x;
-        this.y = y;
-        this.z = z;
-        this.w = w;
 
-        return this;
-    },
+var fnTyped = {
+  arraySet: function (dest, src, src_offs, len, dest_offs) {
+    if (src.subarray && dest.subarray) {
+      dest.set(src.subarray(src_offs, src_offs+len), dest_offs);
+      return;
+    }
+    // Fallback to ordinary array
+    for (var i=0; i<len; i++) {
+      dest[dest_offs + i] = src[src_offs + i];
+    }
+  },
+  // Join array of chunks to single array.
+  flattenChunks: function(chunks) {
+    var i, l, len, pos, chunk, result;
+
+    // calculate data length
+    len = 0;
+    for (i=0, l=chunks.length; i<l; i++) {
+      len += chunks[i].length;
+    }
 
-    copy : function(q) {
-        
-        this.x = q.x;
-        this.y = q.y;
-        this.z = q.z;
-        this.w = q.w;
+    // join chunks
+    result = new Uint8Array(len);
+    pos = 0;
+    for (i=0, l=chunks.length; i<l; i++) {
+      chunk = chunks[i];
+      result.set(chunk, pos);
+      pos += chunk.length;
+    }
 
-        return this;
-    },
+    return result;
+  }
+};
 
-    conjugate : function() {
-        
-        this.x *= -1;
-        this.y *= -1;
-        this.z *= -1;
+var fnUntyped = {
+  arraySet: function (dest, src, src_offs, len, dest_offs) {
+    for (var i=0; i<len; i++) {
+      dest[dest_offs + i] = src[src_offs + i];
+    }
+  },
+  // Join array of chunks to single array.
+  flattenChunks: function(chunks) {
+    return [].concat.apply([], chunks);
+  }
+};
 
-        return this;
-    },
 
-    inverse : function() {
-        
-        return this.conjugate().normalize();
-    },
+// Enable/Disable typed arrays use, for testing
+//
+exports.setTyped = function (on) {
+  if (on) {
+    exports.Buf8  = Uint8Array;
+    exports.Buf16 = Uint16Array;
+    exports.Buf32 = Int32Array;
+    exports.assign(exports, fnTyped);
+  } else {
+    exports.Buf8  = Array;
+    exports.Buf16 = Array;
+    exports.Buf32 = Array;
+    exports.assign(exports, fnUntyped);
+  }
+};
 
-    length : function() {
-        
-        return Math.sqrt(this.x * this.x + this.y * this.y + this.z * this.z + this.w * this.w);
-    },
+exports.setTyped(TYPED_OK);
 
-    normalize : function() {
-        
-        var l = this.length();
+},{}],2:[function(require,module,exports){
+// String encode/decode helpers
+'use strict';
 
-        if (l === 0) {
-            this.x = 0;
-            this.y = 0;
-            this.z = 0;
-            this.w = 1;
-        } else {
-            l = 1 / l;
 
-            this.x *= l;
-            this.y *= l;
-            this.z *= l;
-            this.w *= l;
-        }
+var utils = require('./common');
 
-        return this;
 
-    },
+// Quick check if we can use fast array to bin string conversion
+//
+// - apply(Array) can fail on Android 2.2
+// - apply(Uint8Array) can fail on iOS 5.1 Safary
+//
+var STR_APPLY_OK = true;
+var STR_APPLY_UIA_OK = true;
 
-    multiply : function(q) {
-        
-        return this.multiplyQuaternions(this, q);
-    },
+try { String.fromCharCode.apply(null, [0]); } catch(__) { STR_APPLY_OK = false; }
+try { String.fromCharCode.apply(null, new Uint8Array(1)); } catch(__) { STR_APPLY_UIA_OK = false; }
 
-    multiplyQuaternions : function(a, b) {
 
-        var qax = a.x, qay = a.y, qaz = a.z, qaw = a.w;
-        var qbx = b.x, qby = b.y, qbz = b.z, qbw = b.w;
+// Table with utf8 lengths (calculated by first byte of sequence)
+// Note, that 5 & 6-byte values and some 4-byte values can not be represented in JS,
+// because max possible codepoint is 0x10ffff
+var _utf8len = new utils.Buf8(256);
+for (var q=0; q<256; q++) {
+  _utf8len[q] = (q >= 252 ? 6 : q >= 248 ? 5 : q >= 240 ? 4 : q >= 224 ? 3 : q >= 192 ? 2 : 1);
+}
+_utf8len[254]=_utf8len[254]=1; // Invalid sequence start
+
+
+// convert string to array (typed, when possible)
+exports.string2buf = function (str) {
+  var buf, c, c2, m_pos, i, str_len = str.length, buf_len = 0;
+
+  // count binary size
+  for (m_pos = 0; m_pos < str_len; m_pos++) {
+    c = str.charCodeAt(m_pos);
+    if ((c & 0xfc00) === 0xd800 && (m_pos+1 < str_len)) {
+      c2 = str.charCodeAt(m_pos+1);
+      if ((c2 & 0xfc00) === 0xdc00) {
+        c = 0x10000 + ((c - 0xd800) << 10) + (c2 - 0xdc00);
+        m_pos++;
+      }
+    }
+    buf_len += c < 0x80 ? 1 : c < 0x800 ? 2 : c < 0x10000 ? 3 : 4;
+  }
+
+  // allocate buffer
+  buf = new utils.Buf8(buf_len);
+
+  // convert
+  for (i=0, m_pos = 0; i < buf_len; m_pos++) {
+    c = str.charCodeAt(m_pos);
+    if ((c & 0xfc00) === 0xd800 && (m_pos+1 < str_len)) {
+      c2 = str.charCodeAt(m_pos+1);
+      if ((c2 & 0xfc00) === 0xdc00) {
+        c = 0x10000 + ((c - 0xd800) << 10) + (c2 - 0xdc00);
+        m_pos++;
+      }
+    }
+    if (c < 0x80) {
+      /* one byte */
+      buf[i++] = c;
+    } else if (c < 0x800) {
+      /* two bytes */
+      buf[i++] = 0xC0 | (c >>> 6);
+      buf[i++] = 0x80 | (c & 0x3f);
+    } else if (c < 0x10000) {
+      /* three bytes */
+      buf[i++] = 0xE0 | (c >>> 12);
+      buf[i++] = 0x80 | (c >>> 6 & 0x3f);
+      buf[i++] = 0x80 | (c & 0x3f);
+    } else {
+      /* four bytes */
+      buf[i++] = 0xf0 | (c >>> 18);
+      buf[i++] = 0x80 | (c >>> 12 & 0x3f);
+      buf[i++] = 0x80 | (c >>> 6 & 0x3f);
+      buf[i++] = 0x80 | (c & 0x3f);
+    }
+  }
 
-        this.x = qax * qbw + qaw * qbx + qay * qbz - qaz * qby;
-        this.y = qay * qbw + qaw * qby + qaz * qbx - qax * qbz;
-        this.z = qaz * qbw + qaw * qbz + qax * qby - qay * qbx;
-        this.w = qaw * qbw - qax * qbx - qay * qby - qaz * qbz;
+  return buf;
+};
 
+// Helper (used in 2 places)
+function buf2binstring(buf, len) {
+  // use fallback for big arrays to avoid stack overflow
+  if (len < 65537) {
+    if ((buf.subarray && STR_APPLY_UIA_OK) || (!buf.subarray && STR_APPLY_OK)) {
+      return String.fromCharCode.apply(null, utils.shrinkBuf(buf, len));
     }
-};
+  }
 
-//A 2 Vector
-/** @constructor */
-$3Dmol.Vector2 = function(x, y) {
-    
-    this.x = x || 0.0;
-    this.y = y || 0.0;
-};
+  var result = '';
+  for (var i=0; i < len; i++) {
+    result += String.fromCharCode(buf[i]);
+  }
+  return result;
+}
 
-$3Dmol.Vector2.prototype = {
-    
-    constructor : $3Dmol.Vector2,
-   
-    set : function(x, y) {
-       
-        this.x = x;
-        this.y = y;
-       
-        return this;
-    },
-    
-    subVectors : function(a, b) {
-        
-      this.x = a.x - b.x;
-      this.y = a.y - b.y;
-      
-      return this;
-    },
-   
-    copy : function(v) {
-       
-        this.x = v.x;
-        this.y = v.y;
-       
-        return this;
-    },
-   
-    clone : function() {
-        
-        return new $3Dmol.Vector2(this.x, this.y);
-    }    
-   
+
+// Convert byte array to binary string
+exports.buf2binstring = function(buf) {
+  return buf2binstring(buf, buf.length);
 };
 
-//A 3 Vector
 
-$3Dmol.Vector3 = function(x, y, z) {
-    this.x = x || 0.0;
-    this.y = y || 0.0;
-    this.z = z || 0.0;
+// Convert binary string (typed, when possible)
+exports.binstring2buf = function(str) {
+  var buf = new utils.Buf8(str.length);
+  for (var i=0, len=buf.length; i < len; i++) {
+    buf[i] = str.charCodeAt(i);
+  }
+  return buf;
 };
-/** @this {$3Dmol.Vector3} */
-$3Dmol.Vector3.prototype =  {
-    
-    constructor : $3Dmol.Vector3,
-    
-    set : function(x, y, z) {
-        
-        this.x = x;
-        this.y = y;
-        this.z = z;
-        
-        return this;
-    },
-    
-    copy : function(v) {
-        
-        this.x = v.x;
-        this.y = v.y;
-        this.z = v.z;
-        
-        return this;  
-    },
-    
-    add : function(v) {
-        
-        this.x += v.x;
-        this.y += v.y;
-        this.z += v.z;  
-        
-        return this;
-    },
-    
-    addVectors : function(a, b) {
-        
-        this.x = a.x + b.x;
-        this.y = a.y + b.y;
-        this.z = a.z + b.z;
-        
-        return this;
-    },
-    
-    sub : function(v) {
-        
-        this.x -= v.x;
-        this.y -= v.y;
-        this.z -= v.z;
-        
-        return this;
-    },
-    
-    subVectors : function(a, b) {
-        
-        this.x = a.x - b.x;
-        this.y = a.y - b.y;
-        this.z = a.z - b.z;
-        
-        return this;
-    },
-    
-    multiplyScalar : function(s) {
-        
-        this.x *= s;
-        this.y *= s;
-        this.z *= s;
-        
-        return this;
-    },
-    
-    divideScalar : function(s) {
-        
-        if (s !== 0) {
-            this.x /= s;
-            this.y /= s;
-            this.z /= s;
-        }
-        
-        else {
-            this.x = 0;
-            this.y = 0;
-            this.z = 0;
-        }
-        
-        return this;
-    },
-    
 
-    distanceTo: function(v) {
-        return Math.sqrt(this.distanceToSquared(v));
-    },
 
-    distanceToSquared: function(v) {
-        var dx = this.x - v.x;
-        var dy = this.y - v.y;
-        var dz = this.z - v.z;
+// convert array to string
+exports.buf2string = function (buf, max) {
+  var i, out, c, c_len;
+  var len = max || buf.length;
 
-        return dx * dx + dy * dy + dz * dz;
-    },
-    
-    applyMatrix4 : function(m) {
-    
-        var x = this.x, y = this.y, z = this.z;
-        
-        var e = m.elements;
-        
-        this.x = e[0]*x + e[4]*y + e[8]*z + e[12];
-        this.y = e[1]*x + e[5]*y + e[9]*z + e[13];
-        this.z = e[2]*x + e[6]*y + e[10]*z + e[14];
-        
-        return this;
-    },
-    
-    applyProjection : function(m) {
-        
-        //input: $3Dmol.Matrix4 projection matrix
-        
-        var x = this.x, y = this.y, z = this.z;
-        
-        var e = m.elements;
-        var d = ( e[3]*x + e[7]*y + e[11]*z + e[15]);
-        
-        this.x = (e[0]*x + e[4]*y + e[8]*z + e[12]) / d;
-        this.y = (e[1]*x + e[5]*y + e[9]*z + e[13]) / d;
-        this.z = (e[2]*x + e[6]*y + e[10]*z + e[14]) / d;
-        
-        return this;
-    },
-    
-    applyQuaternion : function(q) { 
-        
-        //save values
-        var x = this.x;
-        var y = this.y;
-        var z = this.z;
-        
-        var qx = q.x;
-        var qy = q.y;
-        var qz = q.z;
-        var qw = q.w;
-        
-        //compute this as
-        //t = 2 * cross(q.xyz, v)
-        //newv = v + q.w * t + cross(q.xyz, t)
-        //this from molecularmusings
-        //http://molecularmusings.wordpress.com/2013/05/24/a-faster-quaternion-vector-multiplication/
-        var t = {};
-        t.x = 2*(y * qz - z * qy);
-        t.y = 2*(z * qx - x * qz);
-        t.z = 2*(x * qy - y * qx);
-        
-        //cross t with q
-        var t2 = {};
-        t2.x = t.y * qz - t.z * qy;
-        t2.y = t.z * qx - t.x * qz;
-        t2.z = t.x * qy - t.y * qx;
-        
-        this.x = x + q.w*t.x + t2.x;
-        this.y = y + q.w*t.y + t2.y;
-        this.z = z + q.w*t.z + t2.z;
-        
-        return this;
-    },
-    
-    negate : function() {
-        
-        return this.multiplyScalar(-1);
-    },
-    
-    dot : function(v) {
-        
-        return this.x * v.x + this.y * v.y + this.z * v.z;
-    },
-    
-    length : function() {
-        
-        return Math.sqrt(this.x*this.x + this.y*this.y + this.z*this.z);
-    },
-    
-    lengthSq : function() {
-    
-        return (this.x*this.x + this.y*this.y + this.z*this.z);
-    },
-    
-    normalize : function() {
-        
-        return this.divideScalar( this.length() );
-    },
-    
-    cross : function (v) {
-        
-        var x = this.x, y = this.y, z = this.z;
-        
-        this.x = y * v.z - z * v.y;
-        this.y = z * v.x - x * v.z;
-        this.z = x * v.y - y * v.x;
-        
-        return this;
-    },
-    
-    crossVectors : function(a, b) {
-        
-        this.x = a.y * b.z - a.z * b.y;
-        this.y = a.z * b.x - a.x * b.z;
-        this.z = a.x * b.y - a.y * b.x;
-        
-        return this;
-    },
-    
-    getPositionFromMatrix : function(m) {
-        
-        this.x = m.elements[12];
-        this.y = m.elements[13];
-        this.z = m.elements[14];
-        
-        return this;
-    },
+  // Reserve max possible length (2 words per char)
+  // NB: by unknown reasons, Array is significantly faster for
+  //     String.fromCharCode.apply than Uint16Array.
+  var utf16buf = new Array(len*2);
 
-    setEulerFromRotationMatrix : function (m, order) {
+  for (out=0, i=0; i<len;) {
+    c = buf[i++];
+    // quick process ascii
+    if (c < 0x80) { utf16buf[out++] = c; continue; }
 
-        // assumes the upper 3x3 of m is a pure rotation matrix (i.e, unscaled)
+    c_len = _utf8len[c];
+    // skip 5 & 6 byte codes
+    if (c_len > 4) { utf16buf[out++] = 0xfffd; i += c_len-1; continue; }
 
-        var te = m.elements;
-        var m11 = te[0], m12 = te[4], m13 = te[8];
-        var m21 = te[1], m22 = te[5], m23 = te[9];
-        var m31 = te[2], m32 = te[6], m33 = te[10];
+    // apply mask on first byte
+    c &= c_len === 2 ? 0x1f : c_len === 3 ? 0x0f : 0x07;
+    // join the rest
+    while (c_len > 1 && i < len) {
+      c = (c << 6) | (buf[i++] & 0x3f);
+      c_len--;
+    }
 
-        if ( order === undefined || order === 'XYZ' ) {
+    // terminated by end of string?
+    if (c_len > 1) { utf16buf[out++] = 0xfffd; continue; }
 
-            this.y = Math.asin( $3Dmol.Math.clamp( m13, -1, 1 ) );
+    if (c < 0x10000) {
+      utf16buf[out++] = c;
+    } else {
+      c -= 0x10000;
+      utf16buf[out++] = 0xd800 | ((c >> 10) & 0x3ff);
+      utf16buf[out++] = 0xdc00 | (c & 0x3ff);
+    }
+  }
 
-            if ( Math.abs( m13 ) < 0.99999 ) {
+  return buf2binstring(utf16buf, out);
+};
 
-                this.x = Math.atan2( - m23, m33 );
-                this.z = Math.atan2( - m12, m11 );
 
-            } else {
+// Calculate max possible position in utf8 buffer,
+// that will not break sequence. If that's not possible
+// - (very small limits) return max size as is.
+//
+// buf[] - utf8 bytes array
+// max   - length limit (mandatory);
+exports.utf8border = function(buf, max) {
+  var pos;
 
-                this.x = Math.atan2( m32, m22 );
-                this.z = 0;
+  max = max || buf.length;
+  if (max > buf.length) { max = buf.length; }
 
-            }
-        }
-        
-        else {
-            console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: " + order);
-        }
-        
-        return this;
+  // go back from last position, until start of sequence found
+  pos = max-1;
+  while (pos >= 0 && (buf[pos] & 0xC0) === 0x80) { pos--; }
 
-    },
-    
-    clone : function() {
-        return new $3Dmol.Vector3(this.x, this.y, this.z);
-    }
-    
-};
+  // Fuckup - very small and broken sequence,
+  // return max, because we should return something anyway.
+  if (pos < 0) { return max; }
 
-//Matrices
+  // If we came to start of buffer - that means vuffer is too small,
+  // return max too.
+  if (pos === 0) { return max; }
 
-//Matrix3
-/** @constructor */
-$3Dmol.Matrix3 = function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
-    
-    this.elements = new Float32Array(9);
-    
-    this.set(
-        (n11 !== undefined) ? n11 : 1, n12 || 0, n13 || 0,
-        n21 || 0, (n22 !== undefined) ? n22 : 1, n23 || 0,
-        n31 || 0, n32 || 0, (n33 !== undefined) ? n33 : 1
-    );
-    
+  return (pos + _utf8len[buf[pos]] > max) ? pos : max;
 };
 
-$3Dmol.Matrix3.prototype = {
-    
-    constructor : $3Dmol.Matrix3,    
-   
-    set : function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
-        var te = this.elements;
-        
-        te[0] = n11; te[3] = n12; te[6] = n13;
-        te[1] = n21; te[4] = n22; te[7] = n23;
-        te[2] = n31; te[5] = n32; te[8] = n33;
-        
-        return this;
-    },
-    
-    identity : function() {   
-        this.set(
-            1,0,0,
-            0,1,0,
-            0,0,1
-        );
-        
-        return this;
-    },
-   
-    copy : function(m) {
-        var me = m.elements;
-       
-        this.set(
-            me[0], me[3], me[6],
-            me[1], me[4], me[7],
-            me[2], me[5], me[8]
-        );
-    },
-    
-    multiplyScalar: function ( s ) {
-        var te = this.elements;
+},{"./common":1}],3:[function(require,module,exports){
+'use strict';
 
-        te[0] *= s; te[3] *= s; te[6] *= s;
-        te[1] *= s; te[4] *= s; te[7] *= s;
-        te[2] *= s; te[5] *= s; te[8] *= s;
+// Note: adler32 takes 12% for level 0 and 2% for level 6.
+// It doesn't worth to make additional optimizationa as in original.
+// Small size is preferable.
 
-        return this;
-    },
+function adler32(adler, buf, len, pos) {
+  var s1 = (adler & 0xffff) |0,
+      s2 = ((adler >>> 16) & 0xffff) |0,
+      n = 0;
 
-    getInverse: function ( matrix, throwOnInvertible ) {
-        // input: Matrix4
+  while (len !== 0) {
+    // Set limit ~ twice less than 5552, to keep
+    // s2 in 31-bits, because we force signed ints.
+    // in other case %= will fail.
+    n = len > 2000 ? 2000 : len;
+    len -= n;
 
-        var me = matrix.elements;
-        var te = this.elements;
+    do {
+      s1 = (s1 + buf[pos++]) |0;
+      s2 = (s2 + s1) |0;
+    } while (--n);
 
-        te[ 0 ] =   me[10] * me[5] - me[6] * me[9];
-        te[ 1 ] = - me[10] * me[1] + me[2] * me[9];
-        te[ 2 ] =   me[6] * me[1] - me[2] * me[5];
-        te[ 3 ] = - me[10] * me[4] + me[6] * me[8];
-        te[ 4 ] =   me[10] * me[0] - me[2] * me[8];
-        te[ 5 ] = - me[6] * me[0] + me[2] * me[4];
-        te[ 6 ] =   me[9] * me[4] - me[5] * me[8];
-        te[ 7 ] = - me[9] * me[0] + me[1] * me[8];
-        te[ 8 ] =   me[5] * me[0] - me[1] * me[4];
+    s1 %= 65521;
+    s2 %= 65521;
+  }
 
-        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 3 ] + me[ 2 ] * te[ 6 ];
+  return (s1 | (s2 << 16)) |0;
+}
 
-        // no inverse
 
-        if ( det === 0 ) {
+module.exports = adler32;
 
-            var msg = "Matrix3.getInverse(): can't invert matrix, determinant is 0";
+},{}],4:[function(require,module,exports){
+module.exports = {
 
-            if ( throwOnInvertible || false ) {
+  /* Allowed flush values; see deflate() and inflate() below for details */
+  Z_NO_FLUSH:         0,
+  Z_PARTIAL_FLUSH:    1,
+  Z_SYNC_FLUSH:       2,
+  Z_FULL_FLUSH:       3,
+  Z_FINISH:           4,
+  Z_BLOCK:            5,
+  Z_TREES:            6,
 
-                throw new Error( msg ); 
+  /* Return codes for the compression/decompression functions. Negative values
+  * are errors, positive values are used for special but normal events.
+  */
+  Z_OK:               0,
+  Z_STREAM_END:       1,
+  Z_NEED_DICT:        2,
+  Z_ERRNO:           -1,
+  Z_STREAM_ERROR:    -2,
+  Z_DATA_ERROR:      -3,
+  //Z_MEM_ERROR:     -4,
+  Z_BUF_ERROR:       -5,
+  //Z_VERSION_ERROR: -6,
+
+  /* compression levels */
+  Z_NO_COMPRESSION:         0,
+  Z_BEST_SPEED:             1,
+  Z_BEST_COMPRESSION:       9,
+  Z_DEFAULT_COMPRESSION:   -1,
+
+
+  Z_FILTERED:               1,
+  Z_HUFFMAN_ONLY:           2,
+  Z_RLE:                    3,
+  Z_FIXED:                  4,
+  Z_DEFAULT_STRATEGY:       0,
+
+  /* Possible values of the data_type field (though see inflate()) */
+  Z_BINARY:                 0,
+  Z_TEXT:                   1,
+  //Z_ASCII:                1, // = Z_TEXT (deprecated)
+  Z_UNKNOWN:                2,
+
+  /* The deflate compression method */
+  Z_DEFLATED:               8
+  //Z_NULL:                 null // Use -1 or null inline, depending on var type
+};
 
-            } else {
+},{}],5:[function(require,module,exports){
+'use strict';
 
-                console.warn( msg );
+// Note: we can't get significant speed boost here.
+// So write code to minimize size - no pregenerated tables
+// and array tools dependencies.
 
-            }
 
-            this.identity();
+// Use ordinary array, since untyped makes no boost here
+function makeTable() {
+  var c, table = [];
 
-            return this;
+  for (var n =0; n < 256; n++) {
+    c = n;
+    for (var k =0; k < 8; k++) {
+      c = ((c&1) ? (0xEDB88320 ^ (c >>> 1)) : (c >>> 1));
+    }
+    table[n] = c;
+  }
 
-        }
+  return table;
+}
 
-        this.multiplyScalar( 1.0 / det );
+// Create table on load. Just 255 signed longs. Not a problem.
+var crcTable = makeTable();
 
-        return this;
-    },
-    
-    transpose: function () {
-        var tmp, m = this.elements;
 
-        tmp = m[1]; m[1] = m[3]; m[3] = tmp;
-        tmp = m[2]; m[2] = m[6]; m[6] = tmp;
-        tmp = m[5]; m[5] = m[7]; m[7] = tmp;
+function crc32(crc, buf, len, pos) {
+  var t = crcTable,
+      end = pos + len;
 
-        return this;
-    },
-    
-    clone: function () {
-        var te = this.elements;
+  crc = crc ^ (-1);
 
-        return new $3Dmol.Matrix3(
+  for (var i = pos; i < end; i++) {
+    crc = (crc >>> 8) ^ t[(crc ^ buf[i]) & 0xFF];
+  }
 
-            te[0], te[3], te[6],
-            te[1], te[4], te[7],
-            te[2], te[5], te[8]
+  return (crc ^ (-1)); // >>> 0;
+}
 
-        );
-    }
-   
-};
 
-//Matrix 4
-/** @constructor */
-$3Dmol.Matrix4 = function(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44) {
+module.exports = crc32;
+
+},{}],6:[function(require,module,exports){
+'use strict';
+
+
+function GZheader() {
+  /* true if compressed data believed to be text */
+  this.text       = 0;
+  /* modification time */
+  this.time       = 0;
+  /* extra flags (not used when writing a gzip file) */
+  this.xflags     = 0;
+  /* operating system */
+  this.os         = 0;
+  /* pointer to extra field or Z_NULL if none */
+  this.extra      = null;
+  /* extra field length (valid if extra != Z_NULL) */
+  this.extra_len  = 0; // Actually, we don't need it in JS,
+                       // but leave for few code modifications
+
+  //
+  // Setup limits is not necessary because in js we should not preallocate memory
+  // for inflate use constant limit in 65536 bytes
+  //
+
+  /* space at extra (only when reading header) */
+  // this.extra_max  = 0;
+  /* pointer to zero-terminated file name or Z_NULL */
+  this.name       = '';
+  /* space at name (only when reading header) */
+  // this.name_max   = 0;
+  /* pointer to zero-terminated comment or Z_NULL */
+  this.comment    = '';
+  /* space at comment (only when reading header) */
+  // this.comm_max   = 0;
+  /* true if there was or will be a header crc */
+  this.hcrc       = 0;
+  /* true when done reading gzip header (not used when writing a gzip file) */
+  this.done       = false;
+}
 
-    var te = this.elements = new Float32Array( 16 );
-    
-    te[0] = ( n11 !== undefined ) ? n11 : 1; te[4] = n12 || 0; te[8] = n13 || 0; te[12] = n14 || 0;
-    te[1] = n21 || 0; te[5] = ( n22 !== undefined ) ? n22 : 1; te[9] = n23 || 0; te[13] = n24 || 0;
-    te[2] = n31 || 0; te[6] = n32 || 0; te[10] = ( n33 !== undefined ) ? n33 : 1; te[14] = n34 || 0;
-    te[3] = n41 || 0; te[7] = n42 || 0; te[11] = n43 || 0; te[15] = ( n44 !== undefined ) ? n44 : 1;
+module.exports = GZheader;
 
-};
+},{}],7:[function(require,module,exports){
+'use strict';
 
-$3Dmol.Matrix4.prototype = {
+// See state defs from inflate.js
+var BAD = 30;       /* got a data error -- remain here until reset */
+var TYPE = 12;      /* i: waiting for type bits, including last-flag bit */
 
-    constructor : $3Dmol.Matrix4,
+/*
+   Decode literal, length, and distance codes and write out the resulting
+   literal and match bytes until either not enough input or output is
+   available, an end-of-block is encountered, or a data error is encountered.
+   When large enough input and output buffers are supplied to inflate(), for
+   example, a 16K input buffer and a 64K output buffer, more than 95% of the
+   inflate execution time is spent in this routine.
+
+   Entry assumptions:
+
+        state.mode === LEN
+        strm.avail_in >= 6
+        strm.avail_out >= 258
+        start >= strm.avail_out
+        state.bits < 8
+
+   On return, state.mode is one of:
+
+        LEN -- ran out of enough output space or enough available input
+        TYPE -- reached end of block code, inflate() to interpret next block
+        BAD -- error in block data
+
+   Notes:
+
+    - The maximum input bits used by a length/distance pair is 15 bits for the
+      length code, 5 bits for the length extra, 15 bits for the distance code,
+      and 13 bits for the distance extra.  This totals 48 bits, or six bytes.
+      Therefore if strm.avail_in >= 6, then there is enough input to avoid
+      checking for available input while decoding.
+
+    - The maximum bytes that a single length/distance pair can output is 258
+      bytes, which is the maximum length that can be coded.  inflate_fast()
+      requires strm.avail_out >= 258 for each loop to avoid checking for
+      output space.
+ */
+module.exports = function inflate_fast(strm, start) {
+  var state;
+  var _in;                    /* local strm.input */
+  var last;                   /* have enough input while in < last */
+  var _out;                   /* local strm.output */
+  var beg;                    /* inflate()'s initial strm.output */
+  var end;                    /* while out < end, enough space available */
+//#ifdef INFLATE_STRICT
+  var dmax;                   /* maximum distance from zlib header */
+//#endif
+  var wsize;                  /* window size or zero if not using window */
+  var whave;                  /* valid bytes in the window */
+  var wnext;                  /* window write index */
+  var window;                 /* allocated sliding window, if wsize != 0 */
+  var hold;                   /* local strm.hold */
+  var bits;                   /* local strm.bits */
+  var lcode;                  /* local strm.lencode */
+  var dcode;                  /* local strm.distcode */
+  var lmask;                  /* mask for first level of length codes */
+  var dmask;                  /* mask for first level of distance codes */
+  var here;                   /* retrieved table entry */
+  var op;                     /* code bits, operation, extra bits, or */
+                              /*  window position, window bytes to copy */
+  var len;                    /* match length, unused bytes */
+  var dist;                   /* match distance */
+  var from;                   /* where to copy match from */
+  var from_source;
+
+
+  var input, output; // JS specific, because we have no pointers
+
+  /* copy state to local variables */
+  state = strm.state;
+  //here = state.here;
+  _in = strm.next_in;
+  input = strm.input;
+  last = _in + (strm.avail_in - 5);
+  _out = strm.next_out;
+  output = strm.output;
+  beg = _out - (start - strm.avail_out);
+  end = _out + (strm.avail_out - 257);
+//#ifdef INFLATE_STRICT
+  dmax = state.dmax;
+//#endif
+  wsize = state.wsize;
+  whave = state.whave;
+  wnext = state.wnext;
+  window = state.window;
+  hold = state.hold;
+  bits = state.bits;
+  lcode = state.lencode;
+  dcode = state.distcode;
+  lmask = (1 << state.lenbits) - 1;
+  dmask = (1 << state.distbits) - 1;
+
+
+  /* decode literals and length/distances until end-of-block or not enough
+     input data or output space */
+
+  top:
+  do {
+    if (bits < 15) {
+      hold += input[_in++] << bits;
+      bits += 8;
+      hold += input[_in++] << bits;
+      bits += 8;
+    }
 
-    set: function ( n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44 ) {
-        var te = this.elements;
+    here = lcode[hold & lmask];
+
+    dolen:
+    for (;;) { // Goto emulation
+      op = here >>> 24/*here.bits*/;
+      hold >>>= op;
+      bits -= op;
+      op = (here >>> 16) & 0xff/*here.op*/;
+      if (op === 0) {                          /* literal */
+        //Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+        //        "inflate:         literal '%c'\n" :
+        //        "inflate:         literal 0x%02x\n", here.val));
+        output[_out++] = here & 0xffff/*here.val*/;
+      }
+      else if (op & 16) {                     /* length base */
+        len = here & 0xffff/*here.val*/;
+        op &= 15;                           /* number of extra bits */
+        if (op) {
+          if (bits < op) {
+            hold += input[_in++] << bits;
+            bits += 8;
+          }
+          len += hold & ((1 << op) - 1);
+          hold >>>= op;
+          bits -= op;
+        }
+        //Tracevv((stderr, "inflate:         length %u\n", len));
+        if (bits < 15) {
+          hold += input[_in++] << bits;
+          bits += 8;
+          hold += input[_in++] << bits;
+          bits += 8;
+        }
+        here = dcode[hold & dmask];
+
+        dodist:
+        for (;;) { // goto emulation
+          op = here >>> 24/*here.bits*/;
+          hold >>>= op;
+          bits -= op;
+          op = (here >>> 16) & 0xff/*here.op*/;
+
+          if (op & 16) {                      /* distance base */
+            dist = here & 0xffff/*here.val*/;
+            op &= 15;                       /* number of extra bits */
+            if (bits < op) {
+              hold += input[_in++] << bits;
+              bits += 8;
+              if (bits < op) {
+                hold += input[_in++] << bits;
+                bits += 8;
+              }
+            }
+            dist += hold & ((1 << op) - 1);
+//#ifdef INFLATE_STRICT
+            if (dist > dmax) {
+              strm.msg = 'invalid distance too far back';
+              state.mode = BAD;
+              break top;
+            }
+//#endif
+            hold >>>= op;
+            bits -= op;
+            //Tracevv((stderr, "inflate:         distance %u\n", dist));
+            op = _out - beg;                /* max distance in output */
+            if (dist > op) {                /* see if copy from window */
+              op = dist - op;               /* distance back in window */
+              if (op > whave) {
+                if (state.sane) {
+                  strm.msg = 'invalid distance too far back';
+                  state.mode = BAD;
+                  break top;
+                }
 
-        te[0] = n11; te[4] = n12; te[8] = n13; te[12] = n14;
-        te[1] = n21; te[5] = n22; te[9] = n23; te[13] = n24;
-        te[2] = n31; te[6] = n32; te[10] = n33; te[14] = n34;
-        te[3] = n41; te[7] = n42; te[11] = n43; te[15] = n44;
+// (!) This block is disabled in zlib defailts,
+// don't enable it for binary compatibility
+//#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+//                if (len <= op - whave) {
+//                  do {
+//                    output[_out++] = 0;
+//                  } while (--len);
+//                  continue top;
+//                }
+//                len -= op - whave;
+//                do {
+//                  output[_out++] = 0;
+//                } while (--op > whave);
+//                if (op === 0) {
+//                  from = _out - dist;
+//                  do {
+//                    output[_out++] = output[from++];
+//                  } while (--len);
+//                  continue top;
+//                }
+//#endif
+              }
+              from = 0; // window index
+              from_source = window;
+              if (wnext === 0) {           /* very common case */
+                from += wsize - op;
+                if (op < len) {         /* some from window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = _out - dist;  /* rest from output */
+                  from_source = output;
+                }
+              }
+              else if (wnext < op) {      /* wrap around window */
+                from += wsize + wnext - op;
+                op -= wnext;
+                if (op < len) {         /* some from end of window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = 0;
+                  if (wnext < len) {  /* some from start of window */
+                    op = wnext;
+                    len -= op;
+                    do {
+                      output[_out++] = window[from++];
+                    } while (--op);
+                    from = _out - dist;      /* rest from output */
+                    from_source = output;
+                  }
+                }
+              }
+              else {                      /* contiguous in window */
+                from += wnext - op;
+                if (op < len) {         /* some from window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = _out - dist;  /* rest from output */
+                  from_source = output;
+                }
+              }
+              while (len > 2) {
+                output[_out++] = from_source[from++];
+                output[_out++] = from_source[from++];
+                output[_out++] = from_source[from++];
+                len -= 3;
+              }
+              if (len) {
+                output[_out++] = from_source[from++];
+                if (len > 1) {
+                  output[_out++] = from_source[from++];
+                }
+              }
+            }
+            else {
+              from = _out - dist;          /* copy direct from output */
+              do {                        /* minimum length is three */
+                output[_out++] = output[from++];
+                output[_out++] = output[from++];
+                output[_out++] = output[from++];
+                len -= 3;
+              } while (len > 2);
+              if (len) {
+                output[_out++] = output[from++];
+                if (len > 1) {
+                  output[_out++] = output[from++];
+                }
+              }
+            }
+          }
+          else if ((op & 64) === 0) {          /* 2nd level distance code */
+            here = dcode[(here & 0xffff)/*here.val*/ + (hold & ((1 << op) - 1))];
+            continue dodist;
+          }
+          else {
+            strm.msg = 'invalid distance code';
+            state.mode = BAD;
+            break top;
+          }
+
+          break; // need to emulate goto via "continue"
+        }
+      }
+      else if ((op & 64) === 0) {              /* 2nd level length code */
+        here = lcode[(here & 0xffff)/*here.val*/ + (hold & ((1 << op) - 1))];
+        continue dolen;
+      }
+      else if (op & 32) {                     /* end-of-block */
+        //Tracevv((stderr, "inflate:         end of block\n"));
+        state.mode = TYPE;
+        break top;
+      }
+      else {
+        strm.msg = 'invalid literal/length code';
+        state.mode = BAD;
+        break top;
+      }
+
+      break; // need to emulate goto via "continue"
+    }
+  } while (_in < last && _out < end);
+
+  /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
+  len = bits >> 3;
+  _in -= len;
+  bits -= len << 3;
+  hold &= (1 << bits) - 1;
+
+  /* update state and return */
+  strm.next_in = _in;
+  strm.next_out = _out;
+  strm.avail_in = (_in < last ? 5 + (last - _in) : 5 - (_in - last));
+  strm.avail_out = (_out < end ? 257 + (end - _out) : 257 - (_out - end));
+  state.hold = hold;
+  state.bits = bits;
+  return;
+};
 
-        return this;
-    },
+},{}],8:[function(require,module,exports){
+'use strict';
 
-    identity: function () {
-        this.set(
 
-            1, 0, 0, 0,
-            0, 1, 0, 0,
-            0, 0, 1, 0,
-            0, 0, 0, 1
+var utils = require('../utils/common');
+var adler32 = require('./adler32');
+var crc32   = require('./crc32');
+var inflate_fast = require('./inffast');
+var inflate_table = require('./inftrees');
 
-        );
+var CODES = 0;
+var LENS = 1;
+var DISTS = 2;
 
-        return this;
-    },
+/* Public constants ==========================================================*/
+/* ===========================================================================*/
 
-    copy: function ( m ) {
-        var me = m.elements;
 
-        this.set(
+/* Allowed flush values; see deflate() and inflate() below for details */
+//var Z_NO_FLUSH      = 0;
+//var Z_PARTIAL_FLUSH = 1;
+//var Z_SYNC_FLUSH    = 2;
+//var Z_FULL_FLUSH    = 3;
+var Z_FINISH        = 4;
+var Z_BLOCK         = 5;
+var Z_TREES         = 6;
 
-            me[0], me[4], me[8], me[12],
-            me[1], me[5], me[9], me[13],
-            me[2], me[6], me[10], me[14],
-            me[3], me[7], me[11], me[15]
 
-        );
+/* Return codes for the compression/decompression functions. Negative values
+ * are errors, positive values are used for special but normal events.
+ */
+var Z_OK            = 0;
+var Z_STREAM_END    = 1;
+var Z_NEED_DICT     = 2;
+//var Z_ERRNO         = -1;
+var Z_STREAM_ERROR  = -2;
+var Z_DATA_ERROR    = -3;
+var Z_MEM_ERROR     = -4;
+var Z_BUF_ERROR     = -5;
+//var Z_VERSION_ERROR = -6;
+
+/* The deflate compression method */
+var Z_DEFLATED  = 8;
+
+
+/* STATES ====================================================================*/
+/* ===========================================================================*/
+
+
+var    HEAD = 1;       /* i: waiting for magic header */
+var    FLAGS = 2;      /* i: waiting for method and flags (gzip) */
+var    TIME = 3;       /* i: waiting for modification time (gzip) */
+var    OS = 4;         /* i: waiting for extra flags and operating system (gzip) */
+var    EXLEN = 5;      /* i: waiting for extra length (gzip) */
+var    EXTRA = 6;      /* i: waiting for extra bytes (gzip) */
+var    NAME = 7;       /* i: waiting for end of file name (gzip) */
+var    COMMENT = 8;    /* i: waiting for end of comment (gzip) */
+var    HCRC = 9;       /* i: waiting for header crc (gzip) */
+var    DICTID = 10;    /* i: waiting for dictionary check value */
+var    DICT = 11;      /* waiting for inflateSetDictionary() call */
+var        TYPE = 12;      /* i: waiting for type bits, including last-flag bit */
+var        TYPEDO = 13;    /* i: same, but skip check to exit inflate on new block */
+var        STORED = 14;    /* i: waiting for stored size (length and complement) */
+var        COPY_ = 15;     /* i/o: same as COPY below, but only first time in */
+var        COPY = 16;      /* i/o: waiting for input or output to copy stored block */
+var        TABLE = 17;     /* i: waiting for dynamic block table lengths */
+var        LENLENS = 18;   /* i: waiting for code length code lengths */
+var        CODELENS = 19;  /* i: waiting for length/lit and distance code lengths */
+var            LEN_ = 20;      /* i: same as LEN below, but only first time in */
+var            LEN = 21;       /* i: waiting for length/lit/eob code */
+var            LENEXT = 22;    /* i: waiting for length extra bits */
+var            DIST = 23;      /* i: waiting for distance code */
+var            DISTEXT = 24;   /* i: waiting for distance extra bits */
+var            MATCH = 25;     /* o: waiting for output space to copy string */
+var            LIT = 26;       /* o: waiting for output space to write literal */
+var    CHECK = 27;     /* i: waiting for 32-bit check value */
+var    LENGTH = 28;    /* i: waiting for 32-bit length (gzip) */
+var    DONE = 29;      /* finished check, done -- remain here until reset */
+var    BAD = 30;       /* got a data error -- remain here until reset */
+var    MEM = 31;       /* got an inflate() memory error -- remain here until reset */
+var    SYNC = 32;      /* looking for synchronization bytes to restart inflate() */
+
+/* ===========================================================================*/
+
+
+
+var ENOUGH_LENS = 852;
+var ENOUGH_DISTS = 592;
+//var ENOUGH =  (ENOUGH_LENS+ENOUGH_DISTS);
+
+var MAX_WBITS = 15;
+/* 32K LZ77 window */
+var DEF_WBITS = MAX_WBITS;
+
+
+function ZSWAP32(q) {
+  return  (((q >>> 24) & 0xff) +
+          ((q >>> 8) & 0xff00) +
+          ((q & 0xff00) << 8) +
+          ((q & 0xff) << 24));
+}
 
-        return this;
-    },
 
-    setRotationFromEuler: function ( v, order ) {
+function InflateState() {
+  this.mode = 0;             /* current inflate mode */
+  this.last = false;          /* true if processing last block */
+  this.wrap = 0;              /* bit 0 true for zlib, bit 1 true for gzip */
+  this.havedict = false;      /* true if dictionary provided */
+  this.flags = 0;             /* gzip header method and flags (0 if zlib) */
+  this.dmax = 0;              /* zlib header max distance (INFLATE_STRICT) */
+  this.check = 0;             /* protected copy of check value */
+  this.total = 0;             /* protected copy of output count */
+  // TODO: may be {}
+  this.head = null;           /* where to save gzip header information */
+
+  /* sliding window */
+  this.wbits = 0;             /* log base 2 of requested window size */
+  this.wsize = 0;             /* window size or zero if not using window */
+  this.whave = 0;             /* valid bytes in the window */
+  this.wnext = 0;             /* window write index */
+  this.window = null;         /* allocated sliding window, if needed */
+
+  /* bit accumulator */
+  this.hold = 0;              /* input bit accumulator */
+  this.bits = 0;              /* number of bits in "in" */
+
+  /* for string and stored block copying */
+  this.length = 0;            /* literal or length of data to copy */
+  this.offset = 0;            /* distance back to copy string from */
+
+  /* for table and code decoding */
+  this.extra = 0;             /* extra bits needed */
+
+  /* fixed and dynamic code tables */
+  this.lencode = null;          /* starting table for length/literal codes */
+  this.distcode = null;         /* starting table for distance codes */
+  this.lenbits = 0;           /* index bits for lencode */
+  this.distbits = 0;          /* index bits for distcode */
+
+  /* dynamic table building */
+  this.ncode = 0;             /* number of code length code lengths */
+  this.nlen = 0;              /* number of length code lengths */
+  this.ndist = 0;             /* number of distance code lengths */
+  this.have = 0;              /* number of code lengths in lens[] */
+  this.next = null;              /* next available space in codes[] */
+
+  this.lens = new utils.Buf16(320); /* temporary storage for code lengths */
+  this.work = new utils.Buf16(288); /* work area for code table building */
+
+  /*
+   because we don't have pointers in js, we use lencode and distcode directly
+   as buffers so we don't need codes
+  */
+  //this.codes = new utils.Buf32(ENOUGH);       /* space for code tables */
+  this.lendyn = null;              /* dynamic table for length/literal codes (JS specific) */
+  this.distdyn = null;             /* dynamic table for distance codes (JS specific) */
+  this.sane = 0;                   /* if false, allow invalid distance too far */
+  this.back = 0;                   /* bits back of last unprocessed length/lit */
+  this.was = 0;                    /* initial length of match */
+}
 
-        var te = this.elements;
+function inflateResetKeep(strm) {
+  var state;
+
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  strm.total_in = strm.total_out = state.total = 0;
+  strm.msg = ''; /*Z_NULL*/
+  if (state.wrap) {       /* to support ill-conceived Java test suite */
+    strm.adler = state.wrap & 1;
+  }
+  state.mode = HEAD;
+  state.last = 0;
+  state.havedict = 0;
+  state.dmax = 32768;
+  state.head = null/*Z_NULL*/;
+  state.hold = 0;
+  state.bits = 0;
+  //state.lencode = state.distcode = state.next = state.codes;
+  state.lencode = state.lendyn = new utils.Buf32(ENOUGH_LENS);
+  state.distcode = state.distdyn = new utils.Buf32(ENOUGH_DISTS);
+
+  state.sane = 1;
+  state.back = -1;
+  //Tracev((stderr, "inflate: reset\n"));
+  return Z_OK;
+}
 
-        var x = v.x, y = v.y, z = v.z;
-        var a = Math.cos( x ), b = Math.sin( x );
-        var c = Math.cos( y ), d = Math.sin( y );
-        var e = Math.cos( z ), f = Math.sin( z );
+function inflateReset(strm) {
+  var state;
 
-        if ( order === undefined || order === 'XYZ' ) {
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  state.wsize = 0;
+  state.whave = 0;
+  state.wnext = 0;
+  return inflateResetKeep(strm);
 
-            var ae = a * e, af = a * f, be = b * e, bf = b * f;
+}
 
-            te[0] = c * e;
-            te[4] = - c * f;
-            te[8] = d;
+function inflateReset2(strm, windowBits) {
+  var wrap;
+  var state;
+
+  /* get the state */
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+
+  /* extract wrap request from windowBits parameter */
+  if (windowBits < 0) {
+    wrap = 0;
+    windowBits = -windowBits;
+  }
+  else {
+    wrap = (windowBits >> 4) + 1;
+    if (windowBits < 48) {
+      windowBits &= 15;
+    }
+  }
+
+  /* set number of window bits, free window if different */
+  if (windowBits && (windowBits < 8 || windowBits > 15)) {
+    return Z_STREAM_ERROR;
+  }
+  if (state.window !== null && state.wbits !== windowBits) {
+    state.window = null;
+  }
+
+  /* update state and reset the rest of it */
+  state.wrap = wrap;
+  state.wbits = windowBits;
+  return inflateReset(strm);
+}
 
-            te[1] = af + be * d;
-            te[5] = ae - bf * d;
-            te[9] = - b * c;
+function inflateInit2(strm, windowBits) {
+  var ret;
+  var state;
 
-            te[2] = bf - ae * d;
-            te[6] = be + af * d;
-            te[10] = a * c;
+  if (!strm) { return Z_STREAM_ERROR; }
+  //strm.msg = Z_NULL;                 /* in case we return an error */
 
-        } 
-        
-        else
-            console.error("Error with matrix4 setRotationFromEuler. Order: " + order);
+  state = new InflateState();
 
-        return this;
+  //if (state === Z_NULL) return Z_MEM_ERROR;
+  //Tracev((stderr, "inflate: allocated\n"));
+  strm.state = state;
+  state.window = null/*Z_NULL*/;
+  ret = inflateReset2(strm, windowBits);
+  if (ret !== Z_OK) {
+    strm.state = null/*Z_NULL*/;
+  }
+  return ret;
+}
 
-    },
+function inflateInit(strm) {
+  return inflateInit2(strm, DEF_WBITS);
+}
 
-    setRotationFromQuaternion: function ( q ) {
-        var te = this.elements;
 
-        var x = q.x, y = q.y, z = q.z, w = q.w;
-        var x2 = x + x, y2 = y + y, z2 = z + z;
-        var xx = x * x2, xy = x * y2, xz = x * z2;
-        var yy = y * y2, yz = y * z2, zz = z * z2;
-        var wx = w * x2, wy = w * y2, wz = w * z2;
+/*
+ Return state with length and distance decoding tables and index sizes set to
+ fixed code decoding.  Normally this returns fixed tables from inffixed.h.
+ If BUILDFIXED is defined, then instead this routine builds the tables the
+ first time it's called, and returns those tables the first time and
+ thereafter.  This reduces the size of the code by about 2K bytes, in
+ exchange for a little execution time.  However, BUILDFIXED should not be
+ used for threaded applications, since the rewriting of the tables and virgin
+ may not be thread-safe.
+ */
+var virgin = true;
 
-        te[0] = 1 - ( yy + zz );
-        te[4] = xy - wz;
-        te[8] = xz + wy;
+var lenfix, distfix; // We have no pointers in JS, so keep tables separate
 
-        te[1] = xy + wz;
-        te[5] = 1 - ( xx + zz );
-        te[9] = yz - wx;
+function fixedtables(state) {
+  /* build fixed huffman tables if first call (may not be thread safe) */
+  if (virgin) {
+    var sym;
 
-        te[2] = xz - wy;
-        te[6] = yz + wx;
-        te[10] = 1 - ( xx + yy );
+    lenfix = new utils.Buf32(512);
+    distfix = new utils.Buf32(32);
 
-        return this;
-    },
+    /* literal/length table */
+    sym = 0;
+    while (sym < 144) { state.lens[sym++] = 8; }
+    while (sym < 256) { state.lens[sym++] = 9; }
+    while (sym < 280) { state.lens[sym++] = 7; }
+    while (sym < 288) { state.lens[sym++] = 8; }
 
-    lookAt: function() {
-        var x = new $3Dmol.Vector3();
-        var y = new $3Dmol.Vector3();
-        var z = new $3Dmol.Vector3();
+    inflate_table(LENS,  state.lens, 0, 288, lenfix,   0, state.work, {bits: 9});
 
-        return function ( eye, target, up ) {
+    /* distance table */
+    sym = 0;
+    while (sym < 32) { state.lens[sym++] = 5; }
 
-            var te = this.elements;
+    inflate_table(DISTS, state.lens, 0, 32,   distfix, 0, state.work, {bits: 5});
 
-            z.subVectors( eye, target ).normalize();
+    /* do this just once */
+    virgin = false;
+  }
 
-            if ( z.length() === 0 ) {
+  state.lencode = lenfix;
+  state.lenbits = 9;
+  state.distcode = distfix;
+  state.distbits = 5;
+}
 
-                z.z = 1;
 
+/*
+ Update the window with the last wsize (normally 32K) bytes written before
+ returning.  If window does not exist yet, create it.  This is only called
+ when a window is already in use, or when output has been written during this
+ inflate call, but the end of the deflate stream has not been reached yet.
+ It is also called to create a window for dictionary data when a dictionary
+ is loaded.
+
+ Providing output buffers larger than 32K to inflate() should provide a speed
+ advantage, since only the last 32K of output is copied to the sliding window
+ upon return from inflate(), and since all distances after the first 32K of
+ output will fall in the output data, making match copies simpler and faster.
+ The advantage may be dependent on the size of the processor's data caches.
+ */
+function updatewindow(strm, src, end, copy) {
+  var dist;
+  var state = strm.state;
+
+  /* if it hasn't been done already, allocate space for the window */
+  if (state.window === null) {
+    state.wsize = 1 << state.wbits;
+    state.wnext = 0;
+    state.whave = 0;
+
+    state.window = new utils.Buf8(state.wsize);
+  }
+
+  /* copy state->wsize or less output bytes into the circular window */
+  if (copy >= state.wsize) {
+    utils.arraySet(state.window,src, end - state.wsize, state.wsize, 0);
+    state.wnext = 0;
+    state.whave = state.wsize;
+  }
+  else {
+    dist = state.wsize - state.wnext;
+    if (dist > copy) {
+      dist = copy;
+    }
+    //zmemcpy(state->window + state->wnext, end - copy, dist);
+    utils.arraySet(state.window,src, end - copy, dist, state.wnext);
+    copy -= dist;
+    if (copy) {
+      //zmemcpy(state->window, end - copy, copy);
+      utils.arraySet(state.window,src, end - copy, copy, 0);
+      state.wnext = copy;
+      state.whave = state.wsize;
+    }
+    else {
+      state.wnext += dist;
+      if (state.wnext === state.wsize) { state.wnext = 0; }
+      if (state.whave < state.wsize) { state.whave += dist; }
+    }
+  }
+  return 0;
+}
+
+function inflate(strm, flush) {
+  var state;
+  var input, output;          // input/output buffers
+  var next;                   /* next input INDEX */
+  var put;                    /* next output INDEX */
+  var have, left;             /* available input and output */
+  var hold;                   /* bit buffer */
+  var bits;                   /* bits in bit buffer */
+  var _in, _out;              /* save starting available input and output */
+  var copy;                   /* number of stored or match bytes to copy */
+  var from;                   /* where to copy match bytes from */
+  var from_source;
+  var here = 0;               /* current decoding table entry */
+  var here_bits, here_op, here_val; // paked "here" denormalized (JS specific)
+  //var last;                   /* parent table entry */
+  var last_bits, last_op, last_val; // paked "last" denormalized (JS specific)
+  var len;                    /* length to copy for repeats, bits to drop */
+  var ret;                    /* return code */
+  var hbuf = new utils.Buf8(4);    /* buffer for gzip header crc calculation */
+  var opts;
+
+  var n; // temporary var for NEED_BITS
+
+  var order = /* permutation of code lengths */
+    [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15];
+
+
+  if (!strm || !strm.state || !strm.output ||
+      (!strm.input && strm.avail_in !== 0)) {
+    return Z_STREAM_ERROR;
+  }
+
+  state = strm.state;
+  if (state.mode === TYPE) { state.mode = TYPEDO; }    /* skip check */
+
+
+  //--- LOAD() ---
+  put = strm.next_out;
+  output = strm.output;
+  left = strm.avail_out;
+  next = strm.next_in;
+  input = strm.input;
+  have = strm.avail_in;
+  hold = state.hold;
+  bits = state.bits;
+  //---
+
+  _in = have;
+  _out = left;
+  ret = Z_OK;
+
+  inf_leave: // goto emulation
+  for (;;) {
+    switch (state.mode) {
+    case HEAD:
+      if (state.wrap === 0) {
+        state.mode = TYPEDO;
+        break;
+      }
+      //=== NEEDBITS(16);
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if ((state.wrap & 2) && hold === 0x8b1f) {  /* gzip header */
+        state.check = 0/*crc32(0L, Z_NULL, 0)*/;
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        state.mode = FLAGS;
+        break;
+      }
+      state.flags = 0;           /* expect zlib header */
+      if (state.head) {
+        state.head.done = false;
+      }
+      if (!(state.wrap & 1) ||   /* check if zlib header allowed */
+        (((hold & 0xff)/*BITS(8)*/ << 8) + (hold >> 8)) % 31) {
+        strm.msg = 'incorrect header check';
+        state.mode = BAD;
+        break;
+      }
+      if ((hold & 0x0f)/*BITS(4)*/ !== Z_DEFLATED) {
+        strm.msg = 'unknown compression method';
+        state.mode = BAD;
+        break;
+      }
+      //--- DROPBITS(4) ---//
+      hold >>>= 4;
+      bits -= 4;
+      //---//
+      len = (hold & 0x0f)/*BITS(4)*/ + 8;
+      if (state.wbits === 0) {
+        state.wbits = len;
+      }
+      else if (len > state.wbits) {
+        strm.msg = 'invalid window size';
+        state.mode = BAD;
+        break;
+      }
+      state.dmax = 1 << len;
+      //Tracev((stderr, "inflate:   zlib header ok\n"));
+      strm.adler = state.check = 1/*adler32(0L, Z_NULL, 0)*/;
+      state.mode = hold & 0x200 ? DICTID : TYPE;
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      break;
+    case FLAGS:
+      //=== NEEDBITS(16); */
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.flags = hold;
+      if ((state.flags & 0xff) !== Z_DEFLATED) {
+        strm.msg = 'unknown compression method';
+        state.mode = BAD;
+        break;
+      }
+      if (state.flags & 0xe000) {
+        strm.msg = 'unknown header flags set';
+        state.mode = BAD;
+        break;
+      }
+      if (state.head) {
+        state.head.text = ((hold >> 8) & 1);
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = TIME;
+      /* falls through */
+    case TIME:
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if (state.head) {
+        state.head.time = hold;
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC4(state.check, hold)
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        hbuf[2] = (hold >>> 16) & 0xff;
+        hbuf[3] = (hold >>> 24) & 0xff;
+        state.check = crc32(state.check, hbuf, 4, 0);
+        //===
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = OS;
+      /* falls through */
+    case OS:
+      //=== NEEDBITS(16); */
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if (state.head) {
+        state.head.xflags = (hold & 0xff);
+        state.head.os = (hold >> 8);
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = EXLEN;
+      /* falls through */
+    case EXLEN:
+      if (state.flags & 0x0400) {
+        //=== NEEDBITS(16); */
+        while (bits < 16) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.length = hold;
+        if (state.head) {
+          state.head.extra_len = hold;
+        }
+        if (state.flags & 0x0200) {
+          //=== CRC2(state.check, hold);
+          hbuf[0] = hold & 0xff;
+          hbuf[1] = (hold >>> 8) & 0xff;
+          state.check = crc32(state.check, hbuf, 2, 0);
+          //===//
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+      }
+      else if (state.head) {
+        state.head.extra = null/*Z_NULL*/;
+      }
+      state.mode = EXTRA;
+      /* falls through */
+    case EXTRA:
+      if (state.flags & 0x0400) {
+        copy = state.length;
+        if (copy > have) { copy = have; }
+        if (copy) {
+          if (state.head) {
+            len = state.head.extra_len - state.length;
+            if (!state.head.extra) {
+              // Use untyped array for more conveniend processing later
+              state.head.extra = new Array(state.head.extra_len);
+            }
+            utils.arraySet(
+              state.head.extra,
+              input,
+              next,
+              // extra field is limited to 65536 bytes
+              // - no need for additional size check
+              copy,
+              /*len + copy > state.head.extra_max - len ? state.head.extra_max : copy,*/
+              len
+            );
+            //zmemcpy(state.head.extra + len, next,
+            //        len + copy > state.head.extra_max ?
+            //        state.head.extra_max - len : copy);
+          }
+          if (state.flags & 0x0200) {
+            state.check = crc32(state.check, input, copy, next);
+          }
+          have -= copy;
+          next += copy;
+          state.length -= copy;
+        }
+        if (state.length) { break inf_leave; }
+      }
+      state.length = 0;
+      state.mode = NAME;
+      /* falls through */
+    case NAME:
+      if (state.flags & 0x0800) {
+        if (have === 0) { break inf_leave; }
+        copy = 0;
+        do {
+          // TODO: 2 or 1 bytes?
+          len = input[next + copy++];
+          /* use constant limit because in js we should not preallocate memory */
+          if (state.head && len &&
+              (state.length < 65536 /*state.head.name_max*/)) {
+            state.head.name += String.fromCharCode(len);
+          }
+        } while (len && copy < have);
+
+        if (state.flags & 0x0200) {
+          state.check = crc32(state.check, input, copy, next);
+        }
+        have -= copy;
+        next += copy;
+        if (len) { break inf_leave; }
+      }
+      else if (state.head) {
+        state.head.name = null;
+      }
+      state.length = 0;
+      state.mode = COMMENT;
+      /* falls through */
+    case COMMENT:
+      if (state.flags & 0x1000) {
+        if (have === 0) { break inf_leave; }
+        copy = 0;
+        do {
+          len = input[next + copy++];
+          /* use constant limit because in js we should not preallocate memory */
+          if (state.head && len &&
+              (state.length < 65536 /*state.head.comm_max*/)) {
+            state.head.comment += String.fromCharCode(len);
+          }
+        } while (len && copy < have);
+        if (state.flags & 0x0200) {
+          state.check = crc32(state.check, input, copy, next);
+        }
+        have -= copy;
+        next += copy;
+        if (len) { break inf_leave; }
+      }
+      else if (state.head) {
+        state.head.comment = null;
+      }
+      state.mode = HCRC;
+      /* falls through */
+    case HCRC:
+      if (state.flags & 0x0200) {
+        //=== NEEDBITS(16); */
+        while (bits < 16) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        if (hold !== (state.check & 0xffff)) {
+          strm.msg = 'header crc mismatch';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+      }
+      if (state.head) {
+        state.head.hcrc = ((state.flags >> 9) & 1);
+        state.head.done = true;
+      }
+      strm.adler = state.check = 0 /*crc32(0L, Z_NULL, 0)*/;
+      state.mode = TYPE;
+      break;
+    case DICTID:
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      strm.adler = state.check = ZSWAP32(hold);
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = DICT;
+      /* falls through */
+    case DICT:
+      if (state.havedict === 0) {
+        //--- RESTORE() ---
+        strm.next_out = put;
+        strm.avail_out = left;
+        strm.next_in = next;
+        strm.avail_in = have;
+        state.hold = hold;
+        state.bits = bits;
+        //---
+        return Z_NEED_DICT;
+      }
+      strm.adler = state.check = 1/*adler32(0L, Z_NULL, 0)*/;
+      state.mode = TYPE;
+      /* falls through */
+    case TYPE:
+      if (flush === Z_BLOCK || flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case TYPEDO:
+      if (state.last) {
+        //--- BYTEBITS() ---//
+        hold >>>= bits & 7;
+        bits -= bits & 7;
+        //---//
+        state.mode = CHECK;
+        break;
+      }
+      //=== NEEDBITS(3); */
+      while (bits < 3) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.last = (hold & 0x01)/*BITS(1)*/;
+      //--- DROPBITS(1) ---//
+      hold >>>= 1;
+      bits -= 1;
+      //---//
+
+      switch ((hold & 0x03)/*BITS(2)*/) {
+      case 0:                             /* stored block */
+        //Tracev((stderr, "inflate:     stored block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = STORED;
+        break;
+      case 1:                             /* fixed block */
+        fixedtables(state);
+        //Tracev((stderr, "inflate:     fixed codes block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = LEN_;             /* decode codes */
+        if (flush === Z_TREES) {
+          //--- DROPBITS(2) ---//
+          hold >>>= 2;
+          bits -= 2;
+          //---//
+          break inf_leave;
+        }
+        break;
+      case 2:                             /* dynamic block */
+        //Tracev((stderr, "inflate:     dynamic codes block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = TABLE;
+        break;
+      case 3:
+        strm.msg = 'invalid block type';
+        state.mode = BAD;
+      }
+      //--- DROPBITS(2) ---//
+      hold >>>= 2;
+      bits -= 2;
+      //---//
+      break;
+    case STORED:
+      //--- BYTEBITS() ---// /* go to byte boundary */
+      hold >>>= bits & 7;
+      bits -= bits & 7;
+      //---//
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if ((hold & 0xffff) !== ((hold >>> 16) ^ 0xffff)) {
+        strm.msg = 'invalid stored block lengths';
+        state.mode = BAD;
+        break;
+      }
+      state.length = hold & 0xffff;
+      //Tracev((stderr, "inflate:       stored length %u\n",
+      //        state.length));
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = COPY_;
+      if (flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case COPY_:
+      state.mode = COPY;
+      /* falls through */
+    case COPY:
+      copy = state.length;
+      if (copy) {
+        if (copy > have) { copy = have; }
+        if (copy > left) { copy = left; }
+        if (copy === 0) { break inf_leave; }
+        //--- zmemcpy(put, next, copy); ---
+        utils.arraySet(output, input, next, copy, put);
+        //---//
+        have -= copy;
+        next += copy;
+        left -= copy;
+        put += copy;
+        state.length -= copy;
+        break;
+      }
+      //Tracev((stderr, "inflate:       stored end\n"));
+      state.mode = TYPE;
+      break;
+    case TABLE:
+      //=== NEEDBITS(14); */
+      while (bits < 14) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.nlen = (hold & 0x1f)/*BITS(5)*/ + 257;
+      //--- DROPBITS(5) ---//
+      hold >>>= 5;
+      bits -= 5;
+      //---//
+      state.ndist = (hold & 0x1f)/*BITS(5)*/ + 1;
+      //--- DROPBITS(5) ---//
+      hold >>>= 5;
+      bits -= 5;
+      //---//
+      state.ncode = (hold & 0x0f)/*BITS(4)*/ + 4;
+      //--- DROPBITS(4) ---//
+      hold >>>= 4;
+      bits -= 4;
+      //---//
+//#ifndef PKZIP_BUG_WORKAROUND
+      if (state.nlen > 286 || state.ndist > 30) {
+        strm.msg = 'too many length or distance symbols';
+        state.mode = BAD;
+        break;
+      }
+//#endif
+      //Tracev((stderr, "inflate:       table sizes ok\n"));
+      state.have = 0;
+      state.mode = LENLENS;
+      /* falls through */
+    case LENLENS:
+      while (state.have < state.ncode) {
+        //=== NEEDBITS(3);
+        while (bits < 3) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.lens[order[state.have++]] = (hold & 0x07);//BITS(3);
+        //--- DROPBITS(3) ---//
+        hold >>>= 3;
+        bits -= 3;
+        //---//
+      }
+      while (state.have < 19) {
+        state.lens[order[state.have++]] = 0;
+      }
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      //state.next = state.codes;
+      //state.lencode = state.next;
+      // Switch to use dynamic table
+      state.lencode = state.lendyn;
+      state.lenbits = 7;
+
+      opts = {bits: state.lenbits};
+      ret = inflate_table(CODES, state.lens, 0, 19, state.lencode, 0, state.work, opts);
+      state.lenbits = opts.bits;
+
+      if (ret) {
+        strm.msg = 'invalid code lengths set';
+        state.mode = BAD;
+        break;
+      }
+      //Tracev((stderr, "inflate:       code lengths ok\n"));
+      state.have = 0;
+      state.mode = CODELENS;
+      /* falls through */
+    case CODELENS:
+      while (state.have < state.nlen + state.ndist) {
+        for (;;) {
+          here = state.lencode[hold & ((1 << state.lenbits) - 1)];/*BITS(state.lenbits)*/
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        if (here_val < 16) {
+          //--- DROPBITS(here.bits) ---//
+          hold >>>= here_bits;
+          bits -= here_bits;
+          //---//
+          state.lens[state.have++] = here_val;
+        }
+        else {
+          if (here_val === 16) {
+            //=== NEEDBITS(here.bits + 2);
+            n = here_bits + 2;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
             }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            if (state.have === 0) {
+              strm.msg = 'invalid bit length repeat';
+              state.mode = BAD;
+              break;
+            }
+            len = state.lens[state.have - 1];
+            copy = 3 + (hold & 0x03);//BITS(2);
+            //--- DROPBITS(2) ---//
+            hold >>>= 2;
+            bits -= 2;
+            //---//
+          }
+          else if (here_val === 17) {
+            //=== NEEDBITS(here.bits + 3);
+            n = here_bits + 3;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
+            }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            len = 0;
+            copy = 3 + (hold & 0x07);//BITS(3);
+            //--- DROPBITS(3) ---//
+            hold >>>= 3;
+            bits -= 3;
+            //---//
+          }
+          else {
+            //=== NEEDBITS(here.bits + 7);
+            n = here_bits + 7;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
+            }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            len = 0;
+            copy = 11 + (hold & 0x7f);//BITS(7);
+            //--- DROPBITS(7) ---//
+            hold >>>= 7;
+            bits -= 7;
+            //---//
+          }
+          if (state.have + copy > state.nlen + state.ndist) {
+            strm.msg = 'invalid bit length repeat';
+            state.mode = BAD;
+            break;
+          }
+          while (copy--) {
+            state.lens[state.have++] = len;
+          }
+        }
+      }
+
+      /* handle error breaks in while */
+      if (state.mode === BAD) { break; }
+
+      /* check for end-of-block code (better have one) */
+      if (state.lens[256] === 0) {
+        strm.msg = 'invalid code -- missing end-of-block';
+        state.mode = BAD;
+        break;
+      }
+
+      /* build code tables -- note: do not change the lenbits or distbits
+         values here (9 and 6) without reading the comments in inftrees.h
+         concerning the ENOUGH constants, which depend on those values */
+      state.lenbits = 9;
+
+      opts = {bits: state.lenbits};
+      ret = inflate_table(LENS, state.lens, 0, state.nlen, state.lencode, 0, state.work, opts);
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      // state.next_index = opts.table_index;
+      state.lenbits = opts.bits;
+      // state.lencode = state.next;
+
+      if (ret) {
+        strm.msg = 'invalid literal/lengths set';
+        state.mode = BAD;
+        break;
+      }
+
+      state.distbits = 6;
+      //state.distcode.copy(state.codes);
+      // Switch to use dynamic table
+      state.distcode = state.distdyn;
+      opts = {bits: state.distbits};
+      ret = inflate_table(DISTS, state.lens, state.nlen, state.ndist, state.distcode, 0, state.work, opts);
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      // state.next_index = opts.table_index;
+      state.distbits = opts.bits;
+      // state.distcode = state.next;
+
+      if (ret) {
+        strm.msg = 'invalid distances set';
+        state.mode = BAD;
+        break;
+      }
+      //Tracev((stderr, 'inflate:       codes ok\n'));
+      state.mode = LEN_;
+      if (flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case LEN_:
+      state.mode = LEN;
+      /* falls through */
+    case LEN:
+      if (have >= 6 && left >= 258) {
+        //--- RESTORE() ---
+        strm.next_out = put;
+        strm.avail_out = left;
+        strm.next_in = next;
+        strm.avail_in = have;
+        state.hold = hold;
+        state.bits = bits;
+        //---
+        inflate_fast(strm, _out);
+        //--- LOAD() ---
+        put = strm.next_out;
+        output = strm.output;
+        left = strm.avail_out;
+        next = strm.next_in;
+        input = strm.input;
+        have = strm.avail_in;
+        hold = state.hold;
+        bits = state.bits;
+        //---
+
+        if (state.mode === TYPE) {
+          state.back = -1;
+        }
+        break;
+      }
+      state.back = 0;
+      for (;;) {
+        here = state.lencode[hold & ((1 << state.lenbits) -1)];  /*BITS(state.lenbits)*/
+        here_bits = here >>> 24;
+        here_op = (here >>> 16) & 0xff;
+        here_val = here & 0xffff;
+
+        if (here_bits <= bits) { break; }
+        //--- PULLBYTE() ---//
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+        //---//
+      }
+      if (here_op && (here_op & 0xf0) === 0) {
+        last_bits = here_bits;
+        last_op = here_op;
+        last_val = here_val;
+        for (;;) {
+          here = state.lencode[last_val +
+                  ((hold & ((1 << (last_bits + last_op)) -1))/*BITS(last.bits + last.op)*/ >> last_bits)];
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((last_bits + here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        //--- DROPBITS(last.bits) ---//
+        hold >>>= last_bits;
+        bits -= last_bits;
+        //---//
+        state.back += last_bits;
+      }
+      //--- DROPBITS(here.bits) ---//
+      hold >>>= here_bits;
+      bits -= here_bits;
+      //---//
+      state.back += here_bits;
+      state.length = here_val;
+      if (here_op === 0) {
+        //Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+        //        "inflate:         literal '%c'\n" :
+        //        "inflate:         literal 0x%02x\n", here.val));
+        state.mode = LIT;
+        break;
+      }
+      if (here_op & 32) {
+        //Tracevv((stderr, "inflate:         end of block\n"));
+        state.back = -1;
+        state.mode = TYPE;
+        break;
+      }
+      if (here_op & 64) {
+        strm.msg = 'invalid literal/length code';
+        state.mode = BAD;
+        break;
+      }
+      state.extra = here_op & 15;
+      state.mode = LENEXT;
+      /* falls through */
+    case LENEXT:
+      if (state.extra) {
+        //=== NEEDBITS(state.extra);
+        n = state.extra;
+        while (bits < n) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.length += hold & ((1 << state.extra) -1)/*BITS(state.extra)*/;
+        //--- DROPBITS(state.extra) ---//
+        hold >>>= state.extra;
+        bits -= state.extra;
+        //---//
+        state.back += state.extra;
+      }
+      //Tracevv((stderr, "inflate:         length %u\n", state.length));
+      state.was = state.length;
+      state.mode = DIST;
+      /* falls through */
+    case DIST:
+      for (;;) {
+        here = state.distcode[hold & ((1 << state.distbits) -1)];/*BITS(state.distbits)*/
+        here_bits = here >>> 24;
+        here_op = (here >>> 16) & 0xff;
+        here_val = here & 0xffff;
+
+        if ((here_bits) <= bits) { break; }
+        //--- PULLBYTE() ---//
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+        //---//
+      }
+      if ((here_op & 0xf0) === 0) {
+        last_bits = here_bits;
+        last_op = here_op;
+        last_val = here_val;
+        for (;;) {
+          here = state.distcode[last_val +
+                  ((hold & ((1 << (last_bits + last_op)) -1))/*BITS(last.bits + last.op)*/ >> last_bits)];
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((last_bits + here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        //--- DROPBITS(last.bits) ---//
+        hold >>>= last_bits;
+        bits -= last_bits;
+        //---//
+        state.back += last_bits;
+      }
+      //--- DROPBITS(here.bits) ---//
+      hold >>>= here_bits;
+      bits -= here_bits;
+      //---//
+      state.back += here_bits;
+      if (here_op & 64) {
+        strm.msg = 'invalid distance code';
+        state.mode = BAD;
+        break;
+      }
+      state.offset = here_val;
+      state.extra = (here_op) & 15;
+      state.mode = DISTEXT;
+      /* falls through */
+    case DISTEXT:
+      if (state.extra) {
+        //=== NEEDBITS(state.extra);
+        n = state.extra;
+        while (bits < n) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.offset += hold & ((1 << state.extra) -1)/*BITS(state.extra)*/;
+        //--- DROPBITS(state.extra) ---//
+        hold >>>= state.extra;
+        bits -= state.extra;
+        //---//
+        state.back += state.extra;
+      }
+//#ifdef INFLATE_STRICT
+      if (state.offset > state.dmax) {
+        strm.msg = 'invalid distance too far back';
+        state.mode = BAD;
+        break;
+      }
+//#endif
+      //Tracevv((stderr, "inflate:         distance %u\n", state.offset));
+      state.mode = MATCH;
+      /* falls through */
+    case MATCH:
+      if (left === 0) { break inf_leave; }
+      copy = _out - left;
+      if (state.offset > copy) {         /* copy from window */
+        copy = state.offset - copy;
+        if (copy > state.whave) {
+          if (state.sane) {
+            strm.msg = 'invalid distance too far back';
+            state.mode = BAD;
+            break;
+          }
+// (!) This block is disabled in zlib defailts,
+// don't enable it for binary compatibility
+//#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+//          Trace((stderr, "inflate.c too far\n"));
+//          copy -= state.whave;
+//          if (copy > state.length) { copy = state.length; }
+//          if (copy > left) { copy = left; }
+//          left -= copy;
+//          state.length -= copy;
+//          do {
+//            output[put++] = 0;
+//          } while (--copy);
+//          if (state.length === 0) { state.mode = LEN; }
+//          break;
+//#endif
+        }
+        if (copy > state.wnext) {
+          copy -= state.wnext;
+          from = state.wsize - copy;
+        }
+        else {
+          from = state.wnext - copy;
+        }
+        if (copy > state.length) { copy = state.length; }
+        from_source = state.window;
+      }
+      else {                              /* copy from output */
+        from_source = output;
+        from = put - state.offset;
+        copy = state.length;
+      }
+      if (copy > left) { copy = left; }
+      left -= copy;
+      state.length -= copy;
+      do {
+        output[put++] = from_source[from++];
+      } while (--copy);
+      if (state.length === 0) { state.mode = LEN; }
+      break;
+    case LIT:
+      if (left === 0) { break inf_leave; }
+      output[put++] = state.length;
+      left--;
+      state.mode = LEN;
+      break;
+    case CHECK:
+      if (state.wrap) {
+        //=== NEEDBITS(32);
+        while (bits < 32) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          // Use '|' insdead of '+' to make sure that result is signed
+          hold |= input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        _out -= left;
+        strm.total_out += _out;
+        state.total += _out;
+        if (_out) {
+          strm.adler = state.check =
+              /*UPDATE(state.check, put - _out, _out);*/
+              (state.flags ? crc32(state.check, output, _out, put - _out) : adler32(state.check, output, _out, put - _out));
 
-            x.crossVectors( up, z ).normalize();
+        }
+        _out = left;
+        // NB: crc32 stored as signed 32-bit int, ZSWAP32 returns signed too
+        if ((state.flags ? hold : ZSWAP32(hold)) !== state.check) {
+          strm.msg = 'incorrect data check';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        //Tracev((stderr, "inflate:   check matches trailer\n"));
+      }
+      state.mode = LENGTH;
+      /* falls through */
+    case LENGTH:
+      if (state.wrap && state.flags) {
+        //=== NEEDBITS(32);
+        while (bits < 32) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        if (hold !== (state.total & 0xffffffff)) {
+          strm.msg = 'incorrect length check';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        //Tracev((stderr, "inflate:   length matches trailer\n"));
+      }
+      state.mode = DONE;
+      /* falls through */
+    case DONE:
+      ret = Z_STREAM_END;
+      break inf_leave;
+    case BAD:
+      ret = Z_DATA_ERROR;
+      break inf_leave;
+    case MEM:
+      return Z_MEM_ERROR;
+    case SYNC:
+      /* falls through */
+    default:
+      return Z_STREAM_ERROR;
+    }
+  }
+
+  // inf_leave <- here is real place for "goto inf_leave", emulated via "break inf_leave"
+
+  /*
+     Return from inflate(), updating the total counts and the check value.
+     If there was no progress during the inflate() call, return a buffer
+     error.  Call updatewindow() to create and/or update the window state.
+     Note: a memory error from inflate() is non-recoverable.
+   */
+
+  //--- RESTORE() ---
+  strm.next_out = put;
+  strm.avail_out = left;
+  strm.next_in = next;
+  strm.avail_in = have;
+  state.hold = hold;
+  state.bits = bits;
+  //---
+
+  if (state.wsize || (_out !== strm.avail_out && state.mode < BAD &&
+                      (state.mode < CHECK || flush !== Z_FINISH))) {
+    if (updatewindow(strm, strm.output, strm.next_out, _out - strm.avail_out)) {
+      state.mode = MEM;
+      return Z_MEM_ERROR;
+    }
+  }
+  _in -= strm.avail_in;
+  _out -= strm.avail_out;
+  strm.total_in += _in;
+  strm.total_out += _out;
+  state.total += _out;
+  if (state.wrap && _out) {
+    strm.adler = state.check = /*UPDATE(state.check, strm.next_out - _out, _out);*/
+      (state.flags ? crc32(state.check, output, _out, strm.next_out - _out) : adler32(state.check, output, _out, strm.next_out - _out));
+  }
+  strm.data_type = state.bits + (state.last ? 64 : 0) +
+                    (state.mode === TYPE ? 128 : 0) +
+                    (state.mode === LEN_ || state.mode === COPY_ ? 256 : 0);
+  if (((_in === 0 && _out === 0) || flush === Z_FINISH) && ret === Z_OK) {
+    ret = Z_BUF_ERROR;
+  }
+  return ret;
+}
 
-            if ( x.length() === 0 ) {
+function inflateEnd(strm) {
 
-                z.x += 0.0001;
-                x.crossVectors( up, z ).normalize();
+  if (!strm || !strm.state /*|| strm->zfree == (free_func)0*/) {
+    return Z_STREAM_ERROR;
+  }
 
-            }
+  var state = strm.state;
+  if (state.window) {
+    state.window = null;
+  }
+  strm.state = null;
+  return Z_OK;
+}
 
-            y.crossVectors( z, x );
+function inflateGetHeader(strm, head) {
+  var state;
 
+  /* check state */
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  if ((state.wrap & 2) === 0) { return Z_STREAM_ERROR; }
 
-            te[0] = x.x; te[4] = y.x; te[8] = z.x;
-            te[1] = x.y; te[5] = y.y; te[9] = z.y;
-            te[2] = x.z; te[6] = y.z; te[10] = z.z;
+  /* save header structure */
+  state.head = head;
+  head.done = false;
+  return Z_OK;
+}
 
-            return this;
-        };
 
-    }(),
+exports.inflateReset = inflateReset;
+exports.inflateReset2 = inflateReset2;
+exports.inflateResetKeep = inflateResetKeep;
+exports.inflateInit = inflateInit;
+exports.inflateInit2 = inflateInit2;
+exports.inflate = inflate;
+exports.inflateEnd = inflateEnd;
+exports.inflateGetHeader = inflateGetHeader;
+exports.inflateInfo = 'pako inflate (from Nodeca project)';
+
+/* Not implemented
+exports.inflateCopy = inflateCopy;
+exports.inflateGetDictionary = inflateGetDictionary;
+exports.inflateMark = inflateMark;
+exports.inflatePrime = inflatePrime;
+exports.inflateSetDictionary = inflateSetDictionary;
+exports.inflateSync = inflateSync;
+exports.inflateSyncPoint = inflateSyncPoint;
+exports.inflateUndermine = inflateUndermine;
+*/
 
-    multiplyMatrices: function ( a, b ) {
-        var ae = a.elements;
-        var be = b.elements;
-        var te = this.elements;
+},{"../utils/common":1,"./adler32":3,"./crc32":5,"./inffast":7,"./inftrees":9}],9:[function(require,module,exports){
+'use strict';
 
-        var a11 = ae[0], a12 = ae[4], a13 = ae[8], a14 = ae[12];
-        var a21 = ae[1], a22 = ae[5], a23 = ae[9], a24 = ae[13];
-        var a31 = ae[2], a32 = ae[6], a33 = ae[10], a34 = ae[14];
-        var a41 = ae[3], a42 = ae[7], a43 = ae[11], a44 = ae[15];
 
-        var b11 = be[0], b12 = be[4], b13 = be[8], b14 = be[12];
-        var b21 = be[1], b22 = be[5], b23 = be[9], b24 = be[13];
-        var b31 = be[2], b32 = be[6], b33 = be[10], b34 = be[14];
-        var b41 = be[3], b42 = be[7], b43 = be[11], b44 = be[15];
+var utils = require('../utils/common');
 
-        te[0] = a11 * b11 + a12 * b21 + a13 * b31 + a14 * b41;
-        te[4] = a11 * b12 + a12 * b22 + a13 * b32 + a14 * b42;
-        te[8] = a11 * b13 + a12 * b23 + a13 * b33 + a14 * b43;
-        te[12] = a11 * b14 + a12 * b24 + a13 * b34 + a14 * b44;
+var MAXBITS = 15;
+var ENOUGH_LENS = 852;
+var ENOUGH_DISTS = 592;
+//var ENOUGH = (ENOUGH_LENS+ENOUGH_DISTS);
 
-        te[1] = a21 * b11 + a22 * b21 + a23 * b31 + a24 * b41;
-        te[5] = a21 * b12 + a22 * b22 + a23 * b32 + a24 * b42;
-        te[9] = a21 * b13 + a22 * b23 + a23 * b33 + a24 * b43;
-        te[13] = a21 * b14 + a22 * b24 + a23 * b34 + a24 * b44;
+var CODES = 0;
+var LENS = 1;
+var DISTS = 2;
 
-        te[2] = a31 * b11 + a32 * b21 + a33 * b31 + a34 * b41;
-        te[6] = a31 * b12 + a32 * b22 + a33 * b32 + a34 * b42;
-        te[10] = a31 * b13 + a32 * b23 + a33 * b33 + a34 * b43;
-        te[14] = a31 * b14 + a32 * b24 + a33 * b34 + a34 * b44;
+var lbase = [ /* Length codes 257..285 base */
+  3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
+  35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0
+];
 
-        te[3] = a41 * b11 + a42 * b21 + a43 * b31 + a44 * b41;
-        te[7] = a41 * b12 + a42 * b22 + a43 * b32 + a44 * b42;
-        te[11] = a41 * b13 + a42 * b23 + a43 * b33 + a44 * b43;
-        te[15] = a41 * b14 + a42 * b24 + a43 * b34 + a44 * b44;
+var lext = [ /* Length codes 257..285 extra */
+  16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
+  19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78
+];
 
-        return this;
-    },
-    
-    multiplyScalar: function ( s ) {
-        var te = this.elements;
-    
-        te[0] *= s; te[4] *= s; te[8] *= s; te[12] *= s;
-        te[1] *= s; te[5] *= s; te[9] *= s; te[13] *= s;
-        te[2] *= s; te[6] *= s; te[10] *= s; te[14] *= s;
-        te[3] *= s; te[7] *= s; te[11] *= s; te[15] *= s;
-    
-        return this;
-    },
-    
-    transpose: function () {
-        var te = this.elements;
-        var tmp;
+var dbase = [ /* Distance codes 0..29 base */
+  1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
+  257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
+  8193, 12289, 16385, 24577, 0, 0
+];
 
-        tmp = te[1]; te[1] = te[4]; te[4] = tmp;
-        tmp = te[2]; te[2] = te[8]; te[8] = tmp;
-        tmp = te[6]; te[6] = te[9]; te[9] = tmp;
+var dext = [ /* Distance codes 0..29 extra */
+  16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
+  23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
+  28, 28, 29, 29, 64, 64
+];
 
-        tmp = te[3]; te[3] = te[12]; te[12] = tmp;
-        tmp = te[7]; te[7] = te[13]; te[13] = tmp;
-        tmp = te[11]; te[11] = te[14]; te[14] = tmp;
+module.exports = function inflate_table(type, lens, lens_index, codes, table, table_index, work, opts)
+{
+  var bits = opts.bits;
+      //here = opts.here; /* table entry for duplication */
+
+  var len = 0;               /* a code's length in bits */
+  var sym = 0;               /* index of code symbols */
+  var min = 0, max = 0;          /* minimum and maximum code lengths */
+  var root = 0;              /* number of index bits for root table */
+  var curr = 0;              /* number of index bits for current table */
+  var drop = 0;              /* code bits to drop for sub-table */
+  var left = 0;                   /* number of prefix codes available */
+  var used = 0;              /* code entries in table used */
+  var huff = 0;              /* Huffman code */
+  var incr;              /* for incrementing code, index */
+  var fill;              /* index for replicating entries */
+  var low;               /* low bits for current root entry */
+  var mask;              /* mask for low root bits */
+  var next;             /* next available space in table */
+  var base = null;     /* base value table to use */
+  var base_index = 0;
+//  var shoextra;    /* extra bits table to use */
+  var end;                    /* use base and extra for symbol > end */
+  var count = new utils.Buf16(MAXBITS+1); //[MAXBITS+1];    /* number of codes of each length */
+  var offs = new utils.Buf16(MAXBITS+1); //[MAXBITS+1];     /* offsets in table for each length */
+  var extra = null;
+  var extra_index = 0;
+
+  var here_bits, here_op, here_val;
+
+  /*
+   Process a set of code lengths to create a canonical Huffman code.  The
+   code lengths are lens[0..codes-1].  Each length corresponds to the
+   symbols 0..codes-1.  The Huffman code is generated by first sorting the
+   symbols by length from short to long, and retaining the symbol order
+   for codes with equal lengths.  Then the code starts with all zero bits
+   for the first code of the shortest length, and the codes are integer
+   increments for the same length, and zeros are appended as the length
+   increases.  For the deflate format, these bits are stored backwards
+   from their more natural integer increment ordering, and so when the
+   decoding tables are built in the large loop below, the integer codes
+   are incremented backwards.
+
+   This routine assumes, but does not check, that all of the entries in
+   lens[] are in the range 0..MAXBITS.  The caller must assure this.
+   1..MAXBITS is interpreted as that code length.  zero means that that
+   symbol does not occur in this code.
+
+   The codes are sorted by computing a count of codes for each length,
+   creating from that a table of starting indices for each length in the
+   sorted table, and then entering the symbols in order in the sorted
+   table.  The sorted table is work[], with that space being provided by
+   the caller.
+
+   The length counts are used for other purposes as well, i.e. finding
+   the minimum and maximum length codes, determining if there are any
+   codes at all, checking for a valid set of lengths, and looking ahead
+   at length counts to determine sub-table sizes when building the
+   decoding tables.
+   */
+
+  /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
+  for (len = 0; len <= MAXBITS; len++) {
+    count[len] = 0;
+  }
+  for (sym = 0; sym < codes; sym++) {
+    count[lens[lens_index + sym]]++;
+  }
+
+  /* bound code lengths, force root to be within code lengths */
+  root = bits;
+  for (max = MAXBITS; max >= 1; max--) {
+    if (count[max] !== 0) { break; }
+  }
+  if (root > max) {
+    root = max;
+  }
+  if (max === 0) {                     /* no symbols to code at all */
+    //table.op[opts.table_index] = 64;  //here.op = (var char)64;    /* invalid code marker */
+    //table.bits[opts.table_index] = 1;   //here.bits = (var char)1;
+    //table.val[opts.table_index++] = 0;   //here.val = (var short)0;
+    table[table_index++] = (1 << 24) | (64 << 16) | 0;
+
+
+    //table.op[opts.table_index] = 64;
+    //table.bits[opts.table_index] = 1;
+    //table.val[opts.table_index++] = 0;
+    table[table_index++] = (1 << 24) | (64 << 16) | 0;
+
+    opts.bits = 1;
+    return 0;     /* no symbols, but wait for decoding to report error */
+  }
+  for (min = 1; min < max; min++) {
+    if (count[min] !== 0) { break; }
+  }
+  if (root < min) {
+    root = min;
+  }
+
+  /* check for an over-subscribed or incomplete set of lengths */
+  left = 1;
+  for (len = 1; len <= MAXBITS; len++) {
+    left <<= 1;
+    left -= count[len];
+    if (left < 0) {
+      return -1;
+    }        /* over-subscribed */
+  }
+  if (left > 0 && (type === CODES || max !== 1)) {
+    return -1;                      /* incomplete set */
+  }
+
+  /* generate offsets into symbol table for each length for sorting */
+  offs[1] = 0;
+  for (len = 1; len < MAXBITS; len++) {
+    offs[len + 1] = offs[len] + count[len];
+  }
+
+  /* sort symbols by length, by symbol order within each length */
+  for (sym = 0; sym < codes; sym++) {
+    if (lens[lens_index + sym] !== 0) {
+      work[offs[lens[lens_index + sym]]++] = sym;
+    }
+  }
+
+  /*
+   Create and fill in decoding tables.  In this loop, the table being
+   filled is at next and has curr index bits.  The code being used is huff
+   with length len.  That code is converted to an index by dropping drop
+   bits off of the bottom.  For codes where len is less than drop + curr,
+   those top drop + curr - len bits are incremented through all values to
+   fill the table with replicated entries.
+
+   root is the number of index bits for the root table.  When len exceeds
+   root, sub-tables are created pointed to by the root entry with an index
+   of the low root bits of huff.  This is saved in low to check for when a
+   new sub-table should be started.  drop is zero when the root table is
+   being filled, and drop is root when sub-tables are being filled.
+
+   When a new sub-table is needed, it is necessary to look ahead in the
+   code lengths to determine what size sub-table is needed.  The length
+   counts are used for this, and so count[] is decremented as codes are
+   entered in the tables.
+
+   used keeps track of how many table entries have been allocated from the
+   provided *table space.  It is checked for LENS and DIST tables against
+   the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
+   the initial root table size constants.  See the comments in inftrees.h
+   for more information.
+
+   sym increments through all symbols, and the loop terminates when
+   all codes of length max, i.e. all codes, have been processed.  This
+   routine permits incomplete codes, so another loop after this one fills
+   in the rest of the decoding tables with invalid code markers.
+   */
+
+  /* set up for code type */
+  // poor man optimization - use if-else instead of switch,
+  // to avoid deopts in old v8
+  if (type === CODES) {
+    base = extra = work;    /* dummy value--not used */
+    end = 19;
+
+  } else if (type === LENS) {
+    base = lbase;
+    base_index -= 257;
+    extra = lext;
+    extra_index -= 257;
+    end = 256;
+
+  } else {                    /* DISTS */
+    base = dbase;
+    extra = dext;
+    end = -1;
+  }
+
+  /* initialize opts for loop */
+  huff = 0;                   /* starting code */
+  sym = 0;                    /* starting code symbol */
+  len = min;                  /* starting code length */
+  next = table_index;              /* current table to fill in */
+  curr = root;                /* current table index bits */
+  drop = 0;                   /* current bits to drop from code for index */
+  low = -1;                   /* trigger new sub-table when len > root */
+  used = 1 << root;          /* use root table entries */
+  mask = used - 1;            /* mask for comparing low */
+
+  /* check available table space */
+  if ((type === LENS && used > ENOUGH_LENS) ||
+    (type === DISTS && used > ENOUGH_DISTS)) {
+    return 1;
+  }
+
+  var i=0;
+  /* process all codes and make table entries */
+  for (;;) {
+    i++;
+    /* create table entry */
+    here_bits = len - drop;
+    if (work[sym] < end) {
+      here_op = 0;
+      here_val = work[sym];
+    }
+    else if (work[sym] > end) {
+      here_op = extra[extra_index + work[sym]];
+      here_val = base[base_index + work[sym]];
+    }
+    else {
+      here_op = 32 + 64;         /* end of block */
+      here_val = 0;
+    }
 
-        return this;
-    },
+    /* replicate for those indices with low len bits equal to huff */
+    incr = 1 << (len - drop);
+    fill = 1 << curr;
+    min = fill;                 /* save offset to next table */
+    do {
+      fill -= incr;
+      table[next + (huff >> drop) + fill] = (here_bits << 24) | (here_op << 16) | here_val |0;
+    } while (fill !== 0);
+
+    /* backwards increment the len-bit code huff */
+    incr = 1 << (len - 1);
+    while (huff & incr) {
+      incr >>= 1;
+    }
+    if (incr !== 0) {
+      huff &= incr - 1;
+      huff += incr;
+    } else {
+      huff = 0;
+    }
 
-    getPosition: function() {
-        var v1 = new $3Dmol.Vector3();
+    /* go to next symbol, update count, len */
+    sym++;
+    if (--count[len] === 0) {
+      if (len === max) { break; }
+      len = lens[lens_index + work[sym]];
+    }
 
-        return function () {
+    /* create new sub-table if needed */
+    if (len > root && (huff & mask) !== low) {
+      /* if first time, transition to sub-tables */
+      if (drop === 0) {
+        drop = root;
+      }
+
+      /* increment past last table */
+      next += min;            /* here min is 1 << curr */
+
+      /* determine length of next table */
+      curr = len - drop;
+      left = 1 << curr;
+      while (curr + drop < max) {
+        left -= count[curr + drop];
+        if (left <= 0) { break; }
+        curr++;
+        left <<= 1;
+      }
+
+      /* check for enough space */
+      used += 1 << curr;
+      if ((type === LENS && used > ENOUGH_LENS) ||
+        (type === DISTS && used > ENOUGH_DISTS)) {
+        return 1;
+      }
+
+      /* point entry in root table to sub-table */
+      low = huff & mask;
+      /*table.op[low] = curr;
+      table.bits[low] = root;
+      table.val[low] = next - opts.table_index;*/
+      table[low] = (root << 24) | (curr << 16) | (next - table_index) |0;
+    }
+  }
+
+  /* fill in remaining table entry if code is incomplete (guaranteed to have
+   at most one remaining entry, since if the code is incomplete, the
+   maximum code length that was allowed to get this far is one bit) */
+  if (huff !== 0) {
+    //table.op[next + huff] = 64;            /* invalid code marker */
+    //table.bits[next + huff] = len - drop;
+    //table.val[next + huff] = 0;
+    table[next + huff] = ((len - drop) << 24) | (64 << 16) |0;
+  }
+
+  /* set return parameters */
+  //opts.table_index += used;
+  opts.bits = root;
+  return 0;
+};
 
-            console.warn( 'DEPRECATED: Matrix4\'s .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.' );
+},{"../utils/common":1}],10:[function(require,module,exports){
+'use strict';
+
+module.exports = {
+  '2':    'need dictionary',     /* Z_NEED_DICT       2  */
+  '1':    'stream end',          /* Z_STREAM_END      1  */
+  '0':    '',                    /* Z_OK              0  */
+  '-1':   'file error',          /* Z_ERRNO         (-1) */
+  '-2':   'stream error',        /* Z_STREAM_ERROR  (-2) */
+  '-3':   'data error',          /* Z_DATA_ERROR    (-3) */
+  '-4':   'insufficient memory', /* Z_MEM_ERROR     (-4) */
+  '-5':   'buffer error',        /* Z_BUF_ERROR     (-5) */
+  '-6':   'incompatible version' /* Z_VERSION_ERROR (-6) */
+};
 
-            var te = this.elements;
-            return v1.set( te[12], te[13], te[14] );
-        };
+},{}],11:[function(require,module,exports){
+'use strict';
+
+
+function ZStream() {
+  /* next input byte */
+  this.input = null; // JS specific, because we have no pointers
+  this.next_in = 0;
+  /* number of bytes available at input */
+  this.avail_in = 0;
+  /* total number of input bytes read so far */
+  this.total_in = 0;
+  /* next output byte should be put there */
+  this.output = null; // JS specific, because we have no pointers
+  this.next_out = 0;
+  /* remaining free space at output */
+  this.avail_out = 0;
+  /* total number of bytes output so far */
+  this.total_out = 0;
+  /* last error message, NULL if no error */
+  this.msg = ''/*Z_NULL*/;
+  /* not visible by applications */
+  this.state = null;
+  /* best guess about the data type: binary or text */
+  this.data_type = 2/*Z_UNKNOWN*/;
+  /* adler32 value of the uncompressed data */
+  this.adler = 0;
+}
 
-    }(),
+module.exports = ZStream;
 
-    setPosition: function ( v ) {
-        var te = this.elements;
+},{}],"/lib/inflate.js":[function(require,module,exports){
+'use strict';
 
-        te[12] = v.x;
-        te[13] = v.y;
-        te[14] = v.z;
 
-        return this;
-    },
-
-    getInverse: function ( m, throwOnInvertible ) {
-        // based on http://www.euclideanspace.com/maths/algebra/matrix/functions/inverse/fourD/index.htm
-        var te = this.elements;
-        var me = m.elements;
-
-        var n11 = me[0], n12 = me[4], n13 = me[8], n14 = me[12];
-        var n21 = me[1], n22 = me[5], n23 = me[9], n24 = me[13];
-        var n31 = me[2], n32 = me[6], n33 = me[10], n34 = me[14];
-        var n41 = me[3], n42 = me[7], n43 = me[11], n44 = me[15];
-
-        te[0] = n23*n34*n42 - n24*n33*n42 + n24*n32*n43 - n22*n34*n43 - n23*n32*n44 + n22*n33*n44;
-        te[4] = n14*n33*n42 - n13*n34*n42 - n14*n32*n43 + n12*n34*n43 + n13*n32*n44 - n12*n33*n44;
-        te[8] = n13*n24*n42 - n14*n23*n42 + n14*n22*n43 - n12*n24*n43 - n13*n22*n44 + n12*n23*n44;
-        te[12] = n14*n23*n32 - n13*n24*n32 - n14*n22*n33 + n12*n24*n33 + n13*n22*n34 - n12*n23*n34;
-        te[1] = n24*n33*n41 - n23*n34*n41 - n24*n31*n43 + n21*n34*n43 + n23*n31*n44 - n21*n33*n44;
-        te[5] = n13*n34*n41 - n14*n33*n41 + n14*n31*n43 - n11*n34*n43 - n13*n31*n44 + n11*n33*n44;
-        te[9] = n14*n23*n41 - n13*n24*n41 - n14*n21*n43 + n11*n24*n43 + n13*n21*n44 - n11*n23*n44;
-        te[13] = n13*n24*n31 - n14*n23*n31 + n14*n21*n33 - n11*n24*n33 - n13*n21*n34 + n11*n23*n34;
-        te[2] = n22*n34*n41 - n24*n32*n41 + n24*n31*n42 - n21*n34*n42 - n22*n31*n44 + n21*n32*n44;
-        te[6] = n14*n32*n41 - n12*n34*n41 - n14*n31*n42 + n11*n34*n42 + n12*n31*n44 - n11*n32*n44;
-        te[10] = n12*n24*n41 - n14*n22*n41 + n14*n21*n42 - n11*n24*n42 - n12*n21*n44 + n11*n22*n44;
-        te[14] = n14*n22*n31 - n12*n24*n31 - n14*n21*n32 + n11*n24*n32 + n12*n21*n34 - n11*n22*n34;
-        te[3] = n23*n32*n41 - n22*n33*n41 - n23*n31*n42 + n21*n33*n42 + n22*n31*n43 - n21*n32*n43;
-        te[7] = n12*n33*n41 - n13*n32*n41 + n13*n31*n42 - n11*n33*n42 - n12*n31*n43 + n11*n32*n43;
-        te[11] = n13*n22*n41 - n12*n23*n41 - n13*n21*n42 + n11*n23*n42 + n12*n21*n43 - n11*n22*n43;
-        te[15] = n12*n23*n31 - n13*n22*n31 + n13*n21*n32 - n11*n23*n32 - n12*n21*n33 + n11*n22*n33;
+var zlib_inflate = require('./zlib/inflate.js');
+var utils = require('./utils/common');
+var strings = require('./utils/strings');
+var c = require('./zlib/constants');
+var msg = require('./zlib/messages');
+var zstream = require('./zlib/zstream');
+var gzheader = require('./zlib/gzheader');
 
-        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 4 ] + me[ 2 ] * te[ 8 ] + me[ 3 ] * te[ 12 ];
+var toString = Object.prototype.toString;
 
-        if ( det === 0 ) {
+/**
+ * class Inflate
+ *
+ * Generic JS-style wrapper for zlib calls. If you don't need
+ * streaming behaviour - use more simple functions: [[inflate]]
+ * and [[inflateRaw]].
+ **/
 
-            var msg = "Matrix4.getInverse(): can't invert matrix, determinant is 0";
+/* internal
+ * inflate.chunks -> Array
+ *
+ * Chunks of output data, if [[Inflate#onData]] not overriden.
+ **/
 
-            if ( throwOnInvertible || false ) {
+/**
+ * Inflate.result -> Uint8Array|Array|String
+ *
+ * Uncompressed result, generated by default [[Inflate#onData]]
+ * and [[Inflate#onEnd]] handlers. Filled after you push last chunk
+ * (call [[Inflate#push]] with `Z_FINISH` / `true` param) or if you
+ * push a chunk with explicit flush (call [[Inflate#push]] with
+ * `Z_SYNC_FLUSH` param).
+ **/
 
-                throw new Error( msg ); 
+/**
+ * Inflate.err -> Number
+ *
+ * Error code after inflate finished. 0 (Z_OK) on success.
+ * Should be checked if broken data possible.
+ **/
 
-            } else {
+/**
+ * Inflate.msg -> String
+ *
+ * Error message, if [[Inflate.err]] != 0
+ **/
 
-                console.warn( msg );
 
-            }
+/**
+ * new Inflate(options)
+ * - options (Object): zlib inflate options.
+ *
+ * Creates new inflator instance with specified params. Throws exception
+ * on bad params. Supported options:
+ *
+ * - `windowBits`
+ *
+ * [http://zlib.net/manual.html#Advanced](http://zlib.net/manual.html#Advanced)
+ * for more information on these.
+ *
+ * Additional options, for internal needs:
+ *
+ * - `chunkSize` - size of generated data chunks (16K by default)
+ * - `raw` (Boolean) - do raw inflate
+ * - `to` (String) - if equal to 'string', then result will be converted
+ *   from utf8 to utf16 (javascript) string. When string output requested,
+ *   chunk length can differ from `chunkSize`, depending on content.
+ *
+ * By default, when no options set, autodetect deflate/gzip data format via
+ * wrapper header.
+ *
+ * ##### Example:
+ *
+ * ```javascript
+ * var pako = require('pako')
+ *   , chunk1 = Uint8Array([1,2,3,4,5,6,7,8,9])
+ *   , chunk2 = Uint8Array([10,11,12,13,14,15,16,17,18,19]);
+ *
+ * var inflate = new pako.Inflate({ level: 3});
+ *
+ * inflate.push(chunk1, false);
+ * inflate.push(chunk2, true);  // true -> last chunk
+ *
+ * if (inflate.err) { throw new Error(inflate.err); }
+ *
+ * console.log(inflate.result);
+ * ```
+ **/
+var Inflate = function(options) {
+
+  this.options = utils.assign({
+    chunkSize: 16384,
+    windowBits: 0,
+    to: ''
+  }, options || {});
+
+  var opt = this.options;
+
+  // Force window size for `raw` data, if not set directly,
+  // because we have no header for autodetect.
+  if (opt.raw && (opt.windowBits >= 0) && (opt.windowBits < 16)) {
+    opt.windowBits = -opt.windowBits;
+    if (opt.windowBits === 0) { opt.windowBits = -15; }
+  }
+
+  // If `windowBits` not defined (and mode not raw) - set autodetect flag for gzip/deflate
+  if ((opt.windowBits >= 0) && (opt.windowBits < 16) &&
+      !(options && options.windowBits)) {
+    opt.windowBits += 32;
+  }
+
+  // Gzip header has no info about windows size, we can do autodetect only
+  // for deflate. So, if window size not set, force it to max when gzip possible
+  if ((opt.windowBits > 15) && (opt.windowBits < 48)) {
+    // bit 3 (16) -> gzipped data
+    // bit 4 (32) -> autodetect gzip/deflate
+    if ((opt.windowBits & 15) === 0) {
+      opt.windowBits |= 15;
+    }
+  }
 
-            this.identity();
+  this.err    = 0;      // error code, if happens (0 = Z_OK)
+  this.msg    = '';     // error message
+  this.ended  = false;  // used to avoid multiple onEnd() calls
+  this.chunks = [];     // chunks of compressed data
 
-            return this;
-        }
+  this.strm   = new zstream();
+  this.strm.avail_out = 0;
 
-        this.multiplyScalar( 1 / det );
+  var status  = zlib_inflate.inflateInit2(
+    this.strm,
+    opt.windowBits
+  );
 
-        return this;
-    },
+  if (status !== c.Z_OK) {
+    throw new Error(msg[status]);
+  }
 
-    compose: function() {
-        var mRotation = new $3Dmol.Matrix4(),
-            mScale = new $3Dmol.Matrix4();
-        
-        return function ( translation, rotation, scale ) {
+  this.header = new gzheader();
 
-            var te = this.elements;
+  zlib_inflate.inflateGetHeader(this.strm, this.header);
+};
 
-            mRotation.identity();
-            mRotation.setRotationFromQuaternion( rotation );
+/**
+ * Inflate#push(data[, mode]) -> Boolean
+ * - data (Uint8Array|Array|ArrayBuffer|String): input data
+ * - mode (Number|Boolean): 0..6 for corresponding Z_NO_FLUSH..Z_TREE modes.
+ *   See constants. Skipped or `false` means Z_NO_FLUSH, `true` meansh Z_FINISH.
+ *
+ * Sends input data to inflate pipe, generating [[Inflate#onData]] calls with
+ * new output chunks. Returns `true` on success. The last data block must have
+ * mode Z_FINISH (or `true`). That will flush internal pending buffers and call
+ * [[Inflate#onEnd]]. For interim explicit flushes (without ending the stream) you
+ * can use mode Z_SYNC_FLUSH, keeping the decompression context.
+ *
+ * On fail call [[Inflate#onEnd]] with error code and return false.
+ *
+ * We strongly recommend to use `Uint8Array` on input for best speed (output
+ * format is detected automatically). Also, don't skip last param and always
+ * use the same type in your code (boolean or number). That will improve JS speed.
+ *
+ * For regular `Array`-s make sure all elements are [0..255].
+ *
+ * ##### Example
+ *
+ * ```javascript
+ * push(chunk, false); // push one of data chunks
+ * ...
+ * push(chunk, true);  // push last chunk
+ * ```
+ **/
+Inflate.prototype.push = function(data, mode) {
+  var strm = this.strm;
+  var chunkSize = this.options.chunkSize;
+  var status, _mode;
+  var next_out_utf8, tail, utf8str;
+
+  if (this.ended) { return false; }
+  _mode = (mode === ~~mode) ? mode : ((mode === true) ? c.Z_FINISH : c.Z_NO_FLUSH);
+
+  // Convert data if needed
+  if (typeof data === 'string') {
+    // Only binary strings can be decompressed on practice
+    strm.input = strings.binstring2buf(data);
+  } else if (toString.call(data) === '[object ArrayBuffer]') {
+    strm.input = new Uint8Array(data);
+  } else {
+    strm.input = data;
+  }
+
+  strm.next_in = 0;
+  strm.avail_in = strm.input.length;
+
+  do {
+    if (strm.avail_out === 0) {
+      strm.output = new utils.Buf8(chunkSize);
+      strm.next_out = 0;
+      strm.avail_out = chunkSize;
+    }
 
-            mScale.makeScale( scale.x, scale.y, scale.z );
+    status = zlib_inflate.inflate(strm, c.Z_NO_FLUSH);    /* no bad return value */
 
-            this.multiplyMatrices( mRotation, mScale );
+    if (status !== c.Z_STREAM_END && status !== c.Z_OK) {
+      this.onEnd(status);
+      this.ended = true;
+      return false;
+    }
 
-            te[12] = translation.x;
-            te[13] = translation.y;
-            te[14] = translation.z;
+    if (strm.next_out) {
+      if (strm.avail_out === 0 || status === c.Z_STREAM_END || (strm.avail_in === 0 && (_mode === c.Z_FINISH || _mode === c.Z_SYNC_FLUSH))) {
 
-            return this;
+        if (this.options.to === 'string') {
 
-        };
-    }(),
+          next_out_utf8 = strings.utf8border(strm.output, strm.next_out);
 
-    decompose: function() {
-        var x = new $3Dmol.Vector3(),
-            y = new $3Dmol.Vector3(),
-            z = new $3Dmol.Vector3(),
-            matrix = new $3Dmol.Matrix4();
+          tail = strm.next_out - next_out_utf8;
+          utf8str = strings.buf2string(strm.output, next_out_utf8);
 
-        return function ( translation, rotation, scale ) {
+          // move tail
+          strm.next_out = tail;
+          strm.avail_out = chunkSize - tail;
+          if (tail) { utils.arraySet(strm.output, strm.output, next_out_utf8, tail, 0); }
 
-            var te = this.elements;
+          this.onData(utf8str);
 
-            // grab the axis vectors
-            x.set( te[0], te[1], te[2] );
-            y.set( te[4], te[5], te[6] );
-            z.set( te[8], te[9], te[10] );
+        } else {
+          this.onData(utils.shrinkBuf(strm.output, strm.next_out));
+        }
+      }
+    }
+  } while ((strm.avail_in > 0) && status !== c.Z_STREAM_END);
+
+  if (status === c.Z_STREAM_END) {
+    _mode = c.Z_FINISH;
+  }
+
+  // Finalize on the last chunk.
+  if (_mode === c.Z_FINISH) {
+    status = zlib_inflate.inflateEnd(this.strm);
+    this.onEnd(status);
+    this.ended = true;
+    return status === c.Z_OK;
+  }
+
+  // callback interim results if Z_SYNC_FLUSH.
+  if (_mode === c.Z_SYNC_FLUSH) {
+    this.onEnd(c.Z_OK);
+    strm.avail_out = 0;
+    return true;
+  }
+
+  return true;
+};
 
-            translation = ( translation instanceof $3Dmol.Vector3 ) ? translation : new $3Dmol.Vector3();
-            rotation = ( rotation instanceof $3Dmol.Quaternion ) ? rotation : new $3Dmol.Quaternion();
-            scale = ( scale instanceof $3Dmol.Vector3 ) ? scale : new $3Dmol.Vector3();
 
-            scale.x = x.length();
-            scale.y = y.length();
-            scale.z = z.length();
+/**
+ * Inflate#onData(chunk) -> Void
+ * - chunk (Uint8Array|Array|String): ouput data. Type of array depends
+ *   on js engine support. When string output requested, each chunk
+ *   will be string.
+ *
+ * By default, stores data blocks in `chunks[]` property and glue
+ * those in `onEnd`. Override this handler, if you need another behaviour.
+ **/
+Inflate.prototype.onData = function(chunk) {
+  this.chunks.push(chunk);
+};
 
-            translation.x = te[12];
-            translation.y = te[13];
-            translation.z = te[14];
 
-            // scale the rotation part
+/**
+ * Inflate#onEnd(status) -> Void
+ * - status (Number): inflate status. 0 (Z_OK) on success,
+ *   other if not.
+ *
+ * Called either after you tell inflate that the input stream is
+ * complete (Z_FINISH) or should be flushed (Z_SYNC_FLUSH)
+ * or if an error happened. By default - join collected chunks,
+ * free memory and fill `results` / `err` properties.
+ **/
+Inflate.prototype.onEnd = function(status) {
+  // On success - join
+  if (status === c.Z_OK) {
+    if (this.options.to === 'string') {
+      // Glue & convert here, until we teach pako to send
+      // utf8 alligned strings to onData
+      this.result = this.chunks.join('');
+    } else {
+      this.result = utils.flattenChunks(this.chunks);
+    }
+  }
+  this.chunks = [];
+  this.err = status;
+  this.msg = this.strm.msg;
+};
 
-            matrix.copy( this );
 
-            matrix.elements[0] /= scale.x;
-            matrix.elements[1] /= scale.x;
-            matrix.elements[2] /= scale.x;
+/**
+ * inflate(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * Decompress `data` with inflate/ungzip and `options`. Autodetect
+ * format via wrapper header by default. That's why we don't provide
+ * separate `ungzip` method.
+ *
+ * Supported options are:
+ *
+ * - windowBits
+ *
+ * [http://zlib.net/manual.html#Advanced](http://zlib.net/manual.html#Advanced)
+ * for more information.
+ *
+ * Sugar (options):
+ *
+ * - `raw` (Boolean) - say that we work with raw stream, if you don't wish to specify
+ *   negative windowBits implicitly.
+ * - `to` (String) - if equal to 'string', then result will be converted
+ *   from utf8 to utf16 (javascript) string. When string output requested,
+ *   chunk length can differ from `chunkSize`, depending on content.
+ *
+ *
+ * ##### Example:
+ *
+ * ```javascript
+ * var pako = require('pako')
+ *   , input = pako.deflate([1,2,3,4,5,6,7,8,9])
+ *   , output;
+ *
+ * try {
+ *   output = pako.inflate(input);
+ * } catch (err)
+ *   console.log(err);
+ * }
+ * ```
+ **/
+function inflate(input, options) {
+  var inflator = new Inflate(options);
+
+  inflator.push(input, true);
+
+  // That will never happens, if you don't cheat with options :)
+  if (inflator.err) { throw inflator.msg; }
+
+  return inflator.result;
+}
 
-            matrix.elements[4] /= scale.y;
-            matrix.elements[5] /= scale.y;
-            matrix.elements[6] /= scale.y;
 
-            matrix.elements[8] /= scale.z;
-            matrix.elements[9] /= scale.z;
-            matrix.elements[10] /= scale.z;
+/**
+ * inflateRaw(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * The same as [[inflate]], but creates raw data, without wrapper
+ * (header and adler32 crc).
+ **/
+function inflateRaw(input, options) {
+  options = options || {};
+  options.raw = true;
+  return inflate(input, options);
+}
 
-            rotation.setFromRotationMatrix( matrix );
 
-            return [ translation, rotation, scale ];
+/**
+ * ungzip(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * Just shortcut to [[inflate]], because it autodetects format
+ * by header.content. Done for convenience.
+ **/
 
-        };
-    }(),
 
-    scale: function ( v ) {
-        var te = this.elements;
-        var x = v.x, y = v.y, z = v.z;
+exports.Inflate = Inflate;
+exports.inflate = inflate;
+exports.inflateRaw = inflateRaw;
+exports.ungzip  = inflate;
 
-        te[0] *= x; te[4] *= y; te[8] *= z;
-        te[1] *= x; te[5] *= y; te[9] *= z;
-        te[2] *= x; te[6] *= y; te[10] *= z;
-        te[3] *= x; te[7] *= y; te[11] *= z;
+},{"./utils/common":1,"./utils/strings":2,"./zlib/constants":4,"./zlib/gzheader":6,"./zlib/inflate.js":8,"./zlib/messages":10,"./zlib/zstream":11}]},{},[])("/lib/inflate.js")
+});
+//This defines the $3Dmol object which is used to create viewers
+//and configure system-wide settings
 
-        return this;
-    },
+/** 
+ * All of the functionality of $3Dmol.js is contained within the
+ * $3Dmol global namespace
+ * @namespace */
+$3Dmol = (function(window) {
     
-    getMaxScaleOnAxis : function() {
-        
-        var te = this.elements;
-        
-        var scaleXSq = te[0] * te[0] + te[1] * te[1] + te[2] * te[2];
-        var scaleYSq = te[4] * te[4] + te[5] * te[5] + te[6] * te[6];
-        var scaleZSq = te[8] * te[8] + te[9] * te[9] + te[10] * te[10];
-        
-        return Math.sqrt(Math.max(scaleXSq, Math.max(scaleYSq, scaleZSq)));
-        
-    },
+    var my = window['$3Dmol'] || {};
+    //var $ = window['jQuery'];
+    
+    return my;
 
-    makeFrustum: function ( left, right, bottom, top, near, far ) {
-        var te = this.elements;
-        var x = 2 * near / ( right - left );
-        var y = 2 * near / ( top - bottom );
+})(window);
 
-        var a = ( right + left ) / ( right - left );
-        var b = ( top + bottom ) / ( top - bottom );
-        var c = - ( far + near ) / ( far - near );
-        var d = - 2 * far * near / ( far - near );
+/* The following code "phones home" to register that an ip 
+   address has loaded 3Dmol.js.  Being able track this usage
+   is very helpful when reporting to funding agencies.  Please
+   leave this code in if you would like to increase the 
+   likelihood of 3Dmol.js remaining supported.
+*/
+if('https:' != document.location.protocol) { //not willing to pay for ssl cert
+    $.get("http://3dmol.csb.pitt.edu/track/report.cgi");
+}
 
-        te[0] = x;  te[4] = 0;  te[8] = a;  te[12] = 0;
-        te[1] = 0;  te[5] = y;  te[9] = b;  te[13] = 0;
-        te[2] = 0;  te[6] = 0;  te[10] = c; te[14] = d;
-        te[3] = 0;  te[7] = 0;  te[11] = - 1;   te[15] = 0;
+/* shims for IE */
+/*
+IE Doesn't have a .startsWith 
+*/
+if (!String.prototype.startsWith) {
+    String.prototype.startsWith = function (str){
+        return this.lastIndexOf(str, 0) === 0;
+    };
+}
 
-        return this;
-    },
+// or endsWith
+if (!String.prototype.endsWith) {
+    String.prototype.endsWith = function(suffix) {
+        return this.indexOf(suffix, this.length - suffix.length) !== -1;
+    };
+}
+    
+/**
+ * Create and initialize an appropriate viewer at supplied HTML element using specification in config
+ * @param {Object | string} element - Either HTML element or string identifier
+ * @param {ViewerSpec} config Viewer specification
+ * @return {$3Dmol.GLViewer} GLViewer, null if unable to instantiate WebGL
+ * 
+ * @example
+ * // Assume there exists an HTML div with id "gldiv"
+ * var element = $("#gldiv");
+ * 
+ * // Viewer config - properties 'defaultcolors' and 'callback'
+ * var config = {defaultcolors: $3Dmol.rasmolElementColors };
+ * 
+ * // Create GLViewer within 'gldiv' 
+ * var myviewer = $3Dmol.createViewer(element, config);
+ * //'data' is a string containing molecule data in pdb format  
+ * myviewer.addModel(data, "pdb");
+ * myviewer.zoomTo();
+ * myviewer.render();                        
+ *                        
+ */
+$3Dmol.createViewer = function(element, config)
+{
+    if($.type(element) === "string")
+        element = $("#"+element);
+    if(!element) return;
 
-    makePerspective: function ( fov, aspect, near, far ) {
-        var ymax = near * Math.tan( $3Dmol.Math.degToRad( fov * 0.5 ) );
-        var ymin = - ymax;
-        var xmin = ymin * aspect;
-        var xmax = ymax * aspect;
+    config = config || {}; 
 
-        return this.makeFrustum( xmin, xmax, ymin, ymax, near, far );
-    },
+    //try to create the  viewer
+    try {
+        return new $3Dmol.GLViewer(element, config);
+    }
+    catch(e) {
+        throw "error creating viewer: "+e;
+    }
     
-    isEqual : function (m) {
-        var me = m.elements;
-        var te = this.elements;
-        
-        if (te[0] == me[0] && te[4] == me[4] && te[8] == me[8] && te[12] == me[12] &&
-            te[1] == me[1] && te[5] == me[5] && te[9] == me[9] && te[13] == me[13] &&
-            te[2] == me[2] && te[6] == me[6] && te[10] == me[10] && te[14] == me[14] &&
-            te[3] == me[3] && te[7] == me[7] && te[11] == me[11] && te[15] == me[15]) {
-            return true;
+    return null;
+};
+   
+/**
+ * Contains a dictionary of embedded viewers created from HTML elements
+ * with a the viewer_3Dmoljs css class indexed by their id (or numerically
+ * if they do not have an id).
+*/
+$3Dmol.viewers = {};
+
+/**
+ * Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model
+ * 
+ * @function $3Dmol.download
+ * @param {string} query - String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively
+ * @param {$3Dmol.GLViewer} viewer - Add new model to existing viewer
+ * @param {Object} options - Specify additional options
+ *                           format: file format to download, if multiple are available, default format is pdb
+ *                           pdbUri: URI to retrieve PDB files, default URI is http://www.rcsb.org/pdb/files/
+ * @param {Function} callback - Function to call with model as argument after data is loaded.
+
+ * @example
+ * var myviewer = $3Dmol.createViewer(gldiv);
+ * 
+ * // GLModel 'm' created and loaded into glviewer for PDB id 2POR
+ * // Note that m will not contain the atomic data until after the network request is completed
+ * var m = $3Dmol.download('pdb: 2POR', myviewer, {format:'cif'});
+ * 
+ * @return {$3Dmol.GLModel} GLModel
+ */ 
+$3Dmol.download = function(query, viewer, options, callback) {
+    var baseURL = '';
+    var type = "";
+    var pdbUri = "";
+    var m = viewer.addModel();
+    if (query.substr(0, 4) === 'pdb:') {
+        pdbUri = options && options.pdbUri ? options.pdbUri : "http://www.rcsb.org/pdb/files/";
+        type = options && options.format ? options.format : "pdb";
+        query = query.substr(4).toUpperCase();
+        if (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) {
+           alert("Wrong PDB ID"); return;
         }
-        else {
-            return false;
+        if (options && options.format)
+            uri = pdbUri + query + "." + options.format;
+        else
+            uri = pdbUri + query + ".pdb";
+
+    } else if (query.substr(0, 4) == 'cid:') {
+        type = "sdf";
+        query = query.substr(4);
+        if (!query.match(/^[0-9]+$/)) {
+           alert("Wrong Compound ID"); return;
         }
-    },
+        uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query + 
+          "/SDF?record_type=3d";
+    }
 
-    clone: function () {
-        var te = this.elements;
+   $.get(uri, function(ret) {
+      m.addMolData(ret, type, options);
+      viewer.zoomTo();
+      viewer.render();
+      if(callback) callback(m);
 
-        return new $3Dmol.Matrix4(
+   });
+   
+   return m;
+};
+       
 
-            te[0], te[4], te[8], te[12],
-            te[1], te[5], te[9], te[13],
-            te[2], te[6], te[10], te[14],
-            te[3], te[7], te[11], te[15]
+/**
+ * $3Dmol surface types
+ * @enum {number}
+ */
+$3Dmol.SurfaceType = {
+    VDW : 1,
+    MS : 2,
+    SAS : 3,
+    SES  : 4
+};
 
-        );
-    },
+
+//Miscellaneous functions and classes - to be incorporated into $3Dmol proper
+/**
+ * 
+ * @param {$3Dmol.Geometry} geometry
+ * @param {$3Dmol.Mesh} mesh
+ * @returns {undefined}
+ */
+$3Dmol.mergeGeos = function(geometry, mesh) {
     
-    isIdentity: function () {
-        var te = this.elements;
-        
-        if (te[0] == 1 && te[4] == 0 && te[8] == 0 && te[12] == 0 &&
-            te[1] == 0 && te[5] == 1 && te[9] == 0 && te[13] == 0 &&
-            te[2] == 0 && te[6] == 0 && te[10] == 1 && te[14] == 0 &&
-            te[3] == 0 && te[7] == 0 && te[11] == 0 && te[15] == 1) {
+    var meshGeo = mesh.geometry;
+    
+    if (meshGeo === undefined) 
+        return;
+    
+    geometry.geometryGroups.push( meshGeo.geometryGroups[0] );
+    
+};
+
+$3Dmol.multiLineString = function(f) {
+    return f.toString()
+            .replace(/^[^\/]+\/\*!?/, '')
+            .replace(/\*\/[^\/]+$/, '');
+            
+};
+
+/** 
+ * Render surface synchronously if true
+ * @param {boolean} [$3Dmol.SyncSurface=false]
+ * @type {boolean} */
+$3Dmol.syncSurface = false;
+
+// Internet Explorer refuses to allow webworkers in data blobs.  I can find
+// no way of checking for this feature directly, so must do a brower check
+if(window.navigator.userAgent.indexOf('MSIE ') >= 0 ||
+        window.navigator.userAgent.indexOf('Trident/') >= 0) {
+    $3Dmol.syncSurface = true; // can't use webworkers
+}
+
+/**
+ * Parse a string that represents a style or atom selection and convert it
+ * into an object.  The goal is to make it easier to write out these specifications
+ * without resorting to json. Objects cannot be defined recursively.
+ * ; - delineates fields of the object 
+ * : - if the field has a value other than an empty object, it comes after a colon
+ * , - delineates key/value pairs of a value object
+ *     If the value object consists of ONLY keys (no = present) the keys are 
+ *     converted to a list.  Otherwise a object of key/value pairs is created with
+ *     any missing values set to null
+ * = OR ~ - separates key/value pairs of a value object, if not provided value is null
+ *     twiddle is supported since = has special meaning in URLs
+ * @param (String) str
+ * @returns {Object}
+ */
+$3Dmol.specStringToObject = function(str) {
+    if(typeof(str) === "object") {
+        return str; //not string, assume was converted already
+    }
+    else if(typeof(str) === "undefined" || str == null) {
+        return str; 
+    }
+    
+    str = str.replace(/%7E/,'~'); //copy/pasting urls sometimes does this
+    //convert things that look like numbers into numbers
+    var massage = function(val) {
+        if($.isNumeric(val)) {
+           //hexadecimal does not parse as float
+           if(Math.floor(parseFloat(val)) == parseInt(val)) {
+              return parseFloat(val);
+           }
+           else if(val.indexOf('.') >= 0) {
+               return parseFloat(val); // ".7" for example, does not parseInt
+           }
+           else {
+               return parseInt(val);
+           }
+        }
+        //boolean conversions
+        else if(val === 'true') {
             return true;
         }
-        else {
+        else if(val === 'false') {
             return false;
         }
+        return val;
     }
     
-};
-/** @constructor */
-$3Dmol.Ray = function(origin, direction) {
+    var ret = {};
+    var fields = str.split(';');
+    for(var i = 0; i < fields.length; i++) {
+        var fv = fields[i].split(':');
+        var f = fv[0];
+        var val = {};
+        var vstr = fv[1];
+        if(vstr) {
+            vstr = vstr.replace(/~/g,"=");
+            if(vstr.indexOf('=') !== -1) {
+                //has key=value pairs, must be object
+                var kvs = vstr.split(',');
+                for(var j = 0; j < kvs.length; j++) {
+                    var kv = kvs[j].split('=',2);
+                    val[kv[0]] = massage(kv[1]);
+                }
+            }
+            else if(vstr.indexOf(',') !== -1) {
+                //has multiple values, must list
+                val = vstr.split(',');
+            }
+            else {
+                val = massage(vstr); //value itself
+            }
+        }
+        ret[f] = val;
+    }
+
+return ret;
+}
+
+
+/**
+ * computes the bounding box around the provided atoms
+ * @param {AtomSpec[]} atomlist
+ * @return {Array}
+ */
+$3Dmol.getExtent = function(atomlist, ignoreSymmetries) {
+    var xmin, ymin, zmin, xmax, ymax, zmax, xsum, ysum, zsum, cnt;
+    var includeSym = !ignoreSymmetries;
+
+    xmin = ymin = zmin = 9999;
+    xmax = ymax = zmax = -9999;
+    xsum = ysum = zsum = cnt = 0;
     
-    this.origin = (origin !== undefined) ? 
-        origin : new $3Dmol.Vector3();
+    if (atomlist.length === 0)
+        return [ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ];
+    for (var i = 0; i < atomlist.length; i++) {
+        var atom = atomlist[i];
+        if (typeof atom === 'undefined' || !isFinite(atom.x) ||
+                !isFinite(atom.y) || !isFinite(atom.z))
+            continue;
+        cnt++;
+        xsum += atom.x;
+        ysum += atom.y;
+        zsum += atom.z;
         
-    this.direction = (direction !== undefined) ?
-        direction : new $3Dmol.Vector3();
-      
+        xmin = (xmin < atom.x) ? xmin : atom.x;
+        ymin = (ymin < atom.y) ? ymin : atom.y;
+        zmin = (zmin < atom.z) ? zmin : atom.z;
+        xmax = (xmax > atom.x) ? xmax : atom.x;
+        ymax = (ymax > atom.y) ? ymax : atom.y;
+        zmax = (zmax > atom.z) ? zmax : atom.z;
+        
+        if (atom.symmetries && includeSym) {
+            for (var n = 0; n < atom.symmetries.length; n++) {
+                cnt++;
+                xsum += atom.symmetries[n].x;
+                ysum += atom.symmetries[n].y;
+                zsum += atom.symmetries[n].z;
+                xmin = (xmin < atom.symmetries[n].x) ? xmin : atom.symmetries[n].x;
+                ymin = (ymin < atom.symmetries[n].y) ? ymin : atom.symmetries[n].y;
+                zmin = (zmin < atom.symmetries[n].z) ? zmin : atom.symmetries[n].z;
+                xmax = (xmax > atom.symmetries[n].x) ? xmax : atom.symmetries[n].x;
+                ymax = (ymax > atom.symmetries[n].y) ? ymax : atom.symmetries[n].y;
+                zmax = (zmax > atom.symmetries[n].z) ? zmax : atom.symmetries[n].z; 
+            }
+        }  
+    }
+
+    return [ [ xmin, ymin, zmin ], [ xmax, ymax, zmax ],
+            [ xsum / cnt, ysum / cnt, zsum / cnt ] ];
 };
 
-//TODO: Remove methods we don't need (intersectPlane ??)
-$3Dmol.Ray.prototype = {
-    
-    constructor : $3Dmol.Ray,
-     
-    set : function(origin, direction){
-        
-        this.origin.copy(origin);
-        this.direction.copy(direction);
+
+//return the value of an atom property prop, or null if non existent
+//looks first in properties, then in the atom itself
+$3Dmol.getAtomProperty = function(atom, prop) {
+    var val = null;
+    if (atom.properties
+            && typeof (atom.properties[prop]) != "undefined") {
+        val = atom.properties[prop];
+    } else if(typeof(atom[prop]) != 'undefined') {
+        val = atom[prop];
+    }
+    return val;
+};
+
+/* get the min and max values of the specified property in the provided
+* @function $3Dmol.getPropertyRange
+* @param {AtomSpec[]} atomlist - list of atoms to evaluate
+* @param {string} prop - name of property 
+* @return {Array} - [min, max] values
+*/
+$3Dmol.getPropertyRange = function (atomlist, prop) {
+    var min = Number.POSITIVE_INFINITY;
+    var max = Number.NEGATIVE_INFINITY;
+
+    for (var i = 0, n = atomlist.length; i < n; i++) {
+        var atom = atomlist[i];
+        var val = $3Dmol.getAtomProperty(atom, prop);
         
-        return this;
-    
-    },
-    
-    copy : function(ray) {
+        if(val != null) {
+            if (val < min)
+                min = val;
+            if (val > max)
+                max = val;                
+        }
+    }
+
+    if (!isFinite(min) && !isFinite(max))
+        min = max = 0;
+    else if (!isFinite(min))
+        min = max;
+    else if (!isFinite(max))
+        max = min;
+
+    return [ min, max ];
+}
+
+/*
+* math-like functionality
+* quaternion, vector, matrix
+*/
+
+var $3Dmol = $3Dmol || {};
+$3Dmol.Math = {
+
+    clamp : function(x, min, max) {
+        return Math.min( Math.max( x, min ), max );
+    },
+
+    degToRad : function() {
+       var degreeToRadiansFactor = Math.PI / 180;
+       
+       return function(deg) {
+           return deg * degreeToRadiansFactor;
+       };
+    
+    }()
+    
+};
+
+
+// Quaternion
+/** @constructor */
+$3Dmol.Quaternion = function(x, y, z, w) {
+
+    this.x = x || 0;
+    this.y = y || 0;
+    this.z = z || 0;
+    this.w = (w !== undefined) ? w : 1;
+
+};
+
+$3Dmol.Quaternion.prototype = {
+
+    constructor : $3Dmol.Quaternion,
+
+    set : function(x, y, z, w) {
         
-        this.origin.copy(ray.origin);
-        this.direction.copy(ray.direction);
+        this.x = x;
+        this.y = y;
+        this.z = z;
+        this.w = w;
+
+        return this;
+    },
+
+    copy : function(q) {
+        
+        this.x = q.x;
+        this.y = q.y;
+        this.z = q.z;
+        this.w = q.w;
+
+        return this;
+    },
+
+    conjugate : function() {
         
+        this.x *= -1;
+        this.y *= -1;
+        this.z *= -1;
+
         return this;
+    },
+
+    inverse : function() {
         
+        return this.conjugate().normalize();
     },
-    
-    at : function(t, optionalTarget) {
+
+    length : function() {
         
-        var result = optionalTarget || new $3Dmol.Vector3();
+        return Math.sqrt(this.x * this.x + this.y * this.y + this.z * this.z + this.w * this.w);
+    },
+
+    normalize : function() {
         
-        return result.copy(this.direction).multiplyScalar(t).add(this.origin);
+        var l = this.length();
+
+        if (l === 0) {
+            this.x = 0;
+            this.y = 0;
+            this.z = 0;
+            this.w = 1;
+        } else {
+            l = 1 / l;
+
+            this.x *= l;
+            this.y *= l;
+            this.z *= l;
+            this.w *= l;
+        }
+
+        return this;
+
+    },
+
+    multiply : function(q) {
         
+        return this.multiplyQuaternions(this, q);
     },
+
+    multiplyQuaternions : function(a, b) {
+
+        var qax = a.x, qay = a.y, qaz = a.z, qaw = a.w;
+        var qbx = b.x, qby = b.y, qbz = b.z, qbw = b.w;
+
+        this.x = qax * qbw + qaw * qbx + qay * qbz - qaz * qby;
+        this.y = qay * qbw + qaw * qby + qaz * qbx - qax * qbz;
+        this.z = qaz * qbw + qaw * qbz + qax * qby - qay * qbx;
+        this.w = qaw * qbw - qax * qbx - qay * qby - qaz * qbz;
+
+    }
+};
+
+//A 2 Vector
+/** @constructor */
+$3Dmol.Vector2 = function(x, y) {
     
-    recast : function() {
-        
-        var v1 = new $3Dmol.Vector3();
+    this.x = x || 0.0;
+    this.y = y || 0.0;
+};
+
+$3Dmol.Vector2.prototype = {
+    
+    constructor : $3Dmol.Vector2,
+   
+    set : function(x, y) {
+       
+        this.x = x;
+        this.y = y;
+       
+        return this;
+    },
+    
+    subVectors : function(a, b) {
         
-        return function(t) {
-            this.origin.copy(this.at(t, v1));
-            
-            return this;
-        };
+      this.x = a.x - b.x;
+      this.y = a.y - b.y;
+      
+      return this;
+    },
+   
+    copy : function(v) {
+       
+        this.x = v.x;
+        this.y = v.y;
+       
+        return this;
+    },
+   
+    clone : function() {
         
-    }(),
+        return new $3Dmol.Vector2(this.x, this.y);
+    }    
+   
+};
+
+//A 3 Vector
+
+$3Dmol.Vector3 = function(x, y, z) {
+    this.x = x || 0.0;
+    this.y = y || 0.0;
+    this.z = z || 0.0;
+};
+/** @this {$3Dmol.Vector3} */
+$3Dmol.Vector3.prototype =  {
     
-    closestPointToPoint : function(point, optionalTarget) {
-        
-        var result = optionalTarget || new $3Dmol.Vector3();
-        result.subVectors(point, this.origin);
-        var directionDistance = result.dot(this.direction);
+    constructor : $3Dmol.Vector3,
+    
+    set : function(x, y, z) {
         
-        //returns a point on this ray
-        return result.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
+        this.x = x;
+        this.y = y;
+        this.z = z;
         
+        return this;
     },
     
-    distanceToPoint : function() {
-        
-        var v1 = new $3Dmol.Vector3();
+    copy : function(v) {
         
-        return function(point) {
-            var directionDistance = v1.subVectors(point, this.origin).dot(this.direction);
-            v1.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
-            
-            return v1.distanceTo(point);
-        };
+        this.x = v.x;
+        this.y = v.y;
+        this.z = v.z;
         
-    }(),
+        return this;  
+    },
     
-    isIntersectionCylinder : function() {
+    add : function(v) {
+        
+        this.x += v.x;
+        this.y += v.y;
+        this.z += v.z;  
         
+        return this;
     },
     
-    isIntersectionSphere : function(sphere) {
-       
-       return (this.distanceToPoint(sphere.center) <= sphere.radius);
-          
+    addVectors : function(a, b) {
+        
+        this.x = a.x + b.x;
+        this.y = a.y + b.y;
+        this.z = a.z + b.z;
+        
+        return this;
     },
     
-    isIntersectionPlane : function(plane) {
+    sub : function(v) {
         
-        var denominator = plane.normal.dot(this.direction);
+        this.x -= v.x;
+        this.y -= v.y;
+        this.z -= v.z;
         
-        //plane and ray are not perpendicular
-        if (denominator !== 0) 
-            return true;
+        return this;
+    },
+    
+    subVectors : function(a, b) {
         
-        if (plane.distanceToPoint(this.origin) === 0) 
-            return true;
+        this.x = a.x - b.x;
+        this.y = a.y - b.y;
+        this.z = a.z - b.z;
         
-        return false;
+        return this;
+    },
+    
+    multiplyScalar : function(s) {
+        
+        this.x *= s;
+        this.y *= s;
+        this.z *= s;
         
+        return this;
     },
     
-    distanceToPlane : function(plane) {
-       
-       var denominator = plane.normal.dot(this.direction);
-       if (denominator === 0) {
-           
-           //line is coplanar
-       if (plane.distanceToPoint(this.origin) === 0)
-           return 0;
-       
-       //ray is parallel
-           return undefined;
-       }
-       
-       var t = - (this.origin.dot(plane.normal) + plane.constant) / denominator;
-       
-       return t;
-       
+    divideScalar : function(s) {
+        
+        if (s !== 0) {
+            this.x /= s;
+            this.y /= s;
+            this.z /= s;
+        }
+        
+        else {
+            this.x = 0;
+            this.y = 0;
+            this.z = 0;
+        }
+        
+        return this;
     },
     
-    intersectPlane : function(plane, optionalTarget) {
-       
-       var t = this.distanceToPlane(plane);
-       
-       if (t === undefined)
-           return undefined;
-       
-       return this.at(t, optionalTarget);
-       
+    //accumulate maximum
+    max : function(s) {
+        
+        this.x = Math.max(this.x,s.x);
+        this.y = Math.max(this.y,s.y);
+        this.z = Math.max(this.z,s.z);
+        
+        return this;
     },
     
-    applyMatrix4 : function(matrix4) {
-       
-       this.direction.add(this.origin).applyMatrix4(matrix4);
-       this.origin.applyMatrix4(matrix4);
-       this.direction.sub(this.origin);
-       
-       return this;
-       
+    //accumulate min
+    min : function(s) {
+        
+        this.x = Math.min(this.x,s.x);
+        this.y = Math.min(this.y,s.y);
+        this.z = Math.min(this.z,s.z);
+        
+        return this;
     },
-    
-    equals : function(ray) {
-       
-       return ray.origin.equals(this.origin) && ray.direction.equals(this.direction);
-       
+    distanceTo: function(v) {
+        return Math.sqrt(this.distanceToSquared(v));
     },
-    
-    clone : function() {
-    
-       return new $3Dmol.Ray().copy(this);
-    
-    }
- 
-     
-};
-
-//Intersection sphere and box shapes.  
-
 
-//Intersection sphere for sphere, stick render
-/** @constructor */
-$3Dmol.Sphere = function(center, radius) {
-
-    this.center = (center !== undefined) ? 
-        center : new $3Dmol.Vector3();
-        
-    this.radius = (radius !== undefined) ?
-        radius : 0;
-        
-};
+    distanceToSquared: function(v) {
+        var dx = this.x - v.x;
+        var dy = this.y - v.y;
+        var dz = this.z - v.z;
 
-$3Dmol.Sphere.prototype = {
+        return dx * dx + dy * dy + dz * dz;
+    },
     
-    constructor : $3Dmol.Sphere,
+    applyMatrix4 : function(m) {
     
-    set : function(center, radius) {
+        var x = this.x, y = this.y, z = this.z;
         
-        this.center.copy(center);
-        this.radius = radius;
+        var e = m.elements;
+        
+        this.x = e[0]*x + e[4]*y + e[8]*z + e[12];
+        this.y = e[1]*x + e[5]*y + e[9]*z + e[13];
+        this.z = e[2]*x + e[6]*y + e[10]*z + e[14];
         
         return this;
+    },
+    
+    applyProjection : function(m) {
+        
+        //input: $3Dmol.Matrix4 projection matrix
+        
+        var x = this.x, y = this.y, z = this.z;
+        
+        var e = m.elements;
+        var d = ( e[3]*x + e[7]*y + e[11]*z + e[15]);
+        
+        this.x = (e[0]*x + e[4]*y + e[8]*z + e[12]) / d;
+        this.y = (e[1]*x + e[5]*y + e[9]*z + e[13]) / d;
+        this.z = (e[2]*x + e[6]*y + e[10]*z + e[14]) / d;
         
+        return this;
     },
     
-    copy : function(sphere) {
+    applyQuaternion : function(q) { 
         
-        this.center.copy(sphere.center);
-        this.radius = sphere.radius;
+        //save values
+        var x = this.x;
+        var y = this.y;
+        var z = this.z;
+        
+        var qx = q.x;
+        var qy = q.y;
+        var qz = q.z;
+        var qw = q.w;
+        
+        //compute this as
+        //t = 2 * cross(q.xyz, v)
+        //newv = v + q.w * t + cross(q.xyz, t)
+        //this from molecularmusings
+        //http://molecularmusings.wordpress.com/2013/05/24/a-faster-quaternion-vector-multiplication/
+        var t = {};
+        t.x = 2*(y * qz - z * qy);
+        t.y = 2*(z * qx - x * qz);
+        t.z = 2*(x * qy - y * qx);
+        
+        //cross t with q
+        var t2 = {};
+        t2.x = t.y * qz - t.z * qy;
+        t2.y = t.z * qx - t.x * qz;
+        t2.z = t.x * qy - t.y * qx;
+        
+        this.x = x + q.w*t.x + t2.x;
+        this.y = y + q.w*t.y + t2.y;
+        this.z = z + q.w*t.z + t2.z;
         
         return this;
+    },
+    
+    negate : function() {
         
+        return this.multiplyScalar(-1);
     },
     
-    applyMatrix4 : function(matrix) {
+    dot : function(v) {
         
-        this.center.applyMatrix4(matrix);
-        this.radius = this.radius * matrix.getMaxScaleOnAxis();
+        return this.x * v.x + this.y * v.y + this.z * v.z;
+    },
+    
+    length : function() {
         
-        return this;
+        return Math.sqrt(this.x*this.x + this.y*this.y + this.z*this.z);
+    },
+    
+    lengthSq : function() {
+    
+        return (this.x*this.x + this.y*this.y + this.z*this.z);
+    },
+    
+    normalize : function() {
         
+        return this.divideScalar( this.length() );
     },
     
-    translate : function(offset) {
+    cross : function (v) {
         
-        this.center.add(offset);
+        var x = this.x, y = this.y, z = this.z;
         
-        return this;
+        this.x = y * v.z - z * v.y;
+        this.y = z * v.x - x * v.z;
+        this.z = x * v.y - y * v.x;
         
+        return this;
     },
     
-    equals : function(sphere) {
+    crossVectors : function(a, b) {
         
-        return sphere.center.equals(this.center) && (sphere.radius === this.radius);
+        this.x = a.y * b.z - a.z * b.y;
+        this.y = a.z * b.x - a.x * b.z;
+        this.z = a.x * b.y - a.y * b.x;
         
+        return this;
     },
-       
-    clone : function() {
+    
+    getPositionFromMatrix : function(m) {
         
-        return new $3Dmol.Sphere().copy(this);
+        this.x = m.elements[12];
+        this.y = m.elements[13];
+        this.z = m.elements[14];
         
-    }
+        return this;
+    },
 
-};
+    setEulerFromRotationMatrix : function (m, order) {
 
+        // assumes the upper 3x3 of m is a pure rotation matrix (i.e, unscaled)
 
-//Bounding cylinder for stick render  
-/** @constructor */
-$3Dmol.Cylinder = function(c1, c2, radius) {
+        var te = m.elements;
+        var m11 = te[0], m12 = te[4], m13 = te[8];
+        var m21 = te[1], m22 = te[5], m23 = te[9];
+        var m31 = te[2], m32 = te[6], m33 = te[10];
 
-    this.c1 = (c1 !== undefined) ?
-        c1 : new $3Dmol.Vector3();
+        if ( order === undefined || order === 'XYZ' ) {
 
-    this.c2 = (c2 !== undefined) ?
-        c2 : new $3Dmol.Vector3();
+            this.y = Math.asin( $3Dmol.Math.clamp( m13, -1, 1 ) );
+
+            if ( Math.abs( m13 ) < 0.99999 ) {
+
+                this.x = Math.atan2( - m23, m33 );
+                this.z = Math.atan2( - m12, m11 );
+
+            } else {
+
+                this.x = Math.atan2( m32, m22 );
+                this.z = 0;
+
+            }
+        }
         
-    this.direction = new $3Dmol.Vector3().subVectors(this.c2, this.c1).normalize();
+        else {
+            console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: " + order);
+        }
+        
+        return this;
 
-    this.radius = (radius !== undefined) ?
-        radius : 0;
-    
-};
+    },
 
-$3Dmol.Cylinder.prototype = {
+    rotateAboutVector : function(axis, ang) {
 
-    constructor : $3Dmol.Cylinder,
+        axis.normalize();
+        var cosang = Math.cos(ang);
+        var sinang = Math.sin(ang); 
+        // Rodrigues' rotation formula, from wikipedia
 
-    copy : function(cylinder) {
+        var term1 = this.clone().multiplyScalar(cosang);
+        var term2 = (axis.clone().cross(this)).multiplyScalar(sinang)
+        var term3 = axis.clone().multiplyScalar(axis.clone().dot(this)).multiplyScalar(1-cosang);
 
-        this.c1.copy(cylinder.c1);
-        this.c2.copy(cylinder.c2);
-        this.direction.copy(cylinder.direction);
-        this.radius = cylinder.radius;
+        var rot = term1.add(term2).add(term3);
+    
+        this.x = rot.x;
+        this.y = rot.y;
+        this.z = rot.z;
 
         return this;
-
     },
     
-    lengthSq : function() {
+    clone : function() {
+        return new $3Dmol.Vector3(this.x, this.y, this.z);
+    }
     
-        var vector = new $3Dmol.Vector3();
-        
-        return function(){
-            return vector.subVectors(this.c2, this.c1).lengthSq();
-        };
-        
-    }(),
-
-    applyMatrix4 : function(matrix) {
-        
-        this.direction.add(this.c1).applyMatrix4(matrix);
-        this.c1.applyMatrix4(matrix);
-        this.c2.applyMatrix4(matrix);
-        this.direction.sub(this.c1).normalize();
-        this.radius = this.radius * matrix.getMaxScaleOnAxis();
-
-        return this;
-
-    }
-
 };
 
+//Matrices
 
-//plane specified by three points
+//Matrix3
 /** @constructor */
-$3Dmol.Triangle = function(a, b, c){
-   
-    this.a = (a !== undefined) ?
-        a : new $3Dmol.Vector3();
-
-    this.b = (b !== undefined) ?
-        b : new $3Dmol.Vector3();
+$3Dmol.Matrix3 = function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
+    
+    this.elements = new Float32Array(9);
+    
+    this.set(
+        (n11 !== undefined) ? n11 : 1, n12 || 0, n13 || 0,
+        n21 || 0, (n22 !== undefined) ? n22 : 1, n23 || 0,
+        n31 || 0, n32 || 0, (n33 !== undefined) ? n33 : 1
+    );
     
-    this.c = (c !== undefined) ?
-        c : new $3Dmol.Vector3();   
-  
 };
 
-$3Dmol.Triangle.prototype = {
-
-    constructor : $3Dmol.Triangle,
+$3Dmol.Matrix3.prototype = {
     
-    copy : function(triangle) {
+    constructor : $3Dmol.Matrix3,    
+   
+    set : function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
+        var te = this.elements;
         
-        this.a.copy(triangle.a);
-        this.b.copy(triangle.b);
-        this.c.copy(triangle.c);
+        te[0] = n11; te[3] = n12; te[6] = n13;
+        te[1] = n21; te[4] = n22; te[7] = n23;
+        te[2] = n31; te[5] = n32; te[8] = n33;
         
         return this;
-        
     },
     
-    applyMatrix4 : function(matrix) {
-        
-        this.a.applyMatrix4(matrix);
-        this.b.applyMatrix4(matrix);
-        this.c.applyMatrix4(matrix);
+    identity : function() {   
+        this.set(
+            1,0,0,
+            0,1,0,
+            0,0,1
+        );
         
         return this;
-        
+    },
+   
+    copy : function(m) {
+        var me = m.elements;
+       
+        this.set(
+            me[0], me[3], me[6],
+            me[1], me[4], me[7],
+            me[2], me[5], me[8]
+        );
     },
     
-    getNormal : function() {
-        
-        var v1 = new $3Dmol.Vector3();
-        
-        return function() {
-            
-            var norm = this.a.clone();
-            norm.sub(this.b);
-            v1.subVectors(this.c, this.b);
-            
-            norm.cross(v1);
-            norm.normalize();
-            
-            return norm;
-            
-        };
-        
-    }()
+    multiplyScalar: function ( s ) {
+        var te = this.elements;
 
-};
+        te[0] *= s; te[3] *= s; te[6] *= s;
+        te[1] *= s; te[4] *= s; te[7] *= s;
+        te[2] *= s; te[5] *= s; te[8] *= s;
 
+        return this;
+    },
 
-/* core Object3D
- * Base class for Scene, Camera, Geometry
- * Geometry class
- */
+    getInverse: function ( matrix, throwOnInvertible ) {
+        // input: Matrix4
 
-//Event Handling
-/** @this {$3Dmol.EventDispatcher} */
-$3Dmol.EventDispatcher = function() {
-  
-    var listeners = {};
-    
-    this.addEventListener = function(type, listener) {
-        if (listeners[type] === undefined)
-            listeners[type] = [];
-        
-        if (listeners[type].indexOf(listener) === -1)
-            listeners[type].push(listener);
-    };  
-    
-    this.removeEventListener = function(type, listener) {
-        
-        var index = listeners[type].indexOf(listener);
-        
-        if (index !== -1)
-            listeners[type].splice(index, 1);
-              
-    };
-    
-    this.dispatchEvent = function(event) {
-        
-        var listenerArray = listeners[event.type];
-        
-        if (listenerArray !== undefined) {
-            event.target = this;
-            
-            for (var i = 0, l = listenerArray.length; i < l; i++)
-                listenerArray[i].call(this, event);
-                
-        }
-            
-    };
-    
-};
+        var me = matrix.elements;
+        var te = this.elements;
 
-$3Dmol.Color = function( color ){
-    
-    if ( arguments.length > 1) {
-            this.r = arguments[0] || 0.0;
-            this.g = arguments[1] || 0.0;
-            this.b = arguments[2] || 0.0;
+        te[ 0 ] =   me[10] * me[5] - me[6] * me[9];
+        te[ 1 ] = - me[10] * me[1] + me[2] * me[9];
+        te[ 2 ] =   me[6] * me[1] - me[2] * me[5];
+        te[ 3 ] = - me[10] * me[4] + me[6] * me[8];
+        te[ 4 ] =   me[10] * me[0] - me[2] * me[8];
+        te[ 5 ] = - me[6] * me[0] + me[2] * me[4];
+        te[ 6 ] =   me[9] * me[4] - me[5] * me[8];
+        te[ 7 ] = - me[9] * me[0] + me[1] * me[8];
+        te[ 8 ] =   me[5] * me[0] - me[1] * me[4];
 
-            return this;
-    }
-    
-    return this.set(color);
-                
-};
+        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 3 ] + me[ 2 ] * te[ 6 ];
 
-$3Dmol.Color.prototype = {
-    
-    constructor: $3Dmol.Color,
-    
-    r: 0.0, g: 0.0, b: 0.0,
-    
-    set : function(val) {
-        
-            if (val instanceof $3Dmol.Color) 
-                return val.clone();
+        // no inverse
 
-            else if (typeof val === 'number')
-                this.setHex(val);
-    },
-    
-    setHex: function(hex) {
-        
-            hex = Math.floor(hex);
+        if ( det === 0 ) {
+
+            var msg = "Matrix3.getInverse(): can't invert matrix, determinant is 0";
+
+            if ( throwOnInvertible || false ) {
+
+                throw new Error( msg ); 
+
+            } else {
+
+                console.warn( msg );
+
+            }
+
+            this.identity();
 
-            this.r = (hex >> 16 & 255) / 255;
-            this.g = (hex >> 8 & 255) / 255;
-            this.b = (hex & 255) / 255;                                                                                     
-        
             return this;
+
+        }
+
+        this.multiplyScalar( 1.0 / det );
+
+        return this;
     },
-    
-    getHex: function() {
-        var R = Math.round(this.r*255);
-        var G = Math.round(this.g*255);
-        var B = Math.round(this.b*255);
-        return R<<16 | G << 8 | B;
+
+    //https://en.wikipedia.org/wiki/Determinant
+    getDeterminant: function() {
+        var m = this.elements;
+
+        /*|a b c|
+          |d e f|
+          |g h i|*/
+
+        var determinant
+            = m[0] * m[4] * m[8] //+aei
+            + m[1] * m[5] * m[6] //+bfg
+            + m[2] * m[3] * m[7] //+cdh
+            - m[2] * m[4] * m[6] //-ceg
+            - m[1] * m[3] * m[8] //-bdi
+            - m[0] * m[5] * m[7];//-afh
+        return determinant;
     },
     
-    clone : function() {
-            return new $3Dmol.Color(this.r, this.g, this.b);
-    },
-        
-    copy : function(color) {
-        this.r = color.r;
-        this.g = color.g;
-        this.b = color.b;
-        
+    transpose: function () {
+        var tmp, m = this.elements;
+
+        tmp = m[1]; m[1] = m[3]; m[3] = tmp;
+        tmp = m[2]; m[2] = m[6]; m[6] = tmp;
+        tmp = m[5]; m[5] = m[7]; m[7] = tmp;
+
         return this;
     },
     
-    //return object that represents color components from 0 to 255
-    scaled : function() {
-        var ret = {};
-        ret.r = Math.round(this.r*255);
-        ret.g = Math.round(this.g*255);
-        ret.b = Math.round(this.b*255);
-        ret.a = 1.0;
-        return ret;
+    clone: function () {
+        var te = this.elements;
+
+        return new $3Dmol.Matrix3(
+
+            te[0], te[3], te[6],
+            te[1], te[4], te[7],
+            te[2], te[5], te[8]
+
+        );
     }
-    
+   
 };
 
-//Object3D base constructor function
-/** @this {$3Dmol.Object3D} */
-$3Dmol.Object3D = function() {
-    
-    this.id = $3Dmol.Object3DIDCount++;
-    
-    this.name = "";
-    
-    this.parent = undefined;
-    this.children = [];
-    
-    this.position = new $3Dmol.Vector3();
-    this.rotation = new $3Dmol.Vector3();
-    this.matrix = new $3Dmol.Matrix4();
-    this.matrixWorld = new $3Dmol.Matrix4();
-    this.quaternion = new $3Dmol.Quaternion();
-    this.eulerOrder = 'XYZ';
-    
-    this.up = new $3Dmol.Vector3(0, 1, 0);
-    this.scale = new $3Dmol.Vector3(1, 1, 1);
-    
-    this.matrixAutoUpdate = true;
-    this.matrixWorldNeedsUpdate = true;
-    this.rotationAutoUpdate = true;
-    this.useQuaternion = false;
-    
-    this.visible = true;
+//Matrix 4
+/** @constructor */
+$3Dmol.Matrix4 = function(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44) {
+
+    var te = this.elements = new Float32Array( 16 );
     
+    te[0] = ( n11 !== undefined ) ? n11 : 1; te[4] = n12 || 0; te[8] = n13 || 0; te[12] = n14 || 0;
+    te[1] = n21 || 0; te[5] = ( n22 !== undefined ) ? n22 : 1; te[9] = n23 || 0; te[13] = n24 || 0;
+    te[2] = n31 || 0; te[6] = n32 || 0; te[10] = ( n33 !== undefined ) ? n33 : 1; te[14] = n34 || 0;
+    te[3] = n41 || 0; te[7] = n42 || 0; te[11] = n43 || 0; te[15] = ( n44 !== undefined ) ? n44 : 1;
+
 };
 
-$3Dmol.Object3D.prototype = {
-    
-    constructor : $3Dmol.Object3D,
-    
-    lookAt : function(vector) {
-        
-        this.matrix.lookAt(vector, this.position, this.up);
-        
-        if (this.rotationAutoUpdate) {
-            
-            if (this.useQuaternion === true) 
-                this.quaternion.copy(this.matrix.decompose()[1]);
-            else
-                this.rotation.setEulerFromRotationMatrix(this.matrix, this.eulerOrder);
-        }
+$3Dmol.Matrix4.prototype = {
+
+    constructor : $3Dmol.Matrix4,
+
+    set: function ( n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44 ) {
+        var te = this.elements;
+
+        te[0] = n11; te[4] = n12; te[8] = n13; te[12] = n14;
+        te[1] = n21; te[5] = n22; te[9] = n23; te[13] = n24;
+        te[2] = n31; te[6] = n32; te[10] = n33; te[14] = n34;
+        te[3] = n41; te[7] = n42; te[11] = n43; te[15] = n44;
+
+        return this;
     },
-    
-    //add child object
-    add : function(object) {
-        if (object === this){
-            console.error("Can't add $3Dmol.Object3D to itself");
-            return;
-        }
-        
-        object.parent = this;
-        this.children.push(object);
-        
-        //add to the scene (i.e. follow up this instance's parents until reach the top)
-        
-        var scene = this;
-        
-        while (scene.parent !== undefined)
-            scene = scene.parent;
-            
-        if (scene !== undefined && scene instanceof $3Dmol.Scene) 
-            scene.__addObject(object);
-        
+
+    identity: function () {
+        this.set(
+
+            1, 0, 0, 0,
+            0, 1, 0, 0,
+            0, 0, 1, 0,
+            0, 0, 0, 1
+
+        );
+
+        return this;
     },
-    
-    remove : function(object) {
-        
-        var index = this.children.indexOf(object);
-        
-        if (index !== -1) {
-            
-            object.parent = undefined;
-            this.children.splice(index, 1);
-            
-            //Remove from scene
-            
-            var scene = this;
-            
-            while (scene.parent !== undefined)
-                scene = scene.parent;
-                
-            if (scene !== undefined && scene instanceof $3Dmol.Scene)
-                scene.__removeObject(object);
-                
-        }
+
+    copy: function ( m ) {
+        var me = m.elements;
+
+        this.set(
+
+            me[0], me[4], me[8], me[12],
+            me[1], me[5], me[9], me[13],
+            me[2], me[6], me[10], me[14],
+            me[3], me[7], me[11], me[15]
+
+        );
+
+        return this;
     },
-    
-    updateMatrix : function() {
-        
-        this.matrix.setPosition(this.position);
-        
-        if (this.useQuaternion === false) 
-            this.matrix.setRotationFromEuler(this.rotation, this.eulerOrder);
-        else
-            this.matrix.setRotationFromQuaternion(this.quaternion);
-        
-        //TODO: Do I need this??
-        if (this.scale.x !== 1 || this.scale.y !== 1 || this.scale.z !== 1)
-            this.matrix.scale(this.scale);
-            
-        this.matrixWorldNeedsUpdate = true;
-        
+
+    matrix3FromTopLeft: function () {
+        var te = this.elements;
+        return new $3Dmol.Matrix3(te[0],te[4],te[8],te[1],te[5],te[9],te[2],te[6],te[10]);
     },
-    
-    updateMatrixWorld : function(force) {
-        
-        if (this.matrixAutoUpdate === true) 
-            this.updateMatrix();
-        
-        if (this.matrixWorldNeedsUpdate === true || force === true) {
-            
-            if (this.parent === undefined)
-                this.matrixWorld.copy(this.matrix);
-            else
-                this.matrixWorld.multiplyMatrices(this.parent.matrixWorld, this.matrix);
-                
-        }
-        
-        this.matrixWorldNeedsUpdate = false;
+
+    setRotationFromEuler: function ( v, order ) {
+
+        var te = this.elements;
+
+        var x = v.x, y = v.y, z = v.z;
+        var a = Math.cos( x ), b = Math.sin( x );
+        var c = Math.cos( y ), d = Math.sin( y );
+        var e = Math.cos( z ), f = Math.sin( z );
+
+        if ( order === undefined || order === 'XYZ' ) {
+
+            var ae = a * e, af = a * f, be = b * e, bf = b * f;
+
+            te[0] = c * e;
+            te[4] = - c * f;
+            te[8] = d;
+
+            te[1] = af + be * d;
+            te[5] = ae - bf * d;
+            te[9] = - b * c;
+
+            te[2] = bf - ae * d;
+            te[6] = be + af * d;
+            te[10] = a * c;
+
+        } 
         
-        //Update matrices of all children
-        for (var i = 0; i < this.children.length; i++) {
-            this.children[i].updateMatrixWorld(true);
-        }
+        else
+            console.error("Error with matrix4 setRotationFromEuler. Order: " + order);
+
+        return this;
+
     },
-    
-    clone : function(object) {
-        
-        if (object === undefined)
-            object = new $3Dmol.Object3D();
-            
-        object.name = this.name;
-        
-        object.up.copy(this.up);
-        object.position.copy(this.position);
-        object.rotation.copy(this.rotation);
-        object.eulerOrder = this.eulerOrder;
-        object.scale.copy(this.scale);
 
-        object.rotationAutoUpdate = this.rotationAutoUpdate;
-        object.matrix.copy(this.matrix);
-        object.matrixWorld.copy(this.matrixWorld);
-        object.quaternion.copy(this.quaternion);
-        object.matrixAutoUpdate = this.matrixAutoUpdate;
-        object.matrixWorldNeedsUpdate = this.matrixWorldNeedsUpdate;
-        
-        object.useQuaternion = this.useQuaternion;
-        
-        object.visible = this.visible;
-        
-        for (var i = 0; i < this.children.length; i++) {
-            var child = this.children[i];
-            object.add(child.clone());
-        }
-        
-        return object;
-        
-    }
-    
-};
+    setRotationFromQuaternion: function ( q ) {
+        var te = this.elements;
 
-$3Dmol.Object3DIDCount = 0;
+        var x = q.x, y = q.y, z = q.z, w = q.w;
+        var x2 = x + x, y2 = y + y, z2 = z + z;
+        var xx = x * x2, xy = x * y2, xz = x * z2;
+        var yy = y * y2, yz = y * z2, zz = z * z2;
+        var wx = w * x2, wy = w * y2, wz = w * z2;
 
-//Geometry class
-//TODO: What can I remove - how can I optimize ?
-$3Dmol.Geometry = (function() {
-   
-    var BUFFERSIZE = 65535; //limited to 16bit indices
-    
-    
-    /** @constructor */
-    var geometryGroup = function(id) {
-        this.id = id || 0;
-        //for performance reasons, callers must directly modify these
-        this.vertexArray = null;
-        this.colorArray = null;
-        this.normalArray = null;
-        this.faceArray = null;
-        this.lineArray = null;
-        this.vertices = 0;
-        this.faceidx = 0;
-        this.lineidx = 0;
-        
-    };
-    
-    geometryGroup.prototype.getNumVertices = function() {
-        return this.vertices;
-    };
-    
-    geometryGroup.prototype.getVertices = function() {
-        return this.vertexArray;
-    };
-    
+        te[0] = 1 - ( yy + zz );
+        te[4] = xy - wz;
+        te[8] = xz + wy;
+
+        te[1] = xy + wz;
+        te[5] = 1 - ( xx + zz );
+        te[9] = yz - wx;
+
+        te[2] = xz - wy;
+        te[6] = yz + wx;
+        te[10] = 1 - ( xx + yy );
+
+        return this;
+    },
+
+    lookAt: function() {
+        var x = new $3Dmol.Vector3();
+        var y = new $3Dmol.Vector3();
+        var z = new $3Dmol.Vector3();
+
+        return function ( eye, target, up ) {
+
+            var te = this.elements;
+
+            z.subVectors( eye, target ).normalize();
+
+            if ( z.length() === 0 ) {
+
+                z.z = 1;
+
+            }
+
+            x.crossVectors( up, z ).normalize();
+
+            if ( x.length() === 0 ) {
+
+                z.x += 0.0001;
+                x.crossVectors( up, z ).normalize();
+
+            }
+
+            y.crossVectors( z, x );
+
+
+            te[0] = x.x; te[4] = y.x; te[8] = z.x;
+            te[1] = x.y; te[5] = y.y; te[9] = z.y;
+            te[2] = x.z; te[6] = y.z; te[10] = z.z;
+
+            return this;
+        };
+
+    }(),
+
+    multiplyMatrices: function ( a, b ) {
+        var ae = a.elements;
+        var be = b.elements;
+        var te = this.elements;
+
+        var a11 = ae[0], a12 = ae[4], a13 = ae[8], a14 = ae[12];
+        var a21 = ae[1], a22 = ae[5], a23 = ae[9], a24 = ae[13];
+        var a31 = ae[2], a32 = ae[6], a33 = ae[10], a34 = ae[14];
+        var a41 = ae[3], a42 = ae[7], a43 = ae[11], a44 = ae[15];
+
+        var b11 = be[0], b12 = be[4], b13 = be[8], b14 = be[12];
+        var b21 = be[1], b22 = be[5], b23 = be[9], b24 = be[13];
+        var b31 = be[2], b32 = be[6], b33 = be[10], b34 = be[14];
+        var b41 = be[3], b42 = be[7], b43 = be[11], b44 = be[15];
+
+        te[0] = a11 * b11 + a12 * b21 + a13 * b31 + a14 * b41;
+        te[4] = a11 * b12 + a12 * b22 + a13 * b32 + a14 * b42;
+        te[8] = a11 * b13 + a12 * b23 + a13 * b33 + a14 * b43;
+        te[12] = a11 * b14 + a12 * b24 + a13 * b34 + a14 * b44;
+
+        te[1] = a21 * b11 + a22 * b21 + a23 * b31 + a24 * b41;
+        te[5] = a21 * b12 + a22 * b22 + a23 * b32 + a24 * b42;
+        te[9] = a21 * b13 + a22 * b23 + a23 * b33 + a24 * b43;
+        te[13] = a21 * b14 + a22 * b24 + a23 * b34 + a24 * b44;
+
+        te[2] = a31 * b11 + a32 * b21 + a33 * b31 + a34 * b41;
+        te[6] = a31 * b12 + a32 * b22 + a33 * b32 + a34 * b42;
+        te[10] = a31 * b13 + a32 * b23 + a33 * b33 + a34 * b43;
+        te[14] = a31 * b14 + a32 * b24 + a33 * b34 + a34 * b44;
+
+        te[3] = a41 * b11 + a42 * b21 + a43 * b31 + a44 * b41;
+        te[7] = a41 * b12 + a42 * b22 + a43 * b32 + a44 * b42;
+        te[11] = a41 * b13 + a42 * b23 + a43 * b33 + a44 * b43;
+        te[15] = a41 * b14 + a42 * b24 + a43 * b34 + a44 * b44;
+
+        return this;
+    },
     
-    geometryGroup.prototype.getCentroid = function() {
-        
-        var centroid = new $3Dmol.Vector3();
-        var offset, x, y, z;
-        
-        for (var i = 0; i < this.vertices; ++i) {
-            offset = i*3;
-            
-            x = this.vertexArray[offset]; y = this.vertexArray[offset+1]; z = this.vertexArray[offset+2];
-            
-            centroid.x += x; centroid.y += y; centroid.z += z;
-        }
-        
-        //divideScalar checks for 0 denom
-        centroid.divideScalar(this.vertices);
-        
-        return centroid;
-    };
+    multiplyScalar: function ( s ) {
+        var te = this.elements;
     
-    //setup normals - vertex and face array must exist
-    geometryGroup.prototype.setNormals = function() {        
-        
-        var faces = this.faceArray;
-        var verts = this.vertexArray;
-        var norms = this.normalArray;
-        
-        if (! this.vertices || ! this.faceidx) 
-            return;
-        
-        //vertex indices
-        var a, b, c, d,
-        //and actual vertices
-        vA, vB, vC, norm;
-            
-        for (var i = 0; i < faces.length / 3; ++i) {
-            
-            a = faces[i * 3] * 3;
-            b = faces[i * 3 + 1] * 3;
-            c = faces[i * 3 + 2] * 3;
-            
-            vA = new $3Dmol.Vector3(verts[a], verts[a+1], verts[a+2]);
-            vB = new $3Dmol.Vector3(verts[b], verts[b+1], verts[b+2]);
-            vC = new $3Dmol.Vector3(verts[c], verts[c+1], verts[c+2]);
-            
-            vA.subVectors(vA, vB);
-            vC.subVectors(vC, vB);
-            vC.cross(vA);
-            
-            //face normal
-            norm = vC;
-            norm.normalize();
-            
-            norms[a] += norm.x; norms[b] += norm.x; norms[c] += norm.x;
-            norms[a + 1] += norm.y; norms[b + 1] += norm.y; norms[c + 1] += norm.y;
-            norms[a + 2] += norm.z; norms[b + 2] += norm.z; norms[c + 2] += norm.z;
-            
-        }             
-                
-    };
+        te[0] *= s; te[4] *= s; te[8] *= s; te[12] *= s;
+        te[1] *= s; te[5] *= s; te[9] *= s; te[13] *= s;
+        te[2] *= s; te[6] *= s; te[10] *= s; te[14] *= s;
+        te[3] *= s; te[7] *= s; te[11] *= s; te[15] *= s;
     
-    //sets line index array from face arr
-    //Note - assumes all faces are triangles (i.e. there will
-    //be an extra diagonal for four-sided faces - user should 
-    //specify linearr for custom shape generation to show wireframe squares
-    //as rectangles rather than two triangles)
-    geometryGroup.prototype.setLineIndices = function() {
-        
-        if (! this.faceidx)
-            return;
-                    
-        var faceArr = this.faceArray, lineArr = this.lineArray = new Uint16Array(this.faceidx*2);      
-        this.lineidx = this.faceidx*2;         
-        var faceoffset;
-            
-        for (var i = 0; i < this.faceidx / 3; ++i) {
-            
-            faceoffset = i*3; lineoffset = faceoffset*2;          
-            var a = faceArr[faceoffset], b = faceArr[faceoffset+1], c = faceArr[faceoffset+2];
-            
-            lineArr[lineoffset] = a; lineArr[lineoffset+1] = b;
-            lineArr[lineoffset+2] = a; lineArr[lineoffset+3] = c;
-            lineArr[lineoffset+4] = b; lineArr[lineoffset+5] = c;
-            
-        }
-    };
+        return this;
+    },
     
-    geometryGroup.prototype.truncateArrayBuffers = function(mesh, reallocatemem) {
-        
-        mesh = (mesh === true) ? true : false;
-        
-        var vertexArr = this.vertexArray,
-            colorArr = this.colorArray,
-            normalArr = this.normalArray,
-            faceArr = this.faceArray,
-            lineArr = this.lineArray;
+    transpose: function () {
+        var te = this.elements;
+        var tmp;
 
-        //subarray to avoid copying and reallocating memory
-        this.vertexArray = vertexArr.subarray(0,this.vertices*3);
-        this.colorArray = colorArr.subarray(0,this.vertices*3);
-        
-        if (mesh) {
-            this.normalArray = normalArr.subarray(0,this.vertices*3);
-            this.faceArray = faceArr.subarray(0,this.faceidx); 
+        tmp = te[1]; te[1] = te[4]; te[4] = tmp;
+        tmp = te[2]; te[2] = te[8]; te[8] = tmp;
+        tmp = te[6]; te[6] = te[9]; te[9] = tmp;
 
-            if(this.lineidx > 0) //not always set so reclaim memory
-                this.lineArray = lineArr.subarray(0,this.lineidx); 
-            else
-                this.lineArray = new Uint16Array();
-        }
-        else {
-            this.normalArray = new Float32Array(); 
-            this.faceArray = new Uint16Array(); 
-            this.lineArray = new Uint16Array(); 
-        }
-        
-        if(reallocatemem) { 
-            //actually copy smaller arrays to save memory
-            if(this.normalArray) this.normalArray = new Float32Array(this.normalArray);
-            if(this.faceArray) this.faceArray = new Uint16Array(this.faceArray);
-            if(this.lineArray) this.lineArray = new Uint16Array(this.lineArray);
-            if(this.vertexArray) this.vertexArray = new Float32Array(this.vertexArray);
-            if(this.colorArray) this.colorArray = new Float32Array(this.colorArray);
-            
-        }
-        this.__inittedArrays = true;        
-        
-    };
-    
-    var addGroup = function(geo) {
-        var ret = new geometryGroup(geo.geometryGroups.length);
-        geo.geometryGroups.push(ret);
-        geo.groups = geo.geometryGroups.length;
-        
-        ret.vertexArray = new Float32Array(BUFFERSIZE*3);
-        ret.colorArray = new Float32Array(BUFFERSIZE*3);
-        
-        //TODO: instantiating uint arrays according to max number of vertices
-        // is dangerous, since there exists the possibility that there will be 
-        // more face or line indices than vertex points - but so far that doesn't
-        // seem to be the case for any of the renders 
-        if (geo.mesh) {
-            ret.normalArray = new Float32Array(BUFFERSIZE*3);
-            ret.faceArray = new Uint16Array(BUFFERSIZE*6);
-            ret.lineArray = new Uint16Array(BUFFERSIZE*6);
-        }
-        
-        
-        return ret;
-    };
-    /** @constructor */
-    var Geometry = function(mesh) {
-        
-        $3Dmol.EventDispatcher.call(this);
-        
-        this.id = $3Dmol.GeometryIDCount++;
-    
-        this.name = '';
-    
-        this.hasTangents = false;
-    
-        this.dynamic = true; // the intermediate typed arrays will be deleted when set to false
-        this.mesh = (mesh === true) ? true : false; // Does this geometry represent a mesh (i.e. do we need Face/Line index buffers?)
-        // update flags
-    
-        this.verticesNeedUpdate = false;
-        this.elementsNeedUpdate = false;
-        this.normalsNeedUpdate = false;
-        this.colorsNeedUpdate = false;
-    
-        this.buffersNeedUpdate = false;
-        
-        this.geometryGroups = [];
-        this.groups = 0;
-        
-    };
-    
-    Geometry.prototype = {
-        
-        constructor : Geometry,
+        tmp = te[3]; te[3] = te[12]; te[12] = tmp;
+        tmp = te[7]; te[7] = te[13]; te[13] = tmp;
+        tmp = te[11]; te[11] = te[14]; te[14] = tmp;
 
-        //Get geometry group to accomodate addVertices new vertices - create 
-        // new group if necessary       
-        updateGeoGroup : function(addVertices) {
-        
-            addVertices = addVertices || 0;
-            
-            var retGroup = this.groups > 0 ? this.geometryGroups[ this.groups - 1 ] : null;
-            
-            if (!retGroup || retGroup.vertices + addVertices > BUFFERSIZE) 
-                retGroup = addGroup(this);
-                
-            return retGroup;
-            
-        },
-        
-        addGeoGroup : function() {
-            return addGroup(this);  
-        },
-        
-        setUpNormals : function(three) {
-            
-            three = three || false;
-            
-            for (var g = 0; g < this.groups; g++) {
-            
-                var geoGroup = this.geometryGroups[g];            
-                
-                geoGroup.setNormals(three);
-                
-            }  
-                      
-        },
-        
-        setUpWireframe : function() {
-            for (var g = 0; g < this.groups; g++) {
-                var geoGroup = this.geometryGroups[g];
-                
-                geoGroup.setLineIndices();
-            }
-        },
-        
-        //After vertices, colors, etc are collected in regular or typed arrays,
-        //  create typed arrays from regular arrays if they don't already exist,
-        initTypedArrays : function() {
-                
-            for (var g = 0; g < this.groups; g++) {
-                
-                var group = this.geometryGroups[g];
-                
-                if (group.__inittedArrays === true)
-                    continue;
-                
-                //do not actually reallocate smaller memory here because
-                //of the performance hit - if you know your geometry is small,
-                //truncate manually with the second parameter true
-                group.truncateArrayBuffers(this.mesh, false);
-            }
-            
-        
-        },
-        
-        dispose : function() {
-            this.dispatchEvent( {type : 'dispose'} );
-        }
-    };
+        return this;
+    },
 
-    
-    return Geometry;
-    
-})();
+    getPosition: function() {
+        var v1 = new $3Dmol.Vector3();
 
-Object.defineProperty($3Dmol.Geometry.prototype, "vertices", {
-    
-    /** @this {$3Dmol.Geometry} */
-    get : function() {
-        var vertices = 0;
-        for (var g = 0; g < this.groups; g++)
-            vertices += this.geometryGroups[g].vertices;
-            
-        return vertices;
-    } 
-        
-});
+        return function () {
 
-$3Dmol.GeometryIDCount = 0;
+            console.warn( 'DEPRECATED: Matrix4\'s .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.' );
 
+            var te = this.elements;
+            return v1.set( te[12], te[13], te[14] );
+        };
 
-//Raycaster
-/** @constructor */
-$3Dmol.Raycaster = (function() {
-    
-    var Raycaster = function(origin, direction, far, near) {
-        
-        this.ray = new $3Dmol.Ray(origin, direction);
-        
-        if (this.ray.direction.lengthSq() > 0) 
-            this.ray.direction.normalize();
-        
-        this.near = near || 0;
-        this.far = far || Infinity;
-    
-    };
-    
-    var sphere = new $3Dmol.Sphere();
-    var cylinder = new $3Dmol.Cylinder();
-    var triangle = new $3Dmol.Triangle();
-    var w_0 = new $3Dmol.Vector3(); // for cylinders, cylinder.c1 - ray.origin
-    var v1 = new $3Dmol.Vector3(); // all purpose local vector
-    var v2 = new $3Dmol.Vector3();
-    var v3 = new $3Dmol.Vector3();
-    //var facePlane = new $3Dmol.Plane();
-    var localRay = new $3Dmol.Ray();
-    var intersectPoint = new $3Dmol.Vector3();
-    var matrixPosition = new $3Dmol.Vector3();
-    
-    var inverseMatrix = new $3Dmol.Matrix4();
-        
-    var descSort = function(a, b) {
-        return a.distance - b.distance;
-    };
+    }(),
 
-    // [-1, 1]
-    var clamp = function(x) {
-        return Math.min(Math.max(x, -1), 1);
-    };
-    
-    //object is a Sphere or (Bounding) Box
-    var intersectObject = function(group, clickable, raycaster, intersects) {
-        
-        matrixPosition.getPositionFromMatrix(group.matrixWorld);
-        
-        if ((clickable.clickable !== true) || (clickable.intersectionShape === undefined))
-            return intersects;
-        
-        var intersectionShape = clickable.intersectionShape;
-        var precision = raycaster.linePrecision;
-        precision *= group.matrixWorld.getMaxScaleOnAxis();
-        var precisionSq = precision*precision;
+    setPosition: function ( v ) {
+        var te = this.elements;
+
+        te[12] = v.x;
+        te[13] = v.y;
+        te[14] = v.z;
+
+        return this;
+    },
+
+    getInverse: function ( m, throwOnInvertible ) {
+        // based on http://www.euclideanspace.com/maths/algebra/matrix/functions/inverse/fourD/index.htm
+        var te = this.elements;
+        var me = m.elements;
+
+        var n11 = me[0], n12 = me[4], n13 = me[8], n14 = me[12];
+        var n21 = me[1], n22 = me[5], n23 = me[9], n24 = me[13];
+        var n31 = me[2], n32 = me[6], n33 = me[10], n34 = me[14];
+        var n41 = me[3], n42 = me[7], n43 = me[11], n44 = me[15];
+
+        te[0] = n23*n34*n42 - n24*n33*n42 + n24*n32*n43 - n22*n34*n43 - n23*n32*n44 + n22*n33*n44;
+        te[4] = n14*n33*n42 - n13*n34*n42 - n14*n32*n43 + n12*n34*n43 + n13*n32*n44 - n12*n33*n44;
+        te[8] = n13*n24*n42 - n14*n23*n42 + n14*n22*n43 - n12*n24*n43 - n13*n22*n44 + n12*n23*n44;
+        te[12] = n14*n23*n32 - n13*n24*n32 - n14*n22*n33 + n12*n24*n33 + n13*n22*n34 - n12*n23*n34;
+        te[1] = n24*n33*n41 - n23*n34*n41 - n24*n31*n43 + n21*n34*n43 + n23*n31*n44 - n21*n33*n44;
+        te[5] = n13*n34*n41 - n14*n33*n41 + n14*n31*n43 - n11*n34*n43 - n13*n31*n44 + n11*n33*n44;
+        te[9] = n14*n23*n41 - n13*n24*n41 - n14*n21*n43 + n11*n24*n43 + n13*n21*n44 - n11*n23*n44;
+        te[13] = n13*n24*n31 - n14*n23*n31 + n14*n21*n33 - n11*n24*n33 - n13*n21*n34 + n11*n23*n34;
+        te[2] = n22*n34*n41 - n24*n32*n41 + n24*n31*n42 - n21*n34*n42 - n22*n31*n44 + n21*n32*n44;
+        te[6] = n14*n32*n41 - n12*n34*n41 - n14*n31*n42 + n11*n34*n42 + n12*n31*n44 - n11*n32*n44;
+        te[10] = n12*n24*n41 - n14*n22*n41 + n14*n21*n42 - n11*n24*n42 - n12*n21*n44 + n11*n22*n44;
+        te[14] = n14*n22*n31 - n12*n24*n31 - n14*n21*n32 + n11*n24*n32 + n12*n21*n34 - n11*n22*n34;
+        te[3] = n23*n32*n41 - n22*n33*n41 - n23*n31*n42 + n21*n33*n42 + n22*n31*n43 - n21*n32*n43;
+        te[7] = n12*n33*n41 - n13*n32*n41 + n13*n31*n42 - n11*n33*n42 - n12*n31*n43 + n11*n32*n43;
+        te[11] = n13*n22*n41 - n12*n23*n41 - n13*n21*n42 + n11*n23*n42 + n12*n21*n43 - n11*n22*n43;
+        te[15] = n12*n23*n31 - n13*n22*n31 + n13*n21*n32 - n11*n23*n32 - n12*n21*n33 + n11*n22*n33;
+
+        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 4 ] + me[ 2 ] * te[ 8 ] + me[ 3 ] * te[ 12 ];
+
+        if ( det === 0 ) {
+
+            var msg = "Matrix4.getInverse(): can't invert matrix, determinant is 0";
+
+            if ( throwOnInvertible || false ) {
+
+                throw new Error( msg ); 
+
+            } else {
+
+                console.warn( msg );
 
-        //Check for intersection with clickable's bounding sphere, if it exists
-        if (clickable.boundingSphere !== undefined && clickable.boundingSphere instanceof $3Dmol.Sphere) {
-            sphere.copy(clickable.boundingSphere);
-            sphere.applyMatrix4(group.matrixWorld);
-            
-            if (!raycaster.ray.isIntersectionSphere(sphere)) {
-                return intersects;
             }
+
+            this.identity();
+
+            return this;
         }
+
+        this.multiplyScalar( 1 / det );
+
+        return this;
+    },
+
+    isReflected: function() {
+        return this.matrix3FromTopLeft().getDeterminant() < 0;
+    },
+
+    compose: function() {
+        var mRotation = new $3Dmol.Matrix4(),
+            mScale = new $3Dmol.Matrix4();
         
-        //Iterate through intersection objects
-        var i, il,
-            norm, normProj, cylProj, rayProj,
-            distance, closestDistSq, denom, discriminant,
-            s, t, s_c, t_c;
-        //triangle faces
-        for (i = 0, il = intersectionShape.triangle.length; i < il; i++) {
-            
-            if (intersectionShape.triangle[i] instanceof $3Dmol.Triangle) {
-                
-                triangle.copy(intersectionShape.triangle[i]);
-                triangle.applyMatrix4(group.matrixWorld);
-                
-                norm = triangle.getNormal();
-                
-                normProj = raycaster.ray.direction.dot(norm);
-                
-                //face culling
-                if (normProj >= 0)
-                    continue;
-                
-                w_0.subVectors(triangle.a, raycaster.ray.origin);
-                
-                distance = (norm.dot(w_0)) / normProj;
-                
-                if (distance < 0)
-                    continue;
-                    
-                //intersects with plane, check if P inside triangle
-                v1.copy(raycaster.ray.direction).multiplyScalar(distance).add(raycaster.ray.origin);
-                v1.sub(triangle.a); // from pt a to intersection point P
-                
-                v2.copy(triangle.b).sub(triangle.a); // from pt a to b
-                v3.copy(triangle.c).sub(triangle.a); // from pt a to c
-                var b_dot_c = v2.dot(v3);
-                var b_sq = v2.lengthSq();
-                var c_sq = v3.lengthSq();
-                
-                // P = A + s(v2) + t(v3), inside trianle if 0 <= s, t <=1  and (s + t) <=0
-                
-                t = ( b_sq*v1.dot(v3) - b_dot_c*v1.dot(v2) ) / ( b_sq*c_sq - b_dot_c*b_dot_c );
-                
-                if (t < 0 || t > 1)
-                    continue;
-                
-                s = ( v1.dot(v2) - t*b_dot_c ) / b_sq;
-                
-                if ( (s < 0 || s > 1) || s + t > 1)
-                    continue;
-                    
-                else
-                    intersects.push({clickable : clickable,
-                                     distance : distance});  
-            }
-        }
-        
-        //cylinders
-        for (i = 0, il = intersectionShape.cylinder.length; i < il; i++) {
-            
-            if (intersectionShape.cylinder[i] instanceof $3Dmol.Cylinder){
-                
-                cylinder.copy(intersectionShape.cylinder[i]);
-                cylinder.applyMatrix4(group.matrixWorld);
-                
-                w_0.subVectors(cylinder.c1, raycaster.ray.origin); 
-                
-                cylProj = w_0.dot(cylinder.direction); // Dela
-                rayProj = w_0.dot(raycaster.ray.direction); // Epsilon
-                
-                normProj = clamp(raycaster.ray.direction.dot(cylinder.direction)); // Beta
-                
-                denom = 1 - normProj*normProj;
-                
-                if (denom === 0.0)
-                    continue;
-                
-                s_c = (normProj*rayProj - cylProj) / denom;
-                t_c = (rayProj - normProj*cylProj) / denom;
-                
-                v1.copy(cylinder.direction).multiplyScalar(s_c).add(cylinder.c1);  // Q_c
-                v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
-                
-                closestDistSq = v3.subVectors(v1, v2).lengthSq();
-                var radiusSq = cylinder.radius*cylinder.radius;
-                
-                //Smoothing?
-                //if (closestDistSq > radiusSq) radiusSq += precisionSq;
-                
-                // closest distance between ray and cylinder axis not greater than cylinder radius;
-                // might intersect this cylinder between atom and bond midpoint
-                if (closestDistSq <= radiusSq){
+        return function ( translation, rotation, scale ) {
 
-                    //Find points where ray intersects sides of cylinder
-                    discriminant = (normProj*cylProj - rayProj)*(normProj*cylProj - rayProj) - 
-                            denom*(w_0.lengthSq() - cylProj*cylProj - radiusSq);
-                    
-                    // ray tangent to cylinder?
-                    if (discriminant <= 0)
-                        t = distance = Math.sqrt(closestDistSq);
-                    else
-                        t = distance = ( (rayProj - normProj*cylProj) - Math.sqrt(discriminant) ) / denom; 
-                    
-                    //find closest intersection point; make sure it's between atom's position and cylinder midpoint
-                    
-                    s = normProj*t - cylProj;
-                    
-                    //does not intersect cylinder between atom and midpoint,
-                    // or intersects cylinder behind camera
-                    if (s < 0 || s*s > cylinder.lengthSq() || t < 0)
-                        continue;
-                    
-                    else
-                        intersects.push({clickable : clickable,
-                                         distance : distance});
-                    
-                }
-                    
-                
-            }
-            
-        }
-         
-        //lines
-        for (i = 0, il = intersectionShape.line.length; i < il; i += 2) {
-            
-            v1.copy(intersectionShape.line[i]);
-            v1.applyMatrix4(group.matrixWorld);
-            v2.copy(intersectionShape.line[i+1]);
-            v2.applyMatrix4(group.matrixWorld);
-            
-            v3.subVectors(v2, v1);
-            var bondLengthSq = v3.lengthSq();
-            v3.normalize();
-            
-            w_0.subVectors(v1, raycaster.ray.origin);
-            
-            lineProj = w_0.dot(v3);
-            rayProj = w_0.dot(raycaster.ray.direction);
-            
-            normProj = clamp(raycaster.ray.direction.dot(v3));
-            
-            denom = 1 - normProj*normProj;
-            
-            if (denom === 0.0)
-                continue;
-            
-            s_c = (normProj*rayProj - lineProj) / denom;
-            t_c = (rayProj - normProj*lineProj) / denom;
-            
-            v1.add(v3.multiplyScalar(s_c)); // Q_c
-            v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
-            
-            closestDistSq = v3.subVectors(v2, v1).lengthSq();
-            
-            if (closestDistSq < precisionSq && s_c*s_c < bondLengthSq)
-                intersects.push({clickable : clickable,
-                                 distance : t_c
-                                });
-            
-        }
+            var te = this.elements;
 
-        for (i = 0, il = intersectionShape.sphere.length; i < il; i++) {
-            //sphere
-            if (intersectionShape.sphere[i] instanceof $3Dmol.Sphere) {
-                
-                sphere.copy(intersectionShape.sphere[i]);
-                sphere.applyMatrix4(group.matrixWorld);
-                
-                if (raycaster.ray.isIntersectionSphere(sphere)) {
-                    
-                    v1.subVectors(sphere.center, raycaster.ray.origin);
-                    
-                    //distance from ray origin to point on the ray normal to sphere's center
-                    //must be less than sphere's radius (since ray intersects sphere)
-                    var distanceToCenter = v1.dot(raycaster.ray.direction);
-                    
-                    discriminant = distanceToCenter*distanceToCenter - (v1.lengthSq() - sphere.radius*sphere.radius);
-                    
-                    //Don't select if sphere center behind camera
-                    if (distanceToCenter < 0) 
-                        return intersects;
-                    
-                    //ray tangent to sphere?
-                    if (discriminant <= 0)
-                        distance = distanceToCenter;
-                    
-                    //This is reversed if sphere is closer than ray origin.  Do we have 
-                    //to worry about handling that case?
-                    else 
-                        distance = distanceToCenter - Math.sqrt(discriminant);
-    
-                    intersects.push({clickable : clickable, 
-                                     distance : distance});
-                    return intersects;
-                }
-            }        
-       }
-        
-    };   
-       
-    Raycaster.prototype.precision = 0.0001;
-    Raycaster.prototype.linePrecision = 0.2;
-    
-    Raycaster.prototype.set = function(origin, direction) {
-        
-        this.ray.set(origin, direction);
-          
-    };
-    
-    Raycaster.prototype.intersectObjects = function(group, objects) {
-        
-        var intersects = [];
-        
-        for (var i = 0, l = objects.length; i < l; i++)            
-            intersectObject(group, objects[i], this, intersects);
-            
-        intersects.sort(descSort);
-        
-        return intersects;
-        
-    };
-    
-    return Raycaster;
-    
-})();
+            mRotation.identity();
+            mRotation.setRotationFromQuaternion( rotation );
 
+            mScale.makeScale( scale.x, scale.y, scale.z );
 
-//$3Dmol Projecion 
-//TODO: can probably strip this down a lot (only used for selection handling)
-/** @constructor */
-$3Dmol.Projector = function () {
+            this.multiplyMatrices( mRotation, mScale );
 
-    var _viewMatrix = new $3Dmol.Matrix4(),
-    _viewProjectionMatrix = new $3Dmol.Matrix4();
+            te[12] = translation.x;
+            te[13] = translation.y;
+            te[14] = translation.z;
 
-    this.projectVector = function ( vector, camera ) {
+            return this;
 
-        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
+        };
+    }(),
 
-        _viewProjectionMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
+    decompose: function() {
+        var x = new $3Dmol.Vector3(),
+            y = new $3Dmol.Vector3(),
+            z = new $3Dmol.Vector3(),
+            matrix = new $3Dmol.Matrix4();
 
-        return vector.applyProjection( _viewProjectionMatrix );
+        return function ( translation, rotation, scale ) {
 
-    };
+            var te = this.elements;
 
-    this.unprojectVector = function ( vector, camera ) {
+            // grab the axis vectors
+            x.set( te[0], te[1], te[2] );
+            y.set( te[4], te[5], te[6] );
+            z.set( te[8], te[9], te[10] );
 
-        camera.projectionMatrixInverse.getInverse(camera.projectionMatrix);
+            translation = ( translation instanceof $3Dmol.Vector3 ) ? translation : new $3Dmol.Vector3();
+            rotation = ( rotation instanceof $3Dmol.Quaternion ) ? rotation : new $3Dmol.Quaternion();
+            scale = ( scale instanceof $3Dmol.Vector3 ) ? scale : new $3Dmol.Vector3();
 
-        _viewProjectionMatrix.multiplyMatrices(camera.matrixWorld, camera.projectionMatrixInverse);
-
-        return vector.applyProjection( _viewProjectionMatrix );
-
-    };
-
-};
-/*
- * Simplified Perspective Camera
- */
-
-/** @constructor */
-$3Dmol.Camera = function(fov, aspect, near, far) {
-    
-    $3Dmol.Object3D.call(this);
-    
-    this.fov = fov !== undefined ? fov : 50;
-    this.aspect = aspect !== undefined ? aspect : 1;
-    this.near = near !== undefined ? near : 0.1;
-    this.far = far !== undefined ? far : 2000;
-
-    this.projectionMatrix = new $3Dmol.Matrix4();
-    this.projectionMatrixInverse = new $3Dmol.Matrix4();
-    this.matrixWorldInverse = new $3Dmol.Matrix4();
-    
-    this.updateProjectionMatrix();
-        
-};
-
-//Inherit Object3D's prototyped methods
-$3Dmol.Camera.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Camera.prototype.lookAt = function(vector){
-    
-    //Why is the parameter order switched (compared to Object3D)?
-    this.matrix.lookAt(this.position, vector, this.up);
-    
-    if (this.rotationAutoUpdate) {    
-        
-        if (this.useQuaternion === false) 
-            this.rotation.setEulerFromRotationMatrix( this.matrix, this.eulerOrder );
-        else
-            this.quaternion.copy( this.matrix.decompose()[ 1 ] );    
-            
-    }
-    
-};
-
-$3Dmol.Camera.prototype.updateProjectionMatrix = function () {
-
-    this.projectionMatrix.makePerspective( this.fov, this.aspect, this.near, this.far );
-
-};
-
-
-//Render plugins go here
-
-/**
- * Sprite render plugin
- * @this {$3Dmol.SpritePlugin}
- */
-
-$3Dmol.SpritePlugin = function () {
-
-    var _gl, _renderer, _precision, _sprite = {};
-
-    this.init = function ( renderer ) {
-
-        _gl = renderer.context;
-        _renderer = renderer;
-
-        _precision = renderer.getPrecision();
-
-        _sprite.vertices = new Float32Array( 8 + 8 );
-        _sprite.faces    = new Uint16Array( 6 );
-
-        var i = 0;
-
-        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = -1; // vertex 0
-        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 0;  // uv 0
-
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = -1; // vertex 1
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 0;  // uv 1
-
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // vertex 2
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // uv 2
-
-        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = 1;  // vertex 3
-        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 1;  // uv 3
-
-        i = 0;
-
-        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 1; _sprite.faces[ i++ ] = 2;
-        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 2; _sprite.faces[ i++ ] = 3;
-
-        _sprite.vertexBuffer  = _gl.createBuffer();
-        _sprite.elementBuffer = _gl.createBuffer();
-
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, _sprite.vertices, _gl.STATIC_DRAW );
-
-        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
-        _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, _sprite.faces, _gl.STATIC_DRAW );
-
-        _sprite.program = createProgram( $3Dmol.ShaderLib.sprite, _precision );
-
-        _sprite.attributes = {};
-        _sprite.uniforms = {};
-
-        _sprite.attributes.position           = _gl.getAttribLocation ( _sprite.program, "position" );
-        _sprite.attributes.uv                 = _gl.getAttribLocation ( _sprite.program, "uv" );
-
-        _sprite.uniforms.uvOffset             = _gl.getUniformLocation( _sprite.program, "uvOffset" );
-        _sprite.uniforms.uvScale              = _gl.getUniformLocation( _sprite.program, "uvScale" );
-
-        _sprite.uniforms.rotation             = _gl.getUniformLocation( _sprite.program, "rotation" );
-        _sprite.uniforms.scale                = _gl.getUniformLocation( _sprite.program, "scale" );
-        _sprite.uniforms.alignment            = _gl.getUniformLocation( _sprite.program, "alignment" );
-
-        _sprite.uniforms.color                = _gl.getUniformLocation( _sprite.program, "color" );
-        _sprite.uniforms.map                  = _gl.getUniformLocation( _sprite.program, "map" );
-        _sprite.uniforms.opacity              = _gl.getUniformLocation( _sprite.program, "opacity" );
-
-        _sprite.uniforms.useScreenCoordinates = _gl.getUniformLocation( _sprite.program, "useScreenCoordinates" );
-        _sprite.uniforms.screenPosition       = _gl.getUniformLocation( _sprite.program, "screenPosition" );
-        _sprite.uniforms.modelViewMatrix      = _gl.getUniformLocation( _sprite.program, "modelViewMatrix" );
-        _sprite.uniforms.projectionMatrix     = _gl.getUniformLocation( _sprite.program, "projectionMatrix" );
-
-        _sprite.uniforms.fogType              = _gl.getUniformLocation( _sprite.program, "fogType" );
-        _sprite.uniforms.fogDensity           = _gl.getUniformLocation( _sprite.program, "fogDensity" );
-        _sprite.uniforms.fogNear              = _gl.getUniformLocation( _sprite.program, "fogNear" );
-        _sprite.uniforms.fogFar               = _gl.getUniformLocation( _sprite.program, "fogFar" );
-        _sprite.uniforms.fogColor             = _gl.getUniformLocation( _sprite.program, "fogColor" );
-
-        _sprite.uniforms.alphaTest            = _gl.getUniformLocation( _sprite.program, "alphaTest" );
-
-    };
-
-    this.render = function ( scene, camera, viewportWidth, viewportHeight ) {
-
-        var sprites = scene.__webglSprites,
-            nSprites = sprites.length;
-
-        if ( ! nSprites ) return;
+            scale.x = x.length();
+            scale.y = y.length();
+            scale.z = z.length();
 
-        var attributes = _sprite.attributes,
-            uniforms = _sprite.uniforms;
+            translation.x = te[12];
+            translation.y = te[13];
+            translation.z = te[14];
 
-        var invAspect = viewportHeight / viewportWidth;
+            // scale the rotation part
 
-        var halfViewportWidth = viewportWidth * 0.5,
-            halfViewportHeight = viewportHeight * 0.5;
+            matrix.copy( this );
 
-        // setup gl
+            matrix.elements[0] /= scale.x;
+            matrix.elements[1] /= scale.x;
+            matrix.elements[2] /= scale.x;
 
-        _gl.useProgram( _sprite.program );
+            matrix.elements[4] /= scale.y;
+            matrix.elements[5] /= scale.y;
+            matrix.elements[6] /= scale.y;
 
-        _gl.enableVertexAttribArray( attributes.position );
-        _gl.enableVertexAttribArray( attributes.uv );
+            matrix.elements[8] /= scale.z;
+            matrix.elements[9] /= scale.z;
+            matrix.elements[10] /= scale.z;
 
-        _gl.disable( _gl.CULL_FACE );
-        _gl.enable( _gl.BLEND );
+            rotation.setFromRotationMatrix( matrix );
 
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
-        _gl.vertexAttribPointer( attributes.position, 2, _gl.FLOAT, false, 2 * 8, 0 );
-        _gl.vertexAttribPointer( attributes.uv, 2, _gl.FLOAT, false, 2 * 8, 8 );
+            return [ translation, rotation, scale ];
 
-        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
+        };
+    }(),
 
-        _gl.uniformMatrix4fv( uniforms.projectionMatrix, false, camera.projectionMatrix.elements );
+    scale: function ( v ) {
+        var te = this.elements;
+        var x = v.x, y = v.y, z = v.z;
 
-        _gl.activeTexture( _gl.TEXTURE0 );
-        _gl.uniform1i( uniforms.map, 0 );
+        te[0] *= x; te[4] *= y; te[8] *= z;
+        te[1] *= x; te[5] *= y; te[9] *= z;
+        te[2] *= x; te[6] *= y; te[10] *= z;
+        te[3] *= x; te[7] *= y; te[11] *= z;
 
-        var oldFogType = 0;
-        var sceneFogType = 0;
-        var fog = scene.fog;
+        return this;
+    },
+    
+    getMaxScaleOnAxis : function() {
+        
+        var te = this.elements;
+        
+        var scaleXSq = te[0] * te[0] + te[1] * te[1] + te[2] * te[2];
+        var scaleYSq = te[4] * te[4] + te[5] * te[5] + te[6] * te[6];
+        var scaleZSq = te[8] * te[8] + te[9] * te[9] + te[10] * te[10];
+        
+        return Math.sqrt(Math.max(scaleXSq, Math.max(scaleYSq, scaleZSq)));
+        
+    },
 
-        if ( fog ) {
+    makeFrustum: function ( left, right, bottom, top, near, far ) {
+        var te = this.elements;
+              
+        var x = 2 * near / ( right - left );
+        var y = 2 * near / ( top - bottom );
 
-            _gl.uniform3f( uniforms.fogColor, fog.color.r, fog.color.g, fog.color.b );
+        var a = ( right + left ) / ( right - left );
+        var b = ( top + bottom ) / ( top - bottom );
+        var c = - ( far + near ) / ( far - near );
+        var d = - 2 * far * near / ( far - near );
 
-            _gl.uniform1f( uniforms.fogNear, fog.near );
-            _gl.uniform1f( uniforms.fogFar, fog.far );
+        te[0] = x;  te[4] = 0;  te[8] = a;  te[12] = 0;
+        te[1] = 0;  te[5] = y;  te[9] = b;  te[13] = 0;
+        te[2] = 0;  te[6] = 0;  te[10] = c; te[14] = d;
+        te[3] = 0;  te[7] = 0;  te[11] = - 1;   te[15] = 0;
 
-            _gl.uniform1i( uniforms.fogType, 1 );
-            oldFogType = 1;
-            sceneFogType = 1;
+        return this;
+    },
 
+    makePerspective: function ( fov, aspect, near, far ) {
+        var ymax = near * Math.tan( $3Dmol.Math.degToRad( fov * 0.5 ) );
+        var ymin = - ymax;
+        var xmin = ymin * aspect;
+        var xmax = ymax * aspect;
 
-        } 
+        return this.makeFrustum( xmin, xmax, ymin, ymax, near, far );
+    },
+    
+    isEqual : function (m) {
+        var me = m.elements;
+        var te = this.elements;
         
+        if (te[0] == me[0] && te[4] == me[4] && te[8] == me[8] && te[12] == me[12] &&
+            te[1] == me[1] && te[5] == me[5] && te[9] == me[9] && te[13] == me[13] &&
+            te[2] == me[2] && te[6] == me[6] && te[10] == me[10] && te[14] == me[14] &&
+            te[3] == me[3] && te[7] == me[7] && te[11] == me[11] && te[15] == me[15]) {
+            return true;
+        }
         else {
-
-            _gl.uniform1i( uniforms.fogType, 0 );
-            oldFogType = 0;
-            sceneFogType = 0;
-
+            return false;
         }
+    },
 
+    clone: function () {
+        var te = this.elements;
 
-        // update positions and sort
-
-        var i, sprite, material, screenPosition, size, fogType, scale = [];
-
-        for( i = 0; i < nSprites; i ++ ) {
-
-            sprite = sprites[ i ];
-            material = sprite.material;
-
-            if ( ! sprite.visible || material.opacity === 0 ) continue;
-
-            if ( ! material.useScreenCoordinates ) {
-
-                sprite._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, sprite.matrixWorld );
-                sprite.z = - sprite._modelViewMatrix.elements[ 14 ];
-
-            } else {
-
-                sprite.z = - sprite.position.z;
-
-            }
-
-        }
-
-        sprites.sort( painterSortStable );
-
-        // render all sprites
-
-        for( i = 0; i < nSprites; i ++ ) {
-
-            sprite = sprites[ i ];
-            material = sprite.material;
-
-            if ( ! sprite.visible || material.opacity === 0 ) continue;
-
-            if ( material.map && material.map.image && material.map.image.width ) {
-
-                _gl.uniform1f( uniforms.alphaTest, material.alphaTest );
-                var w = material.map.image.width;
-                var h = material.map.image.height;
-                
-                scale[ 0 ] = w*_renderer.devicePixelRatio/viewportWidth;
-                scale[ 1 ] = h*_renderer.devicePixelRatio/viewportHeight;
-                
-                if ( material.useScreenCoordinates === true ) {
-
-                    _gl.uniform1i( uniforms.useScreenCoordinates, 1 );
-                    _gl.uniform3f(
-                        uniforms.screenPosition,
-                        ( ( sprite.position.x * _renderer.devicePixelRatio ) - halfViewportWidth  ) / halfViewportWidth,
-                        ( halfViewportHeight - ( sprite.position.y * _renderer.devicePixelRatio ) ) / halfViewportHeight,
-                        Math.max( 0, Math.min( 1, sprite.position.z ) )
-                    );
-
-                } else {
-
-                    _gl.uniform1i( uniforms.useScreenCoordinates, 0 );
-                    _gl.uniformMatrix4fv( uniforms.modelViewMatrix, false, sprite._modelViewMatrix.elements );
-                }
-
-                if ( scene.fog && material.fog ) {
-
-                    fogType = sceneFogType;
-
-                } else {
-
-                    fogType = 0;
-
-                }
-
-                if ( oldFogType !== fogType ) {
-
-                    _gl.uniform1i( uniforms.fogType, fogType );
-                    oldFogType = fogType;
-
-                }
-
-                size = 1 / ( material.scaleByViewport ? viewportHeight : 1 );
-
-                scale[ 0 ] *= size * sprite.scale.x;
-                scale[ 1 ] *= size * sprite.scale.y;
-
-                _gl.uniform2f( uniforms.uvScale, material.uvScale.x, material.uvScale.y );
-                _gl.uniform2f( uniforms.uvOffset, material.uvOffset.x, material.uvOffset.y );
-                _gl.uniform2f( uniforms.alignment, material.alignment.x, material.alignment.y );
-
-                _gl.uniform1f( uniforms.opacity, material.opacity );
-                _gl.uniform3f( uniforms.color, material.color.r, material.color.g, material.color.b );
-
-                _gl.uniform1f( uniforms.rotation, sprite.rotation );
-                _gl.uniform2fv( uniforms.scale, scale );
-
-                //_renderer.setBlending( material.blending, material.blendEquation, material.blendSrc, material.blendDst );
-                _renderer.setDepthTest( material.depthTest );
-                _renderer.setDepthWrite( material.depthWrite );
-                _renderer.setTexture( material.map, 0 );
-
-                _gl.drawElements( _gl.TRIANGLES, 6, _gl.UNSIGNED_SHORT, 0 );
-
-            }
-
-        }
-
-        // restore gl
-
-        _gl.enable( _gl.CULL_FACE );
-
-    };
-
-    function createProgram ( shader, precision ) {
-
-        var program = _gl.createProgram();
-
-        var fragmentShader = _gl.createShader( _gl.FRAGMENT_SHADER );
-        var vertexShader = _gl.createShader( _gl.VERTEX_SHADER );
-
-        var prefix = "precision " + precision + " float;\n";
+        return new $3Dmol.Matrix4(
 
-        _gl.shaderSource( fragmentShader, prefix + shader.fragmentShader );
-        _gl.shaderSource( vertexShader, prefix + shader.vertexShader );
+            te[0], te[4], te[8], te[12],
+            te[1], te[5], te[9], te[13],
+            te[2], te[6], te[10], te[14],
+            te[3], te[7], te[11], te[15]
 
-        _gl.compileShader( fragmentShader );
-        _gl.compileShader( vertexShader );
+        );
+    },
+    
+    isIdentity: function () {
+        var te = this.elements;
         
-        if ( ! _gl.getShaderParameter(fragmentShader, _gl.COMPILE_STATUS) || ! _gl.getShaderParameter(vertexShader,_gl.COMPILE_STATUS) ) {
-
-                console.error(_gl.getShaderInfoLog(fragmentShader));
-                console.error("could not initialize shader");
-                return null;
+        if (te[0] == 1 && te[4] == 0 && te[8] == 0 && te[12] == 0 &&
+            te[1] == 0 && te[5] == 1 && te[9] == 0 && te[13] == 0 &&
+            te[2] == 0 && te[6] == 0 && te[10] == 1 && te[14] == 0 &&
+            te[3] == 0 && te[7] == 0 && te[11] == 0 && te[15] == 1) {
+            return true;
         }
-
-        _gl.attachShader( program, fragmentShader );
-        _gl.attachShader( program, vertexShader );
-
-        _gl.linkProgram( program );
-
-        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
-                console.error("Could not initialize shader");
-
-        return program;
-
-    }
-
-    function painterSortStable ( a, b ) {
-
-        if ( a.z !== b.z ) {
-
-            return b.z - a.z;
-
-        } else {
-
-            return b.id - a.id;
-
+        else {
+            return false;
         }
-
     }
-
+    
+};
+/** @constructor */
+$3Dmol.Ray = function(origin, direction) {
+    
+    this.origin = (origin !== undefined) ? 
+        origin : new $3Dmol.Vector3();
+        
+    this.direction = (direction !== undefined) ?
+        direction : new $3Dmol.Vector3();
+      
 };
 
-$3Dmol.Light = function(hex, intensity) {
+//TODO: Remove methods we don't need (intersectPlane ??)
+$3Dmol.Ray.prototype = {
     
-    $3Dmol.Object3D.call(this);
+    constructor : $3Dmol.Ray,
+     
+    set : function(origin, direction){
+        
+        this.origin.copy(origin);
+        this.direction.copy(direction);
+        
+        return this;
     
-    this.color = new $3Dmol.Color(hex);
-    this.position = new $3Dmol.Vector3( 0, 1, 0 );
-    this.target = new $3Dmol.Object3D();
-
-    this.intensity = ( intensity !== undefined ) ? intensity : 1;
-
-    this.castShadow = false;
-    this.onlyShadow = false;
+    },
     
-};
-
-$3Dmol.Light.prototype = Object.create($3Dmol.Object3D.prototype);
-/**
- * Line and Mesh material types
- * @constructor
- */
-$3Dmol.Material = function () {
-
-    $3Dmol.EventDispatcher.call( this );
-
-    this.id = $3Dmol.MaterialIdCount ++;
-
-    this.name = '';
+    copy : function(ray) {
+        
+        this.origin.copy(ray.origin);
+        this.direction.copy(ray.direction);
+        
+        return this;
+        
+    },
     
-    //TODO: Which of these instance variables can I remove??
-    this.side = $3Dmol.FrontSide;
-
-    this.opacity = 1;
-    this.transparent = false;
-
-    this.depthTest = true;
-    this.depthWrite = true;
-
-    this.polygonOffset = false;
-    this.polygonOffsetFactor = 0;
-    this.polygonOffsetUnits = 0;
-
-    this.alphaTest = 0;
-
-    this.visible = true;
-
-    this.needsUpdate = true;
-
-};
-
-
-$3Dmol.Material.prototype.setValues = function ( values ) {
-
-    if ( values === undefined ) return;
-
-    for ( var key in values ) {
-
-        var newValue = values[ key ];
-
-        if ( newValue === undefined ) {
-
-            console.warn( '$3Dmol.Material: \'' + key + '\' parameter is undefined.' );
-            continue;
-
-        }
-
-        if ( key in this ) {
-
-            var currentValue = this[ key ];
-
-            if ( currentValue instanceof $3Dmol.Color && newValue instanceof $3Dmol.Color ) {
+    at : function(t, optionalTarget) {
+        
+        var result = optionalTarget || new $3Dmol.Vector3();
+        
+        return result.copy(this.direction).multiplyScalar(t).add(this.origin);
+        
+    },
+    
+    recast : function() {
+        
+        var v1 = new $3Dmol.Vector3();
+        
+        return function(t) {
+            this.origin.copy(this.at(t, v1));
+            
+            return this;
+        };
+        
+    }(),
+    
+    closestPointToPoint : function(point, optionalTarget) {
+        
+        var result = optionalTarget || new $3Dmol.Vector3();
+        result.subVectors(point, this.origin);
+        var directionDistance = result.dot(this.direction);
+        
+        //returns a point on this ray
+        return result.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
+        
+    },
+    
+    distanceToPoint : function(point) {
+        
+        var v1 = new $3Dmol.Vector3();
+        
+        return function(point) {
+            var directionDistance = v1.subVectors(point, this.origin).dot(this.direction);
+            v1.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
+            return v1.distanceTo(point);
+        };
+        
+    }(),
+    
+    isIntersectionCylinder : function() {
+        
+    },
+    
+    isIntersectionSphere : function(sphere) {
+       return (this.distanceToPoint(sphere.center) <= sphere.radius);
+          
+    },
+    
+    isIntersectionPlane : function(plane) {
+        
+        var denominator = plane.normal.dot(this.direction);
+        
+        //plane and ray are not perpendicular
+        if (denominator !== 0) 
+            return true;
+        
+        if (plane.distanceToPoint(this.origin) === 0) 
+            return true;
+        
+        return false;
+        
+    },
+    
+    distanceToPlane : function(plane) {
+       
+       var denominator = plane.normal.dot(this.direction);
+       if (denominator === 0) {
+           
+           //line is coplanar
+       if (plane.distanceToPoint(this.origin) === 0)
+           return 0;
+       
+       //ray is parallel
+           return undefined;
+       }
+       
+       var t = - (this.origin.dot(plane.normal) + plane.constant) / denominator;
+       
+       return t;
+       
+    },
+    
+    intersectPlane : function(plane, optionalTarget) {
+       
+       var t = this.distanceToPlane(plane);
+       
+       if (t === undefined)
+           return undefined;
+       
+       return this.at(t, optionalTarget);
+       
+    },
+    
+    applyMatrix4 : function(matrix4) {
+       
+       this.direction.add(this.origin).applyMatrix4(matrix4);
+       this.origin.applyMatrix4(matrix4);
+       this.direction.sub(this.origin);
+       
+       return this;
+       
+    },
+    
+    equals : function(ray) {
+       
+       return ray.origin.equals(this.origin) && ray.direction.equals(this.direction);
+       
+    },
+    
+    clone : function() {
+    
+       return new $3Dmol.Ray().copy(this);
+    
+    }
+ 
+     
+};
 
-                currentValue.copy( newValue );
+//Intersection sphere and box shapes.  
 
-            } else if ( currentValue instanceof $3Dmol.Color ) {
 
-                currentValue.set( newValue );
+//Intersection sphere for sphere, stick render
+/** @constructor */
+$3Dmol.Sphere = function(center, radius) {
 
-            } else if ( currentValue instanceof $3Dmol.Vector3 && newValue instanceof $3Dmol.Vector3 ) {
+    this.center = (center !== undefined) ? 
+        center : new $3Dmol.Vector3();
+        
+    this.radius = (radius !== undefined) ?
+        radius : 0;
+        
+};
 
-                currentValue.copy( newValue );
+$3Dmol.Sphere.prototype = {
+    
+    constructor : $3Dmol.Sphere,
+    
+    set : function(center, radius) {
+        
+        this.center.copy(center);
+        this.radius = radius;
+        
+        return this;
+        
+    },
+    
+    copy : function(sphere) {
+        
+        this.center.copy(sphere.center);
+        this.radius = sphere.radius;
+        
+        return this;
+        
+    },
+    
+    applyMatrix4 : function(matrix) {
+        
+        this.center.applyMatrix4(matrix);
+        this.radius = this.radius * matrix.getMaxScaleOnAxis();
+        
+        return this;
+        
+    },
+    
+    translate : function(offset) {
+        
+        this.center.add(offset);
+        
+        return this;
+        
+    },
+    
+    equals : function(sphere) {
+        
+        return sphere.center.equals(this.center) && (sphere.radius === this.radius);
+        
+    },
+       
+    clone : function() {
+        
+        return new $3Dmol.Sphere().copy(this);
+        
+    }
 
-            } else {
+};
 
-                this[ key ] = newValue;
 
-            }
+//Bounding cylinder for stick render  
+/** @constructor */
+$3Dmol.Cylinder = function(c1, c2, radius) {
 
-        }
+    this.c1 = (c1 !== undefined) ?
+        c1 : new $3Dmol.Vector3();
 
-    }
+    this.c2 = (c2 !== undefined) ?
+        c2 : new $3Dmol.Vector3();
+        
+    this.direction = new $3Dmol.Vector3().subVectors(this.c2, this.c1).normalize();
 
+    this.radius = (radius !== undefined) ?
+        radius : 0;
+    
 };
-//TODO: might want to look into blending equations
-$3Dmol.Material.prototype.clone = function ( material ) {
-
-    if ( material === undefined ) material = new $3Dmol.Material();
 
-    material.name = this.name;
+$3Dmol.Cylinder.prototype = {
 
-    material.side = this.side;
+    constructor : $3Dmol.Cylinder,
 
-    material.opacity = this.opacity;
-    material.transparent = this.transparent;
+    copy : function(cylinder) {
 
-    material.depthTest = this.depthTest;
-    material.depthWrite = this.depthWrite;
+        this.c1.copy(cylinder.c1);
+        this.c2.copy(cylinder.c2);
+        this.direction.copy(cylinder.direction);
+        this.radius = cylinder.radius;
 
-    material.polygonOffset = this.polygonOffset;
-    material.polygonOffsetFactor = this.polygonOffsetFactor;
-    material.polygonOffsetUnits = this.polygonOffsetUnits;
+        return this;
 
-    material.alphaTest = this.alphaTest;
+    },
+    
+    lengthSq : function() {
+    
+        var vector = new $3Dmol.Vector3();
+        
+        return function(){
+            return vector.subVectors(this.c2, this.c1).lengthSq();
+        };
+        
+    }(),
 
-    material.overdraw = this.overdraw;
+    applyMatrix4 : function(matrix) {
+        
+        this.direction.add(this.c1).applyMatrix4(matrix);
+        this.c1.applyMatrix4(matrix);
+        this.c2.applyMatrix4(matrix);
+        this.direction.sub(this.c1).normalize();
+        this.radius = this.radius * matrix.getMaxScaleOnAxis();
 
-    material.visible = this.visible;
+        return this;
 
-    return material;
+    }
 
 };
 
-$3Dmol.Material.prototype.dispose = function () {
 
-    this.dispatchEvent( { type: 'dispose' } );
+//plane specified by three points
+/** @constructor */
+$3Dmol.Triangle = function(a, b, c){
+   
+    this.a = (a !== undefined) ?
+        a : new $3Dmol.Vector3();
 
+    this.b = (b !== undefined) ?
+        b : new $3Dmol.Vector3();
+    
+    this.c = (c !== undefined) ?
+        c : new $3Dmol.Vector3();   
+  
 };
 
-$3Dmol.MaterialIdCount = 0;
+$3Dmol.Triangle.prototype = {
 
-//Line basic material
-/** @constructor */
-$3Dmol.LineBasicMaterial = function(parameters) {
-    
-    $3Dmol.Material.call(this);
-    
-    this.color = new $3Dmol.Color(0xffffff);
-    
-    this.linewidth = 1;
-    this.linecap = 'round';
-    this.linejoin = 'round';
+    constructor : $3Dmol.Triangle,
     
-    this.vertexColors = false;
+    copy : function(triangle) {
+        
+        this.a.copy(triangle.a);
+        this.b.copy(triangle.b);
+        this.c.copy(triangle.c);
+        
+        return this;
+        
+    },
     
-    this.fog = true;
-    this.shaderID = "basic";
-    this.setValues(parameters);
+    applyMatrix4 : function(matrix) {
+        
+        this.a.applyMatrix4(matrix);
+        this.b.applyMatrix4(matrix);
+        this.c.applyMatrix4(matrix);
+        
+        return this;
+        
+    },
     
+    getNormal : function() {
+        
+        var v1 = new $3Dmol.Vector3();
+        
+        return function() {
+            
+            var norm = this.a.clone();
+            norm.sub(this.b);
+            v1.subVectors(this.c, this.b);
+            
+            norm.cross(v1);
+            norm.normalize();
+            
+            return norm;
+            
+        };
+        
+    }()
+
 };
 
-$3Dmol.LineBasicMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-$3Dmol.LineBasicMaterial.prototype.clone = function() {
+/* core Object3D
+ * Base class for Scene, Camera, Geometry
+ * Geometry class
+ */
+
+//Event Handling
+/** @this {$3Dmol.EventDispatcher} */
+$3Dmol.EventDispatcher = function() {
   
-    var material = new $3Dmol.LineBasicMaterial();
-    
-    $3Dmol.Material.prototype.clone.call(this, material);
+    var listeners = {};
     
-    material.color.copy();
-    return material;
-};
-
-//Mesh Lambert material
-/** @constructor */
-$3Dmol.MeshLambertMaterial = function(parameters) {
+    this.addEventListener = function(type, listener) {
+        if (listeners[type] === undefined)
+            listeners[type] = [];
+        
+        if (listeners[type].indexOf(listener) === -1)
+            listeners[type].push(listener);
+    };  
     
-    $3Dmol.Material.call(this);
+    this.removeEventListener = function(type, listener) {
+        
+        var index = listeners[type].indexOf(listener);
+        
+        if (index !== -1)
+            listeners[type].splice(index, 1);
+              
+    };
     
-    this.color = new $3Dmol.Color(0xffffff);
-    this.ambient = new $3Dmol.Color(0xfffff);
-    this.emissive = new $3Dmol.Color(0x000000);
+    this.dispatchEvent = function(event) {
+        
+        var listenerArray = listeners[event.type];
+        
+        if (listenerArray !== undefined) {
+            event.target = this;
+            
+            for (var i = 0, l = listenerArray.length; i < l; i++)
+                listenerArray[i].call(this, event);
+                
+        }
+            
+    };
     
-    //TODO: Which of these instance variables do I really need?
-    this.wrapAround = false;
-    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
+};
+
+$3Dmol.Color = function( color ){
     
-    this.map = null;
+    if ( arguments.length > 1) {
+            this.r = arguments[0] || 0.0;
+            this.g = arguments[1] || 0.0;
+            this.b = arguments[2] || 0.0;
+
+            return this;
+    }
     
-    this.lightMap = null;
+    return this.set(color);
+                
+};
+
+$3Dmol.Color.prototype = {
     
-    this.specularMap = null;
+    constructor: $3Dmol.Color,
     
-    this.envMap = null;
-    this.reflectivity = 1;
-    this.refractionRatio = 0.98;
+    r: 0.0, g: 0.0, b: 0.0,
     
-    this.fog = true;
+    set : function(val) {
+        
+            if (val instanceof $3Dmol.Color) 
+                return val.clone();
+
+            else if (typeof val === 'number')
+                this.setHex(val);
+            
+            else if (typeof val === 'object' && "r" in val && "g" in val && "b" in val) {
+                this.r = val.r;
+                this.g = val.g;
+                this.b = val.b;
+            }
+    },
     
-    this.wireframe = false;
-    this.wireframeLinewidth = 1;
-    this.wireframeLinecap = 'round';
-    this.wireframeLinejoin = 'round';
+    setHex: function(hex) {
+        
+            hex = Math.floor(hex);
+
+            this.r = (hex >> 16 & 255) / 255;
+            this.g = (hex >> 8 & 255) / 255;
+            this.b = (hex & 255) / 255;                                                                                     
+        
+            return this;
+    },
     
-    this.shading = $3Dmol.SmoothShading;
-    this.shaderID = "lambert";
-    this.vertexColors = $3Dmol.NoColors;
+    getHex: function() {
+        var R = Math.round(this.r*255);
+        var G = Math.round(this.g*255);
+        var B = Math.round(this.b*255);
+        return R<<16 | G << 8 | B;
+    },
     
-    this.skinning = false;
+    clone : function() {
+            return new $3Dmol.Color(this.r, this.g, this.b);
+    },
+        
+    copy : function(color) {
+        this.r = color.r;
+        this.g = color.g;
+        this.b = color.b;
+        
+        return this;
+    },
     
-    this.setValues(parameters);
+    //return object that represents color components from 0 to 255
+    scaled : function() {
+        var ret = {};
+        ret.r = Math.round(this.r*255);
+        ret.g = Math.round(this.g*255);
+        ret.b = Math.round(this.b*255);
+        ret.a = 1.0;
+        return ret;
+    }
     
 };
 
-$3Dmol.MeshLambertMaterial.prototype = Object.create($3Dmol.Material.prototype);
-
-$3Dmol.MeshLambertMaterial.prototype.clone = function(material) {
-  
-    if ( typeof material === "undefined" ) material = new $3Dmol.MeshLambertMaterial();
-    
-    $3Dmol.Material.prototype.clone.call(this, material);
-    
-    material.color.copy(this.color);
-    material.ambient.copy(this.ambient);
-    material.emissive.copy(this.emissive);
-    
-    material.wrapAround = this.wrapAround;
-    material.wrapRGB.copy(this.wrapRGB);
-    
-    material.map = this.map;
+//Object3D base constructor function
+/** @this {$3Dmol.Object3D} */
+$3Dmol.Object3D = function() {
     
-    material.lightMap = this.lightMap;
+    this.id = $3Dmol.Object3DIDCount++;
     
-    material.specularMap = this.specularMap;
+    this.name = "";
     
-    material.envMap = this.envMap;
-    material.combine = this.combine;
-    material.reflectivity = this.reflectivity;
-    material.refractionRatio = this.refractionRatio;
+    this.parent = undefined;
+    this.children = [];
     
-    material.fog = this.fog;
+    this.position = new $3Dmol.Vector3();
+    this.rotation = new $3Dmol.Vector3();
+    this.matrix = new $3Dmol.Matrix4();
+    this.matrixWorld = new $3Dmol.Matrix4();
+    this.quaternion = new $3Dmol.Quaternion();
+    this.eulerOrder = 'XYZ';
     
-    material.shading = this.shading;
-    material.shaderID = this.shaderID;
-    material.vertexColors = this.vertexColors;
+    this.up = new $3Dmol.Vector3(0, 1, 0);
+    this.scale = new $3Dmol.Vector3(1, 1, 1);
     
-    material.skinning = this.skinning;
-    material.morphTargets = this.morphTargets;
-    material.morphNormals = this.morphNormals;
+    this.matrixAutoUpdate = true;
+    this.matrixWorldNeedsUpdate = true;
+    this.rotationAutoUpdate = true;
+    this.useQuaternion = false;
     
-    return material;
+    this.visible = true;
     
 };
 
-//Double sided Mesh Lambert material
-/** @constructor */
-$3Dmol.MeshDoubleLambertMaterial = function(parameters) {
-    
-    $3Dmol.MeshLambertMaterial.call(this, parameters);
-
-    this.shaderID = "lambertdouble";
-    this.side = $3Dmol.DoubleSide;    
+$3Dmol.Object3D.prototype = {
     
-};
-
-$3Dmol.MeshDoubleLambertMaterial.prototype = Object.create($3Dmol.MeshLambertMaterial.prototype);
-
-$3Dmol.MeshDoubleLambertMaterial.prototype.clone = function() {
-  
-    var material = new $3Dmol.MeshDoubleLambertMaterial();
+    constructor : $3Dmol.Object3D,
     
-    $3Dmol.MeshLambertMaterial.prototype.clone.call(this, material);
+    lookAt : function(vector) {
         
-    return material;
-    
-};
-
-
-//Imposter material
-/** @constructor */
-$3Dmol.ImposterMaterial = function(parameters) {
-  
-  $3Dmol.Material.call(this);
-  
-  this.color = new $3Dmol.Color(0xffffff);
-  this.ambient = new $3Dmol.Color(0xfffff);
-  this.emissive = new $3Dmol.Color(0x000000);
-  
-  //TODO: Which of these instance variables do I really need?
-  this.wrapAround = false;
-  this.wrapRGB = new $3Dmol.Vector3(1,1,1);
-  
-  this.map = null;
-  
-  this.lightMap = null;
-  
-  this.specularMap = null;
-  
-  this.envMap = null;
-  this.reflectivity = 1;
-  this.refractionRatio = 0.98;
-  
-  this.fog = true;
-  
-  this.wireframe = false;
-  this.wireframeLinewidth = 1;
-  this.wireframeLinecap = 'round';
-  this.wireframeLinejoin = 'round';
-  
-  this.shading = $3Dmol.SmoothShading;
-  this.shaderID = "sphereimposter";
-  this.vertexColors = $3Dmol.NoColors;
-  
-  this.skinning = false;
-  
-  this.setValues(parameters);
-  
-};
-
-$3Dmol.ImposterMaterial.prototype = Object.create($3Dmol.Material.prototype);
-
-$3Dmol.ImposterMaterial.prototype.clone = function() {
-
-  var material = new $3Dmol.ImposterMaterial();
-  
-  $3Dmol.Material.prototype.clone.call(this, material);
-  
-  material.color.copy(this.color);
-  material.ambient.copy(this.ambient);
-  material.emissive.copy(this.emissive);
-  
-  material.wrapAround = this.wrapAround;
-  material.wrapRGB.copy(this.wrapRGB);
-  
-  material.map = this.map;
-  
-  material.lightMap = this.lightMap;
-  
-  material.specularMap = this.specularMap;
-  
-  material.envMap = this.envMap;
-  material.combine = this.combine;
-  material.reflectivity = this.reflectivity;
-  material.refractionRatio = this.refractionRatio;
-  
-  material.fog = this.fog;
-  
-  material.shading = this.shading;
-  material.shaderID = this.shaderID;
-  material.vertexColors = this.vertexColors;
-  
-  material.skinning = this.skinning;
-  material.morphTargets = this.morphTargets;
-  material.morphNormals = this.morphNormals;
-  
-  return material;
-  
-};
-
-
-//Sprite material
-/** @constructor */
-$3Dmol.SpriteMaterial = function(parameters) {
-    
-    $3Dmol.Material.call(this);
-    
-    this.color = new $3Dmol.Color(0xffffff);
-    this.map = new $3Dmol.Texture();
-    
-    this.useScreenCoordinates = true;
-    this.depthTest = !this.useScreenCoordinates;
-    this.sizeAttenuation = !this.useScreenCoordinates;
-    this.scaleByViewPort = !this.sizeAttenuation;
-    this.alignment = $3Dmol.SpriteAlignment.center.clone();
+        this.matrix.lookAt(vector, this.position, this.up);
+        
+        if (this.rotationAutoUpdate) {
+            
+            if (this.useQuaternion === true) 
+                this.quaternion.copy(this.matrix.decompose()[1]);
+            else
+                this.rotation.setEulerFromRotationMatrix(this.matrix, this.eulerOrder);
+        }
+    },
     
-    this.fog = false; // use scene fog
+    //add child object
+    add : function(object) {
+        if (object === this){
+            console.error("Can't add $3Dmol.Object3D to itself");
+            return;
+        }
+        
+        object.parent = this;
+        this.children.push(object);
+        
+        //add to the scene (i.e. follow up this instance's parents until reach the top)
+        
+        var scene = this;
+        
+        while (scene.parent !== undefined)
+            scene = scene.parent;
+            
+        if (scene !== undefined && scene instanceof $3Dmol.Scene) 
+            scene.__addObject(object);
+        
+    },
     
-    this.uvOffset = new $3Dmol.Vector2(0, 0);
-    this.uvScale = new $3Dmol.Vector2(1, 1);
+    remove : function(object) {
+        
+        var index = this.children.indexOf(object);
+        
+        if (index !== -1) {
+            
+            object.parent = undefined;
+            this.children.splice(index, 1);
+            
+            //Remove from scene
+            
+            var scene = this;
+            
+            while (scene.parent !== undefined)
+                scene = scene.parent;
+                
+            if (scene !== undefined && scene instanceof $3Dmol.Scene)
+                scene.__removeObject(object);
+                
+        }
+    },
     
-    this.setValues(parameters);
+    updateMatrix : function() {
+        
+        this.matrix.setPosition(this.position);
+        
+        if (this.useQuaternion === false) 
+            this.matrix.setRotationFromEuler(this.rotation, this.eulerOrder);
+        else
+            this.matrix.setRotationFromQuaternion(this.quaternion);
+        
+        //TODO: Do I need this??
+        if (this.scale.x !== 1 || this.scale.y !== 1 || this.scale.z !== 1)
+            this.matrix.scale(this.scale);
+            
+        this.matrixWorldNeedsUpdate = true;
+        
+    },
     
-    parameters = parameters || {};
+    updateMatrixWorld : function(force) {
+        
+        if (this.matrixAutoUpdate === true) 
+            this.updateMatrix();
+        
+        if (this.matrixWorldNeedsUpdate === true || force === true) {
+            
+            if (this.parent === undefined)
+                this.matrixWorld.copy(this.matrix);
+            else
+                this.matrixWorld.multiplyMatrices(this.parent.matrixWorld, this.matrix);
+                
+        }
+        
+        this.matrixWorldNeedsUpdate = false;
+        
+        //Update matrices of all children
+        for (var i = 0; i < this.children.length; i++) {
+            this.children[i].updateMatrixWorld(true);
+        }
+    },
     
-    if (parameters.depthTest === undefined)
-        this.depthTest = !this.useScreenCoordinates;
-    if (parameters.sizeAttenuation === undefined)
-        this.sizeAttenuation = !this.useScreenCoordinates;
-    if (parameters.scaleByViewPort === undefined)
-        this.scaleByViewPort = !this.sizeAttenuation;
+    clone : function(object) {
+        
+        if (object === undefined)
+            object = new $3Dmol.Object3D();
+            
+        object.name = this.name;
+        
+        object.up.copy(this.up);
+        object.position.copy(this.position);
+        object.rotation.copy(this.rotation);
+        object.eulerOrder = this.eulerOrder;
+        object.scale.copy(this.scale);
+
+        object.rotationAutoUpdate = this.rotationAutoUpdate;
+        object.matrix.copy(this.matrix);
+        object.matrixWorld.copy(this.matrixWorld);
+        object.quaternion.copy(this.quaternion);
+        object.matrixAutoUpdate = this.matrixAutoUpdate;
+        object.matrixWorldNeedsUpdate = this.matrixWorldNeedsUpdate;
+        
+        object.useQuaternion = this.useQuaternion;
+        
+        object.visible = this.visible;
+        
+        for (var i = 0; i < this.children.length; i++) {
+            var child = this.children[i];
+            object.add(child.clone());
+        }
+        
+        return object;
+        
+    },
     
+    setVisible: function(val) { //recursively set visibility
+        this.visible = val;
+        for (var i = 0; i < this.children.length; i++) {
+            var child = this.children[i];
+            child.setVisible(val);
+        }
+    }
 };
 
-$3Dmol.SpriteMaterial.prototype = Object.create($3Dmol.Material.prototype);
+$3Dmol.Object3DIDCount = 0;
 
-$3Dmol.SpriteMaterial.prototype.clone = function() {
-    
-    var material = new $3Dmol.SpriteMaterial();
-    
-    $3Dmol.Material.prototype.clone.call(this, material);
-    
-    material.color.copy(this.color);
-    material.map = this.map;
-    
-    material.useScreenCoordinates = useScreenCoordinates;
-    material.sizeAttenuation = this.sizeAttenuation;
-    material.scaleByViewport = this.scaleByViewPort;
-    material.alignment.copy(this.alignment);
-    
-    material.uvOffset.copy(this.uvOffset);
-    
-    return material;
-    
-};
-
-//Alignment for Sprites
-
-$3Dmol.SpriteAlignment = {};
-$3Dmol.SpriteAlignment.topLeft = new $3Dmol.Vector2(1, -1);
-$3Dmol.SpriteAlignment.topCenter = new $3Dmol.Vector2(0, -1);
-$3Dmol.SpriteAlignment.topRight = new $3Dmol.Vector2(-1, -1);
-$3Dmol.SpriteAlignment.centerLeft = new $3Dmol.Vector2(1, 0);
-$3Dmol.SpriteAlignment.center = new $3Dmol.Vector2(0, 0);
-$3Dmol.SpriteAlignment.centerRight = new $3Dmol.Vector2(-1, 0);
-$3Dmol.SpriteAlignment.bottomLeft = new $3Dmol.Vector2(1, 1);
-$3Dmol.SpriteAlignment.bottomCenter = new $3Dmol.Vector2(0, 1);
-$3Dmol.SpriteAlignment.bottomRight = new $3Dmol.Vector2(-1, 1);
-
-
-//Texture
-//We really only create textures from 2d rendering contexts (to display text labels)
-/** @constructor */
-$3Dmol.Texture = function(image) {
-
-    $3Dmol.EventDispatcher.call(this);
-    
-    this.id = $3Dmol.TextureIdCount++;
-    
-    this.name = "";
-    
-    this.image = image;
-    this.mipmaps = [];
-    
-    this.mapping = new $3Dmol.UVMapping();
+//Geometry class
+//TODO: What can I remove - how can I optimize ?
+$3Dmol.Geometry = (function() {
+   
+    var BUFFERSIZE = 65535; //limited to 16bit indices
     
-    this.wrapS = $3Dmol.ClampToEdgeWrapping;
-    this.wrapT = $3Dmol.ClampToEdgeWrapping;
     
-    this.magFilter = $3Dmol.LinearFilter;
-    this.minFilter = $3Dmol.LinearMipMapLinearFilter;
+    /** @constructor */
+    var geometryGroup = function(id) {
+        this.id = id || 0;
+        //for performance reasons, callers must directly modify these
+        this.vertexArray = null;
+        this.colorArray = null;
+        this.normalArray = null;
+        this.faceArray = null;
+        this.radiusArray = null;
+        //this.adjFaceArray=null;
+        this.lineArray = null;
+        this.vertices = 0;
+        this.faceidx = 0;
+        this.lineidx = 0;
+        
+    };
     
-    this.anisotropy = 1;
+    geometryGroup.prototype.getNumVertices = function() {
+        return this.vertices;
+    };
     
-    this.format = $3Dmol.RGBAFormat;
-    this.type = $3Dmol.UnsignedByteType;
+    geometryGroup.prototype.getVertices = function() {
+        return this.vertexArray;
+    };
     
-    this.offset = new $3Dmol.Vector2(0, 0);
-    this.repeat = new $3Dmol.Vector2(1, 1);
     
-    this.generateMipmaps = true;
-    this.premultiplyAlpha = false;
-    this.flipY = true;
-    this.unpackAlignment = 4;
+    geometryGroup.prototype.getCentroid = function() {
+        
+        var centroid = new $3Dmol.Vector3();
+        var offset, x, y, z;
+        
+        for (var i = 0; i < this.vertices; ++i) {
+            offset = i*3;
+            
+            x = this.vertexArray[offset]; y = this.vertexArray[offset+1]; z = this.vertexArray[offset+2];
+            
+            centroid.x += x; centroid.y += y; centroid.z += z;
+        }
+        
+        //divideScalar checks for 0 denom
+        centroid.divideScalar(this.vertices);
+        
+        return centroid;
+    };
     
-    this.needsUpdate = false;
-    this.onUpdate = null;
+    //setup normals - vertex and face array must exist
+    geometryGroup.prototype.setNormals = function() {        
+        
+        var faces = this.faceArray;
+        var verts = this.vertexArray;
+        var norms = this.normalArray;
+        
+        if (! this.vertices || ! this.faceidx) 
+            return;
+        
+        //vertex indices
+        var a, b, c, d,
+        //and actual vertices
+        vA, vB, vC, norm;
+            
+        for (var i = 0; i < faces.length / 3; ++i) {
+            
+            a = faces[i * 3] * 3;
+            b = faces[i * 3 + 1] * 3;
+            c = faces[i * 3 + 2] * 3;
+            
+            vA = new $3Dmol.Vector3(verts[a], verts[a+1], verts[a+2]);
+            vB = new $3Dmol.Vector3(verts[b], verts[b+1], verts[b+2]);
+            vC = new $3Dmol.Vector3(verts[c], verts[c+1], verts[c+2]);
+            
+            vA.subVectors(vA, vB);
+            vC.subVectors(vC, vB);
+            vC.cross(vA);
+            
+            //face normal
+            norm = vC;
+            norm.normalize();
+            
+            norms[a] += norm.x; norms[b] += norm.x; norms[c] += norm.x;
+            norms[a + 1] += norm.y; norms[b + 1] += norm.y; norms[c + 1] += norm.y;
+            norms[a + 2] += norm.z; norms[b + 2] += norm.z; norms[c + 2] += norm.z;
+            
+        }             
+                
+    };
     
-};
-
-$3Dmol.Texture.prototype = {
-
-    constructor : $3Dmol.Texture,
+    //sets line index array from face arr
+    //Note - assumes all faces are triangles (i.e. there will
+    //be an extra diagonal for four-sided faces - user should 
+    //specify linearr for custom shape generation to show wireframe squares
+    //as rectangles rather than two triangles)
+    geometryGroup.prototype.setLineIndices = function() {
+        
+        if (! this.faceidx)
+            return;
+                    
+        var faceArr = this.faceArray, lineArr = this.lineArray = new Uint16Array(this.faceidx*2);      
+        this.lineidx = this.faceidx*2;         
+        var faceoffset;
+            
+        for (var i = 0; i < this.faceidx / 3; ++i) {
+            
+            faceoffset = i*3; lineoffset = faceoffset*2;          
+            var a = faceArr[faceoffset], b = faceArr[faceoffset+1], c = faceArr[faceoffset+2];
+            
+            lineArr[lineoffset] = a; lineArr[lineoffset+1] = b;
+            lineArr[lineoffset+2] = a; lineArr[lineoffset+3] = c;
+            lineArr[lineoffset+4] = b; lineArr[lineoffset+5] = c;
+            
+        }
+    };
     
-    clone : function(texture) {
+    geometryGroup.prototype.truncateArrayBuffers = function(mesh, reallocatemem) {
         
-        if (texture === undefined)
-            texture = new $3Dmol.Texture();
+        mesh = (mesh === true) ? true : false;
         
-        texture.image = this.image;
-        texture.mipmaps = this.mipmaps.slice(0);
+        var vertexArr = this.vertexArray,
+            colorArr = this.colorArray,
+            normalArr = this.normalArray,
+            faceArr = this.faceArray,
+            lineArr = this.lineArray,
+            radiusArr = this.radiusArray;
+
+        //subarray to avoid copying and reallocating memory
+        this.vertexArray = vertexArr.subarray(0,this.vertices*3);
+        this.colorArray = colorArr.subarray(0,this.vertices*3);
         
-        texture.mapping = this.mapping;
+        if (mesh) {
+            this.normalArray = normalArr.subarray(0,this.vertices*3);
+            this.faceArray = faceArr.subarray(0,this.faceidx); 
+            
+            if(this.lineidx > 0) //not always set so reclaim memory
+                this.lineArray = lineArr.subarray(0,this.lineidx); 
+            else
+                this.lineArray = new Uint16Array();
+                        
+        }        
+        else {
+            this.normalArray = new Float32Array(); 
+            this.faceArray = new Uint16Array(); 
+            this.lineArray = new Uint16Array(); 
+        }
+        if (radiusArr) {
+            this.radiusArray = radiusArr.subarray(0, this.vertices);
+        }
         
-        texture.wrapS = this.wrapS;
-        texture.wrapT = this.wrapT;
+        if(reallocatemem) { 
+            //actually copy smaller arrays to save memory
+            if(this.normalArray) this.normalArray = new Float32Array(this.normalArray);
+            if(this.faceArray) this.faceArray = new Uint16Array(this.faceArray);
+            if(this.lineArray) this.lineArray = new Uint16Array(this.lineArray);
+            if(this.vertexArray) this.vertexArray = new Float32Array(this.vertexArray);
+            if(this.colorArray) this.colorArray = new Float32Array(this.colorArray);
+            if(this.radiusArray) this.radiusArray = new Float32Array(this.radiusArray);
+        }
+        this.__inittedArrays = true;        
         
-        texture.magFilter = this.magFilter;
-        texture.minFilter = this.minFilter;
+    };
+    
+    var addGroup = function(geo) {
+        var ret = new geometryGroup(geo.geometryGroups.length);
+        geo.geometryGroups.push(ret);
+        geo.groups = geo.geometryGroups.length;
         
-        texture.anisotropy = this.anisotropy;
+        ret.vertexArray = new Float32Array(BUFFERSIZE*3);
+        ret.colorArray = new Float32Array(BUFFERSIZE*3);
         
-        texture.format = this.format;
-        texture.type = this.type;
+        //TODO: instantiating uint arrays according to max number of vertices
+        // is dangerous, since there exists the possibility that there will be 
+        // more face or line indices than vertex points - but so far that doesn't
+        // seem to be the case for any of the renders 
+        if (geo.mesh) {
+            ret.normalArray = new Float32Array(BUFFERSIZE*3);
+            ret.faceArray = new Uint16Array(BUFFERSIZE*6);
+            ret.lineArray = new Uint16Array(BUFFERSIZE*6);
+        }
+        if (geo.radii) {
+            ret.radiusArray = new Float32Array(BUFFERSIZE);
+        }
+        ret.useOffset = geo.offset;
         
-        texture.offset.copy(this.offset);
-        texture.repeat.copy(this.repeat);
         
-        texture.generateMipmaps = this.generateMipmaps;
-        texture.premultiplyAlpha = this.premultiplyAlpha;
-        texture.flipY = this.flipY;
-        texture.unpackAlignment = this.unpackAlignment;
+        return ret;
+    };
+    /** @constructor */
+    var Geometry = function(mesh, radii,offset) {
         
-        return texture;
+        $3Dmol.EventDispatcher.call(this);
         
-    },
+        this.id = $3Dmol.GeometryIDCount++;
     
-    dispose : function() {
-        
-        this.dispatchEvent( {type: 'dispose'});
+        this.name = '';
+    
+        this.hasTangents = false;
+    
+        this.dynamic = true; // the intermediate typed arrays will be deleted when set to false
+        this.mesh = (mesh === true) ? true : false; // Does this geometry represent a mesh (i.e. do we need Face/Line index buffers?)
+        this.radii = radii || false;
+        this.offset = offset || false; //offset buffer used for instancing
+        // update flags
+    
+        this.verticesNeedUpdate = false;
+        this.elementsNeedUpdate = false;
+        this.normalsNeedUpdate = false;
+        this.colorsNeedUpdate = false;
+    
+        this.buffersNeedUpdate = false;
         
-    }    
+        this.geometryGroups = [];
+        this.groups = 0;
+        
+    };
     
-};
-
-$3Dmol.TextureIdCount = 0;
-
-
-// sides
-$3Dmol.FrontSide = 0;
-$3Dmol.BackSide = 1;
-$3Dmol.DoubleSide = 2;
-
-// shading
-$3Dmol.NoShading = 0;
-$3Dmol.FlatShading = 1;
-$3Dmol.SmoothShading = 2;
-
-// colors
-$3Dmol.NoColors = 0;
-$3Dmol.FaceColors = 1;
-$3Dmol.VertexColors = 2;
-
-//Texture constants
-//TODO: Which of these do I need (since I only use textures to display label sprites) ?
-$3Dmol.MultiplyOperation = 0;
-$3Dmol.MixOperation = 1;
-$3Dmol.AddOperation = 2;
-
-// mapping modes
-
-$3Dmol.UVMapping = function() {};
-
-// wrapping modes
-$3Dmol.ClampToEdgeWrapping = 1001;
-
-//Filters
-$3Dmol.LinearFilter = 1006;
-$3Dmol.LinearMipMapLinearFilter = 1008;
-
-//Data types
-$3Dmol.UnsignedByteType = 1009;
-
-//Pixel formats
-$3Dmol.RGBAFormat = 1021;/* 
- * $3Dmol Mesh and Line objects
- */
-
-
-//Line Object
-/** @constructor */
-$3Dmol.Line = function (geometry, material, type) {
-
-    $3Dmol.Object3D.call(this);
-
-    this.geometry = geometry;
-        //TODO: update material and type to webgl
-    this.material = (material !== undefined) ? material : new $3Dmol.LineBasicMaterial( { color: Math.random() * 0xffffff } );
-    this.type = (type !== undefined) ? type : $3Dmol.LineStrip;
-
-};
-
-$3Dmol.LineStrip = 0;
-$3Dmol.LinePieces = 1;
-
-$3Dmol.Line.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Line.prototype.clone = function (object) {
-
-    if (object === undefined) object = new $3Dmol.Line(this.geometry, this.material, this.type);
-
-    $3Dmol.Object3D.prototype.clone.call(this, object);
-
-    return object;
-
-};
-
-
-//Mesh Object
-/** @constructor */
-$3Dmol.Mesh = function(geometry, material) {
-
-    $3Dmol.Object3D.call(this);
-
-    this.geometry = geometry;
-    this.material = (material !== undefined) ? material : new $3Dmol.MeshBasicMaterial( { color: Math.random() * 0xffffff, wireframe: true } );
-
-};
-
-$3Dmol.Mesh.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Mesh.prototype.clone = function (object) {
-
-    if (object === undefined) object = new $3Dmol.Mesh(this.geometry, this.material);
-
-    $3Dmol.Object3D.prototype.clone.call(this, object);
-
-    return object;
-
-};
+    Geometry.prototype = {
+        
+        constructor : Geometry,
 
+        //Get geometry group to accomodate addVertices new vertices - create 
+        // new group if necessary       
+        updateGeoGroup : function(addVertices) {
+        
+            addVertices = addVertices || 0;
+            
+            var retGroup = this.groups > 0 ? this.geometryGroups[ this.groups - 1 ] : null;
+            
+            if (!retGroup || retGroup.vertices + addVertices > retGroup.vertexArray.length/3) 
+                retGroup = addGroup(this);
+                
+            return retGroup;
+            
+        },
+        
+        addGeoGroup : function() {
+            return addGroup(this);  
+        },
+        
+        setUpNormals : function(three) {
+            
+            three = three || false;
+            
+            for (var g = 0; g < this.groups; g++) {
+            
+                var geoGroup = this.geometryGroups[g];            
+                
+                geoGroup.setNormals(three);
+                
+            }  
+                      
+        },
+        
+        setUpWireframe : function() {
+            for (var g = 0; g < this.groups; g++) {
+                var geoGroup = this.geometryGroups[g];
+                
+                geoGroup.setLineIndices();
+            }
+        },
+        
+        //After vertices, colors, etc are collected in regular or typed arrays,
+        //  create typed arrays from regular arrays if they don't already exist,
+        initTypedArrays : function() {
+                
+            for (var g = 0; g < this.groups; g++) {
+                
+                var group = this.geometryGroups[g];
+                
+                if (group.__inittedArrays === true)
+                    continue;
+                
+                //do not actually reallocate smaller memory here because
+                //of the performance hit - if you know your geometry is small,
+                //truncate manually with the second parameter true
+                group.truncateArrayBuffers(this.mesh, false);
+            }
+            
+        
+        },
+        
+        dispose : function() {
+            this.dispatchEvent( {type : 'dispose'} );
+        }
+    };
 
-//Sprite object
-/** @constructor */
-$3Dmol.Sprite = function(material) {
     
-    $3Dmol.Object3D.call(this);
+    return Geometry;
     
-    this.material = (material !== undefined) ? material : new $3Dmol.SpriteMaterial();
+})();
 
-    this.rotation3d = this.rotation;
-    this.rotation = 0;
+Object.defineProperty($3Dmol.Geometry.prototype, "vertices", {
     
-};
+    /** @this {$3Dmol.Geometry} */
+    get : function() {
+        var vertices = 0;
+        for (var g = 0; g < this.groups; g++)
+            vertices += this.geometryGroups[g].vertices;
+            
+        return vertices;
+    } 
+        
+});
 
-$3Dmol.Sprite.prototype = Object.create($3Dmol.Object3D.prototype);
+$3Dmol.GeometryIDCount = 0;
 
-$3Dmol.Sprite.prototype.updateMatrix = function() {
-    
-    this.matrix.setPosition(this.position);
-    
-    this.rotation3d.set(0, 0, this.rotation);
-    this.matrix.setRotationFromEuler(this.rotation3d);
-    
-    if (this.scale.x !== 1 || this.scale.y !== 1)
-        this.matrix.scale(this.scale);
-    
-    this.matrixWorldNeedsUpdate = true;
-    
-};
 
-$3Dmol.Sprite.prototype.clone = function(object) {
+//Raycaster
+/** @constructor */
+$3Dmol.Raycaster = (function() {
     
-    if (object === undefined)
-        object = new $3Dmol.Sprite(this.material);
+    var Raycaster = function(origin, direction, far, near) {
+        
+        this.ray = new $3Dmol.Ray(origin, direction);
+        
+        if (this.ray.direction.lengthSq() > 0) 
+            this.ray.direction.normalize();
+        
+        this.near = near || 0;
+        this.far = far || Infinity;
     
-    $3Dmol.Object3D.prototype.clone.call(this, object);
+    };
     
-    return object;
+    var sphere = new $3Dmol.Sphere();
+    var cylinder = new $3Dmol.Cylinder();
+    var triangle = new $3Dmol.Triangle();
+    var w_0 = new $3Dmol.Vector3(); // for cylinders, cylinder.c1 - ray.origin
+    var v1 = new $3Dmol.Vector3(); // all purpose local vector
+    var v2 = new $3Dmol.Vector3();
+    var v3 = new $3Dmol.Vector3();
+    //var facePlane = new $3Dmol.Plane();
+    var localRay = new $3Dmol.Ray();
+    var intersectPoint = new $3Dmol.Vector3();
+    var matrixPosition = new $3Dmol.Vector3();
     
-};
-/**
-Simplified webGL renderer 
- */
+    var inverseMatrix = new $3Dmol.Matrix4();
+        
+    var descSort = function(a, b) {
+        return a.distance - b.distance;
+    };
 
-$3Dmol.Renderer = function ( parameters ) {
+    // [-1, 1]
+    var clamp = function(x) {
+        return Math.min(Math.max(x, -1), 1);
+    };
     
-    parameters = parameters || {};
+    //object is a Sphere or (Bounding) Box
+    var intersectObject = function(group, clickable, raycaster, intersects) {
+        
+        matrixPosition.getPositionFromMatrix(group.matrixWorld);
+        
+        if ((clickable.clickable !== true) || (clickable.intersectionShape === undefined))
+            return intersects;       
+        var intersectionShape = clickable.intersectionShape;
+        var precision = raycaster.linePrecision;
+        precision *= group.matrixWorld.getMaxScaleOnAxis();
+        var precisionSq = precision*precision;
+
+        //Check for intersection with clickable's bounding sphere, if it exists
+        if (clickable.boundingSphere !== undefined && clickable.boundingSphere instanceof $3Dmol.Sphere) {
+            sphere.copy(clickable.boundingSphere);
+            sphere.applyMatrix4(group.matrixWorld);          
+            if (!raycaster.ray.isIntersectionSphere(sphere)) {             
+				return intersects;
+            }
+        }      
+        //Iterate through intersection objects
+        var i, il,
+            norm, normProj, cylProj, rayProj,
+            distance, closestDistSq, denom, discriminant,
+            s, t, s_c, t_c;
+        //triangle faces
+        for (i = 0, il = intersectionShape.triangle.length; i < il; i++) {
+            
+            if (intersectionShape.triangle[i] instanceof $3Dmol.Triangle) {
+                
+                triangle.copy(intersectionShape.triangle[i]);
+                triangle.applyMatrix4(group.matrixWorld);
+                
+                norm = triangle.getNormal();
+                
+                normProj = raycaster.ray.direction.dot(norm);
+                
+                //face culling
+                if (normProj >= 0)
+                    continue;
+                
+                w_0.subVectors(triangle.a, raycaster.ray.origin);
+                
+                distance = (norm.dot(w_0)) / normProj;
+                
+                if (distance < 0)
+                    continue;
+                    
+                //intersects with plane, check if P inside triangle
+                v1.copy(raycaster.ray.direction).multiplyScalar(distance).add(raycaster.ray.origin);
+                v1.sub(triangle.a); // from pt a to intersection point P
+                
+                v2.copy(triangle.b).sub(triangle.a); // from pt a to b
+                v3.copy(triangle.c).sub(triangle.a); // from pt a to c
+                var b_dot_c = v2.dot(v3);
+                var b_sq = v2.lengthSq();
+                var c_sq = v3.lengthSq();
+                
+                // P = A + s(v2) + t(v3), inside trianle if 0 <= s, t <=1  and (s + t) <=0
+                
+                t = ( b_sq*v1.dot(v3) - b_dot_c*v1.dot(v2) ) / ( b_sq*c_sq - b_dot_c*b_dot_c );
+                
+                if (t < 0 || t > 1)
+                    continue;
+                
+                s = ( v1.dot(v2) - t*b_dot_c ) / b_sq;
+                
+                if ( (s < 0 || s > 1) || s + t > 1)
+                    continue;
+                    
+                else{
+                    intersects.push({clickable : clickable,
+                                     distance : distance});
+				}  
+            }
+        }    
+        //cylinders
+        for (i = 0, il = intersectionShape.cylinder.length; i < il; i++) {
+            
+            if (intersectionShape.cylinder[i] instanceof $3Dmol.Cylinder){
+                
+                cylinder.copy(intersectionShape.cylinder[i]);
+                cylinder.applyMatrix4(group.matrixWorld);
+                
+                w_0.subVectors(cylinder.c1, raycaster.ray.origin); 
+                
+                cylProj = w_0.dot(cylinder.direction); // Dela
+                rayProj = w_0.dot(raycaster.ray.direction); // Epsilon
+                
+                normProj = clamp(raycaster.ray.direction.dot(cylinder.direction)); // Beta
+                
+                denom = 1 - normProj*normProj;
+                
+                if (denom === 0.0)
+                    continue;
+                
+                s_c = (normProj*rayProj - cylProj) / denom;
+                t_c = (rayProj - normProj*cylProj) / denom;
+                
+                v1.copy(cylinder.direction).multiplyScalar(s_c).add(cylinder.c1);  // Q_c
+                v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
+                
+                closestDistSq = v3.subVectors(v1, v2).lengthSq();
+                var radiusSq = cylinder.radius*cylinder.radius;
+                
+                //Smoothing?
+                //if (closestDistSq > radiusSq) radiusSq += precisionSq;
+                
+                // closest distance between ray and cylinder axis not greater than cylinder radius;
+                // might intersect this cylinder between atom and bond midpoint
+                if (closestDistSq <= radiusSq){
+
+                    //Find points where ray intersects sides of cylinder
+                    discriminant = (normProj*cylProj - rayProj)*(normProj*cylProj - rayProj) - 
+                            denom*(w_0.lengthSq() - cylProj*cylProj - radiusSq);
+                    
+                    // ray tangent to cylinder?
+                    if (discriminant <= 0)
+                        t = distance = Math.sqrt(closestDistSq);
+                    else
+                        t = distance = ( (rayProj - normProj*cylProj) - Math.sqrt(discriminant) ) / denom; 
+                    
+                    //find closest intersection point; make sure it's between atom's position and cylinder midpoint
+                    
+                    s = normProj*t - cylProj;
+                    
+                    //does not intersect cylinder between atom and midpoint,
+                    // or intersects cylinder behind camera
+                    if (s < 0 || s*s > cylinder.lengthSq() || t < 0)
+                        continue;
+                    
+                    else
+                        intersects.push({clickable : clickable,
+                                         distance : distance});
+                    
+                }
+                    
+                
+            }
+            
+        }       
+        //lines
+        for (i = 0, il = intersectionShape.line.length; i < il; i += 2) {
+            
+            v1.copy(intersectionShape.line[i]);
+            v1.applyMatrix4(group.matrixWorld);
+            v2.copy(intersectionShape.line[i+1]);
+            v2.applyMatrix4(group.matrixWorld);
+            
+            v3.subVectors(v2, v1);
+            var bondLengthSq = v3.lengthSq();
+            v3.normalize();
+            
+            w_0.subVectors(v1, raycaster.ray.origin);
+            
+            lineProj = w_0.dot(v3);
+            rayProj = w_0.dot(raycaster.ray.direction);
+            
+            normProj = clamp(raycaster.ray.direction.dot(v3));
+            
+            denom = 1 - normProj*normProj;
+            
+            if (denom === 0.0)
+                continue;
+            
+            s_c = (normProj*rayProj - lineProj) / denom;
+            t_c = (rayProj - normProj*lineProj) / denom;
+            
+            v1.add(v3.multiplyScalar(s_c)); // Q_c
+            v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
+            
+            closestDistSq = v3.subVectors(v2, v1).lengthSq();
+            
+            if (closestDistSq < precisionSq && s_c*s_c < bondLengthSq)
+                intersects.push({clickable : clickable,
+                                 distance : t_c
+                                });
+            
+        }
+        for (i = 0, il = intersectionShape.sphere.length; i < il; i++) {
+            //sphere
+            if (intersectionShape.sphere[i] instanceof $3Dmol.Sphere) {
+                
+                sphere.copy(intersectionShape.sphere[i]);
+                sphere.applyMatrix4(group.matrixWorld);
+                
+                if (raycaster.ray.isIntersectionSphere(sphere)) {
+                    
+                    v1.subVectors(sphere.center, raycaster.ray.origin);
+                    
+                    //distance from ray origin to point on the ray normal to sphere's center
+                    //must be less than sphere's radius (since ray intersects sphere)
+                    var distanceToCenter = v1.dot(raycaster.ray.direction);
+                    
+                    discriminant = distanceToCenter*distanceToCenter - (v1.lengthSq() - sphere.radius*sphere.radius);
+                    
+                    //Don't select if sphere center behind camera
+                    if (distanceToCenter < 0) 
+                        return intersects;
+                    
+                    //ray tangent to sphere?
+                    if (discriminant <= 0)
+                        distance = distanceToCenter;
+                    
+                    //This is reversed if sphere is closer than ray origin.  Do we have 
+                    //to worry about handling that case?
+                    else 
+                        distance = distanceToCenter - Math.sqrt(discriminant);
+    
+                    intersects.push({clickable : clickable, 
+                                     distance : distance});
+                    return intersects;
+                }
+            }        
+       }
+        
+    };   
+       
+    Raycaster.prototype.precision = 0.0001;
+    Raycaster.prototype.linePrecision = 0.2;
+    
+    Raycaster.prototype.set = function(origin, direction) {
+        
+        this.ray.set(origin, direction);
+          
+    };
+    
+    Raycaster.prototype.intersectObjects = function(group, objects) {     
+        var intersects = [];
+        
+        for (var i = 0, l = objects.length; i < l; i++)            
+            intersectObject(group, objects[i], this, intersects);
+            
+        intersects.sort(descSort);
+        
+        return intersects;
+        
+    };
+    
+    return Raycaster;
     
-    var _canvas = parameters.canvas !== undefined ? parameters.canvas : document.createElement( 'canvas' ),
+})();
 
-    _precision = parameters.precision !== undefined ? parameters.precision : 'highp',
 
-    _alpha = parameters.alpha !== undefined ? parameters.alpha : true,
-    _premultipliedAlpha = parameters.premultipliedAlpha !== undefined ? parameters.premultipliedAlpha : true,
-    _antialias = parameters.antialias !== undefined ? parameters.antialias : false,
-    _stencil = parameters.stencil !== undefined ? parameters.stencil : true,
-    _preserveDrawingBuffer = parameters.preserveDrawingBuffer !== undefined ? parameters.preserveDrawingBuffer : false,
+//$3Dmol Projecion 
+//TODO: can probably strip this down a lot (only used for selection handling)
+/** @constructor */
+$3Dmol.Projector = function () {
 
-    _clearColor = parameters.clearColor !== undefined ? new $3Dmol.Color( parameters.clearColor ) : new $3Dmol.Color( 0x000000 ),
-    _clearAlpha = parameters.clearAlpha !== undefined ? parameters.clearAlpha : 0;
-    
-    this.domElement = _canvas;
-    this.context = null;
-    this.devicePixelRatio = parameters.devicePixelRatio !== undefined ? 
-    parameters.devicePixelRatio : (self.devicePixelRatio !== undefined) ? 
-                                   self.devicePixelRatio : 1;
+    var _viewMatrix = new $3Dmol.Matrix4(),
+    _viewProjectionMatrix = new $3Dmol.Matrix4();
 
-    // clearing
+    this.projectVector = function ( vector, camera ) {
 
-    this.autoClear = true;
-    this.autoClearColor = true;
-    this.autoClearDepth = true;
-    this.autoClearStencil = true;
+        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
 
-    // scene graph
+        _viewProjectionMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
 
-    this.sortObjects = true;
+        return vector.applyProjection( _viewProjectionMatrix );
 
-    this.autoUpdateObjects = true;
-    this.autoUpdateScene = true;
-    
-    this.renderPluginsPost = [];
-    
-    // info
+    };
 
-    this.info = {
+    this.unprojectVector = function ( vector, camera ) {
+
+        camera.projectionMatrixInverse.getInverse(camera.projectionMatrix);
+
+        _viewProjectionMatrix.multiplyMatrices(camera.matrixWorld, camera.projectionMatrixInverse);
+
+        return vector.applyProjection( _viewProjectionMatrix );
+
+    };
+
+};
+/*
+ * Simplified Perspective Camera
+ */
 
-        memory: {
+/** @constructor */
+$3Dmol.Camera = function(fov, aspect, near, far) {
     
-        programs: 0,
-        geometries: 0,
-        textures: 0
+    $3Dmol.Object3D.call(this);
     
-        },
+    this.fov = fov !== undefined ? fov : 50;
+    this.aspect = aspect !== undefined ? aspect : 1;
+    this.near = near !== undefined ? near : 0.1;
+    this.far = far !== undefined ? far : 2000;
+
+    this.projectionMatrix = new $3Dmol.Matrix4();
+    this.projectionMatrixInverse = new $3Dmol.Matrix4();
+    this.matrixWorldInverse = new $3Dmol.Matrix4();
     
-        render: {
+    this.updateProjectionMatrix();
+        
+};
+
+//Inherit Object3D's prototyped methods
+$3Dmol.Camera.prototype = Object.create($3Dmol.Object3D.prototype);
+
+$3Dmol.Camera.prototype.lookAt = function(vector){
     
-        calls: 0,
-        vertices: 0,
-        faces: 0,
-        points: 0
+    //Why is the parameter order switched (compared to Object3D)?
+    this.matrix.lookAt(this.position, vector, this.up);
     
-        }
-
-    };
+    if (this.rotationAutoUpdate) {    
+        
+        if (this.useQuaternion === false) 
+            this.rotation.setEulerFromRotationMatrix( this.matrix, this.eulerOrder );
+        else
+            this.quaternion.copy( this.matrix.decompose()[ 1 ] );    
+            
+    }
+    
+};
 
-    // internal properties
+$3Dmol.Camera.prototype.updateProjectionMatrix = function () {
 
-    var _this = this,
+    this.projectionMatrix.makePerspective( this.fov, this.aspect, this.near, this.far );
+    this.projectionMatrixInverse.getInverse(this.projectionMatrix);
+};
 
-    _programs = [],
-    _programs_counter = 0,
 
-    // internal state cache
+//Render plugins go here
 
-    _currentProgram = null,
-    _currentFramebuffer = null,
-    _currentMaterialId = -1,
-    _currentGeometryGroupHash = null,
-    _currentCamera = null,
-    _geometryGroupCounter = 0,
+/**
+ * Sprite render plugin
+ * @this {$3Dmol.SpritePlugin}
+ */
 
-    _usedTextureUnits = 0,
+$3Dmol.SpritePlugin = function () {
 
-    // GL state cache
+    var _gl, _renderer, _precision, _sprite = {};
 
-    _oldDoubleSided = -1,
-    _oldFlipSided = -1,
+    this.init = function ( renderer ) {
 
-    _oldBlending = -1,
+        _gl = renderer.context;
+        _renderer = renderer;
 
-    _oldBlendEquation = -1,
-    _oldBlendSrc = -1,
-    _oldBlendDst = -1,
+        _precision = renderer.getPrecision();
 
-    _oldDepthTest = -1,
-    _oldDepthWrite = -1,
+        _sprite.vertices = new Float32Array( 8 + 8 );
+        _sprite.faces    = new Uint16Array( 6 );
 
-    _oldPolygonOffset = null,
-    _oldPolygonOffsetFactor = null,
-    _oldPolygonOffsetUnits = null,
+        var i = 0;
 
-    _oldLineWidth = null,
+        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = -1; // vertex 0
+        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 0;  // uv 0
 
-    _viewportX = 0,
-    _viewportY = 0,
-    _viewportWidth = 0,
-    _viewportHeight = 0,
-    _currentWidth = 0,
-    _currentHeight = 0,
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = -1; // vertex 1
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 0;  // uv 1
 
-    _enabledAttributes = {},
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // vertex 2
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // uv 2
 
-     // camera matrices cache
+        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = 1;  // vertex 3
+        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 1;  // uv 3
 
-    _projScreenMatrix = new $3Dmol.Matrix4(),
+        i = 0;
 
-    _vector3 = new $3Dmol.Vector3(),
+        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 1; _sprite.faces[ i++ ] = 2;
+        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 2; _sprite.faces[ i++ ] = 3;
 
-    // light arrays cache
+        _sprite.vertexBuffer  = _gl.createBuffer();
+        _sprite.elementBuffer = _gl.createBuffer();
 
-    _direction = new $3Dmol.Vector3(),
+        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
+        _gl.bufferData( _gl.ARRAY_BUFFER, _sprite.vertices, _gl.STATIC_DRAW );
 
-    _lightsNeedUpdate = true,
+        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
+        _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, _sprite.faces, _gl.STATIC_DRAW );
 
-    _lights = {
+        _sprite.program = createProgram( $3Dmol.ShaderLib.sprite, _precision );
 
-            ambient: [0,0,0],
-            directional: { length: 0, colors: [], positions: [] },
-            point: { length: 0, colors: [], positions: [], distances: [] },
-            spot: { length: 0, colors: [], positions: [], distances: [], directions: [], anglesCos: [], exponents: [] },
-            hemi: { length: 0, skyColors: [], groundColors: [], positions: [] }
+        _sprite.attributes = {};
+        _sprite.uniforms = {};
 
-    };
+        _sprite.attributes.position           = _gl.getAttribLocation ( _sprite.program, "position" );
+        _sprite.attributes.uv                 = _gl.getAttribLocation ( _sprite.program, "uv" );
 
-    // initialize
+        _sprite.uniforms.uvOffset             = _gl.getUniformLocation( _sprite.program, "uvOffset" );
+        _sprite.uniforms.uvScale              = _gl.getUniformLocation( _sprite.program, "uvScale" );
 
-    var _gl;
+        _sprite.uniforms.rotation             = _gl.getUniformLocation( _sprite.program, "rotation" );
+        _sprite.uniforms.scale                = _gl.getUniformLocation( _sprite.program, "scale" );
+        _sprite.uniforms.alignment            = _gl.getUniformLocation( _sprite.program, "alignment" );
 
-    initGL();
+        _sprite.uniforms.color                = _gl.getUniformLocation( _sprite.program, "color" );
+        _sprite.uniforms.map                  = _gl.getUniformLocation( _sprite.program, "map" );
+        _sprite.uniforms.opacity              = _gl.getUniformLocation( _sprite.program, "opacity" );
 
-    setDefaultGLState();
+        _sprite.uniforms.useScreenCoordinates = _gl.getUniformLocation( _sprite.program, "useScreenCoordinates" );
+        _sprite.uniforms.screenPosition       = _gl.getUniformLocation( _sprite.program, "screenPosition" );
+        _sprite.uniforms.modelViewMatrix      = _gl.getUniformLocation( _sprite.program, "modelViewMatrix" );
+        _sprite.uniforms.projectionMatrix     = _gl.getUniformLocation( _sprite.program, "projectionMatrix" );
 
-    this.context = _gl;    
+        _sprite.uniforms.fogType              = _gl.getUniformLocation( _sprite.program, "fogType" );
+        _sprite.uniforms.fogDensity           = _gl.getUniformLocation( _sprite.program, "fogDensity" );
+        _sprite.uniforms.fogNear              = _gl.getUniformLocation( _sprite.program, "fogNear" );
+        _sprite.uniforms.fogFar               = _gl.getUniformLocation( _sprite.program, "fogFar" );
+        _sprite.uniforms.fogColor             = _gl.getUniformLocation( _sprite.program, "fogColor" );
 
-    // API
+        _sprite.uniforms.alphaTest            = _gl.getUniformLocation( _sprite.program, "alphaTest" );
 
-    this.getContext = function () {
+    };
 
-            return _gl;
+    this.render = function ( scene, camera, viewportWidth, viewportHeight ) {
 
-    };
+        var sprites = scene.__webglSprites,
+            nSprites = sprites.length;
 
-    this.getPrecision = function () {
+        if ( ! nSprites ) return;
 
-            return _precision;
+        var attributes = _sprite.attributes,
+            uniforms = _sprite.uniforms;
 
-    };
-    
-    this.setClearColorHex = function ( hex, alpha ) {
+        var invAspect = viewportHeight / viewportWidth;
 
-            _clearColor.setHex( hex );
-            _clearAlpha = alpha;
+        var halfViewportWidth = viewportWidth * 0.5,
+            halfViewportHeight = viewportHeight * 0.5;
 
-            _gl.clearColor( _clearColor.r, _clearColor.g, _clearColor.b, _clearAlpha );
+        // setup gl
 
-    };
+        _gl.useProgram( _sprite.program );
 
-    this.setSize = function ( width, height ) {
+        _gl.enableVertexAttribArray( attributes.position );
+        _gl.enableVertexAttribArray( attributes.uv );
 
-            _canvas.width = width * this.devicePixelRatio;
-            _canvas.height = height * this.devicePixelRatio;
+        _gl.disable( _gl.CULL_FACE );
+        _gl.enable( _gl.BLEND );
 
-            _canvas.style.width = width + 'px';
-            _canvas.style.height = height + 'px';
+        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
+        _gl.vertexAttribPointer( attributes.position, 2, _gl.FLOAT, false, 2 * 8, 0 );
+        _gl.vertexAttribPointer( attributes.uv, 2, _gl.FLOAT, false, 2 * 8, 8 );
 
-            this.setViewport( 0, 0, _canvas.width, _canvas.height );
+        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
 
-    };
+        _gl.uniformMatrix4fv( uniforms.projectionMatrix, false, camera.projectionMatrix.elements );
 
-    this.setViewport = function ( x, y, width, height ) {
+        _gl.activeTexture( _gl.TEXTURE0 );
+        _gl.uniform1i( uniforms.map, 0 );
 
-            _viewportX = x !== undefined ? x : 0;
-            _viewportY = y !== undefined ? y : 0;
+        var oldFogType = 0;
+        var sceneFogType = 0;
+        var fog = scene.fog;
 
-            _viewportWidth = width !== undefined ? width : _canvas.width;
-            _viewportHeight = height !== undefined ? height : _canvas.height;
+        if ( fog ) {
 
-            _gl.viewport( _viewportX, _viewportY, _viewportWidth, _viewportHeight );
+            _gl.uniform3f( uniforms.fogColor, fog.color.r, fog.color.g, fog.color.b );
 
-    };
+            _gl.uniform1f( uniforms.fogNear, fog.near );
+            _gl.uniform1f( uniforms.fogFar, fog.far );
 
-    this.clear = function ( color, depth, stencil ) {
+            _gl.uniform1i( uniforms.fogType, 1 );
+            oldFogType = 1;
+            sceneFogType = 1;
 
-            var bits = 0;
 
-            if ( color === undefined || color ) bits |= _gl.COLOR_BUFFER_BIT;
-            if ( depth === undefined || depth ) bits |= _gl.DEPTH_BUFFER_BIT;
-            if ( stencil === undefined || stencil ) bits |= _gl.STENCIL_BUFFER_BIT;
-            _gl.clear( bits );
+        } 
+        
+        else {
 
-    };
+            _gl.uniform1i( uniforms.fogType, 0 );
+            oldFogType = 0;
+            sceneFogType = 0;
 
-    this.clearTarget = function ( color, depth, stencil ) {
-            
-            this.clear( color, depth, stencil );
+        }
 
-    };
 
-    this.setMaterialFaces = function ( material ) {
+        // update positions and sort
 
-            var doubleSided = material.side === $3Dmol.DoubleSide;
-            var flipSided = material.side === $3Dmol.BackSide;
+        var i, sprite, material, screenPosition, size, fogType, scale = [];
 
-            if ( _oldDoubleSided !== doubleSided ) {
+        for( i = 0; i < nSprites; i ++ ) {
 
-                if ( doubleSided ) {
+            sprite = sprites[ i ];
+            material = sprite.material;
 
-                    _gl.disable( _gl.CULL_FACE );
+            if ( ! sprite.visible || material.opacity === 0 ) continue;
 
-                } else {
+            if ( ! material.useScreenCoordinates ) {
 
-                    _gl.enable( _gl.CULL_FACE );
+                sprite._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, sprite.matrixWorld );
+                sprite.z = - sprite._modelViewMatrix.elements[ 14 ];
 
-                }
+            } else {
 
-                _oldDoubleSided = doubleSided;
+                sprite.z = - sprite.position.z;
 
             }
 
-            if ( _oldFlipSided !== flipSided ) {
+        }
 
-                if ( flipSided ) {
+        sprites.sort( painterSortStable );
 
-                    _gl.frontFace( _gl.CW );
+        // render all sprites
 
-                } else {
+        for( i = 0; i < nSprites; i ++ ) {
 
-                    _gl.frontFace( _gl.CCW );
+            sprite = sprites[ i ];
+            material = sprite.material;
 
-                }
+            if ( ! sprite.visible || material.opacity === 0 ) continue;
+
+            if ( material.map && material.map.image && material.map.image.width ) {
 
-                _oldFlipSided = flipSided;
+                _gl.uniform1f( uniforms.alphaTest, material.alphaTest );
+                var w = material.map.image.width;
+                var h = material.map.image.height;
+                
+                scale[ 0 ] = w*_renderer.devicePixelRatio/viewportWidth;
+                scale[ 1 ] = h*_renderer.devicePixelRatio/viewportHeight;
+                
+                if ( material.useScreenCoordinates === true ) {
 
-            }    
+                    _gl.uniform1i( uniforms.useScreenCoordinates, 1 );
+                    _gl.uniform3f(
+                        uniforms.screenPosition,
+                        ( ( sprite.position.x * _renderer.devicePixelRatio ) - halfViewportWidth  ) / halfViewportWidth,
+                        ( halfViewportHeight - ( sprite.position.y * _renderer.devicePixelRatio ) ) / halfViewportHeight,
+                        Math.max( 0, Math.min( 1, sprite.position.z ) )
+                    );
 
-    };
-    
-    this.setDepthTest = function ( depthTest ) {
+                } else {
 
-            if ( _oldDepthTest !== depthTest ) {
+                    _gl.uniform1i( uniforms.useScreenCoordinates, 0 );
+                    _gl.uniformMatrix4fv( uniforms.modelViewMatrix, false, sprite._modelViewMatrix.elements );
+                }
 
-                if ( depthTest ) {
+                if ( scene.fog && material.fog ) {
 
-                    _gl.enable( _gl.DEPTH_TEST );
+                    fogType = sceneFogType;
 
                 } else {
 
-                    _gl.disable( _gl.DEPTH_TEST );
+                    fogType = 0;
 
                 }
 
-                _oldDepthTest = depthTest;
+                if ( oldFogType !== fogType ) {
 
-            }
+                    _gl.uniform1i( uniforms.fogType, fogType );
+                    oldFogType = fogType;
 
-    };
+                }
 
-    this.setDepthWrite = function ( depthWrite ) {
+                size = 1 / ( material.scaleByViewport ? viewportHeight : 1 );
 
-            if ( _oldDepthWrite !== depthWrite ) {
+                scale[ 0 ] *= size * sprite.scale.x;
+                scale[ 1 ] *= size * sprite.scale.y;
 
-                    _gl.depthMask( depthWrite );
-                    _oldDepthWrite = depthWrite;
+                _gl.uniform2f( uniforms.uvScale, material.uvScale.x, material.uvScale.y );
+                _gl.uniform2f( uniforms.uvOffset, material.uvOffset.x, material.uvOffset.y );
+                _gl.uniform2f( uniforms.alignment, material.alignment.x, material.alignment.y );
 
-            }
+                _gl.uniform1f( uniforms.opacity, material.opacity );
+                _gl.uniform3f( uniforms.color, material.color.r, material.color.g, material.color.b );
 
-    };
+                _gl.uniform1f( uniforms.rotation, sprite.rotation );
+                _gl.uniform2fv( uniforms.scale, scale );
 
-    this.setBlending = function( blending ) {
+                //_renderer.setBlending( material.blending, material.blendEquation, material.blendSrc, material.blendDst );
+                _renderer.setDepthTest( material.depthTest );
+                _renderer.setDepthWrite( material.depthWrite );
+                _renderer.setTexture( material.map, 0 );
 
-        if (!blending) {
-                _gl.disable( _gl.BLEND );
+                _gl.drawElements( _gl.TRIANGLES, 6, _gl.UNSIGNED_SHORT, 0 );
 
-        } 
-        else {
-            _gl.enable( _gl.BLEND );
-            _gl.blendEquationSeparate( _gl.FUNC_ADD, _gl.FUNC_ADD );
-            _gl.blendFuncSeparate( _gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA, _gl.ONE, _gl.ONE_MINUS_SRC_ALPHA );
+            }
 
         }
 
-        _oldBlending = blending;
-    };
-    
-    // Plugins
-    
-    this.addPostPlugin = function(plugin) {
+        // restore gl
 
-        plugin.init(this);
-        this.renderPluginsPost.push(plugin);
+        _gl.enable( _gl.CULL_FACE );
 
     };
 
-    // Sorting
-
-    function numericalSort ( a, b ) {
+    function createProgram ( shader, precision ) {
 
-            return b[ 0 ] - a[ 0 ];
+        var program = _gl.createProgram();
 
-    }
+        var fragmentShader = _gl.createShader( _gl.FRAGMENT_SHADER );
+        var vertexShader = _gl.createShader( _gl.VERTEX_SHADER );
 
-    function enableAttribute( attribute ) {
+        var prefix = "precision " + precision + " float;\n";
 
-        if ( ! _enabledAttributes[ attribute ] ) {
+        _gl.shaderSource( fragmentShader, prefix + shader.fragmentShader );
+        _gl.shaderSource( vertexShader, prefix + shader.vertexShader );
 
-            _gl.enableVertexAttribArray( attribute );
-            _enabledAttributes[ attribute ] = true;
+        _gl.compileShader( fragmentShader );
+        _gl.compileShader( vertexShader );
+        
+        if ( ! _gl.getShaderParameter(fragmentShader, _gl.COMPILE_STATUS) || ! _gl.getShaderParameter(vertexShader,_gl.COMPILE_STATUS) ) {
 
+                console.error(_gl.getShaderInfoLog(fragmentShader));
+                console.error("could not initialize shader");
+                return null;
         }
 
-    }
+        _gl.attachShader( program, fragmentShader );
+        _gl.attachShader( program, vertexShader );
 
-    function disableAttributes() {
+        _gl.linkProgram( program );
 
-        for ( var attribute in _enabledAttributes ) {
+        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
+                console.error("Could not initialize shader");
 
-            if ( _enabledAttributes[ attribute ] ) {
+        return program;
 
-                _gl.disableVertexAttribArray( attribute );
-                _enabledAttributes[ attribute ] = false;
+    }
 
-            }
+    function painterSortStable ( a, b ) {
 
-        }
+        if ( a.z !== b.z ) {
 
-    } 
+            return b.z - a.z;
 
-    function setPolygonOffset ( polygonOffset, factor, units) {
+        } else {
 
-        if ( _oldPolygonOffset !== polygonOffset ) {
+            return b.id - a.id;
 
-            if (polygonOffset)
-                _gl.enable( _gl.POLYGON_OFFSET_FILL );
-            else
-                _gl.disable( _gl.POLYGON_OFFSET_FILL );
         }
-    }
 
-    function setLineWidth ( width ) {
+    }
 
-        if ( width !== _oldLineWidth ) {
-            _gl.lineWidth(width);
-            _oldLineWidth = width;
-        }
+};
 
-    }
+$3Dmol.Light = function(hex, intensity) {
     
-    var onGeometryDispose = function(event) {
-        
-        var geometry = event.target;
-        geometry.removeEventListener('dispose', onGeometryDispose);
-        
-        deallocateGeometry(geometry);
-        
-        _this.info.memory.geometries--;
-        
-    };
+    $3Dmol.Object3D.call(this);
     
-    var onTextureDispose = function(event) {
+    this.color = new $3Dmol.Color(hex);
+    this.position = new $3Dmol.Vector3( 0, 1, 0 );
+    this.target = new $3Dmol.Object3D();
 
-        var texture = event.target;
+    this.intensity = ( intensity !== undefined ) ? intensity : 1;
 
-        texture.removeEventListener('dispose', onTextureDispose);
+    this.castShadow = false;
+    this.onlyShadow = false;
+    
+};
 
-        deallocateTexture(texture);
+$3Dmol.Light.prototype = Object.create($3Dmol.Object3D.prototype);
+/**
+ * Line and Mesh material types
+ * @constructor
+ */
+$3Dmol.Material = function () {
 
-        _this.info.memory.textures--;
+    $3Dmol.EventDispatcher.call( this );
 
+    this.id = $3Dmol.MaterialIdCount ++;
 
-    };
-    
-    var onMaterialDispose = function(event) {
-        
-        var material = event.target;
-        material.removeEventListener('dispose', onMaterialDispose);
-        
-        deallocateMaterial(material);
-        
-    };
+    this.name = '';
     
-    var deallocateGeometry = function(geometry) {
-        
-        geometry.__webglInit = undefined;
-        
-        if (geometry.__webglVertexBuffer !== undefined)
-            _gl.deleteBuffer(geometry.__webglVertexBuffer);
-        
-        if (geometry.__webglColorBuffer !== undefined)
-            _gl.deleteBuffer(geometry.__webglColorBuffer);
-        
-        if (geometry.geometryGroups !== undefined) {
-            
-            for (var g = 0, gl = geometry.groups; g < gl; g++) {  
-                
-                var geometryGroup = geometry.geometryGroups[g];
+    //TODO: Which of these instance variables can I remove??
+    this.side = $3Dmol.FrontSide;
 
-                if (geometryGroup.__webglVertexBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglVertexBuffer);
+    this.opacity = 1;
+    this.transparent = false;
 
-                if (geometryGroup.__webglColorBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglColorBuffer);
-                
-                if (geometryGroup.__webglNormalBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglNormalBuffer);  
-                
-                if (geometryGroup.__webglFaceBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglFaceBuffer);
-                    
-                if (geometryGroup.__webglLineBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglLineBuffer);
-                    
-            }
-        }
-    };
+    this.depthTest = true;
+    this.depthWrite = true;
     
-    var deallocateMaterial = function (material) {
-
-        var program = material.program;
-
-        if ( program === undefined ) return;
+    this.stencilTest = true;
 
-        material.program = undefined;
+    this.polygonOffset = false;
+    this.polygonOffsetFactor = 0;
+    this.polygonOffsetUnits = 0;
 
-        // only deallocate GL program if this was the last use of shared program
-        // assumed there is only single copy of any program in the _programs list
-        // (that's how it's constructed)
+    this.alphaTest = 0;
 
-        var i, il, programInfo;
-        var deleteProgram = false;
+    this.visible = true;
 
-        for ( i = 0, il = _programs.length; i < il; i ++ ) {
+    this.needsUpdate = true;
 
-            programInfo = _programs[ i ];
+};
 
-            if ( programInfo.program === program ) {
 
-                programInfo.usedTimes --;
+$3Dmol.Material.prototype.setValues = function ( values ) {
 
-                if ( programInfo.usedTimes === 0 ) {
+    if ( values === undefined ) return;
 
-                    deleteProgram = true;
+    for ( var key in values ) {
 
-                }
+        var newValue = values[ key ];
 
-                break;
+        if ( newValue === undefined ) {
 
-            }
+            console.warn( '$3Dmol.Material: \'' + key + '\' parameter is undefined.' );
+            continue;
 
         }
 
-        if ( deleteProgram === true ) {
-
-            // avoid using array.splice, this is costlier than creating new array from scratch
+        if ( key in this ) {
 
-            var newPrograms = [];
+            var currentValue = this[ key ];
 
-            for ( i = 0, il = _programs.length; i < il; i ++ ) {
+            if ( currentValue instanceof $3Dmol.Color && newValue instanceof $3Dmol.Color ) {
 
-                programInfo = _programs[ i ];
+                currentValue.copy( newValue );
 
-                if ( programInfo.program !== program ) {
+            } else if ( currentValue instanceof $3Dmol.Color ) {
 
-                    newPrograms.push( programInfo );
+                currentValue.set( newValue );
 
-                }
+            } else if ( currentValue instanceof $3Dmol.Vector3 && newValue instanceof $3Dmol.Vector3 ) {
 
-            }
+                currentValue.copy( newValue );
 
-            _programs = newPrograms;
+            } else {
 
-            _gl.deleteProgram( program );
+                this[ key ] = newValue;
 
-            _this.info.memory.programs --;
+            }
 
         }
 
-    };
-    
-    var deallocateTexture = function(texture) {
-
-        if (texture.image && texture.image.__webglTextureCube) {
+    }
 
-            // cube texture
+};
+//TODO: might want to look into blending equations
+$3Dmol.Material.prototype.clone = function ( material ) {
 
-            _gl.deleteTexture(texture.image.__webglTextureCube);
+    if ( material === undefined ) material = new $3Dmol.Material();
 
-        } 
-        
-        else {
+    material.name = this.name;
 
-            // 2D texture
+    material.side = this.side;
 
-            if ( ! texture.__webglInit ) return;
+    material.opacity = this.opacity;
+    material.transparent = this.transparent;
 
-            texture.__webglInit = false;
-            _gl.deleteTexture( texture.__webglTexture );
+    material.depthTest = this.depthTest;
+    material.depthWrite = this.depthWrite;
+    material.stencilTest = this.stencilTest;
 
-        }
+    material.polygonOffset = this.polygonOffset;
+    material.polygonOffsetFactor = this.polygonOffsetFactor;
+    material.polygonOffsetUnits = this.polygonOffsetUnits;
 
-    };
+    material.alphaTest = this.alphaTest;
 
-    //Compile and return shader
-    function getShader (type, str) {
+    material.overdraw = this.overdraw;
 
-        var shader;
+    material.visible = this.visible;
 
-        if (type === "fragment")
-            shader = _gl.createShader( _gl.FRAGMENT_SHADER );
-        else if (type === "vertex")
-            shader = _gl.createShader( _gl.VERTEX_SHADER );
+    return material;
 
-        _gl.shaderSource(shader, str);
-        _gl.compileShader(shader);
+};
 
-        if ( ! _gl.getShaderParameter(shader, _gl.COMPILE_STATUS) ) {
+$3Dmol.Material.prototype.dispose = function () {
 
-            console.error(_gl.getShaderInfoLog(shader));
-            console.error("could not initialize shader");
-            return null;
+    this.dispatchEvent( { type: 'dispose' } );
 
-        }
+};
 
-        return shader;
+$3Dmol.MaterialIdCount = 0;
 
-    } 
+//Line basic material
+/** @constructor */
+$3Dmol.LineBasicMaterial = function(parameters) {
+    
+    $3Dmol.Material.call(this);
+    
+    this.color = new $3Dmol.Color(0xffffff);
+    
+    this.linewidth = 1;
+    this.linecap = 'round';
+    this.linejoin = 'round';
+    
+    this.vertexColors = false;
+    
+    this.fog = true;
+    this.shaderID = "basic";
+    this.setValues(parameters);
+    
+};
 
+$3Dmol.LineBasicMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-    //Compile appropriate shaders (if necessary) from source code and attach to gl program.
-    function buildProgram(fragmentShader, vertexShader, uniforms, parameters) {
+$3Dmol.LineBasicMaterial.prototype.clone = function() {
+  
+    var material = new $3Dmol.LineBasicMaterial();
+    
+    $3Dmol.Material.prototype.clone.call(this, material);
+    
+    material.color.copy(this.color);
+    return material;
+};
 
-        var p, pl, d, program, code;
-        var chunks = [];
-
-        chunks.push(fragmentShader);
-        chunks.push(vertexShader);
-        
-        for (p in parameters) {
-            chunks.push(p);
-            chunks.push(parameters[p]);
-        }
-        
-        code = chunks.join();
+//Mesh Lambert material
+/** @constructor */
+$3Dmol.MeshLambertMaterial = function(parameters) {
+    
+    $3Dmol.Material.call(this);
+    
+    this.color = new $3Dmol.Color(0xffffff);
+    this.ambient = new $3Dmol.Color(0xfffff);
+    this.emissive = new $3Dmol.Color(0x000000);
+    
+    //TODO: Which of these instance variables do I really need?
+    this.wrapAround = false;
+    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
+    
+    this.map = null;
+    
+    this.lightMap = null;
+    
+    this.specularMap = null;
+    
+    this.envMap = null;
+    this.reflectivity = 1;
+    this.refractionRatio = 0.98;
+    
+    this.fog = true;
+    
+    this.wireframe = false;
+    this.wireframeLinewidth = 1;
+    this.wireframeLinecap = 'round';
+    this.wireframeLinejoin = 'round';
+    
+    this.shading = $3Dmol.SmoothShading;
+    this.shaderID = "lambert";
+    this.vertexColors = $3Dmol.NoColors;
+    
+    this.skinning = false;
+    
+    this.setValues(parameters);
+    
+};
 
-        //check if program has already been compiled
+$3Dmol.MeshLambertMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        for (p = 0, pl = _programs.length; p < pl; p++) {
+$3Dmol.MeshLambertMaterial.prototype.clone = function(material) {
+  
+    if ( typeof material === "undefined" ) material = new $3Dmol.MeshLambertMaterial();
+    
+    $3Dmol.Material.prototype.clone.call(this, material);
+    
+    material.color.copy(this.color);
+    material.ambient.copy(this.ambient);
+    material.emissive.copy(this.emissive);
+    
+    material.wrapAround = this.wrapAround;
+    material.wrapRGB.copy(this.wrapRGB);
+    
+    material.map = this.map;
+    
+    material.lightMap = this.lightMap;
+    
+    material.specularMap = this.specularMap;
+    
+    material.envMap = this.envMap;
+    material.combine = this.combine;
+    material.reflectivity = this.reflectivity;
+    material.refractionRatio = this.refractionRatio;
+    
+    material.fog = this.fog;
+    
+    material.shading = this.shading;
+    material.shaderID = this.shaderID;
+    material.vertexColors = this.vertexColors;
+    
+    material.skinning = this.skinning;
+    material.morphTargets = this.morphTargets;
+    material.morphNormals = this.morphNormals;
+    
+    return material;
+    
+};
 
-            var programInfo = _programs[p];
+//Double sided Mesh Lambert material
+/** @constructor */
+$3Dmol.MeshDoubleLambertMaterial = function(parameters) {
+    
+    $3Dmol.MeshLambertMaterial.call(this, parameters);
 
-            if (programInfo.code === code) {
+    this.shaderID = "lambertdouble";
+    this.side = $3Dmol.DoubleSide;    
+    
+};
 
-                programInfo.usedTimes++;
+$3Dmol.MeshDoubleLambertMaterial.prototype = Object.create($3Dmol.MeshLambertMaterial.prototype);
 
-                return programInfo.program;
-            }
-        }
+$3Dmol.MeshDoubleLambertMaterial.prototype.clone = function() {
+  
+    var material = new $3Dmol.MeshDoubleLambertMaterial();
+    
+    $3Dmol.MeshLambertMaterial.prototype.clone.call(this, material);
+        
+    return material;
+    
+};
 
-        //Set up new program and compile shaders
+//Outlined Mesh Lamert material
+/** @constructor */
+$3Dmol.MeshOutlineMaterial = function(parameters) {
+    $3Dmol.Material.call(this);
+    parameters = parameters || {};
+    this.fog = true;
+    this.shaderID = "outline";
+    this.wireframe=false;
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
+    
+};
 
-        program = _gl.createProgram();
-        
-        //set up precision
-        var precision = _precision;
-        var prefix = "precision " + precision + " float;";
-        
-        var prefix_vertex = [
-                             prefix
-                            ].join("\n");
-                            
-        var prefix_fragment = [                               
-                               parameters.wireframe ? "#define WIREFRAME 1" : "",
-                               prefix
-                              ].join("\n");
-        
-        var glFragmentShader = getShader("fragment", prefix_fragment + fragmentShader);
-        var glVertexShader = getShader("vertex", prefix_vertex + vertexShader);
+$3Dmol.MeshOutlineMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        _gl.attachShader(program, glVertexShader);
-        _gl.attachShader(program, glFragmentShader);
+$3Dmol.MeshOutlineMaterial.prototype.clone = function(material) {
+    if ( typeof material === "undefined" ) material = new $3Dmol.MeshOutlineMaterial();
+    $3Dmol.Material.prototype.clone.call(this, material);
+    material.fog = this.fog;
+    material.shaderID = this.shaderID;
+    material.wireframe = this.wireframe;
+    return material;
+};
 
-        _gl.linkProgram(program);
 
-        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
-            console.error("Could not initialize shader");
+//Imposter material
+/** @constructor */
+$3Dmol.ImposterMaterial = function(parameters) {
+  
+  $3Dmol.Material.call(this);
+  
+  this.color = new $3Dmol.Color(0xffffff);
+  this.ambient = new $3Dmol.Color(0xfffff);
+  this.emissive = new $3Dmol.Color(0x000000);
+  this.imposter = true;
+  
+  //TODO: Which of these instance variables do I really need?
+  this.wrapAround = false;
+  this.wrapRGB = new $3Dmol.Vector3(1,1,1);
+  
+  this.map = null;
+  
+  this.lightMap = null;
+  
+  this.specularMap = null;
+  
+  this.envMap = null;
+  this.reflectivity = 1;
+  this.refractionRatio = 0.98;
+  
+  this.fog = true;
+  
+  this.wireframe = false;
+  this.wireframeLinewidth = 1;
+  this.wireframeLinecap = 'round';
+  this.wireframeLinejoin = 'round';
+  
+  this.shading = $3Dmol.SmoothShading;
+  this.shaderID = null;
+  this.vertexColors = $3Dmol.NoColors;
+  
+  this.skinning = false;
+  
+  this.setValues(parameters);
+  
+};
 
-        //gather and cache uniform variables and attributes
+$3Dmol.ImposterMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        program.uniforms = {};
-        program.attributes = {};
+$3Dmol.ImposterMaterial.prototype.clone = function() {
 
-        var identifiers, u, a, i;
+  var material = new $3Dmol.ImposterMaterial();
+  
+  $3Dmol.Material.prototype.clone.call(this, material);
+  
+  material.color.copy(this.color);
+  material.ambient.copy(this.ambient);
+  material.emissive.copy(this.emissive);
+  
+  material.wrapAround = this.wrapAround;
+  material.wrapRGB.copy(this.wrapRGB);
+  
+  material.map = this.map;
+  
+  material.lightMap = this.lightMap;
+  
+  material.specularMap = this.specularMap;
+  
+  material.envMap = this.envMap;
+  material.combine = this.combine;
+  material.reflectivity = this.reflectivity;
+  material.refractionRatio = this.refractionRatio;
+  
+  material.fog = this.fog;
+  
+  material.shading = this.shading;
+  material.shaderID = this.shaderID;
+  material.vertexColors = this.vertexColors;
+  
+  material.skinning = this.skinning;
+  material.morphTargets = this.morphTargets;
+  material.morphNormals = this.morphNormals;
+  
+  return material;
+  
+};
 
-        //uniform vars
-        identifiers = 
-            [ 'viewMatrix', 'modelViewMatrix', 'projectionMatrix', 'normalMatrix', 'modelMatrix', 'cameraPosition' ];
 
-        //custom uniform vars
-        for (u in uniforms) 
-            identifiers.push(u);
+$3Dmol.SphereImposterMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-        for (i = 0; i < identifiers.length; i++) {
+    this.shaderID = "sphereimposter";    
+    this.setValues(parameters);
+    
+};
 
-            var uniformVar = identifiers[i];
-            program.uniforms[uniformVar] = _gl.getUniformLocation(program, uniformVar);
+$3Dmol.SphereImposterMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-        }
+$3Dmol.SphereImposterMaterial.prototype.clone = function() {
 
-        //attributes
-        identifiers = 
-            [ 'position', 'normal', 'color', 'lineDistance' ];
+    var material = new $3Dmol.SphereImposterMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    return material;
+};
 
-        /*
-        for (a in attributes)
-                identifiers.push(a);
-        */
 
-        for (i = 0; i < identifiers.length; i++) {
+$3Dmol.SphereImposterOutlineMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-            var attributeVar = identifiers[i];
-            program.attributes[attributeVar] = _gl.getAttribLocation(program, attributeVar);
-        }
+    this.shaderID = "sphereimposteroutline";
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
+    
+    this.setValues(parameters);
+    
+};
 
-        program.id = _programs_counter++;
-        _programs.push( {program: program, code: code, usedTimes: 1} );
-        _this.info.memory.programs = _programs.length;
+$3Dmol.SphereImposterOutlineMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-        return program;
-    }
+$3Dmol.SphereImposterOutlineMaterial.prototype.clone = function() {
 
-    //TODO: need to set up shader attributes and uniforms as attributes on material object after attaching prgm
-    //We need to attach appropriate uniform variables to material after shaders have been chosen
-    this.initMaterial = function ( material, lights, fog, object ) {
+    var material = new $3Dmol.SphereImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    material.outlineColor = this.outlineColor;
+    material.outlineWidth = this.outlineWidth;
+    material.outlinePushback = this.outlinePushback;
+    return material;
+};
 
-        material.addEventListener('dispose', onMaterialDispose);
 
-        var u, a, identifiers, i, parameters, maxLightCount, maxBones, maxShadows, shaderID;
+$3Dmol.StickImposterMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-        shaderID = material.shaderID;
+    this.shaderID = "stickimposter";    
+    this.setValues(parameters);
+    
+};
 
-        if (shaderID) {
+$3Dmol.StickImposterMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-            var shader = $3Dmol.ShaderLib[shaderID];
-            material.vertexShader = shader.vertexShader;
-            material.fragmentShader = shader.fragmentShader;
-            material.uniforms = $3Dmol.ShaderUtils.clone(shader.uniforms);
-            //TODO: set material uniforms to shader uniform variables
+$3Dmol.StickImposterMaterial.prototype.clone = function() {
 
-        }
-        
-        parameters = {
-            wireframe: material.wireframe
-        };
-
-        material.program = buildProgram(material.fragmentShader, material.vertexShader, material.uniforms, parameters);
-
-    };
-
-    function setProgram( camera, lights, fog, material, object ) {
+    var material = new $3Dmol.StickImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    return material;
+};
 
-        if ( material.needsUpdate ) {
 
-            if (material.program)
-                deallocateMaterial(material);
+$3Dmol.StickImposterOutlineMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-                _this.initMaterial( material, lights, fog, object );
-                material.needsUpdate = false;
-        }
+    this.shaderID = "stickimposteroutline";
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
+    
+    this.setValues(parameters);
+    
+};
 
-        var refreshMaterial = false;
+$3Dmol.StickImposterOutlineMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-        //p_uniforms: uniformVarName => uniformLocation
-        //m_uniforms: uniformVarName => uniformJsVal
-        var program = material.program,
-            p_uniforms = program.uniforms,
-            m_uniforms = material.uniforms;
+$3Dmol.StickImposterOutlineMaterial.prototype.clone = function() {
 
-        if (program != _currentProgram) {   
-            _gl.useProgram(program);
-            _currentProgram = program;
+    var material = new $3Dmol.StickImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    material.outlineColor = this.outlineColor;
+    material.outlineWidth = this.outlineWidth;
+    material.outlinePushback = this.outlinePushback;
+    return material;
+};
 
-            refreshMaterial = true;
-        }
 
-        if (material.id != _currentMaterialId) {
-            _currentMaterialId = material.id;
-            refreshMaterial = true;
-        }
+$3Dmol.InstancedMaterial = function(parameters) {
 
-        if (camera != _currentCamera) {    
-            _currentCamera = camera;
-            refreshMaterial = true;
-        }
-        
-        _gl.uniformMatrix4fv(p_uniforms.projectionMatrix, false, camera.projectionMatrix.elements);
-        _gl.uniformMatrix4fv(p_uniforms.modelViewMatrix, false, object._modelViewMatrix.elements);
-        _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false, object._normalMatrix.elements);
-        
-        //Send projection matrix to uniform variable in shader
-        if (refreshMaterial) {
+    $3Dmol.Material.call(this);
 
-            //Load projection, model-view matrices for perspective
+    this.color = new $3Dmol.Color(0xffffff);
+    this.ambient = new $3Dmol.Color(0xfffff);
+    this.emissive = new $3Dmol.Color(0x000000);
 
+    //TODO: Which of these instance variables do I really need?
+    this.wrapAround = false;
+    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
 
-            //Set up correct fog uniform vals
-            m_uniforms.fogColor.value = fog.color;
-            m_uniforms.fogNear.value = fog.near;
-            m_uniforms.fogFar.value = fog.far;
+    this.map = null;
 
-            //Set up lights for lambert shader
-            if (material.shaderID.lastIndexOf("lambert",0) === 0) {
+    this.lightMap = null;
 
-                //load view and normal matrices for directional and object lighting
-                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false, camera.matrixWorldInverse.elements);
-                //_gl.uniformMatrix4fv(p_uniforms.modelMatrix, false, object.matrixWorld.elements);
+    this.specularMap = null;
 
-                if (_lightsNeedUpdate) {
-                    setupLights(program, lights);
-                    _lightsNeedUpdate = false;
-                }
+    this.envMap = null;
+    this.reflectivity = 1;
+    this.refractionRatio = 0.98;
 
-                //Set up correct light uniform var vals
-                m_uniforms.ambientLightColor.value = _lights.ambient;
-                m_uniforms.directionalLightColor.value = _lights.directional.colors;
-                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
-                m_uniforms.ambient.value = material.ambient;
-                m_uniforms.emissive.value = material.emissive;
+    this.fog = true;
 
-            }
-            else if( material.shaderID === "sphereimposter") {
-                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false, camera.matrixWorldInverse.elements);
-                _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false, object._normalMatrix.elements);
-            }
-                
+    this.wireframe = false;
+    this.wireframeLinewidth = 1;
+    this.wireframeLinecap = 'round';
+    this.wireframeLinejoin = 'round';
 
-            //opacity, diffuse, emissive, etc
-            m_uniforms.opacity.value = material.opacity;
-            m_uniforms.diffuse.value = material.color;
+    this.shading = $3Dmol.SmoothShading;
+    this.shaderID = "instanced";
+    this.vertexColors = $3Dmol.NoColors;
 
-            //Load any other material specific uniform variables to gl shaders
-            loadMaterialUniforms(p_uniforms, m_uniforms);
+    this.skinning = false;
 
-        }
+    this.sphere = null;
 
-        return program;
+    this.setValues(parameters);
 
-    }
+};
 
-    function loadMaterialUniforms(p_uniforms, m_uniforms) {
-        var uniformVar, type, uniformVal, uniformLoc;
+$3Dmol.InstancedMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        for (uniformVar in m_uniforms) {
-            if (! p_uniforms[uniformVar])
-                continue;
+$3Dmol.InstancedMaterial.prototype.clone = function() {
 
-            type = m_uniforms[uniformVar].type;
-            uniformVal = m_uniforms[uniformVar].value;
-            uniformLoc = p_uniforms[uniformVar];
+    var material = new $3Dmol.InstancedMaterial();
 
-            //single float
-            if (type === 'f')
-                _gl.uniform1f(uniformLoc, uniformVal);
-            //array of floats
-            else if (type === 'fv')
-                _gl.uniform3fv(uniformLoc, uniformVal);
-            //color - r,g,b floats
-            else if (type === 'c')
-                _gl.uniform3f(uniformLoc, uniformVal.r, uniformVal.g, uniformVal.b);
+    $3Dmol.Material.prototype.clone.call(this, material);
 
-        }
+    material.color.copy(this.color);
+    material.ambient.copy(this.ambient);
+    material.emissive.copy(this.emissive);
 
-    }
+    material.wrapAround = this.wrapAround;
+    material.wrapRGB.copy(this.wrapRGB);
 
-    this.renderBuffer = function ( camera, lights, fog, material, geometryGroup, object ) {
+    material.map = this.map;
 
-        if ( ! material.visible )
-            return;
+    material.lightMap = this.lightMap;
 
-        var program, attributes, linewidth, primitives, a, attribute, i, il;
+    material.specularMap = this.specularMap;
 
-        //Sets up proper vertex and fragment shaders and attaches them to webGL program
-        //Also sets appropriate uniform variables 
-        program = setProgram(camera, lights, fog, material, object);
+    material.envMap = this.envMap;
+    material.combine = this.combine;
+    material.reflectivity = this.reflectivity;
+    material.refractionRatio = this.refractionRatio;
 
-        attributes = program.attributes;
+    material.fog = this.fog;
 
-        var updateBuffers = false,
-            wireframeBit = material.wireframe ? 1 : 0,
-            geometryGroupHash = (geometryGroup.id * 0xffffff) + (program.id * 2) + wireframeBit;
+    material.shading = this.shading;
+    material.shaderID = this.shaderID;
+    material.vertexColors = this.vertexColors;
 
-        if (geometryGroupHash !== _currentGeometryGroupHash) {
-            _currentGeometryGroupHash = geometryGroupHash;
-            updateBuffers = true;
-        }
+    material.skinning = this.skinning;
+    material.morphTargets = this.morphTargets;
+    material.morphNormals = this.morphNormals;
 
-        //rebind shader attributes to appropriate (and already initialized) gl buffers
-        if (updateBuffers) {
+    material.sphere = this.sphere;
 
-            disableAttributes();
+  return material;
 
-            // Vertices
-            if (attributes.position >= 0) {            
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer );
-                enableAttribute( attributes.position );
-                _gl.vertexAttribPointer( attributes.position, 3, _gl.FLOAT, false, 0, 0 );    
-            }
+};
 
-            // Colors
-            if (attributes.color >= 0) {
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer);
-                enableAttribute( attributes.color );
-                _gl.vertexAttribPointer( attributes.color, 3, _gl.FLOAT, false, 0, 0 );
-            }
 
-            // Normals (lambert shader only)
-            if (attributes.normal >=0) {
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer );
-                enableAttribute( attributes.normal );
-                _gl.vertexAttribPointer( attributes.normal, 3, _gl.FLOAT, false, 0, 0 );
-            }
+//Sprite material
+/** @constructor */
+$3Dmol.SpriteMaterial = function(parameters) {
+    
+    $3Dmol.Material.call(this);
+    
+    this.color = new $3Dmol.Color(0xffffff);
+    this.map = new $3Dmol.Texture();
+    
+    this.useScreenCoordinates = true;
+    this.depthTest = !this.useScreenCoordinates;
+    this.sizeAttenuation = !this.useScreenCoordinates;
+    this.scaleByViewPort = !this.sizeAttenuation;
+    this.alignment = $3Dmol.SpriteAlignment.center.clone();
+    
+    this.fog = false; // use scene fog
+    
+    this.uvOffset = new $3Dmol.Vector2(0, 0);
+    this.uvScale = new $3Dmol.Vector2(1, 1);
+    
+    this.setValues(parameters);
+    
+    parameters = parameters || {};
+    
+    if (parameters.depthTest === undefined)
+        this.depthTest = !this.useScreenCoordinates;
+    if (parameters.sizeAttenuation === undefined)
+        this.sizeAttenuation = !this.useScreenCoordinates;
+    if (parameters.scaleByViewPort === undefined)
+        this.scaleByViewPort = !this.sizeAttenuation;
+    
+};
 
-        }
+$3Dmol.SpriteMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        //Render
-        var faceCount, lineCount;
-        //lambert shaders - draw triangles
-        //TODO: make sure geometryGroup's face count is setup correctly
-        if (object instanceof $3Dmol.Mesh) {
-            
-            if (material.wireframe) {
-                lineCount = geometryGroup.lineidx;
-                setLineWidth(material.wireframeLinewidth);
-                
-                if (updateBuffers)
-                    _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglLineBuffer );
-                
-                _gl.drawElements( _gl.LINES, lineCount, _gl.UNSIGNED_SHORT, 0 );
-            }
-            
-            else {
-                faceCount = geometryGroup.faceidx;
+$3Dmol.SpriteMaterial.prototype.clone = function() {
+    
+    var material = new $3Dmol.SpriteMaterial();
+    
+    $3Dmol.Material.prototype.clone.call(this, material);
+    
+    material.color.copy(this.color);
+    material.map = this.map;
+    
+    material.useScreenCoordinates = useScreenCoordinates;
+    material.sizeAttenuation = this.sizeAttenuation;
+    material.scaleByViewport = this.scaleByViewPort;
+    material.alignment.copy(this.alignment);
+    
+    material.uvOffset.copy(this.uvOffset);
+    
+    return material;
+    
+};
 
-                if (updateBuffers)
-                    _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglFaceBuffer );
-                
-                _gl.drawElements( _gl.TRIANGLES, faceCount, _gl.UNSIGNED_SHORT, 0 );
-                
-            }
+//Alignment for Sprites
 
+$3Dmol.SpriteAlignment = {};
+$3Dmol.SpriteAlignment.topLeft = new $3Dmol.Vector2(1, -1);
+$3Dmol.SpriteAlignment.topCenter = new $3Dmol.Vector2(0, -1);
+$3Dmol.SpriteAlignment.topRight = new $3Dmol.Vector2(-1, -1);
+$3Dmol.SpriteAlignment.centerLeft = new $3Dmol.Vector2(1, 0);
+$3Dmol.SpriteAlignment.center = new $3Dmol.Vector2(0, 0);
+$3Dmol.SpriteAlignment.centerRight = new $3Dmol.Vector2(-1, 0);
+$3Dmol.SpriteAlignment.bottomLeft = new $3Dmol.Vector2(1, 1);
+$3Dmol.SpriteAlignment.bottomCenter = new $3Dmol.Vector2(0, 1);
+$3Dmol.SpriteAlignment.bottomRight = new $3Dmol.Vector2(-1, 1);
 
-            _this.info.render.calls++;
-            _this.info.render.vertices += faceCount;
-            _this.info.render.faces += faceCount / 3;
-        }
 
-        //basic shaders - draw lines
-        else if (object instanceof $3Dmol.Line) {
-            lineCount = geometryGroup.vertices;
+//Texture
+//We really only create textures from 2d rendering contexts (to display text labels)
+/** @constructor */
+$3Dmol.Texture = function(image) {
 
-            setLineWidth(material.linewidth);
-            _gl.drawArrays( _gl.LINES, 0, lineCount );
+    $3Dmol.EventDispatcher.call(this);
+    
+    this.id = $3Dmol.TextureIdCount++;
+    
+    this.name = "";
+    
+    this.image = image;
+    this.mipmaps = [];
+    
+    this.mapping = new $3Dmol.UVMapping();
+    
+    this.wrapS = $3Dmol.ClampToEdgeWrapping;
+    this.wrapT = $3Dmol.ClampToEdgeWrapping;
+    
+    this.magFilter = $3Dmol.LinearFilter;
+    this.minFilter = $3Dmol.LinearMipMapLinearFilter;
+    
+    this.anisotropy = 1;
+    
+    this.format = $3Dmol.RGBAFormat;
+    this.type = $3Dmol.UnsignedByteType;
+    
+    this.offset = new $3Dmol.Vector2(0, 0);
+    this.repeat = new $3Dmol.Vector2(1, 1);
+    
+    this.generateMipmaps = true;
+    this.premultiplyAlpha = false;
+    this.flipY = true;
+    this.unpackAlignment = 4;
+    
+    this.needsUpdate = false;
+    this.onUpdate = null;
+    
+};
 
-            _this.info.render.calls++;
-        }
+$3Dmol.Texture.prototype = {
 
-    };
+    constructor : $3Dmol.Texture,
+    
+    clone : function(texture) {
+        
+        if (texture === undefined)
+            texture = new $3Dmol.Texture();
+        
+        texture.image = this.image;
+        texture.mipmaps = this.mipmaps.slice(0);
+        
+        texture.mapping = this.mapping;
+        
+        texture.wrapS = this.wrapS;
+        texture.wrapT = this.wrapT;
+        
+        texture.magFilter = this.magFilter;
+        texture.minFilter = this.minFilter;
+        
+        texture.anisotropy = this.anisotropy;
+        
+        texture.format = this.format;
+        texture.type = this.type;
+        
+        texture.offset.copy(this.offset);
+        texture.repeat.copy(this.repeat);
+        
+        texture.generateMipmaps = this.generateMipmaps;
+        texture.premultiplyAlpha = this.premultiplyAlpha;
+        texture.flipY = this.flipY;
+        texture.unpackAlignment = this.unpackAlignment;
+        
+        return texture;
+        
+    },
+    
+    dispose : function() {
+        
+        this.dispatchEvent( {type: 'dispose'});
+        
+    }    
+    
+};
 
-    //rendering
-    function renderObjects ( renderList, reverse, materialType, camera, lights, fog, useBlending, overrideMaterial)  {
+$3Dmol.TextureIdCount = 0;
 
-        var webglObject, object, buffer, material, start, end, delta;
 
-        //Forward or backward render
+// sides
+$3Dmol.FrontSide = 0;
+$3Dmol.BackSide = 1;
+$3Dmol.DoubleSide = 2;
 
-        if (reverse) {
-            start = renderList.length - 1;
-            end = -1;
-            delta = -1;
-        }
+// shading
+$3Dmol.NoShading = 0;
+$3Dmol.FlatShading = 1;
+$3Dmol.SmoothShading = 2;
 
-        else {
-            start = 0;
-            end = renderList.length;
-            delta = 1;
-        }
+// colors
+$3Dmol.NoColors = 0;
+$3Dmol.FaceColors = 1;
+$3Dmol.VertexColors = 2;
 
-        for (var i = start; i !== end; i += delta) {
+//Texture constants
+//TODO: Which of these do I need (since I only use textures to display label sprites) ?
+$3Dmol.MultiplyOperation = 0;
+$3Dmol.MixOperation = 1;
+$3Dmol.AddOperation = 2;
 
-            webglObject = renderList[i];
+// mapping modes
 
-            if (webglObject.render) {
+$3Dmol.UVMapping = function() {};
 
-                object = webglObject.object;
-                buffer = webglObject.buffer;
-                material = webglObject[materialType];
+// wrapping modes
+$3Dmol.ClampToEdgeWrapping = 1001;
 
-                if ( ! material )
-                    continue;
+//Filters
+$3Dmol.LinearFilter = 1006;
+$3Dmol.LinearMipMapLinearFilter = 1008;
 
-                if (useBlending)
-                    _this.setBlending(true);
+//Data types
+$3Dmol.UnsignedByteType = 1009;
 
-                _this.setDepthTest(material.depthTest);
-                _this.setDepthWrite(material.depthWrite);
-                setPolygonOffset(material.polygonOffset, material.polygonOffsetFactor, material.polygonOffsetUnits);
+//Pixel formats
+$3Dmol.RGBAFormat = 1021;
+/* 
+ * $3Dmol Mesh and Line objects
+ */
 
-                _this.setMaterialFaces(material);
 
-                _this.renderBuffer(camera, lights, fog, material, buffer, object);
-            }
-        }
+//Line Object
+/** @constructor */
+$3Dmol.Line = function (geometry, material, type) {
 
-    }
-    
-    this.render = function ( scene, camera, forceClear ) {
+    $3Dmol.Object3D.call(this);
 
-        if ( camera instanceof $3Dmol.Camera === false )  {
+    this.geometry = geometry;
+        //TODO: update material and type to webgl
+    this.material = (material !== undefined) ? material : new $3Dmol.LineBasicMaterial( { color: Math.random() * 0xffffff } );
+    this.type = (type !== undefined) ? type : $3Dmol.LineStrip;
 
-            console.error( '$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.' );
-            return;
+};
 
-        }
+$3Dmol.LineStrip = 0;
+$3Dmol.LinePieces = 1;
 
-        var i, il,
+$3Dmol.Line.prototype = Object.create($3Dmol.Object3D.prototype);
 
-        webglObject, object,
-        renderList,
+$3Dmol.Line.prototype.clone = function (object) {
 
-        lights = scene.__lights,
-        fog = scene.fog;
+    if (object === undefined) object = new $3Dmol.Line(this.geometry, this.material, this.type);
 
-        // reset caching for this frame
+    $3Dmol.Object3D.prototype.clone.call(this, object);
 
-        _currentMaterialId = -1;
-        _lightsNeedUpdate = true;
+    return object;
 
-        // update scene graph
+};
 
-        if ( this.autoUpdateScene ) scene.updateMatrixWorld();
 
-        // update camera matrices
-        //Pretty sure camera's parent is always going to be undefined for our purposes...
-        if ( camera.parent === undefined ) camera.updateMatrixWorld();
+//Mesh Object
+/** @constructor */
+$3Dmol.Mesh = function(geometry, material) {
 
-        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
+    $3Dmol.Object3D.call(this);
 
-        _projScreenMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
+    this.geometry = geometry;
+    this.material = (material !== undefined) ? material : new $3Dmol.MeshBasicMaterial( { color: Math.random() * 0xffffff, wireframe: true } );
 
-        // update WebGL objects
+};
 
-        if ( this.autoUpdateObjects ) this.initWebGLObjects( scene );
+$3Dmol.Mesh.prototype = Object.create($3Dmol.Object3D.prototype);
 
+$3Dmol.Mesh.prototype.clone = function (object) {
 
-        _this.info.render.calls = 0;
-        _this.info.render.vertices = 0;
-        _this.info.render.faces = 0;
-        _this.info.render.points = 0;
+    if (object === undefined) object = new $3Dmol.Mesh(this.geometry, this.material);
 
-        _currentWidth = _viewportWidth;
-        _currentHeight = _viewportHeight;
+    $3Dmol.Object3D.prototype.clone.call(this, object);
 
-        if ( this.autoClear || forceClear ) {
-            this.clear( this.autoClearColor, this.autoClearDepth, this.autoClearStencil );
+    return object;
 
-        }
+};
 
-        // set matrices for regular objects (frustum culled)
 
-        renderList = scene.__webglObjects;
+//Sprite object
+/** @constructor */
+$3Dmol.Sprite = function(material) {
+    
+    $3Dmol.Object3D.call(this);
+    
+    this.material = (material !== undefined) ? material : new $3Dmol.SpriteMaterial();
 
-        for ( i = 0, il = renderList.length; i < il; i ++ ) {
+    this.rotation3d = this.rotation;
+    this.rotation = 0;
+    
+};
 
-            webglObject = renderList[ i ];
-            object = webglObject.object;
+$3Dmol.Sprite.prototype = Object.create($3Dmol.Object3D.prototype);
 
-            webglObject.render = false;
+$3Dmol.Sprite.prototype.updateMatrix = function() {
+    
+    this.matrix.setPosition(this.position);
+    
+    this.rotation3d.set(0, 0, this.rotation);
+    this.matrix.setRotationFromEuler(this.rotation3d);
+    
+    if (this.scale.x !== 1 || this.scale.y !== 1)
+        this.matrix.scale(this.scale);
+    
+    this.matrixWorldNeedsUpdate = true;
+    
+};
 
-            if ( object.visible ) {        
-                setupMatrices( object, camera );
-                unrollBufferMaterial( webglObject );
-                webglObject.render = true;
-            }
-        }
+$3Dmol.Sprite.prototype.clone = function(object) {
+    
+    if (object === undefined)
+        object = new $3Dmol.Sprite(this.material);
+    
+    $3Dmol.Object3D.prototype.clone.call(this, object);
+    
+    return object;
+    
+};
+/**
+ * Simplified webGL renderer
+ */
 
-        // set matrices for immediate objects
+$3Dmol.Renderer = function(parameters) {
 
-        var material = null;
+    parameters = parameters || {};
 
-        // opaque pass (front-to-back order)
+    var _canvas = parameters.canvas !== undefined ? parameters.canvas
+            : document.createElement('canvas'),
+
+    _precision = parameters.precision !== undefined ? parameters.precision
+            : 'highp', _alpha = parameters.alpha !== undefined ? parameters.alpha
+            : true, _premultipliedAlpha = parameters.premultipliedAlpha !== undefined ? parameters.premultipliedAlpha
+            : true, _antialias = parameters.antialias !== undefined ? parameters.antialias
+            : false, _stencil = parameters.stencil !== undefined ? parameters.stencil
+            : true, _preserveDrawingBuffer = parameters.preserveDrawingBuffer !== undefined ? parameters.preserveDrawingBuffer
+            : false, _clearColor = parameters.clearColor !== undefined ? new $3Dmol.Color(
+            parameters.clearColor)
+            : new $3Dmol.Color(0x000000), _clearAlpha = parameters.clearAlpha !== undefined ? parameters.clearAlpha
+            : 0, _outlineMaterial = parameters.outline !== undefined ? new $3Dmol.MeshOutlineMaterial(
+            parameters.outline)
+            : null;
 
-        this.setBlending( false );
+    this.domElement = _canvas;
+    this.context = null;
+    this.devicePixelRatio = parameters.devicePixelRatio !== undefined ? parameters.devicePixelRatio
+            : (self.devicePixelRatio !== undefined) ? self.devicePixelRatio : 1;
 
-        renderObjects( scene.__webglObjects, true, "opaque", camera, lights, fog, false, material );
-        
-        //prime depth buffer
-        renderObjects( scene.__webglObjects, true, "blank", camera, lights, fog, true, material );
+    // clearing
 
-        // transparent pass (back-to-front order)
+    this.autoClear = true;
+    this.autoClearColor = true;
+    this.autoClearDepth = true;
+    this.autoClearStencil = true;
 
-        renderObjects( scene.__webglObjects, false, "transparent", camera, lights, fog, true, material );
+    // scene graph
 
-        // Render plugins (e.g. sprites), and reset state
-        
-        renderPlugins(this.renderPluginsPost, scene, camera);
+    this.sortObjects = true;
 
-        // Ensure depth buffer writing is enabled so it can be cleared on next render
+    this.autoUpdateObjects = true;
+    this.autoUpdateScene = true;
 
-        this.setDepthTest( true );
-        this.setDepthWrite( true );
+    this.renderPluginsPost = [];
 
-        //_gl.finish();
+    // info
 
-    };
-    
-    function renderPlugins(plugins, scene, camera) {
-        
-        //Reset state once regardless
-        //This should also fix cartoon render bug (after transparent surface render)
-        
-        _currentGeometryGroupHash = -1;
-        _currentProgram = null;
-        _currentCamera = null;
-        _oldBlending = -1;
-        _oldDepthWrite = -1;
-        _oldDepthTest = -1;
-        _oldDoubleSided = -1;
-        _currentMaterialId = -1;
-        _oldFlipSided = -1;
-        
-        
-        if (!plugins.length)
-            return;
-        
-        for (var i = 0, il = plugins.length; i < il; i++) {
-            
-            _lightsNeedUpdate = true;
-            
-            plugins[i].render(scene, camera, _currentWidth, _currentHeight);
-            
-            //Reset state after plugin render
-            _currentGeometryGroupHash = -1;
-            _currentProgram = null;
-            _currentCamera = null;
-            _oldBlending = -1;
-            _oldDepthWrite = -1;
-            _oldDepthTest = -1;
-            _oldDoubleSided = -1;
-            _currentMaterialId = -1;
-            _oldFlipSided = -1;       
-                
-        }  
-        
-    }
+    this.info = {
+        memory : {
 
-    this.initWebGLObjects = function ( scene ) {
+            programs : 0,
+            geometries : 0,
+            textures : 0
 
-        if ( !scene.__webglObjects ) {
+        },
+        render : {
 
-            scene.__webglObjects = [];
-            scene.__webglObjectsImmediate = [];
-            scene.__webglSprites = [];
-            scene.__webglFlares = [];
+            calls : 0,
+            vertices : 0,
+            faces : 0,
+            points : 0
 
         }
+    };
 
-        //Add objects; this sets up buffers for each geometryGroup
-        if (scene.__objectsAdded.length) {
-            
-            while(scene.__objectsAdded.length){
-                addObject(scene.__objectsAdded[0], scene);
-                scene.__objectsAdded.splice(0, 1);
-            }
-            
-            //Force buffer update during render
-            //Hackish fix for initial cartoon-render-then-transparent-surface bug
-            _currentGeometryGroupHash = -1;
-            
-        }
+    // internal properties
+    var _this = this,
+    _programs = [], _programs_counter = 0,
+    
+    // internal state cache
+    _currentProgram = null, _currentFramebuffer = null, _currentMaterialId = -1, _currentGeometryGroupHash = null, _currentCamera = null, _geometryGroupCounter = 0,
+    _usedTextureUnits = 0,
 
-        while (scene.__objectsRemoved.length) {
+    // GL state cache
+    _oldDoubleSided = -1, _oldFlipSided = -1,
+    _oldBlending = -1,
+    _oldBlendEquation = -1, _oldBlendSrc = -1, _oldBlendDst = -1,
+    _oldDepthTest = -1, _oldDepthWrite = -1,
+    _oldPolygonOffset = null, _oldPolygonOffsetFactor = null, _oldPolygonOffsetUnits = null,
+    _oldLineWidth = null,
 
-            removeObject(scene.__objectsRemoved[ 0 ], scene);
-            scene.__objectsRemoved.splice(0, 1);
+    _viewportX = 0, _viewportY = 0, _viewportWidth = 0, _viewportHeight = 0, _currentWidth = 0, _currentHeight = 0,
+    _enabledAttributes = {},
+
+    // camera matrices cache
+    _projScreenMatrix = new $3Dmol.Matrix4(),
+    _vector3 = new $3Dmol.Vector3(),
+
+    // light arrays cache
+    _direction = new $3Dmol.Vector3(),
+    _lightsNeedUpdate = true,
 
+    _lights = {
+        ambient : [ 0, 0, 0 ],
+        directional : {
+            length : 0,
+            colors : [],
+            positions : []
+        },
+        point : {
+            length : 0,
+            colors : [],
+            positions : [],
+            distances : []
+        },
+        spot : {
+            length : 0,
+            colors : [],
+            positions : [],
+            distances : [],
+            directions : [],
+            anglesCos : [],
+            exponents : []
+        },
+        hemi : {
+            length : 0,
+            skyColors : [],
+            groundColors : [],
+            positions : []
         }
 
-        // update must be called after objects adding / removal
-        //This sends typed arrays to GL buffers for each geometryGroup
-        for ( var o = 0, ol = scene.__webglObjects.length; o < ol; o ++ ) {
+    };
 
-            updateObject(scene.__webglObjects[ o ].object);
+    // initialize
+    var _gl;
 
-        }
+    initGL();
+    setDefaultGLState();
+
+    this.context = _gl;
+    var _extInstanced = _gl.getExtension("ANGLE_instanced_arrays");
+    var _extFragDepth = _gl.getExtension("EXT_frag_depth");
 
+    // API
+    
+    this.supportedExtensions = function() {
+        return {supportsAIA: Boolean(_extInstanced),
+            supportsImposters:  Boolean(_extFragDepth)
+            };
     };
     
-    // Objects adding
+    this.getContext = function() {
+        return _gl;
+    };
 
-    function addObject (object, scene) {
+    this.getPrecision = function() {
+        return _precision;
+    };
 
-        var g, gl, geometry, material, geometryGroup;
+    this.setClearColorHex = function(hex, alpha) {
+        _clearColor.setHex(hex);
+        _clearAlpha = alpha;
 
-        if ( !object.__webglInit ) {
+        _gl.clearColor(_clearColor.r, _clearColor.g, _clearColor.b,
+                        _clearAlpha);
+    };
 
-            object.__webglInit = true;
+    this.enableOutline = function(parameters) {
+        _outlineMaterial = new $3Dmol.MeshOutlineMaterial(parameters);
+        _outlineSphereImposterMaterial = new $3Dmol.SphereImposterOutlineMaterial(parameters);
+        _outlineStickImposterMaterial = new $3Dmol.StickImposterOutlineMaterial(parameters);
+    };
 
-            object._modelViewMatrix = new $3Dmol.Matrix4();
-            object._normalMatrix = new $3Dmol.Matrix3();
+    this.disableOutline = function() {
+        _outlineMaterial = null;
+        _outlineSphereImposterMaterial = null;
+        _outlineStickImposterMaterial = null;
+    };
 
-            if (object.geometry !== undefined && object.geometry.__webglInit === undefined) {
+    this.setSize = function(width, height) {
 
-                object.geometry.__webglInit = true;
-                object.geometry.addEventListener('dispose', onGeometryDispose);
+        _canvas.width = width * this.devicePixelRatio;
+        _canvas.height = height * this.devicePixelRatio;
 
-            }
-            
-            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
-                geometry = object.geometry;
-                material = object.material;           
-    
-                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
-    
-                    geometryGroup = geometry.geometryGroups[ g ];
-                    
-                    geometryGroup.id = _geometryGroupCounter++;
+        _canvas.style.width = width + 'px';
+        _canvas.style.height = height + 'px';
 
-                    // initialise VBO on the first access
+        this.setViewport(0, 0, _canvas.width, _canvas.height);
 
-                    if ( !geometryGroup.__webglVertexBuffer ) {
-                            
-                        if (object instanceof $3Dmol.Mesh) {
-                            createMeshBuffers(geometryGroup);
-                            geometry.elementsNeedUpdate = true;
-                            geometry.normalsNeedUpdate = true;
-                        }
-                            
-                        else if (object instanceof $3Dmol.Line)
-                            createLineBuffers(geometryGroup);
+    };
 
-                        geometry.verticesNeedUpdate = true;
-                        geometry.colorsNeedUpdate = true;
+    this.setViewport = function(x, y, width, height) {
 
-                    }
-                        
-                }
-                
-            }
-        
-        }
-        
-        if ( ! object.__webglActive ) {
-            
-            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
-                
-                geometry = object.geometry;
+        _viewportX = x !== undefined ? x : 0;
+        _viewportY = y !== undefined ? y : 0;
 
-                for ( g = 0, gl = geometry.geometryGroups.length; g < gl; g++ ) {
-                    geometryGroup = geometry.geometryGroups[g];
+        _viewportWidth = width !== undefined ? width : _canvas.width;
+        _viewportHeight = height !== undefined ? height : _canvas.height;
 
-                    addBuffer(scene.__webglObjects, geometryGroup, object);
-                }
-                
-            }
-            
-            //Sprite
-            else if (object instanceof $3Dmol.Sprite) 
-                scene.__webglSprites.push(object);
-         
-                     
-            object.__webglActive = true;
-            
-        }
+        _gl.viewport(_viewportX, _viewportY, _viewportWidth, _viewportHeight);
 
-    }
+    };
 
-    function updateObject ( object ) {
+    this.clear = function(color, depth, stencil) {
 
-        var geometry = object.geometry, material = object.material,
-                geometryGroup, customAttributesDirty;
-        
-        if ( object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line ) {
-            
-            for (var g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
-                
-                geometryGroup = geometry.geometryGroups[ g ];
+        var bits = 0;
 
-                if ( geometry.verticesNeedUpdate || geometry.elementsNeedUpdate || geometry.colorsNeedUpdate || geometry.normalsNeedUpdate) {
-                    setBuffers( geometryGroup, _gl.STATIC_DRAW );
-                }
-            }
-            
-            geometry.verticesNeedUpdate = false;
-            geometry.elementsNeedUpdate = false;
-            geometry.normalsNeedUpdate = false;
-            geometry.colorsNeedUpdate = false;
+        if (color === undefined || color)
+            bits |= _gl.COLOR_BUFFER_BIT;
+        if (depth === undefined || depth)
+            bits |= _gl.DEPTH_BUFFER_BIT;
+        if (stencil === undefined || stencil)
+            bits |= _gl.STENCIL_BUFFER_BIT;
+        _gl.clear(bits);
 
-            geometry.buffersNeedUpdate = false;
+    };
 
-        }
+    this.clearTarget = function(color, depth, stencil) {
 
-    }
-    
-    function removeObject( object, scene ) {
+        this.clear(color, depth, stencil);
 
-        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line )
-            removeInstances(scene.__webglObjects, object);
+    };
 
-        else if (object instanceof $3Dmol.Sprite)
-            removeInstancesDirect(scene.__webglSprites, object);
-            
-        object.__webglActive = false;
+    this.setMaterialFaces = function(material, reflected) {
 
-    }
+        var doubleSided = material.side === $3Dmol.DoubleSide;
+        var flipSided = material.side === $3Dmol.BackSide;
+        flipSided = reflected ? !flipSided : flipSided;
 
-    function removeInstances( objList, object ) {
+        if (_oldDoubleSided !== doubleSided) {
 
-        for (var o = objList.length - 1; o >= 0; --o) {
+            if (doubleSided) {
 
-            if (objList[o].object === object) 
-                objList.splice(o, 1);
+                _gl.disable(_gl.CULL_FACE);
 
-        }
-    }
+            } else {
 
-    function removeInstancesDirect( objList, object ) {
+                _gl.enable(_gl.CULL_FACE);
 
-        for (var o = objList.length - 1; o >= 0; --o) {
+            }
 
-            if (objList[o] === object) 
-                objList.splice(o, 1);
+            _oldDoubleSided = doubleSided;
 
         }
-    }
 
-    function unrollBufferMaterial( globject ) {
+        if (_oldFlipSided !== flipSided) {
 
-        var object = globject.object;
-        var material = object.material;
+            if (flipSided) {
 
-        if ( material.transparent) {                    
-            globject.opaque = null;
-            globject.transparent = material;
-            var blankMaterial = material.clone();
-            blankMaterial.opacity = 0;
-            globject.blank = blankMaterial;
-        }
+                _gl.frontFace(_gl.CW);
 
-        else {
-            globject.opaque = material;
-            globject.transparent = null;
-        }
+            } else {
 
-    }
+                _gl.frontFace(_gl.CCW);
 
-    function setBuffers( geometryGroup, hint, line ) {
+            }
 
-        var vertexArray = geometryGroup.vertexArray;
-        var colorArray = geometryGroup.colorArray;
-         
-        //vertex buffers
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, vertexArray, hint );        
+            _oldFlipSided = flipSided;
 
-        //color buffers
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, colorArray, hint );    
-              
-        
-        //normal buffers
-        if (geometryGroup.normalArray !== undefined && geometryGroup.__webglNormalBuffer !== undefined) {
-            var normalArray = geometryGroup.normalArray;
-            _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer );
-            _gl.bufferData( _gl.ARRAY_BUFFER, normalArray, hint );       
-             
-        }
-        
-        //face (index) buffers
-        if (geometryGroup.faceArray !== undefined && geometryGroup.__webglFaceBuffer !== undefined) {
-            var faceArray = geometryGroup.faceArray;
-            _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglFaceBuffer );
-            _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, faceArray, hint );  
-                      
-        }
-        
-        //line (index) buffers (for wireframe)
-        if (geometryGroup.lineArray !== undefined && geometryGroup.__webglLineBuffer !== undefined) {
-            var lineArray = geometryGroup.lineArray;            
-            _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglLineBuffer );
-            _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, lineArray, hint );
         }
 
-    }
-    
-    //Creates appropriate gl buffers for geometry chunk
-    //TODO: do we need line buffer for mesh objects?
-    //Also, can we integrate this with createLineBuffers?
-    function createMeshBuffers ( geometryGroup ) {
+    };
 
-        geometryGroup.__webglVertexBuffer = _gl.createBuffer();
-        geometryGroup.__webglNormalBuffer = _gl.createBuffer();
-        geometryGroup.__webglColorBuffer = _gl.createBuffer();
+    this.setDepthTest = function(depthTest) {
 
-        geometryGroup.__webglFaceBuffer = _gl.createBuffer();
-        geometryGroup.__webglLineBuffer = _gl.createBuffer();
+        if (_oldDepthTest !== depthTest) {
 
-        _this.info.memory.geometries++;
-    }
-    
-    function createLineBuffers ( geometry ) {
-        
-        geometry.__webglVertexBuffer = _gl.createBuffer();
-        geometry.__webglColorBuffer = _gl.createBuffer();
-        
-        _this.info.memory.geometries++;
-    }
+            if (depthTest) {
 
-    function addBuffer (objlist, buffer, object) {
+                _gl.enable(_gl.DEPTH_TEST);
+
+            } else {
+
+                _gl.disable(_gl.DEPTH_TEST);
 
-        objlist.push(
-            {
-                buffer: buffer,
-                object: object,
-                opaque: null,
-                transparent: null
             }
-        );
 
-    }
+            _oldDepthTest = depthTest;
 
-    function setupMatrices (object, camera) {
+        }
 
-        object._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, object.matrixWorld );
+    };
 
-        object._normalMatrix.getInverse( object._modelViewMatrix );
-        object._normalMatrix.transpose();
+    this.setDepthWrite = function(depthWrite) {
 
-    }
+        if (_oldDepthWrite !== depthWrite) {
 
-    function isPowerOfTwo ( value ) {
+            _gl.depthMask(depthWrite);
+            _oldDepthWrite = depthWrite;
 
-        return ( value & ( value - 1 ) ) === 0;
+        }
 
-    }
-    
-    // Fallback filters for non-power-of-2 textures
+    };
 
-    function filterFallback ( f ) {
+    this.setBlending = function(blending) {
 
-        return _gl.LINEAR;
+        if (!blending) {
+            _gl.disable(_gl.BLEND);
 
-    }
+        } else {
+            _gl.enable(_gl.BLEND);
+            _gl.blendEquationSeparate(_gl.FUNC_ADD, _gl.FUNC_ADD);
+            _gl.blendFuncSeparate(_gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA,
+                    _gl.ONE, _gl.ONE_MINUS_SRC_ALPHA);
 
-    function setTextureParameters ( textureType, texture, isImagePowerOfTwo ) {
+        }
 
-        if ( isImagePowerOfTwo ) {
+        _oldBlending = blending;
+    };
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_S, paramToGL( texture.wrapS ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_T, paramToGL( texture.wrapT ) );
+    // Plugins
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_MAG_FILTER, paramToGL( texture.magFilter ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_MIN_FILTER, paramToGL( texture.minFilter ) );
+    this.addPostPlugin = function(plugin) {
 
-        } else {
+        plugin.init(this);
+        this.renderPluginsPost.push(plugin);
+
+    };
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_S, _gl.CLAMP_TO_EDGE );
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_T, _gl.CLAMP_TO_EDGE );
+    // Sorting
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_MAG_FILTER, filterFallback( texture.magFilter ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_MIN_FILTER, filterFallback( texture.minFilter ) );
+    function numericalSort(a, b) {
 
-        }
+        return b[0] - a[0];
 
     }
-    
-    this.setTexture = function (texture, slot) {
 
-        if (texture.needsUpdate) {
+    function enableAttribute(attribute) {
 
-            if ( !texture.__webglInit ) {
+        if (!_enabledAttributes[attribute]) {
 
-                texture.__webglInit = true;
+            _gl.enableVertexAttribArray(attribute);
+            _enabledAttributes[attribute] = true;
 
-                texture.addEventListener('dispose', onTextureDispose);
+        }
 
-                texture.__webglTexture = _gl.createTexture();
+    }
 
-                _this.info.memory.textures++;
+    function disableAttributes() {
 
-            }
+        for ( var attribute in _enabledAttributes) {
 
-            _gl.activeTexture(_gl.TEXTURE0 + slot);
-            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
+            if (_enabledAttributes[attribute]) {
 
-            _gl.pixelStorei(_gl.UNPACK_FLIP_Y_WEBGL, texture.flipY);
-            _gl.pixelStorei(_gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL, texture.premultiplyAlpha);
-            _gl.pixelStorei(_gl.UNPACK_ALIGNMENT, texture.unpackAlignment);
+                _gl.disableVertexAttribArray(attribute);
+                _enabledAttributes[attribute] = false;
 
-            var image = texture.image,
-            isImagePowerOfTwo = isPowerOfTwo(image.width) && isPowerOfTwo(image.height),
-            glFormat = paramToGL(texture.format),
-            glType = paramToGL(texture.type);
+            }
 
-            setTextureParameters(_gl.TEXTURE_2D, texture, isImagePowerOfTwo);
+        }
 
-            var mipmap, mipmaps = texture.mipmaps;
+    }
 
-            // regular Texture (image, video, canvas)
+    function setPolygonOffset(polygonOffset, factor, units) {
 
-            // use manually created mipmaps if available
-            // if there are no manual mipmaps
-            // set 0 level mipmap and then use GL to generate other mipmap levels
+        if (_oldPolygonOffset !== polygonOffset) {
 
-            if ( mipmaps.length > 0 && isImagePowerOfTwo ) {
+            if (polygonOffset)
+                _gl.enable(_gl.POLYGON_OFFSET_FILL);
+            else
+                _gl.disable(_gl.POLYGON_OFFSET_FILL);
+        }
+    }
 
-                for ( var i = 0, il = mipmaps.length; i < il; i ++ ) {
-                    mipmap = mipmaps[ i ];
-                    _gl.texImage2D( _gl.TEXTURE_2D, i, glFormat, glFormat, glType, mipmap );
-                }
-                
-                texture.generateMipmaps = false;
-            } 
-            
-            else 
-                _gl.texImage2D( _gl.TEXTURE_2D, 0, glFormat, glFormat, glType, texture.image );
+    function setLineWidth(width) {
 
-            
-            if ( texture.generateMipmaps && isImagePowerOfTwo ) _gl.generateMipmap( _gl.TEXTURE_2D );
+        if (width !== _oldLineWidth) {
+            _gl.lineWidth(width);
+            _oldLineWidth = width;
+        }
 
-            texture.needsUpdate = false;
+    }
 
-            if ( texture.onUpdate ) texture.onUpdate();
+    var onGeometryDispose = function(event) {
 
-        } else {
+        var geometry = event.target;
+        geometry.removeEventListener('dispose', onGeometryDispose);
 
-            _gl.activeTexture( _gl.TEXTURE0 + slot );
-            _gl.bindTexture( _gl.TEXTURE_2D, texture.__webglTexture );
+        deallocateGeometry(geometry);
 
-        }
+        _this.info.memory.geometries--;
 
     };
-    
-    // Map constants to WebGL constants
 
-    function paramToGL ( p ) {
+    var onTextureDispose = function(event) {
 
-        if ( p === $3Dmol.UnsignedByteType ) return _gl.UNSIGNED_BYTE;
-        if ( p === $3Dmol.RGBAFormat ) return _gl.RGBA;
+        var texture = event.target;
 
-        return 0;
+        texture.removeEventListener('dispose', onTextureDispose);
 
-    }
-    
-    function setupLights ( program, lights ) {
-        var l, ll, light, n,
-        r = 0, g = 0, b = 0,
-        color,
-        position,
-        intensity,
-        distance,
-        
-        zlights = _lights,
-        
-        dirColors = zlights.directional.colors,
-        dirPositions = zlights.directional.positions,
-        
-        dirCount = 0,
-        dirLength = 0,
-        dirOffset = 0;
-        
-        for ( l = 0, ll = lights.length; l < ll; l++) {
-            
-            light = lights[l];
-            
-            color = light.color;
-            intensity = light.intensity;
-            distance = light.distance;
-            
-            if (light instanceof $3Dmol.Light) {
-                
-                dirCount++;
-                
-                _direction.getPositionFromMatrix(light.matrixWorld);
-                _vector3.getPositionFromMatrix(light.target.matrixWorld);
-                _direction.sub(_vector3);
-                _direction.normalize();
-                
-                if (_direction.x === 0 && _direction.y === 0 && _direction.z === 0)
-                    continue;
-                
-                dirPositions[dirOffset] = _direction.x;
-                dirPositions[dirOffset + 1] = _direction.y;
-                dirPositions[dirOffset + 2] = _direction.z;
+        deallocateTexture(texture);
 
-                dirColors[dirOffset] = color.r * intensity;
-                dirColors[dirOffset + 1] = color.g * intensity;
-                dirColors[dirOffset + 2] = color.b * intensity;
-                
-                dirOffset += 3;
-                
-                dirLength++;    
-            }
-        
-        }
+        _this.info.memory.textures--;
 
-        zlights.ambient[0] = r;
-        zlights.ambient[1] = g;
-        zlights.ambient[2] = b;
-        zlights.directional.length = dirLength;
-    }
+    };
 
-    function initGL () {
+    var onMaterialDispose = function(event) {
 
-        try {
+        var material = event.target;
+        material.removeEventListener('dispose', onMaterialDispose);
 
-            if ( ! ( _gl = _canvas.getContext( 'experimental-webgl', { alpha: _alpha, premultipliedAlpha: _premultipliedAlpha, antialias: _antialias, stencil: _stencil, preserveDrawingBuffer: _preserveDrawingBuffer } ) ) ) {
-                if ( ! ( _gl = _canvas.getContext( 'webgl', { alpha: _alpha, premultipliedAlpha: _premultipliedAlpha, antialias: _antialias, stencil: _stencil, preserveDrawingBuffer: _preserveDrawingBuffer } ) ) ) {
-                throw 'Error creating WebGL context.';
-                }
-            }
+        deallocateMaterial(material);
 
-        } catch ( error ) {
+    };
 
-            console.error( error );
-        }
-        var ext = _gl.getExtension('EXT_frag_depth');
-    }
+    var deallocateGeometry = function(geometry) {
 
-    function setDefaultGLState () {
+        geometry.__webglInit = undefined;
 
-        _gl.clearColor( 0, 0, 0, 1 );
-        _gl.clearDepth( 1 );
-        _gl.clearStencil( 0 );
+        if (geometry.__webglVertexBuffer !== undefined)
+            _gl.deleteBuffer(geometry.__webglVertexBuffer);
 
-        _gl.enable( _gl.DEPTH_TEST );
-        _gl.depthFunc( _gl.LEQUAL );
+        if (geometry.__webglColorBuffer !== undefined)
+            _gl.deleteBuffer(geometry.__webglColorBuffer);
 
-        _gl.frontFace( _gl.CCW );
-        _gl.cullFace( _gl.BACK );
-        _gl.enable( _gl.CULL_FACE );
+        if (geometry.geometryGroups !== undefined) {
 
-        _gl.enable( _gl.BLEND );
-        _gl.blendEquation( _gl.FUNC_ADD );
-        _gl.blendFunc( _gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA );
+            for (var g = 0, gl = geometry.groups; g < gl; g++) {
 
-        _gl.clearColor( _clearColor.r, _clearColor.g, _clearColor.b, _clearAlpha );
-        var ext = _gl.getExtension('EXT_frag_depth');
+                var geometryGroup = geometry.geometryGroups[g];
 
+                if (geometryGroup.__webglVertexBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglVertexBuffer);
 
-    }
-    
-    this.addPostPlugin(new $3Dmol.SpritePlugin());
-        
-};
+                if (geometryGroup.__webglColorBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglColorBuffer);
 
-/*
- * Scene class
- */
-/** @constructor */
-$3Dmol.Scene = function() {
-    
-    $3Dmol.Object3D.call(this);
-    
-    this.fog = null;
-    
-    //May not need...
-    this.overrideMaterial = null;
-    
-    this.matrixAutoUpdate = false;
-    
-    this.__objects = [];
-    this.__lights = [];
-    
-    this.__objectsAdded = [];
-    this.__objectsRemoved = [];
-    
-};
+                if (geometryGroup.__webglNormalBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglNormalBuffer);
 
-$3Dmol.Scene.prototype = Object.create($3Dmol.Object3D.prototype);
+                if (geometryGroup.__webglFaceBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglFaceBuffer);
 
-$3Dmol.Scene.prototype.__addObject = function(object) {
-    
-    //Directional Lighting
-    if (object instanceof $3Dmol.Light) {
-        
-        if (this.__lights.indexOf(object) === -1)
-            this.__lights.push(object);
-        
-        //TODO: Do I need this??
-        if (object.target && object.target.parent === undefined)
-            this.add(object.target);
-            
-    }
-    
-    //Rotation group
-    else {
-        
-        if (this.__objects.indexOf(object) === -1) {
-            
-            this.__objects.push(object);
-            this.__objectsAdded.push(object);
-            
-            //Check if previously removed
-            
-            var idx = this.__objectsRemoved.indexOf(object);
-            
-            if (idx !== -1)
-                this.__objectsRemoved.splice(i, 1);
-                
-        }
-    }
-    
-    //Add object's children
-    
-    for (var i = 0; i < object.children.length; i++) 
-        this.__addObject(object.children[i]);
-    
-};
+                if (geometryGroup.__webglLineBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglLineBuffer);
 
-$3Dmol.Scene.prototype.__removeObject = function(object) {
-    
-    var idx;
-    if (object instanceof $3Dmol.Light) {
-        
-        idx = this.__lights.indexOf(object);
-        
-        if (idx !== -1)
-            this.__lights.splice(idx, 1);
-            
-    }
-    
-    //Object3D
-    else {
-        
-        idx = this.__objects.indexOf(object);
-        
-        if (idx !== -1) {
-            
-            this.__objects.splice(idx, 1);
-            this.__objectsRemoved.push(object);
-            
-            //Check if previously added
-            
-            var ai = this.__objectsAdded.indexOf(object);
-            
-            if (ai !== -1) 
-                this.__objectsAdded.splice(idx, 1);
-                
+            }
         }
-    
-    }
-    
-    //Remove object's children
-    for (var i = 0; i < object.children.length; i++)
-        this.__removeObject(object.children[i]);
-    
-};
+    };
 
+    var deallocateMaterial = function(material) {
 
-/*
- * Fog Class
- */
+        var program = material.program;
 
-/** @constructor */
-$3Dmol.Fog = function ( hex, near, far ) {
+        if (program === undefined)
+            return;
 
-    this.name = '';
+        material.program = undefined;
 
-    this.color = new $3Dmol.Color( hex );
+        // only deallocate GL program if this was the last use of shared program
+        // assumed there is only single copy of any program in the _programs
+        // list
+        // (that's how it's constructed)
 
-    this.near = ( near !== undefined ) ? near : 1;
-    this.far = ( far !== undefined ) ? far : 1000;
+        var i, il, programInfo;
+        var deleteProgram = false;
 
-};
+        for (i = 0, il = _programs.length; i < il; i++) {
 
-$3Dmol.Fog.prototype.clone = function () {
+            programInfo = _programs[i];
 
-    return new $3Dmol.Fog( this.color.getHex(), this.near, this.far );
+            if (programInfo.program === program) {
 
-};/* 
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
+                programInfo.usedTimes--;
 
-$3Dmol.ShaderUtils = {
-    
-    clone: function ( uniforms_src ) {
-        
-        var u, p, parameter, parameter_src, uniforms_clone = {};
-        
-        for (u in uniforms_src) {
-            uniforms_clone[u] = {};
-            uniforms_clone[u].type = uniforms_src[u].type;
-            
-            var srcValue = uniforms_src[u].value;
-            
-            if (srcValue instanceof $3Dmol.Color)
-                uniforms_clone[u].value = srcValue.clone();
-            else if (typeof srcValue === "number")
-                uniforms_clone[u].value = srcValue;
-            else if (srcValue instanceof Array) 
-                uniforms_clone[u].value = [];
-            else
-                console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform");
-            
-        }
-        
-        return uniforms_clone;
-    }
-};
+                if (programInfo.usedTimes === 0) {
 
-$3Dmol.ShaderLib = { 
-    'basic' : {
-        fragmentShader : [
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 diffuse;",
-"uniform float opacity;",
+                    deleteProgram = true;
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+                }
 
-"varying vec3 vColor;",
+                break;
 
-"void main() {",
-    
-"    gl_FragColor = vec4( diffuse, opacity );",
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-    
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",    
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
-    
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+            }
 
-"}"
-                                                     
-].join("\n"),
-        
-        vertexShader : [
+        }
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
+        if (deleteProgram === true) {
 
-"attribute vec3 position;",
-"attribute vec3 color;",
+            // avoid using array.splice, this is costlier than creating new
+            // array from scratch
 
-"varying vec3 vColor;",
+            var newPrograms = [];
 
-"void main() {",
+            for (i = 0, il = _programs.length; i < il; i++) {
 
-"    vColor = color;",
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-"    gl_Position = projectionMatrix * mvPosition;",
+                programInfo = _programs[i];
 
-"}"
-        
-].join("\n"),
-    
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000}
-        }
+                if (programInfo.program !== program) {
 
-    },
-    
- 'sphereimposter' : {
-        fragmentShader : [
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 diffuse;",
-"uniform float opacity;",
+                    newPrograms.push(programInfo);
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+                }
 
-"varying vec3 vColor;",
-"varying vec2 mapping;",
+            }
 
-"void main() {",
-"    float lensqr = dot(mapping,mapping);",
-"    if(lensqr > 2.0)",
-"       discard;",
-"    float w = sqrt(2.0 - lensqr);",
-"    float z = sqrt(sqrt(2.0)-lensqr);",
-"    gl_FragDepthEXT = -.1*z;",
-"    gl_FragColor = vec4( w*vColor, 1 );",
-    
+            _programs = newPrograms;
 
+            _gl.deleteProgram(program);
 
-"}"
-                                                     
-].join("\n"),
-        
-        vertexShader : [
+            _this.info.memory.programs--;
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
+        }
 
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+    };
 
-"varying vec2 mapping;",
-"varying vec3 vColor;",
+    var deallocateTexture = function(texture) {
 
-"void main() {",
+        if (texture.image && texture.image.__webglTextureCube) {
 
-"    vColor = color;",
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-"    vec4 projPosition = projectionMatrix * mvPosition;",
-"    vec4 adjust = projectionMatrix*vec4(normal, 1.0);  adjust.y *= -1.0; adjust.z = 0.0; adjust.w = 0.0;",
-"    mapping = normal.xy;",
-"    gl_Position = projPosition+adjust;",
+            // cube texture
+
+            _gl.deleteTexture(texture.image.__webglTextureCube);
 
-"}"
-        
-].join("\n"),
-    
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000}
         }
 
-    },
-    
-    
-    'lambert' : { 
-        fragmentShader : [
+        else {
 
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform float opacity;",
+            // 2D texture
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+            if (!texture.__webglInit)
+                return;
 
-"varying vec3 vLightFront;",
-"varying vec3 vColor;",
+            texture.__webglInit = false;
+            _gl.deleteTexture(texture.__webglTexture);
 
-"void main() {",
-    
-"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
-    
-"    #ifndef WIREFRAME",
-"    gl_FragColor.xyz *= vLightFront;",
-"    #endif",
-    
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
-    
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
-    
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+        }
 
-"}"
+    };
 
+    // Compile and return shader
+    function getShader(type, str) {
 
-].join("\n"),
-       
-       vertexShader : [
+        var shader;
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 ambient;",
-"uniform vec3 diffuse;",
-"uniform vec3 emissive;",
-"uniform vec3 ambientLightColor;",
-"uniform vec3 directionalLightColor[ 1 ];",
-"uniform vec3 directionalLightDirection[ 1 ];",
+        if (type === "fragment")
+            shader = _gl.createShader(_gl.FRAGMENT_SHADER);
+        else if (type === "vertex")
+            shader = _gl.createShader(_gl.VERTEX_SHADER);
 
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+        _gl.shaderSource(shader, str);
+        _gl.compileShader(shader);
 
-"varying vec3 vColor;",
-"varying vec3 vLightFront;",
+        if (!_gl.getShaderParameter(shader, _gl.COMPILE_STATUS)) {
 
-"void main() {",
-    
-"    vColor = color;",
-    
-"    vec3 objectNormal = normal;",  
-"    vec3 transformedNormal = normalMatrix * objectNormal;",    
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-    
-"    vLightFront = vec3( 0.0 );",
-    
-"    transformedNormal = normalize( transformedNormal );",
-    
-"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
-"    vec3 dirVector = normalize( lDirection.xyz );",
-"    float dotProduct = dot( transformedNormal, dirVector );",
-"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
-    
-"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
-"    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;",
-    
-"    gl_Position = projectionMatrix * mvPosition;",
-"}"
-           
-].join("\n"),
+            console.error(_gl.getShaderInfoLog(shader));
+            console.error("could not initialize shader");
+            return null;
 
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000},           
-            ambient: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            emissive: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            ambientLightColor: { type: 'fv', value: [] },
-            directionalLightColor: { type: 'fv', value: [] },
-            directionalLightDirection: { type: 'fv', value: [] }
         }
 
-    },
-    
-    //for double sided lighting
-    'lambertdouble' : { 
-        fragmentShader : [
+        return shader;
 
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform float opacity;",
+    }
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+    // Compile appropriate shaders (if necessary) from source code and attach to
+    // gl program.
+    function buildProgram(fragmentShader, vertexShader, uniforms, parameters) {
 
-"varying vec3 vLightFront;",
-"varying vec3 vLightBack;",
+        var p, pl, d, program, code;
+        var chunks = [];
 
-"varying vec3 vColor;",
+        chunks.push(fragmentShader);
+        chunks.push(vertexShader);
 
-"void main() {",
-    
-"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
-    
-"    #ifndef WIREFRAME",
-"    if ( gl_FrontFacing )",
-"       gl_FragColor.xyz *= vLightFront;",
-"    else",
-"       gl_FragColor.xyz *= vLightBack;",
-"    #endif",
-    
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
-    
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
-    
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+        for (p in parameters) {
+            chunks.push(p);
+            chunks.push(parameters[p]);
+        }
 
-"}"
+        code = chunks.join();
 
+        // check if program has already been compiled
 
-].join("\n"),
-       
-       vertexShader : [
+        for (p = 0, pl = _programs.length; p < pl; p++) {
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 ambient;",
-"uniform vec3 diffuse;",
-"uniform vec3 emissive;",
-"uniform vec3 ambientLightColor;",
-"uniform vec3 directionalLightColor[ 1 ];",
-"uniform vec3 directionalLightDirection[ 1 ];",
+            var programInfo = _programs[p];
 
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+            if (programInfo.code === code) {
 
-"varying vec3 vColor;",
-"varying vec3 vLightFront;",
-"varying vec3 vLightBack;",
+                programInfo.usedTimes++;
 
-"void main() {",
-    
-"    vColor = color;",
-    
-"    vec3 objectNormal = normal;",  
-"    vec3 transformedNormal = normalMatrix * objectNormal;",    
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-    
-"    vLightFront = vec3( 0.0 );",
-"    vLightBack = vec3( 0.0 );",
-    
-"    transformedNormal = normalize( transformedNormal );",
-    
-"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
-"    vec3 dirVector = normalize( lDirection.xyz );",
-"    float dotProduct = dot( transformedNormal, dirVector );",
-"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
-"    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );",
+                return programInfo.program;
+            }
+        }
 
-"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
-"    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;",
+        // Set up new program and compile shaders
 
-"    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;",
-"    vLightBack = vLightBack * diffuse + ambient * ambientLightColor + emissive;",
+        program = _gl.createProgram();
 
-"    gl_Position = projectionMatrix * mvPosition;",
-"}"
-           
-].join("\n"),
+        // set up precision
+        var precision = _precision;
+        var prefix = "precision " + precision + " float;";
+
+        var prefix_vertex = [ prefix ].join("\n");
+
+        var prefix_fragment = [
+                parameters.fragdepth ? "#extension GL_EXT_frag_depth: enable"
+                        : "",
+                parameters.wireframe ? "#define WIREFRAME 1" : "", prefix ]
+                .join("\n");
+
+        var glFragmentShader = getShader("fragment", prefix_fragment
+                + fragmentShader);
+        var glVertexShader = getShader("vertex", prefix_vertex + vertexShader);
+
+        _gl.attachShader(program, glVertexShader);
+        _gl.attachShader(program, glFragmentShader);
+
+        _gl.linkProgram(program);
+
+        if (!_gl.getProgramParameter(program, _gl.LINK_STATUS))
+            console.error("Could not initialize shader");
+
+        // gather and cache uniform variables and attributes
+
+        program.uniforms = {};
+        program.attributes = {};
+
+        var identifiers, u, a, i;
+
+        // uniform vars
+        identifiers = [ 'viewMatrix', 'modelViewMatrix', 'projectionMatrix', 
+                'normalMatrix'];
+
+        // custom uniform vars
+        for (u in uniforms)
+            identifiers.push(u);
+
+        for (i = 0; i < identifiers.length; i++) {
+
+            var uniformVar = identifiers[i];
+            program.uniforms[uniformVar] = _gl.getUniformLocation(program,
+                    uniformVar);
 
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000},           
-            ambient: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            emissive: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            ambientLightColor: { type: 'fv', value: [] },
-            directionalLightColor: { type: 'fv', value: [] },
-            directionalLightDirection: { type: 'fv', value: [] }
         }
 
-    },
-    
-    
-    'sprite': {
-        
-        fragmentShader: [
-                                                         
-"uniform vec3 color;",
-"uniform sampler2D map;",
-"uniform float opacity;",
+        // attributes
+        identifiers = [ 'position', 'normal', 'color', 'lineDistance',
+                'offset', 'radius' ];
 
-"uniform int fogType;",
-"uniform vec3 fogColor;",
-"uniform float fogDensity;",
-"uniform float fogNear;",
-"uniform float fogFar;",
-"uniform float alphaTest;",
+        /*
+         * for (a in attributes) identifiers.push(a);
+         */
 
-"varying vec2 vUV;",
+        for (i = 0; i < identifiers.length; i++) {
 
-"void main() {",
-    
-"    vec4 texture = texture2D(map, vUV);",
-    
-"    if (texture.a < alphaTest) discard;",
-    
-"    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);",
-    
-"    if (fogType > 0) {",
-        
-"        float depth = gl_FragCoord.z / gl_FragCoord.w;",
-"        float fogFactor = 0.0;",
-        
-"        if (fogType == 1) {",
-"            fogFactor = smoothstep(fogNear, fogFar, depth);",
-"        }",
-        
-"        else {",
-"            const float LOG2 = 1.442695;",
-"            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);",
-"            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);",
-"        }",
-        
-"        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);",
-        
-"    }",
-"}"                                              
-            
-].join("\n"),
-        
-        vertexShader: [
+            var attributeVar = identifiers[i];
+            program.attributes[attributeVar] = _gl.getAttribLocation(program,
+                    attributeVar);
+        }
 
-"uniform int useScreenCoordinates;",
-"uniform vec3 screenPosition;",
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform float rotation;",
-"uniform vec2 scale;",
-"uniform vec2 alignment;",
-"uniform vec2 uvOffset;",
-"uniform vec2 uvScale;",
+        program.id = _programs_counter++;
+        _programs.push({
+            program : program,
+            code : code,
+            usedTimes : 1
+        });
+        _this.info.memory.programs = _programs.length;
 
-"attribute vec2 position;",
-"attribute vec2 uv;",
+        return program;
+    }
 
-"varying vec2 vUV;",
+    // TODO: need to set up shader attributes and uniforms as attributes on
+    // material object after attaching prgm
+    // We need to attach appropriate uniform variables to material after shaders
+    // have been chosen
+    this.initMaterial = function(material, lights, fog, object) {
 
-"void main() {",
-    
-"    vUV = uvOffset + uv * uvScale;",
-    
-"    vec2 alignedPosition = position + alignment;",
-    
-"    vec2 rotatedPosition;",
-"    rotatedPosition.x = ( cos(rotation) * alignedPosition.x - sin(rotation) * alignedPosition.y ) * scale.x;",
-"    rotatedPosition.y = ( sin(rotation) * alignedPosition.x + cos(rotation) * alignedPosition.y ) * scale.y;",
-    
-"    vec4 finalPosition;",
-    
-"    if(useScreenCoordinates != 0) {",
-"        finalPosition = vec4(screenPosition.xy + rotatedPosition, screenPosition.z, 1.0);",
-"    }",
-    
-"    else {",
-"        finalPosition = projectionMatrix * modelViewMatrix * vec4(0.0, 0.0, 0.0, 1.0); finalPosition /= finalPosition.w;",
-"        finalPosition.xy += rotatedPosition; ",
-"    }",
-    
-"    gl_Position = finalPosition;",
-    
-"}"
-       
-].join("\n"),
+        material.addEventListener('dispose', onMaterialDispose);
+
+        var u, a, identifiers, i, parameters, maxLightCount, maxBones, maxShadows, shaderID;
+
+        shaderID = material.shaderID;
+
+        if (shaderID) {
+
+            var shader = $3Dmol.ShaderLib[shaderID];
+            material.vertexShader = shader.vertexShader;
+            material.fragmentShader = shader.fragmentShader;
+            material.uniforms = $3Dmol.ShaderUtils.clone(shader.uniforms);
+            // TODO: set material uniforms to shader uniform variables
 
-        uniforms : {
-            
         }
-        
+
+        parameters = {
+            wireframe : material.wireframe,
+            fragdepth : material.imposter
+        };
+
+        material.program = buildProgram(material.fragmentShader,
+                material.vertexShader, material.uniforms, parameters);
+
+    };
+
+    function setProgram(camera, lights, fog, material, object) {
+
+        if (material.needsUpdate) {
+
+            if (material.program)
+                deallocateMaterial(material);
+
+            _this.initMaterial(material, lights, fog, object);
+            material.needsUpdate = false;
+        }
+
+        var refreshMaterial = false;
+
+        // p_uniforms: uniformVarName => uniformLocation
+        // m_uniforms: uniformVarName => uniformJsVal
+        var program = material.program, p_uniforms = program.uniforms, m_uniforms = material.uniforms;
+
+        if (program != _currentProgram) {
+            _gl.useProgram(program);
+            _currentProgram = program;
+
+            refreshMaterial = true;
+        }
+
+        if (material.id != _currentMaterialId) {
+            _currentMaterialId = material.id;
+            refreshMaterial = true;
+        }
+
+        if (camera != _currentCamera) {
+            _currentCamera = camera;
+            refreshMaterial = true;
+        }
+
+        _gl.uniformMatrix4fv(p_uniforms.projectionMatrix, false,
+                camera.projectionMatrix.elements);
+        _gl.uniformMatrix4fv(p_uniforms.modelViewMatrix, false,
+                object._modelViewMatrix.elements);
+        _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false,
+                object._normalMatrix.elements);
+
+        // Send projection matrix to uniform variable in shader
+        if (refreshMaterial) {
+
+            // Load projection, model-view matrices for perspective
+
+            // Set up correct fog uniform vals
+            m_uniforms.fogColor.value = fog.color;
+            m_uniforms.fogNear.value = fog.near;
+            m_uniforms.fogFar.value = fog.far;
+
+            // Set up lights for lambert shader
+            if (material.shaderID.startsWith("lambert")
+                    || material.shaderID === "instanced"
+                    || material.shaderID.endsWith("imposter")) {
+
+                // load view and normal matrices for directional and object
+                // lighting
+                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false,
+                        camera.matrixWorldInverse.elements);
+
+                if (_lightsNeedUpdate) {
+                    setupLights(program, lights);
+                    _lightsNeedUpdate = false;
+                }
+
+                // Set up correct light uniform var vals
+                m_uniforms.directionalLightColor.value = _lights.directional.colors;
+                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
+
+            } else if (material.shaderID.endsWith("outline")) {
+                m_uniforms.outlineColor.value = material.outlineColor;
+                m_uniforms.outlineWidth.value = material.outlineWidth;
+                m_uniforms.outlinePushback.value = material.outlinePushback;
+            } else if (material.shaderID === "sphereimposter") {
+                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false,
+                        camera.matrixWorldInverse.elements);
+                _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false,
+                        object._normalMatrix.elements);
+                m_uniforms.directionalLightColor.value = _lights.directional.colors;
+                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
+            }
+
+            // opacity, diffuse, emissive, etc
+            m_uniforms.opacity.value = material.opacity;
+
+            // Load any other material specific uniform variables to gl shaders
+            loadMaterialUniforms(p_uniforms, m_uniforms);
+
+        }
+
+        return program;
+
     }
-    
-};var $3Dmol = $3Dmol || {};
 
-//properties for mapping
+    function loadMaterialUniforms(p_uniforms, m_uniforms) {
+        var uniformVar, type, uniformVal, uniformLoc;
+
+        for (uniformVar in m_uniforms) {
+            if (!p_uniforms[uniformVar])
+                continue;
+
+            type = m_uniforms[uniformVar].type;
+            uniformVal = m_uniforms[uniformVar].value;
+            uniformLoc = p_uniforms[uniformVar];
+
+            // single float
+            if (type === 'f')
+                _gl.uniform1f(uniformLoc, uniformVal);
+            // array of floats
+            else if (type === 'fv')
+                _gl.uniform3fv(uniformLoc, uniformVal);
+            // color - r,g,b floats
+            else if (type === 'c')
+                _gl.uniform3f(uniformLoc, uniformVal.r, uniformVal.g,
+                        uniformVal.b);
+            else if (type === 'f4')
+                _gl.uniform4f(uniformLoc, uniformVal[0], uniformVal[1],
+                        uniformVal[2],uniformVal[3]);
 
-/* partial charges for proteins */
-$3Dmol.partialCharges = {
-"ALA:N": -0.15,
-"ALA:CA": 0.10,
-"ALA:CB": 0.00,
-"ALA:C": 0.60,
-"ALA:O": -0.55,
-"ARG:N": -0.15,
-"ARG:CA": 0.10,
-"ARG:CB": 0.00,
-"ARG:CG": 0.00,
-"ARG:CD": 0.10,
-"ARG:NE": -0.10,
-"ARG:CZ": 0.50,
-"ARG:NH1": 0.25,
-"ARG:NH2": 0.25,
-"ARG:C": 0.60,
-"ARG:O": -0.55,
-"ASN:N": -0.15,
-"ASN:CA": 0.10,
-"ASN:CB": 0.00,
-"ASN:CG": 0.55,
-"ASN:OD1": -0.55,
-"ASN:ND2": 0.00,
-"ASN:C": 0.60,
-"ASN:O": -0.55,
-"ASP:N": -0.15,
-"ASP:CA": 0.10,
-"ASP:CB": 0.00,
-"ASP:CG": 0.14,
-"ASP:OD1": -0.57,
-"ASP:OD2": -0.57,
-"ASP:C": 0.60,
-"ASP:O": -0.55,
-"CYS:N": -0.15,
-"CYS:CA": 0.10,
-"CYS:CB": 0.19,
-"CYS:SG": -0.19,
-"CYS:C": 0.60,
-"CYS:O": -0.55,
-"GLN:N": -0.15,
-"GLN:CA": 0.10,
-"GLN:CB": 0.00,
-"GLN:CG": 0.00,
-"GLN:CD": 0.55,
-"GLN:OE1": -0.55,
-"GLN:NE2": 0.00,
-"GLN:C": 0.60,
-"GLN:O": -0.55,
-"GLU:N": -0.15,
-"GLU:CA": 0.10,
-"GLU:CB": 0.00,
-"GLU:CG": 0.00,
-"GLU:CD": 0.14,
-"GLU:OE1": -0.57,
-"GLU:OE2": -0.57,
-"GLU:C": 0.60,
-"GLU:O": -0.55,
-"GLY:N": -0.15,
-"GLY:CA": 0.10,
-"GLY:C": 0.60,
-"GLY:O": -0.55,
-"HIS:N": -0.15,
-"HIS:CA": 0.10,
-"HIS:CB": 0.00,
-"HIS:CG": 0.10,
-"HIS:ND1": -0.10,
-"HIS:CD2": 0.10,
-"HIS:NE2": -0.40,
-"HIS:CE1": 0.30,
-"HIS:C": 0.60,
-"HIS:O": -0.55,
-"ILE:N": -0.15,
-"ILE:CA": 0.10,
-"ILE:CB": 0.00,
-"ILE:CG2": 0.00,
-"ILE:CG1": 0.00,
-"ILE:CD": 0.00,
-"ILE:C": 0.60,
-"ILE:O": -0.55,
-"LEU:N": -0.15,
-"LEU:CA": 0.10,
-"LEU:CB": 0.00,
-"LEU:CG": 0.00,
-"LEU:CD1": 0.00,
-"LEU:CD2": 0.00,
-"LEU:C": 0.60,
-"LEU:O": -0.55,
-"LYS:N": -0.15,
-"LYS:CA": 0.10,
-"LYS:CB": 0.00,
-"LYS:CG": 0.00,
-"LYS:CD": 0.00,
-"LYS:CE": 0.25,
-"LYS:NZ": 0.75,
-"LYS:C": 0.60,
-"LYS:O": -0.55,
-"MET:N": -0.15,
-"MET:CA": 0.10,
-"MET:CB": 0.00,
-"MET:CG": 0.06,
-"MET:SD": -0.12,
-"MET:CE": 0.06,
-"MET:C": 0.60,
-"MET:O": -0.55,
-"PHE:N": -0.15,
-"PHE:CA": 0.10,
-"PHE:CB": 0.00,
-"PHE:CG": 0.00,
-"PHE:CD1": 0.00,
-"PHE:CD2": 0.00,
-"PHE:CE1": 0.00,
-"PHE:CE2": 0.00,
-"PHE:CZ": 0.00,
-"PHE:C": 0.60,
-"PHE:O": -0.55,
-"PRO:N": -0.25,
-"PRO:CD": 0.10,
-"PRO:CA": 0.10,
-"PRO:CB": 0.00,
-"PRO:CG": 0.00,
-"PRO:C": 0.60,
-"PRO:O": -0.55,
-"SER:N": -0.15,
-"SER:CA": 0.10,
-"SER:CB": 0.25,
-"SER:OG": -0.25,
-"SER:C": 0.60,
-"SER:O": -0.55,
-"THR:N": -0.15,
-"THR:CA": 0.10,
-"THR:CB": 0.25,
-"THR:OG1": -0.25,
-"THR:CG2": 0.00,
-"THR:C": 0.60,
-"THR:O": -0.55,
-"TRP:N": -0.15,
-"TRP:CA": 0.10,
-"TRP:CB": 0.00,
-"TRP:CG": -0.03,
-"TRP:CD2": 0.10,
-"TRP:CE2": -0.04,
-"TRP:CE3": -0.03,
-"TRP:CD1": 0.06,
-"TRP:NE1": -0.06,
-"TRP:CZ2": 0.00,
-"TRP:CZ3": 0.00,
-"TRP:CH2": 0.00,
-"TRP:C": 0.60,
-"TRP:O": -0.55,
-"TYR:N": -0.15,
-"TYR:CA": 0.10,
-"TYR:CB": 0.00,
-"TYR:CG": 0.00,
-"TYR:CD1": 0.00,
-"TYR:CE1": 0.00,
-"TYR:CD2": 0.00,
-"TYR:CE2": 0.00,
-"TYR:CZ": 0.25,
-"TYR:OH": -0.25,
-"TYR:C": 0.60,
-"TYR:O": -0.55,
-"VAL:N": -0.15,
-"VAL:CA": 0.10,
-"VAL:CB": 0.00,
-"VAL:CG1": 0.00,
-"VAL:CG2": 0.00,
-"VAL:C": 0.60,
-"VAL:O": -0.55
-};
-    
-//this can be supplied to mapAtomProperties
-$3Dmol.applyPartialCharges = function(atom, keepexisting) {
-    if(!keepexisting || typeof(atom.partialCharge) === "undefined") {
-        if(atom.resn && atom.atom) {
-            var key = atom.resn+":"+atom.atom;
-            atom.properties['partialCharge'] = $3Dmol.partialCharges[key];
         }
+
     }
-};
-$3Dmol = $3Dmol || {};
-//Encapsulate marching cube algorithm for isosurface generation
-// (currently used by protein surface rendering and generic volumetric data reading)
-$3Dmol.MarchingCube = (function() {
-    
-    //Marching cube algorithm - assume data has been pre-treated so isovalue is 0 
-    // (i.e. select points greater than 0)
-    //origin -  vector of origin of volumetric data (default is (0,0,0))
-    // nX, nY, nZ - specifies number of voxels in each dimension
-    // scale - cube diagonal unit vector scale (3Dmol vector) (specifying distance between data points); diagonal of cube
-    // - default is 1 - assumes unit cube (1,1,1) diag)
-    // fulltable - if true, use full marching cubes and tritables - else use trimmed table (e.g. surf render)
-    // voxel - if true, draws with a blocky voxel style (default false)
-    // verts, faces - vertex and face arrays to fill up
-    
-    //to match with protein surface...
-    var ISDONE = 2;
-    var my = {};
-    
-    my.march = function(data, verts, faces, spec) {
 
-        var fulltable = !!(spec.fulltable);
-        var origin = (spec.hasOwnProperty('origin') && spec.origin.hasOwnProperty('x')) ? spec.origin : {x:0, y:0, z:0};
-        var voxel = !!(spec.voxel);
-        
-        var nX = spec.nX || 0;
-        var nY = spec.nY || 0;
-        var nZ = spec.nZ || 0;
-        
-        var scale = spec.scale || 1.0;
-        
-        var unitCube = new $3Dmol.Vector3(1,1,1).multiplyScalar(scale);
-        
-        //keep track of calculated vertices to avoid repeats
-        var vertnums = new Int32Array(nX*nY*nZ);
-        
-        var i, il;
-        
-        for (i = 0, il = vertnums.length; i < il; ++i)
-            vertnums[i] = -1;
+    this.renderBuffer = function(camera, lights, fog, material, geometryGroup,
+            object) {
 
-        // create (or retrieve) a vertex at the appropriate point for
-        // the edge (p1,p2)
-        
-        var getVertex = function(i, j, k, code, p1, p2) {
-            var pt = new $3Dmol.Vector3();
-            pt.copy(origin);
-            var val1 = !!(code & (1 << p1));
-            var val2 = !!(code & (1 << p2));
-             
-            // p1 if they are the same or if !val1
-            var p = p1;
-            if (!val1 && val2)
-                p = p2;
-            
-            // adjust i,j,k by p
-            if (p & 1)
-                k++;
-            if (p & 2)
-                j++;
-            if (p & 4)
-                i++;
-    
-            pt.x += unitCube.x*i;
-            pt.y += unitCube.y*j;
-            pt.z += unitCube.z*k;
-    
-            var index = ((nY * i) + j) * nZ + k;
-            
-            //Have to add option to do voxels
-            if (!voxel) {
-            
-                if (vertnums[index] < 0) // not created yet
-                {
-                    vertnums[index] = verts.length;
-                    verts.push( pt );
-                }
-                return vertnums[index];
-            
+        if (!material.visible)
+            return;
+
+        var program, attributes, linewidth, primitives, a, attribute, i, il;
+
+        // Sets up proper vertex and fragment shaders and attaches them to webGL
+        // program
+        // Also sets appropriate uniform variables
+        program = setProgram(camera, lights, fog, material, object);
+
+        attributes = program.attributes;
+
+        var updateBuffers = false, wireframeBit = material.wireframe ? 1 : 0, geometryGroupHash = (geometryGroup.id * 0xffffff)
+                + (program.id * 2) + wireframeBit;
+
+        if (geometryGroupHash !== _currentGeometryGroupHash) {
+            _currentGeometryGroupHash = geometryGroupHash;
+            updateBuffers = true;
+        }
+
+        // rebind shader attributes to appropriate (and already initialized) gl
+        // buffers
+        if (updateBuffers) {
+
+            disableAttributes();
+
+            // Vertices
+            if (attributes.position >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglVertexBuffer);
+                enableAttribute(attributes.position);
+                _gl.vertexAttribPointer(attributes.position, 3, _gl.FLOAT,
+                        false, 0, 0);
             }
-            
-            else {
-                verts.push(pt);
-                return verts.length - 1;
+
+            // Colors
+            if (attributes.color >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglColorBuffer);
+                enableAttribute(attributes.color);
+                _gl.vertexAttribPointer(attributes.color, 3, _gl.FLOAT, false,
+                        0, 0);
             }
-            
-        };
-            
-        var intersects = new Int32Array(12);
-        
-        var etable = (fulltable) ? edgeTable2 : edgeTable;
-        var tritable = (fulltable) ? triTable2 : triTable;
-                
-        //Run marching cubes algorithm
-        for (i = 0; i < nX-1; ++i) {
-            
-            for (var j = 0; j < nY-1; ++j){
-                
-                for (var k = 0; k < nZ-1; ++k){
-                    
-                    var code = 0;
-                    
-                    for (var p = 0; p < 8; ++p) {
-                        var index = ((nY * (i + ((p & 4) >> 2))) + j + ((p & 2) >> 1)) *
-                                        nZ + k + (p & 1);
 
-                        //TODO: Need to fix vpBits in protein surface for this to work
-                        var val = !!(data[index] & ISDONE);
-                        //var val = !!(data[index] > 0);   
-                        
-                        code |= val << p;                        
-                    }
-                    
-                    if (code === 0 || code === 255)
-                        continue;
-                    
-                    var ecode = etable[code];
-                    
-                    if (ecode === 0)
-                        continue;
-                        
-                    var ttable = tritable[code];                        
-                    
-                    if (ecode & 1)
-                        intersects[0] = getVertex(i, j, k, code, 0, 1);
-                    if (ecode & 2)
-                        intersects[1] = getVertex(i, j, k, code, 1, 3);
-                    if (ecode & 4)
-                        intersects[2] = getVertex(i, j, k, code, 3, 2);
-                    if (ecode & 8)
-                        intersects[3] = getVertex(i, j, k, code, 2, 0);
-                    if (ecode & 16)
-                        intersects[4] = getVertex(i, j, k, code, 4, 5);
-                    if (ecode & 32)
-                        intersects[5] = getVertex(i, j, k, code, 5, 7);
-                    if (ecode & 64)
-                        intersects[6] = getVertex(i, j, k, code, 7, 6);
-                    if (ecode & 128)
-                        intersects[7] = getVertex(i, j, k, code, 6, 4);
-                    if (ecode & 256)
-                        intersects[8] = getVertex(i, j, k, code, 0, 4);
-                    if (ecode & 512)
-                        intersects[9] = getVertex(i, j, k, code, 1, 5);
-                    if (ecode & 1024)
-                        intersects[10] = getVertex(i, j, k, code, 3, 7);
-                    if (ecode & 2048)
-                        intersects[11] = getVertex(i, j, k, code, 2, 6);       
-                        
-                    for (var t = 0; t < ttable.length; t += 3) {
-                        
-                        var a = intersects[ttable[t]],
-                            b = intersects[ttable[t+1]],
-                            c = intersects[ttable[t+2]];         
-                                           
-                        if (voxel && t >= 3) {
-                            verts.push(verts[a]); a = verts.length - 1;
-                            verts.push(verts[b]); b = verts.length - 1;
-                            verts.push(verts[c]); c = verts.length - 1;
-                        }
+            // Normals
+            if (attributes.normal >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglNormalBuffer);
+                enableAttribute(attributes.normal);
+                _gl.vertexAttribPointer(attributes.normal, 3, _gl.FLOAT, false,
+                        0, 0);
+            }
 
-                        
-                        faces.push(a); faces.push(b); faces.push(c);                               
-                    }              
-                    
+            // Offsets (Instanced only)
+            if (attributes.offset >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglOffsetBuffer);
+                enableAttribute(attributes.offset);
+                _gl.vertexAttribPointer(attributes.offset, 3, _gl.FLOAT, false,
+                        0, 0);
+            }
+
+            // Radii (Instanced only)
+            if (attributes.radius >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglRadiusBuffer);
+                enableAttribute(attributes.radius);
+                _gl.vertexAttribPointer(attributes.radius, 1, _gl.FLOAT, false,
+                        0, 0);
+            }
+
+        }
+
+        // Render
+        var faceCount, lineCount;
+        // lambert shaders - draw triangles
+        // TODO: make sure geometryGroup's face count is setup correctly
+        if (object instanceof $3Dmol.Mesh) {
+
+            if (material.shaderID === "instanced") {
+                var sphereGeometryGroup = material.sphere.geometryGroups[0];
+                if (updateBuffers) {
+                    _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                            geometryGroup.__webglVertexBuffer);
+                    _gl.bufferData(_gl.ARRAY_BUFFER,
+                            sphereGeometryGroup.vertexArray, _gl.STATIC_DRAW);
+                    _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                            geometryGroup.__webglNormalBuffer);
+                    _gl.bufferData(_gl.ARRAY_BUFFER,
+                            sphereGeometryGroup.normalArray, _gl.STATIC_DRAW);
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglFaceBuffer);
+                    _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER,
+                            sphereGeometryGroup.faceArray, _gl.STATIC_DRAW);
                 }
-                
+
+                faceCount = sphereGeometryGroup.faceidx;
+
+                _extInstanced.vertexAttribDivisorANGLE(attributes.offset, 1);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.radius, 1);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.color, 1);
+
+                _extInstanced.drawElementsInstancedANGLE(_gl.TRIANGLES,
+                        faceCount, _gl.UNSIGNED_SHORT, 0,
+                        geometryGroup.radiusArray.length);
+
+                _extInstanced.vertexAttribDivisorANGLE(attributes.offset, 0);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.radius, 0);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.color, 0);
+
             }
-            
+
+            else if (material.wireframe) {
+                lineCount = geometryGroup.lineidx;
+                setLineWidth(material.wireframeLinewidth);
+
+                if (updateBuffers)
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglLineBuffer);
+
+                _gl.drawElements(_gl.LINES, lineCount, _gl.UNSIGNED_SHORT, 0);
+            }
+
+            else {
+                faceCount = geometryGroup.faceidx;
+
+                if (updateBuffers)
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglFaceBuffer);
+                _gl.drawElements(_gl.TRIANGLES, faceCount, _gl.UNSIGNED_SHORT,
+                        0);
+
+            }
+
+            _this.info.render.calls++;
+            _this.info.render.vertices += faceCount;
+            _this.info.render.faces += faceCount / 3;
         }
-             
-        
+
+        // basic shaders - draw lines
+        else if (object instanceof $3Dmol.Line) {
+            lineCount = geometryGroup.vertices;
+
+            setLineWidth(material.linewidth);
+            _gl.drawArrays(_gl.LINES, 0, lineCount);
+
+            _this.info.render.calls++;
+        }
+
     };
 
-    my.laplacianSmooth = function(numiter, verts, faces) {
-            var tps = new Array(verts.length);
-            var i, il, j, jl, k, kl;
-            for (i = 0, il = verts.length; i < il; i++)
-                    tps[i] = {
-                        x : 0,
-                        y : 0,
-                        z : 0
-                    };
-            var vertdeg = new Array(20);
-            var flagvert;
-            for (i = 0; i < 20; i++)
-                    vertdeg[i] = new Array(verts.length);
-            for (i = 0, il = verts.length; i < il; i++)
-                    vertdeg[0][i] = 0;
-            for (i = 0, il = faces.length / 3; i < il; i++) {
-                var aoffset = i*3, boffset = i*3 + 1, coffset = i*3 + 2;
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
-                    if (faces[boffset] == vertdeg[j + 1][faces[aoffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[aoffset]]++;
-                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[boffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
-                    if (faces[coffset] == vertdeg[j + 1][faces[aoffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[aoffset]]++;
-                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[coffset];
-                }
-                // b
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
-                    if (faces[aoffset] == vertdeg[j + 1][faces[boffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[boffset]]++;
-                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[aoffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
-                    if (faces[coffset] == vertdeg[j + 1][faces[boffset]]) {
-                        flagvert = false;
-                        break;
+    // rendering
+    function renderObjects(renderList, reverse, materialType, camera, lights,
+            fog, useBlending, overrideMaterial) {
+
+        var webglObject, object, buffer, material, start, end, delta;
+
+        // Forward or backward render
+
+        if (reverse) {
+            start = renderList.length - 1;
+            end = -1;
+            delta = -1;
+        }
+
+        else {
+            start = 0;
+            end = renderList.length;
+            delta = 1;
+        }
+
+        for (var i = start; i !== end; i += delta) {
+
+            webglObject = renderList[i];
+
+            if (webglObject.render) {
+
+                object = webglObject.object;
+                buffer = webglObject.buffer;
+                material = webglObject[materialType];
+
+                if (!material)
+                    continue;
+
+                if (useBlending)
+                    _this.setBlending(true);
+
+                _this.setDepthTest(material.depthTest);
+                _this.setDepthWrite(material.depthWrite);
+                setPolygonOffset(material.polygonOffset,
+                        material.polygonOffsetFactor,
+                        material.polygonOffsetUnits);
+
+                var reflected = object._modelViewMatrix.isReflected();
+
+                _this.setMaterialFaces(material, reflected);
+
+                _this.renderBuffer(camera, lights, fog, material, buffer,
+                        object);
+                if (_outlineMaterial) {                  
+                    if(material.shaderID == 'sphereimposter') {
+                        _this.renderBuffer(camera, lights, fog, _outlineSphereImposterMaterial,
+                                buffer, object);                        
                     }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[boffset]]++;
-                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[coffset];
-                }
-                // c
-                flagvert = true;
-                for (j = 0; j < vertdeg[0][faces[coffset]]; j++) {
-                    if (faces[aoffset] == vertdeg[j + 1][faces[coffset]]) {
-                        flagvert = false;
-                        break;
+                    else if(material.shaderID == 'stickimposter') {
+                        _this.renderBuffer(camera, lights, fog, _outlineStickImposterMaterial,
+                                buffer, object);                        
                     }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[coffset]]++;
-                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[aoffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[coffset]]; j < jl; j++) {
-                    if (faces[boffset] == vertdeg[j + 1][faces[coffset]]) {
-                        flagvert = false;
-                        break;
+                    else if(!material.wireframe                
+                        && material.shaderID !== 'basic'
+                        && material.opacity !== 0.0) {
+                        _this.renderBuffer(camera, lights, fog, _outlineMaterial,
+                            buffer, object);
                     }
                 }
-                if (flagvert) {
-                    vertdeg[0][faces[coffset]]++;
-                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[boffset];
-                }
             }
+        }
 
-            var wt = 1.00;
-            var wt2 = 0.50;
-            var ssign;
-            var scaleFactor = 1;
-            var outwt = 0.75 / (scaleFactor + 3.5); // area-preserving
-            for (k = 0; k < numiter; k++) {
-                    for (i = 0, il = verts.length; i < il; i++) {
-                            if (vertdeg[0][i] < 3) {
-                                    tps[i].x = verts[i].x;
-                                    tps[i].y = verts[i].y;
-                                    tps[i].z = verts[i].z;
-                            } else if (vertdeg[0][i] == 3 || vertdeg[0][i] == 4) {
-                                    tps[i].x = 0;
-                                    tps[i].y = 0;
-                                    tps[i].z = 0;
-                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
-                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
-                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
-                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
-                                    }
-                                    tps[i].x += wt2 * verts[i].x;
-                                    tps[i].y += wt2 * verts[i].y;
-                                    tps[i].z += wt2 * verts[i].z;
-                                    tps[i].x /= wt2 + vertdeg[0][i];
-                                    tps[i].y /= wt2 + vertdeg[0][i];
-                                    tps[i].z /= wt2 + vertdeg[0][i];
-                            } else {
-                                    tps[i].x = 0;
-                                    tps[i].y = 0;
-                                    tps[i].z = 0;
-                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
-                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
-                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
-                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
-                                    }
-                                    tps[i].x += wt * verts[i].x;
-                                    tps[i].y += wt * verts[i].y;
-                                    tps[i].z += wt * verts[i].z;
-                                    tps[i].x /= wt + vertdeg[0][i];
-                                    tps[i].y /= wt + vertdeg[0][i];
-                                    tps[i].z /= wt + vertdeg[0][i];
-                            }
-                    }
-                    for (i = 0, il = verts.length; i < il; i++) {
-                            verts[i].x = tps[i].x;
-                            verts[i].y = tps[i].y;
-                            verts[i].z = tps[i].z;
-                    }
-                    /*
-                     * computenorm(); for (var i = 0; i < vertnumber; i++) { if
-                     * (verts[i].inout) ssign = 1; else ssign = -1; verts[i].x += ssign *
-                     * outwt * verts[i].pn.x; verts[i].y += ssign * outwt *
-                     * verts[i].pn.y; verts[i].z += ssign * outwt * verts[i].pn.z; }
-                     */
+    }
+
+    this.render = function(scene, camera, forceClear) {
+
+        if (camera instanceof $3Dmol.Camera === false) {
+
+            console
+                    .error('$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.');
+            return;
+
+        }
+
+        var i, il,
+
+        webglObject, object, renderList,
+
+        lights = scene.__lights, fog = scene.fog;
+
+        // reset caching for this frame
+
+        _currentMaterialId = -1;
+        _lightsNeedUpdate = true;
+
+        // update scene graph
+
+        if (this.autoUpdateScene)
+            scene.updateMatrixWorld();
+
+        // update camera matrices
+        // Pretty sure camera's parent is always going to be undefined for our
+        // purposes...
+        if (camera.parent === undefined)
+            camera.updateMatrixWorld();
+
+        camera.matrixWorldInverse.getInverse(camera.matrixWorld);
+
+        _projScreenMatrix.multiplyMatrices(camera.projectionMatrix,
+                camera.matrixWorldInverse);
+
+        // update WebGL objects
+
+        if (this.autoUpdateObjects)
+            this.initWebGLObjects(scene);
+
+        _this.info.render.calls = 0;
+        _this.info.render.vertices = 0;
+        _this.info.render.faces = 0;
+        _this.info.render.points = 0;
+
+        _currentWidth = _viewportWidth;
+        _currentHeight = _viewportHeight;
+
+        if (this.autoClear || forceClear) {
+            this.clear(this.autoClearColor, this.autoClearDepth,
+                    this.autoClearStencil);
+
+        }
+
+        // set matrices for regular objects (frustum culled)
+
+        renderList = scene.__webglObjects;
+
+        for (i = 0, il = renderList.length; i < il; i++) {
+
+            webglObject = renderList[i];
+            object = webglObject.object;
+
+            webglObject.render = false;
+
+            if (object.visible) {
+                setupMatrices(object, camera);
+                unrollBufferMaterial(webglObject);
+                webglObject.render = true;
             }
+        }
+
+        // set matrices for immediate objects
+
+        var material = null;
+
+        // opaque pass (front-to-back order)
+
+        this.setBlending(false);
+
+        renderObjects(scene.__webglObjects, true, "opaque", camera, lights,
+                fog, false, material);
+
+        // prime depth buffer
+        renderObjects(scene.__webglObjects, true, "blank", camera, lights, fog,
+                true, material);
+
+        // transparent pass (back-to-front order)
+
+        renderObjects(scene.__webglObjects, false, "transparent", camera,
+                lights, fog, true, material);
+
+        // Render plugins (e.g. sprites), and reset state
+
+        renderPlugins(this.renderPluginsPost, scene, camera);
+
+        // Ensure depth buffer writing is enabled so it can be cleared on next
+        // render
+
+        this.setDepthTest(true);
+        this.setDepthWrite(true);
+
+        // _gl.finish();
+
     };
 
+    function renderPlugins(plugins, scene, camera) {
 
-    /*
-     * These tables are based off those by Paul Bourke and Geoffrey Heller:
-     * http://paulbourke.net/geometry/polygonise/
-     * http://paulbourke.net/geometry/polygonise/table2.txt
-     * 
-     * However, they have been substantially modified to reflect a more 
-     * sensible corner numbering scheme and the discrete nature of our voxel data
-     * (resulting in fewer faces).
-     */
-    my.edgeTable = [ 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
-            0xb00, 0x0, 0x0, 0x0, 0x700, 0x0, 0xd00, 0xe00, 0xf00, 0x0, 0x0, 0x0,
-            0x8a, 0x0, 0x15, 0x0, 0x86, 0x0, 0x0, 0x0, 0x28c, 0x0, 0x813, 0xf19,
-            0xe10, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x0, 0x0, 0x126, 0x0, 0x0, 0x15, 0x1c,
-            0x0, 0xf23, 0x419, 0xd20, 0x0, 0xa8, 0xa2, 0xaa, 0x0, 0x285, 0x9ab,
-            0x8a2, 0x0, 0x2af, 0x125, 0xac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x0, 0x0,
-            0x0, 0x0, 0x0, 0x45, 0x0, 0x384, 0x0, 0x0, 0x0, 0x700, 0x8a, 0x83,
-            0x648, 0x780, 0x0, 0x51, 0x0, 0x81a, 0x54, 0x55, 0x54, 0x56, 0x0, 0x51,
-            0x0, 0xe5c, 0x14a, 0x451, 0x759, 0x650, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x45,
-            0x0, 0x1f6, 0x0, 0x0, 0x15, 0xdfc, 0x8a, 0x7f3, 0x4f9, 0x5f0, 0xb00,
-            0x68, 0x921, 0x6a, 0x348, 0x245, 0x16f, 0x66, 0xb00, 0xe6f, 0xd65,
-            0xc6c, 0x76a, 0x663, 0x569, 0x460, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
-            0xf46, 0x0, 0x0, 0x45, 0x24c, 0x2a, 0x823, 0x29, 0xb40, 0x0, 0x0, 0x0,
-            0x6ba, 0x0, 0x8f5, 0xfff, 0xef6, 0x0, 0xff, 0x2f5, 0x2fc, 0x9ea, 0x8f3,
-            0xbf9, 0xaf0, 0x0, 0x0, 0x51, 0x152, 0x0, 0xf55, 0x45f, 0xd56, 0x54,
-            0x357, 0x55, 0x154, 0x852, 0xb53, 0x59, 0x950, 0x700, 0x2c8, 0xc2,
-            0x48a, 0xfc4, 0xec5, 0xdcf, 0xcc6, 0x2c4, 0x2cf, 0xc5, 0xcc, 0xbca,
-            0xac3, 0x9c9, 0x8c0, 0x0, 0x0, 0x0, 0x0, 0xa8, 0x1a4, 0xa8, 0x7a6,
-            0xa2, 0xa2, 0x2a4, 0xbac, 0xaa, 0xa3, 0x2a8, 0x3a0, 0xd00, 0xc18,
-            0xd00, 0xe3a, 0x34, 0x35, 0x73f, 0x636, 0x924, 0x83f, 0xb35, 0xa3c,
-            0x12a, 0x33, 0x339, 0x230, 0xe00, 0xe00, 0xc12, 0xd9a, 0x684, 0x795,
-            0x49f, 0x596, 0x92, 0xb9f, 0x815, 0x99c, 0x9a, 0x393, 0x99, 0x190,
-            0xf00, 0xe08, 0xd01, 0xc0a, 0x704, 0x605, 0x50f, 0x406, 0xb02, 0xa0f,
-            0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
-    
-    var edgeTable = new Uint32Array(my.edgeTable);
-    
-    var triTable = my.triTable = [ [], [], [], [], [], [], [], [ 11, 9, 8 ], [], [], [],
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-     
-    var edgeTable2 = [ 0x0, 0x109, 0x203, 0x30a, 0x80c, 0x905, 0xa0f,
-            0xb06, 0x406, 0x50f, 0x605, 0x70c, 0xc0a, 0xd03, 0xe09, 0xf00, 0x190,
-            0x99, 0x393, 0x29a, 0x99c, 0x895, 0xb9f, 0xa96, 0x596, 0x49f, 0x795,
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-            0xd30, 0x3a0, 0x2a9, 0x1a3, 0xaa, 0xbac, 0xaa5, 0x9af, 0x8a6, 0x7a6,
-            0x6af, 0x5a5, 0x4ac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x8c0, 0x9c9, 0xac3,
-            0xbca, 0xcc, 0x1c5, 0x2cf, 0x3c6, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x4ca,
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-            0x406, 0xb06, 0xa0f, 0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
-     
-    var triTable2 = [ [], [ 8, 3, 0 ], [ 9, 0, 1 ], [ 8, 3, 1, 8, 1, 9 ],
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-            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [ 7, 8, 4, 5, 1, 2, 5, 2, 6 ],
-            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ],
-            [ 9, 4, 5, 8, 0, 7, 0, 6, 7, 0, 2, 6 ], [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ],
-            [ 6, 7, 11, 4, 5, 8, 5, 3, 8, 5, 1, 3 ],
-            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
-            [ 9, 4, 5, 7, 11, 6 ], [ 10, 6, 4, 10, 4, 9 ],
-            [ 8, 3, 0, 9, 10, 6, 9, 6, 4 ], [ 1, 10, 0, 10, 6, 0, 0, 6, 4 ],
-            [ 8, 6, 4, 8, 1, 6, 6, 1, 10, 8, 3, 1 ],
-            [ 2, 3, 11, 6, 4, 9, 6, 9, 10 ],
-            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
-            [ 10, 2, 1, 11, 6, 3, 6, 0, 3, 6, 4, 0 ],
-            [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ], [ 9, 1, 4, 1, 2, 4, 4, 2, 6 ],
-            [ 1, 0, 9, 3, 2, 8, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
-            [ 3, 2, 8, 8, 2, 4, 2, 6, 4 ],
-            [ 1, 4, 9, 11, 4, 1, 11, 1, 3, 11, 6, 4 ],
-            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 11, 6, 3, 3, 6, 0, 6, 4, 0 ],
-            [ 8, 6, 4, 8, 11, 6 ], [ 6, 7, 10, 7, 8, 10, 10, 8, 9 ],
-            [ 9, 3, 0, 6, 3, 9, 6, 9, 10, 6, 7, 3 ],
-            [ 6, 1, 10, 6, 7, 1, 7, 0, 1, 7, 8, 0 ],
-            [ 6, 7, 10, 10, 7, 1, 7, 3, 1 ],
-            [ 7, 11, 6, 3, 8, 2, 8, 10, 2, 8, 9, 10 ],
-            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
-            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2, 2, 9, 1, 7, 8, 9 ],
-            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 8, 0, 7, 7, 0, 6, 0, 2, 6 ],
-            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
-            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ],
-            [ 11, 7, 5, 11, 5, 10 ], [ 3, 0, 8, 7, 5, 10, 7, 10, 11 ],
-            [ 9, 0, 1, 10, 11, 7, 10, 7, 5 ],
-            [ 3, 1, 9, 3, 9, 8, 7, 10, 11, 7, 5, 10 ],
-            [ 10, 2, 5, 2, 3, 5, 5, 3, 7 ],
-            [ 5, 10, 2, 8, 5, 2, 8, 7, 5, 8, 2, 0 ],
-            [ 9, 0, 1, 10, 2, 5, 5, 2, 3, 5, 3, 7 ],
-            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 2, 11, 1, 11, 7, 1, 1, 7, 5 ],
-            [ 0, 8, 3, 2, 11, 1, 1, 11, 7, 1, 7, 5 ],
-            [ 9, 0, 2, 9, 2, 7, 2, 11, 7, 9, 7, 5 ],
-            [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ], [ 1, 3, 7, 1, 7, 5 ],
-            [ 8, 7, 0, 0, 7, 1, 7, 5, 1 ], [ 0, 3, 9, 9, 3, 5, 3, 7, 5 ],
-            [ 9, 7, 5, 9, 8, 7 ], [ 4, 5, 8, 5, 10, 8, 8, 10, 11 ],
-            [ 3, 0, 4, 3, 4, 10, 4, 5, 10, 3, 10, 11 ],
-            [ 0, 1, 9, 4, 5, 8, 8, 5, 10, 8, 10, 11 ],
-            [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ],
-            [ 3, 8, 4, 3, 4, 2, 2, 4, 5, 2, 5, 10 ],
-            [ 10, 2, 5, 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
-            [ 2, 1, 10, 9, 4, 5 ], [ 8, 4, 5, 2, 8, 5, 2, 11, 8, 2, 5, 1 ],
-            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
-            [ 11, 3, 2, 9, 4, 5 ], [ 4, 5, 8, 8, 5, 3, 5, 1, 3 ],
-            [ 5, 0, 4, 5, 1, 0 ], [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ],
-            [ 7, 4, 11, 4, 9, 11, 11, 9, 10 ],
-            [ 3, 0, 8, 7, 4, 11, 11, 4, 9, 11, 9, 10 ],
-            [ 11, 7, 4, 1, 11, 4, 1, 10, 11, 1, 4, 0 ],
-            [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
-            [ 2, 3, 7, 2, 7, 9, 7, 4, 9, 2, 9, 10 ],
-            [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ], [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ],
-            [ 10, 2, 1, 8, 7, 4 ], [ 2, 11, 7, 2, 7, 1, 1, 7, 4, 1, 4, 9 ],
-            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 7, 4, 11, 11, 4, 2, 4, 0, 2 ],
-            [ 2, 11, 3, 7, 4, 8 ], [ 9, 1, 4, 4, 1, 7, 1, 3, 7 ],
-            [ 1, 0, 9, 8, 7, 4 ], [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ],
-            [ 8, 9, 10, 8, 10, 11 ], [ 0, 9, 3, 3, 9, 11, 9, 10, 11 ],
-            [ 1, 10, 0, 0, 10, 8, 10, 11, 8 ], [ 10, 3, 1, 10, 11, 3 ],
-            [ 3, 8, 2, 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
-            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 2, 11, 1, 1, 11, 9, 11, 8, 9 ],
-            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
-            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
-            
-            return my;
-})();
+        // Reset state once regardless
+        // This should also fix cartoon render bug (after transparent surface
+        // render)
 
+        _currentGeometryGroupHash = -1;
+        _currentProgram = null;
+        _currentCamera = null;
+        _oldBlending = -1;
+        _oldDepthWrite = -1;
+        _oldDepthTest = -1;
+        _oldDoubleSided = -1;
+        _currentMaterialId = -1;
+        _oldFlipSided = -1;
 
+        if (!plugins.length)
+            return;
 
-/*  ProteinSurface.js by biochem_fan
+        for (var i = 0, il = plugins.length; i < il; i++) {
 
-Ported and modified for Javascript based on EDTSurf,
-  whose license is as follows.
+            _lightsNeedUpdate = true;
 
-Permission to use, copy, modify, and distribute this program for any
-purpose, with or without fee, is hereby granted, provided that this
-copyright notice and the reference information appear in all copies or
-substantial portions of the Software. It is provided "as is" without
-express or implied warranty. 
+            plugins[i].render(scene, camera, _currentWidth, _currentHeight);
 
-Reference:
-http://zhanglab.ccmb.med.umich.edu/EDTSurf/
-D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces
-by Euclidean Distance Transform. PLoS ONE 4(12): e8140.
+            // Reset state after plugin render
+            _currentGeometryGroupHash = -1;
+            _currentProgram = null;
+            _currentCamera = null;
+            _oldBlending = -1;
+            _oldDepthWrite = -1;
+            _oldDepthTest = -1;
+            _oldDoubleSided = -1;
+            _currentMaterialId = -1;
+            _oldFlipSided = -1;
 
-=======
+        }
 
-TODO: Improved performance on Firefox
-      Reduce memory consumption
-      Refactor!
- */
+    }
 
+    this.initWebGLObjects = function(scene) {
+
+        if (!scene.__webglObjects) {
+
+            scene.__webglObjects = [];
+            scene.__webglObjectsImmediate = [];
+            scene.__webglSprites = [];
+            scene.__webglFlares = [];
 
-// dkoes
-// Surface calculations.  This must be safe to use within a web worker.
-if (typeof console === 'undefined') {
-    // this should only be true inside of a webworker
-    console = {
-        log : function() {
         }
-    };
-}
 
-$3Dmol.ProteinSurface = function() {
+        // Add objects; this sets up buffers for each geometryGroup
+        if (scene.__objectsAdded.length) {
 
-    // constants for vpbits bitmasks
-    /** @const */
-    var INOUT = 1;
-    /** @const */
-    var ISDONE = 2;
-    /** @const */
-    var ISBOUND = 4;
+            while (scene.__objectsAdded.length) {
+                addObject(scene.__objectsAdded[0], scene);
+                scene.__objectsAdded.splice(0, 1);
+            }
 
-    var ptranx = 0, ptrany = 0, ptranz = 0;
-    var probeRadius = 1.4;
-    var defaultScaleFactor = 2;
-    var scaleFactor = defaultScaleFactor; // 2 is .5A grid; if this is made user configurable,
-                            // also have to adjust offset used to find non-shown
-                            // atoms
-    var pHeight = 0, pWidth = 0, pLength = 0;
-    var cutRadius = 0;
-    var vpBits = null; // uint8 array of bitmasks
-    var vpDistance = null; // floatarray of _squared_ distances
-    var vpAtomID = null; // intarray
-    var vertnumber = 0, facenumber = 0;
-    var pminx = 0, pminy = 0, pminz = 0, pmaxx = 0, pmaxy = 0, pmaxz = 0;
+            // Force buffer update during render
+            // Hackish fix for initial cartoon-render-then-transparent-surface
+            // bug
+            _currentGeometryGroupHash = -1;
 
-    var vdwRadii = {
-            "H" : 1.2,
-            "Li" : 1.82,
-            "Na" : 2.27,
-            "K" : 2.75,
-            "C" : 1.7,
-            "N" : 1.55,
-            "O" : 1.52,
-            "F" : 1.47,
-            "P" : 1.80,
-            "S" : 1.80,
-            "CL" : 1.75,
-            "BR" : 1.85,
-            "SE" : 1.90,
-            "ZN" : 1.39,
-            "CU" : 1.4,
-            "NI" : 1.63,
-            "X" : 2
-        };
-    
-    /** @param {AtomSpec} atom */
-    var getVDWIndex = function(atom) {
-        if(!atom.elem || typeof(vdwRadii[atom.elem]) == "undefined") {
-            return "X";
         }
-        return atom.elem;
+
+        while (scene.__objectsRemoved.length) {
+
+            removeObject(scene.__objectsRemoved[0], scene);
+            scene.__objectsRemoved.splice(0, 1);
+
+        }
+
+        // update must be called after objects adding / removal
+        // This sends typed arrays to GL buffers for each geometryGroup
+        for (var o = 0, ol = scene.__webglObjects.length; o < ol; o++) {
+
+            updateObject(scene.__webglObjects[o].object);
+
+        }
+
     };
-    
-    var depty = {}, widxz = {};
-    var faces, verts;
-    var nb = [ new Int32Array([ 1, 0, 0 ]), new Int32Array([ -1, 0, 0 ]), 
-               new Int32Array([ 0, 1, 0 ]), new Int32Array([ 0, -1, 0 ]),
-               new Int32Array([ 0, 0, 1 ]), 
-               new Int32Array([ 0, 0, -1 ]), 
-               new Int32Array([ 1, 1, 0 ]), 
-               new Int32Array([ 1, -1, 0 ]), 
-               new Int32Array([ -1, 1, 0 ]),
-               new Int32Array([ -1, -1, 0 ]), 
-               new Int32Array([ 1, 0, 1 ]), 
-               new Int32Array([ 1, 0, -1 ]), 
-               new Int32Array([ -1, 0, 1 ]),
-               new Int32Array([ -1, 0, -1 ]), 
-               new Int32Array([ 0, 1, 1 ]), 
-               new Int32Array([ 0, 1, -1 ]), 
-               new Int32Array([ 0, -1, 1 ]),
-               new Int32Array([ 0, -1, -1 ]), 
-               new Int32Array([ 1, 1, 1 ]), 
-               new Int32Array([ 1, 1, -1 ]), 
-               new Int32Array([ 1, -1, 1 ]),
-               new Int32Array([ -1, 1, 1 ]), 
-               new Int32Array([ 1, -1, -1 ]), 
-               new Int32Array([ -1, -1, 1 ]), 
-               new Int32Array([ -1, 1, -1 ]),
-               new Int32Array([ -1, -1, -1 ]) ];
 
-    var origextent;
+    // Objects adding
 
-    var inOrigExtent = function(x, y, z) {
-        if (x < origextent[0][0] || x > origextent[1][0])
-            return false;
-        if (y < origextent[0][1] || y > origextent[1][1])
-            return false;
-        if (z < origextent[0][2] || z > origextent[1][2])
-            return false;
-        return true;
-    };
+    function addObject(object, scene) {
 
-    this.getFacesAndVertices = function(atomlist) {
-        var atomsToShow = {};
-        var i, il;
-        for (i = 0, il = atomlist.length; i < il; i++)
-            atomsToShow[atomlist[i]] = true;
-        var vertices = verts;
-        for (i = 0, il = vertices.length; i < il; i++) {
-            vertices[i].x = vertices[i].x / scaleFactor - ptranx;
-            vertices[i].y = vertices[i].y / scaleFactor - ptrany;
-            vertices[i].z = vertices[i].z / scaleFactor - ptranz;
-        }
+        var g, gl, geometry, material, geometryGroup;
 
-        var finalfaces = [];
-        for (i = 0, il = faces.length; i < il; i += 3) {
-            //var f = faces[i];
-            var fa = faces[i], fb = faces[i+1], fc = faces[i+2];
-            var a = vertices[fa]['atomid'], b = vertices[fb]['atomid'], c = vertices[fc]['atomid'];
+        if (!object.__webglInit) {
 
-            // must be a unique face for each atom
-            var which = a;
-            if (b < which)
-                which = b;
-            if (c < which)
-                which = c;
-            if (!atomsToShow[which]) {
-                continue;
-            }
-            var av = vertices[faces[i]];
-            var bv = vertices[faces[i+1]];
-            var cv = vertices[faces[i+2]];
+            object.__webglInit = true;
 
-            if (fa !== fb && fb !== fc && fa !== fc){
-                finalfaces.push(fa); 
-                finalfaces.push(fb); 
-                finalfaces.push(fc); 
-            }
-               
-        }
+            object._modelViewMatrix = new $3Dmol.Matrix4();
+            object._normalMatrix = new $3Dmol.Matrix3();
 
-        //try to help the garbage collector
-        vpBits = null; // uint8 array of bitmasks
-        vpDistance = null; // floatarray
-        vpAtomID = null; // intarray
-        
-        return {
-            'vertices' : vertices,
-            'faces' : finalfaces
-        };
-    };
+            if (object.geometry !== undefined
+                    && object.geometry.__webglInit === undefined) {
 
+                object.geometry.__webglInit = true;
+                object.geometry.addEventListener('dispose', onGeometryDispose);
 
-    this.initparm = function(extent, btype, volume) {
-        if(volume > 1000000) //heuristical decrease resolution to avoid large memory consumption
-            scaleFactor = defaultScaleFactor/2;
-        
-        var margin = (1 / scaleFactor) * 5.5; // need margin to avoid
-                                                // boundary/round off effects
-        origextent = extent;
-        pminx = extent[0][0]; pmaxx = extent[1][0];
-        pminy = extent[0][1]; pmaxy = extent[1][1];
-        pminz = extent[0][2]; pmaxz = extent[1][2];
+            }
 
-        if (!btype) {
-            pminx -= margin;
-            pminy -= margin;
-            pminz -= margin;
-            pmaxx += margin;
-            pmaxy += margin;
-            pmaxz += margin;
-        } else {
-            pminx -= probeRadius + margin;
-            pminy -= probeRadius + margin;
-            pminz -= probeRadius + margin;
-            pmaxx += probeRadius + margin;
-            pmaxy += probeRadius + margin;
-            pmaxz += probeRadius + margin;
-        }
+            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
+                geometry = object.geometry;
+                material = object.material;
 
-        pminx = Math.floor(pminx * scaleFactor) / scaleFactor;
-        pminy = Math.floor(pminy * scaleFactor) / scaleFactor;
-        pminz = Math.floor(pminz * scaleFactor) / scaleFactor;
-        pmaxx = Math.ceil(pmaxx * scaleFactor) / scaleFactor;
-        pmaxy = Math.ceil(pmaxy * scaleFactor) / scaleFactor;
-        pmaxz = Math.ceil(pmaxz * scaleFactor) / scaleFactor;
+                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
 
-        ptranx = -pminx;
-        ptrany = -pminy;
-        ptranz = -pminz;
+                    geometryGroup = geometry.geometryGroups[g];
 
-        pLength = Math.ceil(scaleFactor * (pmaxx - pminx)) + 1;
-        pWidth = Math.ceil(scaleFactor * (pmaxy - pminy)) + 1;
-        pHeight = Math.ceil(scaleFactor * (pmaxz - pminz)) + 1;
+                    geometryGroup.id = _geometryGroupCounter++;
 
-        this.boundingatom(btype);
-        cutRadius = probeRadius * scaleFactor;
+                    // initialise VBO on the first access
 
-        vpBits = new Uint8Array(pLength * pWidth * pHeight);
-        vpDistance = new Float64Array(pLength * pWidth * pHeight); // float 32
-        // doesn't
-        // play
-        // nicely
-        // with
-        // native
-        // floats
-        vpAtomID = new Int32Array(pLength * pWidth * pHeight);
-        console.log("Box size: ", pLength, pWidth, pHeight, vpBits.length);
-    };
+                    if (!geometryGroup.__webglVertexBuffer) {
 
-    this.boundingatom = function(btype) {
-        var tradius = [];
-        var txz, tdept, sradius, idx;
-        flagradius = btype;
+                        if (object instanceof $3Dmol.Mesh) {
+                            createMeshBuffers(geometryGroup);
+                            geometry.elementsNeedUpdate = true;
+                            geometry.normalsNeedUpdate = true;
+                        }
 
-        for ( var i in vdwRadii) {
-            if(!vdwRadii.hasOwnProperty(i))
-                continue;
-            var r = vdwRadii[i];
-            if (!btype)
-                tradius[i] = r * scaleFactor + 0.5;
-            else
-                tradius[i] = (r + probeRadius) * scaleFactor + 0.5;
+                        else if (object instanceof $3Dmol.Line)
+                            createLineBuffers(geometryGroup);
+
+                        geometry.verticesNeedUpdate = true;
+                        geometry.colorsNeedUpdate = true;
 
-            sradius = tradius[i] * tradius[i];
-            widxz[i] = Math.floor(tradius[i]) + 1;
-            depty[i] = new Int32Array(widxz[i] * widxz[i]);
-            indx = 0;
-            for (j = 0; j < widxz[i]; j++) {
-                for (k = 0; k < widxz[i]; k++) {
-                    txz = j * j + k * k;
-                    if (txz > sradius)
-                        depty[i][indx] = -1; // outside
-                    else {
-                        tdept = Math.sqrt(sradius - txz);
-                        depty[i][indx] = Math.floor(tdept);
                     }
-                    indx++;
+
                 }
+
             }
-        }
-    };
 
-    this.fillvoxels = function(atoms, atomlist) { // (int seqinit,int
-        // seqterm,bool
-        // atomtype,atom*
-        // proseq,bool bcolor)
-        var i, il;
-        for (i = 0, il = vpBits.length; i < il; i++) {
-            vpBits[i] = 0;
-            vpDistance[i] = -1.0;
-            vpAtomID[i] = -1;
         }
 
-        for (i in atomlist) {
-            var atom = atoms[atomlist[i]];
-            if (atom === undefined)
-                continue;
-            this.fillAtom(atom, atoms);
-        }
+        if (!object.__webglActive) {
 
-        for (i = 0, il = vpBits.length; i < il; i++)
-            if (vpBits[i] & INOUT)
-                vpBits[i] |= ISDONE;
+            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
 
-    };
+                geometry = object.geometry;
 
+                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
+                    geometryGroup = geometry.geometryGroups[g];
 
-    this.fillAtom = function(atom, atoms) {
-        var cx, cy, cz, ox, oy, oz, mi, mj, mk, i, j, k, si, sj, sk;
-        var ii, jj, kk, n;
-        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
-        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
-        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
+                    addBuffer(scene.__webglObjects, geometryGroup, object);
+                }
 
-        var at = getVDWIndex(atom);
-        var nind = 0;
-        var cnt = 0;
-        var pWH = pWidth*pHeight;
-        
-        for (i = 0, n = widxz[at]; i < n; i++) {
-            for (j = 0; j < n; j++) {
-                if (depty[at][nind] != -1) {
-                    for (ii = -1; ii < 2; ii++) {
-                        for (jj = -1; jj < 2; jj++) {
-                            for (kk = -1; kk < 2; kk++) {
-                                if (ii !== 0 && jj !== 0 && kk !== 0) {
-                                    mi = ii * i;
-                                    mk = kk * j;
-                                    for (k = 0; k <= depty[at][nind]; k++) {
-                                        mj = k * jj;
-                                        si = cx + mi;
-                                        sj = cy + mj;
-                                        sk = cz + mk;
-                                        if (si < 0 || sj < 0 || 
-                                                sk < 0 ||
-                                                si >= pLength || 
-                                                sj >= pWidth || 
-                                                sk >= pHeight)
-                                            continue;
-                                        var index = si * pWH + sj * pHeight + sk;
+            }
 
-                                        if (!(vpBits[index] & INOUT)) {
-                                            vpBits[index] |= INOUT;
-                                            vpAtomID[index] = atom.serial;
-                                        } else {
-                                            var atom2 = atoms[vpAtomID[index]];
-                                            if(atom2.serial != atom.serial) {
-                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.x + ptranx));
-                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.y + ptrany));
-                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.z + ptranz));
-                                                if (mi * mi + mj * mj + mk * mk < ox *
-                                                        ox + oy * oy + oz * oz)
-                                                    vpAtomID[index] = atom.serial;
-                                            }
-                                        }
+            // Sprite
+            else if (object instanceof $3Dmol.Sprite)
+                scene.__webglSprites.push(object);
 
-                                    }// k
-                                }// if
-                            }// kk
-                        }// jj
-                    }// ii
-                }// if
-                nind++;
-            }// j
-        }// i
-    };
+            object.__webglActive = true;
 
-    this.fillvoxelswaals = function(atoms, atomlist) {
-        var i, il;
-        for (i = 0, il = vpBits.length; i < il; i++)
-            vpBits[i] &= ~ISDONE; // not isdone
+        }
 
-        for (i in atomlist) {
-            var atom = atoms[atomlist[i]];
-            if (atom === undefined)
-                continue;
+    }
 
-            this.fillAtomWaals(atom, atoms);
-        }
-    };
+    function updateObject(object) {
 
-    this.fillAtomWaals = function(atom, atoms) {
-        var cx, cy, cz, ox, oy, oz, nind = 0;
-        var mi, mj, mk, si, sj, sk, i, j, k, ii, jj, kk, n;
-        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
-        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
-        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
+        var geometry = object.geometry, material = object.material, geometryGroup, customAttributesDirty;
 
-        var at = getVDWIndex(atom);
-        var pWH = pWidth*pHeight;
-        for (i = 0, n = widxz[at]; i < n; i++) {
-            for (j = 0; j < n; j++) {
-                if (depty[at][nind] != -1) {
-                    for (ii = -1; ii < 2; ii++) {
-                        for (jj = -1; jj < 2; jj++) {
-                            for (kk = -1; kk < 2; kk++) {
-                                if (ii !== 0 && jj !== 0 && kk !== 0) {
-                                    mi = ii * i;
-                                    mk = kk * j;
-                                    for (k = 0; k <= depty[at][nind]; k++) {
-                                        mj = k * jj;
-                                        si = cx + mi;
-                                        sj = cy + mj;
-                                        sk = cz + mk;
-                                        if (si < 0 || sj < 0 || 
-                                                sk < 0 || 
-                                                si >= pLength || 
-                                                sj >= pWidth || 
-                                                sk >= pHeight)
-                                            continue;
-                                        var index = si * pWH + sj * pHeight + sk;
-                                        if (!(vpBits[index] & ISDONE)) {
-                                            vpBits[index] |= ISDONE;
-                                            vpAtomID[index] = atom.serial;
-                                        }  else {
-                                            var atom2 = atoms[vpAtomID[index]];
-                                            if(atom2.serial != atom.serial) {
-                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.x + ptranx));
-                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.y + ptrany));
-                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.z + ptranz));
-                                                if (mi * mi + mj * mj + mk * mk < ox *
-                                                        ox + oy * oy + oz * oz)
-                                                    vpAtomID[index] = atom.serial;
-                                            }
-                                        }
-                                    }// k
-                                }// if
-                            }// kk
-                        }// jj
-                    }// ii
-                }// if
-                nind++;
-            }// j
-        }// i
-    };
+        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
 
-    this.buildboundary = function() {
-        var pWH = pWidth*pHeight;
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pHeight; j++) {
-                for (k = 0; k < pWidth; k++) {
-                    var index = i * pWH + k * pHeight + j;
-                    if (vpBits[index] & INOUT) {
-                        var flagbound = false;
-                        var ii = 0;
-                        while (ii < 26) {
-                            var ti = i + nb[ii][0], tj = j + nb[ii][2], tk = k +
-                                    nb[ii][1];
-                            if (ti > -1 && 
-                                ti < pLength && 
-                                tk > -1 && 
-                                tk < pWidth && 
-                                tj > -1 && 
-                                tj < pHeight && 
-                                !(vpBits[ti * pWH + tk * pHeight + tj] & INOUT)) {
-                                vpBits[index] |= ISBOUND;
-                                break;
-                            } else
-                                ii++;
-                        }
-                    }
+            for (var g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
+
+                geometryGroup = geometry.geometryGroups[g];
+
+                if (geometry.verticesNeedUpdate || geometry.elementsNeedUpdate
+                        || geometry.colorsNeedUpdate
+                        || geometry.normalsNeedUpdate) {
+                    setBuffers(geometryGroup, _gl.STATIC_DRAW);
                 }
             }
+
+            geometry.verticesNeedUpdate = false;
+            geometry.elementsNeedUpdate = false;
+            geometry.normalsNeedUpdate = false;
+            geometry.colorsNeedUpdate = false;
+
+            geometry.buffersNeedUpdate = false;
+
         }
-    };
 
-    // a little class for 3d array, should really generalize this and
-    // use throughout...
-    var PointGrid = function(length, width, height) {
-        // the standard says this is zero initialized
-        var data = new Int32Array(length * width * height * 3);
+    }
 
-        // set position x,y,z to pt, which has ix,iy,and iz
-        this.set = function(x, y, z, pt) {
-            var index = ((((x * width) + y) * height) + z) * 3;
-            data[index] = pt.ix;
-            data[index + 1] = pt.iy;
-            data[index + 2] = pt.iz;
-        };
+    function removeObject(object, scene) {
 
-        // return point at x,y,z
-        this.get = function(x, y, z) {
-            var index = ((((x * width) + y) * height) + z) * 3;
-            return {
-                ix : data[index],
-                iy : data[index + 1],
-                iz : data[index + 2]
-            };
-        };
-    };
+        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line)
+            removeInstances(scene.__webglObjects, object);
 
-    this.fastdistancemap = function() {
-        var eliminate = 0;
-        var certificate;
-        var i, j, k, n;
+        else if (object instanceof $3Dmol.Sprite)
+            removeInstancesDirect(scene.__webglSprites, object);
+
+        object.__webglActive = false;
+
+    }
+
+    function removeInstances(objList, object) {
+
+        for (var o = objList.length - 1; o >= 0; --o) {
+
+            if (objList[o].object === object)
+                objList.splice(o, 1);
 
-        var boundPoint = new PointGrid(pLength, pWidth, pHeight);
-        var pWH = pWidth*pHeight;
-        var cutRSq = cutRadius*cutRadius;
-        
-        var inarray = [];
-        var outarray = [];
-        
-        var index;
-        
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pWidth; j++) {
-                for (k = 0; k < pHeight; k++) {
-                    index = i * pWH + j * pHeight + k;
-                    vpBits[index] &= ~ISDONE; // isdone = false
-                    if (vpBits[index] & INOUT) {
-                        if (vpBits[index] & ISBOUND) {
-                            var triple = {
-                                ix : i,
-                                iy : j,
-                                iz : k
-                            };
-                            boundPoint.set(i, j, k, triple);
-                            inarray.push(triple);
-                            vpDistance[index] = 0;
-                            vpBits[index] |= ISDONE;
-                            vpBits[index] &= ~ISBOUND;
-                        } 
-                    }
-                }
-            }
         }
+    }
 
-        do {
-            outarray = this.fastoneshell(inarray, boundPoint);
-            inarray = [];
-            for (i = 0, n = outarray.length; i < n; i++) {
-                index = pWH * outarray[i].ix + pHeight *
-                    outarray[i].iy + outarray[i].iz;
-                vpBits[index] &= ~ISBOUND;
-                if (vpDistance[index] <= 1.0404 * cutRSq) {
-                    inarray.push({
-                        ix : outarray[i].ix,
-                        iy : outarray[i].iy,
-                        iz : outarray[i].iz
-                    });
-                }
-            }
-        } while (inarray.length !== 0);
+    function removeInstancesDirect(objList, object) {
 
-        inarray = [];
-        outarray = [];
-        boundPoint = null;
-        
-        var cutsf = scaleFactor - 0.5;
-        if (cutsf < 0)
-            cutsf = 0;
-        var cutoff = cutRSq - 0.50 / (0.1 + cutsf);
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pWidth; j++) {
-                for (k = 0; k < pHeight; k++) {
-                    index = i * pWH + j * pHeight + k;
-                    vpBits[index] &= ~ISBOUND;
-                    // ses solid
-                    if (vpBits[index] & INOUT) {
-                        if (!(vpBits[index] & ISDONE) ||
-                                ((vpBits[index] & ISDONE) && vpDistance[index] >= cutoff)) {
-                            vpBits[index] |= ISBOUND;
-                        }
-                    }
-                }
+        for (var o = objList.length - 1; o >= 0; --o) {
+
+            if (objList[o] === object)
+                objList.splice(o, 1);
+
+        }
+    }
+
+    function unrollBufferMaterial(globject) {
+
+        var object = globject.object;
+        var material = object.material;
+
+        if (material.transparent) {
+            globject.opaque = null;
+            globject.transparent = material;
+            if (!material.wireframe) {
+                var blankMaterial = material.clone();
+                blankMaterial.opacity = 0.0;
+                globject.blank = blankMaterial;
             }
         }
 
-    };
+        else {
+            globject.opaque = material;
+            globject.transparent = null;
 
-    this.fastoneshell = function(inarray, boundPoint) { // (int* innum,int
-        // *allocout,voxel2
-        // ***boundPoint, int*
-        // outnum, int *elimi)
-        var tx, ty, tz;
-        var dx, dy, dz;
-        var i, j, n;
-        var square;
-        var bp, index;
-        var outarray = [];
-        if (inarray.length === 0)
-            return outarray;
+        }
 
-        tnv = {
-            ix : -1,
-            iy : -1,
-            iz : -1
-        };
-        var pWH = pWidth*pHeight;
-        for ( i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
+    }
 
-            for (j = 0; j < 6; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
-                
-                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
-                    
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
-    
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
-    
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
-    
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
-    
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
-        }
+    function setBuffers(geometryGroup, hint, line) {
 
-        // console.log("part1", positout);
+        var vertexArray = geometryGroup.vertexArray;
+        var colorArray = geometryGroup.colorArray;
 
-        for (i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
+        // offset buffers
+        if (geometryGroup.__webglOffsetBuffer !== undefined ) {
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglOffsetBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, vertexArray, hint);
+        }
+        else {
+            //normal, non-instanced case
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, vertexArray, hint);            
+        }
+        // color buffers
+        _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer);
+        _gl.bufferData(_gl.ARRAY_BUFFER, colorArray, hint);
 
-            for (j = 6; j < 18; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
+        // normal buffers
+        if (geometryGroup.normalArray
+                && geometryGroup.__webglNormalBuffer !== undefined) {
+            var normalArray = geometryGroup.normalArray;
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, normalArray, hint);
 
-                if(tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
-                    
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
-    
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
-    
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
         }
 
-        // console.log("part2", positout);
 
-        for (i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
 
-            for (j = 18; j < 26; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
+        // radius buffers
+        if (geometryGroup.radiusArray
+                && geometryGroup.__webglRadiusBuffer !== undefined) {
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglRadiusBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, geometryGroup.radiusArray, hint);
+        }
 
-                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+        // face (index) buffers
+        if (geometryGroup.faceArray
+                && geometryGroup.__webglFaceBuffer !== undefined) {
+            var faceArray = geometryGroup.faceArray;
+            _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                    geometryGroup.__webglFaceBuffer);
+            _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER, faceArray, hint);
 
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+        }
 
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
+        // line (index) buffers (for wireframe)
+        if (geometryGroup.lineArray
+                && geometryGroup.__webglLineBuffer !== undefined) {
+            var lineArray = geometryGroup.lineArray;
+            _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                    geometryGroup.__webglLineBuffer);
+            _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER, lineArray, hint);
+        }
 
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT)  && (vpBits[index] & ISDONE)) {
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+    }
 
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
+    // Creates appropriate gl buffers for geometry chunk
+    // TODO: do we need line buffer for mesh objects?
+    // Also, can we integrate this with createLineBuffers?
+    function createMeshBuffers(geometryGroup) {
+
+        if (geometryGroup.radiusArray) {
+            geometryGroup.__webglRadiusBuffer = _gl.createBuffer();
+        }
+        if(geometryGroup.useOffset) {
+            geometryGroup.__webglOffsetBuffer = _gl.createBuffer();
         }
+        geometryGroup.__webglVertexBuffer = _gl.createBuffer();
+        geometryGroup.__webglNormalBuffer = _gl.createBuffer();
+        geometryGroup.__webglColorBuffer = _gl.createBuffer();
 
-        // console.log("part3", positout);
-        return outarray;
-    };
+        geometryGroup.__webglFaceBuffer = _gl.createBuffer();
+        geometryGroup.__webglLineBuffer = _gl.createBuffer();
 
-    this.marchingcubeinit = function(stype) {
-        for ( var i = 0, lim = vpBits.length; i < lim; i++) {
-            if (stype == 1) {// vdw
-                vpBits[i] &= ~ISBOUND;
-            } else if (stype == 4) { // ses
-                vpBits[i] &= ~ISDONE;
-                if (vpBits[i] & ISBOUND)
-                    vpBits[i] |= ISDONE;
-                vpBits[i] &= ~ISBOUND;
-            } else if (stype == 2) {// after vdw
-                if ((vpBits[i] & ISBOUND) && (vpBits[i] & ISDONE))
-                    vpBits[i] &= ~ISBOUND;
-                else if ((vpBits[i] & ISBOUND) && !(vpBits[i] & ISDONE))
-                    vpBits[i] |= ISDONE;
-            } else if (stype == 3) { // sas
-                vpBits[i] &= ~ISBOUND;
-            }
-        }
-    };
+        _this.info.memory.geometries++;
+    }
 
-    // this code allows me to empirically prune the marching cubes code tables
-    // to more efficiently handle discrete data
-    var counter = function() {
-        var data = Array(256);
-        for ( var i = 0; i < 256; i++)
-            data[i] = [];
+    function createLineBuffers(geometry) {
 
-        this.incrementUsed = function(i, j) {
-            if (typeof data[i][j] === 'undefined')
-                data[i][j] = {
-                    used : 0,
-                    unused : 0
-                };
-            data[i][j].used++;
-        };
+        geometry.__webglVertexBuffer = _gl.createBuffer();
+        geometry.__webglColorBuffer = _gl.createBuffer();
 
-        this.incrementUnused = function(i, j) {
-            if (typeof data[i][j] === 'undefined')
-                data[i][j] = {
-                    used : 0,
-                    unused : 0
-                };
-            data[i][j].unused++;
+        _this.info.memory.geometries++;
+    }
 
-        };
+    function addBuffer(objlist, buffer, object) {
 
-        var redoTable = function(triTable) {
-            var str = "[";
-            for ( var i = 0; i < triTable.length; i++) {
-                var code = 0;
-                var table = triTable[i];
-                for ( var j = 0; j < table.length; j++) {
-                    code |= (1 << (table[j]));
-                }
-                str += "0x" + code.toString(16) + ", ";
-            }
-            str += "]";
-            console.log(str);
-        };
+        objlist.push({
+            buffer : buffer,
+            object : object,
+            opaque : null,
+            transparent : null
+        });
 
-        this.print = function() {
+    }
 
-            var table = MarchingCube.triTable;
-            var str;
-            var newtable = [];
-            for ( var i = 0; i < table.length; i++) {
-                var newarr = [];
-                for ( var j = 0; j < table[i].length; j += 3) {
-                    var k = j / 3;
-                    if (typeof data[i][k] === 'undefined' || !data[i][k].unused) {
-                        newarr.push(table[i][j]);
-                        newarr.push(table[i][j + 1]);
-                        newarr.push(table[i][j + 2]);
-                    }
-                    if (typeof data[i][k] === 'undefined')
-                        console.log("undef " + i + "," + k);
-                }
-                newtable.push(newarr);
-            }
-            console.log(JSON.stringify(newtable));
-            redoTable(newtable);
-        };
-    };
-    
-    this.marchingcube = function(stype) {
-        this.marchingcubeinit(stype);
-        verts = []; faces = [];   
-        $3Dmol.MarchingCube.march(vpBits, verts, faces, {
-            smooth : 1,
-            nX : pLength,
-            nY : pWidth,
-            nZ : pHeight        
-        });      
-
-        var pWH = pWidth*pHeight;
-        for (var i = 0, vlen = verts.length; i < vlen; i++) {
-            verts[i]['atomid'] = vpAtomID[verts[i].x * pWH + pHeight *
-                    verts[i].y + verts[i].z];
-        }  
+    function setupMatrices(object, camera) {
 
-        $3Dmol.MarchingCube.laplacianSmooth(1, verts, faces);
+        object._modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse,
+                object.matrixWorld);
 
-    };
+        object._normalMatrix.getInverse(object._modelViewMatrix);
+        object._normalMatrix.transpose();
 
+    }
 
-};
+    function isPowerOfTwo(value) {
 
-//This defines the $3Dmol object which is used to create viewers
-//and configure system-wide settings
+        return (value & (value - 1)) === 0;
 
-/** 
- * All of the functionality of $3Dmol.js is contained within the
- * $3Dmol global namespace
- * @namespace */
-$3Dmol = (function(window) {
-    
-    var my = window['$3Dmol'] || {};
-    //var $ = window['jQuery'];
-    
-    return my;
+    }
 
-})(window);
+    // Fallback filters for non-power-of-2 textures
 
-/* The following code "phones home" to register that an ip 
-   address has loaded 3Dmol.js.  Being able track this usage
-   is very helpful when reporting to funding agencies.  Please
-   leave this code in if you would like to increase the 
-   likelihood of 3Dmol.js remaining supported.
-*/
-$.get("http://3dmol.csb.pitt.edu/track/report.cgi");
-    
-/**
- * Create and initialize an appropriate viewer at supplied HTML element using specification in config
- * @param {Object | string} element - Either HTML element or string identifier
- * @param {ViewerSpec} config Viewer specification
- * @return {$3Dmol.GLViewer} GLViewer, null if unable to instantiate WebGL
- * 
- * @example
- * // Assume there exists an HTML div with id "gldiv"
- * var element = $("#gldiv");
- * 
- * // Viewer config - properties 'defaultcolors' and 'callback'
- * var config = {defaultcolors: $3Dmol.rasmolElementColors };
- * 
- * // Create GLViewer within 'gldiv' 
- * var myviewer = $3Dmol.createViewer(element, config);
- * //'data' is a string containing molecule data in pdb format  
- * myviewer.addModel(data, "pdb");
- * myviewer.zoomTo();
- * myviewer.render();                        
- *                        
- */
-$3Dmol.createViewer = function(element, config)
-{
-    if($.type(element) === "string")
-        element = $("#"+element);
-    if(!element) return;
+    function filterFallback(f) {
 
-    config = config || {}; 
+        return _gl.LINEAR;
 
-    //try to create the  viewer
-    try {
-        return new $3Dmol.GLViewer(element, config);
     }
-    catch(e) {
-        throw "error creating viewer: "+e;
-    }
-    
-    return null;
-};
-   
-/**
- * Contains a dictionary of embedded viewers created from HTML elements
- * with a the viewer_3Dmoljs css class indexed by their id (or numerically
- * if they do not have an id).
-*/
-$3Dmol.viewers = {};
 
-/**
- * Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model
- * 
- * @function $3Dmol.download
- * @param {string} query String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively
- * @param {$3Dmol.GLViewer} viewer - Add new model to existing viewer
- * @example
- * var myviewer = $3Dmol.createViewer(gldiv);
- * 
- * // GLModel 'm' created and loaded into glviewer for PDB id 2POR
- * // Note that m will not contain the atomic data until after the network request is completed
- * var m = $3Dmol.download('pdb: 2POR', myviewer);
- * 
- * @return {$3Dmol.GLModel} GLModel
- */ 
-$3Dmol.download = function(query, viewer, options, callback) {
-    var baseURL = '';
-    var type = "";
-    var m = viewer.addModel();
-    if (query.substr(0, 4) === 'pdb:') {
-        type = "pdb";
-        query = query.substr(4).toUpperCase();
-        if (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) {
-           alert("Wrong PDB ID"); return;
-        }
-        uri = "http://www.rcsb.org/pdb/files/" + query + ".pdb";
-    } else if (query.substr(0, 4) == 'cid:') {
-        type = "sdf";
-        query = query.substr(4);
-        if (!query.match(/^[1-9]+$/)) {
-           alert("Wrong Compound ID"); return;
+    function setTextureParameters(textureType, texture, isImagePowerOfTwo) {
+
+        if (isImagePowerOfTwo) {
+
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_S,
+                    paramToGL(texture.wrapS));
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_T,
+                    paramToGL(texture.wrapT));
+
+            _gl.texParameteri(textureType, _gl.TEXTURE_MAG_FILTER,
+                    paramToGL(texture.magFilter));
+            _gl.texParameteri(textureType, _gl.TEXTURE_MIN_FILTER,
+                    paramToGL(texture.minFilter));
+
+        } else {
+
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_S,
+                    _gl.CLAMP_TO_EDGE);
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_T,
+                    _gl.CLAMP_TO_EDGE);
+
+            _gl.texParameteri(textureType, _gl.TEXTURE_MAG_FILTER,
+                    filterFallback(texture.magFilter));
+            _gl.texParameteri(textureType, _gl.TEXTURE_MIN_FILTER,
+                    filterFallback(texture.minFilter));
+
         }
-        uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query + 
-          "/SDF?record_type=3d";
+
     }
 
-   $.get(uri, function(ret) {
-      m.addMolData(ret, type, options);
-      viewer.zoomTo();
-      viewer.render();
-      if(callback) callback(m);
+    this.setTexture = function(texture, slot) {
 
-   });
-   
-   return m;
-};
-       
+        if (texture.needsUpdate) {
 
-/**
- * $3Dmol surface types
- * @enum {number}
- */
-$3Dmol.SurfaceType = {
-    VDW : 1,
-    MS : 2,
-    SAS : 3,
-    SES  : 4
-};
+            if (!texture.__webglInit) {
 
+                texture.__webglInit = true;
 
-//Miscellaneous functions and classes - to be incorporated into $3Dmol proper
-/**
- * 
- * @param {$3Dmol.Geometry} geometry
- * @param {$3Dmol.Mesh} mesh
- * @returns {undefined}
- */
-$3Dmol.mergeGeos = function(geometry, mesh) {
-    
-    var meshGeo = mesh.geometry;
-    
-    if (meshGeo === undefined) 
-        return;
-    
-    geometry.geometryGroups.push( meshGeo.geometryGroups[0] );
-    
-};
+                texture.addEventListener('dispose', onTextureDispose);
 
-$3Dmol.multiLineString = function(f) {
-    return f.toString()
-            .replace(/^[^\/]+\/\*!?/, '')
-            .replace(/\*\/[^\/]+$/, '');
-            
-};
+                texture.__webglTexture = _gl.createTexture();
 
-/** 
- * Render surface synchronously if true
- * @param {boolean} [$3Dmol.SyncSurface=false]
- * @type {boolean} */
-$3Dmol.syncSurface = false;
+                _this.info.memory.textures++;
 
-// Internet Explorer refuses to allow webworkers in data blobs.  I can find
-// no way of checking for this feature directly, so must do a brower check
-if(window.navigator.userAgent.indexOf('MSIE ') >= 0 ||
-        window.navigator.userAgent.indexOf('Trident/') >= 0) {
-    $3Dmol.syncSurface = true; // can't use webworkers
-}
+            }
 
-/**
- * Parse a string that represents a style or atom selection and convert it
- * into an object.  The goal is to make it easier to write out these specifications
- * without resorting to json. Objects cannot be defined recursively.
- * ; - delineates fields of the object 
- * : - if the field has a value other than an empty object, it comes after a colon
- * , - delineates key/value pairs of a value object
- *     If the value object consists of ONLY keys (no = present) the keys are 
- *     converted to a list.  Otherwise a object of key/value pairs is created with
- *     any missing values set to null
- * = OR ~ - separates key/value pairs of a value object, if not provided value is null
- *     twiddle is supported since = has special meaning in URLs
- * @param (String) str
- * @returns {Object}
- */
-$3Dmol.specStringToObject = function(str) {
-    if(typeof(str) === "object") {
-        return str; //not string, assume was converted already
-    }
-    else if(typeof(str) === "undefined" || str == null) {
-        return str; 
-    }
-    var ret = {};
-    var fields = str.split(';');
-    for(var i = 0; i < fields.length; i++) {
-        var fv = fields[i].split(':');
-        var f = fv[0];
-        var val = {};
-        var vstr = fv[1];
-        if(vstr) {
-            vstr = vstr.replace(/~/g,"=");
-            if(vstr.indexOf('=') !== -1) {
-                //has key=value pairs, must be object
-                var kvs = vstr.split(',');
-                for(var j = 0; j < kvs.length; j++) {
-                    var kv = kvs[j].split('=',2);
-                    val[kv[0]] = kv[1];
+            _gl.activeTexture(_gl.TEXTURE0 + slot);
+            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
+
+            _gl.pixelStorei(_gl.UNPACK_FLIP_Y_WEBGL, texture.flipY);
+            _gl.pixelStorei(_gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL,
+                    texture.premultiplyAlpha);
+            _gl.pixelStorei(_gl.UNPACK_ALIGNMENT, texture.unpackAlignment);
+
+            var image = texture.image, isImagePowerOfTwo = isPowerOfTwo(image.width)
+                    && isPowerOfTwo(image.height), glFormat = paramToGL(texture.format), glType = paramToGL(texture.type);
+
+            setTextureParameters(_gl.TEXTURE_2D, texture, isImagePowerOfTwo);
+
+            var mipmap, mipmaps = texture.mipmaps;
+
+            // regular Texture (image, video, canvas)
+
+            // use manually created mipmaps if available
+            // if there are no manual mipmaps
+            // set 0 level mipmap and then use GL to generate other mipmap
+            // levels
+
+            if (mipmaps.length > 0 && isImagePowerOfTwo) {
+
+                for (var i = 0, il = mipmaps.length; i < il; i++) {
+                    mipmap = mipmaps[i];
+                    _gl.texImage2D(_gl.TEXTURE_2D, i, glFormat, glFormat,
+                            glType, mipmap);
                 }
+
+                texture.generateMipmaps = false;
             }
-            else if(vstr.indexOf(',') !== -1) {
-                //has multiple values, must list
-                val = vstr.split(',');
-            }
-            else {
-                val = vstr; //value itself
-            }
-        }
-        ret[f] = val;
-    }
 
-return ret;
-}
+            else
+                _gl.texImage2D(_gl.TEXTURE_2D, 0, glFormat, glFormat, glType,
+                        texture.image);
 
-// computes the bounding box around the provided atoms
-/**
- * @param {AtomSpec[]} atomlist
- * @return {Array}
- */
-$3Dmol.getExtent = function(atomlist, ignoreSymmetries) {
-    var xmin, ymin, zmin, xmax, ymax, zmax, xsum, ysum, zsum, cnt;
-    var includeSym = !ignoreSymmetries;
+            if (texture.generateMipmaps && isImagePowerOfTwo)
+                _gl.generateMipmap(_gl.TEXTURE_2D);
 
-    xmin = ymin = zmin = 9999;
-    xmax = ymax = zmax = -9999;
-    xsum = ysum = zsum = cnt = 0;
-    
-    if (atomlist.length === 0)
-        return [ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ];
-    for (var i = 0; i < atomlist.length; i++) {
-        var atom = atomlist[i];
-        if (atom === undefined)
-            continue;
-        cnt++;
-        xsum += atom.x;
-        ysum += atom.y;
-        zsum += atom.z;
-        
-        xmin = (xmin < atom.x) ? xmin : atom.x;
-        ymin = (ymin < atom.y) ? ymin : atom.y;
-        zmin = (zmin < atom.z) ? zmin : atom.z;
-        xmax = (xmax > atom.x) ? xmax : atom.x;
-        ymax = (ymax > atom.y) ? ymax : atom.y;
-        zmax = (zmax > atom.z) ? zmax : atom.z;
-        
-        if (atom.symmetries && includeSym) {
-            for (var n = 0; n < atom.symmetries.length; n++) {
-                cnt++;
-                xsum += atom.symmetries[n].x;
-                ysum += atom.symmetries[n].y;
-                zsum += atom.symmetries[n].z;
-                xmin = (xmin < atom.symmetries[n].x) ? xmin : atom.symmetries[n].x;
-                ymin = (ymin < atom.symmetries[n].y) ? ymin : atom.symmetries[n].y;
-                zmin = (zmin < atom.symmetries[n].z) ? zmin : atom.symmetries[n].z;
-                xmax = (xmax > atom.symmetries[n].x) ? xmax : atom.symmetries[n].x;
-                ymax = (ymax > atom.symmetries[n].y) ? ymax : atom.symmetries[n].y;
-                zmax = (zmax > atom.symmetries[n].z) ? zmax : atom.symmetries[n].z; 
-            }
-        }  
-    }
+            texture.needsUpdate = false;
 
-    return [ [ xmin, ymin, zmin ], [ xmax, ymax, zmax ],
-            [ xsum / cnt, ysum / cnt, zsum / cnt ] ];
-};
+            if (texture.onUpdate)
+                texture.onUpdate();
 
+        } else {
 
-/*
-//Hackish way to create webworker (independent of $3Dmol namespace) within minified file
-//Had to hard-code uglify-js minified version of worker string in order to work with closure compiler...
-$3Dmol.workerString = function(){
+            _gl.activeTexture(_gl.TEXTURE0 + slot);
+            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
 
-    self.onmessage = function(oEvent) {
-        var obj = oEvent.data;
-        var type = obj.type;
-        if (type < 0) // sending atom data, initialize
-        {
-            self.atomData = obj.atoms;
-            self.volume = obj.volume;
-            self.ps = new ProteinSurface();
-        } else {
-            var ps = self.ps;
-            ps.initparm(obj.expandedExtent, (type == 1) ? false : true, self.volume);
-            ps.fillvoxels(self.atomData, obj.extendedAtoms);
-            ps.buildboundary();
-            if (type === 4 || type === 2) {
-                ps.fastdistancemap();
-                ps.boundingatom(false);
-                ps.fillvoxelswaals(self.atomData, obj.extendedAtoms);    
-            }        
-            ps.marchingcube(type);
-            var VandF = ps.getFacesAndVertices(obj.atomsToShow);
-            self.postMessage(VandF);
         }
+
     };
-    
-}.toString().replace(/(^.*?\{|\}$)/g, "");
-$3Dmol.workerString += ";var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}}"
-$3Dmol.workerString += ";var ISDONE=2";
-$3Dmol.workerString += ",ProteinSurface=" + $3Dmol.ProteinSurface.toString().replace(/$3Dmol.MarchingCube./g, "");
-$3Dmol.workerString += ",march=" + $3Dmol.MarchingCube.march.toString().replace(/$3Dmol./g, "");
-$3Dmol.workerString += ",laplacianSmooth=" + $3Dmol.MarchingCube.laplacianSmooth.toString();
 
-$3Dmol.workerString += ",edgeTable=new Uint32Array([" + $3Dmol.MarchingCube.edgeTable.toString() + "])";
+    // Map constants to WebGL constants
 
-$3Dmol.workerString += ",triTable=[";
+    function paramToGL(p) {
 
-for (var i = 0, il = $3Dmol.MarchingCube.triTable.length; i < il - 1; i++)
-    $3Dmol.workerString += "[" + $3Dmol.MarchingCube.triTable[i].toString() + "],";
+        if (p === $3Dmol.UnsignedByteType)
+            return _gl.UNSIGNED_BYTE;
+        if (p === $3Dmol.RGBAFormat)
+            return _gl.RGBA;
 
-$3Dmol.workerString += "[]]";
-*/
+        return 0;
 
-//TODO: Make this dynamic
-//Otherwise, must uncomment and run the above with 3Dmol-min.js, and cut and paste below everytime ProteinSurface or MarchingCube modified
-$3Dmol.workerString = 'self.onmessage=function(oEvent){var obj=oEvent.data,type=obj.type;if(0>type)self.atomData=obj.atoms,self.volume=obj.volume,self.ps=new ProteinSurface;else{var ps=self.ps;ps.initparm(obj.expandedExtent,1==type?!1:!0,self.volume),ps.fillvoxels(self.atomData,obj.extendedAtoms),ps.buildboundary(),(4===type||2===type)&&(ps.fastdistancemap(),ps.boundingatom(!1),ps.fillvoxelswaals(self.atomData,obj.extendedAtoms)),ps.marchingcube(type);var VandF=ps.getFacesAndVertices(obj.atomsToShow);self.postMessage(VandF)}};var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}};var ISDONE=2,ProteinSurface=function (){var faces,verts,origextent,INOUT=1,ISDONE=2,ISBOUND=4,ptranx=0,ptrany=0,ptranz=0,probeRadius=1.4,defaultScaleFactor=2,scaleFactor=defaultScaleFactor,pHeight=0,pWidth=0,pLength=0,cutRadius=0,vpBits=null,vpDistance=null,vpAtomID=null,pminx=0,pminy=0,pminz=0,pmaxx=0,pmaxy=0,pmaxz=0,vdwRadii={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},getVDWIndex=function(atom){return atom.elem&&"undefined"!=typeof vdwRadii[atom.elem]?atom.elem:"X"},depty={},widxz={},nb=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,-1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];this.getFacesAndVertices=function(atomlist){var i,il,atomsToShow={};for(i=0,il=atomlist.length;il>i;i++)atomsToShow[atomlist[i]]=!0;var vertices=verts;for(i=0,il=vertices.length;il>i;i++)vertices[i].x=vertices[i].x/scaleFactor-ptranx,vertices[i].y=vertices[i].y/scaleFactor-ptrany,vertices[i].z=vertices[i].z/scaleFactor-ptranz;var finalfaces=[];for(i=0,il=faces.length;il>i;i+=3){var fa=faces[i],fb=faces[i+1],fc=faces[i+2],a=vertices[fa].atomid,b=vertices[fb].atomid,c=vertices[fc].atomid,which=a;if(which>b&&(which=b),which>c&&(which=c),atomsToShow[which]){{vertices[faces[i]],vertices[faces[i+1]],vertices[faces[i+2]]}fa!==fb&&fb!==fc&&fa!==fc&&(finalfaces.push(fa),finalfaces.push(fb),finalfaces.push(fc))}}return vpBits=null,vpDistance=null,vpAtomID=null,{vertices:vertices,faces:finalfaces}},this.initparm=function(extent,btype,volume){volume>1e6&&(scaleFactor=defaultScaleFactor/2);var margin=1/scaleFactor*5.5;origextent=extent,pminx=extent[0][0],pmaxx=extent[1][0],pminy=extent[0][1],pmaxy=extent[1][1],pminz=extent[0][2],pmaxz=extent[1][2],btype?(pminx-=probeRadius+margin,pminy-=probeRadius+margin,pminz-=probeRadius+margin,pmaxx+=probeRadius+margin,pmaxy+=probeRadius+margin,pmaxz+=probeRadius+margin):(pminx-=margin,pminy-=margin,pminz-=margin,pmaxx+=margin,pmaxy+=margin,pmaxz+=margin),pminx=Math.floor(pminx*scaleFactor)/scaleFactor,pminy=Math.floor(pminy*scaleFactor)/scaleFactor,pminz=Math.floor(pminz*scaleFactor)/scaleFactor,pmaxx=Math.ceil(pmaxx*scaleFactor)/scaleFactor,pmaxy=Math.ceil(pmaxy*scaleFactor)/scaleFactor,pmaxz=Math.ceil(pmaxz*scaleFactor)/scaleFactor,ptranx=-pminx,ptrany=-pminy,ptranz=-pminz,pLength=Math.ceil(scaleFactor*(pmaxx-pminx))+1,pWidth=Math.ceil(scaleFactor*(pmaxy-pminy))+1,pHeight=Math.ceil(scaleFactor*(pmaxz-pminz))+1,this.boundingatom(btype),cutRadius=probeRadius*scaleFactor,vpBits=new Uint8Array(pLength*pWidth*pHeight),vpDistance=new Float64Array(pLength*pWidth*pHeight),vpAtomID=new Int32Array(pLength*pWidth*pHeight)},this.boundingatom=function(btype){var txz,tdept,sradius,tradius=[];flagradius=btype;for(var i in vdwRadii)if(vdwRadii.hasOwnProperty(i)){var r=vdwRadii[i];for(tradius[i]=btype?(r+probeRadius)*scaleFactor+.5:r*scaleFactor+.5,sradius=tradius[i]*tradius[i],widxz[i]=Math.floor(tradius[i])+1,depty[i]=new Int32Array(widxz[i]*widxz[i]),indx=0,j=0;j<widxz[i];j++)for(k=0;k<widxz[i];k++)txz=j*j+k*k,txz>sradius?depty[i][indx]=-1:(tdept=Math.sqrt(sradius-txz),depty[i][indx]=Math.floor(tdept)),indx++}},this.fillvoxels=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]=0,vpDistance[i]=-1,vpAtomID[i]=-1;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtom(atom,atoms)}for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&INOUT&&(vpBits[i]|=ISDONE)},this.fillAtom=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,i,j,k,si,sj,sk,ii,jj,kk,n;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),nind=0,pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&INOUT){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=INOUT,vpAtomID[index]=atom.serial}nind++}},this.fillvoxelswaals=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&=~ISDONE;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtomWaals(atom,atoms)}},this.fillAtomWaals=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,si,sj,sk,i,j,k,ii,jj,kk,n,nind=0;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&ISDONE){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=ISDONE,vpAtomID[index]=atom.serial}nind++}},this.buildboundary=function(){var pWH=pWidth*pHeight;for(i=0;pLength>i;i++)for(j=0;pHeight>j;j++)for(k=0;pWidth>k;k++){var index=i*pWH+k*pHeight+j;if(vpBits[index]&INOUT)for(var ii=0;26>ii;){var ti=i+nb[ii][0],tj=j+nb[ii][2],tk=k+nb[ii][1];if(ti>-1&&pLength>ti&&tk>-1&&pWidth>tk&&tj>-1&&pHeight>tj&&!(vpBits[ti*pWH+tk*pHeight+tj]&INOUT)){vpBits[index]|=ISBOUND;break}ii++}}};var PointGrid=function(length,width,height){var data=new Int32Array(length*width*height*3);this.set=function(x,y,z,pt){var index=3*((x*width+y)*height+z);data[index]=pt.ix,data[index+1]=pt.iy,data[index+2]=pt.iz},this.get=function(x,y,z){var index=3*((x*width+y)*height+z);return{ix:data[index],iy:data[index+1],iz:data[index+2]}}};this.fastdistancemap=function(){var i,j,k,n,index,boundPoint=new PointGrid(pLength,pWidth,pHeight),pWH=pWidth*pHeight,cutRSq=cutRadius*cutRadius,inarray=[],outarray=[];for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)if(index=i*pWH+j*pHeight+k,vpBits[index]&=~ISDONE,vpBits[index]&INOUT&&vpBits[index]&ISBOUND){var triple={ix:i,iy:j,iz:k};boundPoint.set(i,j,k,triple),inarray.push(triple),vpDistance[index]=0,vpBits[index]|=ISDONE,vpBits[index]&=~ISBOUND}do for(outarray=this.fastoneshell(inarray,boundPoint),inarray=[],i=0,n=outarray.length;n>i;i++)index=pWH*outarray[i].ix+pHeight*outarray[i].iy+outarray[i].iz,vpBits[index]&=~ISBOUND,vpDistance[index]<=1.0404*cutRSq&&inarray.push({ix:outarray[i].ix,iy:outarray[i].iy,iz:outarray[i].iz});while(0!==inarray.length);inarray=[],outarray=[],boundPoint=null;var cutsf=scaleFactor-.5;0>cutsf&&(cutsf=0);var cutoff=cutRSq-.5/(.1+cutsf);for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)index=i*pWH+j*pHeight+k,vpBits[index]&=~ISBOUND,vpBits[index]&INOUT&&(!(vpBits[index]&ISDONE)||vpBits[index]&ISDONE&&vpDistance[index]>=cutoff)&&(vpBits[index]|=ISBOUND)},this.fastoneshell=function(inarray,boundPoint){var tx,ty,tz,dx,dy,dz,i,j,n,square,bp,index,outarray=[];if(0===inarray.length)return outarray;tnv={ix:-1,iy:-1,iz:-1};var pWH=pWidth*pHeight;for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=0;6>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=6;18>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=18;26>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return outarray},this.marchingcubeinit=function(stype){for(var i=0,lim=vpBits.length;lim>i;i++)1==stype?vpBits[i]&=~ISBOUND:4==stype?(vpBits[i]&=~ISDONE,vpBits[i]&ISBOUND&&(vpBits[i]|=ISDONE),vpBits[i]&=~ISBOUND):2==stype?vpBits[i]&ISBOUND&&vpBits[i]&ISDONE?vpBits[i]&=~ISBOUND:vpBits[i]&ISBOUND&&!(vpBits[i]&ISDONE)&&(vpBits[i]|=ISDONE):3==stype&&(vpBits[i]&=~ISBOUND)};this.marchingcube=function(stype){this.marchingcubeinit(stype),verts=[],faces=[],march(vpBits,verts,faces,{smooth:1,nX:pLength,nY:pWidth,nZ:pHeight});for(var pWH=pWidth*pHeight,i=0,vlen=verts.length;vlen>i;i++)verts[i].atomid=vpAtomID[verts[i].x*pWH+pHeight*verts[i].y+verts[i].z];laplacianSmooth(1,verts,faces)}},march=function (data,verts,faces,spec){var i,il,fulltable=!!spec.fulltable,origin=spec.hasOwnProperty("origin")&&spec.origin.hasOwnProperty("x")?spec.origin:{x:0,y:0,z:0},voxel=!!spec.voxel,nX=spec.nX||0,nY=spec.nY||0,nZ=spec.nZ||0,scale=spec.scale||1,unitCube=new Vector3(1,1,1).multiplyScalar(scale),vertnums=new Int32Array(nX*nY*nZ);for(i=0,il=vertnums.length;il>i;++i)vertnums[i]=-1;var getVertex=function(i,j,k,code,p1,p2){var pt=new Vector3;pt.copy(origin);var val1=!!(code&1<<p1),val2=!!(code&1<<p2),p=p1;!val1&&val2&&(p=p2),1&p&&k++,2&p&&j++,4&p&&i++,pt.x+=unitCube.x*i,pt.y+=unitCube.y*j,pt.z+=unitCube.z*k;var index=(nY*i+j)*nZ+k;return voxel?(verts.push(pt),verts.length-1):(vertnums[index]<0&&(vertnums[index]=verts.length,verts.push(pt)),vertnums[index])},intersects=new Int32Array(12),etable=fulltable?edgeTable2:edgeTable,tritable=fulltable?triTable2:triTable;for(i=0;nX-1>i;++i)for(var j=0;nY-1>j;++j)for(var k=0;nZ-1>k;++k){for(var code=0,p=0;8>p;++p){var index=(nY*(i+((4&p)>>2))+j+((2&p)>>1))*nZ+k+(1&p),val=!!(data[index]&ISDONE);code|=val<<p}if(0!==code&&255!==code){var ecode=etable[code];if(0!==ecode){var ttable=tritable[code];1&ecode&&(intersects[0]=getVertex(i,j,k,code,0,1)),2&ecode&&(intersects[1]=getVertex(i,j,k,code,1,3)),4&ecode&&(intersects[2]=getVertex(i,j,k,code,3,2)),8&ecode&&(intersects[3]=getVertex(i,j,k,code,2,0)),16&ecode&&(intersects[4]=getVertex(i,j,k,code,4,5)),32&ecode&&(intersects[5]=getVertex(i,j,k,code,5,7)),64&ecode&&(intersects[6]=getVertex(i,j,k,code,7,6)),128&ecode&&(intersects[7]=getVertex(i,j,k,code,6,4)),256&ecode&&(intersects[8]=getVertex(i,j,k,code,0,4)),512&ecode&&(intersects[9]=getVertex(i,j,k,code,1,5)),1024&ecode&&(intersects[10]=getVertex(i,j,k,code,3,7)),2048&ecode&&(intersects[11]=getVertex(i,j,k,code,2,6));for(var t=0;t<ttable.length;t+=3){var a=intersects[ttable[t]],b=intersects[ttable[t+1]],c=intersects[ttable[t+2]];voxel&&t>=3&&(verts.push(verts[a]),a=verts.length-1,verts.push(verts[b]),b=verts.length-1,verts.push(verts[c]),c=verts.length-1),faces.push(a),faces.push(b),faces.push(c)}}}}},laplacianSmooth=function (numiter,verts,faces){var i,il,j,jl,k,tps=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)tps[i]={x:0,y:0,z:0};var flagvert,vertdeg=new Array(20);for(i=0;20>i;i++)vertdeg[i]=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)vertdeg[0][i]=0;for(i=0,il=faces.length/3;il>i;i++){var aoffset=3*i,boffset=3*i+1,coffset=3*i+2;for(flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[boffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[coffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[aoffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[coffset]),flagvert=!0,j=0;j<vertdeg[0][faces[coffset]];j++)if(faces[aoffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[coffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[boffset])}var wt=1,wt2=.5;for(k=0;numiter>k;k++){for(i=0,il=verts.length;il>i;i++)if(vertdeg[0][i]<3)tps[i].x=verts[i].x,tps[i].y=verts[i].y,tps[i].z=verts[i].z;else if(3==vertdeg[0][i]||4==vertdeg[0][i]){for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt2*verts[i].x,tps[i].y+=wt2*verts[i].y,tps[i].z+=wt2*verts[i].z,tps[i].x/=wt2+vertdeg[0][i],tps[i].y/=wt2+vertdeg[0][i],tps[i].z/=wt2+vertdeg[0][i]}else{for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt*verts[i].x,tps[i].y+=wt*verts[i].y,tps[i].z+=wt*verts[i].z,tps[i].x/=wt+vertdeg[0][i],tps[i].y/=wt+vertdeg[0][i],tps[i].z/=wt+vertdeg[0][i]}for(i=0,il=verts.length;il>i;i++)verts[i].x=tps[i].x,verts[i].y=tps[i].y,verts[i].z=tps[i].z}},edgeTable=new Uint32Array([0,0,0,0,0,0,0,2816,0,0,0,1792,0,3328,3584,3840,0,0,0,138,0,21,0,134,0,0,0,652,0,2067,3865,3600,0,0,0,42,0,0,0,294,0,0,21,28,0,3875,1049,3360,0,168,162,170,0,645,2475,2210,0,687,293,172,4010,3747,3497,3232,0,0,0,0,0,69,0,900,0,0,0,1792,138,131,1608,1920,0,81,0,2074,84,85,84,86,0,81,0,3676,330,1105,1881,1616,0,0,0,42,0,69,0,502,0,0,21,3580,138,2035,1273,1520,2816,104,2337,106,840,581,367,102,2816,3695,3429,3180,1898,1635,1385,1120,0,0,0,0,0,0,0,3910,0,0,69,588,42,2083,41,2880,0,0,0,1722,0,2293,4095,3830,0,255,757,764,2538,2291,3065,2800,0,0,81,338,0,3925,1119,3414,84,855,85,340,2130,2899,89,2384,1792,712,194,1162,4036,3781,3535,3270,708,719,197,204,3018,2755,2505,2240,0,0,0,0,168,420,168,1958,162,162,676,2988,170,163,680,928,3328,3096,3328,3642,52,53,1855,1590,2340,2111,2869,2620,298,51,825,560,3584,3584,3090,3482,1668,1941,1183,1430,146,2975,2069,2460,154,915,153,400,3840,3592,3329,3082,1796,1541,1295,1030,2818,2575,2309,2060,778,515,265,0]),triTable=[[],[],[],[],[],[],[],[11,9,8],[],[],[],[8,10,9],[],[10,8,11],[9,11,10],[8,10,9,8,11,10],[],[],[],[1,7,3],[],[4,2,0],[],[2,1,7],[],[],[],[2,7,3,2,9,7],[],[1,4,11,1,0,4],[3,8,0,11,9,4,11,10,9],[4,11,9,11,10,9],[],[],[],[5,3,1],[],[],[],[2,5,8,2,1,5],[],[],[2,4,0],[3,2,4],[],[0,9,1,8,10,5,8,11,10],[3,4,0,3,10,4],[5,8,10,8,11,10],[],[3,5,7],[7,1,5],[1,7,3,1,5,7],[],[9,2,0,9,7,2],[0,3,8,1,7,11,1,5,7],[11,1,7,1,5,7],[],[9,1,0,5,3,2,5,7,3],[8,2,5,8,0,2],[2,5,3,5,7,3],[3,9,1,3,8,9,7,11,10,7,10,5],[9,1,0,10,7,11,10,5,7],[3,8,0,7,10,5,7,11,10],[11,5,7,11,10,5],[],[],[],[],[],[0,6,2],[],[7,2,9,7,9,8],[],[],[],[8,10,9],[7,1,3],[7,1,0],[6,9,3,6,10,9],[7,10,8,10,9,8],[],[6,0,4],[],[11,1,4,11,3,1],[2,4,6],[2,0,4,2,4,6],[2,4,6],[1,4,2,4,6,2],[],[6,0,4],[],[2,11,3,6,9,4,6,10,9],[8,6,1,8,1,3],[10,0,6,0,4,6],[8,0,3,9,6,10,9,4,6],[10,4,6,10,9,4],[],[],[],[5,3,1],[],[0,6,2],[],[7,4,8,5,2,1,5,6,2],[],[],[2,4,0],[7,4,8,2,11,3,10,5,6],[7,1,3],[5,6,10,0,9,1,8,7,4],[5,6,10,7,0,3,7,4,0],[10,5,6,4,8,7],[9,11,8],[3,5,6],[0,5,11,0,11,8],[6,3,5,3,1,5],[3,9,6,3,8,9],[9,6,0,6,2,0],[0,3,8,2,5,6,2,1,5],[1,6,2,1,5,6],[9,11,8],[1,0,9,6,10,5,11,3,2],[6,10,5,2,8,0,2,11,8],[3,2,11,10,5,6],[10,5,6,9,3,8,9,1,3],[0,9,1,5,6,10],[8,0,3,10,5,6],[10,5,6],[],[],[],[],[],[],[],[1,10,2,9,11,6,9,8,11],[],[],[6,0,2],[3,6,9,3,2,6],[3,5,1],[0,5,1,0,11,5],[0,3,5],[6,9,11,9,8,11],[],[],[],[4,5,9,7,1,10,7,3,1],[],[11,6,7,2,4,5,2,0,4],[11,6,7,8,0,3,1,10,2,9,4,5],[6,7,11,1,10,2,9,4,5],[],[4,1,0,4,5,1,6,7,3,6,3,2],[9,4,5,0,6,7,0,2,6],[4,5,9,6,3,2,6,7,3],[6,7,11,5,3,8,5,1,3],[6,7,11,4,1,0,4,5,1],[4,5,9,3,8,0,11,6,7],[9,4,5,7,11,6],[],[],[0,6,4],[8,6,4,8,1,6],[],[0,10,2,0,9,10,4,8,11,4,11,6],[10,2,1,6,0,3,6,4,0],[10,2,1,11,4,8,11,6,4],[4,2,6],[1,0,9,2,4,8,2,6,4],[2,4,0,2,6,4],[8,2,4,2,6,4],[11,4,1,11,6,4],[0,9,1,4,11,6,4,8,11],[3,6,0,6,4,0],[8,6,4,8,11,6],[10,8,9],[6,3,9,6,7,3],[6,7,1],[10,7,1,7,3,1],[7,11,6,8,10,2,8,9,10],[11,6,7,10,0,9,10,2,0],[2,1,10,7,11,6,8,0,3],[1,10,2,6,7,11],[7,2,6,7,9,2],[1,0,9,3,6,7,3,2,6],[7,0,6,0,2,6],[2,7,3,2,6,7],[7,11,6,3,9,1,3,8,9],[9,1,0,11,6,7],[0,3,8,11,6,7],[11,6,7],[],[],[],[],[5,3,7],[8,5,2,8,7,5],[5,3,7],[1,10,2,5,8,7,5,9,8],[1,7,5],[1,7,5],[9,2,7,9,7,5],[11,3,2,8,5,9,8,7,5],[1,3,7,1,7,5],[0,7,1,7,5,1],[9,3,5,3,7,5],[9,7,5,9,8,7],[8,10,11],[3,4,10,3,10,11],[8,10,11],[5,9,4,1,11,3,1,10,11],[2,4,5],[5,2,4,2,0,4],[0,3,8,5,9,4,10,2,1],[2,1,10,9,4,5],[2,8,5,2,11,8],[3,2,11,1,4,5,1,0,4],[9,4,5,8,2,11,8,0,2],[11,3,2,9,4,5],[8,5,3,5,1,3],[5,0,4,5,1,0],[3,8,0,4,5,9],[9,4,5],[11,9,10],[11,9,10],[1,11,4,1,10,11],[8,7,4,11,1,10,11,3,1],[2,7,9,2,9,10],[4,8,7,0,10,2,0,9,10],[2,1,10,0,7,4,0,3,7],[10,2,1,8,7,4],[1,7,4],[3,2,11,4,8,7,9,1,0],[11,4,2,4,0,2],[2,11,3,7,4,8],[4,1,7,1,3,7],[1,0,9,8,7,4],[3,4,0,3,7,4],[8,7,4],[8,9,10,8,10,11],[3,9,11,9,10,11],[0,10,8,10,11,8],[10,3,1,10,11,3],[2,8,10,8,9,10],[9,2,0,9,10,2],[8,0,3,1,10,2],[10,2,1],[1,11,9,11,8,9],[11,3,2,0,9,1],[11,0,2,11,8,0],[11,3,2],[8,1,3,8,9,1],[9,1,0],[8,0,3],[]]';
+    }
 
-$3Dmol.SurfaceWorker = window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type: 'text/javascript'}));
+    function setupLights(program, lights) {
+        var l, ll, light, n, r = 0, g = 0, b = 0, color, position, intensity, distance,
 
-$3Dmol['workerString'] = $3Dmol.workerString;
-$3Dmol['SurfaceWorker'] = $3Dmol.SurfaceWorker;
-//auto-initialization
-//Create embedded viewer from HTML attributes if true
+        zlights = _lights,
 
-$(document).ready(function() {
+        dirColors = zlights.directional.colors, dirPositions = zlights.directional.positions,
 
-    if ($(".viewer_3Dmoljs")[0] !== undefined)
-        $3Dmol.autoinit = true;
-        
-    if ($3Dmol.autoinit) { 
-        $3Dmol.viewers = {};
-        var nviewers = 0;
-        $(".viewer_3Dmoljs").each( function() {
-            var viewerdiv = $(this);
-            var datauri = null;
-            
-        
-            var callback = (typeof(window[viewerdiv.data("callback")]) === 'function') ? 
-                    window[viewerdiv.data("callback")] : null;
-            
-            var type = null;
-            if (viewerdiv.data("pdb")) {
-                datauri = "http://www.pdb.org/pdb/files/" + viewerdiv.data("pdb") + ".pdb";
-                type = "pdb";
-            } else if(viewerdiv.data("cid")) {
-                //this doesn't actually work since pubchem does have CORS enabled
-                type = "sdf";
-                datauri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.data("cid") + 
-                "/SDF?record_type=3d";
-            }
-            else if (viewerdiv.data("href"))
-                datauri = viewerdiv.data("href");
-                
-            var bgcolor = Number(viewerdiv.data("backgroundcolor")) || 0x000000;
-            var style = {line:{}};
-            if(viewerdiv.data("style")) style = $3Dmol.specStringToObject(viewerdiv.data("style"));
-            var select = {};
-            if(viewerdiv.data("select")) select = $3Dmol.specStringToObject(viewerdiv.data("select"));
-            var selectstylelist = [];
-            var surfaces = [];
-            var labels = [];
-            var d = viewerdiv.data();
-            
-            //let users specify individual but matching select/style tags, eg.
-            //data-select1 data-style1
-            var stylere = /style(.+)/;
-            var surfre = /surface(.*)/;
-            var reslabre = /labelres(.*)/;
-            var keys = [];
-            for(var dataname in d) {
-                if(d.hasOwnProperty(dataname)) {
-                    keys.push(dataname);
-                }
-            }
-            keys.sort();
-            for(var i = 0; i < keys.length; i++) {
-                var dataname = keys[i];
-                var m = stylere.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    selectstylelist.push([newsel,styleobj]);
-                }         
-                m = surfre.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    surfaces.push([newsel,styleobj]);
-                }
-                m = reslabre.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    labels.push([newsel,styleobj]);
-                }
-            }
-            
-            try {
-                var glviewer = $3Dmol.viewers[this.id || nviewers++] = $3Dmol.createViewer(viewerdiv, {defaultcolors: $3Dmol.rasmolElementColors, callback: function(viewer) {            
-                    viewer.setBackgroundColor(bgcolor);            
-                }});
-            } catch ( error ) {
-                //for autoload, provide a useful error message
-                window.location = "http://get.webgl.org";                    
-            }
-            
-            
-            if (datauri) {  
-                
-                type = viewerdiv.data("type") || viewerdiv.data("datatype") || type;
-                if(!type) {
-                    type = datauri.substr(datauri.lastIndexOf('.')+1);
-                }
-                                
-                $.get(datauri, function(ret) {
-                    glviewer.addModel(ret, type);
-                    glviewer.setStyle(select,style);
-                    for(var i = 0; i < selectstylelist.length; i++) {
-                        var sel = selectstylelist[i][0] || {};
-                        var sty = selectstylelist[i][1] || {"line":{}}
-                        glviewer.setStyle(sel, sty);
-                    }
-                    for(var i = 0; i < surfaces.length; i++) {
-                        var sel = surfaces[i][0] || {};
-                        var sty = surfaces[i][1] || {}
-                        glviewer.addSurface($3Dmol.SurfaceType.VDW, sty, sel, sel);
-                    }
-                    for(var i = 0; i < labels.length; i++) {
-                        var sel = labels[i][0] || {};
-                        var sty = labels[i][1] || {}
-                        glviewer.addResLabels(sel, sty);
-                    }
-                    // Allowing us to fire callback after viewer has added model
-                    if (callback) 
-                        callback(glviewer);                    
-                    
-                    glviewer.zoomTo();
-                    glviewer.render();          
-                    
-                }, 'text');
-           
-            }
-            
-            else {
-                
-                if (viewerdiv.data("element")) {
-                    var moldata = $("#" + viewerdiv.data("element")).val() || "";
-                    var type = viewerdiv.data("type") || viewerdiv.data("datatype");
+        dirCount = 0, dirLength = 0, dirOffset = 0;
 
-                    if (!type){
+        for (l = 0, ll = lights.length; l < ll; l++) {
 
-                        console.log("Warning: No type specified for embedded viewer with moldata from " + viewerdiv.data("element") +
-                                    "\n assuming type 'pdb'")
+            light = lights[l];
 
-                        type = 'pdb';
-                    }
+            color = light.color;
+            intensity = light.intensity;
+            distance = light.distance;
 
-                    glviewer.addModel(moldata, type);
-                    glviewer.setStyle(select, style);
-                    for(var i = 0; i < selectstylelist.length; i++) {
-                        var sel = selectstylelist[i][0] || {};
-                        var sty = selectstylelist[i][1] || {"line":{}}
-                        glviewer.setStyle(sel, sty);
-                    }                
-                }
+            if (light instanceof $3Dmol.Light) {
 
+                dirCount++;
 
-                if (callback) 
-                    callback(glviewer);
-                
-                glviewer.zoomTo();
-                glviewer.render();
+                _direction.getPositionFromMatrix(light.matrixWorld);
+                _vector3.getPositionFromMatrix(light.target.matrixWorld);
+                _direction.sub(_vector3);
+                _direction.normalize();
+
+                if (_direction.x === 0 && _direction.y === 0
+                        && _direction.z === 0)
+                    continue;
+
+                dirPositions[dirOffset] = _direction.x;
+                dirPositions[dirOffset + 1] = _direction.y;
+                dirPositions[dirOffset + 2] = _direction.z;
+
+                dirColors[dirOffset] = color.r * intensity;
+                dirColors[dirOffset + 1] = color.g * intensity;
+                dirColors[dirOffset + 2] = color.b * intensity;
+
+                dirOffset += 3;
+
+                dirLength++;
             }
-            
-        });              
+
+        }
+
+        zlights.ambient[0] = r;
+        zlights.ambient[1] = g;
+        zlights.ambient[2] = b;
+        zlights.directional.length = dirLength;
     }
-});
-    
 
+    function initGL() {
 
-// in an attempt to reduce memory overhead, cache all $3Dmol.Colors
-// this makes things a little faster
-$3Dmol.CC = {
-    cache : {},
-    color : function(hex) {
+        try {
 
-        if(typeof(this.cache[hex]) !== "undefined") {
-            return this.cache[hex];
-        }
-        else {
-            hex = this.getHex(hex);
-            var c = new $3Dmol.Color(hex);
-            this.cache[hex] = c;
-            return c;
+            if (!(_gl = _canvas.getContext('experimental-webgl', {
+                alpha : _alpha,
+                premultipliedAlpha : _premultipliedAlpha,
+                antialias : _antialias,
+                stencil : _stencil,
+                preserveDrawingBuffer : _preserveDrawingBuffer
+            }))) {
+                if (!(_gl = _canvas.getContext('webgl', {
+                    alpha : _alpha,
+                    premultipliedAlpha : _premultipliedAlpha,
+                    antialias : _antialias,
+                    stencil : _stencil,
+                    preserveDrawingBuffer : _preserveDrawingBuffer
+                }))) {
+                    throw 'Error creating WebGL context.';
+                }
+            }
+
+        } catch (error) {
+
+            console.error(error);
         }
-    },
-    colorTab : {
-        'white' : 0xFFFFFF,
-        'silver' : 0xC0C0C0,
-        'gray' : 0x808080,
-        'grey' : 0x808080,
-        'black' : 0x000000,
-        'red' : 0xFF0000,
-        'maroon' : 0x800000,
-        'yellow' : 0xFFFF00,
-        'orange' : 0xFF6600,
-        'olive' : 0x808000,
-        'lime' : 0x00FF00,
-        'green' : 0x008000,
-        'aqua' : 0x00FFFF,
-        'cyan' : 0x00FFFF,
-        'teal' : 0x008080,
-        'blue' : 0x0000FF,
-        'navy' : 0x000080,
-        'fuchsia' : 0xFF00FF,
-        'magenta' : 0xFF00FF,
-        'purple' : 0x800080
-    },    
-    getHex : function(hex) {
-        if (parseInt(hex))
-            return parseInt(hex);
+    }
+
+    function setDefaultGLState() {
+
+        _gl.clearColor(0, 0, 0, 1);
+        _gl.clearDepth(1);
+        _gl.clearStencil(0);
+
+        _gl.enable(_gl.DEPTH_TEST);
+        _gl.depthFunc(_gl.LEQUAL);
+
+        _gl.frontFace(_gl.CCW);
+        _gl.cullFace(_gl.BACK);
+        _gl.enable(_gl.CULL_FACE);
+
+        _gl.enable(_gl.BLEND);
+        _gl.blendEquation(_gl.FUNC_ADD);
+        _gl.blendFunc(_gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA);
+
+        _gl.clearColor(_clearColor.r, _clearColor.g, _clearColor.b,
+                        _clearAlpha);
+    }
+
+    this.addPostPlugin(new $3Dmol.SpritePlugin());
+
+};
+/*
+ * Scene class
+ */
+/** @constructor */
+$3Dmol.Scene = function() {
+    
+    $3Dmol.Object3D.call(this);
+    
+    this.fog = null;
+    
+    //May not need...
+    this.overrideMaterial = null;
+    
+    this.matrixAutoUpdate = false;
+    
+    this.__objects = [];
+    this.__lights = [];
+    
+    this.__objectsAdded = [];
+    this.__objectsRemoved = [];
+    
+};
+
+$3Dmol.Scene.prototype = Object.create($3Dmol.Object3D.prototype);
+
+$3Dmol.Scene.prototype.__addObject = function(object) {
+    
+    //Directional Lighting
+    if (object instanceof $3Dmol.Light) {
         
-        else if (typeof(hex) === 'string') {
+        if (this.__lights.indexOf(object) === -1)
+            this.__lights.push(object);
+        
+        //TODO: Do I need this??
+        if (object.target && object.target.parent === undefined)
+            this.add(object.target);
             
-            return this.colorTab[hex.trim().toLowerCase()] || 0x000000;
+    }
+    
+    //Rotation group
+    else {
+        
+        if (this.__objects.indexOf(object) === -1) {
+            
+            this.__objects.push(object);
+            this.__objectsAdded.push(object);
+            
+            //Check if previously removed
+            
+            var idx = this.__objectsRemoved.indexOf(object);
+            
+            if (idx !== -1)
+                this.__objectsRemoved.splice(i, 1);
+                
         }
+    }
+    
+    //Add object's children
+    
+    for (var i = 0; i < object.children.length; i++) 
+        this.__addObject(object.children[i]);
+    
+};
+
+$3Dmol.Scene.prototype.__removeObject = function(object) {
+    
+    var idx;
+    if (object instanceof $3Dmol.Light) {
+        
+        idx = this.__lights.indexOf(object);
+        
+        if (idx !== -1)
+            this.__lights.splice(idx, 1);
+            
+    }
+    
+    //Object3D
+    else {
+        
+        idx = this.__objects.indexOf(object);
         
+        if (idx !== -1) {
+            
+            this.__objects.splice(idx, 1);
+            this.__objectsRemoved.push(object);
+            
+            //Check if previously added
+            
+            var ai = this.__objectsAdded.indexOf(object);
+            
+            if (ai !== -1) 
+                this.__objectsAdded.splice(idx, 1);
+                
+        }
+    
     }
     
+    //Remove object's children
+    for (var i = 0; i < object.children.length; i++)
+        this.__removeObject(object.children[i]);
+    
 };
 
 
-$3Dmol['CC'] = $3Dmol.CC;
-$3Dmol['CC']['color'] = $3Dmol.CC.color;
+/*
+ * Fog Class
+ */
 
+/** @constructor */
+$3Dmol.Fog = function ( hex, near, far ) {
 
+    this.name = '';
 
-/** Return proper color for atom given style
- * @param {AtomSpec} atom
- * @param {AtomStyle} style
- * @return {$3Dmol.Color}
- */
-$3Dmol.getColorFromStyle = function(atom, style) {
-    var color = atom.color;
-    if (typeof (style.color) != "undefined" && style.color != "spectrum")
-        color = style.color;
-    if(typeof(style.colorscheme) != "undefined") {
-        if(typeof($3Dmol.elementColors[style.colorscheme]) != "undefined") {
-            //name of builtin colorscheme
-            var scheme = $3Dmol.elementColors[style.colorscheme];
-            if(typeof(scheme[atom.elem]) != "undefined") {
-                color = scheme[atom.elem];
-            }
-        } else if(typeof(style.colorscheme[atom.elem]) != 'undefined') {
-            //actual color scheme provided
-            color = style.colorscheme[atom.elem];
-        }
-    }
-    var C = $3Dmol.CC.color(color);
-    return C;
-}
+    this.color = new $3Dmol.Color( hex );
 
-/** Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
- * @struct
- */
-$3Dmol.elementColors = $3Dmol.elementColors || {};
+    this.near = ( near !== undefined ) ? near : 1;
+    this.far = ( far !== undefined ) ? far : 1000;
 
-$3Dmol.elementColors.defaultColor = 0xff1493;
+};
+
+$3Dmol.Fog.prototype.clone = function () {
+
+    return new $3Dmol.Fog( this.color.getHex(), this.near, this.far );
 
-/** @property Jmol-like element colors*/
-$3Dmol.elementColors.Jmol = {
-        'H': 0xFFFFFF,
-        'He': 0xD9FFFF,
-        'HE': 0xD9FFFF,
-        'Li': 0xCC80FF,
-        'LI': 0xCC80FF,
-        'B': 0xFFB5B5,
-        'C': 0x909090,
-        'N': 0x3050F8,
-        'O': 0xFF0D0D,
-        'F': 0x90E050,
-        'Na': 0xAB5CF2,
-        'NA': 0xAB5CF2,
-        'Mg': 0x8AFF00,
-        'MG': 0x8AFF00,
-        'Al': 0xBFA6A6,
-        'AL': 0xBFA6A6,
-        'Si': 0xF0C8A0,
-        'SI': 0xF0C8A0,
-        'P': 0xFF8000,
-        'S': 0xFFFF30,
-        'Cl': 0x1FF01F,
-        'CL': 0x1FF01F,
-        'Ca': 0x3DFF00,
-        'CA': 0x3DFF00,
-        'Ti': 0xBFC2C7,
-        'TI': 0xBFC2C7,
-        'Cr': 0x8A99C7,
-        'CR': 0x8A99C7,
-        'Mn': 0x9C7AC7,
-        'MN': 0x9C7AC7,
-        'Fe': 0xE06633,
-        'FE': 0xE06633,
-        'Ni': 0x50D050,
-        'NI': 0x50D050,
-        'Cu': 0xC88033,
-        'CU': 0xC88033,
-        'Zn': 0x7D80B0,
-        'ZN': 0x7D80B0,
-        'Br': 0xA62929,
-        'BR': 0xA62929,
-        'Ag': 0xC0C0C0,
-        'AG': 0xC0C0C0,
-        'I': 0x940094,
-        'Ba': 0x00C900,
-        'BA': 0x00C900,
-        'Au': 0xFFD123,
-        'AU': 0xFFD123
 };
 
-/** @property rasmol-like element colors */
-$3Dmol.elementColors.rasmol = {
-        'H': 0xFFFFFF,
-        'He': 0xFFC0CB,
-        'HE': 0xFFC0CB,
-        'Li': 0xB22222,
-        'LI': 0xB22222,
-        'B': 0x00FF00,
-        'C': 0xC8C8C8,
-        'N': 0x8F8FFF,
-        'O': 0xF00000,
-        'F': 0xDAA520,
-        'Na': 0x0000FF,
-        'NA': 0x0000FF,
-        'Mg': 0x228B22,
-        'MG': 0x228B22,
-        'Al': 0x808090,
-        'AL': 0x808090,
-        'Si': 0xDAA520,
-        'SI': 0xDAA520,
-        'P': 0xFFA500,
-        'S': 0xFFC832,
-        'Cl': 0x00FF00,
-        'CL': 0x00FF00,
-        'Ca': 0x808090,
-        'CA': 0x808090,
-        'Ti': 0x808090,
-        'TI': 0x808090,
-        'Cr': 0x808090,
-        'CR': 0x808090,
-        'Mn': 0x808090,
-        'MN': 0x808090,
-        'Fe': 0xFFA500,
-        'FE': 0xFFA500,
-        'Ni': 0xA52A2A,
-        'NI': 0xA52A2A,
-        'Cu': 0xA52A2A,
-        'CU': 0xA52A2A,
-        'Zn': 0xA52A2A,
-        'ZN': 0xA52A2A,
-        'Br': 0xA52A2A,
-        'BR': 0xA52A2A,
-        'Ag': 0x808090,
-        'AG': 0x808090,
-        'I': 0xA020F0,
-        'Ba': 0xFFA500,
-        'BA': 0xFFA500,
-        'Au': 0xDAA520,
-        'AU': 0xDAA520    
+$3Dmol.ShaderUtils = {
+    
+    clone: function ( uniforms_src ) {
+        
+        var u, p, parameter, parameter_src, uniforms_clone = {};
+        
+        for (u in uniforms_src) {
+            uniforms_clone[u] = {};
+            uniforms_clone[u].type = uniforms_src[u].type;
+            
+            var srcValue = uniforms_src[u].value;
+            
+            if (srcValue instanceof $3Dmol.Color)
+                uniforms_clone[u].value = srcValue.clone();
+            else if (typeof srcValue === "number")
+                uniforms_clone[u].value = srcValue;
+            else if (srcValue instanceof Array) 
+                uniforms_clone[u].value = [];
+            else
+                console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform");
+            
+        }
+        
+        return uniforms_clone;
+    },
+    //fragment shader reused by outline shader
+    stickimposterFragmentShader: [
+     "uniform float opacity;",
+     "uniform mat4 projectionMatrix;",
+
+     "uniform vec3 fogColor;",
+     "uniform float fogNear;",
+     "uniform float fogFar;",
+
+     "varying vec3 vLight;",
+     "varying vec3 vColor;",
+     "varying vec3 cposition;",
+     "varying vec3 p1;",
+     "varying vec3 p2;",
+     "varying float r;",
+
+
+     //cylinder-ray intersection testing taken from http://mrl.nyu.edu/~dzorin/cg05/lecture12.pdf
+     //also useful: http://stackoverflow.com/questions/9595300/cylinder-impostor-in-glsl
+     //with a bit more care (caps) this could be a general cylinder imposter (see also outline)
+     "void main() {",   
+     "    vec3 color = abs(vColor);",
+     "    vec3 pos = cposition;",
+     "    vec3 p = pos;", //ray point
+     "    vec3 v = normalize(pos);", //ray normal
+     "    vec3 pa = p1;", //cyl start
+     "    vec3 va = normalize(p2-p1);", //cyl norm
+     "    vec3 tmp1 = v-(dot(v,va)*va);",
+     "    vec3 deltap = p-pa;",
+     "    float A = dot(tmp1,tmp1);",
+     "    if(A == 0.0) discard;",
+     "    vec3 tmp2 = deltap-(dot(deltap,va)*va);",
+     "    float B = 2.0*dot(tmp1, tmp2);",
+     "    float C = dot(tmp2,tmp2)-r*r;",
+     //quadratic equation!
+     "    float det = (B*B) - (4.0*A*C);",
+     "    if(det < 0.0) discard;",
+     "    float sqrtDet = sqrt(det);",
+     "    float posT = (-B+sqrtDet)/(2.0*A);",
+     "    float negT = (-B-sqrtDet)/(2.0*A);",
+     "    float intersectionT = min(posT,negT);",
+     "    vec3 qi = p+v*intersectionT;", 
+     "    float dotp1 = dot(va,qi-p1);",
+     "    float dotp2 = dot(va,qi-p2);",
+     "    vec3 norm;",
+     "    if( dotp1 < 0.0 || dotp2 > 0.0) {", //(p-c)^2 + 2(p-c)vt +v^2+t^2 - r^2 = 0
+     "       vec3 cp;",
+     "       if( dotp1 < 0.0) {" +
+     //"        if(vColor.x < 0.0 ) discard;", //color sign bit indicates if we should cap or not
+     "        cp = p1;",
+     "       } else {",
+     //"          if(vColor.y < 0.0 ) discard;",
+     "          cp = p2;",
+     "       }",
+     "       vec3 diff = p-cp;",
+     "       A = dot(v,v);",
+     "       B = dot(diff,v)*2.0;",
+     "       C = dot(diff,diff)-r*r;",
+     "       det = (B*B) - (4.0*C);",
+     "       if(det < 0.0) discard;",
+     "       sqrtDet = sqrt(det);",
+     "       posT = (-B+sqrtDet)/(2.0);",
+     "       negT = (-B-sqrtDet)/(2.0);",
+     "       float t = min(posT,negT);",
+     "       qi = p+v*t;",
+     "       norm = normalize(qi-cp);",
+     "    } else {",
+     "       norm = normalize(qi-(dotp1*va + p1));",
+     "    }",
+     "    vec4 clipPos = projectionMatrix * vec4(qi, 1.0);",
+     "    float ndcDepth = clipPos.z / clipPos.w;",
+     "    float depth = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+     "    gl_FragDepthEXT = depth;",
+    ].join("\n")  
 };
 
-$3Dmol.elementColors.defaultColors = $3Dmol.elementColors.rasmol;
+$3Dmol.ShaderLib = { 
+    'basic' : {
+        fragmentShader : [                    
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-$3Dmol.elementColors.greenCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-$3Dmol.elementColors.cyanCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
+"varying vec3 vColor;",
 
-$3Dmol.elementColors.magentaCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
+"void main() {",
+    
+"    gl_FragColor = vec4( vColor, opacity );",
+    
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-$3Dmol.elementColors.yellowCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
+"}"
+                                                     
+].join("\n"),
+        
+        vertexShader : [
 
-$3Dmol.elementColors.whiteCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
 
-$3Dmol.elementColors.orangeCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
+"attribute vec3 position;",
+"attribute vec3 color;",
 
-$3Dmol.elementColors.purpleCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
+"varying vec3 vColor;",
 
-$3Dmol.elementColors.blueCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
-//glcartoon.js
-//This contains all the routines for rendering a cartoon given a set
-//of atoms with assigned secondary structure
+"void main() {",
 
-//TODO: generate normals directly in drawStrip and drawThinStrip
+"    vColor = color;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    gl_Position = projectionMatrix * mvPosition;",
 
-var $3Dmol = $3Dmol || {};
+"}"
+        
+].join("\n"),
+    
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000}
+        }
 
+    },
+    
+ 'sphereimposter' : {
+        fragmentShader : [
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
+"uniform mat4 projectionMatrix;",
 
-/**@typedef CartoonStyleSpec
- * @prop {string} color - solid color, may specify as 'spectrum'
- * @prop {string} style - style of cartoon rendering (currently just default and trace)
- * @prop {number} thickness - cartoon strand thickness, default is 0.4
- * In nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which
- * is 'N1' for purines (resn: '  A', '  G', ' DA', ' DG') and 'N3' for pyrimidines (resn: '  C', '  U', ' DC', ' DT').
- * The different nucleobases can therefore be distinguished as follows:
- * @example
- * viewer.setStyle({resn:' DA', atom:'N1'}, {cartoon:{color:'red'}});
- * viewer.setStyle({resn:' DG', atom:'N1'}, {cartoon:{color:'green'}});
- * viewer.setStyle({resn:' DC', atom:'N3'}, {cartoon:{color:'blue'}});
- * viewer.setStyle({resn:' DT', atom:'N3'}, {cartoon:{color:'yellow'}});
- */
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform float uDepth;",
+"uniform vec3 directionalLightColor[ 1 ];",
 
-/**
- * @ignore
- * @param {$3Dmol.Object3D} group
- * @param {AtomSpec} atomlist
- * @param {$3Dmol.Gradient} gradientscheme
- */
-$3Dmol.drawCartoon = (function() {
+"varying vec3 vColor;",
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 vLight;",
+"varying vec3 center;",
 
-    var axisDIV = 5; // 3 still gives acceptable quality
-    var strandDIV = 6;
-    var nucleicAcidStrandDIV = 4;
-    var tubeDIV = 8;
-    var coilWidth = 0.3;
-    var helixSheetWidth = 1.3;
-    var nucleicAcidWidth = 0.8;
-    var defaultThickness = 0.4; 
 
-    // helper functions
+"void main() {",
+"    float lensqr = dot(mapping,mapping);",
+"    float rsqr = rval*rval;",
+"    if(lensqr > rsqr)",
+"       discard;",
+"    float z = sqrt(rsqr-lensqr);",
+"    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z);",
+"    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);",
+"    float ndcDepth = clipPos.z / clipPos.w;",
+"    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+"    vec3 norm = normalize(vec3(mapping.x,mapping.y,z));",
+"    float dotProduct = dot( norm, vLight );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",    
+"    vec3 vLight = directionalLightColor[ 0 ] * directionalLightWeighting;",
+"    gl_FragColor = vec4(vLight*vColor, opacity*opacity );", 
+"    float fogFactor = smoothstep( fogNear, fogFar, gl_FragDepthEXT/gl_FragCoord.w );",
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-    // Catmull-Rom subdivision
-    var subdivide = function(_points, DIV) { // points as Vector3
-        var ret = [];
-        var points = _points;
-        points = []; // Smoothing test
-        points.push(_points[0]);
-        
-        var i, lim, size;
-        var p0, p1, p2, p3, v0, v1;
-        
-        for (i = 1, lim = _points.length - 1; i < lim; i++) {
-            p1 = _points[i]; p2 = _points[i + 1];
-            if (p1.smoothen)
-                points.push(new $3Dmol.Vector3((p1.x + p2.x) / 2, (p1.y + p2.y) / 2,
-                        (p1.z + p2.z) / 2));
-            else
-                points.push(p1);
-        }
-        points.push(_points[_points.length - 1]);
 
+"}"
+                                                     
+].join("\n"),
         
-        for (i = -1, size = points.length; i <= size - 3; i++) {
-            p0 = points[(i === -1) ? 0 : i];
-            p1 = points[i + 1]; p2 = points[i + 2];
-            p3 = points[(i === size - 3) ? size - 1 : i + 3];
-            v0 = new $3Dmol.Vector3().subVectors(p2, p0).multiplyScalar(0.5);
-            v1 = new $3Dmol.Vector3().subVectors(p3, p1).multiplyScalar(0.5);
+        vertexShader : [
 
-            for ( var j = 0; j < DIV; j++) {
-                var t = 1.0 / DIV * j;
-                var x = p1.x + t * v0.x + t * t * 
-                        (-3 * p1.x + 3 * p2.x - 2 * v0.x - v1.x) + t * t * t *
-                        (2 * p1.x - 2 * p2.x + v0.x + v1.x);
-                var y = p1.y + t * v0.y + t * t * 
-                        (-3 * p1.y + 3 * p2.y - 2 * v0.y - v1.y) + t * t * t *
-                        (2 * p1.y - 2 * p2.y + v0.y + v1.y);
-                var z = p1.z + t * v0.z + t * t * 
-                        (-3 * p1.z + 3 * p2.z - 2 * v0.z - v1.z) + t * t * t * 
-                        (2 * p1.z - 2 * p2.z + v0.z + v1.z);
-                        
-                var pt = new $3Dmol.Vector3(x, y, z);
-                
-                var atomIndex = Math.floor( (ret.length+2) / DIV);
-                
-                if (_points[atomIndex] !== undefined && _points[atomIndex].atom !== undefined)
-                    pt.atom = _points[atomIndex].atom;
-                    
-                ret.push(pt);
-            }
-        }
-        ret.push(points[points.length - 1]);
-        return ret;
-    };
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-    var drawThinStrip = function(group, p1, p2, colors, div) {
-    
-        var geo = new $3Dmol.Geometry(true);       
-        var offset, vertoffset;
-        var color;
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-        
-        for ( var i = 0, lim = p1.length; i < lim; i++) {
-            
-            color = $3Dmol.CC.color(colors[Math.round((i - 1) / div)]);
-           
-            geoGroup = geo.updateGeoGroup(2);
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var faceArray = geoGroup.faceArray;
-            offset = geoGroup.vertices; vertoffset = offset*3;
-            
-            vertexArray[vertoffset] = p1[i].x;
-            vertexArray[vertoffset+1] = p1[i].y;
-            vertexArray[vertoffset+2] = p1[i].z;
-            
-            vertexArray[vertoffset+3] = p2[i].x;
-            vertexArray[vertoffset+4] = p2[i].y;
-            vertexArray[vertoffset+5] = p2[i].z;
-            
-            for (var j = 0; j < 6; ++j) {                
-                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
-            }            
-           
-            if (i > 0) {
-                var faces = [offset, offset + 1, offset - 1, offset - 2];
-                var faceoffset = geoGroup.faceidx;
-                
-                faceArray[faceoffset] = faces[0]; faceArray[faceoffset+1] = faces[1]; faceArray[faceoffset+2] = faces[3];
-                faceArray[faceoffset+3] = faces[1]; faceArray[faceoffset+4] = faces[2]; faceArray[faceoffset+5] = faces[3];
+"varying vec2 mapping;",
+"varying vec3 vColor;",
+"varying float rval;",
+"varying vec3 vLight;",
+"varying vec3 center;",
 
-                geoGroup.faceidx += 6;
-            }
-            
-            geoGroup.vertices += 2;
-        }
-        
-        geo.initTypedArrays();
-        geo.setUpNormals();
-        
-        var material = new $3Dmol.MeshLambertMaterial();
-        material.vertexColors = $3Dmol.FaceColors;
-                material.side = $3Dmol.DoubleSide;
-        var mesh = new $3Dmol.Mesh(geo, material);
-        group.add(mesh);
-    };
+"void main() {",
 
-    var drawStrip = function(group, p1, p2, colors, div, thickness) {
-        if ((p1.length) < 2)
-            return;
-        div = div || axisDIV;
-        p1 = subdivide(p1, div);
-        p2 = subdivide(p2, div);
-        if (!thickness)
-            return drawThinStrip(group, p1, p2, colors, div);
+"    vColor = color;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    center = mvPosition.xyz;",
+"    vec4 projPosition = projectionMatrix * mvPosition;",
+"    vec4 adjust = projectionMatrix* vec4(normal,0.0); adjust.z = 0.0; adjust.w = 0.0;",
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vLight = normalize( lDirection.xyz );",
+"    mapping = normal.xy;",
+"    rval = abs(normal.x);",
+"    gl_Position = projPosition+adjust;",
 
-        var geo = new $3Dmol.Geometry(true);
+"}"
         
-        //var vs = geo.vertices, fs = geo.faces;
-                var vs = [], fs = [];
-        var axis, p1v, p2v, a1v, a2v;
-        
-        var faces = [ [ 0, 2, -6, -8 ], [ -4, -2, 6, 4 ], [ 7, -1, -5, 3 ],
-                [ -3, 5, 1, -7 ] ];
-                
-        var offset, vertoffset, faceoffset;
-        var color;
-        var currentAtom, lastAtom;
-        var i, lim, j;
-        var face1, face2, face3;
-        var geoGroup;
-        
-        for (i = 0, lim = p1.length; i < lim; i++) {
-        
-            color = $3Dmol.CC.color(colors[Math.round((i - 1) / div)]);
-            
-            vs.push(p1v = p1[i]); // 0
-            vs.push(p1v); // 1
-            vs.push(p2v = p2[i]); // 2
-            vs.push(p2v); // 3
-            if (i < lim - 1) {
-                var toNext = p1[i + 1].clone().sub(p1[i]);
-                var toSide = p2[i].clone().sub(p1[i]);
-                axis = toSide.cross(toNext).normalize().multiplyScalar(
-                        thickness);
-            }
-            vs.push(a1v = p1[i].clone().add(axis)); // 4
-            vs.push(a1v); // 5
-            vs.push(a2v = p2[i].clone().add(axis)); // 6
-            vs.push(a2v); // 7
-            
-            if (p1v.atom !== undefined)
-                currentAtom = p1v.atom;
-            
-            geoGroup = geo.updateGeoGroup(8);
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var faceArray = geoGroup.faceArray;
-            offset = geoGroup.vertices; vertoffset = offset*3;
-            
-            vertexArray[vertoffset] = p1v.x; vertexArray[vertoffset+1] = p1v.y; vertexArray[vertoffset+2] = p1v.z;
-            vertexArray[vertoffset+3] = p1v.x; vertexArray[vertoffset+4] = p1v.y; vertexArray[vertoffset+5] = p1v.z;
-            vertexArray[vertoffset+6] = p2v.x; vertexArray[vertoffset+7] = p2v.y; vertexArray[vertoffset+8] = p2v.z;
-            vertexArray[vertoffset+9] = p2v.x; vertexArray[vertoffset+10] = p2v.y; vertexArray[vertoffset+11] = p2v.z;
-            vertexArray[vertoffset+12] = a1v.x; vertexArray[vertoffset+13] = a1v.y; vertexArray[vertoffset+14] = a1v.z;
-            vertexArray[vertoffset+15] = a1v.x; vertexArray[vertoffset+16] = a1v.y; vertexArray[vertoffset+17] = a1v.z;
-            vertexArray[vertoffset+18] = a2v.x; vertexArray[vertoffset+19] = a2v.y; vertexArray[vertoffset+20] = a2v.z;
-            vertexArray[vertoffset+21] = a2v.x; vertexArray[vertoffset+22] = a2v.y; vertexArray[vertoffset+23] = a2v.z;
-            
-            for (j = 0; j < 8; ++j) {                
-                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
-            }
-            
-            if (i > 0) {
-             
-                //both points have distinct atoms
-                var diffAtoms = ((lastAtom !== undefined && currentAtom !== undefined) && lastAtom.serial !== currentAtom.serial);
-                
-                for (j = 0; j < 4; j++ ) {
-                
-                    var face = [offset + faces[j][0], offset + faces[j][1], offset + faces[j][2], offset + faces[j][3]];
-                    
-                    faceoffset = geoGroup.faceidx;    
-                    
-                    faceArray[faceoffset] = face[0]; faceArray[faceoffset+1] = face[1]; faceArray[faceoffset+2] = face[3];
-                    faceArray[faceoffset+3] = face[1]; faceArray[faceoffset+4] = face[2]; faceArray[faceoffset+5] = face[3];
-                    
-                    geoGroup.faceidx += 6;
-                    
-                    if (currentAtom.clickable || lastAtom.clickable) {
-                        
-                        var p1a = vs[face[3]].clone(), p1b = vs[face[0]].clone(),
-                            p2a = vs[face[2]].clone(), p2b = vs[face[1]].clone();
-                        
-                        p1a.atom = vs[face[3]].atom || null; //should be same
-                        p2a.atom = vs[face[2]].atom || null; 
-                        
-                        
-                        p1b.atom = vs[face[0]].atom || null; //should be same                      
-                        p2b.atom = vs[face[1]].atom || null; 
-                        
-                        if (diffAtoms) {
-                            var m1 = p1a.clone().add(p1b).multiplyScalar(0.5);
-                            var m2 = p2a.clone().add(p2b).multiplyScalar(0.5);
-                            var m = p1a.clone().add(p2b).multiplyScalar(0.5);
-                            
-                            if (j % 2 === 0)
-                            {
-                                if (lastAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
-                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
-                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
-                                    lastAtom.intersectionShape.triangle.push(face1);
-                                    lastAtom.intersectionShape.triangle.push(face2);
-                                    lastAtom.intersectionShape.triangle.push(face3);
-                                }
-                                
-                                if (currentAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
-                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
-                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
-                                    currentAtom.intersectionShape.triangle.push(face1);
-                                    currentAtom.intersectionShape.triangle.push(face2);
-                                    currentAtom.intersectionShape.triangle.push(face3);
-                                }
-                            }
-                            else {
-                                if (currentAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
-                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
-                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
-                                    currentAtom.intersectionShape.triangle.push(face1);
-                                    currentAtom.intersectionShape.triangle.push(face2);
-                                    currentAtom.intersectionShape.triangle.push(face3);
-                                }
-                                
-                                if (lastAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
-                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
-                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
-                                    lastAtom.intersectionShape.triangle.push(face1);
-                                    lastAtom.intersectionShape.triangle.push(face2);
-                                    lastAtom.intersectionShape.triangle.push(face3);
-                                }                          
-                            }
-                            
-                        }
-                        
-                        //face for single atom
-                        else if (currentAtom.clickable) {
-                            face1 = new $3Dmol.Triangle(p1b, p2b, p1a);
-                            face2 = new $3Dmol.Triangle(p2b, p2a, p1a);
-                            currentAtom.intersectionShape.triangle.push(face1);
-                            currentAtom.intersectionShape.triangle.push(face2);
-                        }
-                        
-                    }
-                    
-                }
-            }
-            
-            geoGroup.vertices += 8;
-            lastAtom = currentAtom;
+].join("\n"),
+    
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
         }
-        
-
-        var vsize = vs.length - 8; // Cap
-        
-        geoGroup = geo.updateGeoGroup(8);
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        offset = geoGroup.vertices; vertoffset = offset*3; faceoffset = geoGroup.faceidx;
-        
-        for (i = 0; i < 4; i++) {
-            vs.push(vs[i * 2]);
-            vs.push(vs[vsize + i * 2]);
-            
-            var v1 = vs[i * 2], v2 = vs[vsize + i * 2];
-            
-            vertexArray[vertoffset+6*i] = v1.x; vertexArray[vertoffset+1+6*i] = v1.y; vertexArray[vertoffset+2+6*i] = v1.z;
-            vertexArray[vertoffset+3+6*i] = v2.x; vertexArray[vertoffset+4+6*i] = v2.y; vertexArray[vertoffset+5+6*i] = v2.z;
-            
-            colorArray[vertoffset+6*i] = color.r; colorArray[vertoffset+1+6*i] = color.g; colorArray[vertoffset+2+6*i] = color.b;
-            colorArray[vertoffset+3+6*i] = color.r; colorArray[vertoffset+4+6*i] = color.g; colorArray[vertoffset+5+6*i] = color.b;
 
-        }
-        
-        vsize += 8;
-                
-        face1 = [offset, offset + 2, offset + 6, offset + 4];
-        face2 = [offset + 1, offset + 5, offset + 7, offset + 3];
-        
-        faceArray[faceoffset] = face1[0]; faceArray[faceoffset+1] = face1[1]; faceArray[faceoffset+2] = face1[3];
-        faceArray[faceoffset+3] = face1[1]; faceArray[faceoffset+4] = face1[2]; faceArray[faceoffset+5] = face1[3];
-        faceArray[faceoffset+6] = face2[0]; faceArray[faceoffset+7] = face2[1]; faceArray[faceoffset+8] = face2[3];
-        faceArray[faceoffset+9] = face2[1]; faceArray[faceoffset+10] = face2[2]; faceArray[faceoffset+11] = face2[3];
-        
-        geoGroup.faceidx += 12;
-        geoGroup.vertices += 8;
-        
-        //TODO: Add intersection planes for caps
-        
-        geo.initTypedArrays();
-        geo.setUpNormals();
-        
-        var material = new $3Dmol.MeshLambertMaterial();
-        material.vertexColors = $3Dmol.FaceColors;
-        material.side = $3Dmol.DoubleSide;
-        var mesh = new $3Dmol.Mesh(geo, material);
-        group.add(mesh);
-        
-    };
+    },
+    
+    
+    'lambert' : { 
+        fragmentShader : [
 
-    //TODO: Need to update this (will we ever use this?)
-    var drawSmoothCurve = function(group, _points, width, colors, div) {
-        if (_points.length === 0)
-            return;
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-        div = (div === undefined) ? 5 : div;
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-        var geo = new $3Dmol.Geometry();
-        var points = subdivide(_points, div);
-                /*
-        for ( var i = 0; i < points.length; i++) {
-            geo.vertices.push(points[i]);
-            geo.colors.push($3Dmol.color(colors[(i == 0) ? 0 : Math.round((i - 1)
-                    / div)]));
-        }
-                */
-        var lineMaterial = new $3Dmol.LineBasicMaterial({
-            linewidth : width
-        });
-        lineMaterial.vertexColors = true;
-        var line = new $3Dmol.Line(geo, lineMaterial);
-        line.type = $3Dmol.LineStrip;
-        group.add(line);
-    };
+"varying vec3 vLightFront;",
+"varying vec3 vColor;",
 
-    var drawStrand = function(group, atomList, num, div, fill, coilWidth, helixSheetWidth, doNotSmoothen, gradientScheme, geo)
-    {
-        num = num || strandDIV;
-        div = div || axisDIV;
-        doNotSmoothen = !!(doNotSmoothen);
+"void main() {",
+    
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    
+"    #ifndef WIREFRAME",
+"    gl_FragColor.xyz *= vLightFront;",
+"    #endif",
+    
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-                        //  proteins    na backbone  na terminus                  nucleobases
-        var cartoonAtoms = ["CA", "O",  "P", "OP2",  "O5'", "O3'", "C5'", "C2'",  "N1", "N3"];
-        var purResns = [" DA", " DG", "  A", "  G"];
-        var pyrResns = [" DT", " DC", "  U", "  C"];
+"}"
 
-        var cartoon, curr, next, currColor, nextColor, thickness, i;
-        var backbonePt, orientPt, prevOrientPt, terminalPt, termOrientPt, baseStartPt, baseEndPt;
-        var traceGeo = null;
-        var colors = [];
-        var points = [];
-        for (var i = 0; i < num; i++)
-            points[i] = [];
 
-        for (i in atomList)
-        {
-            next = atomList[i];
-            
-            if (next === undefined || $.inArray(next.atom, cartoonAtoms) === -1 || next.hetflag)
-                continue; // skip array holes, heteroatoms, and atoms not involved in cartoon drawing
+].join("\n"),
+       
+       vertexShader : [
 
-            // determine cartoon style
-            cartoon = next.style.cartoon;
-            if (cartoon.style === "trace") // draw cylinders connecting consecutive 'backbone' atoms
-            {
-                /* "trace" style just draws cylinders between consecutive 'backbone' atoms,
-                    such as alpha carbon for polypeptides and phosphorus for DNA. */
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-                if (!traceGeo) traceGeo = new $3Dmol.Geometry(true);
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-                if (next.atom === "CA" || next.atom === "P")
-                {
-                    // determine cylinder color
-                    if (gradientScheme)
-                        nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
-                    else
-                        nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                    colors.push(nextColor);
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
 
-                    // determine cylinder thickness
-                    if ($.isNumeric(cartoon.thickness))
-                        thickness = cartoon.thickness;
-                    else
-                        thickness = defaultThickness;
+"void main() {",
+    
+"    vColor = color;",
+    
+"    vec3 objectNormal = normal;",  
+"    vec3 transformedNormal = normalMatrix * objectNormal;",    
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    
+"    vLightFront = vec3( 0.0 );",
+    
+"    transformedNormal = normalize( transformedNormal );",
+    
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
+    
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
+    
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
+           
+].join("\n"),
 
-                    /* do not draw connections between different chains, but ignore
-                       differences in reschain to properly support CA-only files */
-                    if (curr && curr.chain === next.chain && curr.resi + 1 === next.resi)
-                    {
-                        // if both atoms are same color, draw single cylinder
-                        if (nextColor == currColor)
-                        {
-                            var color = $3Dmol.CC.color(nextColor);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, next, thickness, color, true, true);
-                        }
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-                        else // otherwise draw cylinders for each color (split down the middle)
-                        {
-                            var midpoint = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
-                            var color1 = $3Dmol.CC.color(currColor);
-                            var color2 = $3Dmol.CC.color(nextColor);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, midpoint, thickness, color1, true, false);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, midpoint, next, thickness, color2, false, true);
-                        } // note that an atom object can be duck-typed as a 3-vector in this case
-                    }
+    },
 
-                    curr = next;
-                    currColor = nextColor;
-                }
-            }
 
-            else // draw default-style cartoons based on secondary structure
-            {
-                // draw backbone through these atoms
-                if (next.atom === "CA" || next.atom === "P" || next.atom === "O5'")
-                {
-                    // end of a chain of connected residues
-                    if (curr != undefined && (curr.chain != next.chain || !(curr.resi === next.resi || curr.resi + 1 === next.resi)
-                        || curr.reschain != next.reschain))
-                    { 
+    'instanced' : {
+        fragmentShader : [
 
-                        if (baseEndPt) // draw the last base if it's a NA chain
-                        {
-                            if (terminalPt)
-                                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
-                            else
-                                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-                            addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr);
-                            colors.push(nextColor);
-                            
-                            baseStartPt = null;
-                            baseEndPt = null;
-                        }
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-                        // draw accumulated strand points
-                        for (i = 0; !thickness && i < num; i++)
-                            drawSmoothCurve(group, points[i], 1, colors, div);
-                        if (fill)
-                            drawStrip(group, points[0], points[num - 1], colors, div, thickness);
+"varying vec3 vLightFront;",
+"varying vec3 vColor;",
 
-                        // clear arrays for points and colors
-                        points = [];
-                        for (i = 0; i < num; i++)
-                            points[i] = [];
-                        colors = [];
-                    }
+"void main() {",
 
-                    // backbone atom of next residue
-                    if (curr === undefined || curr.resi != next.resi)
-                    {
-                        if (baseEndPt) // draw last NA residue's base
-                        {
-                            // start the cylinder at the midpoint between consecutive backbone atoms
-                            baseStartPt = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
-                            //var startFix = baseStartPt.clone().sub(baseEndPt).multiplyScalar(0.04);
-                            //baseStartPt.add(startFix);
-                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-                            baseStartPt = null;
-                            baseEndPt = null;   
-                        }
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
 
-                        // determine color and thickness of the next strand segment
-                        if (gradientScheme)
-                            nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
-                        else
-                            nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                        colors.push(nextColor);
-                        if ($.isNumeric(cartoon.thickness))
-                            thickness = cartoon.thickness;
-                        else
-                            thickness = defaultThickness;
+"    #ifndef WIREFRAME",
+"    gl_FragColor.xyz *= vLightFront;",
+"    #endif",
 
-                        curr = next; // advance pointer
-                        backbonePt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
-                        backbonePt.resi = curr.resi;
-                        currColor = nextColor; // used for NA bases
-                    }
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
 
-                    // click handling
-                    if (next.clickable === true &&
-                        (next.intersectionShape === undefined || next.intersectionShape.triangle === undefined)) 
-                        next.intersectionShape = {sphere : null, cylinder : [], line : [], triangle : []};
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
 
-                }
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-                // atoms used to orient the backbone strand
-                else if (next.atom === "O"  && curr.atom === "CA"
-                      || next.atom === "OP2" && curr.atom === "P"
-                      || next.atom === "C5'" && curr.atom === "O5'")
-                {
-                    orientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                    orientPt.resi = next.resi;
-                    if (next.atom === "OP2") // for NA 3' terminus
-                        termOrientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                }
+"}"
 
-                // NA 3' terminus is an edge case, need a vector for most recent O3'
-                else if (next.atom === "O3'")
-                {
-                    terminalPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                }
 
-                // atoms used for drawing the NA base cylinders (diff for purines and pyramidines)
-                else if ((next.atom === "N1" && $.inArray(next.resn, purResns) != -1) ||
-                         (next.atom === "N3" && $.inArray(next.resn, pyrResns) != -1))
-                {
-                    baseEndPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                    baseEndPt.color = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                }
+].join("\n"),
 
-                // when we have a backbone point and orientation point in the same residue, accumulate strand points
-                if (orientPt && backbonePt && orientPt.resi === backbonePt.resi)
-                {
-                    addBackbonePoints(points, num, !doNotSmoothen, backbonePt, orientPt, prevOrientPt, curr);
-                    prevOrientPt = orientPt;
-                    backbonePt = null;
-                    orientPt = null;
-                }
-            }  
-        }
+       vertexShader : [
 
-        if (baseEndPt) // draw last NA base if needed
-        {
-            if (terminalPt)
-                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
-            else
-                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-            addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr);
-            colors.push(nextColor);
-        }
+"attribute vec3 offset;",
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-        // for default style, draw the last strand
-        for (i = 0; !thickness && i < num; i++)
-            drawSmoothCurve(group, points[i], 1, colors, div);
-        if (fill)
-            drawStrip(group, points[0], points[num - 1], colors, div, thickness);
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
 
-        if (traceGeo) // generate mesh for trace geometry
-        {
-            var traceMaterial = new $3Dmol.MeshLambertMaterial();
-            traceMaterial.vertexColors = $3Dmol.FaceColors;
-            traceMaterial.side = $3Dmol.DoubleSide;
-            var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
-            group.add(traceMesh);
-        }
-    };
+"void main() {",
 
-    //TODO document me
-    var addBackbonePoints = function(pointsArray, num, smoothen, backbonePt, orientPt, prevOrientPt, backboneAtom)
-    {
-        var widthScalar, i, delta, v;
-        orientPt.sub(backbonePt);
-        orientPt.normalize();
-        if (backboneAtom.ss === "c")
-        {
-            if (backboneAtom.atom === "P")
-                widthScalar = nucleicAcidWidth;
-            else
-                widthScalar = coilWidth;
-        } else
-            widthScalar = helixSheetWidth;
-        orientPt.multiplyScalar(widthScalar);
+"    vColor = color;",
 
-        if (prevOrientPt != null && orientPt.dot(prevOrientPt) < 0)
-        {
-            orientPt.negate();
-        }
+"    vec3 objectNormal = normal;",
+"    vec3 transformedNormal = normalMatrix * objectNormal;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position * radius + offset, 1.0 );",
 
-        for (i = 0; i < num; i++)
-        {
-            delta = -1 + i * 2 /(num - 1); // produces num increments from -1 to 1
-            v = new $3Dmol.Vector3(backbonePt.x + delta * orientPt.x,
-                                   backbonePt.y + delta * orientPt.y,
-                                   backbonePt.z + delta * orientPt.z);
-            v.atom = backboneAtom;
-            if (smoothen && backboneAtom.ss === "s") 
-                v.smoothen = true;
-            pointsArray[i].push(v);
-        }
-    }
+"    vLightFront = vec3( 0.0 );",
 
-    // actual function call
-    var drawCartoon = function(group, atomlist, geo, gradientscheme) {
-        
-        drawStrand(group, atomlist, 2, undefined, true, coilWidth, helixSheetWidth,
-                false, gradientscheme, geo);
-    };
+"    transformedNormal = normalize( transformedNormal );",
 
-    return drawCartoon;
-})();
-//
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
 
-var $3Dmol = $3Dmol || {};
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
 
-/**
- * Lower level utilities for creating WebGL shape geometries.
- * These are not intended for general consumption.
- * @namespace $3Dmol.GLDraw
-  */
-$3Dmol.GLDraw = (function() {
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
 
-    var draw = {}; // object for exporting functions
+].join("\n"),
 
-    // Rotation matrix around z and x axis -
-    // according to y basis vector
-    // TODO: Try to optimize this (square roots?)
-    var getRotationMatrix = function() {
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-        var d = new $3Dmol.Vector3();
-        // var rot = new Float32Array(9);
+    },
+ 
+//for outline
+     'outline' : { 
+        fragmentShader : [
 
-        return function(dir) {
+"uniform float opacity;",
+"uniform vec3 outlineColor;",
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-            d.set(dir[0], dir[1], dir[2]);
+"void main() {",
+    
+"    gl_FragColor = vec4( outlineColor, 1 );",
+"}"
 
-            var dx = d.x, dy = d.y, dz = d.z;
 
-            var dxy = Math.sqrt(dx * dx + dy * dy);
-            var dxz, dyz;
-
-            var sinA, cosA, sinB, cosB, sinC, cosC;
+].join("\n"),
+       
+       vertexShader : [
 
-            // about z axis - Phi
-            if (dxy < 0.0001) {
-                sinA = 0;
-                cosA = 1;
-            }
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-            else {
-                sinA = -dx / dxy;
-                cosA = dy / dxy;
-            }
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-            // recast dy in terms of new axes - z is the same
+"void main() {",
 
-            dy = -sinA * dx + cosA * dy;
-            dyz = Math.sqrt(dy * dy + dz * dz);
+"    vec4 norm = modelViewMatrix*vec4(normalize(normal),0.0);",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    mvPosition.xy += norm.xy*outlineWidth;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    mvPosition.z -= outlinePushback;", //go backwards in model space
+"    vec4 pushpos = projectionMatrix*mvPosition;", //project to get z in projection space, I'm probably missing some simple math to do the same thing..
+"    gl_Position.z = gl_Position.w*pushpos.z/pushpos.w;",
+"}"
+           
+].join("\n"),
 
-            // about new x axis - Theta
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},           
+            outlineWidth: { type: 'f', value: 0.1 },
+            outlinePushback: { type: 'f', value: 1.0 },
+        }
 
-            if (dyz < 0.0001) {
-                sinB = 0;
-                cosB = 1;
-            }
+    },
+//for outlining sphere imposter
+    'sphereimposteroutline' : { 
+       fragmentShader : [
 
-            else {
-                sinB = dz / dyz;
-                cosB = dy / dyz;
-            }
+"uniform float opacity;",
+"uniform vec3 outlineColor;",
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform mat4 projectionMatrix;",
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 center;",
 
-            var rot = new Float32Array(9);
-            rot[0] = cosA;
-            rot[1] = sinA;
-            rot[2] = 0;
-            rot[3] = -sinA * cosB;
-            rot[4] = cosA * cosB;
-            rot[5] = sinB;
-            rot[6] = sinA * sinB;
-            rot[7] = -cosA * sinB;
-            rot[8] = cosB;
+"uniform float outlinePushback;",
 
-            return rot;
 
-        };
+"void main() {",
+"    float lensqr = dot(mapping,mapping);",
+"    float rsqr = rval*rval;",
+"    if(lensqr > rsqr)",
+"       discard;",
+"    float z = sqrt(rsqr-lensqr);",
+"    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z-outlinePushback);",
+"    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);",
+"    float ndcDepth = clipPos.z / clipPos.w;",
+"    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+"    gl_FragColor = vec4(outlineColor, 1 );",
+"}"
 
-    }();
-    
-    // Ortho normal vectors for cylinder radius/ sphere cap equator and cones
-    // Direction is j basis (0,1,0)
-    var basisVectors = function() {
 
-        var ret = {
-            vertices : [],
-            norms : []
-        };
+].join("\n"),
+      
+      vertexShader : [
 
-        var nvecs = [];
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-        var subdivisions = 4; // including the initial 2, eg. 4 => 16 subintervals
-        var N = Math.pow(2, subdivisions);  // eg. 2**4 = 16 subintervals in total
-        var i = 2;  // start with 2 subdivisions already done
-        var M = Math.pow(2, i); // 4
-        var spacing = N/M;  // 16/4 = 4; if there were 5 subdivs, then 32/4 = 8.
-        var j;
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-        nvecs[0] = new $3Dmol.Vector3(-1, 0, 0);
-        nvecs[spacing] = new $3Dmol.Vector3(0, 0, 1);
-        nvecs[spacing*2] = new $3Dmol.Vector3(1, 0, 0);
-        nvecs[spacing*3] = new $3Dmol.Vector3(0, 0, -1);
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 center;",
 
-        for ( i = 3; i <= subdivisions; i ++ ) {
-            // eg. i=3, we need to add 2**(3-1) = 4 new vecs. Call it M.
-            // their spacing is N/M, eg. N=16, M=4, N/M=4; M=8, N/M=2.
-            // they start off at half this spacing
-            // and are equal to the average of the two vectors on either side
-            M = Math.pow(2, (i-1));
-            spacing = N/M;
-            for ( j = 0; j < (M-1); j ++ ) {
-                nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[(j+1)*spacing]).normalize();
-            }
-            // treat the last one specially so it wraps around to zero
-            j = M - 1;
-            nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[0]).normalize();
-        }
+"void main() {",
 
-        /*
-         * nvecs[0] = new $3Dmol.Vector3(-1,0,0); nvecs[1] = new
-         * $3Dmol.Vector3(0,0,1); nvecs[2] = new $3Dmol.Vector3(1,0,0);
-         * nvecs[3] = new $3Dmol.Vector3(0,0,-1);
-         */
-        return nvecs;
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    center = mvPosition.xyz;",
+"    vec4 projPosition = projectionMatrix * mvPosition;",
+"    vec2 norm = normal.xy + vec2(sign(normal.x)*outlineWidth,sign(normal.y)*outlineWidth);", 
+"    vec4 adjust = projectionMatrix* vec4(norm,normal.z,0.0); adjust.z = 0.0; adjust.w = 0.0;",
+"    mapping = norm.xy;",
+"    rval = abs(norm.x);",
+"    gl_Position = projPosition+adjust;",
+"}"
+          
+].join("\n"),
 
-    }();
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},           
+           outlineWidth: { type: 'f', value: 0.1 },
+           outlinePushback: { type: 'f', value: 1.0 },
+       }
 
-    // memoize capped cylinder for given radius
-    var cylVertexCache = {
+   },
+   //stick imposters
+   'stickimposter' : { 
+      fragmentShader : [$3Dmol.ShaderUtils.stickimposterFragmentShader,
+    "    float dotProduct = dot( norm, vLight );",
+    "    vec3 light = vec3( max( dotProduct, 0.0 ) );",    
+    "    gl_FragColor = vec4(light*color, opacity*opacity );", 
+    "    float fogFactor = smoothstep( fogNear, fogFar, depth );",   
+    "    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+    "}"].join("\n"),
+      vertexShader : [
 
-        cache : {},
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-        getVerticesForRadius : function(radius) {
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-            if (this.cache[radius] !== undefined)
-                return this.cache[radius];
+"varying vec3 vColor;",
+"varying vec3 vLight;",
+"varying vec3 cposition;",
+"varying vec3 p1;",
+"varying vec3 p2;",
+"varying float r;",
 
-            var dir = new $3Dmol.Vector3(0, 1, 0);
-            var w = basisVectors.length;
-            var nvecs = [], norms = [];
-            var n;
+"void main() {",
+   
+"    vColor = color; vColor.z = abs(vColor.z);", //z indicates which vertex and so would vary
+"    r = abs(radius);",
+"    vec4 to = modelViewMatrix*vec4(normal, 1.0);", //normal is other point of cylinder
+"    vec4 pt = modelViewMatrix*vec4(position, 1.0);",
+"    vec4 mvPosition = pt;",
+"    p1 = pt.xyz; p2 = to.xyz;",
+"    vec3 norm = to.xyz-pt.xyz;","" +
+"    float mult = 1.1;", //slop to account for perspective of sphere
+"    if(length(p1) > length(p2)) {", //billboard at level of closest point
+"       mvPosition = to;",
+"    }",
+"    vec3 n = normalize(mvPosition.xyz);",
+//intersect with the plane defined by the camera looking at the billboard point
+"    if(color.z >= 0.0) {", //p1
+"       vec3 pnorm = normalize(p1);",
+"       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p1+t*pnorm;",
+"    } else {",
+"       vec3 pnorm = normalize(p2);",
+"       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p2+t*pnorm;",
+"       mult *= -1.0;",
+"    }",
+"    vec3 cr = normalize(cross(mvPosition.xyz,norm))*radius;", 
+"    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*radius;", 
+"    mvPosition.xy +=  mult*(cr + doublecr).xy;",
+"    cposition = mvPosition.xyz;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vLight = normalize( lDirection.xyz )*directionalLightColor[0];", //not really sure this is right, but color is always white so..
+"}"
+          
+].join("\n"),
 
-            for (var i = 0; i < w; i++) {
-                // bottom
-                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
-                // top
-                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},         
+           directionalLightColor: { type: 'fv', value: [] },
+           directionalLightDirection: { type: 'fv', value: [] }
+       }
 
-                // NOTE: this normal is used for constructing sphere caps -
-                // cylinder normals taken care of in drawCylinder
-                n = basisVectors[i].clone().normalize();
-                norms.push(n);
-                norms.push(n);
-            }
+   },
+   //stick imposter outlines
+   'stickimposteroutline' : { 
+      fragmentShader : $3Dmol.ShaderUtils.stickimposterFragmentShader + 'gl_FragColor = vec4(color,1.0);}',   
+      vertexShader : [
 
-            // norms[0]
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
+"uniform vec3 outlineColor;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-            var verticesRows = [];
 
-            // Require that heightSegments is even and >= 2
-            // Equator points at h/2 (theta = pi/2)
-            // (repeated) polar points at 0 and h (theta = 0 and pi)
-            var heightSegments = 10, widthSegments = w; // 16 or however many
-                                                        // basis vectors for
-                                                        // cylinder
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-            if (heightSegments % 2 !== 0 || !heightSegments) {
-                console.error("heightSegments must be even");
+"varying vec3 vColor;",
+"varying vec3 vLight;",
+"varying vec3 cposition;",
+"varying vec3 p1;",
+"varying vec3 p2;",
+"varying float r;",
 
-                return null;
-            }
+"void main() {",
+   
+"    vColor = outlineColor;",
+"    float rad = radius+sign(radius)*outlineWidth;",
+"    r = abs(rad);",
+"    vec4 to = modelViewMatrix*vec4(normal, 1.0);", //normal is other point of cylinder
+"    vec4 pt = modelViewMatrix*vec4(position, 1.0);",
+//pushback
+"    to.xyz += normalize(to.xyz)*outlinePushback;",
+"    pt.xyz += normalize(pt.xyz)*outlinePushback;",
+
+"    vec4 mvPosition = pt;",
+"    p1 = pt.xyz; p2 = to.xyz;",
+"    vec3 norm = to.xyz-pt.xyz;","" +
+"    float mult = 1.1;", //slop to account for perspective of sphere
+"    if(length(p1) > length(p2)) {", //billboard at level of closest point
+"       mvPosition = to;",
+"    }",
+"    vec3 n = normalize(mvPosition.xyz);",
+//intersect with the plane defined by the camera looking at the billboard point
+"    if(color.z >= 0.0) {", //p1
+"       vec3 pnorm = normalize(p1);",
+"       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p1+t*pnorm;",
+"    } else {",
+"       vec3 pnorm = normalize(p2);",
+"       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p2+t*pnorm;",
+"       mult *= -1.0;",
+"    }",
+"    vec3 cr = normalize(cross(mvPosition.xyz,norm))*rad;", 
+"    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*rad;", 
+"    mvPosition.xy +=  mult*(cr + doublecr).xy;",
+"    cposition = mvPosition.xyz;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    vLight = vec3(1.0,1.0,1.0);",
+"}"
+          
+].join("\n"),
 
-            var phiStart = 0;
-            var phiLength = Math.PI * 2;
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},         
+           outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },         
+           outlineWidth: { type: 'f', value: 0.1 },
+           outlinePushback: { type: 'f', value: 1.0 },         
+       }
 
-            var thetaStart = 0;
-            var thetaLength = Math.PI;
+   },
+    //for double sided lighting
+    'lambertdouble' : { 
+        fragmentShader : [
 
-            var x, y;
-            var polar = false, equator = false;
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-            for (y = 0; y <= heightSegments; y++) {
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-                polar = (y === 0 || y === heightSegments) ? true : false;
-                equator = (y === heightSegments / 2) ? true : false;
+"varying vec3 vLightFront;",
+"varying vec3 vLightBack;",
 
-                var verticesRow = [], toRow = [];
+"varying vec3 vColor;",
 
-                for (x = 0; x <= widthSegments; x++) {
+"void main() {",
+    
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    
+"    #ifndef WIREFRAME",
+"    if ( gl_FrontFacing )",
+"       gl_FragColor.xyz *= vLightFront;",
+"    else",
+"       gl_FragColor.xyz *= vLightBack;",
+"    #endif",
+    
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-                    // Two vertices rows for equator pointing to previously
-                    // constructed cyl points
-                    if (equator) {
-                        var xi = (x < widthSegments) ? 2 * x : 0;
-                        toRow.push(xi + 1);
-                        verticesRow.push(xi);
+"}"
 
-                        continue;
-                    }
 
-                    var u = x / widthSegments;
-                    var v = y / heightSegments;
+].join("\n"),
+       
+       vertexShader : [
 
-                    // Only push first polar point
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-                    if (!polar || x === 0) {
-
-                        if (x < widthSegments) {
-                            var vertex = new $3Dmol.Vector3();
-                            vertex.x = -radius
-                                    * Math.cos(phiStart + u * phiLength)
-                                    * Math.sin(thetaStart + v * thetaLength);
-                            vertex.y = radius
-                                    * Math.cos(thetaStart + v * thetaLength);
-                            vertex.z = radius
-                                    * Math.sin(phiStart + u * phiLength)
-                                    * Math.sin(thetaStart + v * thetaLength);
-
-                            if (Math.abs(vertex.x) < 1e-5)
-                                vertex.x = 0;
-                            if (Math.abs(vertex.y) < 1e-5)
-                                vertex.y = 0;
-                            if (Math.abs(vertex.z) < 1e-5)
-                                vertex.z = 0;
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-                            n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
-                            n.normalize();
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
+"varying vec3 vLightBack;",
 
-                            nvecs.push(vertex);
-                            norms.push(n);
+"void main() {",
+    
+"    vColor = color;",
+    
+"    vec3 objectNormal = normal;",  
+"    vec3 transformedNormal = normalMatrix * objectNormal;",    
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    
+"    vLightFront = vec3( 0.0 );",
+"    vLightBack = vec3( 0.0 );",
+    
+"    transformedNormal = normalize( transformedNormal );",
+    
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
+"    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );",
 
-                            verticesRow.push(nvecs.length - 1);
-                        }
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
+"    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;",
 
-                        // last point is just the first point for this row
-                        else {
-                            verticesRow.push(nvecs.length - widthSegments);
-                        }
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
+           
+].join("\n"),
 
-                    }
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},           
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-                    // x > 0; index to already added point
-                    else if (polar)
-                        verticesRow.push(nvecs.length - 1);
+    },
+    
+    
+    'sprite': {
+        
+        fragmentShader: [
+                                                         
+"uniform vec3 color;",
+"uniform sampler2D map;",
+"uniform float opacity;",
 
-                }
+"uniform int fogType;",
+"uniform vec3 fogColor;",
+"uniform float fogDensity;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform float alphaTest;",
 
-                // extra equator row
-                if (equator)
-                    verticesRows.push(toRow);
+"varying vec2 vUV;",
 
-                verticesRows.push(verticesRow);
+"void main() {",
+    
+"    vec4 texture = texture2D(map, vUV);",
+    
+"    if (texture.a < alphaTest) discard;",
+    
+"    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);",
+    
+"    if (fogType > 0) {",
+        
+"        float depth = gl_FragCoord.z / gl_FragCoord.w;",
+"        float fogFactor = 0.0;",
+        
+"        if (fogType == 1) {",
+"            fogFactor = smoothstep(fogNear, fogFar, depth);",
+"        }",
+        
+"        else {",
+"            const float LOG2 = 1.442695;",
+"            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);",
+"            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);",
+"        }",
+        
+"        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);",
+        
+"    }",
+"}"                                              
+            
+].join("\n"),
+        
+        vertexShader: [
 
-            }
+"uniform int useScreenCoordinates;",
+"uniform vec3 screenPosition;",
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float rotation;",
+"uniform vec2 scale;",
+"uniform vec2 alignment;",
+"uniform vec2 uvOffset;",
+"uniform vec2 uvScale;",
 
-            var obj = {
-                vertices : nvecs,
-                normals : norms,
-                verticesRows : verticesRows,
-                w : widthSegments,
-                h : heightSegments
-            };
+"attribute vec2 position;",
+"attribute vec2 uv;",
 
-            this.cache[radius] = obj;
+"varying vec2 vUV;",
 
-            return obj;
+"void main() {",
+    
+"    vUV = uvOffset + uv * uvScale;",
+    
+"    vec2 alignedPosition = position + alignment;",
+    
+"    vec2 rotatedPosition;",
+"    rotatedPosition.x = ( cos(rotation) * alignedPosition.x - sin(rotation) * alignedPosition.y ) * scale.x;",
+"    rotatedPosition.y = ( sin(rotation) * alignedPosition.x + cos(rotation) * alignedPosition.y ) * scale.y;",
+    
+"    vec4 finalPosition;",
+    
+"    if(useScreenCoordinates != 0) {",
+"        finalPosition = vec4(screenPosition.xy + rotatedPosition, screenPosition.z, 1.0);",
+"    }",
+    
+"    else {",
+"        finalPosition = projectionMatrix * modelViewMatrix * vec4(0.0, 0.0, 0.0, 1.0); finalPosition /= finalPosition.w;",
+"        finalPosition.xy += rotatedPosition; ",
+"    }",
+    
+"    gl_Position = finalPosition;",
+    
+"}"
+       
+].join("\n"),
 
+        uniforms : {
+            
         }
-    };
-
-    // creates a cylinder
-    var drawnC = 0;
+        
+    }
     
-    /** Create a cylinder 
-     * @function $3Dmol.GLDraw.drawCylinder
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            from
-     * @param {Point}
-     *            to
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     * @param {boolean} fromCap
-     * @param {boolean} toCap
-     *            
-     * */
-    draw.drawCylinder = function(geo, from, to, radius, color, fromCap, toCap) {
-        if (!from || !to)
-            return;
-        drawnC++;
-        // vertices
-        var drawcaps = fromCap || toCap;
-        color = color || {r:0, g:0, b:0};
+};
+/*  ProteinSurface.js by biochem_fan
 
-        /** @type {Array.<number>} */
-        var dir = [ to.x, to.y, to.z ];
-        dir[0] -= from.x;
-        dir[1] -= from.y;
-        dir[2] -= from.z;
+Ported and modified for Javascript based on EDTSurf,
+  whose license is as follows.
 
-        var e = getRotationMatrix(dir);
-        // get orthonormal vectors from cache
-        // TODO: Will have orient with model view matrix according to direction
-        var vobj = cylVertexCache.getVerticesForRadius(radius);
+Permission to use, copy, modify, and distribute this program for any
+purpose, with or without fee, is hereby granted, provided that this
+copyright notice and the reference information appear in all copies or
+substantial portions of the Software. It is provided "as is" without
+express or implied warranty. 
 
-        // w (n) corresponds to the number of orthonormal vectors for cylinder
-        // (default 16)
-        var n = vobj.w, h = vobj.h;
-        var w = n;
-        // get orthonormal vector
-        var n_verts = (drawcaps) ? h * n + 2 : 2 * n;
+Reference:
+http://zhanglab.ccmb.med.umich.edu/EDTSurf/
+D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces
+by Euclidean Distance Transform. PLoS ONE 4(12): e8140.
 
-        var geoGroup = geo.updateGeoGroup(n_verts);
+=======
 
-        var vertices = vobj.vertices, normals = vobj.normals, verticesRows = vobj.verticesRows;
-        var toRow = verticesRows[h / 2], fromRow = verticesRows[h / 2 + 1];
+TODO: Improved performance on Firefox
+      Reduce memory consumption
+      Refactor!
+ */
 
-        var start = geoGroup.vertices;
-        var offset, faceoffset;
-        var i, x, y, z;
 
-        var vertexArray = geoGroup.vertexArray;
-        var normalArray = geoGroup.normalArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        // add vertices, opposing vertices paired together
-        for (i = 0; i < n; ++i) {
+// dkoes
+// Surface calculations.  This must be safe to use within a web worker.
+if (typeof console === 'undefined') {
+    // this should only be true inside of a webworker
+    console = {
+        log : function() {
+        }
+    };
+}
 
-            var vi = 2 * i;
+$3Dmol.ProteinSurface = function() {
 
-            x = e[0] * vertices[vi].x + e[3] * vertices[vi].y + e[6]
-                    * vertices[vi].z;
-            y = e[1] * vertices[vi].x + e[4] * vertices[vi].y + e[7]
-                    * vertices[vi].z;
-            z = e[5] * vertices[vi].y + e[8] * vertices[vi].z;
+    // constants for vpbits bitmasks
+    /** @const */
+    var INOUT = 1;
+    /** @const */
+    var ISDONE = 2;
+    /** @const */
+    var ISBOUND = 4;
 
-            // var xn = x/radius, yn = y/radius, zn = z/radius;
+    var ptranx = 0, ptrany = 0, ptranz = 0;
+    var probeRadius = 1.4;
+    var defaultScaleFactor = 2;
+    var scaleFactor = defaultScaleFactor; // 2 is .5A grid; if this is made user configurable,
+                            // also have to adjust offset used to find non-shown
+                            // atoms
+    var pHeight = 0, pWidth = 0, pLength = 0;
+    var cutRadius = 0;
+    var vpBits = null; // uint8 array of bitmasks
+    var vpDistance = null; // floatarray of _squared_ distances
+    var vpAtomID = null; // intarray
+    var vertnumber = 0, facenumber = 0;
+    var pminx = 0, pminy = 0, pminz = 0, pmaxx = 0, pmaxy = 0, pmaxz = 0;
 
-            offset = 3 * (start + vi);
-            faceoffset = geoGroup.faceidx;
+    var vdwRadii = {
+            "H" : 1.2,
+            "Li" : 1.82,
+            "Na" : 2.27,
+            "K" : 2.75,
+            "C" : 1.7,
+            "N" : 1.55,
+            "O" : 1.52,
+            "F" : 1.47,
+            "P" : 1.80,
+            "S" : 1.80,
+            "CL" : 1.75,
+            "BR" : 1.85,
+            "SE" : 1.90,
+            "ZN" : 1.39,
+            "CU" : 1.4,
+            "NI" : 1.63,
+            "X" : 2
+        };
+    
+    /** @param {AtomSpec} atom */
+    var getVDWIndex = function(atom) {
+        if(!atom.elem || typeof(vdwRadii[atom.elem]) == "undefined") {
+            return "X";
+        }
+        return atom.elem;
+    };
+    
+    var depty = {}, widxz = {};
+    var faces, verts;
+    var nb = [ new Int32Array([ 1, 0, 0 ]), new Int32Array([ -1, 0, 0 ]), 
+               new Int32Array([ 0, 1, 0 ]), new Int32Array([ 0, -1, 0 ]),
+               new Int32Array([ 0, 0, 1 ]), 
+               new Int32Array([ 0, 0, -1 ]), 
+               new Int32Array([ 1, 1, 0 ]), 
+               new Int32Array([ 1, -1, 0 ]), 
+               new Int32Array([ -1, 1, 0 ]),
+               new Int32Array([ -1, -1, 0 ]), 
+               new Int32Array([ 1, 0, 1 ]), 
+               new Int32Array([ 1, 0, -1 ]), 
+               new Int32Array([ -1, 0, 1 ]),
+               new Int32Array([ -1, 0, -1 ]), 
+               new Int32Array([ 0, 1, 1 ]), 
+               new Int32Array([ 0, 1, -1 ]), 
+               new Int32Array([ 0, -1, 1 ]),
+               new Int32Array([ 0, -1, -1 ]), 
+               new Int32Array([ 1, 1, 1 ]), 
+               new Int32Array([ 1, 1, -1 ]), 
+               new Int32Array([ 1, -1, 1 ]),
+               new Int32Array([ -1, 1, 1 ]), 
+               new Int32Array([ 1, -1, -1 ]), 
+               new Int32Array([ -1, -1, 1 ]), 
+               new Int32Array([ -1, 1, -1 ]),
+               new Int32Array([ -1, -1, -1 ]) ];
 
-            // from
-            vertexArray[offset] = x + from.x;
-            vertexArray[offset + 1] = y + from.y;
-            vertexArray[offset + 2] = z + from.z;
-            // to
-            vertexArray[offset + 3] = x + to.x;
-            vertexArray[offset + 4] = y + to.y;
-            vertexArray[offset + 5] = z + to.z;
+    var origextent;
 
-            // normals
-            normalArray[offset] = x;
-            normalArray[offset + 3] = x;
-            normalArray[offset + 1] = y;
-            normalArray[offset + 4] = y;
-            normalArray[offset + 2] = z;
-            normalArray[offset + 5] = z;
+    var inOrigExtent = function(x, y, z) {
+        if (x < origextent[0][0] || x > origextent[1][0])
+            return false;
+        if (y < origextent[0][1] || y > origextent[1][1])
+            return false;
+        if (z < origextent[0][2] || z > origextent[1][2])
+            return false;
+        return true;
+    };
 
-            // colors
-            colorArray[offset] = color.r;
-            colorArray[offset + 3] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 4] = color.g;
-            colorArray[offset + 2] = color.b;
-            colorArray[offset + 5] = color.b;
+    this.getFacesAndVertices = function(atomlist) {
+        var atomsToShow = {};
+        var i, il;
+        for (i = 0, il = atomlist.length; i < il; i++)
+            atomsToShow[atomlist[i]] = true;
+        var vertices = verts;
+        for (i = 0, il = vertices.length; i < il; i++) {
+            vertices[i].x = vertices[i].x / scaleFactor - ptranx;
+            vertices[i].y = vertices[i].y / scaleFactor - ptrany;
+            vertices[i].z = vertices[i].z / scaleFactor - ptranz;
+        }
 
-            // faces
-            // 0 - 2 - 1
-            faceArray[faceoffset] = fromRow[i] + start;
-            faceArray[faceoffset + 1] = fromRow[i + 1] + start;
-            faceArray[faceoffset + 2] = toRow[i] + start;
-            // 1 - 2 - 3
-            faceArray[faceoffset + 3] = toRow[i] + start;
-            faceArray[faceoffset + 4] = fromRow[i + 1] + start;
-            faceArray[faceoffset + 5] = toRow[i + 1] + start;
+        var finalfaces = [];
+        for (i = 0, il = faces.length; i < il; i += 3) {
+            //var f = faces[i];
+            var fa = faces[i], fb = faces[i+1], fc = faces[i+2];
+            var a = vertices[fa]['atomid'], b = vertices[fb]['atomid'], c = vertices[fc]['atomid'];
 
-            geoGroup.faceidx += 6;
+            // must be a unique face for each atom
+            var which = a;
+            if (b < which)
+                which = b;
+            if (c < which)
+                which = c;
+            if (!atomsToShow[which]) {
+                continue;
+            }
+            var av = vertices[faces[i]];
+            var bv = vertices[faces[i+1]];
+            var cv = vertices[faces[i+2]];
 
+            if (fa !== fb && fb !== fc && fa !== fc){
+                finalfaces.push(fa); 
+                finalfaces.push(fb); 
+                finalfaces.push(fc); 
+            }
+               
         }
 
-        // SPHERE CAPS
+        //try to help the garbage collector
+        vpBits = null; // uint8 array of bitmasks
+        vpDistance = null; // floatarray
+        vpAtomID = null; // intarray
+        
+        return {
+            'vertices' : vertices,
+            'faces' : finalfaces
+        };
+    };
 
-        if (drawcaps) {
 
-            // h - sphere rows, verticesRows.length - 2
-            var ystart = (toCap) ? 0 : h / 2;
-            var yend = (fromCap) ? h + 1 : h / 2 + 1;
+    this.initparm = function(extent, btype, volume) {
+        if(volume > 1000000) //heuristical decrease resolution to avoid large memory consumption
+            scaleFactor = defaultScaleFactor/2;
+        
+        var margin = (1 / scaleFactor) * 5.5; // need margin to avoid
+                                                // boundary/round off effects
+        origextent = extent;
+        pminx = extent[0][0]; pmaxx = extent[1][0];
+        pminy = extent[0][1]; pmaxy = extent[1][1];
+        pminz = extent[0][2]; pmaxz = extent[1][2];
 
-            var v1, v2, v3, v4, x1, x2, x3, x4, y1, y2, y3, y4, z1, z2, z3, z4, nx1, nx2, nx3, nx4, ny1, ny2, ny3, ny4, nz1, nz2, nz3, nz4, v1offset, v2offset, v3offset, v4offset;
+        if (!btype) {
+            pminx -= margin;
+            pminy -= margin;
+            pminz -= margin;
+            pmaxx += margin;
+            pmaxy += margin;
+            pmaxz += margin;
+        } else {
+            pminx -= probeRadius + margin;
+            pminy -= probeRadius + margin;
+            pminz -= probeRadius + margin;
+            pmaxx += probeRadius + margin;
+            pmaxy += probeRadius + margin;
+            pmaxz += probeRadius + margin;
+        }
 
-            for (y = ystart; y < yend; y++) {
-                if (y === h / 2)
-                    continue;
-                // n number of points for each level (verticesRows[i].length -
-                // 1)
-                var cap = (y <= h / 2) ? to : from;
+        pminx = Math.floor(pminx * scaleFactor) / scaleFactor;
+        pminy = Math.floor(pminy * scaleFactor) / scaleFactor;
+        pminz = Math.floor(pminz * scaleFactor) / scaleFactor;
+        pmaxx = Math.ceil(pmaxx * scaleFactor) / scaleFactor;
+        pmaxy = Math.ceil(pmaxy * scaleFactor) / scaleFactor;
+        pmaxz = Math.ceil(pmaxz * scaleFactor) / scaleFactor;
 
-                for (x = 0; x < n; x++) {
+        ptranx = -pminx;
+        ptrany = -pminy;
+        ptranz = -pminz;
 
-                    faceoffset = geoGroup.faceidx;
+        pLength = Math.ceil(scaleFactor * (pmaxx - pminx)) + 1;
+        pWidth = Math.ceil(scaleFactor * (pmaxy - pminy)) + 1;
+        pHeight = Math.ceil(scaleFactor * (pmaxz - pminz)) + 1;
 
-                    v1 = verticesRows[y][x + 1];
-                    v1offset = (v1 + start) * 3;
-                    v2 = verticesRows[y][x];
-                    v2offset = (v2 + start) * 3;
-                    v3 = verticesRows[y + 1][x];
-                    v3offset = (v3 + start) * 3;
-                    v4 = verticesRows[y + 1][x + 1];
-                    v4offset = (v4 + start) * 3;
+        this.boundingatom(btype);
+        cutRadius = probeRadius * scaleFactor;
 
-                    // rotate sphere vectors
-                    x1 = e[0] * vertices[v1].x + e[3] * vertices[v1].y + e[6]
-                            * vertices[v1].z;
-                    x2 = e[0] * vertices[v2].x + e[3] * vertices[v2].y + e[6]
-                            * vertices[v2].z;
-                    x3 = e[0] * vertices[v3].x + e[3] * vertices[v3].y + e[6]
-                            * vertices[v3].z;
-                    x4 = e[0] * vertices[v4].x + e[3] * vertices[v4].y + e[6]
-                            * vertices[v4].z;
+        vpBits = new Uint8Array(pLength * pWidth * pHeight);
+        vpDistance = new Float64Array(pLength * pWidth * pHeight); // float 32
+        // doesn't
+        // play
+        // nicely
+        // with
+        // native
+        // floats
+        vpAtomID = new Int32Array(pLength * pWidth * pHeight);
+        //console.log("Box size: ", pLength, pWidth, pHeight, vpBits.length);
+    };
 
-                    y1 = e[1] * vertices[v1].x + e[4] * vertices[v1].y + e[7]
-                            * vertices[v1].z;
-                    y2 = e[1] * vertices[v2].x + e[4] * vertices[v2].y + e[7]
-                            * vertices[v2].z;
-                    y3 = e[1] * vertices[v3].x + e[4] * vertices[v3].y + e[7]
-                            * vertices[v3].z;
-                    y4 = e[1] * vertices[v4].x + e[4] * vertices[v4].y + e[7]
-                            * vertices[v4].z;
+    this.boundingatom = function(btype) {
+        var tradius = [];
+        var txz, tdept, sradius, idx;
+        flagradius = btype;
 
-                    z1 = e[5] * vertices[v1].y + e[8] * vertices[v1].z;
-                    z2 = e[5] * vertices[v2].y + e[8] * vertices[v2].z;
-                    z3 = e[5] * vertices[v3].y + e[8] * vertices[v3].z;
-                    z4 = e[5] * vertices[v4].y + e[8] * vertices[v4].z;
-
-                    vertexArray[v1offset] = x1 + cap.x;
-                    vertexArray[v2offset] = x2 + cap.x;
-                    vertexArray[v3offset] = x3 + cap.x;
-                    vertexArray[v4offset] = x4 + cap.x;
-
-                    vertexArray[v1offset + 1] = y1 + cap.y;
-                    vertexArray[v2offset + 1] = y2 + cap.y;
-                    vertexArray[v3offset + 1] = y3 + cap.y;
-                    vertexArray[v4offset + 1] = y4 + cap.y;
-
-                    vertexArray[v1offset + 2] = z1 + cap.z;
-                    vertexArray[v2offset + 2] = z2 + cap.z;
-                    vertexArray[v3offset + 2] = z3 + cap.z;
-                    vertexArray[v4offset + 2] = z4 + cap.z;
-
-                    colorArray[v1offset] = color.r;
-                    colorArray[v2offset] = color.r;
-                    colorArray[v3offset] = color.r;
-                    colorArray[v4offset] = color.r;
-
-                    colorArray[v1offset + 1] = color.g;
-                    colorArray[v2offset + 1] = color.g;
-                    colorArray[v3offset + 1] = color.g;
-                    colorArray[v4offset + 1] = color.g;
-
-                    colorArray[v1offset + 2] = color.b;
-                    colorArray[v2offset + 2] = color.b;
-                    colorArray[v3offset + 2] = color.b;
-                    colorArray[v4offset + 2] = color.b;
-
-                    nx1 = e[0] * normals[v1].x + e[3] * normals[v1].y + e[6]
-                            * normals[v1].z;
-                    nx2 = e[0] * normals[v2].x + e[3] * normals[v2].y + e[6]
-                            * normals[v2].z;
-                    nx3 = e[0] * normals[v3].x + e[3] * normals[v3].y + e[6]
-                            * normals[v3].z;
-                    nx4 = e[0] * normals[v4].x + e[3] * normals[v4].y + e[6]
-                            * normals[v4].z;
-
-                    ny1 = e[1] * normals[v1].x + e[4] * normals[v1].y + e[7]
-                            * normals[v1].z;
-                    ny2 = e[1] * normals[v2].x + e[4] * normals[v2].y + e[7]
-                            * normals[v2].z;
-                    ny3 = e[1] * normals[v3].x + e[4] * normals[v3].y + e[7]
-                            * normals[v3].z;
-                    ny4 = e[1] * normals[v4].x + e[4] * normals[v4].y + e[7]
-                            * normals[v4].z;
-
-                    nz1 = e[5] * normals[v1].y + e[8] * normals[v1].z;
-                    nz2 = e[5] * normals[v2].y + e[8] * normals[v2].z;
-                    nz3 = e[5] * normals[v3].y + e[8] * normals[v3].z;
-                    nz4 = e[5] * normals[v4].y + e[8] * normals[v4].z;
-
-                    // if (Math.abs(vobj.sphereVertices[v1].y) === radius) {
-                    if (y === 0) {
-                        // face = [v1, v3, v4];
-                        // norm = [n1, n3, n4];
-
-                        normalArray[v1offset] = nx1;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v3offset + 2] = nz3;
-                        normalArray[v4offset + 2] = nz4;
-
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v3 + start;
-                        faceArray[faceoffset + 2] = v4 + start;
-
-                        geoGroup.faceidx += 3;
+        for ( var i in vdwRadii) {
+            if(!vdwRadii.hasOwnProperty(i))
+                continue;
+            var r = vdwRadii[i];
+            if (!btype)
+                tradius[i] = r * scaleFactor + 0.5;
+            else
+                tradius[i] = (r + probeRadius) * scaleFactor + 0.5;
 
+            sradius = tradius[i] * tradius[i];
+            widxz[i] = Math.floor(tradius[i]) + 1;
+            depty[i] = new Int32Array(widxz[i] * widxz[i]);
+            indx = 0;
+            for (j = 0; j < widxz[i]; j++) {
+                for (k = 0; k < widxz[i]; k++) {
+                    txz = j * j + k * k;
+                    if (txz > sradius)
+                        depty[i][indx] = -1; // outside
+                    else {
+                        tdept = Math.sqrt(sradius - txz);
+                        depty[i][indx] = Math.floor(tdept);
                     }
+                    indx++;
+                }
+            }
+        }
+    };
 
-                    // else if (Math.abs(vobj.sphereVertices[v3].y) === radius)
-                    // {
-                    else if (y === yend - 1) {
-                        // face = [v1, v2, v3];
-                        // norm = [n1, n2, n3];
-
-                        normalArray[v1offset] = nx1;
-                        normalArray[v2offset] = nx2;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v3offset + 2] = nz3;
+    this.fillvoxels = function(atoms, atomlist) { // (int seqinit,int
+        // seqterm,bool
+        // atomtype,atom*
+        // proseq,bool bcolor)
+        var i, il;
+        for (i = 0, il = vpBits.length; i < il; i++) {
+            vpBits[i] = 0;
+            vpDistance[i] = -1.0;
+            vpAtomID[i] = -1;
+        }
 
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v2 + start;
-                        faceArray[faceoffset + 2] = v3 + start;
+        for (i in atomlist) {
+            var atom = atoms[atomlist[i]];
+            if (atom === undefined)
+                continue;
+            this.fillAtom(atom, atoms);
+        }
 
-                        geoGroup.faceidx += 3;
+        for (i = 0, il = vpBits.length; i < il; i++)
+            if (vpBits[i] & INOUT)
+                vpBits[i] |= ISDONE;
 
-                    }
+    };
 
-                    else {
-                        // face = [v1, v2, v3, v4];
-                        // norm = [n1, n2, n3, n4];
 
-                        normalArray[v1offset] = nx1;
-                        normalArray[v2offset] = nx2;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v4offset + 2] = nz4;
+    this.fillAtom = function(atom, atoms) {
+        var cx, cy, cz, ox, oy, oz, mi, mj, mk, i, j, k, si, sj, sk;
+        var ii, jj, kk, n;
+        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
+        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
+        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
 
-                        normalArray[v2offset] = nx2;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v3offset + 2] = nz3;
-                        normalArray[v4offset + 2] = nz4;
+        var at = getVDWIndex(atom);
+        var nind = 0;
+        var cnt = 0;
+        var pWH = pWidth*pHeight;
+        
+        for (i = 0, n = widxz[at]; i < n; i++) {
+            for (j = 0; j < n; j++) {
+                if (depty[at][nind] != -1) {
+                    for (ii = -1; ii < 2; ii++) {
+                        for (jj = -1; jj < 2; jj++) {
+                            for (kk = -1; kk < 2; kk++) {
+                                if (ii !== 0 && jj !== 0 && kk !== 0) {
+                                    mi = ii * i;
+                                    mk = kk * j;
+                                    for (k = 0; k <= depty[at][nind]; k++) {
+                                        mj = k * jj;
+                                        si = cx + mi;
+                                        sj = cy + mj;
+                                        sk = cz + mk;
+                                        if (si < 0 || sj < 0 || 
+                                                sk < 0 ||
+                                                si >= pLength || 
+                                                sj >= pWidth || 
+                                                sk >= pHeight)
+                                            continue;
+                                        var index = si * pWH + sj * pHeight + sk;
 
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v2 + start;
-                        faceArray[faceoffset + 2] = v4 + start;
+                                        if (!(vpBits[index] & INOUT)) {
+                                            vpBits[index] |= INOUT;
+                                            vpAtomID[index] = atom.serial;
+                                        } else {
+                                            var atom2 = atoms[vpAtomID[index]];
+                                            if(atom2.serial != atom.serial) {
+                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.x + ptranx));
+                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.y + ptrany));
+                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.z + ptranz));
+                                                if (mi * mi + mj * mj + mk * mk < ox *
+                                                        ox + oy * oy + oz * oz)
+                                                    vpAtomID[index] = atom.serial;
+                                            }
+                                        }
 
-                        faceArray[faceoffset + 3] = v2 + start;
-                        faceArray[faceoffset + 4] = v3 + start;
-                        faceArray[faceoffset + 5] = v4 + start;
+                                    }// k
+                                }// if
+                            }// kk
+                        }// jj
+                    }// ii
+                }// if
+                nind++;
+            }// j
+        }// i
+    };
 
-                        geoGroup.faceidx += 6;
-                    }
+    this.fillvoxelswaals = function(atoms, atomlist) {
+        var i, il;
+        for (i = 0, il = vpBits.length; i < il; i++)
+            vpBits[i] &= ~ISDONE; // not isdone
 
-                }
-            }
+        for (i in atomlist) {
+            var atom = atoms[atomlist[i]];
+            if (atom === undefined)
+                continue;
 
+            this.fillAtomWaals(atom, atoms);
         }
-
-        geoGroup.vertices += n_verts;
     };
 
-    /** Create a cone 
-     * @function $3Dmol.GLDraw.drawCone
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            from
-     * @param {Point}
-     *            to
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     *            */
-    draw.drawCone = function(geo, from, to, radius, color) {
-        if (!from || !to)
-            return;
+    this.fillAtomWaals = function(atom, atoms) {
+        var cx, cy, cz, ox, oy, oz, nind = 0;
+        var mi, mj, mk, si, sj, sk, i, j, k, ii, jj, kk, n;
+        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
+        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
+        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
 
-        color = color || {r:0, g:0, b:0};
+        var at = getVDWIndex(atom);
+        var pWH = pWidth*pHeight;
+        for (i = 0, n = widxz[at]; i < n; i++) {
+            for (j = 0; j < n; j++) {
+                if (depty[at][nind] != -1) {
+                    for (ii = -1; ii < 2; ii++) {
+                        for (jj = -1; jj < 2; jj++) {
+                            for (kk = -1; kk < 2; kk++) {
+                                if (ii !== 0 && jj !== 0 && kk !== 0) {
+                                    mi = ii * i;
+                                    mk = kk * j;
+                                    for (k = 0; k <= depty[at][nind]; k++) {
+                                        mj = k * jj;
+                                        si = cx + mi;
+                                        sj = cy + mj;
+                                        sk = cz + mk;
+                                        if (si < 0 || sj < 0 || 
+                                                sk < 0 || 
+                                                si >= pLength || 
+                                                sj >= pWidth || 
+                                                sk >= pHeight)
+                                            continue;
+                                        var index = si * pWH + sj * pHeight + sk;
+                                        if (!(vpBits[index] & ISDONE)) {
+                                            vpBits[index] |= ISDONE;
+                                            vpAtomID[index] = atom.serial;
+                                        }  else {
+                                            var atom2 = atoms[vpAtomID[index]];
+                                            if(atom2.serial != atom.serial) {
+                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.x + ptranx));
+                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.y + ptrany));
+                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.z + ptranz));
+                                                if (mi * mi + mj * mj + mk * mk < ox *
+                                                        ox + oy * oy + oz * oz)
+                                                    vpAtomID[index] = atom.serial;
+                                            }
+                                        }
+                                    }// k
+                                }// if
+                            }// kk
+                        }// jj
+                    }// ii
+                }// if
+                nind++;
+            }// j
+        }// i
+    };
 
-        var dir =[to.x, to.y, to.z ];        
-        dir.x -= from.x;
-        dir.y -= from.y;
-        dir.z -= from.z;
+    this.buildboundary = function() {
+        var pWH = pWidth*pHeight;
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pHeight; j++) {
+                for (k = 0; k < pWidth; k++) {
+                    var index = i * pWH + k * pHeight + j;
+                    if (vpBits[index] & INOUT) {
+                        var flagbound = false;
+                        var ii = 0;
+                        while (ii < 26) {
+                            var ti = i + nb[ii][0], tj = j + nb[ii][2], tk = k +
+                                    nb[ii][1];
+                            if (ti > -1 && 
+                                ti < pLength && 
+                                tk > -1 && 
+                                tk < pWidth && 
+                                tj > -1 && 
+                                tj < pHeight && 
+                                !(vpBits[ti * pWH + tk * pHeight + tj] & INOUT)) {
+                                vpBits[index] |= ISBOUND;
+                                break;
+                            } else
+                                ii++;
+                        }
+                    }
+                }
+            }
+        }
+    };
 
-        var e = getRotationMatrix(dir);
+    // a little class for 3d array, should really generalize this and
+    // use throughout...
+    var PointGrid = function(length, width, height) {
+        // the standard says this is zero initialized
+        var data = new Int32Array(length * width * height * 3);
 
+        // set position x,y,z to pt, which has ix,iy,and iz
+        this.set = function(x, y, z, pt) {
+            var index = ((((x * width) + y) * height) + z) * 3;
+            data[index] = pt.ix;
+            data[index + 1] = pt.iy;
+            data[index + 2] = pt.iz;
+        };
 
-        // n vertices around bottom plust the two points
-        var n = basisVectors.length;
-        var basis = basisVectors;
-        var n_verts =  n + 2;
+        // return point at x,y,z
+        this.get = function(x, y, z) {
+            var index = ((((x * width) + y) * height) + z) * 3;
+            return {
+                ix : data[index],
+                iy : data[index + 1],
+                iz : data[index + 2]
+            };
+        };
+    };
 
+    this.fastdistancemap = function() {
+        var eliminate = 0;
+        var certificate;
+        var i, j, k, n;
+
+        var boundPoint = new PointGrid(pLength, pWidth, pHeight);
+        var pWH = pWidth*pHeight;
+        var cutRSq = cutRadius*cutRadius;
         
-        //setup geo structures
-        var geoGroup = geo.updateGeoGroup(n_verts);
-        var start = geoGroup.vertices;    
-        var offset, faceoffset;
-        var i, x, y, z;
-        var vertexArray = geoGroup.vertexArray;
-        var normalArray = geoGroup.normalArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        
-        var offset = start*3;
-        var ndir = new $3Dmol.Vector3(dir[0],dir[1],dir[2]).normalize();
-        //base point first vertex
-        vertexArray[offset] = from.x;
-        vertexArray[offset+1] = from.y;
-        vertexArray[offset+2] = from.z;
-        normalArray[offset] = -ndir.x;
-        normalArray[offset + 1] = -ndir.y;
-        normalArray[offset + 2] = -ndir.z;
-        colorArray[offset] = color.r;
-        colorArray[offset + 1] = color.g;
-        colorArray[offset + 2] = color.b;
-        
-        //second vertex top
-        vertexArray[offset+3] = to.x;
-        vertexArray[offset+4] = to.y;
-        vertexArray[offset+5] = to.z;
-        
-        normalArray[offset+3] = ndir.x;
-        normalArray[offset+4] = ndir.y;
-        normalArray[offset+5] = ndir.z;
-        colorArray[offset+3] = color.r;
-        colorArray[offset + 4] = color.g;
-        colorArray[offset + 5] = color.b;
+        var inarray = [];
+        var outarray = [];
         
-        offset += 6;
+        var index;
         
-        // add circle vertices
-        for (i = 0; i < n; ++i) {
-            var vec = basis[i].clone();
-            vec.multiplyScalar(radius);
-            x = e[0] * vec.x + e[3] * vec.y + e[6]
-                    * vec.z;
-            y = e[1] * vec.x + e[4] * vec.y + e[7]
-                    * vec.z;
-            z = e[5] * vec.y + e[8] * vec.z;
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pWidth; j++) {
+                for (k = 0; k < pHeight; k++) {
+                    index = i * pWH + j * pHeight + k;
+                    vpBits[index] &= ~ISDONE; // isdone = false
+                    if (vpBits[index] & INOUT) {
+                        if (vpBits[index] & ISBOUND) {
+                            var triple = {
+                                ix : i,
+                                iy : j,
+                                iz : k
+                            };
+                            boundPoint.set(i, j, k, triple);
+                            inarray.push(triple);
+                            vpDistance[index] = 0;
+                            vpBits[index] |= ISDONE;
+                            vpBits[index] &= ~ISBOUND;
+                        } 
+                    }
+                }
+            }
+        }
 
-            // from
-            vertexArray[offset] = x + from.x;
-            vertexArray[offset + 1] = y + from.y;
-            vertexArray[offset + 2] = z + from.z;
+        do {
+            outarray = this.fastoneshell(inarray, boundPoint);
+            inarray = [];
+            for (i = 0, n = outarray.length; i < n; i++) {
+                index = pWH * outarray[i].ix + pHeight *
+                    outarray[i].iy + outarray[i].iz;
+                vpBits[index] &= ~ISBOUND;
+                if (vpDistance[index] <= 1.0404 * cutRSq) {
+                    inarray.push({
+                        ix : outarray[i].ix,
+                        iy : outarray[i].iy,
+                        iz : outarray[i].iz
+                    });
+                }
+            }
+        } while (inarray.length !== 0);
 
-            // normals
-            normalArray[offset] = x;
-            normalArray[offset + 1] = y;
-            normalArray[offset + 2] = z;
+        inarray = [];
+        outarray = [];
+        boundPoint = null;
+        
+        var cutsf = scaleFactor - 0.5;
+        if (cutsf < 0)
+            cutsf = 0;
+        var cutoff = cutRSq - 0.50 / (0.1 + cutsf);
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pWidth; j++) {
+                for (k = 0; k < pHeight; k++) {
+                    index = i * pWH + j * pHeight + k;
+                    vpBits[index] &= ~ISBOUND;
+                    // ses solid
+                    if (vpBits[index] & INOUT) {
+                        if (!(vpBits[index] & ISDONE) ||
+                                ((vpBits[index] & ISDONE) && vpDistance[index] >= cutoff)) {
+                            vpBits[index] |= ISBOUND;
+                        }
+                    }
+                }
+            }
+        }
 
-            // colors
-            colorArray[offset] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 2] = color.b;
-            
-            offset += 3;
+    };
 
-        }
-        geoGroup.vertices += (n+2);
-        //faces
-        var faceoffset = geoGroup.faceidx;
-        for( i = 0; i < n; i++) {
-            //two neighboring circle vertices
-            var v1 = start+2+i;
-            var v2 = start+2+ ((i+1)%n);
-            
-            faceArray[faceoffset] = v1;
-            faceArray[faceoffset+1] = v2;
-            faceArray[faceoffset+2] = start;
-            faceoffset += 3;
-            faceArray[faceoffset] = v1;
-            faceArray[faceoffset+1] = v2;
-            faceArray[faceoffset+2] = start+1;
-            faceoffset += 3;
-        }
-        geoGroup.faceidx += 6*n;
-    };
-
-    
-    // Sphere component
-    var sphereVertexCache = {
-        cache : {},
-        getVerticesForRadius : function(radius) {
+    this.fastoneshell = function(inarray, boundPoint) { // (int* innum,int
+        // *allocout,voxel2
+        // ***boundPoint, int*
+        // outnum, int *elimi)
+        var tx, ty, tz;
+        var dx, dy, dz;
+        var i, j, n;
+        var square;
+        var bp, index;
+        var outarray = [];
+        if (inarray.length === 0)
+            return outarray;
 
-            if (typeof (this.cache[radius]) !== "undefined")
-                return this.cache[radius];
+        tnv = {
+            ix : -1,
+            iy : -1,
+            iz : -1
+        };
+        var pWH = pWidth*pHeight;
+        for ( i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-            var obj = {
-                vertices : [],
-                verticesRows : [],
-                normals : []
-            };
-            // scale quality with radius heuristically
-            var sphereQuality = 1;
-            var widthSegments = 16 * sphereQuality;
-            var heightSegments = 10 * sphereQuality;
-            if (radius < 1) {
-                widthSegments = 10 * sphereQuality;
-                heightSegments = 8 * sphereQuality;
+            for (j = 0; j < 6; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
+                
+                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+                    
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+    
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
+    
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
+    
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+    
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
+                            }
+                        }
+                    }
+                }
             }
+        }
 
-            var phiStart = 0;
-            var phiLength = Math.PI * 2;
+        // console.log("part1", positout);
 
-            var thetaStart = 0;
-            var thetaLength = Math.PI;
+        for (i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-            var x, y, vertices = [], uvs = [];
+            for (j = 6; j < 18; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
 
-            for (y = 0; y <= heightSegments; y++) {
+                if(tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+                    
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+    
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
+    
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
+                            }
+                        }
+                    }
+                }
+            }
+        }
 
-                var verticesRow = [];
-                for (x = 0; x <= widthSegments; x++) {
+        // console.log("part2", positout);
 
-                    var u = x / widthSegments;
-                    var v = y / heightSegments;
+        for (i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-                    var vertex = {};
-                    vertex.x = -radius * Math.cos(phiStart + u * phiLength)
-                            * Math.sin(thetaStart + v * thetaLength);
-                    vertex.y = radius * Math.cos(thetaStart + v * thetaLength);
-                    vertex.z = radius * Math.sin(phiStart + u * phiLength)
-                            * Math.sin(thetaStart + v * thetaLength);
+            for (j = 18; j < 26; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
 
-                    var n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
-                    n.normalize();
+                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
 
-                    obj.vertices.push(vertex);
-                    obj.normals.push(n);
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
 
-                    verticesRow.push(obj.vertices.length - 1);
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
+
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT)  && (vpBits[index] & ISDONE)) {
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
 
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
+                            }
+                        }
+                    }
                 }
+            }
+        }
 
-                obj.verticesRows.push(verticesRow);
+        // console.log("part3", positout);
+        return outarray;
+    };
 
+    this.marchingcubeinit = function(stype) {
+        for ( var i = 0, lim = vpBits.length; i < lim; i++) {
+            if (stype == 1) {// vdw
+                vpBits[i] &= ~ISBOUND;
+            } else if (stype == 4) { // ses
+                vpBits[i] &= ~ISDONE;
+                if (vpBits[i] & ISBOUND)
+                    vpBits[i] |= ISDONE;
+                vpBits[i] &= ~ISBOUND;
+            } else if (stype == 2) {// after vdw
+                if ((vpBits[i] & ISBOUND) && (vpBits[i] & ISDONE))
+                    vpBits[i] &= ~ISBOUND;
+                else if ((vpBits[i] & ISBOUND) && !(vpBits[i] & ISDONE))
+                    vpBits[i] |= ISDONE;
+            } else if (stype == 3) { // sas
+                vpBits[i] &= ~ISBOUND;
             }
-
-            this.cache[radius] = obj;
-            return obj;
         }
-
     };
 
-    /** Create a sphere.
-     * @function $3Dmol.GLDraw.drawSphere
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            pos
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     */
-    draw.drawSphere = function(geo, pos, radius, color) {
-
-        var center = new $3Dmol.Vector3(pos.x, pos.y, pos.z);
-
-        var x, y;
-        var vobj = sphereVertexCache.getVerticesForRadius(radius);
+    // this code allows me to empirically prune the marching cubes code tables
+    // to more efficiently handle discrete data
+    var counter = function() {
+        var data = Array(256);
+        for ( var i = 0; i < 256; i++)
+            data[i] = [];
 
-        var vertices = vobj.vertices;
-        var normals = vobj.normals;
+        this.incrementUsed = function(i, j) {
+            if (typeof data[i][j] === 'undefined')
+                data[i][j] = {
+                    used : 0,
+                    unused : 0
+                };
+            data[i][j].used++;
+        };
 
-        var geoGroup = geo.updateGeoGroup(vertices.length);
+        this.incrementUnused = function(i, j) {
+            if (typeof data[i][j] === 'undefined')
+                data[i][j] = {
+                    used : 0,
+                    unused : 0
+                };
+            data[i][j].unused++;
 
-        var start = geoGroup.vertices;
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        var lineArray = geoGroup.lineArray;
-        var normalArray = geoGroup.normalArray;
+        };
 
-        for (var i = 0, il = vertices.length; i < il; ++i) {
-            var offset = 3 * (start + i);
-            var v = vertices[i];
+        var redoTable = function(triTable) {
+            var str = "[";
+            for ( var i = 0; i < triTable.length; i++) {
+                var code = 0;
+                var table = triTable[i];
+                for ( var j = 0; j < table.length; j++) {
+                    code |= (1 << (table[j]));
+                }
+                str += "0x" + code.toString(16) + ", ";
+            }
+            str += "]";
+            console.log(str);
+        };
 
-            vertexArray[offset] = (v.x + pos.x);
-            vertexArray[offset + 1] = (v.y + pos.y);
-            vertexArray[offset + 2] = (v.z + pos.z);
+        this.print = function() {
 
-            colorArray[offset] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 2] = color.b;
+            var table = MarchingCube.triTable;
+            var str;
+            var newtable = [];
+            for ( var i = 0; i < table.length; i++) {
+                var newarr = [];
+                for ( var j = 0; j < table[i].length; j += 3) {
+                    var k = j / 3;
+                    if (typeof data[i][k] === 'undefined' || !data[i][k].unused) {
+                        newarr.push(table[i][j]);
+                        newarr.push(table[i][j + 1]);
+                        newarr.push(table[i][j + 2]);
+                    }
+                    if (typeof data[i][k] === 'undefined')
+                        console.log("undef " + i + "," + k);
+                }
+                newtable.push(newarr);
+            }
+            console.log(JSON.stringify(newtable));
+            redoTable(newtable);
+        };
+    };
+    
+    this.marchingcube = function(stype) {
+        this.marchingcubeinit(stype);
+        verts = []; faces = [];   
+        $3Dmol.MarchingCube.march(vpBits, verts, faces, {
+            smooth : 1,
+            nX : pLength,
+            nY : pWidth,
+            nZ : pHeight        
+        });      
 
-        }
+        var pWH = pWidth*pHeight;
+        for (var i = 0, vlen = verts.length; i < vlen; i++) {
+            verts[i]['atomid'] = vpAtomID[verts[i].x * pWH + pHeight *
+                    verts[i].y + verts[i].z];
+        }  
 
-        geoGroup.vertices += vertices.length;
+        $3Dmol.MarchingCube.laplacianSmooth(1, verts, faces);
 
-        var verticesRows = vobj.verticesRows;
-        var h = verticesRows.length - 1;
+    };
 
-        for (y = 0; y < h; y++) {
-            var w = verticesRows[y].length - 1;
-            for (x = 0; x < w; x++) {
 
-                var faceoffset = geoGroup.faceidx, lineoffset = geoGroup.lineidx;
+};
+//auto-initialization
+//Create embedded viewer from HTML attributes if true
 
-                var v1 = verticesRows[y][x + 1] + start, v1offset = v1 * 3;
-                var v2 = verticesRows[y][x] + start, v2offset = v2 * 3;
-                var v3 = verticesRows[y + 1][x] + start, v3offset = v3 * 3;
-                var v4 = verticesRows[y + 1][x + 1] + start, v4offset = v4 * 3;
+$(document).ready(function() {
 
-                var n1 = normals[v1 - start];
-                var n2 = normals[v2 - start];
-                var n3 = normals[v3 - start];
-                var n4 = normals[v4 - start];
-                var face, norm;
-                if (Math.abs(vertices[v1 - start].y) === radius) {
-                    // face = [v1, v3, v4];
-                    // norm = [n1, n3, n4];
+    if ($(".viewer_3Dmoljs")[0] !== undefined)
+        $3Dmol.autoinit = true;
+        
+    if ($3Dmol.autoinit) { 
+        $3Dmol.viewers = {};
+        var nviewers = 0;
+        $(".viewer_3Dmoljs").each( function() {
+            var viewerdiv = $(this);
+            var datauri = null;
+            
+        
+            var callback = (typeof(window[viewerdiv.data("callback")]) === 'function') ? 
+                    window[viewerdiv.data("callback")] : null;
+            
+            var type = null;
+            if (viewerdiv.data("pdb")) {
+                datauri = "http://www.rcsb.org/pdb/files/" + viewerdiv.data("pdb") + ".pdb";
+                type = "pdb";
+            } else if(viewerdiv.data("cid")) {
+                //this doesn't actually work since pubchem does have CORS enabled
+                type = "sdf";
+                datauri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.data("cid") + 
+                "/SDF?record_type=3d";
+            }
+            else if (viewerdiv.data("href"))
+                datauri = viewerdiv.data("href");
+                
+            var bgcolor = $3Dmol.CC.color(viewerdiv.data("backgroundcolor"));
+            var style = {line:{}};
+            if(viewerdiv.data("style")) style = $3Dmol.specStringToObject(viewerdiv.data("style"));
+            var select = {};
+            if(viewerdiv.data("select")) select = $3Dmol.specStringToObject(viewerdiv.data("select"));
+            var selectstylelist = [];
+            var surfaces = [];
+            var labels = [];
+            var d = viewerdiv.data();
+            
+            //let users specify individual but matching select/style tags, eg.
+            //data-select1 data-style1
+            var stylere = /style(.+)/;
+            var surfre = /surface(.*)/;
+            var reslabre = /labelres(.*)/;
+            var keys = [];
+            for(var dataname in d) {
+                if(d.hasOwnProperty(dataname)) {
+                    keys.push(dataname);
+                }
+            }
+            keys.sort();
+            for(var i = 0; i < keys.length; i++) {
+                var dataname = keys[i];
+                var m = stylere.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    selectstylelist.push([newsel,styleobj]);
+                }         
+                m = surfre.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    surfaces.push([newsel,styleobj]);
+                }
+                m = reslabre.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    labels.push([newsel,styleobj]);
+                }
+            }
+            
+            //apply all the selections/styles parsed out above to the passed viewer
+            var applyStyles = function(glviewer) {
+                glviewer.setStyle(select,style);
+                for(var i = 0; i < selectstylelist.length; i++) {
+                    var sel = selectstylelist[i][0] || {};
+                    var sty = selectstylelist[i][1] || {"line":{}}
+                    glviewer.setStyle(sel, sty);
+                }
+                for(var i = 0; i < surfaces.length; i++) {
+                    var sel = surfaces[i][0] || {};
+                    var sty = surfaces[i][1] || {}
+                    glviewer.addSurface($3Dmol.SurfaceType.VDW, sty, sel, sel);
+                }
+                for(var i = 0; i < labels.length; i++) {
+                    var sel = labels[i][0] || {};
+                    var sty = labels[i][1] || {}
+                    glviewer.addResLabels(sel, sty);
+                }               
+                
+                glviewer.zoomTo();
+                glviewer.render();             
+            }
+            
+            
+            var glviewer = null;
+            try {
+                glviewer = $3Dmol.viewers[this.id || nviewers++] = $3Dmol.createViewer(viewerdiv, {defaultcolors: $3Dmol.rasmolElementColors});
+                glviewer.setBackgroundColor(bgcolor);                            
+            } catch ( error ) {
+                //for autoload, provide a useful error message
+                window.location = "http://get.webgl.org";                    
+            }           
+            
+            if (datauri) {  
+                
+                type = viewerdiv.data("type") || viewerdiv.data("datatype") || type;
+                if(!type) {
+                    type = datauri.substr(datauri.lastIndexOf('.')+1);
+                }
+                                
+                $.get(datauri, function(ret) {
+                    glviewer.addModel(ret, type);
+                    applyStyles(glviewer);       
+                    if (callback) 
+                        callback(glviewer);
+                }, 'text');         
+            }
+            
+            else {
+                
+                if (viewerdiv.data("element")) {
+                    var moldata = $("#" + viewerdiv.data("element")).val() || "";
+                    var type = viewerdiv.data("type") || viewerdiv.data("datatype");
 
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v3offset + 2] = n3.z;
-                    normalArray[v4offset + 2] = n4.z;
+                    if (!type){
 
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v3;
-                    faceArray[faceoffset + 2] = v4;
+                        console.log("Warning: No type specified for embedded viewer with moldata from " + viewerdiv.data("element") +
+                                    "\n assuming type 'pdb'")
 
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v3;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v4;
-                    lineArray[lineoffset + 4] = v3;
-                    lineArray[lineoffset + 5] = v4;
+                        type = 'pdb';
+                    }
 
-                    geoGroup.faceidx += 3;
-                    geoGroup.lineidx += 6;
+                    glviewer.addModel(moldata, type);        
+                }
 
-                } else if (Math.abs(vertices[v3 - start].y) === radius) {
-                    // face = [v1, v2, v3];
-                    // norm = [n1, n2, n3];
-
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v3offset + 2] = n3.z;
-
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v2;
-                    faceArray[faceoffset + 2] = v3;
-
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v2;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v3;
-                    lineArray[lineoffset + 4] = v2;
-                    lineArray[lineoffset + 5] = v3;
-
-                    geoGroup.faceidx += 3;
-                    geoGroup.lineidx += 6;
+                applyStyles(glviewer);                
+                if (callback) 
+                    callback(glviewer);
+            }
+            
+        });              
+    }
+});
+    
+//this is only used for create the enum documentation in JSDoc
+(function() {
+/**
+ * Color representation. 
+ * @typedef ColorSpec
+ * @prop {string} 0xAF10AB - any hex number
+ * @prop {string} white   - 0xFFFFFF
+ * @prop {string} silver  - 0xC0C0C0
+ * @prop {string} gray    - 0x808080
+ * @prop {string} grey    - 0x808080
+ * @prop {string} black   - 0x000000
+ * @prop {string} red     - 0xFF0000
+ * @prop {string} maroon  - 0x800000
+ * @prop {string} yellow  - 0xFFFF00
+ * @prop {string} orange  - 0xFF6600
+ * @prop {string} olive   - 0x808000
+ * @prop {string} lime    - 0x00FF00
+ * @prop {string} green   - 0x008000
+ * @prop {string} aqua    - 0x00FFFF
+ * @prop {string} cyan    - 0x00FFFF
+ * @prop {string} teal    - 0x008080
+ * @prop {string} blue    - 0x0000FF
+ * @prop {string} navy    - 0x000080
+ * @prop {string} fuchsia - 0xFF00FF
+ * @prop {string} magenta - 0xFF00FF
+ * @prop {string} purple  - 0x800080
+ */
 
-                } else {
-                    // face = [v1, v2, v3, v4];
-                    // norm = [n1, n2, n3, n4];
+$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
 
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v4offset + 2] = n4.z;
 
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v3offset + 2] = n3.z;
-                    normalArray[v4offset + 2] = n4.z;
+$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
 
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v2;
-                    faceArray[faceoffset + 2] = v4;
 
-                    faceArray[faceoffset + 3] = v2;
-                    faceArray[faceoffset + 4] = v3;
-                    faceArray[faceoffset + 5] = v4;
+$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
 
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v2;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v4;
 
-                    lineArray[lineoffset + 4] = v2;
-                    lineArray[lineoffset + 5] = v3;
-                    lineArray[lineoffset + 6] = v3;
-                    lineArray[lineoffset + 7] = v4;
+$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
 
-                    geoGroup.faceidx += 6;
-                    geoGroup.lineidx += 8;
 
-                }
+$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
 
-            }
-        }
 
-    };
+$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
 
-    return draw;
 
-})();// A model is a collection of related atoms.  Bonds are only allowed between
-//atoms in the same model.  An atom is uniquely specified by its model id and
-//its serial number.
-//A glmodel knows how to apply the styles on each atom to create a gl object
+$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
 
-var $3Dmol = $3Dmol || {};
+$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
 
-/**
- * GLModel represents a group of related atoms
- * @constructor 
- * @param {number=} mid 
- * @param {Object=} defaultcolors Object defining default atom colors as atom => color property value pairs
- * @see $3Dmol.download
+ /**
+ * Color scheme representation. 
+ * @typedef ColorschemeSpec
+ * @prop {string} greenCarbon   - 0x00FF00
+ * @prop {string} cyanCarbon    - 0x00FFFF
+ * @prop {string} magentaCarbon - 0xFF00FF
+ * @prop {string} yellowCarbon  - 0xFFFF00
+ * @prop {string} whiteCarbon   - 0xFFFFFF
+ * @prop {string} orangeCarbon  - 0xFF6600
+ * @prop {string} purpleCarbon  - 0x100080
+ * @prop {string} blueCarbon    - 0x0000FF
  */
-$3Dmol.GLModel = (function() {
-
-    // class variables go here
-    var defaultAtomStyle = {
-        line : {}
-    };
-
-    var Nucleotides = [ '  G', '  A', '  T', '  C', '  U', ' DG', ' DA', ' DT',
-            ' DC', ' DU' ];
+ 
+});
 
-    var defaultlineWidth = 1.0;
+// in an attempt to reduce memory overhead, cache all $3Dmol.Colors
+// this makes things a little faster
+$3Dmol.CC = {
+    cache : {0:new $3Dmol.Color(0)},
+    color : function color_(hex) {
+        // Undefined values default to black
+        if(!hex)
+            return this.cache[0];
+        // cache hits
+        if(typeof(this.cache[hex]) !== "undefined") {
+            return this.cache[hex];
+        }
+        // arrays
+        else if(hex && hex.constructor === Array) {
+            // parse elements recursively
+            return hex.map(color_,this);
+        }
+        // numbers and hex strings
+        hex = this.getHex(hex);
+        if(typeof hex === 'number') {
+            var c = new $3Dmol.Color(hex);
+            this.cache[hex] = c;
+            return c;
+        } else {
+            // pass through $3Dmol.Color & other objects
+            return hex;
+        }
+    },
+ 
+    colorTab : {
+        'white' : 0xFFFFFF,
+        'silver' : 0xC0C0C0,
+        'gray' : 0x808080,
+        'grey' : 0x808080,
+        'black' : 0x000000,
+        'red' : 0xFF0000,
+        'maroon' : 0x800000,
+        'yellow' : 0xFFFF00,
+        'orange' : 0xFF6600,
+        'olive' : 0x808000,
+        'lime' : 0x00FF00,
+        'green' : 0x008000,
+        'aqua' : 0x00FFFF,
+        'cyan' : 0x00FFFF,
+        'teal' : 0x008080,
+        'blue' : 0x0000FF,
+        'navy' : 0x000080,
+        'fuchsia' : 0xFF00FF,
+        'magenta' : 0xFF00FF,
+        'purple' : 0x800080
+    },    
+    getHex : function(hex) {
+        if (!isNaN(parseInt(hex)))
+            return parseInt(hex);
+        
+        else if (typeof(hex) === 'string') {
+            
+            return this.colorTab[hex.trim().toLowerCase()] || 0x000000;
+        }
+        return hex;
+    }
+    
+};
 
-    // Reference: A. Bondi, J. Phys. Chem., 1964, 68, 441.
-    var vdwRadii = {
-        "H" : 1.2,
-        "Li" : 1.82,
-        "LI" : 1.82,
-        "Na" : 2.27,
-        "NA" : 2.27,
-        "K" : 2.75,
-        "C" : 1.7,
-        "N" : 1.55,
-        "O" : 1.52,
-        "F" : 1.47,
-        "P" : 1.80,
-        "S" : 1.80,
-        "CL" : 1.75,
-        "Cl" : 1.75,
-        "BR" : 1.85,
-        "Br" : 1.85,
-        "SE" : 1.90,
-        "Se" : 1.90,
-        "ZN" : 1.39,
-        "Zn" : 1.39,
-        "CU" : 1.4,
-        "Cu" : 1.4,
-        "NI" : 1.63,
-        "Ni" : 1.63
-    };
 
-    // class functions
+$3Dmol['CC'] = $3Dmol.CC;
+$3Dmol['CC']['color'] = $3Dmol.CC.color;
 
-    // return true if a and b represent the same style
-    var sameObj = function(a,b) {
-        if(a && b)
-            return JSON.stringify(a) == JSON.stringify(b);
-        else
-            return a == b;
-    };    
 
-   
-    function GLModel(mid, defaultcolors) {
-        // private variables
-        var atoms = [];
-        var id = mid;
-        var molObj = null;
-        var renderedMolObj = null;
-        var lastColors = null;
-        var copyMatrices = []; //transformation + rot matrices
-        var idMatrix = new $3Dmol.Matrix4();
-        idMatrix.identity();
-        var noAssembly;
-        var dontDuplicateAtoms;
-        
-        var defaultColor = $3Dmol.elementColors.defaultColor;
-        
-        var ElementColors = (defaultcolors) ? defaultcolors : $3Dmol.elementColors.defaultColors;
 
+/** Return proper color for atom given style
+ * @param {AtomSpec} atom
+ * @param {AtomStyle} style
+ * @return {$3Dmol.Color}
+ */
+$3Dmol.getColorFromStyle = function(atom, style) {
+    var color = atom.color;
+    if (typeof (style.color) != "undefined" && style.color != "spectrum")
+        color = style.color;
+    if(typeof(style.colorscheme) != "undefined") {
+        if(typeof($3Dmol.elementColors[style.colorscheme]) != "undefined") {
+            //name of builtin colorscheme
+            var scheme = $3Dmol.elementColors[style.colorscheme];
+            if(typeof(scheme[atom.elem]) != "undefined") {
+                color = scheme[atom.elem];
+            }
+        } else if(typeof(style.colorscheme[atom.elem]) != 'undefined') {
+            //actual color scheme provided
+            color = style.colorscheme[atom.elem];
+        } else if(typeof(style.colorscheme.prop) != 'undefined' &&
+                typeof(style.colorscheme.gradient) != 'undefined') {         
+            //apply a property mapping
+            var prop = style.colorscheme.prop;
+            var scheme = style.colorscheme.gradient;
+            var range = scheme.range() || [-1,1]; //sensible default
+            var val = $3Dmol.getAtomProperty(atom, prop);
+            if(val != null) {
+                color = scheme.valueToHex(val, range);
+            }
+        }
+    } 
+    else if(typeof(style.colorfunc) != "undefined") {
+    	//this is a user provided function for turning an atom into a color
+    	color = style.colorfunc(atom);
+    }
+    
+    var C = $3Dmol.CC.color(color);
+    return C;
+}
 
-        // drawing functions must be associated with model object since
-        // geometries can't span multiple canvases
+/** Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
+ * @struct
+ */
+$3Dmol.elementColors = $3Dmol.elementColors || {};
 
-        // sphere drawing
-        var defaultSphereRadius = 1.5;
+$3Dmol.elementColors.defaultColor = 0xff1493;
 
-        // return proper radius for atom given style
-        /** 
-         * 
-         * @param {AtomSpec} atom
-         * @param {atomstyle} style
-         * @return {number} 
-         * 
-         */
-        var getRadiusFromStyle = function(atom, style) {
-            var r = defaultSphereRadius;
-            if (typeof (style.radius) != "undefined")
-                r = style.radius;
-            else if (vdwRadii[atom.elem])
-                r = vdwRadii[atom.elem];
+/** @property Jmol-like element colors*/
+$3Dmol.elementColors.Jmol = {
+        'H': 0xFFFFFF,
+        'He': 0xD9FFFF,
+        'HE': 0xD9FFFF,
+        'Li': 0xCC80FF,
+        'LI': 0xCC80FF,
+        'B': 0xFFB5B5,
+        'C': 0x909090,
+        'N': 0x3050F8,
+        'O': 0xFF0D0D,
+        'F': 0x90E050,
+        'Na': 0xAB5CF2,
+        'NA': 0xAB5CF2,
+        'Mg': 0x8AFF00,
+        'MG': 0x8AFF00,
+        'Al': 0xBFA6A6,
+        'AL': 0xBFA6A6,
+        'Si': 0xF0C8A0,
+        'SI': 0xF0C8A0,
+        'P': 0xFF8000,
+        'S': 0xFFFF30,
+        'Cl': 0x1FF01F,
+        'CL': 0x1FF01F,
+        'Ca': 0x3DFF00,
+        'CA': 0x3DFF00,
+        'Ti': 0xBFC2C7,
+        'TI': 0xBFC2C7,
+        'Cr': 0x8A99C7,
+        'CR': 0x8A99C7,
+        'Mn': 0x9C7AC7,
+        'MN': 0x9C7AC7,
+        'Fe': 0xE06633,
+        'FE': 0xE06633,
+        'Ni': 0x50D050,
+        'NI': 0x50D050,
+        'Cu': 0xC88033,
+        'CU': 0xC88033,
+        'Zn': 0x7D80B0,
+        'ZN': 0x7D80B0,
+        'Br': 0xA62929,
+        'BR': 0xA62929,
+        'Ag': 0xC0C0C0,
+        'AG': 0xC0C0C0,
+        'I': 0x940094,
+        'Ba': 0x00C900,
+        'BA': 0x00C900,
+        'Au': 0xFFD123,
+        'AU': 0xFFD123
+};
 
-            if (typeof (style.scale) != "undefined")
-                r *= style.scale;
-            return r;
-        };
+/** @property rasmol-like element colors */
+$3Dmol.elementColors.rasmol = {
+        'H': 0xFFFFFF,
+        'He': 0xFFC0CB,
+        'HE': 0xFFC0CB,
+        'Li': 0xB22222,
+        'LI': 0xB22222,
+        'B': 0x00FF00,
+        'C': 0xC8C8C8,
+        'N': 0x8F8FFF,
+        'O': 0xF00000,
+        'F': 0xDAA520,
+        'Na': 0x0000FF,
+        'NA': 0x0000FF,
+        'Mg': 0x228B22,
+        'MG': 0x228B22,
+        'Al': 0x808090,
+        'AL': 0x808090,
+        'Si': 0xDAA520,
+        'SI': 0xDAA520,
+        'P': 0xFFA500,
+        'S': 0xFFC832,
+        'Cl': 0x00FF00,
+        'CL': 0x00FF00,
+        'Ca': 0x808090,
+        'CA': 0x808090,
+        'Ti': 0x808090,
+        'TI': 0x808090,
+        'Cr': 0x808090,
+        'CR': 0x808090,
+        'Mn': 0x808090,
+        'MN': 0x808090,
+        'Fe': 0xFFA500,
+        'FE': 0xFFA500,
+        'Ni': 0xA52A2A,
+        'NI': 0xA52A2A,
+        'Cu': 0xA52A2A,
+        'CU': 0xA52A2A,
+        'Zn': 0xA52A2A,
+        'ZN': 0xA52A2A,
+        'Br': 0xA52A2A,
+        'BR': 0xA52A2A,
+        'Ag': 0x808090,
+        'AG': 0x808090,
+        'I': 0xA020F0,
+        'Ba': 0xFFA500,
+        'BA': 0xFFA500,
+        'Au': 0xDAA520,
+        'AU': 0xDAA520    
+};
 
-        // cross drawing
-        /** @typedef CrossStyleSpec
-         * @prop {boolean} hidden - do not show 
-         * @prop {number} linewidth 
-         * @prop {number} radius 
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        /**
-         * 
-         * @param {AtomSpec} atom
-         * @param {$3Dmol.Geometry[]} geos
-         */
-        var drawAtomCross = function(atom, geos) {
-            if (!atom.style.cross)
-                return;
-            var style = atom.style.cross;
-            if (style.hidden)
-                return;
-            var linewidth = (style.linewidth || defaultlineWidth);
-            if (!geos[linewidth])
-                geos[linewidth] = new $3Dmol.Geometry();
-                
-            var geoGroup = geos[linewidth].updateGeoGroup(6);
-            
-            var delta = getRadiusFromStyle(atom, style);
+$3Dmol.elementColors.defaultColors = $3Dmol.elementColors.rasmol;
 
-            var points = [ [ delta, 0, 0 ], [ -delta, 0, 0 ], [ 0, delta, 0 ],
-                    [ 0, -delta, 0 ], [ 0, 0, delta ], [ 0, 0, -delta ] ];
+$3Dmol.elementColors.greenCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
 
-            var clickable = atom.clickable;
-            if (clickable && atom.intersectionShape === undefined)
-                atom.intersectionShape = {sphere : [], cylinder : [], line : []};
-            
-            var c = $3Dmol.getColorFromStyle(atom, style);
-            
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            
-            for ( var j = 0; j < 6; j++) {
-                
-                var offset = geoGroup.vertices*3;
-                
-                geoGroup.vertices++;
-                vertexArray[offset] = atom.x + points[j][0];
-                vertexArray[offset+1] = atom.y + points[j][1];
-                vertexArray[offset+2] = atom.z + points[j][2];
-                colorArray[offset] = c.r;
-                colorArray[offset+1] = c.g;
-                colorArray[offset+2] = c.b;
-                
-                if (clickable){
-                    var point = new $3Dmol.Vector3(points[j][0], points[j][1], points[j][2]);
-                    
-                    //decrease cross size for selection to prevent misselection from atom overlap
-                    point.multiplyScalar(0.1);
-                    point.set(point.x+atom.x, point.y+atom.y, point.z+atom.z);
-                    atom.intersectionShape.line.push(point);
-                }
+$3Dmol.elementColors.cyanCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
 
-            }
-                        
-        };
+$3Dmol.elementColors.magentaCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
 
-        //from atom, return a normalized vector v that is orthogonal and along which
-        //it is appropraite to draw multiple bonds
-        var getSideBondV = function(atom, atom2, i) {
+$3Dmol.elementColors.yellowCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
 
-            var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-            var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
+$3Dmol.elementColors.whiteCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
 
-            var dir = p2.clone();
-            var v = null;
-            dir.sub(p1);
+$3Dmol.elementColors.orangeCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
 
-            var p1a, p1b, p2a, p2b;
-            var i2, j2, atom3, p3, dir2;
-            if (atom.bonds.length === 1) {
-                if (atom2.bonds.length === 1) {
-                    v = dir.clone();
-                    if (Math.abs(v.x) > 0.0001)
-                        v.y += 1;
-                    else
-                        v.x += 1;
-                } else {
-                    i2 = (i + 1) % atom2.bonds.length;
-                    j2 = atom2.bonds[i2];
-                    atom3 = atoms[j2];
-                    p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+$3Dmol.elementColors.purpleCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
 
-                    dir2 = p3.clone();
-                    dir2.sub(p1);
+$3Dmol.elementColors.blueCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
+//glcartoon.js
+//This contains all the routines for rendering a cartoon given a set
+//of atoms with assigned secondary structure
 
-                    v = dir2.clone();
-                    v.cross(dir);
-                }
-            } else {
-                // get vector 2 different neighboring atom
-                i2 = (i + 1) % atom.bonds.length;
-                j2 = atom.bonds[i2];
-                atom3 = atoms[j2];
-                p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+//TODO: generate normals directly in drawStrip and drawThinStrip
 
-                dir2 = p3.clone();
-                dir2.sub(p1);
+var $3Dmol = $3Dmol || {};
 
-                v = dir2.clone();
-                v.cross(dir);
-            }
 
-            // especially for C#C (triple bond) dir and dir2
-            // may be opposites resulting in a zero v
-            if (v.lengthSq() < 0.01) {
-                v = dir.clone();
-                if (Math.abs(v.x) > 0.0001)
-                    v.y += 1;
-                else
-                    v.x += 1;
-            }
+/**@typedef CartoonStyleSpec
+ * @prop {ColorSpec} color - strand color, may specify as 'spectrum'
+ * @prop {string} style - style of cartoon rendering (trace, oval, rectangle (default), parabola, edged)
+ * @prop {boolean} ribbon - whether to use constant strand width, disregarding secondary structure; use thickness to adjust radius
+ * @prop {boolean} arrows - whether to add arrows showing beta-sheet directionality; does not apply to trace or ribbon
+ * @prop {boolean} tubes - whether to display alpha helices as simple cylinders; does not apply to trace
+ * @prop {number} thickness - cartoon strand thickness, default is 0.4
+ * @prop {number} width - cartoon strand width, default is secondary structure-dependent; does not apply to trace or ribbon
+ * @prop {number} opacity - set opacity from 0-1; transparency is set per-chain with a warning outputted in the event of ambiguity
+ * @prop {}
+ * In nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which
+ * is 'N1' for purines (resn: 'A', 'G', 'DA', 'DG') and 'N3' for pyrimidines (resn: 'C', 'U', 'DC', 'DT').
+ * The different nucleobases can therefore be distinguished as follows:
+ * @example
+ * viewer.setStyle({resn:'DA', atom:'N1'}, {cartoon:{color:'red'}});
+ * viewer.setStyle({resn:'DG', atom:'N1'}, {cartoon:{color:'green'}});
+ * viewer.setStyle({resn:'DC', atom:'N3'}, {cartoon:{color:'blue'}});
+ * viewer.setStyle({resn:'DT', atom:'N3'}, {cartoon:{color:'yellow'}});
+ */
 
-            v.cross(dir);
-            v.normalize();
-            
-            return v;
-            
-            v.multiplyScalar(r * 1.5);
+/**
+ * @ignore
+ * @param {$3Dmol.Object3D} group
+ * @param {AtomSpec} atomlist
+ * @param {$3Dmol.Gradient} gradientscheme
+ */
+$3Dmol.drawCartoon = (function() {
 
-        }
-        
-        var getTripleBondPoints = function() {
-            
-            v.cross(dir);
-            v.normalize();
-            v.multiplyScalar(r * 3);
+    var defaultNum = 5; // for cross-sectional shape
+    var defaultDiv = 5; // for length-wise splicing
 
-            p1a = p1.clone();
-            p1a.add(v);
-            p1b = p1.clone();
-            p1b.sub(v);
+    var coilWidth = 0.5;
+    var helixSheetWidth = 1.3;
+    var nucleicAcidWidth = 0.8;
+    var arrowTipWidth = 0.1;
+    var defaultThickness = 0.4; 
 
-            p2a = p1a.clone();
-            p2a.add(dir);
-            p2b = p1b.clone();
-            p2b.add(dir);
+    // helper functions
+
+    // Catmull-Rom subdivision
+    var subdivide = function(_points, DIV) { // points as Vector3
+        var ret = [];
+        var points = _points;
+        points = []; // Smoothing test
+        points.push(_points[0]);
+        
+        var i, lim, size;
+        var p0, p1, p2, p3, v0, v1;
+        
+        for (i = 1, lim = _points.length - 1; i < lim; i++) {
+            p1 = _points[i]; p2 = _points[i + 1];
+            if (p1.smoothen)
+                points.push(new $3Dmol.Vector3((p1.x + p2.x) / 2, (p1.y + p2.y) / 2,
+                        (p1.z + p2.z) / 2));
+            else
+                points.push(p1);
         }
+        points.push(_points[_points.length - 1]);
+
         
-        var addLine = function(vertexArray, colorArray, offset, p1, p2, c1) {
-            //make line from p1 to p2, does not incremeant counts
-            vertexArray[offset] = p1.x; vertexArray[offset+1] = p1.y; vertexArray[offset+2] = p1.z;
-            colorArray[offset] = c1.r; colorArray[offset+1] = c1.g; colorArray[offset+2] = c1.b;
-            vertexArray[offset+3] = p2.x; vertexArray[offset+4] = p2.y; vertexArray[offset+5] = p2.z;
-            colorArray[offset+3] = c1.r; colorArray[offset+4] = c1.g; colorArray[offset+5] = c1.b;            
+        for (i = -1, size = points.length; i <= size - 3; i++) {
+            p0 = points[(i === -1) ? 0 : i];
+            p1 = points[i + 1]; p2 = points[i + 2];
+            p3 = points[(i === size - 3) ? size - 1 : i + 3];
+            v0 = new $3Dmol.Vector3().subVectors(p2, p0).multiplyScalar(0.5);
+            v1 = new $3Dmol.Vector3().subVectors(p3, p1).multiplyScalar(0.5);
+            if (p2.skip) continue;
+
+            for ( var j = 0; j < DIV; j++) {
+                var t = 1.0 / DIV * j;
+                var x = p1.x + t * v0.x + t * t * 
+                        (-3 * p1.x + 3 * p2.x - 2 * v0.x - v1.x) + t * t * t *
+                        (2 * p1.x - 2 * p2.x + v0.x + v1.x);
+                var y = p1.y + t * v0.y + t * t * 
+                        (-3 * p1.y + 3 * p2.y - 2 * v0.y - v1.y) + t * t * t *
+                        (2 * p1.y - 2 * p2.y + v0.y + v1.y);
+                var z = p1.z + t * v0.z + t * t * 
+                        (-3 * p1.z + 3 * p2.z - 2 * v0.z - v1.z) + t * t * t * 
+                        (2 * p1.z - 2 * p2.z + v0.z + v1.z);
+                        
+                var pt = new $3Dmol.Vector3(x, y, z);
+                
+                var atomIndex = Math.floor( (ret.length+2) / DIV);
+                
+                if (_points[atomIndex] !== undefined && _points[atomIndex].atom !== undefined)
+                    pt.atom = _points[atomIndex].atom;
+                    
+                ret.push(pt);
+            }
         }
+        ret.push(points[points.length - 1]);
+        return ret;
+    };
+
+    var drawThinStrip = function(group, p1, p2, colors, div, opacity) {
+    
+        var geo = new $3Dmol.Geometry(true);       
+        var offset, vertoffset;
+        var color, colori;
+
         
-        /**@typedef LineStyleSpec
-         * @prop {boolean} hidden - do not show line
-         * @prop {number} linewidth 
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
+        for ( var i = 0, lim = p1.length; i < lim; i++) {
+            
+            colori = Math.round(i*(colors.length-1)/lim);
+            color = $3Dmol.CC.color(colors[colori]);
+           
+            geoGroup = geo.updateGeoGroup(2);
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            offset = geoGroup.vertices; vertoffset = offset*3;
+            
+            vertexArray[vertoffset] = p1[i].x;
+            vertexArray[vertoffset+1] = p1[i].y;
+            vertexArray[vertoffset+2] = p1[i].z;
+            
+            vertexArray[vertoffset+3] = p2[i].x;
+            vertexArray[vertoffset+4] = p2[i].y;
+            vertexArray[vertoffset+5] = p2[i].z;
+            
+            for (var j = 0; j < 6; ++j)
+            {
+                colorArray[vertoffset+3*j] = color.r;
+                colorArray[vertoffset+1+3*j] = color.g;
+                colorArray[vertoffset+2+3*j] = color.b;
+            }
+           
+            if (i > 0) {
+                var faces = [offset, offset + 1, offset - 1, offset - 2];
+                var faceoffset = geoGroup.faceidx;
+                
+                faceArray[faceoffset] = faces[0]; faceArray[faceoffset+1] = faces[1]; faceArray[faceoffset+2] = faces[3];
+                faceArray[faceoffset+3] = faces[1]; faceArray[faceoffset+4] = faces[2]; faceArray[faceoffset+5] = faces[3];
+
+                geoGroup.faceidx += 6;
+            }
+            
+            geoGroup.vertices += 2;
+        }
         
-        // bonds - both atoms must match bond style
-        // standardize on only drawing for lowest to highest
-        /**
-         * 
-         * @param {AtomSpec}
-         *            atom
-         * @param {AtomSpec[]} atoms
-         * @param {$3Dmol.Geometry[]} geos
-         */
-        var drawBondLines = function(atom, atoms, geos) {
-            if (!atom.style.line)
-                return;
-            var style = atom.style.line;
-            if (style.hidden)
-                return;
+        geo.initTypedArrays();
+        geo.setUpNormals();
+        
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        if(typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        material.vertexColors = $3Dmol.FaceColors;
+        var mesh = new $3Dmol.Mesh(geo, material);
 
-            // have a separate geometry for each linewidth
-            var linewidth = (style.linewidth || defaultlineWidth);
+        group.add(mesh);
+    };
 
-            if (!geos[linewidth])
-                geos[linewidth] = new $3Dmol.Geometry();
-            /** @type {geometryGroup} */
-            var geoGroup = geos[linewidth].updateGeoGroup(2*atom.bonds.length);
+    var drawShapeStrip = function(group, points, colors, div, thickness, opacity, shape) {
+
+        // points is a 2D array, dimensionality given by [num = cross-sectional resolution][len = length of strip]
+        var i, j, num, len;
+        num = points.length;
+        if (num < 2 || points[0].length < 2) return;
+
+        div = div || axisDIV;
+        for (i = 0; i < num; i++) { // spline to generate greater length-wise resolution
+            points[i] = subdivide(points[i], div)
+        }
+        len = points[0].length;
+
+        if (!thickness) // if thickness is 0, we can use a smaller geometry than this function generates
+            return drawThinStrip(group, points[0], points[num-1], colors, div, opacity);
+
+
+        var geo = new $3Dmol.Geometry(true);
+        var axis, cs_shape, cs_bottom, cs_top, last_cs_bottom, last_cs_top;
+
+        // cache the available cross-sectional shapes
+        var cs_ellipse = [], cs_rectangle = [], cs_parabola = [];
+        for (j=0; j < num; j++) {
+            cs_ellipse.push(0.25 + 1.5*Math.sqrt((num-1)*j - Math.pow(j, 2))/(num-1));
+            cs_rectangle.push(0.5);
+            cs_parabola.push(2*(Math.pow(j/num, 2) - j/num) + 0.6);
+        }
+
+        /* face_refs array is used to generate faces from vertexArray iteratively.
+           As we move through each cross-sectional segment of points, we draw lateral
+           faces backwards to the previous cross-sectional segment.
+
+           To correctly identify the points needed to make each face we use this
+           array as a lookup table for the relative indices of each needed point
+           in the vertices array.
+
+           4 points are used to create 2 faces.
+        */
+
+        var face_refs = [];
+        for (j = 0; j < num*2-1; j++) {
+            /* [curr vertex in curr cross-section,
+                next vertex in curr cross-section,
+                next vertex in prev cross-section,
+                curr vertex in prev cross-section] */
+            face_refs[j] = [j, j+1, j+1-2*num, j-2*num];
+        }
+        // last face is different. easier to conceptualize this by drawing a diagram
+        face_refs[num*2-1] = [j, j+1-2*num, j+1-4*num, j-2*num];
+
+                
+        var v_offset, va_offset, f_offset;
+        var currentAtom, lastAtom
+        var color, colori;
+        var geoGroup = geo.updateGeoGroup(2*num*len); // ensure vertex capacity
+        
+        for (i = 0; i < len; i++) {
+        
+            colori = Math.round(i*(colors.length-1)/len);
+            color = $3Dmol.CC.color(colors[colori]);
+            
+            last_cs_bottom = cs_bottom;
+            last_cs_top = cs_top;
+            cs_bottom = [];
+            cs_top = [];
+            axis = [];
+
+            if (points[0][i].atom !== undefined) // TODO better edge case handling
+            {
+                currentAtom = points[0][i].atom;
+                if (shape === "oval")
+                    cs_shape = cs_ellipse;
+                else if (shape === "rectangle")
+                    cs_shape = cs_rectangle;
+                else if (shape === "parabola")
+                    cs_shape = cs_parabola;
+            }
+            if (!cs_shape) cs_shape = cs_rectangle;
+
+            
+            // calculate thickness at each width point, from cross-sectional shape
+            var toNext, toSide;
+            for (j = 0; j < num; j++)
+            {
+                if (i < len-1)
+                    toNext = points[j][i+1].clone().sub(points[j][i]);
+                else
+                    toNext = points[j][i-1].clone().sub(points[j][i]).negate();
+
+                if (j < num-1)
+                    toSide = points[j+1][i].clone().sub(points[j][i]);
+                else
+                    toSide = points[j-1][i].clone().sub(points[j][i]).negate();
+
+                axis[j] = toSide.cross(toNext).normalize().multiplyScalar(thickness*cs_shape[j]);
+            }
+
+            // generate vertices by applying cross-sectional shape thickness to input points
+            for (j = 0; j < num; j++)
+                cs_bottom[j] = points[j][i].clone().add(axis[j].clone().negate());
+            for (j = 0; j < num; j++)
+                cs_top[j] = points[j][i].clone().add(axis[j]);
             
+
+            /* Until this point the vertices have been dealt with as $3Dmol.Vector3() objects,
+               but we need to serialize them into the geoGroup.vertexArray, where every three
+               indices represents the next vertex. The colorArray is analogous.
+
+               In the following for-loops, j iterates through VERTICES so we need to index
+               them in vertexArray by 3*j + either 0, 1, or 2 for xyz or rgb component.
+            */
+
             var vertexArray = geoGroup.vertexArray;
             var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            v_offset = geoGroup.vertices; va_offset = v_offset*3; // in case geoGroup already contains vertices
+
+            // bottom edge of cross-section, vertices [0, num)
+            for (j = 0; j < num; j++) {
+                vertexArray[va_offset + 3*j + 0] = cs_bottom[j].x;
+                vertexArray[va_offset + 3*j + 1] = cs_bottom[j].y;
+                vertexArray[va_offset + 3*j + 2] = cs_bottom[j].z;
+            }
+
+            // top edge of cross-section, vertices [num, 2*num)
+            // add these backwards, so that each cross-section's vertices are added sequentially to vertexArray
+            for (j = 0; j < num; j++) {
+                vertexArray[va_offset + 3*j + 0 + 3*num] = cs_top[num-1-j].x;
+                vertexArray[va_offset + 3*j + 1 + 3*num] = cs_top[num-1-j].y;
+                vertexArray[va_offset + 3*j + 2 + 3*num] = cs_top[num-1-j].z;
+            }
             
-            for ( var i = 0; i < atom.bonds.length; i++) {
-                var j = atom.bonds[i]; // our neighbor
+            for (j = 0; j < 2*num; ++j) {
+                colorArray[va_offset + 3*j + 0] = color.r;
+                colorArray[va_offset + 3*j + 1] = color.g;
+                colorArray[va_offset + 3*j + 2] = color.b;
+            }
+            
+            if (i > 0) {
+             
+                for (j = 0; j < num*2; j++) {
                 
-                var atom2 = atoms[j];
-                if (!atom2.style.line)
-                    continue; // don't sweat the details
+                    // get VERTEX indices of the 4 points of a rectangular face (as opposed to literal vertexArray indices)
+                    var face = [v_offset + face_refs[j][0],
+                                v_offset + face_refs[j][1],
+                                v_offset + face_refs[j][2],
+                                v_offset + face_refs[j][3]];
+                    
+                    f_offset = geoGroup.faceidx;    
+                    
+                    // need 2 triangles to draw a face between 4 points
+                    faceArray[f_offset]   = face[0];
+                    faceArray[f_offset+1] = face[1]; 
+                    faceArray[f_offset+2] = face[3];
+
+                    faceArray[f_offset+3] = face[1];
+                    faceArray[f_offset+4] = face[2];
+                    faceArray[f_offset+5] = face[3];
+                    
+                    geoGroup.faceidx += 6;
 
-                if (atom.serial >= atom2.serial) // only draw if less, this way we can do multi bonds correctly
-                    continue;
-                var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);                
-                var mp = p1.clone().add(p2).multiplyScalar(0.5);
-                var singleBond = false;               
-                
-                if (atom.clickable){
-                    if (atom.intersectionShape === undefined)
-                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                    atom.intersectionShape.line.push(p1);
-                    atom.intersectionShape.line.push(p2);
+                    // TODO implement clickable the right way. midpoints of strand between consecutive atoms
                 }
+                    
+                if (currentAtom.clickable)
+                {
+                    var faces = [];
 
-                if (atom2.clickable){
-                    if (atom2.intersectionShape === undefined)
-                        atom2.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                    atom2.intersectionShape.line.push(p2);
-                    atom2.intersectionShape.line.push(p1);
-                }
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[0], cs_bottom[0], cs_bottom[num-1]));
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[0], cs_bottom[num-1], last_cs_bottom[num-1]));
 
-                var c1 = $3Dmol.getColorFromStyle(atom, atom.style.line);
-                var c2 = $3Dmol.getColorFromStyle(atom2, atom2.style.line);
-               
-                if(atom.bondStyles && atom.bondStyles[i]) {
-                    var bstyle = atom.bondStyles[i];
-                    if(!bstyle.iswire) {
-                        continue;
-                    }
-                    if(bstyle.radius) bondR = bstyle.radius;
-                    if(bstyle.singleBond) singleBond = true;
-                    if(typeof(bstyle.color1) != "undefined") {
-                        c1 = $3Dmol.CC.color(bstyle.color1);
-                    }
-                    if(typeof(bstyle.color2) != "undefined") {
-                        c2 = $3Dmol.CC.color(bstyle.color2);
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[num-1], cs_bottom[num-1], cs_top[num-1]));
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[num-1], cs_top[num-1], last_cs_top[num-1]));
+
+                    faces.push(new $3Dmol.Triangle(cs_top[0], last_cs_top[0], last_cs_top[num-1]));
+                    faces.push(new $3Dmol.Triangle(cs_top[num-1], cs_top[0], last_cs_top[num-1]));
+
+                    faces.push(new $3Dmol.Triangle(cs_bottom[0], last_cs_bottom[0], last_cs_top[0]));
+                    faces.push(new $3Dmol.Triangle(cs_top[0], cs_bottom[0], last_cs_top[0]));
+
+                    for (j in faces)
+                    {
+                        currentAtom.intersectionShape.triangle.push(faces[j]);
+                        
                     }
                 }
 
-                var offset = geoGroup.vertices*3;
-                
-                if(atom.bondOrder[i] > 1 && atom.bondOrder[i] < 4 && !singleBond) {
-                    var v = getSideBondV(atom, atom2, i);
-                    var dir = p2.clone();
-                    dir.sub(p1);
-                    
-                    if(atom.bondOrder[i] == 2) { //double
-                        
-                        v.multiplyScalar(.1);
-                           p1a = p1.clone();
-                        p1a.add(v);
-                        p1b = p1.clone();
-                        p1b.sub(v);
+            }
+            
+            geoGroup.vertices += 2*num;
+            lastAtom = currentAtom;
+        }
 
-                        p2a = p1a.clone();
-                        p2a.add(dir);
-                        p2b = p1b.clone();
-                        p2b.add(dir);
-                        
-                        if(c1 == c2) {
-                            geoGroup.vertices += 4;
-                            addLine(vertexArray, colorArray, offset, p1a, p2a, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, p1b, p2b, c1);                            
-                        }
-                        else {
-                            geoGroup.vertices += 8;
-                            dir.multiplyScalar(0.5);
-                            var mpa = p1a.clone();
-                            mpa.add(dir);
-                            var mpb = p1b.clone();
-                            mpb.add(dir);
-                            
-                            addLine(vertexArray, colorArray, offset, p1a, mpa, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, mpa, p2a, c2);                            
-                            addLine(vertexArray, colorArray, offset+12, p1b, mpb, c1); 
-                            addLine(vertexArray, colorArray, offset+18, mpb, p2b, c2); 
-                        }
-                    }
-                    else if(atom.bondOrder[i] == 3) { //triple
-                        
-                        v.multiplyScalar(.1);
-                           p1a = p1.clone();
-                        p1a.add(v);
-                        p1b = p1.clone();
-                        p1b.sub(v);
+        // for terminal faces
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        v_offset = geoGroup.vertices; va_offset = v_offset*3; f_offset = geoGroup.faceidx;
 
-                        p2a = p1a.clone();
-                        p2a.add(dir);
-                        p2b = p1b.clone();
-                        p2b.add(dir);
-                        
-                        if(c1 == c2) {
-                            geoGroup.vertices += 6;
-                            addLine(vertexArray, colorArray, offset, p1, p2, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, p1a, p2a, c1);                            
-                            addLine(vertexArray, colorArray, offset+12, p1b, p2b, c1);                            
-                        }
-                        else {
-                            geoGroup.vertices += 12;
-                            dir.multiplyScalar(0.5);
-                            var mpa = p1a.clone();
-                            mpa.add(dir);
-                            var mpb = p1b.clone();
-                            mpb.add(dir);
+        for (i = 0; i<num-1; i++) // "rear" face
+        {
+            var face = [i, i+1, 2*num-2-i, 2*num-1-i];
 
-                            addLine(vertexArray, colorArray, offset, p1, mp, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, mp, p2, c2);
-                            addLine(vertexArray, colorArray, offset+12, p1a, mpa, c1);                            
-                            addLine(vertexArray, colorArray, offset+18, mpa, p2a, c2);                            
-                            addLine(vertexArray, colorArray, offset+24, p1b, mpb, c1); 
-                            addLine(vertexArray, colorArray, offset+30, mpb, p2b, c2); 
-                        }
-                    }
-                }
-                else { //single bond                                    
-                    if(c1 == c2) {
-                        geoGroup.vertices += 2;
-                        addLine(vertexArray, colorArray, offset, p1, p2, c1);
-                    } else {
-                        geoGroup.vertices += 4;
-                        addLine(vertexArray, colorArray, offset, p1, mp, c1);
-                        addLine(vertexArray, colorArray, offset+6, mp, p2, c2);                        
-                    }
-                    
-                }
-            }
+            f_offset = geoGroup.faceidx;
 
-        };
+            faceArray[f_offset]   = face[0];
+            faceArray[f_offset+1] = face[1]; 
+            faceArray[f_offset+2] = face[3];
 
-        // bonds as cylinders
-        var defaultStickRadius = 0.25;
+            faceArray[f_offset+3] = face[1];
+            faceArray[f_offset+4] = face[2];
+            faceArray[f_offset+5] = face[3];
 
-        /**@typedef SphereStyleSpec
-         * @prop {boolean} hidden - do not show atom
-         * @prop {number} radius - override van der waals radius
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
+            geoGroup.faceidx += 6;
+        }
+
+        for (i = 0; i<num-1; i++) // "front" face
+        {
+            var face = [v_offset-1-i, v_offset-2-i, v_offset-2*num+i+1, v_offset-2*num+i];
+
+            f_offset = geoGroup.faceidx;
+
+            faceArray[f_offset]   = face[0];
+            faceArray[f_offset+1] = face[1]; 
+            faceArray[f_offset+2] = face[3];
+
+            faceArray[f_offset+3] = face[1];
+            faceArray[f_offset+4] = face[2];
+            faceArray[f_offset+5] = face[3];
+
+            geoGroup.faceidx += 6;
+        }
         
-        //sphere drawing
-        //See also: drawCylinder
-        /** 
-         * 
-         * @param {AtomSpec} atom
-         * @param {$3Dmol.Geometry} geo
-         */
-        var drawAtomSphere = function(atom, geo) {
-            
-            if (!atom.style.sphere)
-                return;
-            var style = atom.style.sphere;
-            if (style.hidden)
-                return;
-                                                                 
-            var C = $3Dmol.getColorFromStyle(atom, style);
-            
-            var x, y;
-            var radius = getRadiusFromStyle(atom, style);
-            
-            if ((atom.clickable === true) && (atom.intersectionShape !== undefined)) {
-                var center = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                atom.intersectionShape.sphere.push(new $3Dmol.Sphere(center, radius));
-            }
-            
-            $3Dmol.GLDraw.drawSphere(geo, atom, radius, C);    
-            
-        };
+        geo.initTypedArrays();
+        geo.setUpNormals();
         
-        //dkoes - test code for sphere imposters
-        var drawAtomImposter = function(atom, geo) {
-            
-            if (!atom.style.spherei)
-                return;
-            var style = atom.style.spherei;
-            if (style.hidden)
-                return;
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        material.vertexColors = $3Dmol.FaceColors;
+        if (typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        var mesh = new $3Dmol.Mesh(geo, material);
+        group.add(mesh);
+    };
+
+    var drawPlainStrip = function(group, points, colors, div, thickness, opacity) {
+        if ((points.length) < 2)
+            return;
+
+        var p1, p2;
+        p1 = points[0];
+        p2 = points[points.length-1];
+
+        div = div || axisDIV;
+        p1 = subdivide(p1, div);
+        p2 = subdivide(p2, div);
+        if (!thickness)
+            return drawThinStrip(group, p1, p2, colors, div, opacity);
+
+        var geo = new $3Dmol.Geometry(true);
+        
+        //var vs = geo.vertices, fs = geo.faces;
+        var vs = [], fs = [];
+        var axis, p1v, p2v, a1v, a2v;
+        
+        var faces = [ [ 0, 2, -6, -8 ],
+                      [ -4, -2, 6, 4 ],
+                      [ 7, -1, -5, 3 ],
+                      [ -3, 5, 1, -7 ] ];
+                
+        var offset, vertoffset, faceoffset;
+        var color, colori;
+        var currentAtom, lastAtom;
+        var i, lim, j;
+        var face1, face2, face3;
+        var geoGroup;
+        
+        for (i = 0, lim = p1.length; i < lim; i++) {
+        
+            colori = Math.round(i*(colors.length-1)/lim);
+            color = $3Dmol.CC.color(colors[colori]);
             
-            var radius = getRadiusFromStyle(atom, style);
-            var C = $3Dmol.getColorFromStyle(atom, style);
+            vs.push(p1v = p1[i]); // 0
+            vs.push(p1v);         // 1
+            vs.push(p2v = p2[i]); // 2
+            vs.push(p2v);         // 3
+            if (i < lim - 1) {
+                var toNext = p1[i + 1].clone().sub(p1[i]);
+                var toSide = p2[i].clone().sub(p1[i]);
+                axis = toSide.cross(toNext).normalize().multiplyScalar(
+                        thickness);
+            }
+            vs.push(a1v = p1[i].clone().add(axis)); // 4
+            vs.push(a1v); // 5
+            vs.push(a2v = p2[i].clone().add(axis)); // 6
+            vs.push(a2v); // 7
             
-            //create flat square                       
+            if (p1v.atom !== undefined)
+                currentAtom = p1v.atom;
             
-            var geoGroup = geo.updateGeoGroup(4);
-            var startv =  geoGroup.vertices;
-            var start = startv*3;
+            geoGroup = geo.updateGeoGroup(8);
             var vertexArray = geoGroup.vertexArray;
             var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            offset = geoGroup.vertices; vertoffset = offset*3;
             
-            //use center point for each vertex
-            for(var i = 0; i < 4; i++) {
-                vertexArray[start+3*i] = atom.x;
-                vertexArray[start+3*i+1] = atom.y ;
-                vertexArray[start+3*i+2] = atom.z;                           
-            }
+            vertexArray[vertoffset]    = p1v.x; vertexArray[vertoffset+1]  = p1v.y; vertexArray[vertoffset+2]  = p1v.z;
+            vertexArray[vertoffset+3]  = p1v.x; vertexArray[vertoffset+4]  = p1v.y; vertexArray[vertoffset+5]  = p1v.z;
+            vertexArray[vertoffset+6]  = p2v.x; vertexArray[vertoffset+7]  = p2v.y; vertexArray[vertoffset+8]  = p2v.z;
+            vertexArray[vertoffset+9]  = p2v.x; vertexArray[vertoffset+10] = p2v.y; vertexArray[vertoffset+11] = p2v.z;
+            vertexArray[vertoffset+12] = a1v.x; vertexArray[vertoffset+13] = a1v.y; vertexArray[vertoffset+14] = a1v.z;
+            vertexArray[vertoffset+15] = a1v.x; vertexArray[vertoffset+16] = a1v.y; vertexArray[vertoffset+17] = a1v.z;
+            vertexArray[vertoffset+18] = a2v.x; vertexArray[vertoffset+19] = a2v.y; vertexArray[vertoffset+20] = a2v.z;
+            vertexArray[vertoffset+21] = a2v.x; vertexArray[vertoffset+22] = a2v.y; vertexArray[vertoffset+23] = a2v.z;
             
-
-            //same colors for all 4 vertices
-            var normalArray = geoGroup.normalArray;
-            var colorArray = geoGroup.colorArray;
-            for(var i = 0; i < 4; i++) {
-                colorArray[start+3*i] = C.r;
-                colorArray[start+3*i+1] = C.g;
-                colorArray[start+3*i+2] = C.b;
-                
+            for (j = 0; j < 8; ++j) {                
+                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
             }
             
-            normalArray[start+0] = -radius;
-            normalArray[start+1] = -radius;
-            normalArray[start+2] = 0;
-            
-            normalArray[start+3] = -radius;
-            normalArray[start+4] = radius;
-            normalArray[start+5] = 0;
-            
-            normalArray[start+6] = radius;
-            normalArray[start+7] = radius;
-            normalArray[start+8] = 0;
-            
-            normalArray[start+9] = radius;
-            normalArray[start+10] = -radius;
-            normalArray[start+11] = 0;
-            
-            geoGroup.vertices += 4;
-            
-            //two faces
-            var faceArray = geoGroup.faceArray;
-            var faceoffset = geoGroup.faceidx; //not number faces, but index
-            faceArray[faceoffset+0] = startv;
-            faceArray[faceoffset+1] = startv+1;
-            faceArray[faceoffset+2] = startv+2;
-            faceArray[faceoffset+3] = startv+2;
-            faceArray[faceoffset+4] = startv+3;
-            faceArray[faceoffset+5] = startv;
-            geoGroup.faceidx += 6;
-            
-        };
-                
-           
-        /**@typedef StickStyleSpec
-         * @prop {boolean} hidden - do not show 
-         * @prop {number} radius 
-         * @prop {boolean} singleBonds - draw all bonds as single bonds if set
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        // draws cylinders and small spheres (at bond radius)
-        var drawBondSticks = function(atom, atoms, geo) {
-            if (!atom.style.stick)
-                return;
-            var style = atom.style.stick;
-            if (style.hidden)
-                return;
-
-            var atomBondR = style.radius || defaultStickRadius;
-            var bondR = atomBondR;
-            var atomSingleBond = style.singleBonds || false;
-            var fromCap = false, toCap = false;
-
-            var C1 = $3Dmol.getColorFromStyle(atom, style);
-
-            var mp, mp1, mp2;
-            
-            if (!atom.capDrawn && atom.bonds.length < 4)
-                fromCap = true;              
+            if (i > 0) {
+             
+                //both points have distinct atoms
+                var diffAtoms = ((lastAtom !== undefined && currentAtom !== undefined) && lastAtom.serial !== currentAtom.serial);
                 
-            for (var i = 0; i < atom.bonds.length; i++) {
-                var j = atom.bonds[i]; // our neighbor
-                var atom2 = atoms[j]; //parsePDB, etc should only add defined bonds
+                for (j = 0; j < 4; j++ ) {
                 
-                if (atom.serial < atom2.serial) {// only draw if less, this
-                    // lets us combine
-                    // cylinders of the same
-                    // color
-                    var style2 = atom2.style;
-                    if (!style2.stick)
-                        continue; // don't sweat the details                     
-                   
-                    var C2 = $3Dmol.getColorFromStyle(atom2, style2.stick);
+                    var face = [offset + faces[j][0], offset + faces[j][1], offset + faces[j][2], offset + faces[j][3]];
                     
-                    //support bond specific styles
-                    bondR = atomBondR;                    
-                    var singleBond = atomSingleBond;
-                    if(atom.bondStyles && atom.bondStyles[i]) {
-                        var bstyle = atom.bondStyles[i];
-                        if(bstyle.iswire) {
-                            continue;
-                        }
-                        if(bstyle.radius) bondR = bstyle.radius;
-                        if(bstyle.singleBond) singleBond = true;
-                        if(typeof(bstyle.color1) != "undefined") {
-                            C1 = $3Dmol.CC.color(bstyle.color1);
-                        }
-                        if(typeof(bstyle.color2) != "undefined") {
-                            C2 = $3Dmol.CC.color(bstyle.color2);
-                        }
-                    }
-                    var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                    var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
-
-                    // draw cylinders
-                    if (atom.bondOrder[i] === 1 || singleBond) {
-
-                        if (!atom2.capDrawn && atom2.bonds.length < 4)
-                            toCap = true;       
-                                                
-                        if (C1 != C2) {
-                            mp = new $3Dmol.Vector3().addVectors(p1, p2)
-                                    .multiplyScalar(0.5);
-                            $3Dmol.GLDraw.drawCylinder(geo, p1, mp, bondR, C1, fromCap, false);
-                            $3Dmol.GLDraw.drawCylinder(geo, mp, p2, bondR, C2, false, toCap);
-                        } else {
-                            $3Dmol.GLDraw.drawCylinder(geo, p1, p2, bondR, C1, fromCap, toCap);
-                        }
-                        
-                        if (atom.clickable || atom2.clickable) {
-                            mp = new $3Dmol.Vector3().addVectors(p1, p2).multiplyScalar(0.5);
-                            if (atom.clickable){
-                                var cylinder1 = new $3Dmol.Cylinder(p1 , mp , bondR);
-                                var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                atom.intersectionShape.cylinder.push(cylinder1);   
-                                atom.intersectionShape.sphere.push(sphere1);                             
-                            }
-                            if (atom2.clickable){
-                                var cylinder2 = new $3Dmol.Cylinder(p2 , mp , bondR);
-                                var sphere2 = new $3Dmol.Sphere(p2 , bondR);
-                                atom2.intersectionShape.cylinder.push(cylinder2);
-                                atom2.intersectionShape.sphere.push(sphere2);
-                            }
-
-                        }
-                        
-                    } 
+                    faceoffset = geoGroup.faceidx;    
                     
-                    else if (atom.bondOrder[i] > 1) {
-                        var mfromCap = false; mtoCap = false; //multi bond caps
+                    faceArray[faceoffset] = face[0]; faceArray[faceoffset+1] = face[1]; faceArray[faceoffset+2] = face[3];
+                    faceArray[faceoffset+3] = face[1]; faceArray[faceoffset+4] = face[2]; faceArray[faceoffset+5] = face[3];
+                    
+                    geoGroup.faceidx += 6;
+                    
+                    if (currentAtom.clickable || lastAtom.clickable) {
                         
-                        if(bondR != atomBondR) {
-                            //assume jmol style multiple bonds - the radius doesn't fit within atom sphere
-                            mfromCap = true;
-                            mtoCap = true;
-                        }
+                        var p1a = vs[face[3]].clone(), p1b = vs[face[0]].clone(),
+                            p2a = vs[face[2]].clone(), p2b = vs[face[1]].clone();
                         
-                        var dir = p2.clone();
-                        var v = null;
-                        dir.sub(p1);
+                        p1a.atom = vs[face[3]].atom || null; //should be same
+                        p2a.atom = vs[face[2]].atom || null; 
                         
-                        var r, p1a, p1b, p2a, p2b;
-                        var v = getSideBondV(atom, atom2, i);
                         
-                        if (atom.bondOrder[i] == 2) {
-                            var r = bondR/2.5;
-                            var v = getSideBondV(atom, atom2, i);
+                        p1b.atom = vs[face[0]].atom || null; //should be same                      
+                        p2b.atom = vs[face[1]].atom || null; 
+                        
+                        if (diffAtoms) {
+                            var m1 = p1a.clone().add(p1b).multiplyScalar(0.5);
+                            var m2 = p2a.clone().add(p2b).multiplyScalar(0.5);
+                            var m = p1a.clone().add(p2b).multiplyScalar(0.5);
                             
-                            v.multiplyScalar(r*1.5);
-                            p1a = p1.clone();
-                            p1a.add(v);
-                            p1b = p1.clone();
-                            p1b.sub(v);
-
-                            p2a = p1a.clone();
-                            p2a.add(dir);
-                            p2b = p1b.clone();
-                            p2b.add(dir);
-
-                                                                 
-                            if (C1 != C2) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, mp, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp, p2a, r, C2, false, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, mp2, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp2, p2b, r, C2, false, mtoCap);
-                            } else {
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
-                            }
-                            if (atom.clickable || atom2.clickable){
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                               .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                                .multiplyScalar(0.5);
-                                if (atom.clickable) {
-                                    cylinder1a = new $3Dmol.Cylinder(p1a , mp , r);
-                                    cylinder1b = new $3Dmol.Cylinder(p1b , mp2 , r);
-                                    atom.intersectionShape.cylinder.push(cylinder1a);
-                                    atom.intersectionShape.cylinder.push(cylinder1b);
-                                    
-                                    var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                    atom.intersectionShape.sphere.push(sphere1);                             
+                            if (j % 2 === 0)
+                            {
+                                if (lastAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
+                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
+                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
+                                    lastAtom.intersectionShape.triangle.push(face1);
+                                    lastAtom.intersectionShape.triangle.push(face2);
+                                    lastAtom.intersectionShape.triangle.push(face3);
                                 }
-                                if (atom2.clickable) {
-                                    cylinder2a = new $3Dmol.Cylinder(p2a , mp , r);
-                                    cylinder2b = new $3Dmol.Cylinder(p2b , mp2 , r);
-                                    atom2.intersectionShape.cylinder.push(cylinder2a);
-                                    atom2.intersectionShape.cylinder.push(cylinder2b);          
-                                    var sphere2 = new $3Dmol.Sphere(p2, bondR);
-                                    atom2.intersectionShape.sphere.push(sphere1);  
+                                
+                                if (currentAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
+                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
+                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
+                                    currentAtom.intersectionShape.triangle.push(face1);
+                                    currentAtom.intersectionShape.triangle.push(face2);
+                                    currentAtom.intersectionShape.triangle.push(face3);
                                 }
                             }
-                        } 
-                        else if (atom.bondOrder[i] == 3) {
-                            r = bondR / 4;
-                            v.cross(dir);
-                            v.normalize();
-                            v.multiplyScalar(r * 3);
-
-                            p1a = p1.clone();
-                            p1a.add(v);
-                            p1b = p1.clone();
-                            p1b.sub(v);
-
-                            p2a = p1a.clone();
-                            p2a.add(dir);
-                            p2b = p1b.clone();
-                            p2b.add(dir);
-
-                            if (C1 != C2) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
-                                        .multiplyScalar(0.5);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, mp, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp, p2a, r, C2, false, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1, mp3, r, C1, fromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp3, p2, r, C2, false, toCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, mp2, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp2, p2b, r, C2, false, mtoCap);
-                            } else {
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1, p2, r, C1, fromCap, toCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
-
-                            }
-                            if (atom.clickable || atom2.clickable) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
-                                        .multiplyScalar(0.5);
-                                                                
-                                if (atom.clickable) {
-                                    cylinder1a = new $3Dmol.Cylinder(p1a.clone(), mp.clone(), r);
-                                    cylinder1b = new $3Dmol.Cylinder(p1b.clone(), mp2.clone(), r);
-                                    cylinder1c = new $3Dmol.Cylinder(p1.clone(), mp3.clone(), r);
-                                    atom.intersectionShape.cylinder.push(cylinder1a);
-                                    atom.intersectionShape.cylinder.push(cylinder1b);
-                                    atom.intersectionShape.cylinder.push(cylinder1c);
-                                    var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                    atom.intersectionShape.sphere.push(sphere1);  
-                                } 
-                                if (atom2.clickable) {                               
-                                    cylinder2a = new $3Dmol.Cylinder(p2a.clone(), mp.clone(), r);
-                                    cylinder2b = new $3Dmol.Cylinder(p2b.clone(), mp2.clone(), r);
-                                    cylinder2c = new $3Dmol.Cylinder(p2.clone(), mp3.clone(), r);
-                                    atom2.intersectionShape.cylinder.push(cylinder2a);
-                                    atom2.intersectionShape.cylinder.push(cylinder2b);
-                                    atom2.intersectionShape.cylinder.push(cylinder2c);      
-                                    var sphere1 = new $3Dmol.Sphere(p2 , bondR);
-                                    atom2.intersectionShape.sphere.push(sphere1);  
+                            else {
+                                if (currentAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
+                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
+                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
+                                    currentAtom.intersectionShape.triangle.push(face1);
+                                    currentAtom.intersectionShape.triangle.push(face2);
+                                    currentAtom.intersectionShape.triangle.push(face3);
                                 }
+                                
+                                if (lastAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
+                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
+                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
+                                    lastAtom.intersectionShape.triangle.push(face1);
+                                    lastAtom.intersectionShape.triangle.push(face2);
+                                    lastAtom.intersectionShape.triangle.push(face3);
+                                }                          
                             }
+                            
                         }
+                        
+                        //face for single atom
+                        else if (currentAtom.clickable) {
+                            face1 = new $3Dmol.Triangle(p1b, p2b, p1a);
+                            face2 = new $3Dmol.Triangle(p2b, p2a, p1a);
+                            currentAtom.intersectionShape.triangle.push(face1);
+                            currentAtom.intersectionShape.triangle.push(face2);
+                        }
+                        
                     }
-                     
-                }                   
-                                 
-            }            
-
-            // draw non bonded heteroatoms as spheres
-            var drawSphere = false;
-            var numsinglebonds = 0;
-            var differentradii = false;
-            //also, if any bonds were drawn as multiples, need sphere
-            for(var i = 0; i < atom.bonds.length; i++) {
-                var singleBond = atomSingleBond;
-                if(atom.bondStyles && atom.bondStyles[i]) {
-                    var bstyle = atom.bondStyles[i];
-                    if(bstyle.singleBond) singleBond = true;
-                    if(bstyle.radius && bstyle.radius != atomBondR) {
-                        differentradii = true;
-                    }
-                }
-                if(singleBond || atom.bondOrder[i] == 1) {
-                    numsinglebonds++;
+                    
                 }
             }
             
-            if(differentradii) { //jmol style double/triple bonds - no sphere
-                if(numsinglebonds > 0) drawSphere = true; //unless needed as a cap
-            }
-            else if(numsinglebonds == 0 && atom.bonds.length > 0) {
-                drawSphere = true;
-            }
-           
-            if (drawSphere) {
-                var savedstyle = atom.style;
-                bondR = atomBondR;
-                //do not use bond style as this can be variable, particularly
-                //with jmol export of double/triple bonds
-                $3Dmol.GLDraw.drawSphere(geo, atom, bondR, C1);    
-            }
-            
-        };
-
-        // go through all the atoms and regenerate their geometries
-        // we try to have one geometry for each style since this is much much
-        // faster
-        // at some point we should optimize this to avoid unnecessary
-        // recalculation
-        /** param {AtomSpec[]} atoms */
-        var createMolObj = function(atoms) {
+            geoGroup.vertices += 8;
+            lastAtom = currentAtom;
+        }
+        
 
-            //console.log("creating for "+id);
-            var ret = new $3Dmol.Object3D();
-            var cartoonAtoms = [];
-            var lineGeometries = {};
-            var crossGeometries = {};
-            var sphereGeometry = new $3Dmol.Geometry(true);                                                         
-            var imposterGeometry = new $3Dmol.Geometry(true);                                                         
-            var stickGeometry = new $3Dmol.Geometry(true);
-            var cartoonGeometry = new $3Dmol.Geometry(true);
-            var i, n;
-            var range = [Number.POSITIVE_INFINITY, Number.NEGATIVE_INFINITY];
-            for (i = 0, n = atoms.length; i < n; i++) {
-                var atom = atoms[i];
-                // recreate gl info for each atom as necessary
-                // set up appropriate intersection spheres for clickable atoms
-                if (atom && atom.style) {
-                    if (atom.clickable && atom.intersectionShape === undefined)
-                        atom.intersectionShape = {sphere: [], cylinder: [], line: [], triangle : []};                    
-                    drawAtomSphere(atom, sphereGeometry);
-                    drawAtomImposter(atom, imposterGeometry);
-                    drawAtomCross(atom, crossGeometries);
-                    drawBondLines(atom, atoms, lineGeometries);
-                    drawBondSticks(atom, atoms, stickGeometry);
-                    if (typeof (atom.style.cartoon) !== "undefined" && !atom.style.cartoon.hidden) {
-                        //gradient color scheme range
-                        if (atom.style.cartoon.color === 'spectrum' && typeof(atom.resi) === "number") {                            
-                            if (atom.resi < range[0])
-                                range[0] = atom.resi;
-                            if (atom.resi > range[1])
-                                range[1] = atom.resi;
-                        }
-                        
-                        cartoonAtoms.push(atom);
-                    }
-                    
-
-                }
-            }
-            // create cartoon if needed - this is a whole model analysis
-            if (cartoonAtoms.length > 0) {
-                var gradientscheme = null;
-                //TODO: Should have an option to choose gradient type
-                if (range[0] < range[1])
-                    gradientscheme = new $3Dmol.Gradient.Sinebow(range[0], range[1]);
-
-                $3Dmol.drawCartoon(ret, cartoonAtoms, cartoonGeometry, gradientscheme);
-                
-                for (i = 0; i < ret.children.length; i++){
-                    var geo = ret.children[i].geometry;
-                }
-            }
+        var vsize = vs.length - 8; // Cap
+        
+        geoGroup = geo.updateGeoGroup(8);
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        offset = geoGroup.vertices; vertoffset = offset*3; faceoffset = geoGroup.faceidx;
+        
+        for (i = 0; i < 4; i++) {
+            vs.push(vs[i * 2]);
+            vs.push(vs[vsize + i * 2]);
+            
+            var v1 = vs[i * 2], v2 = vs[vsize + i * 2];
+            
+            vertexArray[vertoffset+6*i] = v1.x; vertexArray[vertoffset+1+6*i] = v1.y; vertexArray[vertoffset+2+6*i] = v1.z;
+            vertexArray[vertoffset+3+6*i] = v2.x; vertexArray[vertoffset+4+6*i] = v2.y; vertexArray[vertoffset+5+6*i] = v2.z;
+            
+            colorArray[vertoffset+6*i] = color.r; colorArray[vertoffset+1+6*i] = color.g; colorArray[vertoffset+2+6*i] = color.b;
+            colorArray[vertoffset+3+6*i] = color.r; colorArray[vertoffset+4+6*i] = color.g; colorArray[vertoffset+5+6*i] = color.b;
 
-            // add sphere geometry
-            if (sphereGeometry.vertices > 0) {
-                var sphereMaterial = new $3Dmol.MeshLambertMaterial({
-                    ambient : 0x000000,
-                    vertexColors : true,
-                    reflectivity : 0,
-                });
-                
-                //Initialize buffers in geometry                
-                sphereGeometry.initTypedArrays();
+        }
+        
+        vsize += 8;
                 
-                var sphere = new $3Dmol.Mesh(sphereGeometry, sphereMaterial);
-                ret.add(sphere);
-            }
+        face1 = [offset, offset + 2, offset + 6, offset + 4];
+        face2 = [offset + 1, offset + 5, offset + 7, offset + 3];
+        
+        faceArray[faceoffset] = face1[0]; faceArray[faceoffset+1] = face1[1]; faceArray[faceoffset+2] = face1[3];
+        faceArray[faceoffset+3] = face1[1]; faceArray[faceoffset+4] = face1[2]; faceArray[faceoffset+5] = face1[3];
+        faceArray[faceoffset+6] = face2[0]; faceArray[faceoffset+7] = face2[1]; faceArray[faceoffset+8] = face2[3];
+        faceArray[faceoffset+9] = face2[1]; faceArray[faceoffset+10] = face2[2]; faceArray[faceoffset+11] = face2[3];
+        
+        geoGroup.faceidx += 12;
+        geoGroup.vertices += 8;
+        
+        //TODO: Add intersection planes for caps
+        
+        geo.initTypedArrays();
+        geo.setUpNormals();
+        
+                // HalfEdgeRec used to store adjacency info of mesh
+        var HalfEdge=function(vertIdx){
+            this.vert=vertIdx; // Vertex index at the end of this half-edge
+            this.twin=null;    // Oppositely oriented adjacent half-edge
+            this.next=null;    //Next half-edge around the face
+        };
+        
+        var computeAdjacency=function(faces,faceCount,vertCount){
+            //all pieces of the half-edge data structure
+            edges=[];
             
-            // add imposter geometry
-            if (imposterGeometry.vertices > 0) {
-                var imposterMaterial = new $3Dmol.ImposterMaterial({
-                    ambient : 0x000000,
-                    vertexColors : true,
-                    reflectivity : 0
-                });
-                
-                //Initialize buffers in geometry                
-                imposterGeometry.initTypedArrays();
-                
-                var spherei = new $3Dmol.Mesh(imposterGeometry, imposterMaterial);
-                console
-                        .log("spherei geometry " + imposterGeometry.vertices.length);
-
-                ret.add(spherei);
-            }
+            // a hash table to hold the adjaceney info
+            // - Keys are pairs of vertex indices
+            // - Values are pointers to half-edge
+            var edgeTable={};
+            var len=0;
             
-            // add stick geometry
-            if (stickGeometry.vertices > 0) {
-                var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
-                    vertexColors : true,
-                    ambient : 0x000000,
-                    reflectivity : 0
-                });
-
-                //Initialize buffers in geometry                
-                stickGeometry.initTypedArrays();
+            //Plow through faces and fill all half-edge info except twin pointers:
+            for(var i=0;i<faceCount;i+=3){
+                var A=faces[i];
+                var B=faces[i+1];
+                var C=faces[i+2];
+               // console.log("A="+A+ " B="+ B+ " C="+C);
                 
-                if (cylinderMaterial.wireframe)
-                    stickGeometry.setUpWireframe();
+                //create the half-edge that goes from C to A
+                var CA=new HalfEdge(A);
+                edges.push(CA);
+                //create the half-edge that goes from A to B
+                var AB=new HalfEdge(B);
+                edges.push(AB);
+                //create the half-edge that goes from B to C
+                var BC=new HalfEdge(C);
+                edges.push(BC);
                 
-                var sticks = new $3Dmol.Mesh(stickGeometry, cylinderMaterial);
-                ret.add(sticks);
-            }
-
-            // This is only for DNA ladder rendering right now
-            if (cartoonGeometry.vertices > 0) {
-                var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
-                    vertexColors : true,
-                    ambient : 0x000000,
-                    reflectivity : 0
-                });
-
-                cartoonGeometry.initTypedArrays();
-
-                if (cylinderMaterial.wireframe)
-                    cartoonGeometry.setUpWireframe();
-
-                var ladder = new $3Dmol.Mesh(cartoonGeometry, cylinderMaterial);
-                ret.add(ladder);
+                CA.next=AB;
+                AB.next=BC;
+                BC.next=CA;
+                
+                edgeTable[C|(A<<16)]=CA; 
+                edgeTable[A|(B<<16)]=AB; 
+                edgeTable[B|(C<<16)]=BC;
             }
             
-            //var linewidth;
-            // add any line geometries, distinguished by line width
-            for (i in lineGeometries) {
-                if (lineGeometries.hasOwnProperty(i)) {
-                    var linewidth = i;
-                    var lineMaterial = new $3Dmol.LineBasicMaterial({
-                        linewidth : linewidth,
-                        vertexColors : true
-                    });
-                    
-                    lineGeometries[i].initTypedArrays();
-                    
-                    var line = new $3Dmol.Line(lineGeometries[i], lineMaterial,
-                            $3Dmol.LinePieces);
-
-                    ret.add(line);
+            //verify that the mesh is clean
+            for(var key in edgeTable){
+                if(edgeTable.hasOwnProperty(key)){
+                    len++;
                 }
             }
-
-            // add any cross geometries
-            for (i in crossGeometries) {
-                if (crossGeometries.hasOwnProperty(i)) {
-                    var linewidth = i;
-                    var crossMaterial = new $3Dmol.LineBasicMaterial({
-                        linewidth : linewidth,
-                        vertexColors : true
-                    });
-
-                    crossGeometries[i].initTypedArrays();
-                    
-                    var cross = new $3Dmol.Line(crossGeometries[i], crossMaterial,
-                            $3Dmol.LinePieces);
-
-                    ret.add(cross);
+            if(len!=faceCount*3){
+                console.warn("Bad mesh: duplicated edges or inconsistent winding.len="+len+" faceCount="+faceCount+" vertCount="+vertCount);
+            }
+            
+            //Populate the twin pointers by iterating over the hash table
+            var boundaryCount=0;
+            for(var key in edgeTable){
+                if(edgeTable.hasOwnProperty(key)){
+                    var twinKey=((key&0xffff)<<16)|(key>>16);
+                    if(edgeTable.hasOwnProperty(twinKey)){
+                        edgeTable[key].twin=edgeTable[twinKey];
+                        edgeTable[twinKey].twin=edgeTable[key];
+                    }else{
+                        boundaryCount+=1;
+                    }
                 }
             }
             
-            //for BIOMT assembly
-            if (dontDuplicateAtoms && !noAssembly) {
-                var symRet = new $3Dmol.Object3D();
-                var t;
-                for (t = 0; t < copyMatrices.length; t++) {
-                    var transformedRet = new $3Dmol.Object3D();
-                    transformedRet = ret.clone();
-                    transformedRet.matrix.copy(copyMatrices[t]);
-                    transformedRet.matrixAutoUpdate = false;
-                    symRet.add(transformedRet);
+            var ret=new Uint16Array(faceCount*6);
+            // Now that we have a half-edge structure, it's easy to create adjacency info for WebGL
+            if(boundaryCount>0){
+                console.log("Mesh is not watertight. Contains "+boundaryCount +" edges");
+                
+                for(var i=0;i<faceCount;i+=3){
+                    ret[i*2+0]=edges[i+2].vert;
+                    ret[i*2+1]=edges[i+0].twin==null?ret[i*2+0]:edges[i+0].twin.next.vert;
+                    ret[i*2+2]=edges[i+0].vert;
+                    ret[i*2+3]=edges[i+1].twin==null?ret[i*2+1]:edges[i+1].twin.next.vert;                  
+                    ret[i*2+4]=edges[i+1].vert;
+                    ret[i*2+5]=edges[i+2].twin==null?ret[i*2+2]:edges[i+2].twin.next.vert;
                 }
-                ret = symRet;
+            }
+            else{
+                for(var i=0;i<faceCount;i+=3){
+                    ret[i*2+0]=edges[i+2].vert;
+                    ret[i*2+1]=edges[i+0].twin.next.vert;
+                    ret[i*2+2]=edges[i+0].vert;
+                    ret[i*2+3]=edges[i+1].twin.next.vert;                   
+                    ret[i*2+4]=edges[i+1].vert;
+                    ret[i*2+5]=edges[i+2].twin.next.vert;
+                } 
             }
             
             return ret;
-            
         };
         
-        /**
-         * Returns list of rotational/translational matrices if there is BIOMT data
-         * Otherwise returns a list of just the ID matrix
-         *
-         * @function $3Dmol.GlModel#getSymmetries
-         * @return {Array<$3Dmol.Matrix4>}
-         *
-         */
-        this.getSymmetries = function() {
-            if (copyMatrices.length > 0) {
-                return copyMatrices;
-            }
-            else {
-                var idList = [idMatrix];
-                return idList;
-            }
-        };
+        //geoGroup.adjFaceArray = computeAdjacency(faceArray,faceArray.length,offset);
         
-        /**
-         * Sets symmetries based on specified matrices in list
-         *
-         * @function $3Dmol.GlModel#setSymmetries
-         * @param {Array<$3Dmol.Matrix4>} list
-         *
-         */
-        this.setSymmetries = function(list) {
-            if (typeof(list) == "undefined") { //delete sym data
-                var idList = [idMatrix];
-                copyMatrices = idList;
-            }
-            else {
-                copyMatrices = list;
-            }
-        };
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        material.vertexColors = $3Dmol.FaceColors;
+        if(typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        var mesh = new $3Dmol.Mesh(geo, material);
+        group.add(mesh);   
+    };
 
-        /**
-         * Returns model id number
-         * 
-         * @function $3Dmol.GLMode#getID
-         * @return {number} Model ID
-         */
-        this.getID = function() {
-            return id;
-        };
+    //TODO: Need to update this (will we ever use this?)
+    var drawSmoothCurve = function(group, _points, width, colors, div) {
+        if (_points.length === 0)
+            return;
 
-        // set default style and colors for atoms
-        var setAtomDefaults = function(atoms, id) {
-            for ( var i = 0; i < atoms.length; i++) {
-                var atom = atoms[i];
-                if (atom) {
-                    atom.style = atom.style || defaultAtomStyle;
-                    atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
-                    atom.model = id;
-                    if (atom.clickable)
-                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                }
+        div = (div === undefined) ? 5 : div;
+
+        var geo = new $3Dmol.Geometry();
+        var points = subdivide(_points, div);
+                /*
+        for ( var i = 0; i < points.length; i++) {
+            geo.vertices.push(points[i]);
+            geo.colors.push($3Dmol.color(colors[(i == 0) ? 0 : Math.round((i - 1)
+                    / div)]));
+        }
+                */
+        var lineMaterial = new $3Dmol.LineBasicMaterial({
+            linewidth : width
+        });
+        lineMaterial.vertexColors = true;
+        var line = new $3Dmol.Line(geo, lineMaterial);
+        line.type = $3Dmol.LineStrip;
+        group.add(line);
+    };
+
+    var drawStrip = function(group, points, colors, div, thickness, opacity, shape)
+    {    
+        if (!shape || shape === "default")
+            shape = "rectangle";
+        if(shape === 'edged')
+            drawPlainStrip(group, points, colors, div, thickness, opacity);
+        else if (shape === "rectangle" || shape === "oval" || shape === "parabola")
+            drawShapeStrip(group, points, colors, div, thickness, opacity, shape);
+    }
+
+    // check if given atom is an alpha carbon
+    var isAlphaCarbon = function(atom)
+    {
+        return atom && atom.elem === "C" && atom.atom === "CA"; // note that calcium is also CA
+    }
+
+    // check whether two atoms are members of the same residue or subsequent, connected residues (a before b)
+    var inConnectedResidues = function(a, b)
+    {
+        if(a && b && a.chain === b.chain) {
+            if((a.reschain === b.reschain) && (a.resi === b.resi || a.resi === b.resi-1))
+                return true;
+            if(a.resi < b.resi) {
+                //some PDBs have gaps in the numbering but the residues are still connected
+                //assume if within 4A they are connected
+                var av = new $3Dmol.Vector3(a.x, a.y, a.z);
+                var bv = new $3Dmol.Vector3(b.x, b.y, b.z);
+                var dist = av.distanceToSquared(bv);
+                if(dist < 16.0) return true; //calpha dist
             }
-        };
+        }
 
-        /** add atoms to this model from molecular data string
-         * 
-         * @function $3Dmol.GLModel#addMolData
-         * @param {string} data - atom structure file input data string
-         * @param {string} format - input file string format (e.g 'pdb', 'sdf', etc.)
-         * @param {Object} options - format dependent options (e.g. 'options.keepH' to keep hydrogens)
-         */
-        this.addMolData = function(data, format, options) {
-            options = options || {}; 
-            format = format || "";
-            if (!data)
-                return; //leave an empty model
-            if(typeof($3Dmol.Parsers[format]) == "undefined") {
-            	//let someone provide a file name and get format from extension
-            	format = format.split('.').pop();
-            	if(typeof($3Dmol.Parsers[format] == "undefined")) {            	
-	                console.log("Unknown format: "+format);
-	                //try to guess correct format from data contents
-	                if(data.match(/^@<TRIPOS>MOLECULE/)) {
-	                    format = "mol2";
-	                } else if(data.match(/^HETATM/) || data.match(/^ATOM/)) {
-	                    format = "pdb";
-	                } else if(data.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/)){
-	                    format = "sdf"; //could look at line 3
-	                } else {
-	                    format = "xyz";
-	                }
-	                console.log("Best guess: "+format);
-            	}
-            }
-            var parse = $3Dmol.Parsers[format];
-            parse(atoms, data, options, copyMatrices)
-            noAssembly = !options.doAssembly; //for BIOMT uses
-            dontDuplicateAtoms = !options.duplicateAssemblyAtoms;
-            setAtomDefaults(atoms, id);
-        };
-        
-        /** given a selection specification, return true if atom is selected
-         * 
-         * @function $3Dmol.GLModel#atomIsSelected
-         * @param {AtomSpec} atom
-         * @param {AtomSelectionSpec} sel
-         * @return {boolean}
-         */
-        this.atomIsSelected = function(atom, sel) {
-            if (typeof (sel) === "undefined")
-                return true; // undef gets all
-            var invert = !!sel.invert;
-            var ret = true;
-            for ( var key in sel) {
-                if(key === 'predicate') { //a user supplied function for evaluating atoms
-                    if(!sel['predicate'](atom) ) {
-                        ret = false;
-                        break;
-                    }
-                }
+        return false;
 
-                else if (sel.hasOwnProperty(key) && key != "props" && key != "invert" && key != "model" && key != "byres" && key != "expand" && key != "within") {
+    }
 
-                    // if something is in sel, atom must have it                    
-                    if (typeof (atom[key]) === "undefined") {
-                        ret = false;
-                        break;
-                    }
-                    var isokay = false;
-                    if(key === "bonds") {
-                        //special case counting number of bonds, for selecting nonbonded mostly
-                        var val = sel[key];
-                        if(val != atom.bonds.length) {
-                            ret = false;
-                            break;
-                        }
-                    }
-                    else if ($.isArray(sel[key])) {
-                        // can be any of the listed values
-                        var valarr = sel[key];
-                        for ( var i = 0; i < valarr.length; i++) {
-                            if (atom[key] == valarr[i]) {
-                                isokay = true;
-                                break;
-                            }
-                        }
-                        if (!isokay) {
-                            ret = false;
-                            break;
-                        }
-                    } else { // single match
-                        var val = sel[key];
-                        if (atom[key] != val) {
-                            ret = false;
-                            break;
-                        }
+    var drawCartoon = function(group, atomList, gradientScheme, fill, doNotSmoothen, num, div)
+    {
+        num = num || defaultNum;
+        div = div || defaultDiv;
+
+                        //  proteins    na backbone  na terminus                  nucleobases
+        var cartoonAtoms = ["CA", "O",  "P", "OP2", "O2P", "O5'", "O3'", "C5'", "C2'","O5*", "O3*", "C5*", "C2*", "N1", "N3"];
+        var purResns = ["DA", "DG", "A", "G"];
+        var pyrResns = ["DT", "DC", "U", "C", "T"];
+        var naResns  =  purResns.concat(pyrResns);
+
+        var geo, cartoon, prev, curr, next, currColor, nextColor, thickness, i, nextResAtom, arrow;
+        var backbonePt, orientPt, prevOrientPt, terminalPt, termOrientPt, baseStartPt, baseEndPt;
+        var tubeStart, tubeEnd, drawingTube;
+        var traceGeo = null;
+        var colors = [];
+        var points = [];
+        for (var i = 0; i < num; i++)
+            points[i] = [];
+
+        // first determine where beta sheet arrows and alpha helix tubes belong
+        var inSheet = false;
+        var inHelix = false;
+        i = 0;
+        for (i in atomList)
+        {
+            next = atomList[i];
+            if (next.elem === 'C' && next.atom === 'CA')
+            {
+                var connected = inConnectedResidues(curr, next);
+
+                // last two residues in a beta sheet become arrowhead
+                if (connected && next.ss === "s")
+                {
+                    inSheet = true;
+                }
+                else if (inSheet)
+                {   
+                    if (curr && prev && curr.style.cartoon.arrows && prev.style.cartoon.arrows)
+                    {
+                        curr.ss = "arrow end";
+                        prev.ss = "arrow start";
                     }
+                    inSheet = false; 
                 }
+
+                // first and last residues in a helix are used to draw tube
+                if (connected && curr.ss === "h")
+                {
+                    if (!inHelix && next.style.cartoon.tubes) next.ss = "tube start";
+                    inHelix = true;
+                }
+                else if (inHelix && curr.ss !== "tube start")
+                {
+                    if (prev && prev.style.cartoon.tubes) prev.ss = "tube end";
+                    inHelix = false;
+                }
+                prev = curr;
+                curr = next;
             }
+        }
+
+        // then accumulate points
+        curr = undefined;
+        for (i in atomList)
+        {
+            next = atomList[i];
             
-            return invert ? !ret : ret;
-        };
+            if (next === undefined || $.inArray(next.atom, cartoonAtoms) === -1)
+                continue; // skip array holes, heteroatoms, and atoms not involved in cartoon drawing
 
+            var inNucleicAcid = ($.inArray(next.resn.trim(), naResns) != -1)
 
-        /** return list of atoms selected by sel, this is specific to glmodel
-         * 
-         * @function $3Dmol.GLModel#selectedAtoms
-         * @param {AtomSelectionSpec} sel
-         * @return {Array.<Object>}
-         */
-        this.selectedAtoms = function(sel, from) {
-            var ret = [];
-            if (!from) from = atoms;
-            var aLength = from.length;
-            for ( var i = 0; i < aLength; i++) {
-                var atom = from[i];
-                if (atom) {
-                    if (this.atomIsSelected(atom, sel))
-                        ret.push(atom);
-                }
-            }
+            // determine cartoon style
+            cartoon = next.style.cartoon;
+            if (cartoon.style === "trace") // draw cylinders connecting consecutive 'backbone' atoms
+            {
+                /* "trace" style just draws cylinders between consecutive 'backbone' atoms,
+                    such as alpha carbon for polypeptides and phosphorus for DNA. */
 
-            // expand selection by some distance
-            if (sel.hasOwnProperty("expand")) {
+                if (!traceGeo) traceGeo = new $3Dmol.Geometry(true);
 
-                // get atoms in expanded bounding box
-                var expand = expandAtomList(ret, sel.expand)
-                var retlen = ret.length
-                for (var i = 0; i < expand.length; i++) {
-                    for (var j = 0; j < retlen; j++) {
+                if (next.elem === 'C' && next.atom === 'CA' || inNucleicAcid && next.atom === "P")
+                {
+                    // determine cylinder color
+                    if (gradientScheme && cartoon.color === 'spectrum')
+                        nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
+                    else
+                        nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                    colors.push(nextColor);
 
-                        var dist = squaredDistance(expand[i], ret[j]);
-                        var thresh = Math.pow(sel.expand, 2);
-                        if (dist < thresh && dist > 0) {
-                            ret.push(expand[i]);
+                    // determine cylinder thickness
+                    if ($.isNumeric(cartoon.thickness))
+                        thickness = cartoon.thickness;
+                    else
+                        thickness = defaultThickness;
+
+                    if (inConnectedResidues(curr, next))
+                    {
+                        // if both atoms are same color, draw single cylinder
+                        if (nextColor == currColor)
+                        {
+                            var color = $3Dmol.CC.color(nextColor);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, next, thickness, color, 2, 2);
+                        }
+
+                        else // otherwise draw cylinders for each color (split down the middle)
+                        {
+                            var midpoint = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
+                            var color1 = $3Dmol.CC.color(currColor);
+                            var color2 = $3Dmol.CC.color(nextColor);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, midpoint, thickness, color1, 2, 0);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, midpoint, next, thickness, color2, 0, 2);
+                        } // note that an atom object can be duck-typed as a $3Dmol.Vector3 in this case
+                    }
+
+                    if (curr && traceGeo && (curr.style.cartoon && curr.style.cartoon.style != "trace"
+                        || curr.chain != next.chain))
+                    {
+                        var traceMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+                        traceMaterial.vertexColors = $3Dmol.FaceColors;
+                        if ( typeof(traceGeo.opacity) === "number" && traceGeo.opacity >= 0 && traceGeo.opacity < 1) {
+                            traceMaterial.transparent = true;
+                            traceMaterial.opacity = traceGeo.opacity;
+                            delete traceGeo.opacity;
+                        }
+                        var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
+                        group.add(traceMesh);
+                        traceGeo = null;
+                    } else if (curr) // make sure whole chain is same opacity
+                    {
+                        if (traceGeo.opacity && curr.style.cartoon.opacity)
+                        {
+                            if (traceGeo.opacity != curr.style.cartoon.opacity)
+                            {
+                                console.log("Warning: a trace-style chain's opacity is ambiguous");
+                                traceGeo.opacity = 1;
+                            }
                         }
+                        else traceGeo.opacity = parseFloat(curr.style.cartoon.opacity) || 1;
                     }
+
+                    curr = next;
+                    currColor = nextColor;
                 }
             }
 
-            // selection within distance of sub-selection
-            if (sel.hasOwnProperty("within") && sel.within.hasOwnProperty("sel") && sel.within.hasOwnProperty("distance")) {
+            else // draw default-style cartoons based on secondary structure
+            {
+                if (!geo) geo = new $3Dmol.Geometry(true);
 
-                // get atoms in second selection
-                var sel2 = this.selectedAtoms(sel.within.sel, atoms)
-                var within = []
-                for (var i = 0; i < sel2.length; i++) {
-                    for (var j = 0; j < ret.length; j++) {
+                // draw backbone through these atoms
+                if (isAlphaCarbon(next) ||
+                    inNucleicAcid && (next.atom === "P" || next.atom.indexOf('O5') == 0))
+                {
+                    if (drawingTube)
+                    {
+                        if (next.ss === "tube end")
+                        {
+                            drawingTube = false;
+                            tubeEnd = new $3Dmol.Vector3(next.x, next.y, next.z);
+                            $3Dmol.GLDraw.drawCylinder(geo, tubeStart, tubeEnd, 2, $3Dmol.CC.color(currColor), 1, 1);
+                            next.ss = "h";
 
-                        var dist = squaredDistance(sel2[i], ret[j]);
-                        var thresh = Math.pow(sel.within.distance, 2);
-                        if (dist < thresh && dist > 0) {
-                            within.push(ret[j]);
                         }
+                        else continue; // don't accumulate strand points while in the middle of drawing a tube
                     }
-                }
-                ret = within;
-            }
 
-            // byres selection flag
-            if (sel.hasOwnProperty("byres")) {
+                    // end of a chain of connected residues (of same style)
+                    if (curr && (!inConnectedResidues(curr, next) || curr.style.cartoon.style !== next.style.cartoon.style ||
+                        curr.ss === "tube start"))
+                    { 
+                        if (curr.ss === "tube start")
+                        {
+                            drawingTube = true;
+                            tubeStart = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+                            curr.ss = "h";
+                        }
 
-                // Keep track of visited residues, visited atoms, and atom stack
-                var vResis = {};
-                var vAtoms = [];
-                var stack = [];
+                        if (baseEndPt) // draw the last base if it's a NA chain
+                        {
+                            if (terminalPt)
+                                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
+                            else
+                                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
 
-                for (var i = 0; i < ret.length; i++) {
-                    
-                    // Check if atom is part of a residue, and that the residue hasn't been traversed yet
-                    var atom = ret[i];
-                    var c = atom.chain;
-                    var r = atom.resi;
-                    if (vResis[c] === undefined) vResis[c] = {};
-                    if (atom.hasOwnProperty("resi") && vResis[c][r] === undefined) {
+                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+                            arrow = addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr, atomList, i);
+                            colors.push(nextColor);
+                            if (arrow) colors.push(nextColor);
+                            
+                            baseStartPt = null;
+                            baseEndPt = null;
+                        }
 
-                        // Perform a depth-first search of atoms with the same resi
-                        vResis[c][r] = true;
-                        stack.push(atom);
-                        while(stack.length > 0) {
-                            atom = stack.pop();
-                            c = atom.chain;
-                            r = atom.resi;
-                            if (vAtoms[atom.index] === undefined) {
-                                vAtoms[atom.index] = true;
-                                for (var j = 0; j < atom.bonds.length; j++) {
-                                    var atom2 = atoms[atom.bonds[j]];
-                                    if (vAtoms[atom2.index] === undefined && atom2.hasOwnProperty("resi") && atom2.chain == c && atom2.resi == r) {
-                                        stack.push(atom2);
-                                        ret.push(atom2);
-                                    }
-                                }
+                        // draw accumulated strand points
+                        for (i = 0; !thickness && i < num; i++)
+                            drawSmoothCurve(group, points[i], 1, colors, div, points.opacity);
+                        if (fill && points[0].length > 0) 
+                            drawStrip(group, points, colors, div, thickness, points.opacity, points.style);
+                        
+                        if (geo != null && geo.vertices > 0)
+                        {
+                            var cartoonMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+                            cartoonMaterial.vertexColors = $3Dmol.FaceColors;
+                            if (typeof(points.opacity) === "number" && points.opacity >= 0 && points.opacity < 1) {
+                                cartoonMaterial.transparent = true;
+                                cartoonMaterial.opacity = points.opacity;
                             }
+                            var cartoonMesh = new $3Dmol.Mesh(geo, cartoonMaterial);
+                            group.add(cartoonMesh);
+                            geo = null;
                         }
-                    }   
-                }
-            }
 
-            return ret;
-        };
+                        // clear arrays for points and colors
+                        points = [];
+                        for (i = 0; i < num; i++)
+                            points[i] = [];
+                        colors = [];
+                    }
 
-        var squaredDistance = function(atom1, atom2) {
-            var xd = atom2.x - atom1.x;
-            var yd = atom2.y - atom1.y;
-            var zd = atom2.z - atom1.z;
-            return (Math.pow(xd, 2) + Math.pow(yd, 2) + Math.pow(zd, 2));
-        };
+                    // reached next residue (potentially the first residue)
+                    if (curr === undefined || curr.rescode != next.rescode || curr.resi != next.resi)
+                    {
+                        if (baseEndPt) // draw last NA residue's base
+                        {
+                            // start the cylinder at the midpoint between consecutive backbone atoms
+                            baseStartPt = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
+                            var startFix = baseStartPt.clone().sub(baseEndPt).multiplyScalar(0.02); //TODO: apply this as function of thickness
+                            baseStartPt.add(startFix);
 
-        /** returns a list of atoms in the expanded bounding box, but not in the current one
-         *
-         *  Bounding box:
-         *
-         *    [ [ xmin, ymin, zmin ],
-         *      [ xmax, ymax, zmax ],
-         *      [ xctr, yctr, zctr ] ]
-         *
-         **/
-        var expandAtomList = function(atomList, amt) {
+                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+                            baseStartPt = null;
+                            baseEndPt = null;   
+                        }
 
-            var pb = $3Dmol.getExtent(atomList);
-            var nb = [[],[],[]];
+                        // determine color and thickness of the next strand segment
+                        if (gradientScheme && cartoon.color === 'spectrum')
+                            nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
+                        else
+                            nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                        colors.push(nextColor);
+                        if ($.isNumeric(cartoon.thickness))
+                            thickness = cartoon.thickness;
+                        else
+                            thickness = defaultThickness;
 
-            for (var i = 0; i < 3; i++)
-            {
-                nb[0][i] = pb[0][i]-amt;
-                nb[1][i] = pb[1][i]+amt;
-                nb[2][i] = pb[2][i];
-            }
+                        
+                        curr = next; // advance backbone
+                        //nextResAtom = atomList[parseInt(i) + resSize[curr.resn]];
+                        backbonePt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+                        backbonePt.resi = curr.resi;
+                        currColor = nextColor;
+                    }
 
-            // look in added box "shell" for new atoms
-            var expand = [];
-            for (var i = 0; i < atoms.length; i++) {
+                    // click handling
+                    if (next.clickable === true &&
+                        (next.intersectionShape === undefined || next.intersectionShape.triangle === undefined)) 
+                        next.intersectionShape = {sphere : null, cylinder : [], line : [], triangle : []};
+                }
 
-                var x = atoms[i].x;
-                var y = atoms[i].y;
-                var z = atoms[i].z;
+                // atoms used to orient the backbone strand
+                else if (isAlphaCarbon(curr) && next.atom === "O"
+                      || inNucleicAcid && curr.atom === "P" && (next.atom === "OP2" || next.atom === "O2P")
+                      || inNucleicAcid && curr.atom.indexOf("O5") == 0 && next.atom.indexOf("C5") == 0)
+                {
+                    orientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                    orientPt.resi = next.resi;
+                    if (next.atom === "OP2" || next.atom === "O2P") // for NA 3' terminus
+                        termOrientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                }
 
-                if (x >= nb[0][0] && x < pb[0][0] || x > pb[1][0] && x <= nb[1][0]) {
-                    if (y >= nb[0][1] && y < pb[0][1] || y > pb[1][1] && y <= nb[1][1]) {
-                        if (z >= nb[0][2] && z < pb[0][2] || z > pb[1][2] && z <= nb[1][2]) {
-                            expand.push(atoms[i]);
-                        }
-                    }
+                // NA 3' terminus is an edge case, need a vector for most recent O3'
+                else if (inNucleicAcid && next.atom.indexOf("O3") == 0)
+                {
+                    terminalPt = new $3Dmol.Vector3(next.x, next.y, next.z);
                 }
-            }
-            return expand;
-        };
-        
-        /** Add list of new atoms to model.  Adjusts bonds appropriately.
-         * 
-         * @function $3Dmol.GLModel#addAtoms
-         * @param {type} newatoms
-         */        
-        this.addAtoms = function(newatoms) {
-            molObj = null;
-            var start = atoms.length;
-            var indexmap = [];
-            // mapping from old index to new index
-            var i;
-            for(i = 0; i < newatoms.length; i++) {
-                indexmap[newatoms[i].index] = start+i;
-            }
-            
-            // copy and push newatoms onto atoms
-            for(i = 0; i < newatoms.length; i++) {
-                var olda = newatoms[i];
-                var nindex = indexmap[olda.index];
-                var a = $.extend(false, {}, olda);
-                a.index = nindex;
-                a.bonds = [];
-                a.bondOrder = [];
-                // copy over all bonds contained in selection,
-                // updating indices appropriately
-                for(var j = 0; j < olda.bonds.length; j++) {
-                    var neigh = indexmap[olda.bonds[j]];
-                    if(typeof(neigh) != "undefined") {
-                        a.bonds.push(neigh);
-                        a.bondOrder.push(olda.bondOrder[j]);
-                    }                
+
+                // atoms used for drawing the NA base cylinders (diff for purines and pyramidines)
+                else if ((next.atom === "N1" && $.inArray(next.resn.trim(), purResns) != -1) ||
+                         (next.atom === "N3" && $.inArray(next.resn.trim(), pyrResns) != -1))
+                {
+                    baseEndPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                    baseEndPt.color = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                }
+
+                // when we have a backbone point and orientation point in the same residue, accumulate strand points
+                if (orientPt && backbonePt && orientPt.resi === backbonePt.resi)
+                {
+                    arrow = addBackbonePoints(points, num, !doNotSmoothen, backbonePt, orientPt, prevOrientPt, curr, atomList, i);
+                    prevOrientPt = orientPt;
+                    backbonePt = null;
+                    orientPt = null;
+                    colors.push(nextColor);
+                    if (arrow) colors.push(nextColor);
                 }
-                atoms.push(a);
             }
-        };
+        }
 
-        /** Remove specified atoms from model
-         * 
-         * @function $3Dmol.GLModel#removeAtoms
-         * @param {type} badatoms
-         * @return {removeAtoms}
-         */
-        this.removeAtoms = function(badatoms) {
-            molObj = null;
-            // make map of all baddies
-            var baddies = [];
-            var i;
-            for(i = 0; i < badatoms.length; i++) {
-                baddies[badatoms[i].index] = true;
+        if (baseEndPt) // draw last NA base if needed
+        {
+            if (terminalPt)
+                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
+            else
+                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+
+            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+            arrow = addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr, atomList, i);
+            colors.push(nextColor);
+            if (arrow) colors.push(nextColor);
+        }
+
+        // for default style, draw the last strand
+        for (i = 0; !thickness && i < num; i++)
+            drawSmoothCurve(group, points[i], 1, colors, div, points.opacity);
+        if (fill && points[0].length > 0)
+        {
+            drawStrip(group, points, colors, div, thickness, points.opacity, points.style);
+        }
+        if (geo != null && geo.vertices > 0)
+        {
+            var cartoonMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+            cartoonMaterial.vertexColors = $3Dmol.FaceColors;
+            if (typeof(points.opacity) === "number" && points.opacity >= 0 && points.opacity < 1) {
+                cartoonMaterial.transparent = true;
+                cartoonMaterial.opacity = points.opacity;
             }
-            
-            // create list of good atoms
-            var newatoms = [];
-            for(i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                if(!baddies[a.index])
-                    newatoms.push(a);
+            var cartoonMesh = new $3Dmol.Mesh(geo, cartoonMaterial);
+            group.add(cartoonMesh);
+            geo = null;
+        }
+
+        if (traceGeo != null && traceGeo.vertices > 0) // generate last mesh for trace geometry
+        {
+            var traceMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+            traceMaterial.vertexColors = $3Dmol.FaceColors;
+            if (typeof(traceGeo.opacity) === "number" && traceGeo.opacity >= 0 && traceGeo.opacity < 1) {
+                traceMaterial.transparent = true;
+                traceMaterial.opacity = traceGeo.opacity;
+                delete traceGeo.opacity;
             }
-            
-            // clear it all out
-            atoms = [];
-            // and add back in to get updated bonds
-            this.addAtoms(newatoms);
-        };
+            var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
+            group.add(traceMesh);
+        }
+    };
+
+    var addBackbonePoints = function(points, num, smoothen, backbonePt, orientPt, prevOrientPt, backboneAtom, atomList, atomi)
+    {
+        var widthScalar, i, delta, v, addArrowPoints, testOpacity, testStyle;
         
+        // dictionary of standard amino acid sizes, in number of atoms
+        var resSize = {ALA: 5, ARG: 11, ASN:8, ASP:8, CYS:6, GLN:9, GLU: 9, GLY:4, HIS:10,
+            ILE:8, LEU: 8, LYS: 9, MET:8, PHE:11, PRO:7, SER:6, THR:7, TRP:14, TYR:12, VAL:7}
         
-        /** Set atom style of selected atoms
-         * 
-         * @function $3Dmol.GLModel#setStyle
-         * @param {AtomSelectionSpec} sel
-         * @param {AtomStyleSpec} style
-         * @param {boolean} add - if true, add to current style, don't replace
-         */
-        this.setStyle = function(sel, style, add) {           
+        if(!backbonePt || !orientPt || !backboneAtom)
+            return;
+        
+        // the side vector points along the axis from backbone atom to orientation atom (eg. CA to O, in peptides)
+        var sideVec = orientPt.sub(backbonePt);
+        sideVec.normalize();
 
-            // do a copy to enforce style changes through this function
-            var mystyle = $.extend(true, {}, style);
-            var changedAtoms = false;
-            // somethings we only calculate if there is a change in a certain
-            // style, although these checks will only catch cases where both
-            // are either null or undefined
+        // the forward vector points along the axis from backbone atom to next backbone atom
+        var forwardVec = atomList[parseInt(atomi) + resSize[backboneAtom.resn]];
+        forwardVec = forwardVec ? new $3Dmol.Vector3(forwardVec.x, forwardVec.y, forwardVec.z) : new $3Dmol.Vector3(0, 0, 0);
+        forwardVec.sub(backbonePt);
 
-            var selected = this.selectedAtoms(sel, atoms);
-            for ( var i = 0; i < atoms.length; i++) {
-                if(atoms[i]) atoms[i].capDrawn = false; //reset for proper stick render
-            }
+        // adjustments for proper beta arrow appearance
+        if (backboneAtom.ss === "arrow start")
+        {
+            var adjustment = forwardVec.clone().multiplyScalar(0.3).cross(orientPt); // adjust perpendicularly to strand face
+            backbonePt.add(adjustment);
+
+            var upVec = forwardVec.clone().cross(sideVec).normalize();
+            sideVec.rotateAboutVector(upVec, 0.43);
+        }
+
+        // determine from cartoon style or secondary structure how wide the strand should be here
+        // ribbon shape should have same width as thickness
+        if (backboneAtom.style.cartoon.ribbon)
+        {
+            widthScalar = backboneAtom.style.cartoon.thickness || defaultThickness;
+
+        } else // depending on secondary structure, multiply the orientation vector by some scalar
+        {
+            if (!backboneAtom.style.cartoon.width)
+            {
+                if (backboneAtom.ss === "c")
+                {
+                    if (backboneAtom.atom === "P")
+                        widthScalar = nucleicAcidWidth;
+                    else
+                        widthScalar = coilWidth;
+                } else if (backboneAtom.ss === "arrow start")
+                {
+                    widthScalar = helixSheetWidth;
+                    addArrowPoints = true;
 
-            for ( var i = 0; i < selected.length; i++) {                
-                changedAtoms = true;
-                //even though clickable and callback are atom properties, let them
-                //be set through styles
-                if(typeof(mystyle.clickable) != 'undefined') 
-                    selected[i].clickable = mystyle.clickable;
-                if(typeof(mystyle.callback) != 'undefined') 
-                    selected[i].callback = mystyle.callback;
+                } else if (backboneAtom.ss === "arrow end")
+                    widthScalar = coilWidth;
                 
-                if (selected[i].clickable) 
-                    selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};                    
-                   
-                if(!add) selected[i].style = {};
-                for(var s in mystyle) {
-                    if(mystyle.hasOwnProperty(s)) {
-                        selected[i].style[s] = mystyle[s];
-                    }
-                }
-            }
-            
-            if (changedAtoms)
-                molObj = null; //force rebuild
-            
-        };
-        
-        /** given a mapping from element to color, set atom colors
-         * 
-         * @function $3Dmol.GLModel#setColorByElement
-         * @param {type} sel
-         * @param {type} colors
-         */
-        this.setColorByElement = function(sel, colors) {
-            
-            if(molObj !== null && sameObj(colors,lastColors))
-                return; // don't recompute
-            lastColors = colors;
-            var atoms = this.selectedAtoms(sel, atoms);
-            if(atoms.length > 0)
-                molObj = null; // force rebuild
-            for ( var i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                if(typeof(colors[a.elem]) !== "undefined") {
-                    a.color = colors[a.elem];
-                }
+                else if (backboneAtom.ss === "h" && backboneAtom.style.cartoon.tubes || backboneAtom.ss === "tube start")
+                    widthScalar = coilWidth;
+
+                else
+                    widthScalar = helixSheetWidth;
             }
-        };
-        
-        /**
-         * @function $3Dmol.GLModel.setColorByProperty
-         * @param {type} sel
-         * @param {type} prop
-         * @param {type} scheme
-         */
-        this.setColorByProperty = function(sel, prop, scheme) {
-            var atoms = this.selectedAtoms(sel, atoms);
-            lastColors = null; // don't bother memoizing
-            if(atoms.length > 0)
-                molObj = null; // force rebuild
-            var min =  Number.POSITIVE_INFINITY;
-            var max =  Number.NEGATIVE_INFINITY;
-            var i, a;
-            // compute the range            
-            for (i = 0; i < atoms.length; i++) {
-                a = atoms[i];
-                if(a.properties && typeof(a.properties[prop]) !== undefined) {
-                    var p = parseFloat(a.properties[prop]);
-                    if(p < min) min = p;
-                    if(p > max) max = p;
-                }                    
+            else widthScalar = backboneAtom.style.cartoon.width;  
+        }
+
+        // make sure the strand orientation doesn't twist more than 90 degrees
+        if (prevOrientPt != null && sideVec.dot(prevOrientPt) < 0)
+            sideVec.negate();
+
+
+        sideVec.multiplyScalar(widthScalar);
+        for (i = 0; i < num; i++)
+        {
+            // produces NUM incremental points from backbone atom minus orientation vector
+            //  to backbone atom plus orientation vector
+            delta = -1 + i * 2/(num - 1); // -1 to 1 incrementing by num
+            v = new $3Dmol.Vector3(backbonePt.x + delta * sideVec.x,
+                                   backbonePt.y + delta * sideVec.y,
+                                   backbonePt.z + delta * sideVec.z);
+            v.atom = backboneAtom;
+            if (smoothen && backboneAtom.ss === "s") 
+                v.smoothen = true;
+            points[i].push(v); // a num-length array of arrays, where each inner array contains length-wise points
+                               // along the backbone offset by some constant pertaining to its cell in the outer array
+        }
+
+        if (addArrowPoints)
+        {
+
+            sideVec.multiplyScalar(2);
+            for (i = 0; i < num; i++)
+            {
+                delta = -1 + i * 2/(num - 1); // -1 to 1 incrementing by num
+                v = new $3Dmol.Vector3(backbonePt.x + delta * sideVec.x,
+                                       backbonePt.y + delta * sideVec.y,
+                                       backbonePt.z + delta * sideVec.z);
+                v.atom = backboneAtom;
+                v.smoothen = false;
+                v.skip = true;
+                points[i].push(v);
             }
-            // now apply colors using scheme
-            for (i = 0; i < atoms.length; i++) {
-                a = atoms[i];
-                if(a.properties && typeof(a.properties[prop]) !== undefined) {
-                    var c = scheme.valueToHex(parseFloat(a.properties[prop]), [min,max]);
-                    a.color = c;
-                }                    
+        }
+
+        // make sure the strand is all the same opacity and style
+        testOpacity = parseFloat(backboneAtom.style.cartoon.opacity) || 1;
+        if (points.opacity)
+        {
+            if (points.opacity != testOpacity)
+            {
+                console.log("Warning: a cartoon-style chain's opacity is ambiguous");
+                points.opacity = 1;
             }
-        };
 
+        } else points.opacity = testOpacity;
 
-        /** manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
-         * 
-         * @function $3Dmol.GLModel#globj
-         * @param {$3Dmol.Object3D} group
-         */
-        this.globj = function(group) {
-            var time = new Date();
-            if(molObj === null) { // have to regenerate
-                molObj = createMolObj(atoms);
-                var time2 = new Date();
-                //console.log("object creation time: " + (time2 - time));
-                if(renderedMolObj) { // previously rendered, remove
-                    group.remove(renderedMolObj);
-                    renderedMolObj = null;
-                }
-                renderedMolObj = molObj.clone();
-                group.add(renderedMolObj);
-            }
-        };
-        
-        /** Remove any renderable mol object from scene
-         * 
-         * @function $3Dmol.GLModel#removegl
-         * @param {$3Dmol.Object3D} group
-         */
-        this.removegl = function(group) {
-            if(renderedMolObj) {
-                //dispose of geos and materials
-                if (renderedMolObj.geometry !== undefined) renderedMolObj.geometry.dispose();             
-                if (renderedMolObj.material !== undefined) renderedMolObj.material.dispose();
-                group.remove(renderedMolObj);
-                renderedMolObj = null;
+        testStyle = backboneAtom.style.cartoon.style || 'default';
+        if (points.style)
+        {
+            if (points.style != testStyle)
+            {
+                console.log("Warning: a cartoon chain's strand-style is ambiguous");
+                points.style = 'default';
             }
-            molObj = null;
-        };
-        
-        /** Create labels for residues of selected atoms.
-         * Will create a single label at the center of mass of all atoms
-         * with the same chain,resn, and resi.
-         * @function $3Dmol.GLModel#addResLabels
-         * 
-         * @param {AtomSelectionSpec} sel
-         * @param {$3Dmol.GLViewer} viewer
-         */
-        this.addResLabels = function(sel, viewer, style) {
-            var atoms = this.selectedAtoms(sel, atoms);
-            var bylabel = {}
-            //collect by chain:resn:resi
-            for(var i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                var c = a.chain;
-                var resn = a.resn;
-                var resi = a.resi;
-                var label =  resn + '' + resi;
-                if(!bylabel[c]) bylabel[c] = {};
-                if(!bylabel[c][label]) bylabel[c][label] = []
-                bylabel[c][label].push(a);
-            }
-            
-            var mystyle = $.extend(true, {}, style);
-            //now compute centers of mass
-            for(var c in bylabel) {
-                if(bylabel.hasOwnProperty(c)) {
-                    var labels = bylabel[c];
-                    for(var label in labels) {
-                        if(labels.hasOwnProperty(label)) {
-                            var atoms = labels[label];
-                            var sum = new $3Dmol.Vector3(0,0,0);
-                            for(var i = 0; i < atoms.length; i++) {
-                                var a = atoms[i];
-                                sum.x += a.x;
-                                sum.y += a.y;
-                                sum.z += a.z;
-                            }
-                            sum.divideScalar(atoms.length);
-                            mystyle.position = sum;
-                            viewer.addLabel(label, mystyle);
-                        }                        
-                    }
-                }
-            }
-        }
 
+        } else points.style = testStyle;
+
+        // revert ss keywords used for arrow rendering back to original value
+        if (backboneAtom.ss === "arrow start" || backboneAtom.ss === "arrow end")
+            backboneAtom.ss = "s";
+
+        return addArrowPoints;
+    };
+
+    var defaultDrawCartoon = function(group, atomList, gradientScheme, quality)
+    {
+        quality = parseInt(parseFloat(quality)*5) || 5;
+        drawCartoon(group, atomList, gradientScheme, fill=true, doNotSmoothen=false, num=quality, div=quality);
     }
 
-    return GLModel;
-    
+    return defaultDrawCartoon;
 })();
-/**
- * A GLShape is a collection of user specified shapes.
- * 
- * @constructor $3Dmol.GLShape
- * @extends {ShapeSpec}
- * @param {number} sid - Unique identifier
- * @param {ShapeSpec} stylespec - shape style specification
- */
-$3Dmol.GLShape = (function() {
+//
 
-    // Marching cube, to match with protein surface generation
-    var ISDONE = 2;
+var $3Dmol = $3Dmol || {};
 
-    /**
-     * 
-     * @param {$3Dmol.Geometry}
-     *            geo
-     * @param {$3Dmol.Color |
-     *            colorlike} color
-     */
-    var updateColor = function(geo, color) {
+/**
+ * Lower level utilities for creating WebGL shape geometries.
+ * These are not intended for general consumption.
+ * @namespace $3Dmol.GLDraw
+  */
+$3Dmol.GLDraw = (function() {
 
-        var C = color || $3Dmol.CC.color(color);
-        geo.colorsNeedUpdate = true;
+    var draw = {}; // object for exporting functions
 
-        for ( var g in geo.geometryGroups) {
+    // Rotation matrix around z and x axis -
+    // according to y basis vector
+    // TODO: Try to optimize this (square roots?)
+    var getRotationMatrix = function() {
 
-            var geoGroup = geo.geometryGroups[g];
-            var colorArr = geoGroup.colorArray;
+        var d = new $3Dmol.Vector3();
+        // var rot = new Float32Array(9);
 
-            for (var i = 0, il = geoGroup.vertices; i < il; ++i) {
-                colorArr[i * 3] = C.r;
-                colorArr[i * 3 + 1] = C.g;
-                colorArr[i * 3 + 2] = C.b;
-            }
-        }
+        return function(dir) {
 
-    };
+            d.set(dir[0], dir[1], dir[2]);
 
+            var dx = d.x, dy = d.y, dz = d.z;
 
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {ArrowSpec}
-     *            spec
-     */
-    var drawArrow = function(shape, geoGroup, spec) {
+            var dxy = Math.sqrt(dx * dx + dy * dy);
+            var dxz, dyz;
 
-        var from = spec.start, end = spec.end, radius = spec.radius, radiusRatio = spec.radiusRatio, mid = spec.mid;
+            var sinA, cosA, sinB, cosB, sinC, cosC;
 
-        if (!(from && end))
-            return;
+            // about z axis - Phi
+            if (dxy < 0.0001) {
+                sinA = 0;
+                cosA = 1;
+            }
 
-        // vertices
+            else {
+                sinA = -dx / dxy;
+                cosA = dy / dxy;
+            }
 
-        var dir = end.clone();
-        dir.sub(from).multiplyScalar(mid);
-        var to = from.clone().add(dir);
-        var negDir = dir.clone().negate();
+            // recast dy in terms of new axes - z is the same
 
-        shape.intersectionShape.cylinder.push(new $3Dmol.Cylinder(from.clone(),
-                to.clone(), radius));
-        shape.intersectionShape.sphere.push(new $3Dmol.Sphere(from.clone(),
-                radius));
+            dy = -sinA * dx + cosA * dy;
+            dyz = Math.sqrt(dy * dy + dz * dz);
 
-        // get orthonormal vector
-        var nvecs = [];
-        nvecs[0] = dir.clone();
-        if (Math.abs(nvecs[0].x) > 0.0001)
-            nvecs[0].y += 1;
-        else
-            nvecs[0].x += 1;
-        nvecs[0].cross(dir);
-        nvecs[0].normalize();
+            // about new x axis - Theta
 
-        nvecs[0] = nvecs[0];
-        // another orth vector
-        nvecs[4] = nvecs[0].clone();
-        nvecs[4].crossVectors(nvecs[0], dir);
-        nvecs[4].normalize();
-        nvecs[8] = nvecs[0].clone().negate();
-        nvecs[12] = nvecs[4].clone().negate();
+            if (dyz < 0.0001) {
+                sinB = 0;
+                cosB = 1;
+            }
 
-        // now quarter positions
-        nvecs[2] = nvecs[0].clone().add(nvecs[4]).normalize();
-        nvecs[6] = nvecs[4].clone().add(nvecs[8]).normalize();
-        nvecs[10] = nvecs[8].clone().add(nvecs[12]).normalize();
-        nvecs[14] = nvecs[12].clone().add(nvecs[0]).normalize();
+            else {
+                sinB = dz / dyz;
+                cosB = dy / dyz;
+            }
 
-        // eights
-        nvecs[1] = nvecs[0].clone().add(nvecs[2]).normalize();
-        nvecs[3] = nvecs[2].clone().add(nvecs[4]).normalize();
-        nvecs[5] = nvecs[4].clone().add(nvecs[6]).normalize();
-        nvecs[7] = nvecs[6].clone().add(nvecs[8]).normalize();
-        nvecs[9] = nvecs[8].clone().add(nvecs[10]).normalize();
-        nvecs[11] = nvecs[10].clone().add(nvecs[12]).normalize();
-        nvecs[13] = nvecs[12].clone().add(nvecs[14]).normalize();
-        nvecs[15] = nvecs[14].clone().add(nvecs[0]).normalize();
+            var rot = new Float32Array(9);
+            rot[0] = cosA;
+            rot[1] = sinA;
+            rot[2] = 0;
+            rot[3] = -sinA * cosB;
+            rot[4] = cosA * cosB;
+            rot[5] = sinB;
+            rot[6] = sinA * sinB;
+            rot[7] = -cosA * sinB;
+            rot[8] = cosB;
 
-        // var start = geo.vertices.length;
-        var start = geoGroup.vertices;
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        var normalArray = geoGroup.normalArray;
-        var lineArray = geoGroup.lineArray;
+            return rot;
 
-        var offset, i, n;
-        // add vertices, opposing vertices paired together
-        for (i = 0, n = nvecs.length; i < n; ++i) {
-            offset = 3 * (start + 3 * i);
-            var bottom = nvecs[i].clone().multiplyScalar(radius).add(from);
-            var top = nvecs[i].clone().multiplyScalar(radius).add(to);
-            var conebase = nvecs[i].clone()
-                    .multiplyScalar(radius * radiusRatio).add(to);
+        };
 
-            vertexArray[offset] = bottom.x;
-            vertexArray[offset + 1] = bottom.y;
-            vertexArray[offset + 2] = bottom.z;
+    }();
+    
+    // Ortho normal vectors for cylinder radius/ sphere cap equator and cones
+    // Direction is j basis (0,1,0)
+    var basisVectors = function() {
 
-            vertexArray[offset + 3] = top.x;
-            vertexArray[offset + 4] = top.y;
-            vertexArray[offset + 5] = top.z;
+        var ret = {
+            vertices : [],
+            norms : []
+        };
 
-            vertexArray[offset + 6] = conebase.x;
-            vertexArray[offset + 7] = conebase.y;
-            vertexArray[offset + 8] = conebase.z;
+        var nvecs = [];
 
-            if (i > 0) {
-                var prev_x = vertexArray[offset - 3];
-                var prev_y = vertexArray[offset - 2];
-                var prev_z = vertexArray[offset - 1];
+        var subdivisions = 4; // including the initial 2, eg. 4 => 16 subintervals
+        var N = Math.pow(2, subdivisions);  // eg. 2**4 = 16 subintervals in total
+        var i = 2;  // start with 2 subdivisions already done
+        var M = Math.pow(2, i); // 4
+        var spacing = N/M;  // 16/4 = 4; if there were 5 subdivs, then 32/4 = 8.
+        var j;
 
-                var c = new $3Dmol.Vector3(prev_x, prev_y, prev_z);
-                var b = end.clone(), b2 = to.clone();
-                var a = new $3Dmol.Vector3(conebase.x, conebase.y, conebase.z);
+        nvecs[0] = new $3Dmol.Vector3(-1, 0, 0);
+        nvecs[spacing] = new $3Dmol.Vector3(0, 0, 1);
+        nvecs[spacing*2] = new $3Dmol.Vector3(1, 0, 0);
+        nvecs[spacing*3] = new $3Dmol.Vector3(0, 0, -1);
 
-                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(a, b,
-                        c));
-                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(c
-                        .clone(), b2, a.clone()));
+        for ( i = 3; i <= subdivisions; i ++ ) {
+            // eg. i=3, we need to add 2**(3-1) = 4 new vecs. Call it M.
+            // their spacing is N/M, eg. N=16, M=4, N/M=4; M=8, N/M=2.
+            // they start off at half this spacing
+            // and are equal to the average of the two vectors on either side
+            M = Math.pow(2, (i-1));
+            spacing = N/M;
+            for ( j = 0; j < (M-1); j ++ ) {
+                nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[(j+1)*spacing]).normalize();
             }
+            // treat the last one specially so it wraps around to zero
+            j = M - 1;
+            nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[0]).normalize();
         }
 
-        geoGroup.vertices += 48;
-        offset = geoGroup.vertices * 3;
+        /*
+         * nvecs[0] = new $3Dmol.Vector3(-1,0,0); nvecs[1] = new
+         * $3Dmol.Vector3(0,0,1); nvecs[2] = new $3Dmol.Vector3(1,0,0);
+         * nvecs[3] = new $3Dmol.Vector3(0,0,-1);
+         */
+        return nvecs;
 
-        // caps
-        vertexArray[offset] = from.x;
-        vertexArray[offset + 1] = from.y;
-        vertexArray[offset + 2] = from.z;
+    }();
 
-        vertexArray[offset + 3] = to.x;
-        vertexArray[offset + 4] = to.y;
-        vertexArray[offset + 5] = to.z;
+    // memoize capped cylinder for given radius
+    var cylVertexCache = {
 
-        vertexArray[offset + 6] = end.x;
-        vertexArray[offset + 7] = end.y;
-        vertexArray[offset + 8] = end.z;
+        // memoize both rounded and flat caps (hemisphere and circle)
+        cache : {false:{}, true:{}},
 
-        geoGroup.vertices += 3;
+        getVerticesForRadius : function(radius, flat) {
 
-        // now faces
-        var face, norm, faceoffset, lineoffset;
-        var t1, t2, t2b, t3, t3b, t4, t1offset, t2offset, t2boffset, t3offset, t3boffset, t4offset;
-        var n1, n2, n3, n4;
-        var n_vertices = 0;
-        var fromi = geoGroup.vertices - 3, toi = geoGroup.vertices - 2, endi = geoGroup.vertices - 1;
-        var fromoffset = fromi * 3, tooffset = toi * 3, endoffset = endi * 3;
-        for (i = 0, n = nvecs.length - 1; i < n; ++i) {
+            if (this.cache[flat][radius] !== undefined)
+                return this.cache[flat][radius];
 
-            var ti = start + 3 * i;
-            offset = ti * 3;
-            faceoffset = geoGroup.faceidx;
-            lineoffset = geoGroup.lineidx;
+            var dir = new $3Dmol.Vector3(0, 1, 0);
+            var w = basisVectors.length;
+            var nvecs = [], norms = [];
+            var n;
 
-            t1 = ti;
-            t1offset = t1 * 3;
-            t2 = ti + 1;
-            t2offset = t2 * 3;
-            t2b = ti + 2;
-            t2boffset = t2b * 3;
-            t3 = ti + 4;
-            t3offset = t3 * 3;
-            t3b = ti + 5;
-            t3boffset = t3b * 3;
-            t4 = ti + 3;
-            t4offset = t4 * 3;
+            for (var i = 0; i < w; i++) {
+                // bottom
+                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
+                // top
+                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
 
-            // face = [t1, t2, t4], [t2, t3, t4];
-            // face = [t1, t2, t3, t4];
+                // NOTE: this normal is used for constructing sphere caps -
+                // cylinder normals taken care of in drawCylinder
+                n = basisVectors[i].clone().normalize();
+                norms.push(n);
+                norms.push(n);
+            }
 
-            norm = [ nvecs[i], nvecs[i], nvecs[i + 1], nvecs[i + 1] ];
+            // norms[0]
 
-            n1 = n2 = nvecs[i];
-            n3 = n4 = nvecs[i + 1];
+            var verticesRows = [];
 
-            normalArray[t1offset] = n1.x;
-            normalArray[t2offset] = n2.x;
-            normalArray[t4offset] = n4.x;
-            normalArray[t1offset + 1] = n1.y;
-            normalArray[t2offset + 1] = n2.y;
-            normalArray[t4offset + 1] = n4.y;
-            normalArray[t1offset + 2] = n1.z;
-            normalArray[t2offset + 2] = n2.z;
-            normalArray[t4offset + 2] = n4.z;
+            // Require that heightSegments is even and >= 2
+            // Equator points at h/2 (theta = pi/2)
+            // (repeated) polar points at 0 and h (theta = 0 and pi)
+            var heightSegments = 10, widthSegments = w; // 16 or however many
+                                                        // basis vectors for
+                                                        // cylinder
 
-            normalArray[t2offset] = n2.x;
-            normalArray[t3offset] = n3.x;
-            normalArray[t4offset] = n4.x;
-            normalArray[t2offset + 1] = n2.y;
-            normalArray[t3offset + 1] = n3.y;
-            normalArray[t4offset + 1] = n4.y;
-            normalArray[t2offset + 2] = n2.z;
-            normalArray[t3offset + 2] = n3.z;
-            normalArray[t4offset + 2] = n4.z;
+            if (heightSegments % 2 !== 0 || !heightSegments) {
+                console.error("heightSegments must be even");
 
-            normalArray[t2boffset] = n2.x;
-            normalArray[t3boffset] = n3.x;
-            normalArray[t2boffset + 1] = n2.y;
-            normalArray[t3boffset + 1] = n3.y;
-            normalArray[t2boffset + 2] = n2.z;
-            normalArray[t3boffset + 2] = n3.z;
+                return null;
+            }
 
-            // sides
-            faceArray[faceoffset] = t1;
-            faceArray[faceoffset + 1] = t2;
-            faceArray[faceoffset + 2] = t4;
-            faceArray[faceoffset + 3] = t2;
-            faceArray[faceoffset + 4] = t3;
-            faceArray[faceoffset + 5] = t4;
-            // caps
-            faceArray[faceoffset + 6] = t1;
-            faceArray[faceoffset + 7] = t4;
-            faceArray[faceoffset + 8] = fromi;
-            faceArray[faceoffset + 9] = t2b;
-            faceArray[faceoffset + 10] = toi;
-            faceArray[faceoffset + 11] = t3b;
-            // arrowhead
-            faceArray[faceoffset + 12] = t2b;
-            faceArray[faceoffset + 13] = endi;
-            faceArray[faceoffset + 14] = t3b;
+            var phiStart = 0;
+            var phiLength = Math.PI * 2;
 
-            // sides
-            lineArray[lineoffset] = t1;
-            lineArray[lineoffset + 1] = t2;
-            lineArray[lineoffset + 2] = t1;
-            lineArray[lineoffset + 3] = t4;
-            // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
-            lineArray[lineoffset + 4] = t3;
-            lineArray[lineoffset + 5] = t4;
-            // caps
-            lineArray[lineoffset + 6] = t1;
-            lineArray[lineoffset + 7] = t4;
-            // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
-            // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+            var thetaStart = 0;
+            var thetaLength = Math.PI;
 
-            lineArray[lineoffset + 8] = t2b;
-            lineArray[lineoffset + 9] = t2; // toi
-            lineArray[lineoffset + 10] = t2b;
-            lineArray[lineoffset + 11] = t3b;
-            lineArray[lineoffset + 12] = t3;
-            lineArray[lineoffset + 13] = t3b; // toi
-            // arrowhead
-            lineArray[lineoffset + 14] = t2b;
-            lineArray[lineoffset + 15] = endi;
-            lineArray[lineoffset + 16] = t2b;
-            lineArray[lineoffset + 17] = t3b;
-            lineArray[lineoffset + 18] = endi;
-            lineArray[lineoffset + 19] = t3b;
+            var x, y;
+            var polar = false, equator = false;
 
-            geoGroup.faceidx += 15;
-            geoGroup.lineidx += 20;
+            for (y = 0; y <= heightSegments; y++) {
 
-        }
-        // final face
+                polar = (y === 0 || y === heightSegments) ? true : false;
+                equator = (y === heightSegments / 2) ? true : false;
 
-        face = [ start + 45, start + 46, start + 1, start, start + 47,
-                start + 2 ];
-        norm = [ nvecs[15], nvecs[15], nvecs[0], nvecs[0] ];
+                var verticesRow = [], toRow = [];
 
-        faceoffset = geoGroup.faceidx;
-        lineoffset = geoGroup.lineidx;
+                for (x = 0; x <= widthSegments; x++) {
 
-        t1 = face[0];
-        t1offset = t1 * 3;
-        t2 = face[1];
-        t2offset = t2 * 3;
-        t2b = face[4];
-        t2boffset = t2b * 3;
-        t3 = face[2];
-        t3offset = t3 * 3;
-        t3b = face[5];
-        t3boffset = t3b * 3;
-        t4 = face[3];
-        t4offset = t4 * 3;
+                    // Two vertices rows for equator pointing to previously
+                    // constructed cyl points
+                    if (equator) {
+                        var xi = (x < widthSegments) ? 2 * x : 0;
+                        toRow.push(xi + 1);
+                        verticesRow.push(xi);
 
-        n1 = n2 = nvecs[15];
-        n3 = n4 = nvecs[0];
+                        continue;
+                    }
 
-        normalArray[t1offset] = n1.x;
-        normalArray[t2offset] = n2.x;
-        normalArray[t4offset] = n4.x;
-        normalArray[t1offset + 1] = n1.y;
-        normalArray[t2offset + 1] = n2.y;
-        normalArray[t4offset + 1] = n4.y;
-        normalArray[t1offset + 2] = n1.z;
-        normalArray[t2offset + 2] = n2.z;
-        normalArray[t4offset + 2] = n4.z;
+                    var u = x / widthSegments;
+                    var v = y / heightSegments;
 
-        normalArray[t2offset] = n2.x;
-        normalArray[t3offset] = n3.x;
-        normalArray[t4offset] = n4.x;
-        normalArray[t2offset + 1] = n2.y;
-        normalArray[t3offset + 1] = n3.y;
-        normalArray[t4offset + 1] = n4.y;
-        normalArray[t2offset + 2] = n2.z;
-        normalArray[t3offset + 2] = n3.z;
-        normalArray[t4offset + 2] = n4.z;
+                    // Only push first polar point
 
-        normalArray[t2boffset] = n2.x;
-        normalArray[t3boffset] = n3.x;
-        normalArray[t2boffset + 1] = n2.y;
-        normalArray[t3boffset + 1] = n3.y;
-        normalArray[t2boffset + 2] = n2.z;
-        normalArray[t3boffset + 2] = n3.z;
+                    if (!polar || x === 0) {
 
-        // Cap normals
-        dir.normalize();
-        negDir.normalize();
-        normalArray[fromoffset] = negDir.x;
-        normalArray[tooffset] = normalArray[endoffset] = dir.x;
-        normalArray[fromoffset + 1] = negDir.y;
-        normalArray[tooffset + 1] = normalArray[endoffset + 1] = dir.y;
-        normalArray[fromoffset + 2] = negDir.z;
-        normalArray[tooffset + 2] = normalArray[endoffset + 2] = dir.z;
+                        if (x < widthSegments) {
+                            var vertex = new $3Dmol.Vector3();
+                            vertex.x = -radius
+                                    * Math.cos(phiStart + u * phiLength)
+                                    * Math.sin(thetaStart + v * thetaLength);
+                            vertex.y = flat ? 0 : radius * Math.cos(thetaStart + v * thetaLength);
+                            vertex.z = radius
+                                    * Math.sin(phiStart + u * phiLength)
+                                    * Math.sin(thetaStart + v * thetaLength);
 
-        // Final side
-        faceArray[faceoffset] = t1;
-        faceArray[faceoffset + 1] = t2;
-        faceArray[faceoffset + 2] = t4;
-        faceArray[faceoffset + 3] = t2;
-        faceArray[faceoffset + 4] = t3;
-        faceArray[faceoffset + 5] = t4;
-        // final caps
-        faceArray[faceoffset + 6] = t1;
-        faceArray[faceoffset + 7] = t4;
-        faceArray[faceoffset + 8] = fromi;
-        faceArray[faceoffset + 9] = t2b;
-        faceArray[faceoffset + 10] = toi;
-        faceArray[faceoffset + 11] = t3b;
-        // final arrowhead
-        faceArray[faceoffset + 12] = t2b;
-        faceArray[faceoffset + 13] = endi;
-        faceArray[faceoffset + 14] = t3b;
+                            if (Math.abs(vertex.x) < 1e-5)
+                                vertex.x = 0;
+                            if (Math.abs(vertex.y) < 1e-5)
+                                vertex.y = 0;
+                            if (Math.abs(vertex.z) < 1e-5)
+                                vertex.z = 0;
 
-        // sides
-        lineArray[lineoffset] = t1;
-        lineArray[lineoffset + 1] = t2;
-        lineArray[lineoffset + 2] = t1;
-        lineArray[lineoffset + 3] = t4;
-        // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
-        lineArray[lineoffset + 4] = t3;
-        lineArray[lineoffset + 5] = t4;
-        // caps
-        lineArray[lineoffset + 6] = t1;
-        lineArray[lineoffset + 7] = t4;
-        // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
-        // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
-
-        lineArray[lineoffset + 8] = t2b;
-        lineArray[lineoffset + 9] = t2; // toi
-        lineArray[lineoffset + 10] = t2b;
-        lineArray[lineoffset + 11] = t3b;
-        lineArray[lineoffset + 12] = t3;
-        lineArray[lineoffset + 13] = t3b; // toi
-        // arrowhead
-        lineArray[lineoffset + 14] = t2b;
-        lineArray[lineoffset + 15] = endi;
-        lineArray[lineoffset + 16] = t2b;
-        lineArray[lineoffset + 17] = t3b;
-        lineArray[lineoffset + 18] = endi;
-        lineArray[lineoffset + 19] = t3b;
+                            if (flat) {
+                                n = new $3Dmol.Vector3(0, Math.cos(thetaStart + v * thetaLength), 0);
+                                n.normalize();
+                            }
+                            else {
+                                n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
+                                n.normalize();
+                            }
 
-        geoGroup.faceidx += 15;
-        geoGroup.lineidx += 20;
+                            nvecs.push(vertex);
+                            norms.push(n);
 
-    };
+                            verticesRow.push(nvecs.length - 1);
+                        }
 
-    // handles custom shape generation from user supplied arrays
-    // May need to generate normal and/or line indices
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {CustomSpec}
-     *            customSpec
-     */
-    var drawCustom = function(shape, geoGroup, customSpec) {
+                        // last point is just the first point for this row
+                        else {
+                            verticesRow.push(nvecs.length - widthSegments);
+                        }
 
-        var vertexArr = customSpec.vertexArr, normalArr = customSpec.normalArr, faceArr = customSpec.faceArr, lineArr = customSpec.lineArr;
+                    }
 
-        if (vertexArr.length === 0 || faceArr.length === 0) {
-            console
-                    .warn("Error adding custom shape component: No vertices and/or face indices supplied!");
-        }
+                    // x > 0; index to already added point
+                    else if (polar)
+                        verticesRow.push(nvecs.length - 1);
 
-        geoGroup.vertices = vertexArr.length;
-        geoGroup.faceidx = faceArr.length;
+                }
 
-        var offset, v, a, b, c, i, il;
+                // extra equator row
+                if (equator)
+                    verticesRows.push(toRow);
 
-        for (i = 0, il = geoGroup.vertices; i < il; ++i) {
-            offset = i * 3;
-            v = vertexArr[i];
-            geoGroup.vertexArray[offset] = v.x;
-            geoGroup.vertexArray[offset + 1] = v.y;
-            geoGroup.vertexArray[offset + 2] = v.z;
-        }
+                verticesRows.push(verticesRow);
 
-        for (i = 0, il = geoGroup.faceidx / 3; i < il; ++i) {
-            offset = i * 3;
-            a = faceArr[offset];
-            b = faceArr[offset + 1];
-            c = faceArr[offset + 2];
-            var vA = new $3Dmol.Vector3(), vB = new $3Dmol.Vector3(), vC = new $3Dmol.Vector3();
-            shape.intersectionShape.triangle.push(new $3Dmol.Triangle(vA
-                    .copy(vertexArr[a]), vB.copy(vertexArr[b]), vC
-                    .copy(vertexArr[c])));
-        }
+            }
 
-        geoGroup.faceArray = new Uint16Array(faceArr);
+            var obj = {
+                vertices : nvecs,
+                normals : norms,
+                verticesRows : verticesRows,
+                w : widthSegments,
+                h : heightSegments
+            };
 
-        geoGroup.truncateArrayBuffers(true, true);
+            this.cache[flat][radius] = obj;
 
-        if (normalArr.length < geoGroup.vertices)
-            geoGroup.setNormals();
-        else {
+            return obj;
 
-            geoGroup.normalArray = new Float32Array(geoGroup.vertices * 3);
-            var n;
-            for (i = 0, il = geoGroup.vertices; i < il; ++i) {
-                offset = i * 3;
-                n = normalArr[i];
-                geoGroup.normalArray[offset] = n.x;
-                geoGroup.normalArray[offset + 1] = n.y;
-                geoGroup.normalArray[offset + 2] = n.z;
-            }
         }
-
-        if (!lineArr.length)
-            geoGroup.setLineIndices();
-        else
-            geoGroup.lineArray = new Uint16Array(lineArr);
-
-        geoGroup.lineidx = geoGroup.lineArray.length;
-
     };
 
-    // Read a cube file - generate model and possibly shape(s)
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {string}
-     *            str
-     * @param {number}
-     *            isoval
-     * @param {boolean}
-     *            voxel
-     */
-    var parseCube = function(shape, geoGroup, str, isoval, voxel) {
-
-        var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
-
-        if (lines.length < 6)
+    // creates a cylinder
+    var drawnC = 0;
+    
+    /** Create a cylinder 
+     * @function $3Dmol.GLDraw.drawCylinder
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            from
+     * @param {Point}
+     *            to
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     * @param {integer} fromCap - 0 for none, 1 for flat, 2 for round; Note: currently do not support different styles of caps on the same cylinder.
+     * @param {integer} toCap = 0 for none, 1 for flat, 2 for round
+     *            
+     * */
+    draw.drawCylinder = function(geo, from, to, radius, color, fromCap, toCap) {
+        if (!from || !to)
             return;
+        drawnC++;
+        // vertices
+        var drawcaps = fromCap || toCap;
 
-        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
-                " ");
+        var flat = false;
+        if (fromCap == 1 && toCap == 1) // 0 is none, 1 is flat, 2 is round
+          	flat = true;
 
-        var natoms = Math.abs(parseFloat(lineArr[0]));
-        var origin = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]));
+        color = color || {r:0, g:0, b:0};
 
-        lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+        /** @type {Array.<number>} */
+        var dir = [ to.x, to.y, to.z ];
+        dir[0] -= from.x;
+        dir[1] -= from.y;
+        dir[2] -= from.z;
 
-        // might have to convert from bohr units to angstroms
-        var convFactor = (parseFloat(lineArr[0]) > 0) ? 0.529177 : 1;
+        var e = getRotationMatrix(dir);
+        // get orthonormal vectors from cache
+        // TODO: Will have orient with model view matrix according to direction
+        var vobj = cylVertexCache.getVerticesForRadius(radius, flat);
 
-        origin.multiplyScalar(convFactor);
+        // w (n) corresponds to the number of orthonormal vectors for cylinder
+        // (default 16)
+        var n = vobj.w, h = vobj.h;
+        var w = n;
+        // get orthonormal vector
+        var n_verts = (drawcaps) ? h * n + 2 : 2 * n;
 
-        var nX = Math.abs(lineArr[0]);
-        var xVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
+        var geoGroup = geo.updateGeoGroup(n_verts);
 
-        lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+        var vertices = vobj.vertices, normals = vobj.normals, verticesRows = vobj.verticesRows;
+        var toRow = verticesRows[h / 2], fromRow = verticesRows[h / 2 + 1];
 
-        var nY = Math.abs(lineArr[0]);
-        var yVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
+        var start = geoGroup.vertices;
+        var offset, faceoffset;
+        var i, x, y, z;
 
-        lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+        var vertexArray = geoGroup.vertexArray;
+        var normalArray = geoGroup.normalArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        // add vertices, opposing vertices paired together
+        for (i = 0; i < n; ++i) {
 
-        var nZ = Math.abs(lineArr[0]);
-        var zVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
+            var vi = 2 * i;
 
-        // lines.splice(6, natoms).join("\n");
+            x = e[0] * vertices[vi].x + e[3] * vertices[vi].y + e[6]
+                    * vertices[vi].z;
+            y = e[1] * vertices[vi].x + e[4] * vertices[vi].y + e[7]
+                    * vertices[vi].z;
+            z = e[5] * vertices[vi].y + e[8] * vertices[vi].z;
 
-        lines = new Float32Array(lines.splice(natoms + 7).join(" ").replace(
-                /^\s+/, "").split(/[\s\r]+/));
+            // var xn = x/radius, yn = y/radius, zn = z/radius;
 
-        var vertnums = new Int16Array(nX * nY * nZ);
+            offset = 3 * (start + vi);
+            faceoffset = geoGroup.faceidx;
 
-        var i, il;
+            // from
+            vertexArray[offset] = x + from.x;
+            vertexArray[offset + 1] = y + from.y;
+            vertexArray[offset + 2] = z + from.z;
+            // to
+            vertexArray[offset + 3] = x + to.x;
+            vertexArray[offset + 4] = y + to.y;
+            vertexArray[offset + 5] = z + to.z;
 
-        for (i = 0, il = vertnums.length; i < il; ++i)
-            vertnums[i] = -1;
+            // normals
+            normalArray[offset] = x;
+            normalArray[offset + 3] = x;
+            normalArray[offset + 1] = y;
+            normalArray[offset + 4] = y;
+            normalArray[offset + 2] = z;
+            normalArray[offset + 5] = z;
 
-        var bitdata = new Uint8Array(nX * nY * nZ);
+            // colors
+            colorArray[offset] = color.r;
+            colorArray[offset + 3] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 4] = color.g;
+            colorArray[offset + 2] = color.b;
+            colorArray[offset + 5] = color.b;
 
-        for (i = 0, il = lines.length; i < il; ++i) {
-            var val = (isoval >= 0) ? lines[i] - isoval : isoval - lines[i];
+            // faces
+            // 0 - 2 - 1
+            faceArray[faceoffset] = fromRow[i] + start;
+            faceArray[faceoffset + 1] = fromRow[i + 1] + start;
+            faceArray[faceoffset + 2] = toRow[i] + start;
+            // 1 - 2 - 3
+            faceArray[faceoffset + 3] = toRow[i] + start;
+            faceArray[faceoffset + 4] = fromRow[i + 1] + start;
+            faceArray[faceoffset + 5] = toRow[i + 1] + start;
 
-            if (val > 0)
-                bitdata[i] |= ISDONE;
+            geoGroup.faceidx += 6;
 
         }
 
-        var verts = [], faces = [];
+        // SPHERE CAPS
 
-        $3Dmol.MarchingCube.march(bitdata, verts, faces, {
-            fulltable : true,
-            voxel : voxel,
-            scale : xVec.length(),
-            origin : origin,
-            nX : nX,
-            nY : nY,
-            nZ : nZ
-        });
+        if (drawcaps) {
 
-        if (!voxel)
-            $3Dmol.MarchingCube.laplacianSmooth(10, verts, faces);
+            // h - sphere rows, verticesRows.length - 2
+            var ystart = (toCap) ? 0 : h / 2;
+            var yend = (fromCap) ? h + 1 : h / 2 + 1;
 
-        drawCustom(shape, geoGroup, {
-            vertexArr : verts,
-            faceArr : faces,
-            normalArr : [],
-            lineArr : []
-        });
+            var v1, v2, v3, v4, x1, x2, x3, x4, y1, y2, y3, y4, z1, z2, z3, z4, nx1, nx2, nx3, nx4, ny1, ny2, ny3, ny4, nz1, nz2, nz3, nz4, v1offset, v2offset, v3offset, v4offset;
 
-    };
+            for (y = ystart; y < yend; y++) {
+                if (y === h / 2)
+                    continue;
+                // n number of points for each level (verticesRows[i].length -
+                // 1)
+                var cap = (y <= h / 2) ? to : from;
 
-    // Update a bounding sphere's position and radius
-    // from list of centroids and new points
-    /**
-     * @param {$3Dmol.Sphere}
-     *            sphere
-     * @param {Object}
-     *            components
-     * @param {Array}
-     *            points
-     */
-    var updateBoundingFromPoints = function(sphere, components, points) {
+                for (x = 0; x < n; x++) {
 
-        sphere.center.set(0, 0, 0);
+                    faceoffset = geoGroup.faceidx;
 
-        var i, il;
+                    v1 = verticesRows[y][x + 1];
+                    v1offset = (v1 + start) * 3;
+                    v2 = verticesRows[y][x];
+                    v2offset = (v2 + start) * 3;
+                    v3 = verticesRows[y + 1][x];
+                    v3offset = (v3 + start) * 3;
+                    v4 = verticesRows[y + 1][x + 1];
+                    v4offset = (v4 + start) * 3;
 
-        if (components.length > 0) {
+                    // rotate sphere vectors
+                    x1 = e[0] * vertices[v1].x + e[3] * vertices[v1].y + e[6]
+                            * vertices[v1].z;
+                    x2 = e[0] * vertices[v2].x + e[3] * vertices[v2].y + e[6]
+                            * vertices[v2].z;
+                    x3 = e[0] * vertices[v3].x + e[3] * vertices[v3].y + e[6]
+                            * vertices[v3].z;
+                    x4 = e[0] * vertices[v4].x + e[3] * vertices[v4].y + e[6]
+                            * vertices[v4].z;
 
-            for (i = 0, il = components.length; i < il; ++i) {
-                var centroid = components[i].centroid;
-                sphere.center.add(centroid);
-            }
+                    y1 = e[1] * vertices[v1].x + e[4] * vertices[v1].y + e[7]
+                            * vertices[v1].z;
+                    y2 = e[1] * vertices[v2].x + e[4] * vertices[v2].y + e[7]
+                            * vertices[v2].z;
+                    y3 = e[1] * vertices[v3].x + e[4] * vertices[v3].y + e[7]
+                            * vertices[v3].z;
+                    y4 = e[1] * vertices[v4].x + e[4] * vertices[v4].y + e[7]
+                            * vertices[v4].z;
 
-            sphere.center.divideScalar(components.length);
-        }
-
-        var maxRadiusSq = sphere.radius * sphere.radius;
+                    z1 = e[5] * vertices[v1].y + e[8] * vertices[v1].z;
+                    z2 = e[5] * vertices[v2].y + e[8] * vertices[v2].z;
+                    z3 = e[5] * vertices[v3].y + e[8] * vertices[v3].z;
+                    z4 = e[5] * vertices[v4].y + e[8] * vertices[v4].z;
 
-        for (i = 0, il = points.length / 3; i < il; i++) {
-            var x = points[i * 3], y = points[i * 3 + 1], z = points[i * 3 + 2];
-            var radiusSq = sphere.center.distanceToSquared({
-                x : x,
-                y : y,
-                z : z
-            });
-            maxRadiusSq = Math.max(maxRadiusSq, radiusSq);
-        }
+                    vertexArray[v1offset] = x1 + cap.x;
+                    vertexArray[v2offset] = x2 + cap.x;
+                    vertexArray[v3offset] = x3 + cap.x;
+                    vertexArray[v4offset] = x4 + cap.x;
 
-        sphere.radius = Math.sqrt(maxRadiusSq);
+                    vertexArray[v1offset + 1] = y1 + cap.y;
+                    vertexArray[v2offset + 1] = y2 + cap.y;
+                    vertexArray[v3offset + 1] = y3 + cap.y;
+                    vertexArray[v4offset + 1] = y4 + cap.y;
 
-    };
+                    vertexArray[v1offset + 2] = z1 + cap.z;
+                    vertexArray[v2offset + 2] = z2 + cap.z;
+                    vertexArray[v3offset + 2] = z3 + cap.z;
+                    vertexArray[v4offset + 2] = z4 + cap.z;
 
-    /**
-     * 
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {ShapeSpec}
-     *            stylespec
-     * @returns {undefined}
-     */
-    var updateFromStyle = function(shape, stylespec) {
-        shape.color = stylespec.color || new $3Dmol.Color();
-        if(! (stylespec.color instanceof $3Dmol.Color))
-            shape.color = $3Dmol.CC.color(stylespec.color);
-        shape.wireframe = stylespec.wireframe ? true : false;
-        shape.alpha = stylespec.alpha ? $3Dmol.Math.clamp(stylespec.alpha, 0.0,
-                1.0) : 1.0;
-        shape.side = (stylespec.side !== undefined) ? stylespec.side
-                : $3Dmol.DoubleSide;
-        shape.linewidth = typeof(stylespec.linewidth) == 'undefined' ? 1 : stylespec.linewidth;
-        // Click handling
-        shape.clickable = stylespec.clickable ? true : false;
-        shape.callback = typeof (stylespec.callback) === "function" ? stylespec.callback
-                : null;
-    };
+                    colorArray[v1offset] = color.r;
+                    colorArray[v2offset] = color.r;
+                    colorArray[v3offset] = color.r;
+                    colorArray[v4offset] = color.r;
 
-    /**
-     * Custom renderable shape
-     * 
-     * @constructor $3Dmol.GLShape
-     * 
-     * @param {Object}
-     *            stylespec
-     * @returns {$3Dmol.GLShape}
-     */
-    function GLShape(stylespec) {
+                    colorArray[v1offset + 1] = color.g;
+                    colorArray[v2offset + 1] = color.g;
+                    colorArray[v3offset + 1] = color.g;
+                    colorArray[v4offset + 1] = color.g;
 
-        stylespec = stylespec || {};
-        $3Dmol.ShapeIDCount++;
+                    colorArray[v1offset + 2] = color.b;
+                    colorArray[v2offset + 2] = color.b;
+                    colorArray[v3offset + 2] = color.b;
+                    colorArray[v4offset + 2] = color.b;
 
-        this.boundingSphere = new $3Dmol.Sphere();
-        /** @type {IntersectionShapes} */
-        this.intersectionShape = {
-            sphere : [],
-            cylinder : [],
-            line : [],
-            triangle : []
-        };
+                    nx1 = e[0] * normals[v1].x + e[3] * normals[v1].y + e[6]
+                            * normals[v1].z;
+                    nx2 = e[0] * normals[v2].x + e[3] * normals[v2].y + e[6]
+                            * normals[v2].z;
+                    nx3 = e[0] * normals[v3].x + e[3] * normals[v3].y + e[6]
+                            * normals[v3].z;
+                    nx4 = e[0] * normals[v4].x + e[3] * normals[v4].y + e[6]
+                            * normals[v4].z;
 
-        updateFromStyle(this, stylespec);
+                    ny1 = e[1] * normals[v1].x + e[4] * normals[v1].y + e[7]
+                            * normals[v1].z;
+                    ny2 = e[1] * normals[v2].x + e[4] * normals[v2].y + e[7]
+                            * normals[v2].z;
+                    ny3 = e[1] * normals[v3].x + e[4] * normals[v3].y + e[7]
+                            * normals[v3].z;
+                    ny4 = e[1] * normals[v4].x + e[4] * normals[v4].y + e[7]
+                            * normals[v4].z;
 
-        // Keep track of shape components and their centroids
-        var components = [];
-        var shapeObj = null;
-        var renderedShapeObj = null;
+                    nz1 = e[5] * normals[v1].y + e[8] * normals[v1].z;
+                    nz2 = e[5] * normals[v2].y + e[8] * normals[v2].z;
+                    nz3 = e[5] * normals[v3].y + e[8] * normals[v3].z;
+                    nz4 = e[5] * normals[v4].y + e[8] * normals[v4].z;
 
-        var geo = new $3Dmol.Geometry(true);
-        var linegeo = new $3Dmol.Geometry(true);
+                    // if (Math.abs(vobj.sphereVertices[v1].y) === radius) {
+                    if (y === 0) {
+                        // face = [v1, v3, v4];
+                        // norm = [n1, n3, n4];
 
-        /** Update shape with new style specification
-         * @param {ShapeSpec} newspec
-         * @return {$3Dmol.GLShape}
-         */
-        this.updateStyle = function(newspec) {
+                        normalArray[v1offset] = nx1;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v3offset + 2] = nz3;
+                        normalArray[v4offset + 2] = nz4;
 
-            for ( var prop in newspec) {
-                stylespec[prop] = newspec[prop];
-            }
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v3 + start;
+                        faceArray[faceoffset + 2] = v4 + start;
 
-            updateFromStyle(this, stylespec);
-        };
+                        geoGroup.faceidx += 3;
 
-        /**
-         * Creates a custom shape from supplied vertex and face arrays
-         * @param {CustomSpec} customSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCustom = function(customSpec) {
+                    }
 
-            customSpec.vertexArr = customSpec.vertexArr || [];
-            customSpec.faceArr = customSpec.faceArr || [];
-            customSpec.normalArr = customSpec.normalArr || [];
-            customSpec.lineArr = customSpec.lineArr || [];
+                    // else if (Math.abs(vobj.sphereVertices[v3].y) === radius)
+                    // {
+                    else if (y === yend - 1) {
+                        // face = [v1, v2, v3];
+                        // norm = [n1, n2, n3];
 
-            // Force creation of new geometryGroup for each added component
-            var geoGroup = geo.addGeoGroup();
-            drawCustom(this, geoGroup, customSpec);
-            geoGroup.truncateArrayBuffers(true, true);
+                        normalArray[v1offset] = nx1;
+                        normalArray[v2offset] = nx2;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v3offset + 2] = nz3;
 
-            for (var i = 0; i < geoGroup.colorArray.length / 3; ++i) {
-                geoGroup.colorArray[i * 3] = this.color.r;
-                geoGroup.colorArray[i * 3 + 1] = this.color.g;
-                geoGroup.colorArray[i * 3 + 2] = this.color.b;
-            }
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v2 + start;
+                        faceArray[faceoffset + 2] = v3 + start;
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : geoGroup.getCentroid()
-            });
+                        geoGroup.faceidx += 3;
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
-        };
+                    }
 
-        /**
-         * Creates a sphere shape
-         * @param {SphereSpec} sphereSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addSphere = function(sphereSpec) {
+                    else {
+                        // face = [v1, v2, v3, v4];
+                        // norm = [n1, n2, n3, n4];
 
-            sphereSpec.center = sphereSpec.center || {
-                x : 0,
-                y : 0,
-                z : 0
-            };
-            sphereSpec.radius = sphereSpec.radius ? $3Dmol.Math.clamp(
-                    sphereSpec.radius, 0, Infinity) : 1.5;
-            sphereSpec.color = $3Dmol.CC.color(sphereSpec.color);
-            
-            this.intersectionShape.sphere.push(new $3Dmol.Sphere(
-                    sphereSpec.center, sphereSpec.radius));
+                        normalArray[v1offset] = nx1;
+                        normalArray[v2offset] = nx2;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v4offset + 2] = nz4;
 
-            var geoGroup = geo.addGeoGroup();
-            $3Dmol.GLDraw.drawSphere(geo, sphereSpec.center,
-                    sphereSpec.radius, sphereSpec.color);
-            geoGroup.truncateArrayBuffers(true, true);
+                        normalArray[v2offset] = nx2;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v3offset + 2] = nz3;
+                        normalArray[v4offset + 2] = nz4;
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup, // has to be last group added
-                centroid : new $3Dmol.Vector3(sphereSpec.center.x,
-                        sphereSpec.center.y, sphereSpec.center.z)
-            });
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v2 + start;
+                        faceArray[faceoffset + 2] = v4 + start;
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
-        };
+                        faceArray[faceoffset + 3] = v2 + start;
+                        faceArray[faceoffset + 4] = v3 + start;
+                        faceArray[faceoffset + 5] = v4 + start;
 
-        /**
-         * Creates a cylinder shape
-         * @param {CylinderSpec} cylinderSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCylinder = function(cylinderSpec) {
+                        geoGroup.faceidx += 6;
+                    }
 
-            cylinderSpec.start = cylinderSpec.start || {};
-            cylinderSpec.end = cylinderSpec.end || {};
+                }
+            }
 
-            var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
-                    cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
-            var end = new $3Dmol.Vector3(cylinderSpec.end.x,
-                    cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
-        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+        }
 
-            var radius = cylinderSpec.radius || 0.1;
-            var color = $3Dmol.CC.color(cylinderSpec.color);
-            
-            this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(start, end, radius));
+        geoGroup.vertices += n_verts;
+    };
 
-            var geoGroup = geo.addGeoGroup();
-            $3Dmol.GLDraw.drawCylinder(geo, start, end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);            
-            geoGroup.truncateArrayBuffers(true, true);
-            
-            var centroid = new $3Dmol.Vector3();
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
-            });
+    /** Create a cone 
+     * @function $3Dmol.GLDraw.drawCone
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            from
+     * @param {Point}
+     *            to
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     *            */
+    draw.drawCone = function(geo, from, to, radius, color) {
+        if (!from || !to)
+            return;
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
+        color = color || {r:0, g:0, b:0};
 
-        };
+        var dir =[to.x, to.y, to.z ];        
+        dir.x -= from.x;
+        dir.y -= from.y;
+        dir.z -= from.z;
 
-        /**
-         * Creates a line shape
-         * @param {LineSpec} lineSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addLine = function(lineSpec) {
-        	lineSpec.start = lineSpec.start || {};
-        	lineSpec.end = lineSpec.end || {};
+        var e = getRotationMatrix(dir);
 
-        	var start = new $3Dmol.Vector3(lineSpec.start.x || 0,
-        			lineSpec.start.y || 0, lineSpec.start.z || 0);
-        	var end = new $3Dmol.Vector3(lineSpec.end.x,
-        			lineSpec.end.y || 0, lineSpec.end.z || 0);            
-        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
-    
-            var geoGroup = geo.addGeoGroup();
 
-            //make line from start to end
-            //for consistency with rest of shapes, uses vertices and lines rather
-            //than a separate line geometry
-            var vstart = geoGroup.vertices;
-            var i = vstart*3;
-            var vertexArray = geoGroup.vertexArray;
-            vertexArray[i] = start.x;
-            vertexArray[i+1] = start.y;
-            vertexArray[i+2] = start.z;
-            vertexArray[i+3] = end.x;
-            vertexArray[i+4] = end.y;
-            vertexArray[i+5] = end.z;
-            geoGroup.vertices += 2;
+        // n vertices around bottom plust the two points
+        var n = basisVectors.length;
+        var basis = basisVectors;
+        var n_verts =  n + 2;
+
+        
+        //setup geo structures
+        var geoGroup = geo.updateGeoGroup(n_verts);
+        var start = geoGroup.vertices;    
+        var offset, faceoffset;
+        var i, x, y, z;
+        var vertexArray = geoGroup.vertexArray;
+        var normalArray = geoGroup.normalArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        
+        var offset = start*3;
+        var ndir = new $3Dmol.Vector3(dir[0],dir[1],dir[2]).normalize();
+        //base point first vertex
+        vertexArray[offset] = from.x;
+        vertexArray[offset+1] = from.y;
+        vertexArray[offset+2] = from.z;
+        normalArray[offset] = -ndir.x;
+        normalArray[offset + 1] = -ndir.y;
+        normalArray[offset + 2] = -ndir.z;
+        colorArray[offset] = color.r;
+        colorArray[offset + 1] = color.g;
+        colorArray[offset + 2] = color.b;
+        
+        //second vertex top
+        vertexArray[offset+3] = to.x;
+        vertexArray[offset+4] = to.y;
+        vertexArray[offset+5] = to.z;
+        
+        normalArray[offset+3] = ndir.x;
+        normalArray[offset+4] = ndir.y;
+        normalArray[offset+5] = ndir.z;
+        colorArray[offset+3] = color.r;
+        colorArray[offset + 4] = color.g;
+        colorArray[offset + 5] = color.b;
+        
+        offset += 6;
+        
+        // add circle vertices
+        for (i = 0; i < n; ++i) {
+            var vec = basis[i].clone();
+            vec.multiplyScalar(radius);
+            x = e[0] * vec.x + e[3] * vec.y + e[6]
+                    * vec.z;
+            y = e[1] * vec.x + e[4] * vec.y + e[7]
+                    * vec.z;
+            z = e[5] * vec.y + e[8] * vec.z;
+
+            // from
+            vertexArray[offset] = x + from.x;
+            vertexArray[offset + 1] = y + from.y;
+            vertexArray[offset + 2] = z + from.z;
+
+            // normals
+            normalArray[offset] = x;
+            normalArray[offset + 1] = y;
+            normalArray[offset + 2] = z;
+
+            // colors
+            colorArray[offset] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 2] = color.b;
             
-            var lineArray = geoGroup.lineArray;
-            var li =  geoGroup.lineidx;
-            lineArray[li] = vstart;
-            lineArray[li+1] = vstart+1;
-            geoGroup.lineidx += 2;
+            offset += 3;
+
+        }
+        geoGroup.vertices += (n+2);
+        //faces
+        var faceoffset = geoGroup.faceidx;
+        for( i = 0; i < n; i++) {
+            //two neighboring circle vertices
+            var v1 = start+2+i;
+            var v2 = start+2+ ((i+1)%n);
             
-            geoGroup.truncateArrayBuffers(true, true);
+            faceArray[faceoffset] = v1;
+            faceArray[faceoffset+1] = v2;
+            faceArray[faceoffset+2] = start;
+            faceoffset += 3;
+            faceArray[faceoffset] = v1;
+            faceArray[faceoffset+1] = v2;
+            faceArray[faceoffset+2] = start+1;
+            faceoffset += 3;
         }
-        /**
-         * Creates an arrow shape
-         * @param {ArrowSpec} arrowSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addArrow = function(arrowSpec) {
+        geoGroup.faceidx += 6*n;
+    };
 
-            arrowSpec.start = arrowSpec.start || {};
-            arrowSpec.end = arrowSpec.end || {};
+    
+    // Sphere component
+    var sphereVertexCache = {
+        cache : {},
+        getVerticesForRadius : function(radius) {
 
-            arrowSpec.start = new $3Dmol.Vector3(arrowSpec.start.x || 0,
-                    arrowSpec.start.y || 0, arrowSpec.start.z || 0);
+            if (typeof (this.cache[radius]) !== "undefined")
+                return this.cache[radius];
 
-            if (arrowSpec.dir instanceof $3Dmol.Vector3
-                    && arrowSpec.length instanceof number) {
-                var end = arrowSpec.dir.clone().multiplyScalar(arrowSpec.length).add(
-                        start);
-                arrowSpec.end = end;
+            var obj = {
+                vertices : [],
+                verticesRows : [],
+                normals : []
+            };
+            // scale quality with radius heuristically
+            var sphereQuality = 1;
+            var widthSegments = 16 * sphereQuality;
+            var heightSegments = 10 * sphereQuality;
+            if (radius < 1) {
+                widthSegments = 10 * sphereQuality;
+                heightSegments = 8 * sphereQuality;
             }
 
-            else {
-                arrowSpec.end = new $3Dmol.Vector3(arrowSpec.end.x,
-                        arrowSpec.end.y || 0, arrowSpec.end.z || 0);
-            	if(typeof(arrowSpec.end.x) == 'undefined') arrowSpec.end.x = 3; //show something even if undefined
-            }
+            var phiStart = 0;
+            var phiLength = Math.PI * 2;
 
-            arrowSpec.radius = arrowSpec.radius || 0.1;
+            var thetaStart = 0;
+            var thetaLength = Math.PI;
 
-            arrowSpec.radiusRatio = arrowSpec.radiusRatio || 1.618034;
-            arrowSpec.mid = (0 < arrowSpec.mid && arrowSpec.mid < 1) ? arrowSpec.mid
-                    : 0.618034;
+            var x, y, vertices = [], uvs = [];
 
-            var geoGroup = geo.addGeoGroup();
+            for (y = 0; y <= heightSegments; y++) {
 
-            drawArrow(this, geoGroup, arrowSpec);
-            geoGroup.truncateArrayBuffers(true, true);
+                var verticesRow = [];
+                for (x = 0; x <= widthSegments; x++) {
 
-            var centroid = new $3Dmol.Vector3();
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : centroid.addVectors(arrowSpec.start, arrowSpec.end)
-                        .multiplyScalar(0.5)
-            });
+                    var u = x / widthSegments;
+                    var v = y / heightSegments;
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
+                    var vertex = {};
+                    vertex.x = -radius * Math.cos(phiStart + u * phiLength)
+                            * Math.sin(thetaStart + v * thetaLength);
+                    vertex.y = radius * Math.cos(thetaStart + v * thetaLength);
+                    vertex.z = radius * Math.sin(phiStart + u * phiLength)
+                            * Math.sin(thetaStart + v * thetaLength);
 
-        };
-        
-        /** 
-         * Creates custom shape from volumetric data 
-         * @param {string} data - Volumetric input data 
-         * @param {string} fmt - Input data format (e.g. 'cube' for cube file format)
-         * @param {VolSpec} volSpec - Volumetric data shape specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addVolumetricData = function(data, fmt, volSpec) {
+                    var n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
+                    n.normalize();
 
-            // str, fmt, isoval, vxl
-            var isoval = (volSpec.isoval !== undefined && typeof (volSpec.isoval) === "number") ? volSpec.isoval
-                    : 0.0;
-            var vxl = (volSpec.voxel) ? true : false;
+                    obj.vertices.push(vertex);
+                    obj.normals.push(n);
 
-            var geoGroup = geo.addGeoGroup();
+                    verticesRow.push(obj.vertices.length - 1);
 
-            // TODO: Initialize geometry group here (parseCube currently calls
-            // addCustom...)
-            switch (fmt) {
-            case "cube":
-                parseCube(this, geoGroup, data, isoval, vxl);
-                break;
-            }
+                }
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : geoGroup.getCentroid()
-            });
+                obj.verticesRows.push(verticesRow);
 
-            this.updateStyle(volSpec);
+            }
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
+            this.cache[radius] = obj;
+            return obj;
+        }
 
-        };
+    };
 
-        /**
-         * Initialize webgl objects for rendering
-         * @param {$3Dmol.Object3D} group
-         * 
-         */  
-        this.globj = function(group) {
+    /** Create a sphere.
+     * @function $3Dmol.GLDraw.drawSphere
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            pos
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     */
+    draw.drawSphere = function(geo, pos, radius, color) {
 
-            geo.initTypedArrays();
+        var center = new $3Dmol.Vector3(pos.x, pos.y, pos.z);
 
-            updateColor(geo, this.color);
+        var x, y;
+        var vobj = sphereVertexCache.getVerticesForRadius(radius);
 
-            shapeObj = new $3Dmol.Object3D();
-            var material = new $3Dmol.MeshLambertMaterial({
-                wireframe : this.wireframe,
-                vertexColors : true,
-                ambient : 0x000000,
-                reflectivity : 0,
-                side : this.side,
-                transparent : (this.alpha < 1) ? true : false,
-                opacity : this.alpha,
-                wireframeLinewidth: this.linewidth
-            });
-            
-            var mesh = new $3Dmol.Mesh(geo, material);
-            shapeObj.add(mesh);
-            
-            var lineMaterial = new $3Dmol.LineBasicMaterial({
-                linewidth : this.linewidth,
-                color: this.color
-            });
-            var line = new $3Dmol.Line(linegeo, lineMaterial,
-                    $3Dmol.LinePieces);
-            shapeObj.add(line);
+        var vertices = vobj.vertices;
+        var normals = vobj.normals;
 
-            if (renderedShapeObj) {
-                group.remove(renderedShapeObj);
-                renderedShapeObj = null;
-            }
-            renderedShapeObj = shapeObj.clone();
-            group.add(renderedShapeObj);
+        var geoGroup = geo.updateGeoGroup(vertices.length);
 
-        };
+        var start = geoGroup.vertices;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        var lineArray = geoGroup.lineArray;
+        var normalArray = geoGroup.normalArray;
 
-        this.removegl = function(group) {
-            if (renderedShapeObj) {
-                // dispose of geos and materials
-                if (renderedShapeObj.geometry !== undefined)
-                    renderedShapeObj.geometry.dispose();
-                if (renderedShapeObj.material !== undefined)
-                    renderedShapeObj.material.dispose();
-                group.remove(renderedShapeObj);
-                renderedShapeObj = null;
-            }
-            shapeObj = null;
-        };
+        for (var i = 0, il = vertices.length; i < il; ++i) {
+            var offset = 3 * (start + i);
+            var v = vertices[i];
 
-    };
+            vertexArray[offset] = (v.x + pos.x);
+            vertexArray[offset + 1] = (v.y + pos.y);
+            vertexArray[offset + 2] = (v.z + pos.z);
 
-    Object.defineProperty(GLShape.prototype, "position", {
+            colorArray[offset] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 2] = color.b;
 
-        get : function() {
-            return this.boundingSphere.center;
         }
 
-    });
+        geoGroup.vertices += vertices.length;
 
-    Object.defineProperty(GLShape.prototype, "x", {
+        var verticesRows = vobj.verticesRows;
+        var h = verticesRows.length - 1;
 
-        get : function() {
-            return this.boundingSphere.center.x;
-        }
+        for (y = 0; y < h; y++) {
+            var w = verticesRows[y].length - 1;
+            for (x = 0; x < w; x++) {
 
-    });
+                var faceoffset = geoGroup.faceidx, lineoffset = geoGroup.lineidx;
 
-    Object.defineProperty(GLShape.prototype, "y", {
+                var v1 = verticesRows[y][x + 1] + start, v1offset = v1 * 3;
+                var v2 = verticesRows[y][x] + start, v2offset = v2 * 3;
+                var v3 = verticesRows[y + 1][x] + start, v3offset = v3 * 3;
+                var v4 = verticesRows[y + 1][x + 1] + start, v4offset = v4 * 3;
 
-        get : function() {
-            return this.boundingSphere.center.y;
-        }
+                var n1 = normals[v1 - start];
+                var n2 = normals[v2 - start];
+                var n3 = normals[v3 - start];
+                var n4 = normals[v4 - start];
+                var face, norm;
+                if (Math.abs(vertices[v1 - start].y) === radius) {
+                    // face = [v1, v3, v4];
+                    // norm = [n1, n3, n4];
 
-    });
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v3offset + 2] = n3.z;
+                    normalArray[v4offset + 2] = n4.z;
 
-    Object.defineProperty(GLShape.prototype, "z", {
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v3;
+                    faceArray[faceoffset + 2] = v4;
 
-        get : function() {
-            return this.boundingSphere.center.z;
-        }
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v3;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v4;
+                    lineArray[lineoffset + 4] = v3;
+                    lineArray[lineoffset + 5] = v4;
 
-    });
+                    geoGroup.faceidx += 3;
+                    geoGroup.lineidx += 6;
 
-    return GLShape;
+                } else if (Math.abs(vertices[v3 - start].y) === radius) {
+                    // face = [v1, v2, v3];
+                    // norm = [n1, n2, n3];
 
-}());
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v3offset + 2] = n3.z;
 
-$3Dmol.ShapeIDCount = 0;//a molecular viewer based on GLMol
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v2;
+                    faceArray[faceoffset + 2] = v3;
 
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v2;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v3;
+                    lineArray[lineoffset + 4] = v2;
+                    lineArray[lineoffset + 5] = v3;
 
+                    geoGroup.faceidx += 3;
+                    geoGroup.lineidx += 6;
 
-/**
- * WebGL-based 3Dmol.js viewer
- * Note: The preferred method of instantiating a GLViewer is through {@link $3Dmol.createViewer} 
- * 
- * @constructor 
- * @param {Object} element HTML element within which to create viewer
- * @param {function} callback - Callback function to be immediately executed on this viewer
- * @param {Object} defaultcolors - Object defining default atom colors as atom => color property value pairs for all models within this viewer
- */
-$3Dmol.GLViewer = (function() {
-    // private class variables
-    var numWorkers = 4; // number of threads for surface generation
-    var maxVolume = 64000; // how much to break up surface calculations
+                } else {
+                    // face = [v1, v2, v3, v4];
+                    // norm = [n1, n2, n3, n4];
 
-    // private class helper functions
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v4offset + 2] = n4.z;
 
-    function GLViewer(element, config) { 
-        // set variables
-    	config = config || {};
-    	var callback = config.callback;
-    	var defaultcolors = config.defaultcolors;    	
-        if(!defaultcolors)
-            defaultcolors = $3Dmol.elementColors.defaultColors;
-    	var nomouse = config.nomouse;
-    	var bgColor = 0;
-    	
-    	if(typeof(config.backgroundColor) != undefined) {
-            bgColor = $3Dmol.CC.color(config.backgroundColor).getHex();
-    	}
-        var _viewer = this;
-        var container = element;
-        var id = container.id;
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v3offset + 2] = n3.z;
+                    normalArray[v4offset + 2] = n4.z;
 
-        var models = []; // atomistic molecular models
-        var surfaces = [];
-        var shapes = []; // Generic shapes
-        var labels = [];
-        var clickables = []; //things you can click on
-        var WIDTH = container.width();
-        var HEIGHT = container.height();
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v2;
+                    faceArray[faceoffset + 2] = v4;
 
-        // set dimensions
-        // $(container).width(WIDTH);
-        // $(container).height(HEIGHT);
+                    faceArray[faceoffset + 3] = v2;
+                    faceArray[faceoffset + 4] = v3;
+                    faceArray[faceoffset + 5] = v4;
 
-        var ASPECT = WIDTH / HEIGHT;
-        var NEAR = 1, FAR = 800;
-        var CAMERA_Z = 150;
-        var fov = 20;
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v2;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v4;
 
+                    lineArray[lineoffset + 4] = v2;
+                    lineArray[lineoffset + 5] = v3;
+                    lineArray[lineoffset + 6] = v3;
+                    lineArray[lineoffset + 7] = v4;
 
-        var renderer = new $3Dmol.Renderer({
-            antialias : true,
-            premultipliedAlpha : false /* more traditional compositing with background */
-        });
+                    geoGroup.faceidx += 6;
+                    geoGroup.lineidx += 8;
 
-        renderer.domElement.style.width = "100%";
-        renderer.domElement.style.height = "100%";
-        renderer.domElement.style.padding = "0";
-        renderer.domElement.style.position = "absolute"; //TODO: get rid of this
-        renderer.domElement.style.top = "0px";
-        renderer.domElement.style.zIndex = "0";
-        container.append(renderer.domElement);
-        renderer.setSize(WIDTH, HEIGHT);
-        var camera = new $3Dmol.Camera(fov, ASPECT, NEAR, FAR);
-        camera.position = new $3Dmol.Vector3(0, 0, CAMERA_Z);
-        var lookingAt = new $3Dmol.Vector3();
-        camera.lookAt(lookingAt);
+                }
 
-        var raycaster = new $3Dmol.Raycaster(new $3Dmol.Vector3(0, 0, 0),
-                new $3Dmol.Vector3(0, 0, 0));
-        var projector = new $3Dmol.Projector();
-        var mouseVector = new $3Dmol.Vector3(0, 0, 0);
+            }
+        }
 
-        var scene = null;
-        var rotationGroup = null; // which contains modelGroup
-        var modelGroup = null;
+    };
 
-        var fogStart = 0.4;
-        var slabNear = -50; // relative to the center of rotationGroup
-        var slabFar = 50;
+    return draw;
 
-        // UI variables
-        var cq = new $3Dmol.Quaternion(0, 0, 0, 1);
-        var dq = new $3Dmol.Quaternion(0, 0, 0, 1);
-        var isDragging = false;
-        var mouseStartX = 0;
-        var mouseStartY = 0;
-        var touchDistanceStart = 0;
-        var currentModelPos = 0;
-        var cz = 0;
-        var cslabNear = 0;
-        var cslabFar = 0;
+})();// A model is a collection of related atoms.  Bonds are only allowed between
+//atoms in the same model.  An atom is uniquely specified by its model id and
+//its serial number.
+//A glmodel knows how to apply the styles on each atom to create a gl object
 
-        var setSlabAndFog = function() {
-            var center = camera.position.z - rotationGroup.position.z;
-            if (center < 1)
-                center = 1;
-            camera.near = center + slabNear;
-            if (camera.near < 1)
-                camera.near = 1;
-            camera.far = center + slabFar;
-            if (camera.near + 1 > camera.far)
-                camera.far = camera.near + 1;
-            if (camera instanceof $3Dmol.Camera) {
-                camera.fov = fov;
-            } else {
-                camera.right = center * Math.tan(Math.PI / 180 * fov);
-                camera.left = -camera.right;
-                camera.top = camera.right / ASPECT;
-                camera.bottom = -camera.top;
-            }
-            camera.updateProjectionMatrix();
-            scene.fog.near = camera.near + fogStart
-                    * (camera.far - camera.near);
-            // if (scene.fog.near > center) scene.fog.near = center;
-            scene.fog.far = camera.far;
-        };
+var $3Dmol = $3Dmol || {};
 
-        // display scene
-        var show = function() {
-            if (!scene)
-                return;
+/**
+ * GLModel represents a group of related atoms
+ * @constructor 
+ * @param {number=} mid 
+ * @param {Object=} defaultcolors Object defining default atom colors as atom => color property value pairs
+ * @see $3Dmol.download
+ */
+$3Dmol.GLModel = (function() {
 
-            // var time = new Date();
-            setSlabAndFog();
-            renderer.render(scene, camera);
-            // console.log("rendered in " + (+new Date() - time) + "ms");
-        };
+    // class variables go here
+    var defaultAtomStyle = {
+        line : {}
+    };
 
-        var initializeScene = function() {
+    var Nucleotides = [ '  G', '  A', '  T', '  C', '  U', ' DG', ' DA', ' DT',
+            ' DC', ' DU' ];
 
-            scene = new $3Dmol.Scene();
-            scene.fog = new $3Dmol.Fog(bgColor, 100, 200);
+    var defaultlineWidth = 1.0;
 
-            modelGroup = new $3Dmol.Object3D();
-            rotationGroup = new $3Dmol.Object3D();
-            rotationGroup.useQuaternion = true;
-            rotationGroup.quaternion = new $3Dmol.Quaternion(0, 0, 0, 1);
-            rotationGroup.add(modelGroup);
+    // Reference: A. Bondi, J. Phys. Chem., 1964, 68, 441.
+    var vdwRadii = {
+        "H" : 1.2,
+        "Li" : 1.82,
+        "LI" : 1.82,
+        "Na" : 2.27,
+        "NA" : 2.27,
+        "K" : 2.75,
+        "C" : 1.7,
+        "N" : 1.55,
+        "O" : 1.52,
+        "F" : 1.47,
+        "P" : 1.80,
+        "S" : 1.80,
+        "CL" : 1.75,
+        "Cl" : 1.75,
+        "BR" : 1.85,
+        "Br" : 1.85,
+        "SE" : 1.90,
+        "Se" : 1.90,
+        "ZN" : 1.39,
+        "Zn" : 1.39,
+        "CU" : 1.4,
+        "Cu" : 1.4,
+        "NI" : 1.63,
+        "Ni" : 1.63
+    };
 
-            scene.add(rotationGroup);
+    var validAtomSpecs = [
+        "resn", // Parent residue name
+        "x", // Atom's x coordinate
+        "y", // Atom's y coordinate
+        "z", // Atom's z coordinate
+        "color", // Atom's color, as hex code
+        "surfaceColor", // Hex code for color to be used for surface patch over this atom
+        "elem", // Element abbreviation (e.g. 'H', 'Ca', etc)
+        "hetflag", // Set to true if atom is a heteroatom
+        "chain", // Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)
+        "resi", // Residue number 
+        "icode",
+        "rescode",
+        "serial", // Atom's serial id numbermodels
+        "atom", // Atom name; may be more specific than 'elem' (e.g 'CA' for alpha carbon)
+        "bonds", // Array of atom ids this atom is bonded to
+        "ss", // Secondary structure identifier (for cartoon render; e.g. 'h' for helix)
+        "singleBonds", // true if this atom forms only single bonds or no bonds at all
+        "bondOrder", // Array of this atom's bond orders, corresponding to bonds identfied by 'bonds'
+        "properties", // Optional mapping of additional properties
+        "b", // Atom b factor data
+        "pdbline", // If applicable, this atom's record entry from the input PDB file (used to output new PDB from models)
+        "clickable", // Set this flag to true to enable click selection handling for this atom
+        "callback", // Callback click handler function to be executed on this atom and its parent viewer
+        "invert" // for selection, inverts the meaning of the selection
+    ];
+
+    var validAtomSelectionSpecs = validAtomSpecs.concat([  // valid atom specs are ok too
+        "model", // a single model or list of models from which atoms should be selected
+        "bonds", // overloaded to select number of bonds, e.g. {bonds: 0} will select all nonbonded atoms
+        "predicate", // user supplied function that gets passed an {AtomSpec} and should return true if the atom should be selected
+        "invert", // if set, inverts the meaning of the selection
+        "byres", // if set, expands the selection to include all atoms of any residue that has any atom selected
+        "expand", // expands the selection to include all atoms within a given distance from the selection
+        "within" // intersects the selection with the set of atoms within a given distance from another selection
+    ]);
+
+    var validAtomStyleSpecs = [
+        "line", // draw bonds as lines
+        "cross", // draw atoms as crossed lines (aka stars)
+        "stick", // draw bonds as capped cylinders
+        "sphere", // draw atoms as spheres
+        "cartoon" // draw cartoon representation of secondary structure
+    ];
 
-            // setup lights
-            var directionalLight = new $3Dmol.Light(0xFFFFFF);
-            directionalLight.position = new $3Dmol.Vector3(0.2, 0.2, 1)
-                    .normalize();
-            directionalLight.intensity = 1.0;
-            scene.add(directionalLight);
-        };
+    // class functions
 
-        initializeScene();
+    // return true if a and b represent the same style
+    var sameObj = function(a,b) {
+        if(a && b)
+            return JSON.stringify(a) == JSON.stringify(b);
+        else
+            return a == b;
+    };    
 
-        renderer.setClearColorHex(bgColor, 1.0);
-        scene.fog.color = $3Dmol.CC.color(bgColor);
+   
+    function GLModel(mid, defaultcolors) {
+        // private variables
+        var atoms = [];
+        var frames = [];
+        var id = mid;
+        var hidden = false;
+        var molObj = null;
+        var renderedMolObj = null;
+        var lastColors = null;
+        var modelData = {};
+        var idMatrix = new $3Dmol.Matrix4();
+        var dontDuplicateAtoms;
+        var defaultColor = $3Dmol.elementColors.defaultColor;
+        
+        var ElementColors = (defaultcolors) ? defaultcolors : $3Dmol.elementColors.defaultColors;
 
-        var clickedAtom = null;
-        // enable mouse support
-        var glDOM = $(renderer.domElement);
 
-        //regenerate the list of clickables
-        var updateClickables = function() {
-            clickables = [];
-            var i, il;
+        // drawing functions must be associated with model object since
+        // geometries can't span multiple canvases
 
-            for (i = 0, il = models.length; i < il; i++) {
-                var model = models[i];
-                if(model) {
-                    var atoms = model.selectedAtoms({
-                        clickable : true
-                    });
-                    clickables = clickables.concat(atoms);
-                }
-            }
+        // sphere drawing
+        var defaultSphereRadius = 1.5;
 
-            for (i = 0, il = shapes.length; i < il; i++) {
+        // return proper radius for atom given style
+        /** 
+         * 
+         * @param {AtomSpec} atom
+         * @param {atomstyle} style
+         * @return {number} 
+         * 
+         */
+        var getRadiusFromStyle = function(atom, style) {
+            var r = defaultSphereRadius;
+            if (typeof (style.radius) != "undefined")
+                r = style.radius;
+            else if (vdwRadii[atom.elem])
+                r = vdwRadii[atom.elem];
 
-                var shape = shapes[i];
-                if (shape && shape.clickable) {
-                    clickables.push(shape);
-                }
-            }
+            if (typeof (style.scale) != "undefined")
+                r *= style.scale;
+            return r;
         };
-        
-        // Checks for selection intersects on mousedown
-        var handleClickSelection = function(mouseX, mouseY, event) {
-            if(clickables.length == 0) return;
-            var mouse = {
-                x : mouseX,
-                y : mouseY,
-                z : -1.0
-            };
-            mouseVector.set(mouse.x, mouse.y, mouse.z);
-            projector.unprojectVector(mouseVector, camera);
-            mouseVector.sub(camera.position).normalize();
-
-            raycaster.set(camera.position, mouseVector);
 
-            var intersects = [];
+        // cross drawing
+        /** @typedef CrossStyleSpec
+         * @prop {boolean} hidden - do not show 
+         * @prop {number} linewidth 
+         * @prop {number} radius 
+         * @prop {number} scale - scale radius by specified amount
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+         */
+        
+        /**
+         * 
+         * @param {AtomSpec} atom
+         * @param {$3Dmol.Geometry[]} geos
+         */
+        var drawAtomCross = function(atom, geos) {
+            if (!atom.style.cross)
+                return;
+            var style = atom.style.cross;
+            if (style.hidden)
+                return;
+            var linewidth = (style.linewidth || defaultlineWidth);
+            if (!geos[linewidth])
+                geos[linewidth] = new $3Dmol.Geometry();
+                
+            var geoGroup = geos[linewidth].updateGeoGroup(6);
+            
+            var delta = getRadiusFromStyle(atom, style);
 
-            intersects = raycaster.intersectObjects(modelGroup, clickables);
+            var points = [ [ delta, 0, 0 ], [ -delta, 0, 0 ], [ 0, delta, 0 ],
+                    [ 0, -delta, 0 ], [ 0, 0, delta ], [ 0, 0, -delta ] ];
 
-            if (intersects.length) {
-                var selected = intersects[0].clickable;
-                if (selected.callback !== undefined
-                        && typeof (selected.callback) === "function") {
-                    selected.callback(selected, _viewer, event, container);
+            var clickable = atom.clickable;
+            if (clickable && atom.intersectionShape === undefined)
+                atom.intersectionShape = {sphere : [], cylinder : [], line : []};
+            
+            var c = $3Dmol.getColorFromStyle(atom, style);
+            
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            
+            for ( var j = 0; j < 6; j++) {
+                
+                var offset = geoGroup.vertices*3;
+                
+                geoGroup.vertices++;
+                vertexArray[offset] = atom.x + points[j][0];
+                vertexArray[offset+1] = atom.y + points[j][1];
+                vertexArray[offset+2] = atom.z + points[j][2];
+                colorArray[offset] = c.r;
+                colorArray[offset+1] = c.g;
+                colorArray[offset+2] = c.b;
+                
+                if (clickable){
+                    var point = new $3Dmol.Vector3(points[j][0], points[j][1], points[j][2]);
+                    
+                    //decrease cross size for selection to prevent misselection from atom overlap
+                    point.multiplyScalar(0.1);
+                    point.set(point.x+atom.x, point.y+atom.y, point.z+atom.z);
+                    atom.intersectionShape.line.push(point);
                 }
-            }
-        };
 
-        var calcTouchDistance = function(ev) { // distance between first two
-                                                // fingers
-            var xdiff = ev.originalEvent.targetTouches[0].pageX
-                    - ev.originalEvent.targetTouches[1].pageX;
-            var ydiff = ev.originalEvent.targetTouches[0].pageY
-                    - ev.originalEvent.targetTouches[1].pageY;
-            return Math.sqrt(xdiff * xdiff + ydiff * ydiff);
-        }
-        
-        //check targetTouches as well
-        var getXY = function(ev) {
-            var x = ev.pageX, y = ev.pageY;
-            if (ev.originalEvent.targetTouches
-                    && ev.originalEvent.targetTouches[0]) {
-                x = ev.originalEvent.targetTouches[0].pageX;
-                y = ev.originalEvent.targetTouches[0].pageY;
             }
-            else if (ev.originalEvent.changedTouches
-                    && ev.originalEvent.changedTouches[0]) {
-                x = ev.originalEvent.changedTouches[0].pageX;
-                y = ev.originalEvent.changedTouches[0].pageY;
-            }            
-            return [x,y];
+                        
         };
 
-        //for a given screen (x,y) displacement return model displacement 
-        var screenXY2model = function(x,y) {
-            var dx = x/WIDTH;
-            var dy = y/HEIGHT;
-            var zpos = rotationGroup.position.z; 
-            var q = rotationGroup.quaternion;                        
-            var t = new $3Dmol.Vector3(0,0,zpos);
-            projector.projectVector(t, camera);
-            t.x += dx*2;
-            t.y -= dy*2;
-            projector.unprojectVector(t, camera);
-            t.z = 0;                            
-            t.applyQuaternion(q);
-            return t;
-        }
-        
-        if (!nomouse) {
-            // user can request that the mouse handlers not be installed
-            glDOM.bind('mousedown touchstart', function(ev) {
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                var xy = getXY(ev);
-                var x = xy[0];
-                var y = xy[1];
-                
-                if (x === undefined)
-                    return;
-                isDragging = true;
-                clickedAtom = null;
-                mouseButton = ev.which;
-                mouseStartX = x;
-                mouseStartY = y;
-                touchDistanceStart = 0;
-                if (ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 2) {
-                    touchDistanceStart = calcTouchDistance(ev);
-                }
-                cq = rotationGroup.quaternion;
-                cz = rotationGroup.position.z;
-                currentModelPos = modelGroup.position.clone();
-                cslabNear = slabNear;
-                cslabFar = slabFar;
+        //from atom, return a normalized vector v that is orthogonal and along which
+        //it is appropraite to draw multiple bonds
+        var getSideBondV = function(atom, atom2, i) {
 
-            });
+            var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+            var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
 
-            glDOM.bind('DOMMouseScroll mousewheel', function(ev) { // Zoom
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                var scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
-                if (ev.originalEvent.detail) { // Webkit
-                    rotationGroup.position.z += scaleFactor
-                            * ev.originalEvent.detail / 10;
-                } else if (ev.originalEvent.wheelDelta) { // Firefox
-                    rotationGroup.position.z -= scaleFactor
-                            * ev.originalEvent.wheelDelta / 400;
-                }
-                if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+            var dir = p2.clone();
+            var v = null;
+            dir.sub(p1);
 
-                show();
-            });
+            var p1a, p1b, p2a, p2b;
+            var i2, j2, atom3, p3, dir2;
+            if (atom.bonds.length === 1) {
+                if (atom2.bonds.length === 1) {
+                    v = dir.clone();
+                    if (Math.abs(v.x) > 0.0001)
+                        v.y += 1;
+                    else
+                        v.x += 1;
+                } else {
+                    i2 = (i + 1) % atom2.bonds.length;
+                    j2 = atom2.bonds[i2];
+                    atom3 = atoms[j2];
+                    p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
 
-            glDOM.bind("contextmenu", function(ev) {
-                ev.preventDefault();
-            });
-            $('body').bind('mouseup touchend', function(ev) {
-                // handle selection
-                if(isDragging && scene) { //saw mousedown, haven't moved
-                    var xy = getXY(ev);
-                    var x = xy[0];
-                    var y = xy[1];
-                    if(x == mouseStartX && y == mouseStartY) {
-                        var offset = $(container).offset();
-                        var mouseX = ((x - offset.left) / WIDTH) * 2 - 1;
-                        var mouseY = -((y - offset.top) / HEIGHT) * 2 + 1;
-
-                        handleClickSelection(mouseX, mouseY, ev, container);
-                    }
-                }
-                
-                isDragging = false;
+                    dir2 = p3.clone();
+                    dir2.sub(p1);
 
-            });
+                    v = dir2.clone();
+                    v.cross(dir);
+                }
+            } else {
+                // get vector 2 different neighboring atom
+                i2 = (i + 1) % atom.bonds.length;
+                j2 = atom.bonds[i2];
+                atom3 = atoms[j2];
+                p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
 
-            glDOM.bind('mousemove touchmove', function(ev) { // touchmove
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                if (!isDragging)
-                    return;
-                var mode = 0;
+                dir2 = p3.clone();
+                dir2.sub(p1);
 
-                var xy = getXY(ev);
-                var x = xy[0];
-                var y = xy[1];
-                if (x === undefined)
-                    return;
-                var dx = (x - mouseStartX) / WIDTH;
-                var dy = (y - mouseStartY) / HEIGHT;
-                // check for pinch
-                if (touchDistanceStart != 0
-                        && ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 2) {
-                    var newdist = calcTouchDistance(ev);
-                    // change to zoom
-                    mode = 2;
-                    dy = (touchDistanceStart - newdist) * 2
-                            / (WIDTH + HEIGHT);
-                } else if (ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 3) {
-                    // translate
-                    mode = 1;
-                }
-
-                var r = Math.sqrt(dx * dx + dy * dy);
-                var scaleFactor;
-                if (mode == 3
-                        || (mouseButton == 3 && ev.ctrlKey)) { // Slab
-                    slabNear = cslabNear + dx * 100;
-                    slabFar = cslabFar + dy * 100;
-                } else if (mode == 2 || mouseButton == 3
-                        || ev.shiftKey) { // Zoom
-                    scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
-                    if (scaleFactor < 80)
-                        scaleFactor = 80;
-                    rotationGroup.position.z = cz - dy
-                            * scaleFactor;
-                    if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
-                } else if (mode == 1 || mouseButton == 2
-                        || ev.ctrlKey) { // Translate
-                    var t = screenXY2model(x-mouseStartX, y-mouseStartY);
-                    modelGroup.position.addVectors(currentModelPos,t);
-                    
-                } else if ((mode === 0 || mouseButton == 1)
-                        && r !== 0) { // Rotate
-                    var rs = Math.sin(r * Math.PI) / r;
-                    dq.x = Math.cos(r * Math.PI);
-                    dq.y = 0;
-                    dq.z = rs * dx;
-                    dq.w = -rs * dy;
-                    rotationGroup.quaternion = new $3Dmol.Quaternion(
-                            1, 0, 0, 0);
-                    rotationGroup.quaternion.multiply(dq);
-                    rotationGroup.quaternion.multiply(cq);
-                }
-                show();
-            });
-        }
-        // public methods
-        /**
-         * Set the background color (default white)
-         * 
-         * @function $3Dmol.GLViewer#setBackgroundColor
-         * @param {number}
-         *            hex Hexcode specified background color, or standard color spec
-         * @param {number}
-         *            a Alpha level (default 1.0)
-         * 
-         * @example
-         * 
-         * //Set 'myviewer' background color to white
-         * myviewer.setBackgroundColor(0xffffff)
-         * 
-         */
-        this.setBackgroundColor = function(hex, a) {
-            if(typeof(a) == "undefined") {
-                a = 1.0;
-            }
-            else if(a < 0 || a > 1.0) {
-                a = 1.0;
+                v = dir2.clone();
+                v.cross(dir);
             }
-            var c = $3Dmol.CC.color(hex);
-            scene.fog.color = c;
-            bgColor = c.getHex();
-            renderer.setClearColorHex(c.getHex(), a);
-            show();
-        };
 
-        /**
-         * Set viewer width
-         * 
-         * @function $3Dmol.GLViewer#setWidth
-         * @param {number}
-         *            w Width in pixels
-         */
-        this.setWidth = function(w) {
-            WIDTH = w || WIDTH;
-            renderer.setSize(WIDTH, HEIGHT);
-        };
+            // especially for C#C (triple bond) dir and dir2
+            // may be opposites resulting in a zero v
+            if (v.lengthSq() < 0.01) {
+                v = dir.clone();
+                if (Math.abs(v.x) > 0.0001)
+                    v.y += 1;
+                else
+                    v.x += 1;
+            }
 
-        /**
-         * Set viewer height
-         * 
-         * @function $3Dmol.GLViewer#setHeight
-         * @param {number}
-         *            h Height in pixels
-         */
-        this.setHeight = function(h) {
-            HEIGHT = h || HEIGHT;
-            renderer.setSize(WIDTH, HEIGHT);
-        };
+            v.cross(dir);
+            v.normalize();
+            
+            return v;
+            
+            //v.multiplyScalar(r * 1.5);
 
-        /**
-         * Resize viewer according to containing HTML element's dimensions
-         * 
-         * @function $3Dmol.GLViewer#resize
-         */
-        this.resize = function() {
-            WIDTH = container.width();
-            HEIGHT = container.height();
-            ASPECT = WIDTH / HEIGHT;
-            renderer.setSize(WIDTH, HEIGHT);
-            camera.aspect = ASPECT;
-            camera.updateProjectionMatrix();
-            show();
-        };
+        }
+        
+        var getTripleBondPoints = function() {
+            
+            v.cross(dir);
+            v.normalize();
+            v.multiplyScalar(r * 3);
 
-        $(window).resize(this.resize);
+            p1a = p1.clone();
+            p1a.add(v);
+            p1b = p1.clone();
+            p1b.sub(v);
 
-        /**
-         * Return specified model
-         * 
-         * @function $3Dmol.GLViewer#getModel
-         * @param {number}
-         *            [id=last model id] - Retrieve model with specified id
-         * @default Returns last model added to viewer
-         * @return {GLModel}
-         * 
-         * @example // Retrieve reference to first GLModel added var m =
-         *          glviewer.getModel(0);
+            p2a = p1a.clone();
+            p2a.add(dir);
+            p2b = p1b.clone();
+            p2b.add(dir);
+        }
+        
+        var addLine = function(vertexArray, colorArray, offset, p1, p2, c1) {
+            //make line from p1 to p2, does not incremeant counts
+            vertexArray[offset] = p1.x; vertexArray[offset+1] = p1.y; vertexArray[offset+2] = p1.z;
+            colorArray[offset] = c1.r; colorArray[offset+1] = c1.g; colorArray[offset+2] = c1.b;
+            vertexArray[offset+3] = p2.x; vertexArray[offset+4] = p2.y; vertexArray[offset+5] = p2.z;
+            colorArray[offset+3] = c1.r; colorArray[offset+4] = c1.g; colorArray[offset+5] = c1.b;            
+        }
+        
+        /**@typedef LineStyleSpec
+         * @prop {boolean} hidden - do not show line
+         * @prop {number} linewidth 
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
          */
-        this.getModel = function(id) {
-            id = id || models.length - 1;
-            return models[id];
-        };
-
+        
+        // bonds - both atoms must match bond style
+        // standardize on only drawing for lowest to highest
         /**
-         * Rotate scene by angle degrees around axis
-         * 
-         * @function $3Dmol.GLViewer#rotate
-         * @param {number}
-         *            [angle] - Angle, in degrees, to rotate by.
-         * @param {string}
-         *            [angle] - Axis ("x", "y", or "z") to rotate around.
-         *            Default "y"
          * 
+         * @param {AtomSpec}
+         *            atom
+         * @param {AtomSpec[]} atoms
+         * @param {$3Dmol.Geometry[]} geos
          */
-        this.rotate = function(angle, axis) {
-            if (typeof (axis) === "undefined") {
-                axis = "y";
-            }
-            var i = 0, j = 0, k = 0;
-            var rangle = Math.PI * angle / 180.0;
-            var s = Math.sin(rangle / 2.0);
-            var c = Math.cos(rangle / 2.0);
-            if (axis == "x")
-                i = s;
-            if (axis == "y")
-                j = s;
-            if (axis == "z")
-                k = s;
-
-            var q = new $3Dmol.Quaternion(i, j, k, c).normalize();
-            rotationGroup.quaternion.multiply(q);
-            show();
-        };
-
-        /** Returns an array representing the current viewpoint.
-         * Translation, zoom, and rotation quaternion. 
-         * @function $3Dmol.GLViewer#getView
-         * @returns {Array.<number>} arg
-         *  */
-        this.getView = function() {
-            if (!modelGroup)
-                return [ 0, 0, 0, 0, 0, 0, 0, 1 ];
-            var pos = modelGroup.position;
-            var q = rotationGroup.quaternion;
-            return [ pos.x, pos.y, pos.z, rotationGroup.position.z, q.x, q.y,
-                    q.z, q.w ];
-        };
-
-        /** Sets the view to the specified translation, zoom, and rotation.
-         * 
-         * @function $3Dmol.GLViewer#setView
-         * @param {Array.<number>} arg Array formatted identically to the return value of getView */
-        this.setView = function(arg) {
-
-            if (arg === undefined
-                    || !(arg instanceof Array || arg.length !== 8))
+        var drawBondLines = function(atom, atoms, geos) {
+            if (!atom.style.line)
                 return;
-
-            if (!modelGroup || !rotationGroup)
+            var style = atom.style.line;
+            if (style.hidden)
                 return;
-            modelGroup.position.x = arg[0];
-            modelGroup.position.y = arg[1];
-            modelGroup.position.z = arg[2];
-            rotationGroup.position.z = arg[3];
-            rotationGroup.quaternion.x = arg[4];
-            rotationGroup.quaternion.y = arg[5];
-            rotationGroup.quaternion.z = arg[6];
-            rotationGroup.quaternion.w = arg[7];
-            if(typeof(arg[8]) != "undefined") {
-                rotationGroup.position.x = arg[8];
-                rotationGroup.position.y = arg[9];
-            }
-            show();
-        };
 
-        // apply styles, models, etc in viewer
-        /**
-         * Render current state of viewer, after 
-         * adding/removing models, applying styles, etc.
-         * 
-         * @function $3Dmol.GLViewer#render
-         */
-        this.render = function() {
+            // have a separate geometry for each linewidth
+            var linewidth = (style.linewidth || defaultlineWidth);
 
-            updateClickables(); //must render for clickable styles to take effect
-            var time1 = new Date();
-            var view = this.getView();
+            if (!geos[linewidth])
+                geos[linewidth] = new $3Dmol.Geometry();
+            /** @type {geometryGroup} */
+            var geoGroup = geos[linewidth].updateGeoGroup(6*atom.bonds.length); //reserve enough space even for triple bonds
             
-            var i, n;
-            for (i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    models[i].globj(modelGroup);
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            
+            for ( var i = 0; i < atom.bonds.length; i++) {
+                var j = atom.bonds[i]; // our neighbor
+                
+                var atom2 = atoms[j];
+                if (!atom2.style.line)
+                    continue; // don't sweat the details
+
+                if (atom.serial >= atom2.serial) // only draw if less, this way we can do multi bonds correctly
+                    continue;
+                var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);                
+                var mp = p1.clone().add(p2).multiplyScalar(0.5);
+                var singleBond = false;               
+                
+                if (atom.clickable){
+                    if (atom.intersectionShape === undefined)
+                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                    atom.intersectionShape.line.push(p1);
+                    atom.intersectionShape.line.push(p2);
                 }
-            }
 
-            for (i = 0; i < shapes.length; i++) {
-                if (shapes[i]) {
-                    shapes[i].globj(modelGroup);
+                var c1 = $3Dmol.getColorFromStyle(atom, atom.style.line);
+                var c2 = $3Dmol.getColorFromStyle(atom2, atom2.style.line);
+               
+                if(atom.bondStyles && atom.bondStyles[i]) {
+                    var bstyle = atom.bondStyles[i];
+                    if(!bstyle.iswire) {
+                        continue;
+                    }
+                    if(bstyle.radius) bondR = bstyle.radius;
+                    if(bstyle.singleBond) singleBond = true;
+                    if(typeof(bstyle.color1) != "undefined") {
+                        c1 = $3Dmol.CC.color(bstyle.color1);
+                    }
+                    if(typeof(bstyle.color2) != "undefined") {
+                        c2 = $3Dmol.CC.color(bstyle.color2);
+                    }
                 }
-            }
-            
-            for (i in surfaces) { // this is an array with possible holes
-                var surfArr = surfaces[i];
-                for (n = 0; n < surfArr.length; n++) {
-                    if (surfArr.hasOwnProperty(n)) {
-                        var geo = surfArr[n].geo;
-                        // async surface generation can cause
-                        // the geometry to be webgl initialized before it is fully
-                        // formed; force various recalculations until full surface
-                        // is
-                        // available
-                        if (!surfArr[n].finished) {
-                            geo.verticesNeedUpdate = true;
-                            geo.elementsNeedUpdate = true;
-                            geo.normalsNeedUpdate = true;
-                            geo.colorsNeedUpdate = true;
-                            geo.buffersNeedUpdate = true;
-                            geo.boundingSphere = null;
 
-                            if (surfArr[n].done)
-                                surfArr[n].finished = true;
+                var offset = geoGroup.vertices*3;
+                
+                if(atom.bondOrder[i] > 1 && atom.bondOrder[i] < 4 && !singleBond) {
+                    var v = getSideBondV(atom, atom2, i);
+                    var dir = p2.clone();
+                    dir.sub(p1);
+                    
+                    if(atom.bondOrder[i] == 2) { //double
+                        
+                        v.multiplyScalar(.1);
+                           p1a = p1.clone();
+                        p1a.add(v);
+                        p1b = p1.clone();
+                        p1b.sub(v);
 
-                            // remove partially rendered surface
-                            if (surfArr[n].lastGL)
-                                modelGroup.remove(surfArr[n].lastGL);
+                        p2a = p1a.clone();
+                        p2a.add(dir);
+                        p2b = p1b.clone();
+                        p2b.add(dir);
+                        
+                        if(c1 == c2) {
+                            geoGroup.vertices += 4;
+                            addLine(vertexArray, colorArray, offset, p1a, p2a, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, p1b, p2b, c1);                            
+                        }
+                        else {
+                            geoGroup.vertices += 8;
+                            dir.multiplyScalar(0.5);
+                            var mpa = p1a.clone();
+                            mpa.add(dir);
+                            var mpb = p1b.clone();
+                            mpb.add(dir);
+                            
+                            addLine(vertexArray, colorArray, offset, p1a, mpa, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, mpa, p2a, c2);                            
+                            addLine(vertexArray, colorArray, offset+12, p1b, mpb, c1); 
+                            addLine(vertexArray, colorArray, offset+18, mpb, p2b, c2); 
+                        }
+                    }
+                    else if(atom.bondOrder[i] == 3) { //triple
+                        
+                        v.multiplyScalar(.1);
+                           p1a = p1.clone();
+                        p1a.add(v);
+                        p1b = p1.clone();
+                        p1b.sub(v);
 
-                            // create new surface
-                            var smesh = null;
+                        p2a = p1a.clone();
+                        p2a.add(dir);
+                        p2b = p1b.clone();
+                        p2b.add(dir);
+                        
+                        if(c1 == c2) {
+                            geoGroup.vertices += 6;
+                            addLine(vertexArray, colorArray, offset, p1, p2, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, p1a, p2a, c1);                            
+                            addLine(vertexArray, colorArray, offset+12, p1b, p2b, c1);                            
+                        }
+                        else {
+                            geoGroup.vertices += 12;
+                            dir.multiplyScalar(0.5);
+                            var mpa = p1a.clone();
+                            mpa.add(dir);
+                            var mpb = p1b.clone();
+                            mpb.add(dir);
 
-                            if(surfArr[n].mat instanceof $3Dmol.LineBasicMaterial) {
-                                //special case line meshes
-                                smesh = new $3Dmol.Line(geo, surfArr[n].mat);
-                            }
-                            else {
-                                smesh = new $3Dmol.Mesh(geo, surfArr[n].mat);
-                            }
-                            if(surfArr[n].mat.transparent && surfArr[n].mat.opacity == 0) {
-                                //don't bother with hidden surfaces
-                                smesh.visible = false;
-                            } else {
-                                smesh.visible = true;
-                            }
-                            if (surfArr[n].symmetries.length > 1 || 
-                            (surfArr[n].symmetries.length == 1 && 
-                            !(surfArr[n].symmetries[n].isIdentity()))) {
-                                var j;
-                                var tmeshes = new $3Dmol.Object3D(); //transformed meshes
-                                for (j = 0; j < surfArr[n].symmetries.length; j++) {
-                                    var tmesh = smesh.clone();
-                                    tmesh.matrix = surfArr[n].symmetries[j];
-                                    tmesh.matrixAutoUpdate = false;
-                                    tmeshes.add(tmesh);
-                                }
-                                surfArr[n].lastGL = tmeshes;
-                                modelGroup.add(tmeshes);
-                            }
-                            else {
-                                surfArr[n].lastGL = smesh;
-                                modelGroup.add(smesh);
-                            }
-                        } // else final surface already there
+                            addLine(vertexArray, colorArray, offset, p1, mp, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, mp, p2, c2);
+                            addLine(vertexArray, colorArray, offset+12, p1a, mpa, c1);                            
+                            addLine(vertexArray, colorArray, offset+18, mpa, p2a, c2);                            
+                            addLine(vertexArray, colorArray, offset+24, p1b, mpb, c1); 
+                            addLine(vertexArray, colorArray, offset+30, mpb, p2b, c2); 
+                        }
                     }
                 }
-            }
-            
-            this.setView(view); // Calls show() => renderer render
-            var time2 = new Date();
-            //console.log("render time: " + (time2 - time1));
-        };
-
-        /**
-         * 
-         * @param {AtomSelectionSpec}
-         *            sel
-         * @return {AtomSpec[]}
-         */
-        function getAtomsFromSel(sel) {
-            var atoms = [];
-            if (typeof (sel) === "undefined")
-                sel = {};
-
-            var ms = [];
-            var i;
-
-            if (typeof sel.model === "undefined") {
-                for (i = 0; i < models.length; i++) {
-                    if (models[i])
-                        ms.push(models[i]);
+                else { //single bond                                    
+                    if(c1 == c2) {
+                        geoGroup.vertices += 2;
+                        addLine(vertexArray, colorArray, offset, p1, p2, c1);
+                    } else {
+                        geoGroup.vertices += 4;
+                        addLine(vertexArray, colorArray, offset, p1, mp, c1);
+                        addLine(vertexArray, colorArray, offset+6, mp, p2, c2);                        
+                    }
+                    
                 }
-            } else { // specific to some models
-                ms = sel.model;
-                if (!$.isArray(ms))
-                    ms = [ ms ];
             }
 
-            for (i = 0; i < ms.length; i++) {
-                atoms = atoms.concat(ms[i].selectedAtoms(sel));
-            }
+        };
 
-            return atoms;
-        }
+        // bonds as cylinders
+        var defaultStickRadius = 0.25;
 
-        /**
-         * 
-         * @param {AtomSpec}
-         *            atom
-         * @param {AtomSpec}
-         *            sel
-         * @return {boolean}
+        /**@typedef SphereStyleSpec
+         * @prop {boolean} hidden - do not show atom
+         * @prop {number} radius - override van der waals radius
+         * @prop {number} scale - scale radius by specified amount
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
          */
-        function atomIsSelected(atom, sel) {
-            if (typeof (sel) === "undefined")
-                sel = {};
-
-            var ms = [];
-            var i;
-
-            if (typeof sel.model === "undefined") {
-                for (i = 0; i < models.length; i++) {
-                    if (models[i])
-                        ms.push(models[i]);
-                }
-            } else { // specific to some models
-                ms = sel.model;
-                if (!$.isArray(ms))
-                    ms = [ ms ];
-            }
-
-            for (i = 0; i < ms.length; i++) {
-                if (ms[i].atomIsSelected(atom, sel))
-                    return true;
-            }
-
-            return false;
-        }
-
-        /**
-         * Return pdb output of selected atoms (if atoms from pdb input)
+        
+        //sphere drawing
+        //See also: drawCylinder
+        /** 
          * 
-         * @function $3Dmol.GLViewer#pdbData  
-         * @param {Object=} [sel] - Selection specification specifying model and atom properties to select.  Default: all atoms in viewer
-         * @return {string} PDB string of selected atoms
+         * @param {AtomSpec} atom
+         * @param {$3Dmol.Geometry} geo
          */
-        this.pdbData = function(sel) {
-            var atoms = getAtomsFromSel(sel);
-            var ret = "";
-            for (var i = 0, n = atoms.length; i < n; ++i) {
-                ret += atoms[i].pdbline + "\n";
+        var drawAtomSphere = function(atom, geo) {
+            
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
+                                                                 
+            var C = $3Dmol.getColorFromStyle(atom, style);
+            
+            var x, y;
+            var radius = getRadiusFromStyle(atom, style);
+            
+            if ((atom.clickable === true) && (atom.intersectionShape !== undefined)) {
+                var center = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                atom.intersectionShape.sphere.push(new $3Dmol.Sphere(center, radius));
             }
-            return ret;
+            
+            $3Dmol.GLDraw.drawSphere(geo, atom, radius, C);    
+            
         };
 
-        /**
-         * Zoom current view by a constant factor
-         * 
-         * @function $3Dmol.GLViewer#zoom
-         * @param {number}
-         *            [factor] - Magnification factor. Values greater than 1
-         *            will zoom in, less than one will zoom out. Default 2.
-         * 
-         */
-        this.zoom = function(factor) {
-            var factor = factor || 2;
-            var scale = (CAMERA_Z - rotationGroup.position.z) / factor;
-            rotationGroup.position.z = CAMERA_Z - scale;
-            show();
-        };
-        
-        /**
-         * Translate current view by x,y screen coordinates
-         * This pans the camera rather than translating the model.
-         * 
-         * @function $3Dmol.GLViewer#translate
-         * @param {number} x
-         * @param {number} y
-         * 
-         */
-        this.translate = function(x, y) {
-            
-            var dx = x/WIDTH;
-            var dy = y/HEIGHT;
-            var v = new $3Dmol.Vector3(0,0,-CAMERA_Z);
+        var drawAtomInstanced = function(atom, geo) {
 
-            projector.projectVector(v, camera);
-            v.x -= dx;
-            v.y -= dy;
-            projector.unprojectVector(v, camera);
-            v.z = 0;            
-            lookingAt.add(v);
-            camera.lookAt(lookingAt);
-            show();
-        };
-        
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
 
-        /**
-         * Zoom to center of atom selection
-         * 
-         * @function $3Dmol.GLViewer#zoomTo
-         * @param {Object}
-         *            [sel] - Selection specification specifying model and atom
-         *            properties to select. Default: all atoms in viewer
-         * @example // Assuming we have created a model of a protein with
-         *          multiple chains (e.g. from a PDB file), focus on atoms in
-         *          chain B glviewer.zoomTo({chain: 'B'});
-         *  // Focus on centroid of all atoms of all models in this
-         * viewer glviewer.zoomTo(); // (equivalent to glviewer.zoomTo({}) )
-         */
-        this.zoomTo = function(sel) {
-            var allatoms, alltmp;
-            sel = sel || {};
-            var atoms = getAtomsFromSel(sel);
-            var tmp = $3Dmol.getExtent(atoms);
+            var radius = getRadiusFromStyle(atom, style);
+            var C = $3Dmol.getColorFromStyle(atom, style);
 
-            if($.isEmptyObject(sel)) {
-                //include shapes when zooming to full scene
-                //TODO: figure out a good way to specify shapes as part of a selection
-                $.each(shapes, function(i, shape) {
-                	if(shape.boundingSphere && shape.boundingSphere.center)
-                		atoms.push(shape.boundingSphere.center);
-                });
-                tmp = $3Dmol.getExtent(atoms);
-                allatoms = atoms;
-                alltmp = tmp;
+            var geoGroup = geo.updateGeoGroup(1);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var radiusArray = geoGroup.radiusArray;
 
-            }
-            else {
-                allatoms = getAtomsFromSel({});
-                alltmp = $3Dmol.getExtent(allatoms);
-            }
+            vertexArray[start] = atom.x;
+            vertexArray[start+1] = atom.y ;
+            vertexArray[start+2] = atom.z;
 
-            // use selection for center
-            var center = new $3Dmol.Vector3(tmp[2][0], tmp[2][1], tmp[2][2]);
-            modelGroup.position = center.clone().multiplyScalar(-1);
-            // but all for bounding box
-            var x = alltmp[1][0] - alltmp[0][0], y = alltmp[1][1]
-                    - alltmp[0][1], z = alltmp[1][2] - alltmp[0][2];
+            var normalArray = geoGroup.normalArray;
+            var colorArray = geoGroup.colorArray;
+            colorArray[start] = C.r;
+            colorArray[start+1] = C.g;
+            colorArray[start+2] = C.b;
 
-            var maxD = Math.sqrt(x * x + y * y + z * z);
-            if (maxD < 5)
-                maxD = 5;
+            radiusArray[startv] = radius;
 
-            // use full bounding box for slab/fog
-            slabNear = -maxD / 1.9;
-            slabFar = maxD / 2;
+            geoGroup.vertices += 1;
 
-            // for zoom, use selection box
-            x = tmp[1][0] - tmp[0][0];
-            y = tmp[1][1] - tmp[0][1];
-            z = tmp[1][2] - tmp[0][2];
-            maxD = Math.sqrt(x * x + y * y + z * z);
-            if (maxD < 5)
-                maxD = 5;
+        };
+
+        var drawSphereImposter = function(geo, center, radius, C) {
+            //create flat square                                   
+            var geoGroup = geo.updateGeoGroup(4);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
             
-            //find the farthest atom from center to get max distance needed for view
-            var maxDsq = 25;
-            for (var i = 0; i < atoms.length; i++) {
-                if(atoms[i]) {
-                    var dsq = center.distanceToSquared(atoms[i]);
-                    if(dsq > maxDsq)
-                        maxDsq = dsq;
-                }
+            //use center point for each vertex
+            for(var i = 0; i < 4; i++) {
+                vertexArray[start+3*i] = center.x;
+                vertexArray[start+3*i+1] = center.y ;
+                vertexArray[start+3*i+2] = center.z;                           
             }
             
-            var maxD = Math.sqrt(maxDsq)*2;
 
-            rotationGroup.position.z = -(maxD * 0.5
-                    / Math.tan(Math.PI / 180.0 * camera.fov / 2) - CAMERA_Z);
-            show();
-        };
-        /**
-         * Add label to viewer
-         * 
-         * @function $3Dmol.GLViewer#addLabel
-         * @param {string}
-         *            text - Label text
-         * @param {Object}
-         *            data - Label style specification
-         * @return {$3Dmol.Label}
-         * 
-         * @example
-         *  // Assuming glviewer contains a model representing a protein, label
-         * all alpha carbons with their residue name
-         *  // Select all alpha carbons (have property atom : "CA") from last
-         * model added var atoms =
-         * glviewer.getModel().selectedAtoms({atom:"CA"}); var labels = [];
-         * 
-         * for (var a in atoms) { var atom = atoms[a];
-         *  // Create label at alpha carbon's position displaying atom's residue
-         * and residue number var labelText = atom.resname + " " + atom.resi;
-         * 
-         * var l = glviewer.createLabel(labelText, {fontSize: 12, position: {x:
-         * atom.x, y: atom.y, z: atom.z});
-         * 
-         * labels.push(l); }
-         *  // Render labels glviewer.render();
-         */
-        this.addLabel = function(text, data) {
-            var label = new $3Dmol.Label(text, data);
-            label.setContext();
-            modelGroup.add(label.sprite);
-            labels.push(label);
-            show();
-            return label;
+            //same colors for all 4 vertices
+            var normalArray = geoGroup.normalArray;
+            var colorArray = geoGroup.colorArray;
+            for(var i = 0; i < 4; i++) {
+                colorArray[start+3*i] = C.r;
+                colorArray[start+3*i+1] = C.g;
+                colorArray[start+3*i+2] = C.b;                
+            }
+            
+            normalArray[start+0] = -radius;
+            normalArray[start+1] = radius;
+            normalArray[start+2] = 0;
+            
+            normalArray[start+3] = -radius;
+            normalArray[start+4] = -radius;
+            normalArray[start+5] = 0;
+            
+            normalArray[start+6] = radius;
+            normalArray[start+7] = -radius;
+            normalArray[start+8] = 0;
+            
+            normalArray[start+9] = radius;
+            normalArray[start+10] = radius;
+            normalArray[start+11] = 0;
+            
+            geoGroup.vertices += 4;
+            
+            //two faces
+            var faceArray = geoGroup.faceArray;
+            var faceoffset = geoGroup.faceidx; //not number faces, but index
+            faceArray[faceoffset+0] = startv;
+            faceArray[faceoffset+1] = startv+1;
+            faceArray[faceoffset+2] = startv+2;
+            faceArray[faceoffset+3] = startv+2;
+            faceArray[faceoffset+4] = startv+3;
+            faceArray[faceoffset+5] = startv;
+            geoGroup.faceidx += 6;
         };
         
-        /** Add residue labels.  This will generate one label per a
-         * residue within the selected atoms.  The label will be at the
-         * centroid of the atoms and styled according to the passed style.
-         * The label text will be [resn][resi]
-         * 
-         * @param {Object} sel
-         * @param {Object} style
-         */
-        this.addResLabels = function(sel, style) {
-            applyToModels("addResLabels", sel, this, style);
-        }
-
-        /**
-         * Remove label from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeLabel
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * 
-         * @example // Remove labels created in [addLabel example]{@link $3Dmol.GLViewer#addLabel}
-         * 
-         * for (var i = 0; i < labels.length; i++) {
-         * glviewer.removeLabel(label); }
-         * 
-         * glviewer.render();
-         */
-        this.removeLabel = function(label) {
-            //todo: don't do the linear search
-            for(var i = 0; i < labels.length; i++) {
-                if(labels[i] == label) {
-                    labels.splice(i,1);
-                    label.dispose();
-                    modelGroup.remove(label.sprite);
-                    break;
-                }
+        //dkoes -  code for sphere imposters
+        var drawAtomImposter = function(atom, geo) {
+            
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
+            
+            var radius = getRadiusFromStyle(atom, style);
+            var C = $3Dmol.getColorFromStyle(atom, style);
+            
+            drawSphereImposter(geo, atom, radius, C);            
+        };
+                
+          
+        var drawStickImposter =  function(geo, from, to, radius, color, fromCap, toCap) {
+           //we need the four corners - two have from coord, two have to coord, the normal
+            //is the opposing point, from which we can get the normal and length
+            //also need the radius
+            var geoGroup = geo.updateGeoGroup(4);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var radiusArray = geoGroup.radiusArray;
+            var normalArray = geoGroup.normalArray;
+            //encode extra bits of information in the color
+            var r = color.r;
+            var g = color.g;
+            var b = color.b;
+            
+            var negateColor = function(c) {
+                //set sign bit
+                var n = -c;
+                if(n == 0) n = -0.0001;
+                return n;
+            };
+            
+            /* for sticks, always draw caps, but we could in theory set caps in color */
+            
+            //4 vertices, distinguish between p1 and p2 with neg blue
+            var pos = start;
+            for(var i = 0; i < 4; i++) {
+                vertexArray[pos] = from.x;
+                normalArray[pos] = to.x;
+                colorArray[pos] = r;
+                pos++;
+                vertexArray[pos] = from.y;
+                normalArray[pos] = to.y;
+                colorArray[pos] = g;
+                pos++;
+                vertexArray[pos] = from.z;
+                normalArray[pos] = to.z;
+                if(i < 2)
+                    colorArray[pos] = b;
+                else
+                    colorArray[pos] = negateColor(b);
+                pos++;
             }
 
-        };
+            geoGroup.vertices += 4;
 
-        /**
-         * Remove all labels from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeAllLabels
-         */
-        this.removeAllLabels = function() {
-            for (var i = 0; i < labels.length; i++) {
-                modelGroup.remove(labels[i].sprite);
-            }
-            labels = [];
+            radiusArray[startv] = -radius;
+            radiusArray[startv+1] = radius;
+            radiusArray[startv+2] = -radius;
+            radiusArray[startv+3] = radius;      
+                        
+            //two faces
+            var faceArray = geoGroup.faceArray;
+            var faceoffset = geoGroup.faceidx; //not number faces, but index
+            faceArray[faceoffset+0] = startv;
+            faceArray[faceoffset+1] = startv+1;
+            faceArray[faceoffset+2] = startv+2;
+            faceArray[faceoffset+3] = startv+2;
+            faceArray[faceoffset+4] = startv+3;
+            faceArray[faceoffset+5] = startv;
+            geoGroup.faceidx += 6;          
         };
         
-        // Modify label style
-        /**
-         * Modify existing label's style
-         * 
-         * @function $3Dmol.GLViewer#setLabelStyle
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * @param {Object}
-         *            stylespec - Label style specification
-         * @return {$3Dmol.Label}
-         */
-        this.setLabelStyle = function(label, stylespec) {
-            modelGroup.remove(label.sprite);
-            label.dispose();
-            label.stylespec = stylespec;
-            label.setContext();
-            modelGroup.add(label.sprite);
-            show();
-            return label;
-
-        };
-
-        // Change label text
-        /**
-         * Modify existing label's text
-         * 
-         * @function $3Dmol.GLViewer#setLabelText
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * @param {String}
-         *            text - Label text
-         * @return {$3Dmol.Label}
+        /**@typedef StickStyleSpec
+         * @prop {boolean} hidden - do not show 
+         * @prop {number} radius 
+         * @prop {boolean} singleBonds - draw all bonds as single bonds if set
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
          */
-        this.setLabelText = function(label, text) {
-            modelGroup.remove(label.sprite);
-            label.dispose();
-            label.text = text;
-            label.setContext();
-            modelGroup.add(label.sprite);
-            show();
-            return label;
-
-        };
+        
+        // draws cylinders and small spheres (at bond radius)
+        var drawBondSticks = function(atom, atoms, geo) {
+            if (!atom.style.stick)
+                return;
+            var style = atom.style.stick;
+            if (style.hidden)
+                return;
 
-        /**
-         * Add shape object to viewer 
-         * @see {@link $3Dmol.GLShape}
-         * 
-         * @function $3Dmol.GLViewer#addShape
-         * @param {ShapeSpec} shapeSpec - style specification for label
-         * @return {$3Dmol.GLShape}
-         */
-        this.addShape = function(shapeSpec) {
-            shapeSpec = shapeSpec || {};
-            var shape = new $3Dmol.GLShape(shapeSpec);
-            shape.shapePosition = shapes.length;
-            shapes.push(shape);
+            var atomBondR = style.radius || defaultStickRadius;
+            var bondR = atomBondR;
+            var atomSingleBond = style.singleBonds || false;
+            var fromCap = 0, toCap = 0;
 
-            return shape;
+            var C1 = $3Dmol.getColorFromStyle(atom, style);
 
-        };
+            var mp, mp1, mp2;
+            
+            if (!atom.capDrawn && atom.bonds.length < 4)
+                fromCap = 2;
+            
+            var drawCyl = $3Dmol.GLDraw.drawCylinder; //mesh cylinder
+            if(geo.imposter) 
+                drawCyl = drawStickImposter;
 
-        /**
-         * Remove shape object from viewer
-         *
-         * @function $3Dmol.GLViewer#removeShape
-         * @param {$3Dmol.GLShape} shape - Reference to shape object to remove
-         */
-        this.removeShape = function(shape) {
-            if (!shape)
-                return;
-            shape.removegl(modelGroup);
-            delete shapes[shape.shapePosition];
-            // clear off back of model array
-            while (shapes.length > 0
-                    && typeof (shapes[shapes.length - 1]) === "undefined")
-                shapes.pop();
-        };
-        
-        /**
-         * Remove all shape objects from viewer
-         * @function $3Dmol.GLViewer#removeAllShapes
-         */
-        this.removeAllShapes = function() {
-            for (var i = 0; i < shapes.length; i++) {
-                var shape = shapes[i];
-                shape.removegl(modelGroup);
-            }
-            shapes = [];
-        }
+                
+            for (var i = 0; i < atom.bonds.length; i++) {
+                var j = atom.bonds[i]; // our neighbor
+                var atom2 = atoms[j]; //parsePDB, etc should only add defined bonds
+                
+                if (atom.serial < atom2.serial) {// only draw if less, this
+                    // lets us combine
+                    // cylinders of the same
+                    // color
+                    var style2 = atom2.style;
+                    if (!style2.stick)
+                        continue; // don't sweat the details                     
+                   
+                    var C2 = $3Dmol.getColorFromStyle(atom2, style2.stick);
+                    
+                    //support bond specific styles
+                    bondR = atomBondR;                    
+                    var singleBond = atomSingleBond;
+                    if(atom.bondStyles && atom.bondStyles[i]) {
+                        var bstyle = atom.bondStyles[i];
+                        if(bstyle.iswire) {
+                            continue;
+                        }
+                        if(bstyle.radius) bondR = bstyle.radius;
+                        if(bstyle.singleBond) singleBond = true;
+                        if(typeof(bstyle.color1) != "undefined") {
+                            C1 = $3Dmol.CC.color(bstyle.color1);
+                        }
+                        if(typeof(bstyle.color2) != "undefined") {
+                            C2 = $3Dmol.CC.color(bstyle.color2);
+                        }
+                    }
+                    var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                    var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
 
-        /**
-         * Create and add sphere shape. This method provides a shorthand 
-         * way to create a spherical shape object
-         * 
-         * @function $3Dmol.GLViewer#addSphere
-         * @param {SphereSpec} spec - Sphere shape style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addSphere = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addSphere(spec);
-            shapes.push(s);
+                    // draw cylinders
+                    if (atom.bondOrder[i] === 1 || singleBond) {
 
-            return s;
-        };
+                        if (!atom2.capDrawn && atom2.bonds.length < 4)
+                            toCap = 2;       
+                                                
+                        if (C1 != C2) {
+                            mp = new $3Dmol.Vector3().addVectors(p1, p2)
+                                    .multiplyScalar(0.5);
+                            drawCyl(geo, p1, mp, bondR, C1, fromCap, 0);
+                            drawCyl(geo, mp, p2, bondR, C2, 0, toCap);
+                        } else {
+                            drawCyl(geo, p1, p2, bondR, C1, fromCap, toCap);
+                        }
+                        
+                        if (atom.clickable || atom2.clickable) {
+                            mp = new $3Dmol.Vector3().addVectors(p1, p2).multiplyScalar(0.5);
+                            if (atom.clickable){
+                                var cylinder1 = new $3Dmol.Cylinder(p1 , mp , bondR);
+                                var sphere1 = new $3Dmol.Sphere(p1 , bondR);
+                                atom.intersectionShape.cylinder.push(cylinder1);   
+                                atom.intersectionShape.sphere.push(sphere1);                             
+                            }
+                            if (atom2.clickable){
+                                var cylinder2 = new $3Dmol.Cylinder(p2 , mp , bondR);
+                                var sphere2 = new $3Dmol.Sphere(p2 , bondR);
+                                atom2.intersectionShape.cylinder.push(cylinder2);
+                                atom2.intersectionShape.sphere.push(sphere2);
+                            }
 
-        /**
-         * Create and add arrow shape
-         * 
-         * @function $3Dmol.GLViewer#addArrow
-         * @param {ArrowSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addArrow = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addArrow(spec);
-            shapes.push(s);
+                        }
+                        
+                    } 
+                    
+                    else if (atom.bondOrder[i] > 1) {
+                        var mfromCap = 0; mtoCap = 0; //multi bond caps
+                        
+                        if(bondR != atomBondR) {
+                            //assume jmol style multiple bonds - the radius doesn't fit within atom sphere
+                            mfromCap = 2;
+                            mtoCap = 2;
+                        }
+                        
+                        var dir = p2.clone();
+                        var v = null;
+                        dir.sub(p1);
+                        
+                        var r, p1a, p1b, p2a, p2b;
+                        var v = getSideBondV(atom, atom2, i);
+                        
+                        if (atom.bondOrder[i] == 2) {
+                            var r = bondR/2.5;
+                            var v = getSideBondV(atom, atom2, i);
+                            
+                            v.multiplyScalar(r*1.5);
+                            p1a = p1.clone();
+                            p1a.add(v);
+                            p1b = p1.clone();
+                            p1b.sub(v);
 
-            return s;
-        };
-        
-        /**
-         * Create and add cylinder shape
-         * 
-         * @function $3Dmol.GLViewer#addCylinder
-         * @param {CylinderSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCylinder = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addCylinder(spec);
-            shapes.push(s);
+                            p2a = p1a.clone();
+                            p2a.add(dir);
+                            p2b = p1b.clone();
+                            p2b.add(dir);
 
-            return s;
-        };
+                                                                 
+                            if (C1 != C2) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                drawCyl(geo, p1a, mp, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp, p2a, r, C2, 0, mtoCap);
+                                drawCyl(geo, p1b, mp2, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp2, p2b, r, C2, 0, mtoCap);
+                            } else {
+                                drawCyl(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
+                                drawCyl(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
+                            }
+                            if (atom.clickable || atom2.clickable){
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                               .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                                .multiplyScalar(0.5);
+                                if (atom.clickable) {
+                                    cylinder1a = new $3Dmol.Cylinder(p1a , mp , r);
+                                    cylinder1b = new $3Dmol.Cylinder(p1b , mp2 , r);
+                                    atom.intersectionShape.cylinder.push(cylinder1a);
+                                    atom.intersectionShape.cylinder.push(cylinder1b);
+                                }
+                                if (atom2.clickable) {
+                                    cylinder2a = new $3Dmol.Cylinder(p2a , mp , r);
+                                    cylinder2b = new $3Dmol.Cylinder(p2b , mp2 , r);
+                                    atom2.intersectionShape.cylinder.push(cylinder2a);
+                                    atom2.intersectionShape.cylinder.push(cylinder2b);                               
+                                }
+                            }
+                        } 
+                        else if (atom.bondOrder[i] == 3) {
+                            r = bondR / 4;
+                            v.cross(dir);
+                            v.normalize();
+                            v.multiplyScalar(r * 3);
 
-        /**
-         * Create and add line shape
-         * 
-         * @function $3Dmol.GLViewer#addLine
-         * @param {LineSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addLine = function(spec) {
-            spec = spec || {};
-            spec.wireframe = true;
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addLine(spec);
-            shapes.push(s);
+                            p1a = p1.clone();
+                            p1a.add(v);
+                            p1b = p1.clone();
+                            p1b.sub(v);
 
-            return s;
-        };
+                            p2a = p1a.clone();
+                            p2a.add(dir);
+                            p2b = p1b.clone();
+                            p2b.add(dir);
 
-        /**
-         * Add custom shape component from user supplied function
-         * 
-         * @function $3Dmol.GLViewer#addCustom
-         * @param {CustomSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCustom = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addCustom(spec);
-            shapes.push(s);
+                            if (C1 != C2) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
+                                        .multiplyScalar(0.5);
+                                drawCyl(geo, p1a, mp, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp, p2a, r, C2, 0, mtoCap);
+                                drawCyl(geo, p1, mp3, r, C1, fromCap, 0);
+                                drawCyl(geo, mp3, p2, r, C2, 0, toCap);
+                                drawCyl(geo, p1b, mp2, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp2, p2b, r, C2, 0, mtoCap);
+                            } else {
+                                drawCyl(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
+                                drawCyl(geo, p1, p2, r, C1, fromCap, toCap);
+                                drawCyl(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
 
-            return s;
+                            }
+                            if (atom.clickable || atom2.clickable) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
+                                        .multiplyScalar(0.5);
+                                                                
+                                if (atom.clickable) {
+                                    cylinder1a = new $3Dmol.Cylinder(p1a.clone(), mp.clone(), r);
+                                    cylinder1b = new $3Dmol.Cylinder(p1b.clone(), mp2.clone(), r);
+                                    cylinder1c = new $3Dmol.Cylinder(p1.clone(), mp3.clone(), r);
+                                    atom.intersectionShape.cylinder.push(cylinder1a);
+                                    atom.intersectionShape.cylinder.push(cylinder1b);
+                                    atom.intersectionShape.cylinder.push(cylinder1c);
+                                } 
+                                if (atom2.clickable) {                               
+                                    cylinder2a = new $3Dmol.Cylinder(p2a.clone(), mp.clone(), r);
+                                    cylinder2b = new $3Dmol.Cylinder(p2b.clone(), mp2.clone(), r);
+                                    cylinder2c = new $3Dmol.Cylinder(p2.clone(), mp3.clone(), r);
+                                    atom2.intersectionShape.cylinder.push(cylinder2a);
+                                    atom2.intersectionShape.cylinder.push(cylinder2b);
+                                    atom2.intersectionShape.cylinder.push(cylinder2c);                                
+                                }
+                            }
+                        }
+                    }
+                     
+                }                   
+                                 
+            }            
+
+            // draw non bonded heteroatoms as spheres
+            var drawSphere = false;
+            var numsinglebonds = 0;
+            var differentradii = false;
+            //also, if any bonds were drawn as multiples, need sphere
+            for(var i = 0; i < atom.bonds.length; i++) {
+                var singleBond = atomSingleBond;
+                if(atom.bondStyles && atom.bondStyles[i]) {
+                    var bstyle = atom.bondStyles[i];
+                    if(bstyle.singleBond) singleBond = true;
+                    if(bstyle.radius && bstyle.radius != atomBondR) {
+                        differentradii = true;
+                    }
+                }
+                if(singleBond || atom.bondOrder[i] == 1) {
+                    numsinglebonds++;
+                }
+            }
+            
+            if(differentradii) { //jmol style double/triple bonds - no sphere
+                if(numsinglebonds > 0) drawSphere = true; //unless needed as a cap
+            }
+            else if(numsinglebonds == 0 && atom.bonds.length > 0) {
+                drawSphere = true;
+            }
+           
+            if (drawSphere) {
+                var savedstyle = atom.style;
+                bondR = atomBondR;
+                //do not use bond style as this can be variable, particularly
+                //with jmol export of double/triple bonds
+                if(geo.imposter) {
+                    drawSphereImposter(geo.sphereGeometry, atom, bondR, C1);
+                }
+                else {
+                    $3Dmol.GLDraw.drawSphere(geo, atom, bondR, C1);
+                }
+            }
+            
         };
+        
+        
 
-        /**
-         * Construct isosurface from volumetric data in gaussian cube format
-         * 
-         * @function $3Dmol.GLViewer#addVolumetricData
-         * @param {String} data - Input file contents 
-         * @param {String} format - Input file format (currently only supports "cube")
-         * @param {VolSpec} spec - Shape style specification
-         * @return {$3Dmol.GLShape}
-         * 
-         * @example
-         * viewer.addVolumetricData(data, "cube", {isoval: 0.01, color: "blue", alpha: 0.95});              
-         * viewer.addVolumetricData(data, "cube", {isoval: -0.01, color: "red", alpha: 0.95}); 
-         */
-        this.addVolumetricData = function(data, format, spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addVolumetricData(data, format, spec);
-            shapes.push(s);
+        // go through all the atoms and regenerate their geometries
+        // we try to have one geometry for each style since this is much much
+        // faster
+        // at some point we should optimize this to avoid unnecessary
+        // recalculation
+        /** param {AtomSpec[]} atoms */
+        var createMolObj = function(atoms, options) {
 
-            return s;
-        };
+            options = options || {};
 
-        /**
-         * Create and add model to viewer, given molecular data and its format 
-         * (pdb, sdf, xyz, or mol2)
-         * 
-         * @function $3Dmol.GLViewer#addModel
-         * @param {string} data - Input data
-         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
-         * @return {$3Dmol.GLModel}
-         */
-        this.addModel = function(data, format, options) {
+            var ret = new $3Dmol.Object3D();
+            var cartoonAtoms = [];
+            var lineGeometries = {};
+            var crossGeometries = {};
+            
+            var drawSphereFunc = drawAtomSphere;
+            var sphereGeometry = null;
+            var stickGeometry = null;
+            if (options.supportsImposters) {
+                drawSphereFunc = drawAtomImposter;
+                sphereGeometry = new $3Dmol.Geometry(true);
+                sphereGeometry.imposter = true;
+                stickGeometry = new $3Dmol.Geometry(true, true);
+                stickGeometry.imposter = true;
+                stickGeometry.sphereGeometry = sphereGeometry; //for caps
+                stickGeometry.drawnCaps = {};
+            }
+            else if (options.supportsAIA) {
+                drawSphereFunc = drawAtomInstanced;
+                sphereGeometry = new $3Dmol.Geometry(false, true,true);
+                sphereGeometry.instanced = true;
+                stickGeometry = new $3Dmol.Geometry(true); //don't actually have instanced sticks
+            }  else {
+                sphereGeometry = new $3Dmol.Geometry(true);
+                stickGeometry = new $3Dmol.Geometry(true);
+            }
+            
+            var i, j, n, testOpacities;
+            var opacities = {};
+            var range = [Number.POSITIVE_INFINITY, Number.NEGATIVE_INFINITY];
+            for (i = 0, n = atoms.length; i < n; i++) {
+                var atom = atoms[i];
+                // recreate gl info for each atom as necessary
+                // set up appropriate intersection spheres for clickable atoms
 
-            var m = new $3Dmol.GLModel(models.length, defaultcolors);
-            m.addMolData(data, format, options);
-            models.push(m);
+                if (atom && atom.style) {
 
-            return m;
-        };
+                    if (atom.clickable && atom.intersectionShape === undefined)
+                        atom.intersectionShape = {sphere: [], cylinder: [], line: [], triangle : []};
 
-        /**
-         * Delete specified model from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeModel
-         * @param {$3Dmol.GLModel} model
-         */
-        this.removeModel = function(model) {
-            if (!model)
-                return;
-            model.removegl(modelGroup);
-            delete models[model.getID()];
-            // clear off back of model array
-            while (models.length > 0
-                    && typeof (models[models.length - 1]) === "undefined")
-                models.pop();
-        };
+                    testOpacities = {line:undefined, cross:undefined, stick:undefined, sphere:undefined};
+                    for (j in testOpacities)
+                    {
+                        if (atom.style[j])
+                        {
+                            if (atom.style[j].opacity)
+                                testOpacities[j] = parseFloat(atom.style[j].opacity);
+                            else
+                                testOpacities[j] = 1;
 
-        /** 
-         * Delete all existing models
-         * @function $3Dmol.GLViewer#removeAllModels
-         */
-        this.removeAllModels = function() {
-            for (var i = 0; i < models.length; i++) {
-                var model = models[i];
-                model.removegl(modelGroup);
+                        } else testOpacities[j] = undefined;
+
+                        if (opacities[j])
+                        {
+                            if (testOpacities[j] != undefined && opacities[j] != testOpacities[j])
+                            {
+                                console.log("Warning: " + j + " opacity is ambiguous");
+                                opacities[j] = 1;
+                            }
+
+                        } else opacities[j] = testOpacities[j];
+                    }
+
+                    drawSphereFunc(atom, sphereGeometry);
+                   
+                    drawAtomCross(atom, crossGeometries);
+                    drawBondLines(atom, atoms, lineGeometries);
+                    drawBondSticks(atom, atoms, stickGeometry);
+
+                    if (typeof (atom.style.cartoon) !== "undefined" && !atom.style.cartoon.hidden) {
+                        //gradient color scheme range
+                        if (atom.style.cartoon.color === "spectrum" && typeof(atom.resi) === "number" && !atom.hetflag) {                            
+                            if (atom.resi < range[0])
+                                range[0] = atom.resi;
+                            if (atom.resi > range[1])
+                                range[1] = atom.resi;
+                        }
 
+                        cartoonAtoms.push(atom);
+                    }                   
+                }
             }
-            models = [];
-        };
+            // create cartoon if needed - this is a whole model analysis
+            if (cartoonAtoms.length > 0) {
+                var gradientscheme = null;
+                //TODO: Should have an option to choose gradient type
+                if (range[0] < range[1])
+                    gradientscheme = new $3Dmol.Gradient.Sinebow(range[0], range[1]);
 
-        /**
-         * Create a new model from atoms specified by sel.
-         * If extract, removes selected atoms from existing models 
-         * 
-         * @function $3Dmol.GLViewer#createModelFrom
-         * @param {Object} sel - Atom selection specification
-         * @param {boolean=} extract - If true, remove selected atoms from existing models
-         * @return {$3Dmol.GLModel}
-         */
-        this.createModelFrom = function(sel, extract) {
-            var m = new $3Dmol.GLModel(models.length, defaultcolors);
-            for (var i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    var atoms = models[i].selectedAtoms(sel);
-                    m.addAtoms(atoms);
-                    if (extract)
-                        models[i].removeAtoms(atoms);
+                $3Dmol.drawCartoon(ret, cartoonAtoms, gradientscheme);
+
+            }
+
+            // add sphere geometry
+            if (sphereGeometry && sphereGeometry.vertices > 0) {
+                //Initialize buffers in geometry                
+                sphereGeometry.initTypedArrays();                
+                var sphereMaterial = null;
+                
+                //create appropriate material
+                if(sphereGeometry.imposter) {
+                    sphereMaterial = new $3Dmol.SphereImposterMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0
+                    });            
+                }
+                else if(sphereGeometry.instanced) {
+                    var sphere = new $3Dmol.Geometry(true);
+                    $3Dmol.GLDraw.drawSphere(sphere, {x:0, y:0, z:0}, 1, new $3Dmol.Color(0.5, 0.5, 0.5));
+                    sphere.initTypedArrays();
+                    sphereMaterial = new $3Dmol.InstancedMaterial({
+                        sphereMaterial : new $3Dmol.MeshLambertMaterial({
+                            ambient : 0x000000,
+                            vertexColors : true,
+                            reflectivity : 0,
+                        }),
+                        sphere : sphere
+                    });                
+                }
+                else { //regular mesh
+                    var sphereMaterial = new $3Dmol.MeshLambertMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0,
+                    });
                 }
+                if (opacities.sphere < 1 && opacities.sphere >= 0)
+                {
+                    sphereMaterial.transparent = true;
+                    sphereMaterial.opacity = opacities.sphere;
+                }
+                
+                var sphere = new $3Dmol.Mesh(sphereGeometry, sphereMaterial);
+                ret.add(sphere);
             }
-            models.push(m);
-            return m;
-        };
+            
+            // add stick geometry
+            if (stickGeometry.vertices > 0) {
+                
+                if(stickGeometry.imposter) {
+                    var imposterMaterial = new $3Dmol.StickImposterMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0
+                    });
+                    
+                    //Initialize buffers in geometry                
+                    stickGeometry.initTypedArrays();
+                    
+                    var sticks = new $3Dmol.Mesh(stickGeometry, imposterMaterial);
+                    ret.add(sticks);                    
+                } else {                
+                    var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
+                        vertexColors : true,
+                        ambient : 0x000000,
+                        reflectivity : 0
+                    });
+                    if (opacities.stick < 1 && opacities.stick >= 0)
+                    {
+                        cylinderMaterial.transparent = true;
+                        cylinderMaterial.opacity = opacities.stick;
+                    }
+    
+                    //Initialize buffers in geometry                
+                    stickGeometry.initTypedArrays();
+                    
+                    if (cylinderMaterial.wireframe)
+                        stickGeometry.setUpWireframe();
+                
+                    var sticks = new $3Dmol.Mesh(stickGeometry, cylinderMaterial);
+                    ret.add(sticks);
+                }
+            }
+            
+            //var linewidth;
+            // add any line geometries, distinguished by line width
+            for (i in lineGeometries) {
+                if (lineGeometries.hasOwnProperty(i)) {
+                    var linewidth = i;
+                    var lineMaterial = new $3Dmol.LineBasicMaterial({
+                        linewidth : linewidth,
+                        vertexColors : true
+                    });
+                    if (opacities.line < 1 && opacities.line >= 0)
+                    {
+                        lineMaterial.transparent = true;
+                        lineMaterial.opacity = opacities.line;
+                    }
+                    
+                    lineGeometries[i].initTypedArrays();
+                    
+                    var line = new $3Dmol.Line(lineGeometries[i], lineMaterial,
+                            $3Dmol.LinePieces);
 
-        function applyToModels(func, sel, value1, value2) {
-            for (var i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    models[i][func](sel, value1, value2);
+                    ret.add(line);
                 }
             }
+
+            // add any cross geometries
+            for (i in crossGeometries) {
+                if (crossGeometries.hasOwnProperty(i)) {
+                    var linewidth = i;
+                    var crossMaterial = new $3Dmol.LineBasicMaterial({
+                        linewidth : linewidth,
+                        vertexColors : true
+                    });
+                    if (opacities.cross < 1 && opacities.cross >= 0)
+                    {
+                        crossMaterial.transparent = true;
+                        crossMaterial.opacity = opacities.cross;
+                    }
+
+                    crossGeometries[i].initTypedArrays();
+                    
+                    var cross = new $3Dmol.Line(crossGeometries[i], crossMaterial,
+                            $3Dmol.LinePieces);
+
+                    ret.add(cross);
+                }
+            }
+            
+            //for BIOMT assembly
+            if (dontDuplicateAtoms && modelData.symmetries && modelData.symmetries.length > 0) {
+                var finalRet = new $3Dmol.Object3D();
+                var t;
+                for (t = 0; t < modelData.symmetries.length; t++) {
+                    var transformedRet = new $3Dmol.Object3D();
+                    transformedRet = ret.clone();
+                    transformedRet.matrix.copy(modelData.symmetries[t]);
+                    transformedRet.matrixAutoUpdate = false;
+                    finalRet.add(transformedRet);
+                }
+                return finalRet;
+            }
+
+            return ret;
+        };
+        
+        
+        this.getCrystData = function() {
+            if (modelData.cryst) {
+                return modelData.cryst;
+            }
+            else {
+                return null;
+            }
         }
+        
+        /**
+         * Returns list of rotational/translational matrices if there is BIOMT data
+         * Otherwise returns a list of just the ID matrix
+         *
+         * @function $3Dmol.GlModel#getSymmetries
+         * @return {Array<$3Dmol.Matrix4>}
+         *
+         */
+        this.getSymmetries = function() {
+            
+            if (typeof(modelData.symmetries) == 'undefined') {
+                modelData.symmetries = [idMatrix];
+            }
+            return modelData.symmetries; 
+        };
+        
+        /**
+         * Sets symmetries based on specified matrices in list
+         *
+         * @function $3Dmol.GlModel#setSymmetries
+         * @param {Array<$3Dmol.Matrix4>} list
+         *
+         */
+        this.setSymmetries = function(list) {
+            if (typeof(list) == "undefined") { //delete sym data
+                modelData.symmetries = [idMatrix];
+            }
+            else {
+                modelData.symmetries = list;
+            }
+        };
 
         /**
-         * Set style properties to all selected atoms
-         * 
-         * @function $3Dmol.GLViewer#setStyle
-         * @param {AtomSelectionSpec} sel - Atom selection specification
-         * @param {AtomStyleSpec} style - Style spec to apply to specified atoms
+         * Returns model id number
          * 
-         * @example
-         * viewer.setStyle({}, {stick:{}}); //set all atoms to stick
-         * viewer.setStyle({chain: 'B'}, {carton: {color: spectrum}}); //set chain B to rainbow cartoon
+         * @function $3Dmol.GLModel#getID
+         * @return {number} Model ID
          */
-        this.setStyle = function(sel, style) {
-            applyToModels("setStyle", sel, style, false);
+        this.getID = function() {
+            return id;
         };
-
+        
         /**
-         * Add style properties to all selected atoms
+         * Returns model's frames property, a list of atom lists
          * 
-         * @function $3Dmol.GLViewer#addStyle
-         * @param {AtomSelectionSpec} sel - Atom selection specification
-         * @param {AtomStyleSpec} style - style spec to add to specified atoms
+         * @function $3Dmol.GLModel#getFrames
+         * @return {Array.<Object>}
          */
-        this.addStyle = function(sel, style) {
-            applyToModels("setStyle", sel, style, true);
+        this.getFrames = function() {
+            return frames;
         };
-
+        
         /**
-         * @function $3Dmol.GLViewer#setColorByProperty
-         * @param {AtomSelectionSpec} sel
-         * @param {type} prop
-         * @param {type} scheme
+         * Sets model's atomlist to specified frame
+         * Sets to last frame if framenum out of range
+         * 
+         * @function $3Dmol.GLModel#setFrame
+         * @param {number} framenum - model's atoms are set to this index in frames list
          */
-        this.setColorByProperty = function(sel, prop, scheme) {
-            applyToModels("setColorByProperty", sel, prop, scheme);
+        this.setFrame = function(framenum) {
+            if (frames.length == 0) {
+                return;
+            }
+            if (framenum >= 0 && framenum < frames.length) {
+                atoms = frames[framenum];
+            }
+            else {
+                atoms = frames[frames.length-1];
+            }
+            molObj = null;
         };
-
+        
         /**
-         * @function $3Dmol.GLViewer#setColorByElement
-         * @param {AtomSelectionSpec} sel
-         * @param {type} colors
+         * Add atoms as frames of model
+         * 
+         * @function $3Dmol.GLModel#addFrame
+         * @param {AtomSpec} atom - atoms to be added
          */
-        this.setColorByElement = function(sel, colors) {
-            applyToModels("setColorByElement", sel, colors);
+        this.addFrame = function(atoms) {
+            frames.push(atoms);
         };
 
+        
         /**
+         * If model atoms have dx, dy, dz properties (in some xyz files), vibrate populates the model's frame property based on parameters.
+         * Model can then be animated
          * 
-         * @param {AtomSpec[]} atomlist
-         * @param {Array}
-         *            extent
-         * @return {Array}
+         * @function $3Dmol.GLModel#vibrate
+         * @param {number} numFrames - number of frames to be created, default to 10
+         * @param {number} amplitude - amplitude of distortion, default to 1 (full)
          */
-        var getAtomsWithin = function(atomlist, extent) {
-            var ret = [];
-
-            for (var i = 0; i < atomlist.length; i++) {
-                var atom = atomlist[i];
-                if (typeof (atom) == "undefined")
-                    continue;
-
-                if (atom.x < extent[0][0] || atom.x > extent[1][0])
-                    continue;
-                if (atom.y < extent[0][1] || atom.y > extent[1][1])
-                    continue;
-                if (atom.z < extent[0][2] || atom.z > extent[1][2])
-                    continue;
-                ret.push(i);
+        this.vibrate = function(numFrames, amplitude) {
+            var vectors = [];
+            var amplitude = amplitude || 1;
+            var numFrames = numFrames || 10; 
+            for (var i = 0; i < atoms.length; i++) {
+                var vector = new $3Dmol.Vector3(atoms[i].dx, atoms[i].dy, atoms[i].dz);
+                vectors.push(vector);
+            }
+            numFrames--;
+            for (var i = 1; i <= numFrames; i++) {
+                var newAtoms = [];
+                for (var j = 0; j < atoms.length; j++) {
+                    var newVector = new $3Dmol.Vector3(atoms[j].dx, atoms[j].dy, atoms[j].dz);
+                    var starting = new $3Dmol.Vector3(atoms[j].x, atoms[j].y, atoms[j].z);
+                    newVector.sub(starting);
+                    newVector.multiplyScalar((i*amplitude)/numFrames);
+                    starting.add(newVector);
+                    var newAtom = {};
+                    for (var k in atoms[j]) {
+                        newAtom[k] = atoms[j][k];
+                    }
+                    newAtom.x = starting.x;
+                    newAtom.y = starting.y;
+                    newAtom.z = starting.z;
+                    newAtoms.push(newAtom);
+                }
+                frames.push(newAtoms);
+            }
+            frames.unshift(atoms); //add 1st frame
+        };
+        
+        // set default style and colors for atoms
+        this.setAtomDefaults = function(atoms) {
+            for ( var i = 0; i < atoms.length; i++) {
+                var atom = atoms[i];
+                if (atom) {
+                    atom.style = atom.style || defaultAtomStyle;
+                    atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
+                    atom.model = id;
+                    if (atom.clickable)
+                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                }
             }
-            return ret;
         };
 
-        // return volume of extent
-        var volume = function(extent) {
-            var w = extent[1][0] - extent[0][0];
-            var h = extent[1][1] - extent[0][1];
-            var d = extent[1][2] - extent[0][2];
-            return w * h * d;
-        }; // volume
-        /*
-         * Break up bounding box/atoms into smaller pieces so we can parallelize
-         * with webworkers and also limit the size of the working memory Returns
-         * a list of bounding boxes with the corresponding atoms. These extents
-         * are expanded by 4 angstroms on each side.
-         */
-        /**
+        /** add atoms to this model from molecular data string
          * 
-         * @param {Array}
-         *            extent
-         * @param {AtomSpec[]} atomlist
-         * @param {AtomSpec[]} atomstoshow
-         * @return {Array}
+         * @function $3Dmol.GLModel#addMolData
+         * @param {string|ArrayBuffer} data - atom structure file input data string, for gzipped input use ArrayBuffer
+         * @param {string} format - input file string format (e.g 'pdb', 'sdf', 'sdf.gz', etc.)
+         * @param {Object} options - format dependent options (e.g. 'options.keepH' to keep hydrogens)
          */
-        var carveUpExtent = function(extent, atomlist, atomstoshow) {
-            var ret = [];
-
-            var copyExtent = function(extent) {
-                // copy just the dimensions
-                var ret = [];
-                ret[0] = [ extent[0][0], extent[0][1], extent[0][2] ];
-                ret[1] = [ extent[1][0], extent[1][1], extent[1][2] ];
-                return ret;
-            }; // copyExtent
-            var splitExtentR = function(extent) {
-                // recursively split until volume is below maxVol
-                if (volume(extent) < maxVolume) {
-                    return [ extent ];
+        this.addMolData = function(data, format, options) {
+            options = options || {};
+            var parsedAtoms = $3Dmol.GLModel.parseMolData(data, format, options);
+            dontDuplicateAtoms = !options.duplicateAssemblyAtoms;
+            var mData = parsedAtoms.modelData;
+            if (mData) {
+                if (Array.isArray(mData)) {
+                    modelData = mData[0];
                 } else {
-                    // find longest edge
-                    var w = extent[1][0] - extent[0][0];
-                    var h = extent[1][1] - extent[0][1];
-                    var d = extent[1][2] - extent[0][2];
-
-                    var index;
+                    modelData = mData;
+                }
+            }
 
-                    if (w > h && w > d) {
-                        index = 0;
-                    } else if (h > w && h > d) {
-                        index = 1;
-                    } else {
-                        index = 2;
+            if (frames.length == 0) { //first call
+                for (var i = 0; i < parsedAtoms.length; i++) {
+                    if (parsedAtoms[i].length != 0)
+                        frames.push(parsedAtoms[i]);
+                }
+                if(frames[0])
+                    atoms = frames[0];
+            }
+            
+            else { //subsequent calls
+                if (options.frames) { //add to new frame
+                    for (var i = 0; i < parsedAtoms.length; i++) {
+                        frames.push(parsedAtoms[i]);
                     }
-
-                    // create two halves, splitting at index
-                    var a = copyExtent(extent);
-                    var b = copyExtent(extent);
-                    var mid = (extent[1][index] - extent[0][index]) / 2
-                            + extent[0][index];
-                    a[1][index] = mid;
-                    b[0][index] = mid;
-
-                    var alist = splitExtentR(a);
-                    var blist = splitExtentR(b);
-                    return alist.concat(blist);
                 }
-            }; // splitExtentR
-
-            // divide up extent
-            var splits = splitExtentR(extent);
-            // now compute atoms within expanded (this could be more efficient)
-            var off = 6; // enough for water and 2*r, also depends on scale
-            // factor
-            for (var i = 0, n = splits.length; i < n; i++) {
-                var e = copyExtent(splits[i]);
-                e[0][0] -= off;
-                e[0][1] -= off;
-                e[0][2] -= off;
-                e[1][0] += off;
-                e[1][1] += off;
-                e[1][2] += off;
-
-                var atoms = getAtomsWithin(atomlist, e);
-                var toshow = getAtomsWithin(atomstoshow, splits[i]);
-
-                // ultimately, divide up by atom for best meshing
-                ret.push({
-                    extent : splits[i],
-                    atoms : atoms,
-                    toshow : toshow
-                });
+                else { //add atoms to current frame
+                    for (var i = 0; i < parsedAtoms.length; i++) {
+                        this.addAtoms(parsedAtoms[i]); 
+                    }
+                }
+            }
+            
+            for (var i = 0; i < frames.length; i++) {
+                this.setAtomDefaults(frames[i], id);
             }
 
-            return ret;
         };
 
-        // create a mesh defined from the passed vertices and faces and material
-        // Just create a single geometry chunk - broken up whether sync or not
-        /**
+        this.setDontDuplicateAtoms = function(dup) {
+            dontDuplicateAtoms = dup;
+        }
+
+        this.setModelData = function(mData) {
+            modelData = mData;
+        }
+        
+        /** given a selection specification, return true if atom is selected
          * 
-         * @param {AtomSpec[]} atoms
-         * @param {{vertices:number,faces:number}}
-         *            VandF
-         * @param {$3Dmol.MeshLambertMaterial}
-         *            mat
-         * @return {$3Dmol.Mesh}
+         * @function $3Dmol.GLModel#atomIsSelected
+         * @param {AtomSpec} atom
+         * @param {AtomSelectionSpec} sel
+         * @return {boolean}
          */
-        var generateSurfaceMesh = function(atoms, VandF, mat) {
-
-            var geo = new $3Dmol.Geometry(true);
-            // Only one group per call to generate surface mesh (addSurface
-            // should split up mesh render)
-            var geoGroup = geo.updateGeoGroup(0);
+        this.atomIsSelected = function(atom, sel) {
+            if (typeof (sel) === "undefined")
+                return true; // undef gets all
+            var invert = !!sel.invert;
+            var ret = true;
+            for ( var key in sel) {
+                if(key === 'predicate') { //a user supplied function for evaluating atoms
+                    if(!sel['predicate'](atom) ) {
+                        ret = false;
+                        break;
+                    }
+                }
+                else if(key == "properties" && atom[key]) {
+                    for (var propkey in sel.properties) {
+                        if(typeof(atom.properties[propkey]) === 'undefined') {
+                            ret = false;
+                            break
+                        }
+                        if(atom.properties[propkey] != sel.properties[propkey]) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                }
+                else if (sel.hasOwnProperty(key) && key != "props" && key != "invert" && key != "model" && key != "byres" && key != "expand" && key != "within") {
 
-            var vertexArray = geoGroup.vertexArray;
-            // reconstruct vertices and faces
-            var v = VandF['vertices'];
-            var offset;
-            var i, il;
-            for (i = 0, il = v.length; i < il; i++) {
-                offset = geoGroup.vertices * 3;
-                vertexArray[offset] = v[i].x;
-                vertexArray[offset + 1] = v[i].y;
-                vertexArray[offset + 2] = v[i].z;
-                geoGroup.vertices++;
+                    // if something is in sel, atom must have it                    
+                    if (typeof (atom[key]) === "undefined") {
+                        ret = false;
+                        break;
+                    }
+                    var isokay = false;
+                    if(key === "bonds") {
+                        //special case counting number of bonds, for selecting nonbonded mostly
+                        var val = sel[key];
+                        if(val != atom.bonds.length) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                    else if ($.isArray(sel[key])) {
+                        // can be any of the listed values
+                        var valarr = sel[key];
+                        for ( var i = 0; i < valarr.length; i++) {
+                            if (atom[key] == valarr[i]) {
+                                isokay = true;
+                                break;
+                            }
+                        }
+                        if (!isokay) {
+                            ret = false;
+                            break;
+                        }
+                    } else { // single match
+                        var val = sel[key];
+                        if (atom[key] != val) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                }
             }
+            
+            return invert ? !ret : ret;
+        };
 
-            var faces = VandF['faces'];
-            geoGroup.faceidx = faces.length;// *3;
-            geo.initTypedArrays();
 
-            // set colors for vertices
-            var colors = [];
-            for (i = 0, il = atoms.length; i < il; i++) {
-                var atom = atoms[i];
+        /** return list of atoms selected by sel, this is specific to glmodel
+         * 
+         * @function $3Dmol.GLModel#selectedAtoms
+         * @param {AtomSelectionSpec} sel
+         * @return {Array.<Object>}
+         */
+        this.selectedAtoms = function(sel, from) {
+            var ret = [];
+            sel = sel || {};
+            if (!from) from = atoms;
+            var aLength = from.length;
+            for ( var i = 0; i < aLength; i++) {
+                var atom = from[i];
                 if (atom) {
-                    if (typeof (atom.surfaceColor) != "undefined") {
-                        colors[i] = atom.surfaceColor;
-                    } else if (atom.color) // map from atom
-                        colors[i] = $3Dmol.CC.color(atom.color);
+                    if (this.atomIsSelected(atom, sel))
+                        ret.push(atom);
                 }
             }
 
-            var verts = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var normalArray = geoGroup.normalArray;
-            var vA, vB, vC, norm;
-
-            // Setup colors, faces, and normals
-            for (i = 0, il = faces.length; i < il; i += 3) {
-
-                // var a = faces[i].a, b = faces[i].b, c = faces[i].c;
-                var a = faces[i], b = faces[i + 1], c = faces[i + 2];
-                var A = v[a]['atomid'];
-                var B = v[b]['atomid'];
-                var C = v[c]['atomid'];
-
-                var offsetA = a * 3, offsetB = b * 3, offsetC = c * 3;
+            // expand selection by some distance
+            if (sel.hasOwnProperty("expand")) {
 
-                colorArray[offsetA] = colors[A].r;
-                colorArray[offsetA + 1] = colors[A].g;
-                colorArray[offsetA + 2] = colors[A].b;
-                colorArray[offsetB] = colors[B].r;
-                colorArray[offsetB + 1] = colors[B].g;
-                colorArray[offsetB + 2] = colors[B].b;
-                colorArray[offsetC] = colors[C].r;
-                colorArray[offsetC + 1] = colors[C].g;
-                colorArray[offsetC + 2] = colors[C].b;
+                // get atoms in expanded bounding box
 
-                // setup Normals
+                var expand = expandAtomList(ret, parseFloat(sel.expand));
+                var retlen = ret.length;
+                for (var i = 0; i < expand.length; i++) {
+                    for (var j = 0; j < retlen; j++) {
 
-                vA = new $3Dmol.Vector3(verts[offsetA], verts[offsetA + 1],
-                        verts[offsetA + 2]);
-                vB = new $3Dmol.Vector3(verts[offsetB], verts[offsetB + 1],
-                        verts[offsetB + 2]);
-                vC = new $3Dmol.Vector3(verts[offsetC], verts[offsetC + 1],
-                        verts[offsetC + 2]);
-
-                vC.subVectors(vC, vB);
-                vA.subVectors(vA, vB);
-                vC.cross(vA);
+                        var dist = squaredDistance(expand[i], ret[j]);
+                        var thresh = Math.pow(sel.expand, 2);
+                        if (dist < thresh && dist > 0) {
+                            ret.push(expand[i]);
+                        }
+                    }
+                }
+            }
 
-                // face normal
-                norm = vC;
-                norm.normalize();
+            // selection within distance of sub-selection
+            if (sel.hasOwnProperty("within") && sel.within.hasOwnProperty("sel") && sel.within.hasOwnProperty("distance")) {
 
-                normalArray[offsetA] += norm.x;
-                normalArray[offsetB] += norm.x;
-                normalArray[offsetC] += norm.x;
-                normalArray[offsetA + 1] += norm.y;
-                normalArray[offsetB + 1] += norm.y;
-                normalArray[offsetC + 1] += norm.y;
-                normalArray[offsetA + 2] += norm.z;
-                normalArray[offsetB + 2] += norm.z;
-                normalArray[offsetC + 2] += norm.z;
+                // get atoms in second selection
+                var sel2 = this.selectedAtoms(sel.within.sel, atoms);
+                var within = [];
+                for (var i = 0; i < sel2.length; i++) {
+                    for (var j = 0; j < ret.length; j++) {
 
+                        var dist = squaredDistance(sel2[i], ret[j]);
+                        var thresh = Math.pow(parseFloat(sel.within.distance), 2);
+                        if (dist < thresh && dist > 0) {
+                            within.push(ret[j]);
+                        }
+                    }
+                }
+                ret = within;
             }
-            geoGroup.faceArray = new Uint16Array(faces);
-            var mesh = new $3Dmol.Mesh(geo, mat);
-            mesh.doubleSided = true;
-            
-            return mesh;
-        };
-
-        // do same thing as worker in main thread
-        /**
-         * 
-         * @param {$3Dmol.SurfaceType}
-         *            type
-         * @param {Array}
-         *            expandedExtent
-         * @param {Array}
-         *            extendedAtoms
-         * @param {Array}
-         *            atomsToShow
-         * @param {AtomSpec[]} atoms
-         * @param {number}
-         *            vol
-         * @return {Object}
-         */
-        var generateMeshSyncHelper = function(type, expandedExtent,
-                extendedAtoms, atomsToShow, atoms, vol) {
-            var time = new Date();
-            var ps = new $3Dmol.ProteinSurface();
-            ps.initparm(expandedExtent, (type === 1) ? false : true, vol);
-
-            var time2 = new Date();
-            //console.log("initialize " + (time2 - time) + "ms");
 
-            ps.fillvoxels(atoms, extendedAtoms);
+            // byres selection flag
+            if (sel.hasOwnProperty("byres")) {
 
-            var time3 = new Date();
-            //console.log("fillvoxels " + (time3 - time2) + "  " + (time3 - time) + "ms");
+                // Keep track of visited residues, visited atoms, and atom stack
+                var vResis = {};
+                var vAtoms = [];
+                var stack = [];
 
-            ps.buildboundary();
+                for (var i = 0; i < ret.length; i++) {
+                    
+                    // Check if atom is part of a residue, and that the residue hasn't been traversed yet
+                    var atom = ret[i];
+                    var c = atom.chain;
+                    var r = atom.resi;
+                    if (vResis[c] === undefined) vResis[c] = {};
+                    if (atom.hasOwnProperty("resi") && vResis[c][r] === undefined) {
 
-            if (type == $3Dmol.SurfaceType.SES) {
-                ps.fastdistancemap();
-                ps.boundingatom(false);
-                ps.fillvoxelswaals(atoms, extendedAtoms);
+                        // Perform a depth-first search of atoms with the same resi
+                        vResis[c][r] = true;
+                        stack.push(atom);
+                        while(stack.length > 0) {
+                            atom = stack.pop();
+                            c = atom.chain;
+                            r = atom.resi;
+                            if (vAtoms[atom.index] === undefined) {
+                                vAtoms[atom.index] = true;
+                                for (var j = 0; j < atom.bonds.length; j++) {
+                                    var atom2 = atoms[atom.bonds[j]];
+                                    if (vAtoms[atom2.index] === undefined && atom2.hasOwnProperty("resi") && atom2.chain == c && atom2.resi == r) {
+                                        stack.push(atom2);
+                                        ret.push(atom2);
+                                    }
+                                }
+                            }
+                        }
+                    }   
+                }
             }
 
-            var time4 = new Date();
-            console.log("buildboundaryetc " + (time4 - time3) + "  "
-                    + (time4 - time) + "ms");
+            return ret;
+        };
 
-            ps.marchingcube(type);
+        var squaredDistance = function(atom1, atom2) {
+            var xd = atom2.x - atom1.x;
+            var yd = atom2.y - atom1.y;
+            var zd = atom2.z - atom1.z;
+            return (Math.pow(xd, 2) + Math.pow(yd, 2) + Math.pow(zd, 2));
+        };
 
-            var time5 = new Date();
-            //console.log("marching cube " + (time5 - time4) + "  "+ (time5 - time) + "ms");
+        /** returns a list of atoms in the expanded bounding box, but not in the current one
+         *
+         *  Bounding box:
+         *
+         *    [ [ xmin, ymin, zmin ],
+         *      [ xmax, ymax, zmax ],
+         *      [ xctr, yctr, zctr ] ]
+         *
+         **/
+        var expandAtomList = function(atomList, amt) {
 
-            return ps.getFacesAndVertices(atomsToShow);
-        };
+            if (amt <= 0) return atomList;
 
-        /**
-         * 
-         * @param {matSpec}
-         *            style
-         * @return {$3Dmol.MeshLambertMaterial}
-         */
-        function getMatWithStyle(style) {
-            var mat = new $3Dmol.MeshLambertMaterial();
-            mat.vertexColors = $3Dmol.VertexColors;
+            var pb = $3Dmol.getExtent(atomList); // previous bounding box
+            var nb = [[], [], []]; // expanded bounding box
 
-            for ( var prop in style) {
-                if (prop === "color" || prop === "map") {
-                    // ignore
-                } else if (style.hasOwnProperty(prop))
-                    mat[prop] = style[prop];
-            }
-            if (style.opacity !== undefined) {
-                if (style.opacity === 1)
-                    mat.transparent = false;
-                else
-                    mat.transparent = true;
+            for (var i = 0; i < 3; i++)
+            {
+                nb[0][i] = pb[0][i]-amt;
+                nb[1][i] = pb[1][i]+amt;
+                nb[2][i] = pb[2][i];
             }
 
-            return mat;
-        }
+            // look in added box "shell" for new atoms
+            var expand = [];
+            for (var i = 0; i < atoms.length; i++) {
 
-        // get the min and max values of the specified property in the provided
-        // atoms
-        function getPropertyRange(atomlist, prop) {
-            var min = Number.POSITIVE_INFINITY;
-            var max = Number.NEGATIVE_INFINITY;
+                var x = atoms[i].x;
+                var y = atoms[i].y;
+                var z = atoms[i].z;
 
-            for (var i = 0, n = atomlist.length; i < n; i++) {
-                var atom = atomlist[i];
-                if (atom.properties
-                        && typeof (atom.properties[prop]) != "undefined") {
-                    var val = atom.properties[prop];
-                    if (val < min)
-                        min = val;
-                    if (val > max)
-                        max = val;
+                if (x >= nb[0][0] && x <= nb[1][0] && y >= nb[0][1] && y <= nb[1][1] && z >= nb[0][2] && z <= nb[1][2]) {
+                    if (!(x >= pb[0][0] && x <= pb[1][0] && y >= pb[0][1] && y <= pb[1][1] && z >= pb[0][2] && z <= pb[1][2])) {
+                        expand.push(atoms[i]);
+                    }
                 }
             }
-
-            if (!isFinite(min) && !isFinite(max))
-                min = max = 0;
-            else if (!isFinite(min))
-                min = max;
-            else if (!isFinite(max))
-                max = min;
-
-            return [ min, max ];
-        }
-
+            return expand;
+        };
         
-        /**
-         * Adds an explicit mesh as a surface object.
+        /** Add list of new atoms to model.  Adjusts bonds appropriately.
          * 
-         * @param {$3Dmol.Mesh}
-         *            mesh
-         * @param {Object}
-         *            style
-         * @returns {Number} surfid
-         */
-        this.addMesh = function(mesh) {
-            var surfobj = {
-                geo : mesh.geometry,
-                mat : mesh.material,
-                done : true,
-                finished : false //the rendered finishes surfaces when they are done
-            };
-            var surfid = surfaces.length;
-            surfaces[surfid] = surfobj;
-            return surfid;
-        }
+         * @function $3Dmol.GLModel#addAtoms
+         * @param {type} newatoms
+         */        
+        this.addAtoms = function(newatoms) {
+            molObj = null;
+            var start = atoms.length;
+            var indexmap = [];
+            // mapping from old index to new index
+            var i;
+            for(i = 0; i < newatoms.length; i++) {
+                if(typeof(newatoms[i].index) == "undefined")
+                    newatoms[i].index = i;
+                if(typeof(newatoms[i].serial) == "undefined")
+                    newatoms[i].serial = i;
+                indexmap[newatoms[i].index] = start+i;
+            }
+            
+            // copy and push newatoms onto atoms
+            for(i = 0; i < newatoms.length; i++) {
+                var olda = newatoms[i];
+                var nindex = indexmap[olda.index];
+                var a = $.extend(false, {}, olda);
+                a.index = nindex;
+                a.bonds = [];
+                a.bondOrder = [];
+                a.model = id;
+                a.style = a.style || defaultAtomStyle;
+                if(typeof(a.color) == "undefined")
+                    a.color = ElementColors[a.elem] || defaultColor;                
+                // copy over all bonds contained in selection,
+                // updating indices appropriately
+                var nbonds = olda.bonds ? olda.bonds.length : 0;
+                for(var j = 0; j < nbonds; j++) {
+                    var neigh = indexmap[olda.bonds[j]];
+                    if(typeof(neigh) != "undefined") {
+                        a.bonds.push(neigh);
+                        a.bondOrder.push(olda.bondOrder ? olda.bondOrder[j] : 1);
+                    }                
+                }
+                atoms.push(a);
+            }
+        };
 
-        //return a shallow copy of list l, e.g., for atoms so we can
-        //ignore superficial changes (ie surfacecolor, position) that happen
-        //while we're surface building
-        var shallowCopy = function(l) {
-            var ret = [];
-            $.each(l, function(k,v) {
-                ret[k] = $.extend({},v);
-            });
-            return ret;
-        }
-        /**
-         * Add surface representation to atoms
-         *  @function $3Dmol.GLViewer#addSurface
-         * @param {$3Dmol.SurfaceType} type - Surface type
-         * @param {SurfaceStyleSpec} style - optional style specification for surface material (e.g. for different coloring scheme, etc)
-         * @param {AtomSelectionSpec} atomsel - Show surface for atoms in this selection
-         * @param {AtomSelectionSpec} allsel - Use atoms in this selection to calculate surface; may be larger group than 'atomsel' 
-         * @param {AtomSelectionSpec} focus - Optionally begin rendering surface specified atoms
+        /** Remove specified atoms from model
          * 
-         * @return {number} surfid - Identifying number for this surface
+         * @function $3Dmol.GLModel#removeAtoms
+         * @param {type} badatoms
+         * @return {removeAtoms}
          */
-        this.addSurface = function(type, style, atomsel, allsel, focus) {
-            // type 1: VDW 3: SAS 4: MS 2: SES
-            // if sync is true, does all work in main thread, otherwise uses
-            // workers
-            // with workers, must ensure group is the actual modelgroup since
-            // surface
-            // will get added asynchronously
-            // all atoms in atomlist are used to compute surfaces, but only the
-            // surfaces
-            // of atomsToShow are displayed (e.g., for showing cavities)
-            // if focusSele is specified, will start rending surface around the
-            // atoms specified by this selection
-            var atomlist = null, focusSele = null;
-            //TODO: currently generating a shallow copy to avoid problems when atoms are chagned
-            //during surface generation - come up with a better solution
-            var atomsToShow = shallowCopy(getAtomsFromSel(atomsel));
-            if(!allsel) {
-                atomlist = atomsToShow;
+        this.removeAtoms = function(badatoms) {
+            molObj = null;
+            // make map of all baddies
+            var baddies = [];
+            var i;
+            for(i = 0; i < badatoms.length; i++) {
+                baddies[badatoms[i].index] = true;
             }
-            else {
-                atomlist = shallowCopy(getAtomsFromSel(allsel));
+            
+            // create list of good atoms
+            var newatoms = [];
+            for(i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                if(!baddies[a.index])
+                    newatoms.push(a);
             }
             
-            var symmetries = false;
-            var n;
-            for (n = 0; n < models.length; n++) { 
-                var symMatrices = models[n].getSymmetries();
-                if (symMatrices.length > 1 || (symMatrices.length == 1 && !(symMatrices[0].isIdentity()))) {
-                    symmetries = true;
-                    break;
+            // clear it all out
+            atoms = [];
+            // and add back in to get updated bonds
+            this.addAtoms(newatoms);
+        };
+        
+        
+        /** Set atom style of selected atoms
+         * 
+         * @function $3Dmol.GLModel#setStyle
+         * @param {AtomSelectionSpec} sel
+         * @param {AtomStyleSpec} style
+         * @param {boolean} add - if true, add to current style, don't replace
+         */
+        this.setStyle = function(sel, style, add) {
+            
+            if(typeof(style) === 'undefined' && typeof(add) == 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            
+            // report to console if this is not a valid selector
+            var s;
+            for (s in sel) {
+                if(validAtomSelectionSpecs.indexOf(s) === -1) {
+                    console.log('Unknown selector ' + s);
+                }
+            }
+            // report to console if this is not a valid style
+            for (s in style) {
+                if(validAtomStyleSpecs.indexOf(s) === -1) {
+                    console.log('Unknown style ' + s);
                 }
             }
 
-            var addSurfaceHelper = function addSurfaceHelper(surfobj, atomlist, atomsToShow) {
+            var changedAtoms = false;
+            // somethings we only calculate if there is a change in a certain
+            // style, although these checks will only catch cases where both
+            // are either null or undefined
             
-                if(!focus) {
-                    focusSele = atomsToShow;
-                } else {
-                    focusSele = shallowCopy(getAtomsFromSel(focus));
+            var setStyleHelper = function(atomArr) {
+                var selected = that.selectedAtoms(sel, atomArr);
+                for (var i = 0; i < atomArr.length; i++) {
+                    if (atomArr[i]) atomArr[i].capDrawn = false; //reset for proper stick render
                 }
+            
+                for ( var i = 0; i < selected.length; i++) {                
+                    changedAtoms = true;
+                    if (selected[i].clickable) 
+                        selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};                    
+                   
 
-                var atom;
-                var time = new Date();
-                var extent = $3Dmol.getExtent(atomsToShow, true);
-
-                var i, il;
-                if (style['map'] && style['map']['prop']) {
-                    // map color space using already set atom properties
-                    /** @type {AtomSpec} */
-                    var prop = style['map']['prop'];
-                    /** @type {Gradient} */
-                    var scheme = style['map']['scheme'] || new $3Dmol.Gradient.RWB();
-                    var range = scheme.range();
-                    if (!range) {
-                        range = getPropertyRange(atomsToShow, prop);
-                    }
-
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        atom.surfaceColor = $3Dmol.CC.color(scheme.valueToHex(
-                                atom.properties[prop], range));
-                    }
-                }
-                else if(typeof(style['color']) != 'undefined') {
-                    //explicitly set color, otherwise material color just blends
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        atom.surfaceColor = $3Dmol.CC.color(style['color']);
-                    }
-                }
-                else if(typeof(style['colorscheme']) != 'undefined') {
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        var scheme = $3Dmol.elementColors[style.colorscheme];
-                                if(scheme && typeof(scheme[atom.elem]) != "undefined") {
-                                    atom.surfaceColor = $3Dmol.CC.color(scheme[atom.elem]);
-                                }
+                    if(!add) selected[i].style = {};
+                    for(s in style) {
+                        if(style.hasOwnProperty(s)) {
+                            selected[i].style[s]=selected[i].style[s]||{}; //create distinct object for each atom
+                            for(var prop in style[s]){
+                                selected[i].style[s][prop]=style[s][prop];
+                            }
+                        }
                     }
                 }
+            }
+            
+            var that = this;
+            setStyleHelper(atoms);
+            for (var i = 0; i < frames.length; i++) {
+                setStyleHelper(frames[i]);
+            }
+            
+            if (changedAtoms)
+                molObj = null; //force rebuild
+            
+        };
 
-                var totalVol = volume(extent); // used to scale resolution
-                var extents = carveUpExtent(extent, atomlist, atomsToShow);
-
-                if (focusSele && focusSele.length && focusSele.length > 0) {
-                    var seleExtent = $3Dmol.getExtent(focusSele, true);
-                    // sort by how close to center of seleExtent
-                    var sortFunc = function(a, b) {
-                        var distSq = function(ex, sele) {
-                            // distance from e (which has no center of mass) and
-                            // sele which does
-                            var e = ex.extent;
-                            var x = e[1][0] - e[0][0];
-                            var y = e[1][1] - e[0][1];
-                            var z = e[1][2] - e[0][2];
-                            var dx = (x - sele[2][0]);
-                            dx *= dx;
-                            var dy = (y - sele[2][1]);
-                            dy *= dy;
-                            var dz = (z - sele[2][2]);
-                            dz *= dz;
+        /** Set clickable and callback of selected atoms
+         * 
+         * @function $3Dmol.GLModel#setClickable
+         * @param {AtomSelectionSpec} sel - atom selection to apply clickable settings to
+         * @param {boolean} clickable - whether click-handling is enabled for the selection
+         * @param {function} callback - function called when an atom in the selection is clicked
+         */
+        this.setClickable = function(sel, clickable, callback) {           
 
-                            return dx + dy + dz;
-                        };
-                        var d1 = distSq(a, seleExtent);
-                        var d2 = distSq(b, seleExtent);
-                        return d1 - d2;
-                    };
-                    extents.sort(sortFunc);
+            // report to console if this is not a valid selector
+            var s;
+            for (s in sel) {
+                if (validAtomSelectionSpecs.indexOf(s) === -1) {
+                    console.log('Unknown selector ' + s);
                 }
+            }
 
-                //console.log("Extents " + extents.length + "  "+ (+new Date() - time) + "ms");
+            // make sure clickable is a boolean
+            clickable = !!clickable;
 
+            // report to console if callback is not a valid function
+            if (callback && typeof callback != "function") {
+                console.log("Callback is not a function");
+                return;
+            }
 
-                var reducedAtoms = [];
-                // to reduce amount data transfered, just pass x,y,z,serial and elem
-                for (i = 0, il = atomlist.length; i < il; i++) {
-                    atom = atomlist[i];
-                    reducedAtoms[i] = {
-                        x : atom.x,
-                        y : atom.y,
-                        z : atom.z,
-                        serial : i,
-                        elem : atom.elem
-                    };
-                }
+            var i;
+            var selected = this.selectedAtoms(sel, atoms);
+            var len = selected.length;
+            for (i = 0; i < len; i++) {                
 
-                var sync = !!($3Dmol.syncSurface);
-                if (sync) { // don't use worker, still break up for memory purposes
+                selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                selected[i].clickable = clickable;
+                if (callback) selected[i].callback = callback;
 
-                    // to keep the browser from locking up, call through setTimeout
-                    var callSyncHelper = function callSyncHelper(i) {
-                        if (i >= extents.length)
-                            return;
+            }
 
-                        var VandF = generateMeshSyncHelper(type, extents[i].extent,
-                                extents[i].atoms, extents[i].toshow, reducedAtoms,
-                                totalVol);
-                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
-                        $3Dmol.mergeGeos(surfobj.geo, mesh);
-                        _viewer.render();
+            if (len > 0) molObj = null; // force rebuild to get correct intersection shapes         
+        };
+        
+        /** given a mapping from element to color, set atom colors
+         * 
+         * @function $3Dmol.GLModel#setColorByElement
+         * @param {type} sel
+         * @param {type} colors
+         */
+        this.setColorByElement = function(sel, colors) {
+            
+            if(molObj !== null && sameObj(colors,lastColors))
+                return; // don't recompute
+            lastColors = colors;
+            var atoms = this.selectedAtoms(sel, atoms);
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            for ( var i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                if(typeof(colors[a.elem]) !== "undefined") {
+                    a.color = colors[a.elem];
+                }
+            }
+        };
+        
+        /**
+         * @function $3Dmol.GLModel.setColorByProperty
+         * @param {type} sel
+         * @param {type} prop
+         * @param {type} scheme
+         */
+        this.setColorByProperty = function(sel, prop, scheme, range) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            lastColors = null; // don't bother memoizing
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            var min =  Number.POSITIVE_INFINITY;
+            var max =  Number.NEGATIVE_INFINITY;
+            var i, a;
+            
+            if(!range) { //no explicit range, get from scheme
+                range = scheme.range();
+            }
+            
+            if(!range) { //no range in scheme, compute the range for this model
+                range = $3Dmol.getPropertyRange(atoms, prop);
+            }
+            // now apply colors using scheme
+            for (i = 0; i < atoms.length; i++) {
+                a = atoms[i];
+                var val = $3Dmol.getAtomProperty(a, prop);
+                if(val != null) {
+                    a.color = scheme.valueToHex(parseFloat(a.properties[prop]), [range[0],range[1]]);
+                }                    
+            }
+        };
+        
+        /**
+         * @function $3Dmol.GLModel.setColorByFunction
+         * @param {type} sel
+         * @param {type} func
+         */
+        this.setColorByFunction = function(sel, colorfun) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            lastColors = null; // don't bother memoizing
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            
+            // now apply colorfun
+            for (i = 0; i < atoms.length; i++) {
+                a = atoms[i];
+                a.color = colorfun(a);
+            }
+        };
 
-                        setTimeout(callSyncHelper, 1, i + 1);
+        /** Convert the model into an object in the format of a ChemDoodle JSON model.
+         *
+         * @function $3Dmol.GLModel#toCDObject
+         * @param {boolean} whether or not to include style information. Defaults to false.
+         * @return {Object}
+         */
+        this.toCDObject = function(includeStyles) {
+            var out = { a:[], b:[] };
+            if (includeStyles) {
+                out.s = [];
+            }
+            for (var i = 0; i < atoms.length; i++) {
+                var atomJSON = {};
+                var atom = atoms[i];
+                atomJSON.x = atom.x;
+                atomJSON.y = atom.y;
+                atomJSON.z = atom.z;
+                if (atom.elem != "C") {
+                    atomJSON.l = atom.elem;
+                }
+                if (includeStyles) {
+                    var s = 0;
+                    while (s < out.s.length &&
+                          (JSON.stringify(atom.style) !== JSON.stringify(out.s[s]))) {
+                        s++;
                     }
-
-                    setTimeout(callSyncHelper, 1, 0);
-
-                    // TODO: Asynchronously generate geometryGroups (not separate
-                    // meshes) and merge them into a single geometry
-                } else { // use worker
-
-                    var workers = [];
-                    if (type < 0)
-                        type = 0; // negative reserved for atom data
-                    for (i = 0, il = numWorkers; i < il; i++) {
-                        // var w = new Worker('3Dmol/SurfaceWorker.js');
-                        var w = new Worker($3Dmol.SurfaceWorker);
-                        workers.push(w);
-                        w.postMessage({
-                            'type' : -1,
-                            'atoms' : reducedAtoms,
-                            'volume' : totalVol
-                        });
+                    if (s === out.s.length) {
+                        out.s.push(atom.style);
                     }
-                    var cnt = 0;
+                    if (s !== 0) {
+                        atomJSON.s = s;
+                    }
+                }
+                
+                out.a.push(atomJSON);
 
-                    var rfunction = function(event) {
-                        var VandF = event.data;
-                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
-                        $3Dmol.mergeGeos(surfobj.geo, mesh);
-                        _viewer.render();
-                    //    console.log("async mesh generation " + (+new Date() - time) + "ms");
-                        cnt++;
-                        if (cnt == extents.length)
-                            surfobj.done = true;
+                for (var b = 0; b < atom.bonds.length; b++) {
+                    var firstAtom = i;
+                    var secondAtom = atom.bonds[b];
+                    if (firstAtom >= secondAtom)
+                        continue;
+                    var bond = {
+                        b: firstAtom,
+                        e: secondAtom
                     };
-
-                    var efunction = function(event) {
-                        console.log(event.message + " (" + event.filename + ":" + event.lineno + ")");
-                    };
-
-                    for (i = 0; i < extents.length; i++) {
-                        var worker = workers[i % workers.length];
-                        worker.onmessage = rfunction;
-
-                        worker.onerror = efunction;
-
-                        worker.postMessage({
-                            'type' : type,
-                            'expandedExtent' : extents[i].extent,
-                            'extendedAtoms' : extents[i].atoms,
-                            'atomsToShow' : extents[i].toshow
-                        });
+                    var bondOrder =  atom.bondOrder[b];
+                    if (bondOrder != 1) {
+                        bond.o = bondOrder;
                     }
-                }
-
-                // NOTE: This is misleading if 'async' mesh generation - returns
-                // immediately
-                //console.log("full mesh generation " + (+new Date() - time) + "ms");
-            }
-            
-            style = style || {};
-            var mat = getMatWithStyle(style);
-            var surfobj = [];
-            
-            if (symmetries) { //do preprocessing
-                var modelsAtomList = {};
-                var modelsAtomsToShow = {};
-                for (n = 0; n < models.length; n++) {
-                    modelsAtomList[n] = [];
-                    modelsAtomsToShow[n] = [];
-                }
-                for (n = 0; n < atomlist.length; n++) {
-                    modelsAtomList[atomlist[n].model].push(atomlist[n]);
-                }
-                for (n = 0; n < atomsToShow.length; n++) {
-                    modelsAtomsToShow[atomsToShow[n].model].push(atomsToShow[n]);
-                }
-                for (n = 0; n < models.length; n++) {
-                    surfobj.push({
-                        geo : new $3Dmol.Geometry(true),
-                        mat : mat,
-                        done : false,
-                        finished : false,
-                        symmetries : models[n].getSymmetries()
-                    // also webgl initialized
-                    });
-                    addSurfaceHelper(surfobj[n], modelsAtomList[n], modelsAtomsToShow[n]);
+                    out.b.push(bond);
                 }
             }
-            else {
-                surfobj.push({
-                    geo : new $3Dmol.Geometry(true),
-                    mat : mat,
-                    done : false,
-                    finished : false,
-                    symmetries : [new $3Dmol.Matrix4()]
-                });
-                addSurfaceHelper(surfobj[surfobj.length-1], atomlist, atomsToShow);
-            } 
-            var surfid = surfaces.length;
-            surfaces[surfid] = surfobj;
-            
-            return surfid;
+            return out;
+        }
 
-        };
 
-        /**
-         * Set the surface material to something else, must render change
+        /** manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
          * 
-         * @param {number} surf - Surface ID to apply changes to
-         * @param {matSpec} style - new material style specification
-         */ 
-        this.setSurfaceMaterialStyle = function(surf, style) {
-            if (surfaces[surf]) {
-                surfArr = surfaces[surf];
-                for (var i = 0; i < surfArr.length; i++) {
-                    surfArr[i].mat = getMatWithStyle(style);
-                    surfArr[i].mat.side = $3Dmol.FrontSide;
-                    surfArr[i].finished = false; // trigger redraw
+         * @function $3Dmol.GLModel#globj
+         * @param {$3Dmol.Object3D} group
+         * @param Object options
+         */
+        this.globj = function(group, options) {
+            var time = new Date();
+            if(molObj === null) { // have to regenerate
+                molObj = createMolObj(atoms, options);
+                var time2 = new Date();
+                //console.log("object creation time: " + (time2 - time));
+                if(renderedMolObj) { // previously rendered, remove
+                    group.remove(renderedMolObj);
+                    renderedMolObj = null;
+                }
+                renderedMolObj = molObj.clone();
+                if(hidden) {
+                    renderedMolObj.setVisible(false);
+                    molObj.setVisible(false);
                 }
+                group.add(renderedMolObj);              
             }
         };
-
-        /**
-         * Remove surface with given ID
+        
+        /** Remove any renderable mol object from scene
          * 
-         * @param {number} surf - surface id
+         * @function $3Dmol.GLModel#removegl
+         * @param {$3Dmol.Object3D} group
          */
-        this.removeSurface = function(surf) {
-            var surfArr = surfaces[surf];
-            for (var i = 0; i < surfArr.length; i++) {
-                if (surfArr[i] && surfArr[i].lastGL) {
-                    if (surfArr[i].geo !== undefined)
-                        surfArr[i].geo.dispose();
-                    if (surfArr[i].mat !== undefined)
-                        surfArr[i].mat.dispose();
-                    modelGroup.remove(surfArr[i].lastGL); // remove from scene
-                }
+        this.removegl = function(group) {
+            if(renderedMolObj) {
+                //dispose of geos and materials
+                if (renderedMolObj.geometry !== undefined) renderedMolObj.geometry.dispose();             
+                if (renderedMolObj.material !== undefined) renderedMolObj.material.dispose();
+                group.remove(renderedMolObj);
+                renderedMolObj = null;
             }
-            delete surfaces[surf];
-            show();
+            molObj = null;
         };
         
-        /** Remove all surfaces.
-         * @function $3Dmol.GLViewer#removeAllSurfaces */
-        this.removeAllSurfaces = function() {
-            for (var n = 0; n < surfaces.length; n++) {
-                surfArr = surfaces[n];
-                for(var i = 0; i < surfArr.length; i++) {
-                    if (surfArr[i] && surfArr[i].lastGL) {
-                        if (surfArr[i].geo !== undefined)
-                            surfArr[i].geo.dispose();
-                        if (surfArr[i].mat !== undefined)
-                            surfArr[i].mat.dispose();
-                        modelGroup.remove(surfArr[i].lastGL); // remove from scene
-                    }
-                }
-                delete surfaces[n];
-            }
-            show();
-            
-        };
-
-        /** return Jmol moveto command to position this scene */
-        this.jmolMoveTo = function() {
-            var pos = modelGroup.position;
-            // center on same position
-            var ret = "center { " + (-pos.x) + " " + (-pos.y) + " " + (-pos.z)
-                    + " }; ";
-            // apply rotation
-            var q = rotationGroup.quaternion;
-            ret += "moveto .5 quaternion { " + q.x + " " + q.y + " " + q.z
-                    + " " + q.w + " };";
-            // zoom is tricky.. maybe i would be best to let callee zoom on
-            // selection?
-            // can either do a bunch of math, or maybe zoom to the center with a
-            // fixed
-            // but reasonable percentage
-
-            return ret;
-        };
-
-        /** Clear scene of all objects 
-         * @function $3Dmol.GLViewer#clear
-         * */
-        this.clear = function() {
-            this.removeAllSurfaces();
-            this.removeAllModels();
-            this.removeAllLabels();
-            this.removeAllShapes();
-            show();
-        };
-
-        // props is a list of objects that select certain atoms and enumerate
-        // properties for those atoms
-        /**
-         * Add specified properties to all atoms matching input argument
-         * @param {Object} props, either array of atom selectors with associated props, or function that takes atom and sets its properties
+        /** Don't show this model is future renderings.  Keep all styles and state
+         * so it can be efficiencly shown again.
+         * 
+         * @function $3Dmol.GLModel#hide
+         */
+        this.hide = function() {
+            hidden = true;
+            if(renderedMolObj) renderedMolObj.setVisible(false);
+            if(molObj) molObj.setVisible(false);
+        }
+        
+        this.show = function() {
+            hidden = false;
+            if(renderedMolObj) renderedMolObj.setVisible(true);
+            if(molObj) molObj.setVisible(true);
+        }
+        
+        /** Create labels for residues of selected atoms.
+         * Will create a single label at the center of mass of all atoms
+         * with the same chain,resn, and resi.
+         * @function $3Dmol.GLModel#addResLabels
+         * 
          * @param {AtomSelectionSpec} sel
+         * @param {$3Dmol.GLViewer} viewer
          */
-        this.mapAtomProperties = function(props, sel) {
-            sel = sel || {};
-            var atoms = getAtomsFromSel(sel);
-            
-            if(typeof(props) == "function") {
-                for (var a = 0, numa = atoms.length; a < numa; a++) {
-                    var atom = atoms[a];
-                    props(atom);
-                }
+        this.addResLabels = function(sel, viewer, style) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            var bylabel = {}
+            //collect by chain:resn:resi
+            for(var i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                var c = a.chain;
+                var resn = a.resn;
+                var resi = a.resi;
+                var label =  resn + '' + resi;
+                if(!bylabel[c]) bylabel[c] = {};
+                if(!bylabel[c][label]) bylabel[c][label] = []
+                bylabel[c][label].push(a);
             }
-            else {
-                for (var a = 0, numa = atoms.length; a < numa; a++) {
-                    var atom = atoms[a];
-                    for (var i = 0, n = props.length; i < n; i++) {
-                        var prop = props[i];
-                        if (prop.props) {
-                            for ( var p in prop.props) {
-                                if (prop.props.hasOwnProperty(p)) {
-                                    // check the atom
-                                    if (atomIsSelected(atom, prop)) {
-                                        if (!atom.properties)
-                                            atom.properties = {};
-                                        atom.properties[p] = prop.props[p];
-                                    }
-                                }
+            
+            var mystyle = $.extend(true, {}, style);
+            //now compute centers of mass
+            for(var c in bylabel) {
+                if(bylabel.hasOwnProperty(c)) {
+                    var labels = bylabel[c];
+                    for(var label in labels) {
+                        if(labels.hasOwnProperty(label)) {
+                            var atoms = labels[label];
+                            var sum = new $3Dmol.Vector3(0,0,0);
+                            for(var i = 0; i < atoms.length; i++) {
+                                var a = atoms[i];
+                                sum.x += a.x;
+                                sum.y += a.y;
+                                sum.z += a.z;
                             }
-                        }
+                            sum.divideScalar(atoms.length);
+                            mystyle.position = sum;
+                            viewer.addLabel(label, mystyle);
+                        }                        
                     }
                 }
             }
-        };
-
-        var getModelGroup = function() {
-            return modelGroup;
-        };
-
-        try {
-            if (typeof (callback) === "function")
-                callback(this);
-        } catch (e) {
-            // errors in callback shouldn't invalidate the viewer
-            console.log("error with glviewer callback: " + e);
         }
-    }
 
-    return GLViewer;
+    }
 
-})();
+    GLModel.parseMolData = function(data, format, options) {
+        format = format || "";
 
-$3Dmol['glmolViewer'] = $3Dmol.GLViewer;
-//color scheme mappings
-var $3Dmol = $3Dmol || {};
+        if (!data)
+            return []; //leave an empty model
 
-/** Color mapping gradiens
- * @interface
- * @param {number} min
- * @param {number} max
- */
-$3Dmol.Gradient = function(min, max) {};
-
-/**
- * Map value to hex color
- * @param {number} val
- * @param {number} range
- * @returns {number}
- */
-$3Dmol.Gradient.valueToHex = function(val, range) {};
-$3Dmol.Gradient.jmolID = function() {};
-//return range used for color mapping, null if none set
-$3Dmol.Gradient.range = function() {};
-
-
-
-/**
- * Color scheme red to white to blue, for charges
- * @constructor
- * @implements {$3Dmol.Gradient}
- */
-$3Dmol.Gradient.RWB = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
-    
-        if(val === undefined)
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var middle = (hi+lo)/2;
-        var scale, color;
-        
-        //scale bottom from red to white
-        if(val <= middle) {
-            scale = Math.floor(255*Math.sqrt((val-lo)/(middle-lo)));
-            color = 0xff0000 + 0x100*scale + scale;
-            return color;
+        if(/\.gz$/.test(format)) {
+            //unzip gzipped files
+            format = format.replace(/\.gz$/,'');
+            try {
+                data = pako.inflate(data, {to: 'string'});
+            } catch(err) {
+                console.log(err);
+            }
         }
-        else { //form white to blue
-            scale = Math.floor(255*Math.sqrt((1-(val-middle)/(hi-middle))));
-            color =  0x10000*scale+0x100*scale+0xff;
-            return color;
+
+        if(typeof($3Dmol.Parsers[format]) == "undefined") {
+            //let someone provide a file name and get format from extension
+            format = format.split('.').pop();
+            if(typeof($3Dmol.Parsers[format]) == "undefined") {
+                console.log("Unknown format: "+format);
+                //try to guess correct format from data contents
+                if(data.match(/^@<TRIPOS>MOLECULE/gm)) {
+                    format = "mol2";
+                } else if(data.match(/^HETATM/gm) || data.match(/^ATOM/gm)) {
+                    format = "pdb";
+                } else if(data.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/gm)){
+                    format = "sdf"; //could look at line 3
+                } else {
+                    format = "xyz";
+                }
+                console.log("Best guess: "+format);
+            }
         }
-    };
-    
-    this.jmolID = function() {
-        return "rwb";
+        var parse = $3Dmol.Parsers[format];
+        var parsedAtoms = parse(data, options);
+
+        return parsedAtoms;
     };
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
+
+    // set default style and colors for atoms
+    GLModel.setAtomDefaults = function(atoms, id) {
+        for ( var i = 0; i < atoms.length; i++) {
+            var atom = atoms[i];
+            if (atom) {
+                atom.style = atom.style || defaultAtomStyle;
+                atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
+                atom.model = id;
+                if (atom.clickable)
+                    atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+            }
         }
-        return null;
     };
 
-};
-
+    return GLModel;
+    
+})();
 /**
- * rainbow gradient, but without purple to match jmol
- * @constructor
- * @implements {$3Dmol.Gradient}
+ * A GLShape is a collection of user specified shapes.
+ * 
+ * @constructor $3Dmol.GLShape
+ * @extends {ShapeSpec}
+ * @param {number} sid - Unique identifier
+ * @param {ShapeSpec} stylespec - shape style specification
  */
-$3Dmol.Gradient.ROYGB = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
+$3Dmol.GLShape = (function() {
+
+    // Marching cube, to match with protein surface generation
+    var ISDONE = 2;
+
     
-        if(typeof(val) == "undefined")
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var mid = (lo+hi)/2;
-        var q1 = (lo+mid)/2;
-        var q3 = (mid+hi)/2;
-        
-        var scale, color;
-        
-        if(val < q1) { //scale green up, red up, blue down
-            scale = Math.floor(255*Math.sqrt((val-lo)/(q1-lo)));
-            color = 0xff0000 + 0x100*scale + 0;
-            return color;
-        }
-        else if(val < mid) { //scale red down, green up, blue down
-            scale = Math.floor(255*Math.sqrt((1-(val-q1)/(mid-q1))));
-            color =  0x010000*scale+0xff00+0x0;
-            return color;
-        }
-        else if(val < q3) { //scale blue up, red down, green up
-            scale = Math.floor(255*Math.sqrt((val-mid)/(q3-mid)));
-            color = 0x000000 + 0xff00 + 0x1*scale;
-            return color;
+    var finalizeGeo = function(geo) {
+        //to avoid creating a bunch of geometries, we leave geoGroup untruncated
+        //until render is called, at which point we truncate; 
+        //successive called up updateGeo will return a new geometry
+        var geoGroup = geo.updateGeoGroup(0);
+        if(geoGroup.vertices > 0) {
+            geoGroup.truncateArrayBuffers(true, true);
         }
-        else { //scale green down, blue up, red down
-            scale = Math.floor(255*Math.sqrt((1-(val-q3)/(hi-q3))));
-            color =  0x000000+0x0100*scale+0xff;
-            return color;
-        }        
     };
     
-    this.jmolID = function() {
-        return "roygb";
-    };
+    /**
+     * 
+     * @param {$3Dmol.Geometry}
+     *            geo
+     * @param {$3Dmol.Color |
+     *            colorlike} color
+     */
+    var updateColor = function(geo, color) {
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
+        var C = color || $3Dmol.CC.color(color);
+        geo.colorsNeedUpdate = true;
+        
+        var r,g,b;
+        if(! (color.constructor === Array)) {
+            r = color.r;
+            g = color.g;
+            b = color.b;
         }
-        return null;
-    };
 
-};
 
-/**
- * rainbow gradient with constant saturation, all the way to purple!
- * @constructor
- * @implements {$3Dmol.Gradient}
- */
-$3Dmol.Gradient.Sinebow = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
-    
-        if(typeof(val) == "undefined")
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var scale = (val-lo)/(hi-lo);
-        var h = (5*scale/6.0+0.5);
-        var r = Math.sin(Math.PI*h);
-        r *= r*255;
-        var g = Math.sin(Math.PI*(h+1/3.0));
-        g *= g*255;
-        var b = Math.sin(Math.PI*(h+2/3.0));
-        b *= b*255;
-        
-        return 0x10000*Math.floor(r)+0x100*Math.floor(b)+0x1*Math.floor(g);
-    };
-    
-    this.jmolID = function() {
-        return "sinebow";
-    };
+        for ( var gg in geo.geometryGroups) {
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
+            var geoGroup = geo.geometryGroups[gg];
+            var colorArr = geoGroup.colorArray;
+
+            for (var i = 0, il = geoGroup.vertices; i < il; ++i) {
+            
+                if( color.constructor === Array) {
+                    var c = color[i];
+                    r = c.r;
+                    g = c.g;
+                    b = c.b;
+                }
+
+                colorArr[i * 3] = r;
+                colorArr[i * 3 + 1] = g;
+                colorArr[i * 3 + 2] = b;
+            }
         }
-        return null;
-    };
 
-};
-//Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
+    };
 
-$3Dmol.LabelCount = 0;
 
-/**
- * Renderable labels
- * @constructor $3Dmol.Label
- * @param {string} tag - Label text
- * @param {LabelSpec} parameters Label style and font specifications
- */
-$3Dmol.Label = function(text, parameters) {
+    /**
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {geometryGroup}
+     *            geoGroup
+     * @param {ArrowSpec}
+     *            spec
+     */
+    var drawArrow = function(shape, geo, spec) {
 
-    this.id = $3Dmol.LabelCount++;
-    this.stylespec = parameters || {};
+        var from = spec.start, end = spec.end, radius = spec.radius, radiusRatio = spec.radiusRatio, mid = spec.mid;
 
-    this.canvas = document.createElement('canvas');
-    //todo: implement resizing canvas..
-    this.canvas.width = 134;
-    this.canvas.height = 35;
-    this.context = this.canvas.getContext('2d');
-    this.sprite = new $3Dmol.Sprite();
-    this.text = text;
+        if (!(from && end))
+            return;
 
-};
+        var geoGroup = geo.updateGeoGroup(51);
 
-$3Dmol.Label.prototype = {
+        // vertices
 
-    constructor : $3Dmol.Label,
+        var dir = end.clone();
+        dir.sub(from).multiplyScalar(mid);
+        var to = from.clone().add(dir);
+        var negDir = dir.clone().negate();
 
-    getStyle : function () { return this.stylespec; }, 
-    
-    setContext : function() {
-        // function for drawing rounded rectangles - for Label drawing
-        var roundRect = function(ctx, x, y, w, h, r, drawBorder) {
+        shape.intersectionShape.cylinder.push(new $3Dmol.Cylinder(from.clone(),
+                to.clone(), radius));
+        shape.intersectionShape.sphere.push(new $3Dmol.Sphere(from.clone(),
+                radius));
 
-            ctx.beginPath();
-            ctx.moveTo(x + r, y);
-            ctx.lineTo(x + w - r, y);
-            ctx.quadraticCurveTo(x + w, y, x + w, y + r);
-            ctx.lineTo(x + w, y + h - r);
-            ctx.quadraticCurveTo(x + w, y + h, x + w - r, y + h);
-            ctx.lineTo(x + r, y + h);
-            ctx.quadraticCurveTo(x, y + h, x, y + h - r);
-            ctx.lineTo(x, y + r);
-            ctx.quadraticCurveTo(x, y, x + r, y);
-            ctx.closePath();
-            ctx.fill();
-            if(drawBorder)
-                ctx.stroke();
+        // get orthonormal vector
+        var nvecs = [];
+        nvecs[0] = dir.clone();
+        if (Math.abs(nvecs[0].x) > 0.0001)
+            nvecs[0].y += 1;
+        else
+            nvecs[0].x += 1;
+        nvecs[0].cross(dir);
+        nvecs[0].normalize();
 
-        };
-        
-        //do all the checks to figure out what color is desired
-        var getColor = function(style, stylealpha, init) {
-            var ret = init;
-            if(typeof(style) != 'undefined') {
-                //convet regular colors
-                 if(style instanceof $3Dmol.Color) 
-                     ret = style.scaled();
-                 else //hex or name
-                    ret = $3Dmol.CC.color(style).scaled();                    
-            }
-            if(typeof(stylealpha) != 'undefined') {
-                ret.a = parseFloat(stylealpha);
+        nvecs[0] = nvecs[0];
+        // another orth vector
+        nvecs[4] = nvecs[0].clone();
+        nvecs[4].crossVectors(nvecs[0], dir);
+        nvecs[4].normalize();
+        nvecs[8] = nvecs[0].clone().negate();
+        nvecs[12] = nvecs[4].clone().negate();
+
+        // now quarter positions
+        nvecs[2] = nvecs[0].clone().add(nvecs[4]).normalize();
+        nvecs[6] = nvecs[4].clone().add(nvecs[8]).normalize();
+        nvecs[10] = nvecs[8].clone().add(nvecs[12]).normalize();
+        nvecs[14] = nvecs[12].clone().add(nvecs[0]).normalize();
+
+        // eights
+        nvecs[1] = nvecs[0].clone().add(nvecs[2]).normalize();
+        nvecs[3] = nvecs[2].clone().add(nvecs[4]).normalize();
+        nvecs[5] = nvecs[4].clone().add(nvecs[6]).normalize();
+        nvecs[7] = nvecs[6].clone().add(nvecs[8]).normalize();
+        nvecs[9] = nvecs[8].clone().add(nvecs[10]).normalize();
+        nvecs[11] = nvecs[10].clone().add(nvecs[12]).normalize();
+        nvecs[13] = nvecs[12].clone().add(nvecs[14]).normalize();
+        nvecs[15] = nvecs[14].clone().add(nvecs[0]).normalize();
+
+        var start = geoGroup.vertices;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        var normalArray = geoGroup.normalArray;
+        var lineArray = geoGroup.lineArray;
+
+        var offset, i, n;
+        // add vertices, opposing vertices paired together
+        for (i = 0, n = nvecs.length; i < n; ++i) {
+            offset = 3 * (start + 3 * i);
+            var bottom = nvecs[i].clone().multiplyScalar(radius).add(from);
+            var top = nvecs[i].clone().multiplyScalar(radius).add(to);
+            var conebase = nvecs[i].clone()
+                    .multiplyScalar(radius * radiusRatio).add(to);
+
+            vertexArray[offset] = bottom.x;
+            vertexArray[offset + 1] = bottom.y;
+            vertexArray[offset + 2] = bottom.z;
+
+            vertexArray[offset + 3] = top.x;
+            vertexArray[offset + 4] = top.y;
+            vertexArray[offset + 5] = top.z;
+
+            vertexArray[offset + 6] = conebase.x;
+            vertexArray[offset + 7] = conebase.y;
+            vertexArray[offset + 8] = conebase.z;
+
+            if (i > 0) {
+                var prev_x = vertexArray[offset - 3];
+                var prev_y = vertexArray[offset - 2];
+                var prev_z = vertexArray[offset - 1];
+
+                var c = new $3Dmol.Vector3(prev_x, prev_y, prev_z);
+                var b = end.clone(), b2 = to.clone();
+                var a = new $3Dmol.Vector3(conebase.x, conebase.y, conebase.z);
+
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(a, b,
+                        c));
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(c
+                        .clone(), b2, a.clone()));
             }
-            return ret;
         }
 
-        /**
-         * Label type specification
-         * @typedef LabelSpec
-         * @struct
-         * @prop {string} font - font name, default sans-serif
-         * @prop {number} fontSize - height of text, default 18
-         * @prop {string} fontColor - font color, default white
-         * @prop {number} fontOpacity - font opacity, default 1
-         * @prop {number} borderThickness - line width of border around label, default 0
-         * @prop {string} borderColor - color of border, default backgroundColor
-         * @prop {string} borderOpacity - color of border
-         * @prop {string} backgroundColor - color of background, default black
-         * @prop {string} backgroundOpacity - opacity of background, default 1
-         * @prop {Object} position - x,y,z coordinates for label
-         * @prop {boolean} inFront - always put labels in from of model
-         * @prop {boolean} showBackground - show background rounded rectangle, default true
-         */
-        return function() {
-            
-            var style = this.stylespec;
-            var useScreen =  typeof(style.useScreen) == "undefined" ? false : style.useScreen;
+        geoGroup.vertices += 48;
+        offset = geoGroup.vertices * 3;
+
+        // caps
+        vertexArray[offset] = from.x;
+        vertexArray[offset + 1] = from.y;
+        vertexArray[offset + 2] = from.z;
+
+        vertexArray[offset + 3] = to.x;
+        vertexArray[offset + 4] = to.y;
+        vertexArray[offset + 5] = to.z;
+
+        vertexArray[offset + 6] = end.x;
+        vertexArray[offset + 7] = end.y;
+        vertexArray[offset + 8] = end.z;
+
+        geoGroup.vertices += 3;
+
+        // now faces
+        var face, norm, faceoffset, lineoffset;
+        var t1, t2, t2b, t3, t3b, t4, t1offset, t2offset, t2boffset, t3offset, t3boffset, t4offset;
+        var n1, n2, n3, n4;
+        var n_vertices = 0;
+        var fromi = geoGroup.vertices - 3, toi = geoGroup.vertices - 2, endi = geoGroup.vertices - 1;
+        var fromoffset = fromi * 3, tooffset = toi * 3, endoffset = endi * 3;
+        for (i = 0, n = nvecs.length - 1; i < n; ++i) {
+
+            var ti = start + 3 * i;
+            offset = ti * 3;
+            faceoffset = geoGroup.faceidx;
+            lineoffset = geoGroup.lineidx;
+
+            t1 = ti;
+            t1offset = t1 * 3;
+            t2 = ti + 1;
+            t2offset = t2 * 3;
+            t2b = ti + 2;
+            t2boffset = t2b * 3;
+            t3 = ti + 4;
+            t3offset = t3 * 3;
+            t3b = ti + 5;
+            t3boffset = t3b * 3;
+            t4 = ti + 3;
+            t4offset = t4 * 3;
+
+            // face = [t1, t2, t4], [t2, t3, t4];
+            // face = [t1, t2, t3, t4];
+
+            norm = [ nvecs[i], nvecs[i], nvecs[i + 1], nvecs[i + 1] ];
+
+            n1 = n2 = nvecs[i];
+            n3 = n4 = nvecs[i + 1];
+
+            normalArray[t1offset] = n1.x;
+            normalArray[t2offset] = n2.x;
+            normalArray[t4offset] = n4.x;
+            normalArray[t1offset + 1] = n1.y;
+            normalArray[t2offset + 1] = n2.y;
+            normalArray[t4offset + 1] = n4.y;
+            normalArray[t1offset + 2] = n1.z;
+            normalArray[t2offset + 2] = n2.z;
+            normalArray[t4offset + 2] = n4.z;
+
+            normalArray[t2offset] = n2.x;
+            normalArray[t3offset] = n3.x;
+            normalArray[t4offset] = n4.x;
+            normalArray[t2offset + 1] = n2.y;
+            normalArray[t3offset + 1] = n3.y;
+            normalArray[t4offset + 1] = n4.y;
+            normalArray[t2offset + 2] = n2.z;
+            normalArray[t3offset + 2] = n3.z;
+            normalArray[t4offset + 2] = n4.z;
+
+            normalArray[t2boffset] = n2.x;
+            normalArray[t3boffset] = n3.x;
+            normalArray[t2boffset + 1] = n2.y;
+            normalArray[t3boffset + 1] = n3.y;
+            normalArray[t2boffset + 2] = n2.z;
+            normalArray[t3boffset + 2] = n3.z;
+
+            // sides
+            faceArray[faceoffset] = t1;
+            faceArray[faceoffset + 1] = t2;
+            faceArray[faceoffset + 2] = t4;
+            faceArray[faceoffset + 3] = t2;
+            faceArray[faceoffset + 4] = t3;
+            faceArray[faceoffset + 5] = t4;
+            // caps
+            faceArray[faceoffset + 6] = t1;
+            faceArray[faceoffset + 7] = t4;
+            faceArray[faceoffset + 8] = fromi;
+            faceArray[faceoffset + 9] = t2b;
+            faceArray[faceoffset + 10] = toi;
+            faceArray[faceoffset + 11] = t3b;
+            // arrowhead
+            faceArray[faceoffset + 12] = t2b;
+            faceArray[faceoffset + 13] = endi;
+            faceArray[faceoffset + 14] = t3b;
+
+            // sides
+            lineArray[lineoffset] = t1;
+            lineArray[lineoffset + 1] = t2;
+            lineArray[lineoffset + 2] = t1;
+            lineArray[lineoffset + 3] = t4;
+            // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
+            lineArray[lineoffset + 4] = t3;
+            lineArray[lineoffset + 5] = t4;
+            // caps
+            lineArray[lineoffset + 6] = t1;
+            lineArray[lineoffset + 7] = t4;
+            // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
+            // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+
+            lineArray[lineoffset + 8] = t2b;
+            lineArray[lineoffset + 9] = t2; // toi
+            lineArray[lineoffset + 10] = t2b;
+            lineArray[lineoffset + 11] = t3b;
+            lineArray[lineoffset + 12] = t3;
+            lineArray[lineoffset + 13] = t3b; // toi
+            // arrowhead
+            lineArray[lineoffset + 14] = t2b;
+            lineArray[lineoffset + 15] = endi;
+            lineArray[lineoffset + 16] = t2b;
+            lineArray[lineoffset + 17] = t3b;
+            lineArray[lineoffset + 18] = endi;
+            lineArray[lineoffset + 19] = t3b;
+
+            geoGroup.faceidx += 15;
+            geoGroup.lineidx += 20;
+
+        }
+        // final face
+
+        face = [ start + 45, start + 46, start + 1, start, start + 47,
+                start + 2 ];
+        norm = [ nvecs[15], nvecs[15], nvecs[0], nvecs[0] ];
+
+        faceoffset = geoGroup.faceidx;
+        lineoffset = geoGroup.lineidx;
+
+        t1 = face[0];
+        t1offset = t1 * 3;
+        t2 = face[1];
+        t2offset = t2 * 3;
+        t2b = face[4];
+        t2boffset = t2b * 3;
+        t3 = face[2];
+        t3offset = t3 * 3;
+        t3b = face[5];
+        t3boffset = t3b * 3;
+        t4 = face[3];
+        t4offset = t4 * 3;
+
+        n1 = n2 = nvecs[15];
+        n3 = n4 = nvecs[0];
+
+        normalArray[t1offset] = n1.x;
+        normalArray[t2offset] = n2.x;
+        normalArray[t4offset] = n4.x;
+        normalArray[t1offset + 1] = n1.y;
+        normalArray[t2offset + 1] = n2.y;
+        normalArray[t4offset + 1] = n4.y;
+        normalArray[t1offset + 2] = n1.z;
+        normalArray[t2offset + 2] = n2.z;
+        normalArray[t4offset + 2] = n4.z;
+
+        normalArray[t2offset] = n2.x;
+        normalArray[t3offset] = n3.x;
+        normalArray[t4offset] = n4.x;
+        normalArray[t2offset + 1] = n2.y;
+        normalArray[t3offset + 1] = n3.y;
+        normalArray[t4offset + 1] = n4.y;
+        normalArray[t2offset + 2] = n2.z;
+        normalArray[t3offset + 2] = n3.z;
+        normalArray[t4offset + 2] = n4.z;
+
+        normalArray[t2boffset] = n2.x;
+        normalArray[t3boffset] = n3.x;
+        normalArray[t2boffset + 1] = n2.y;
+        normalArray[t3boffset + 1] = n3.y;
+        normalArray[t2boffset + 2] = n2.z;
+        normalArray[t3boffset + 2] = n3.z;
+
+        // Cap normals
+        dir.normalize();
+        negDir.normalize();
+        normalArray[fromoffset] = negDir.x;
+        normalArray[tooffset] = normalArray[endoffset] = dir.x;
+        normalArray[fromoffset + 1] = negDir.y;
+        normalArray[tooffset + 1] = normalArray[endoffset + 1] = dir.y;
+        normalArray[fromoffset + 2] = negDir.z;
+        normalArray[tooffset + 2] = normalArray[endoffset + 2] = dir.z;
+
+        // Final side
+        faceArray[faceoffset] = t1;
+        faceArray[faceoffset + 1] = t2;
+        faceArray[faceoffset + 2] = t4;
+        faceArray[faceoffset + 3] = t2;
+        faceArray[faceoffset + 4] = t3;
+        faceArray[faceoffset + 5] = t4;
+        // final caps
+        faceArray[faceoffset + 6] = t1;
+        faceArray[faceoffset + 7] = t4;
+        faceArray[faceoffset + 8] = fromi;
+        faceArray[faceoffset + 9] = t2b;
+        faceArray[faceoffset + 10] = toi;
+        faceArray[faceoffset + 11] = t3b;
+        // final arrowhead
+        faceArray[faceoffset + 12] = t2b;
+        faceArray[faceoffset + 13] = endi;
+        faceArray[faceoffset + 14] = t3b;
+
+        // sides
+        lineArray[lineoffset] = t1;
+        lineArray[lineoffset + 1] = t2;
+        lineArray[lineoffset + 2] = t1;
+        lineArray[lineoffset + 3] = t4;
+        // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
+        lineArray[lineoffset + 4] = t3;
+        lineArray[lineoffset + 5] = t4;
+        // caps
+        lineArray[lineoffset + 6] = t1;
+        lineArray[lineoffset + 7] = t4;
+        // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
+        // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+
+        lineArray[lineoffset + 8] = t2b;
+        lineArray[lineoffset + 9] = t2; // toi
+        lineArray[lineoffset + 10] = t2b;
+        lineArray[lineoffset + 11] = t3b;
+        lineArray[lineoffset + 12] = t3;
+        lineArray[lineoffset + 13] = t3b; // toi
+        // arrowhead
+        lineArray[lineoffset + 14] = t2b;
+        lineArray[lineoffset + 15] = endi;
+        lineArray[lineoffset + 16] = t2b;
+        lineArray[lineoffset + 17] = t3b;
+        lineArray[lineoffset + 18] = endi;
+        lineArray[lineoffset + 19] = t3b;
+
+        geoGroup.faceidx += 15;
+        geoGroup.lineidx += 20;
+
+    };
+
+    //helper function for adding an appropriately sized mesh
+    var addCustomGeo = function(shape, geo, mesh, color, clickable) {
+        var geoGroup = geo.addGeoGroup();
+        var vertexArr = mesh.vertexArr, normalArr = mesh.normalArr, 
+            faceArr = mesh.faceArr;
+
+        geoGroup.vertices = vertexArr.length;
+        geoGroup.faceidx = faceArr.length;
+
+        var offset, v, a, b, c, i, il;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        
+        if(! (color.constructor === Array)) {
+            var r = color.r;
+            var g = color.g;
+            var b = color.b;
+        }
+        for (i = 0, il = geoGroup.vertices; i < il; ++i) {
+            offset = i * 3;
+            v = vertexArr[i];
+            vertexArray[offset] = v.x;
+            vertexArray[offset + 1] = v.y;
+            vertexArray[offset + 2] = v.z;
+            
+            if( color.constructor === Array) {
+                var c = color[i];
+                var r = c.r;
+                var g = c.g;
+                var b = c.b;
+            }
+            
+            colorArray[offset] = r;
+            colorArray[offset + 1] = g;
+            colorArray[offset + 2] = b;
+        }
+        
+        if(clickable) {
+            for (i = 0, il = geoGroup.faceidx / 3; i < il; ++i) {
+                offset = i * 3;
+                a = faceArr[offset];
+                b = faceArr[offset + 1];
+                c = faceArr[offset + 2];
+                var vA = new $3Dmol.Vector3(), vB = new $3Dmol.Vector3(), vC = new $3Dmol.Vector3();
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(vA
+                        .copy(vertexArr[a]), vB.copy(vertexArr[b]), vC
+                        .copy(vertexArr[c])));
+            }
+        }
+        
+        if(clickable) {
+            
+            var center = new $3Dmol.Vector3(0,0,0);
+            var cnt = 0;
+            for(var g = 0; g < geo.geometryGroups.length; g++) {
+                center.add(geo.geometryGroups[g].getCentroid());
+                cnt++;
+            }
+            center.divideScalar(cnt);
+            
+            
+            updateBoundingFromPoints(shape.boundingSphere, {centroid: center}, vertexArray);
+        }
+
+        geoGroup.faceArray = new Uint16Array(faceArr);
+
+        geoGroup.truncateArrayBuffers(true, true);
+
+        if (normalArr.length < geoGroup.vertices)
+            geoGroup.setNormals();
+        else {
+
+            var normalArray = geoGroup.normalArray = new Float32Array(geoGroup.vertices * 3);
+            var n;
+            for (i = 0, il = geoGroup.vertices; i < il; ++i) {
+                offset = i * 3;
+                n = normalArr[i];
+                normalArray[offset] = n.x;
+                normalArray[offset + 1] = n.y;
+                normalArray[offset + 2] = n.z;
+            }
+        }
+        
+        geoGroup.setLineIndices();
+        geoGroup.lineidx = geoGroup.lineArray.length;
+    };
+    
+
+    
+    // handles custom shape generation from user supplied arrays
+    // May need to generate normal and/or line indices
+    /**
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {geometry}
+     *            geo
+     * @param {CustomSpec}
+     *            customSpec
+     */
+    var drawCustom = function(shape, geo, customSpec) {
+        var mesh = customSpec;
+        var vertexArr = mesh.vertexArr, normalArr = mesh.normalArr, 
+        faceArr = mesh.faceArr;
+        if (vertexArr.length === 0 || faceArr.length === 0) {
+            console
+                    .warn("Error adding custom shape component: No vertices and/or face indices supplied!");
+        }
+
+        var color = customSpec.color;
+        if(typeof(color) == 'undefined') {
+            color = shape.color;
+        }
+        color =  $3Dmol.CC.color(color);
+
+        //var firstgeo = geo.geometryGroups.length;
+        var splits = $3Dmol.splitMesh(mesh);
+        for(var i = 0, n = splits.length; i < n; i++) {
+            addCustomGeo(shape, geo, splits[i], splits[i].colorArr ? splits[i].colorArr : color, customSpec.clickable);
+        } 
+    }; 
+
+    // Update a bounding sphere's position and radius
+    // from list of centroids and new points
+    /**
+     * @param {$3Dmol.Sphere}
+     *            sphere
+     * @param {Object}
+     *            components
+     * @param {Array}
+     *            points
+     */
+    var updateBoundingFromPoints = function(sphere, components, points) {
+
+        sphere.center.set(0, 0, 0);
+
+        var i, il;
+
+        if (components.length > 0) {
+
+            for (i = 0, il = components.length; i < il; ++i) {
+                var centroid = components[i].centroid;
+                sphere.center.add(centroid);
+            }
+
+            sphere.center.divideScalar(components.length);
+        }
+
+        var maxRadiusSq = sphere.radius * sphere.radius;
+
+        for (i = 0, il = points.length / 3; i < il; i++) {
+            var x = points[i * 3], y = points[i * 3 + 1], z = points[i * 3 + 2];
+            var radiusSq = sphere.center.distanceToSquared({
+                x : x,
+                y : y,
+                z : z
+            });
+            maxRadiusSq = Math.max(maxRadiusSq, radiusSq);
+        }
+
+        sphere.radius = Math.sqrt(maxRadiusSq);
+
+    };
+
+    /**
+     * 
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {ShapeSpec}
+     *            stylespec
+     * @returns {undefined}
+     */
+    var updateFromStyle = function(shape, stylespec) {
+        if(typeof(stylespec.color) != 'undefined') {
+            shape.color = stylespec.color || new $3Dmol.Color();
+            if(! (stylespec.color instanceof $3Dmol.Color))
+                shape.color = $3Dmol.CC.color(stylespec.color);
+        }
+        shape.wireframe = stylespec.wireframe ? true : false;
+        //opacity is the preferred nomenclature, support alpha for backwards compat
+        shape.opacity = stylespec.alpha ? $3Dmol.Math.clamp(stylespec.alpha, 0.0,
+                1.0) : 1.0;
+        if(typeof(stylespec.opacity) != 'undefined') {
+            shape.opacity = $3Dmol.Math.clamp(stylespec.opacity, 0.0, 1.0);
+        }
+        shape.side = (stylespec.side !== undefined) ? stylespec.side
+                : $3Dmol.DoubleSide;
+
+        shape.linewidth = typeof(stylespec.linewidth) == 'undefined' ? 1 : stylespec.linewidth;
+        // Click handling
+        shape.clickable = stylespec.clickable ? true : false;
+        shape.callback = typeof (stylespec.callback) === "function" ? stylespec.callback
+                : null;
+        shape.hidden = stylespec.hidden;
+    };
+
+    /**
+     * Custom renderable shape
+     * 
+     * @constructor $3Dmol.GLShape
+     * 
+     * @param {Object}
+     *            stylespec
+     * @returns {$3Dmol.GLShape}
+     */
+    function GLShape(stylespec) {
+
+        stylespec = stylespec || {};
+        $3Dmol.ShapeIDCount++;
+
+        this.boundingSphere = new $3Dmol.Sphere();
+        /** @type {IntersectionShapes} */
+        this.intersectionShape = {
+            sphere : [],
+            cylinder : [],
+            line : [],
+            triangle : []
+        };
+
+        updateFromStyle(this, stylespec);
+
+        // Keep track of shape components and their centroids
+        var components = [];
+        var shapeObj = null;
+        var renderedShapeObj = null;
+
+        var geo = new $3Dmol.Geometry(true);
+        var linegeo = new $3Dmol.Geometry(true);
+
+        /** Update shape with new style specification
+         * @param {ShapeSpec} newspec
+         * @return {$3Dmol.GLShape}
+         */
+        this.updateStyle = function(newspec) {
+
+            for ( var prop in newspec) {
+                stylespec[prop] = newspec[prop];
+            }
+
+            updateFromStyle(this, stylespec);
+        };
+
+        /**
+         * Creates a custom shape from supplied vertex and face arrays
+         * @function $3Dmol.GLShape#addCustom
+         * @param {CustomSpec} customSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCustom = function(customSpec) {
+
+            customSpec.vertexArr = customSpec.vertexArr || [];
+            customSpec.faceArr = customSpec.faceArr || [];
+            customSpec.normalArr = customSpec.normalArr || [];
+
+            var firstgeo = geo.geometryGroups.length;
+            // will split mesh as needed
+            drawCustom(this, geo, customSpec);
+        };
+
+        /**
+         * Creates a sphere shape
+         * @function $3Dmol.GLShape#addSphere
+         * @param {SphereSpec} sphereSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addSphere = function(sphereSpec) {
+
+            sphereSpec.center = sphereSpec.center || {
+                x : 0,
+                y : 0,
+                z : 0
+            };
+            sphereSpec.radius = sphereSpec.radius ? $3Dmol.Math.clamp(
+                    sphereSpec.radius, 0, Infinity) : 1.5;
+            sphereSpec.color = $3Dmol.CC.color(sphereSpec.color);
+            
+            this.intersectionShape.sphere.push(new $3Dmol.Sphere(
+                    sphereSpec.center, sphereSpec.radius));
+
+            $3Dmol.GLDraw.drawSphere(geo, sphereSpec.center,
+                    sphereSpec.radius, sphereSpec.color);
+
+            components.push({
+                centroid : new $3Dmol.Vector3(sphereSpec.center.x,
+                        sphereSpec.center.y, sphereSpec.center.z)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+        };
+
+        /**
+         * Creates a cylinder shape
+         * @function $3Dmol.GLShape#addCylinder
+         * @param {CylinderSpec} cylinderSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCylinder = function(cylinderSpec) {
+
+            cylinderSpec.start = cylinderSpec.start || {};
+            cylinderSpec.end = cylinderSpec.end || {};
+
+            var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
+                    cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
+            var end = new $3Dmol.Vector3(cylinderSpec.end.x,
+                    cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
+        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+
+            var radius = cylinderSpec.radius || 0.1;
+            var color = $3Dmol.CC.color(cylinderSpec.color);
+            
+            this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(start, end, radius));
+
+            $3Dmol.GLDraw.drawCylinder(geo, start, end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);            
+            
+            var centroid = new $3Dmol.Vector3();
+            components.push({
+                centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+
+        };
+
+        /**
+         * Creates a line shape
+         * @function $3Dmol.GLShape#addLine         
+         * @param {LineSpec} lineSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addLine = function(lineSpec) {
+            lineSpec.start = lineSpec.start || {};
+            lineSpec.end = lineSpec.end || {};
+
+            var start = new $3Dmol.Vector3(lineSpec.start.x || 0,
+                    lineSpec.start.y || 0, lineSpec.start.z || 0);
+            var end = new $3Dmol.Vector3(lineSpec.end.x,
+                    lineSpec.end.y || 0, lineSpec.end.z || 0);            
+            if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+
+            var geoGroup = geo.updateGeoGroup(2);
+
+            //make line from start to end
+            //for consistency with rest of shapes, uses vertices and lines rather
+            //than a separate line geometry
+            var vstart = geoGroup.vertices;
+            var i = vstart*3;
+            var vertexArray = geoGroup.vertexArray;
+            vertexArray[i] = start.x;
+            vertexArray[i+1] = start.y;
+            vertexArray[i+2] = start.z;
+            vertexArray[i+3] = end.x;
+            vertexArray[i+4] = end.y;
+            vertexArray[i+5] = end.z;
+            geoGroup.vertices += 2;
+            
+            var lineArray = geoGroup.lineArray;
+            var li =  geoGroup.lineidx;
+            lineArray[li] = vstart;
+            lineArray[li+1] = vstart+1;
+            geoGroup.lineidx += 2;
+            
+        }
+        /**
+         * Creates an arrow shape
+         * @function $3Dmol.GLShape#addArrow        
+         * @param {ArrowSpec} arrowSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addArrow = function(arrowSpec) {
+
+            arrowSpec.start = arrowSpec.start || {};
+            arrowSpec.end = arrowSpec.end || {};
+
+            arrowSpec.start = new $3Dmol.Vector3(arrowSpec.start.x || 0,
+                    arrowSpec.start.y || 0, arrowSpec.start.z || 0);
+
+            if (arrowSpec.dir instanceof $3Dmol.Vector3
+                    && arrowSpec.length instanceof number) {
+                var end = arrowSpec.dir.clone().multiplyScalar(arrowSpec.length).add(
+                        start);
+                arrowSpec.end = end;
+            }
+
+            else {
+                arrowSpec.end = new $3Dmol.Vector3(arrowSpec.end.x,
+                        arrowSpec.end.y || 0, arrowSpec.end.z || 0);
+            	if(typeof(arrowSpec.end.x) == 'undefined') arrowSpec.end.x = 3; //show something even if undefined
+            }
+
+            arrowSpec.radius = arrowSpec.radius || 0.1;
+
+            arrowSpec.radiusRatio = arrowSpec.radiusRatio || 1.618034;
+            arrowSpec.mid = (0 < arrowSpec.mid && arrowSpec.mid < 1) ? arrowSpec.mid
+                    : 0.618034;
+
+
+            drawArrow(this, geo, arrowSpec);
+
+            var centroid = new $3Dmol.Vector3();
+            components.push({
+                centroid : centroid.addVectors(arrowSpec.start, arrowSpec.end)
+                        .multiplyScalar(0.5)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+
+        };
+        
+        /**
+         * Create isosurface from voluemetric data.
+         * @function $3Dmol.GLShape#addIsosurface         
+         * @param {$3Dmol.VolumeData} data - volumetric input data
+         * @param {IsoSurfaceSpec} isoSpec - volumetric data shape specification
+         */
+        this.addIsosurface = function(data, volSpec) {
+            var isoval = (volSpec.isoval !== undefined && typeof (volSpec.isoval) === "number") ? volSpec.isoval
+                    : 0.0;
+            var voxel = (volSpec.voxel) ? true : false;
+            var smoothness = (volSpec.smoothness === undefined) ? 1 : volSpec.smoothness;
+
+            var nX = data.size.x;
+            var nY = data.size.y;
+            var nZ = data.size.z;
+            var vertnums = new Int16Array(nX * nY * nZ);
+            var vals = data.data;
+            var i, il;
+
+            for (i = 0, il = vertnums.length; i < il; ++i)
+                vertnums[i] = -1;
+
+            //mark locations partitioned by isoval
+            var bitdata = new Uint8Array(nX * nY * nZ);
+
+            for (i = 0, il = vals.length; i < il; ++i) {
+                var val = (isoval >= 0) ? vals[i] - isoval : isoval - vals[i];
+
+                if (val > 0)
+                    bitdata[i] |= ISDONE;
+
+            }
+
+            var verts = [], faces = [];
+
+            $3Dmol.MarchingCube.march(bitdata, verts, faces, {
+                fulltable : true,
+                voxel : voxel,
+                unitCube : data.unit,
+                origin : data.origin,
+                nX : nX,
+                nY : nY,
+                nZ : nZ
+            });
+
+            if (!voxel)
+                $3Dmol.MarchingCube.laplacianSmooth(smoothness, verts, faces);
+
+            drawCustom(this, geo, {
+                vertexArr : verts,
+                faceArr : faces,
+                normalArr : [],
+                clickable : volSpec.clickable
+            });
+           
+            this.updateStyle(volSpec);
+            
+            //computing bounding sphere from vertices
+            var origin = new $3Dmol.Vector3(data.origin.x, data.origin.y, data.origin.z);
+            var size = new $3Dmol.Vector3(data.size.x*data.unit.x, data.size.y*data.unit.y, data.size.z*data.unit.z);            
+
+            var total = new $3Dmol.Vector3(0,0,0);
+            var maxv = origin.clone();
+            var minv = origin.clone().add(size);
+            for(var i = 0; i < verts.length; i++) {
+                total.add(verts[i]);
+                maxv.max(verts[i]);
+                minv.min(verts[i]);
+            }
+            total.divideScalar(verts.length);
+            var len1 = total.distanceTo(minv);
+            var len2 = total.distanceTo(maxv);
+            this.boundingSphere.center = total;
+            this.boundingSphere.radius = Math.max(len1,len2);
+           
+        };
+        
+        /** 
+         * @deprecated Use addIsosurface instead
+         * Creates custom shape from volumetric data 
+         * @param {string} data - Volumetric input data 
+         * @param {string} fmt - Input data format (e.g. 'cube' for cube file format)
+         * @param {IsoSurfaceSpec} isoSpec - Volumetric data shape specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addVolumetricData = function(data, fmt, volSpec) {
+            var data = new $3Dmol.VolumeData(data, fmt);
+            this.addIsosurface(data, volSpec);
+        };
+
+        /**
+         * Initialize webgl objects for rendering
+         * @param {$3Dmol.Object3D} group
+         * 
+         */  
+        this.globj = function(group) {
+
+            if (renderedShapeObj) {
+                group.remove(renderedShapeObj);
+                renderedShapeObj = null;
+            }
+            
+            if(this.hidden)
+                return;
+            finalizeGeo(geo);
+            geo.initTypedArrays();
+
+            if(typeof(this.color) != 'undefined')
+                updateColor(geo, this.color);
+
+            shapeObj = new $3Dmol.Object3D();
+            var material = null;
+            if(this.side == $3Dmol.DoubleSide) {
+                var material = new $3Dmol.MeshDoubleLambertMaterial({
+                    wireframe : this.wireframe,
+                    side : this.side,
+                    transparent : (this.opacity < 1) ? true : false,
+                    opacity : this.opacity,
+                    wireframeLinewidth: this.linewidth
+                });
+            } else {
+                var material = new $3Dmol.MeshLambertMaterial({
+                    wireframe : this.wireframe,
+                    side : this.side,
+                    transparent : (this.opacity < 1) ? true : false,
+                    opacity : this.opacity,
+                    wireframeLinewidth: this.linewidth
+                });
+            }
+            
+            var mesh = new $3Dmol.Mesh(geo, material);
+
+            shapeObj.add(mesh);
+            
+            var lineMaterial = new $3Dmol.LineBasicMaterial({
+                linewidth : this.linewidth,
+                color: this.color
+            });
+            var line = new $3Dmol.Line(linegeo, lineMaterial,
+                    $3Dmol.LinePieces);
+            shapeObj.add(line);
+
+            renderedShapeObj = shapeObj.clone();
+            group.add(renderedShapeObj);
+
+        };
+
+        this.removegl = function(group) {
+            if (renderedShapeObj) {
+                // dispose of geos and materials
+                if (renderedShapeObj.geometry !== undefined)
+                    renderedShapeObj.geometry.dispose();
+                if (renderedShapeObj.material !== undefined)
+                    renderedShapeObj.material.dispose();
+                group.remove(renderedShapeObj);
+                renderedShapeObj = null;
+            }
+            shapeObj = null;
+        };
+
+    };
+
+    Object.defineProperty(GLShape.prototype, "position", {
+
+        get : function() {
+            return this.boundingSphere.center;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "x", {
+
+        get : function() {
+            return this.boundingSphere.center.x;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "y", {
+
+        get : function() {
+            return this.boundingSphere.center.y;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "z", {
+
+        get : function() {
+            return this.boundingSphere.center.z;
+        }
+
+    });
+
+    return GLShape;
+
+}());
+
+$3Dmol.ShapeIDCount = 0;
+
+
+$3Dmol.splitMesh = function(mesh) {
+	    var MAXVERT = 64000; //webgl only supports 2^16 elements, leave a little breathing room (require at least 2)
+    //peel off 64k vertices rsvh into their own mesh
+    //duplicating vertices and normals as necessary to preserve faces and lines
+	
+        if(mesh.vertexArr.length < MAXVERT) return [mesh]; //typical case
+        
+        var nverts = mesh.vertexArr.length;
+        var slices = [{vertexArr: [], normalArr: [], faceArr: []}];
+        if(mesh.colorArr) slices.colorArr = [];
+        var vertSlice = []; //indexed by original vertex to get current slice
+        var vertIndex =[]; //indexed by original vertex to get index within slice
+        var currentSlice = 0;
+        
+        //for each face, make sure all three vertices (or copies) are in the same slice
+        var faces = mesh.faceArr;
+        var vs = [0,0,0];
+        for(var i = 0, nf = faces.length; i < nf; i += 3) {
+            var slice = slices[currentSlice];
+            for(var j = 0; j < 3; j++) {
+                //process each vertex to make sure it is assigned a slice
+                //all vertices of a face must belong to the same slice
+                var v = faces[i+j];
+                if(vertSlice[v] !== currentSlice) { //true if undefined
+                    vertSlice[v] = currentSlice;
+                    vertIndex[v] = slice.vertexArr.length;
+                    slice.vertexArr.push(mesh.vertexArr[v]);
+                    if(mesh.normalArr && mesh.normalArr[v]) slice.normalArr.push(mesh.normalArr[v]);
+                    if(mesh.colorArr && mesh.colorArr[v]) slice.colorArr.push(mesh.colorArr[v]);
+                }
+                slice.faceArr.push(vertIndex[v]);
+            }
+            
+            if(slice.vertexArr.length >= MAXVERT) {
+                //new slice
+                slices.push({vertexArr: [], normalArr: [], faceArr: []});
+                if(mesh.colorArr) slices.colorArr = [];
+                currentSlice++;
+            }
+        }
+        return slices;
+    }
+//a molecular viewer based on GLMol
+
+
+
+/**
+ * WebGL-based 3Dmol.js viewer
+ * Note: The preferred method of instantiating a GLViewer is through {@link $3Dmol.createViewer} 
+ * 
+ * @constructor 
+ * @param {Object} element HTML element within which to create viewer
+ * @param {function} callback - Callback function to be immediately executed on this viewer
+ * @param {Object} defaultcolors - Object defining default atom colors as atom => color property value pairs for all models within this viewer
+ */
+$3Dmol.GLViewer = (function() {
+    // private class variables
+    var numWorkers = 4; // number of threads for surface generation
+    var maxVolume = 64000; // how much to break up surface calculations
+
+    // private class helper functions
+
+    function GLViewer(element, config) { 
+        // set variables
+        config = config || {};
+        var callback = config.callback;
+        var defaultcolors = config.defaultcolors;    	
+        if(!defaultcolors)
+            defaultcolors = $3Dmol.elementColors.defaultColors;
+        var nomouse = config.nomouse;
+        var bgColor = 0;
+
+        if(typeof(config.backgroundColor) != undefined) {
+            bgColor = $3Dmol.CC.color(config.backgroundColor).getHex();
+        }
+
+        var camerax = 0;
+        if(typeof(config.camerax) != undefined) {
+            camerax = parseFloat(config.camerax);
+        }
+        var _viewer = this;
+        var container = element;
+        var id = container.id;
+        var glDOM = null;
+
+        var models = []; // atomistic molecular models
+        var surfaces = {};
+        var shapes = []; // Generic shapes
+        var labels = [];
+        var clickables = []; //things you can click on
+        
+        var WIDTH = container.width();
+        var HEIGHT = container.height();
+
+        // set dimensions
+        // $(container).width(WIDTH);
+        // $(container).height(HEIGHT);
+
+        var ASPECT = WIDTH / HEIGHT;
+        var NEAR = 1, FAR = 800;
+        var CAMERA_Z = 150;
+        var fov = 20;
+
+        var linkedViewers = [];
+
+        var renderer = new $3Dmol.Renderer({
+            antialias : true,
+            preserveDrawingBuffer: true, //so we can export images
+            premultipliedAlpha : false/* more traditional compositing with background */
+        });
+
+        renderer.domElement.style.width = "100%";
+        renderer.domElement.style.height = "100%";
+        renderer.domElement.style.padding = "0";
+        renderer.domElement.style.position = "absolute"; //TODO: get rid of this
+        renderer.domElement.style.top = "0px";
+        renderer.domElement.style.left = "0px";
+        renderer.domElement.style.zIndex = "0";
+
+        var camera = new $3Dmol.Camera(fov, ASPECT, NEAR, FAR);
+        camera.position = new $3Dmol.Vector3(camerax, 0, CAMERA_Z);
+        var lookingAt = new $3Dmol.Vector3();
+        camera.lookAt(lookingAt);
+
+        var raycaster = new $3Dmol.Raycaster(new $3Dmol.Vector3(0, 0, 0),
+                new $3Dmol.Vector3(0, 0, 0));
+        var projector = new $3Dmol.Projector();
+        var mouseVector = new $3Dmol.Vector3(0, 0, 0);
+
+        var scene = null;
+        var rotationGroup = null; // which contains modelGroup
+        var modelGroup = null;
+
+        var fogStart = 0.4;
+        var slabNear = -50; // relative to the center of rotationGroup
+        var slabFar = 50;
+
+        // UI variables
+        var cq = new $3Dmol.Quaternion(0, 0, 0, 1);
+        var dq = new $3Dmol.Quaternion(0, 0, 0, 1);
+        var animated = false;
+        var isDragging = false;
+        var mouseStartX = 0;
+        var mouseStartY = 0;
+        var touchDistanceStart = 0;
+        var currentModelPos = 0;
+        var cz = 0;
+        var cslabNear = 0;
+        var cslabFar = 0;      
+        
+        var nextSurfID = function() {
+            //compute the next highest surface id directly from surfaces
+            //this is necessary to support linking of model data
+            var max = 0;
+            for (i in surfaces) { // this is an object with possible holes
+                if(!surfaces.hasOwnProperty(i)) continue;
+                if(i > max) max = i;
+            }
+            return max+1;
+        };
+
+        var setSlabAndFog = function() {
+            var center = camera.position.z - rotationGroup.position.z;
+            if (center < 1)
+                center = 1;
+            camera.near = center + slabNear;
+            if (camera.near < 1)
+                camera.near = 1;
+            camera.far = center + slabFar;
+            if (camera.near + 1 > camera.far)
+                camera.far = camera.near + 1;
+            if (camera instanceof $3Dmol.Camera) {
+                camera.fov = fov;
+            } else {
+                camera.right = center * Math.tan(Math.PI / 180 * fov);
+                camera.left = -camera.right;
+                camera.top = camera.right / ASPECT;
+                camera.bottom = -camera.top;
+            }
+            camera.updateProjectionMatrix();
+            scene.fog.near = camera.near + fogStart
+                    * (camera.far - camera.near);
+            // if (scene.fog.near > center) scene.fog.near = center;
+            scene.fog.far = camera.far;
+        };
+
+        // display scene
+        //if nolink is set/true, don't propagate changes to linked viewers
+        var show = function(nolink) {
+            if (!scene)
+                return;
+
+            // var time = new Date();
+            setSlabAndFog();
+            renderer.render(scene, camera);
+            // console.log("rendered in " + (+new Date() - time) + "ms");
+            
+            if(!nolink && linkedViewers.length > 0) {
+                var view = _viewer.getView();
+                for(var i = 0; i < linkedViewers.length; i++) {
+                    var other = linkedViewers[i];
+                    other.setView(view, true);
+                }
+            }
+        };
+
+        var initializeScene = function() {
+
+            scene = new $3Dmol.Scene();
+            scene.fog = new $3Dmol.Fog(bgColor, 100, 200);
+
+            modelGroup = new $3Dmol.Object3D();
+            rotationGroup = new $3Dmol.Object3D();
+            rotationGroup.useQuaternion = true;
+            rotationGroup.quaternion = new $3Dmol.Quaternion(0, 0, 0, 1);
+            rotationGroup.add(modelGroup);
+
+            scene.add(rotationGroup);
+
+            // setup lights
+            var directionalLight = new $3Dmol.Light(0xFFFFFF);
+            directionalLight.position = new $3Dmol.Vector3(0.2, 0.2, 1)
+                    .normalize();
+            directionalLight.intensity = 1.0;
+            scene.add(directionalLight);
+        };
+
+        initializeScene();
+
+        renderer.setClearColorHex(bgColor, 1.0);
+        scene.fog.color = $3Dmol.CC.color(bgColor);
+
+        var clickedAtom = null;
+
+        // enable mouse support
+
+        //regenerate the list of clickables
+        var updateClickables = function() {
+            clickables.splice(0,clickables.length);
+            var i, il;
+
+            for (i = 0, il = models.length; i < il; i++) {
+                var model = models[i];
+                if(model) {
+                    var atoms = model.selectedAtoms({
+                        clickable : true
+                    });
+                    Array.prototype.push.apply(clickables, atoms); //add atoms into clickables
+                }
+            }
+
+            for (i = 0, il = shapes.length; i < il; i++) {
+
+                var shape = shapes[i];
+                if (shape && shape.clickable) {
+                    clickables.push(shape);
+                }
+            }
+        };
+        
+        // Checks for selection intersects on mousedown
+        var handleClickSelection = function(mouseX, mouseY, event) {
+            if(clickables.length == 0) return;
+            var mouse = {
+                x : mouseX,
+                y : mouseY,
+                z : -1.0
+            };
+            mouseVector.set(mouse.x, mouse.y, mouse.z);
+            projector.unprojectVector(mouseVector, camera);
+            mouseVector.sub(camera.position).normalize();
+
+            raycaster.set(camera.position, mouseVector);
+
+            var intersects = [];
+
+            intersects = raycaster.intersectObjects(modelGroup, clickables);
+            if (intersects.length) {
+                var selected = intersects[0].clickable;
+                if (selected.callback !== undefined
+                        && typeof (selected.callback) === "function") {
+                    selected.callback(selected, _viewer, event, container);
+                }
+            }
+        };
+
+        var calcTouchDistance = function(ev) { // distance between first two
+                                                // fingers
+            var xdiff = ev.originalEvent.targetTouches[0].pageX
+                    - ev.originalEvent.targetTouches[1].pageX;
+            var ydiff = ev.originalEvent.targetTouches[0].pageY
+                    - ev.originalEvent.targetTouches[1].pageY;
+            return Math.sqrt(xdiff * xdiff + ydiff * ydiff);
+        }
+        
+        //check targetTouches as well
+        var getXY = function(ev) {
+            var x = ev.pageX, y = ev.pageY;
+            if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches[0]) {
+                x = ev.originalEvent.targetTouches[0].pageX;
+                y = ev.originalEvent.targetTouches[0].pageY;
+            }
+            else if (ev.originalEvent.changedTouches
+                    && ev.originalEvent.changedTouches[0]) {
+                x = ev.originalEvent.changedTouches[0].pageX;
+                y = ev.originalEvent.changedTouches[0].pageY;
+            }            
+            return [x,y];
+        };
+
+        //for a given screen (x,y) displacement return model displacement 
+        var screenXY2model = function(x,y) {
+            var dx = x/WIDTH;
+            var dy = y/HEIGHT;
+            var zpos = rotationGroup.position.z; 
+            var q = rotationGroup.quaternion;                        
+            var t = new $3Dmol.Vector3(0,0,zpos);
+            projector.projectVector(t, camera);
+            t.x += dx*2;
+            t.y -= dy*2;
+            projector.unprojectVector(t, camera);
+            t.z = 0;                            
+            t.applyQuaternion(q);
+            return t;
+        }
+
+        // this event is bound to the body element, not the container,
+        // so no need to put it inside initContainer()
+        $('body').bind('mouseup touchend', function(ev) {
+            // handle selection
+            if(isDragging && scene) { //saw mousedown, haven't moved
+                var xy = getXY(ev);
+                var x = xy[0];
+                var y = xy[1];
+                if(x == mouseStartX && y == mouseStartY) {
+                    var offset = $('canvas',container).offset();
+                    var mouseX = ((x - offset.left) / WIDTH) * 2 - 1;
+                    var mouseY = -((y - offset.top) / HEIGHT) * 2 + 1;
+
+                    handleClickSelection(mouseX, mouseY, ev, container);
+                }
+            }
+            
+            isDragging = false;
+
+        });
+        
+        var _handleMouseDown = this._handleMouseDown = function(ev) {
+            ev.preventDefault();
+            if (!scene)
+                return;
+            var xy = getXY(ev);
+            var x = xy[0];
+            var y = xy[1];
+            
+            if (x === undefined)
+                return;
+            isDragging = true;
+            clickedAtom = null;
+            mouseButton = ev.which;
+            mouseStartX = x;
+            mouseStartY = y;
+            touchDistanceStart = 0;
+            if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 2) {
+                touchDistanceStart = calcTouchDistance(ev);
+            }
+            cq = rotationGroup.quaternion;
+            cz = rotationGroup.position.z;
+            currentModelPos = modelGroup.position.clone();
+            cslabNear = slabNear;
+            cslabFar = slabFar;
+
+        };
+        
+        var _handleMouseScroll  = this._handleMouseScroll = function(ev) { // Zoom
+            ev.preventDefault();
+            if (!scene)
+                return;
+            var scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
+            if (ev.originalEvent.detail) { // Webkit
+                rotationGroup.position.z += scaleFactor
+                        * ev.originalEvent.detail / 10;
+            } else if (ev.originalEvent.wheelDelta) { // Firefox
+                rotationGroup.position.z -= scaleFactor
+                        * ev.originalEvent.wheelDelta / 400;
+            }
+            if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+
+            show();
+        };
+        
+        var _handleMouseMove = this._handleMouseMove = function(ev) { // touchmove
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ev.preventDefault();
+            if (!scene)
+                return;
+            if (!isDragging)
+                return;
+            var mode = 0;
+
+            var xy = getXY(ev);
+            var x = xy[0];
+            var y = xy[1];
+            if (x === undefined)
+                return;
+            var dx = (x - mouseStartX) / WIDTH;
+            var dy = (y - mouseStartY) / HEIGHT;
+            // check for pinch
+            if (touchDistanceStart != 0
+                    && ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 2) {
+                var newdist = calcTouchDistance(ev);
+                // change to zoom
+                mode = 2;
+                dy = (newdist - touchDistanceStart) * 2
+                        / (WIDTH + HEIGHT);
+            } else if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 3) {
+                // translate
+                mode = 1;
+            }
+
+            var r = Math.sqrt(dx * dx + dy * dy);
+            var scaleFactor;
+            if (mode == 3
+                    || (mouseButton == 3 && ev.ctrlKey)) { // Slab
+                slabNear = cslabNear + dx * 100;
+                slabFar = cslabFar + dy * 100;
+            } else if (mode == 2 || mouseButton == 3
+                    || ev.shiftKey) { // Zoom
+                scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
+                if (scaleFactor < 80)
+                    scaleFactor = 80;
+                rotationGroup.position.z = cz + dy * scaleFactor;
+                if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+            } else if (mode == 1 || mouseButton == 2
+                    || ev.ctrlKey) { // Translate
+                var t = screenXY2model(x-mouseStartX, y-mouseStartY);
+                modelGroup.position.addVectors(currentModelPos,t);
+                
+            } else if ((mode === 0 || mouseButton == 1)
+                    && r !== 0) { // Rotate
+                var rs = Math.sin(r * Math.PI) / r;
+                dq.x = Math.cos(r * Math.PI);
+                dq.y = 0;
+                dq.z = rs * dx;
+                dq.w = -rs * dy;
+                rotationGroup.quaternion = new $3Dmol.Quaternion(
+                        1, 0, 0, 0);
+                rotationGroup.quaternion.multiply(dq);
+                rotationGroup.quaternion.multiply(cq);
+            }
+            show();
+        };
+        
+        var initContainer = function(element) {
+            container = element;
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ASPECT = WIDTH / HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            container.append(renderer.domElement);
+            glDOM = $(renderer.domElement);
+
+            if (!nomouse) {
+                // user can request that the mouse handlers not be installed
+                glDOM.bind('mousedown touchstart', _handleMouseDown);
+                glDOM.bind('DOMMouseScroll mousewheel', _handleMouseScroll);
+                glDOM.bind('mousemove touchmove', _handleMouseMove);
+                
+                glDOM.bind("contextmenu", function(ev) {
+                    ev.preventDefault();
+                });
+            }
+        };
+        initContainer(container);
+
+        // public methods
+        /**
+         * Change the viewer's container element 
+         * Also useful if the original container element was removed from the DOM.
+         * 
+         * @function $3Dmol.GLViewer#resetContainer
+         *
+         * @param {Object | string} element
+         *            Either HTML element or string identifier. Defaults to the element used to initialize the viewer.
+
+         * @example
+         * // Assume there exist HTML divs with ids "gldiv", "gldiv2"
+         * var element = $("#gldiv"), element2 = $("#gldiv2");
+         * // Create GLViewer within 'gldiv'
+         * var myviewer = $3Dmol.createViewer(element);
+         * // Move the canvas to the other div
+         * myviewer.setContainer(element2)
+         *
+         * @example
+         * // Assume there exists an HTML div with id "gldiv"
+         * var element = $("#gldiv");
+         * // Create GLViewer within 'gldiv'
+         * var myviewer = $3Dmol.createViewer(element);
+         * // Remove the element from the DOM, and add a new element
+         * element.remove()
+         * $('body').prepend("<div id='newdiv'></div>")
+         * // Show the canvas in the new element
+         * myviewer.setContainer('newdiv')
+         */
+        this.setContainer = function(element) {
+            if($.type(element) === "string")
+                element = $("#"+element);
+            if(!element) {
+                element = container
+            };
+            initContainer(element);
+            return this;
+        };
+        
+        /**
+         * Set the background color (default white)
+         * 
+         * @function $3Dmol.GLViewer#setBackgroundColor
+         * @param {number}
+         *            hex Hexcode specified background color, or standard color spec
+         * @param {number}
+         *            a Alpha level (default 1.0)
+         * 
+         * @example
+         * 
+         * //Set 'myviewer' background color to white
+         * myviewer.setBackgroundColor(0xffffff)
+         * 
+         */
+        this.setBackgroundColor = function(hex, a) {
+            if(typeof(a) == "undefined") {
+                a = 1.0;
+            }
+            else if(a < 0 || a > 1.0) {
+                a = 1.0;
+            }
+            var c = $3Dmol.CC.color(hex);
+            scene.fog.color = c;
+            bgColor = c.getHex();
+            renderer.setClearColorHex(c.getHex(), a);
+            show();
+            return this;
+        };
+        
+        /**
+         * Enable outline 
+         * @function $eDmol.GLViewer#outline
+         * 
+         * @example
+         * myviewer.outline()
+         * 
+         */
+         this.setViewStyle = function(parameters) {
+            if (parameters["style"] === "outline") {
+                var params = {};
+                if(parameters.color) params.color =  $3Dmol.CC.color(parameters.color);
+                if(parameters.width) params.width = parameters.width;
+                renderer.enableOutline(params);
+            } else {
+                renderer.disableOutline();
+            }
+            return this;
+        }
+         
+        if(config.style) { //enable setting style in constructor
+             this.setViewStyle(config.style);
+        }
+
+        /**
+         * Set viewer width
+         * 
+         * @function $3Dmol.GLViewer#setWidth
+         * @param {number}
+         *            w Width in pixels
+         */
+        this.setWidth = function(w) {
+            WIDTH = w || WIDTH;
+            renderer.setSize(WIDTH, HEIGHT);
+            return this;
+        };
+
+        /**
+         * Set viewer height
+         * 
+         * @function $3Dmol.GLViewer#setHeight
+         * @param {number}
+         *            h Height in pixels
+         */
+        this.setHeight = function(h) {
+            HEIGHT = h || HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            return this;
+        };
+
+        /**
+         * Resize viewer according to containing HTML element's dimensions
+         * 
+         * @function $3Dmol.GLViewer#resize
+         */
+        this.resize = function() {
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ASPECT = WIDTH / HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            camera.aspect = ASPECT;
+            camera.updateProjectionMatrix();
+            show();
+            return this;
+        };
+
+        $(window).resize(this.resize);
+
+        /**
+         * Return specified model
+         * 
+         * @function $3Dmol.GLViewer#getModel
+         * @param {number}
+         *            [id=last model id] - Retrieve model with specified id
+         * @default Returns last model added to viewer
+         * @return {GLModel}
+         * 
+         * @example // Retrieve reference to first GLModel added var m =
+         *          glviewer.getModel(0);
+         */
+        this.getModel = function(id) {
+            id = id || models.length - 1;
+            return models[id];
+        };
+
+        /**
+         * Rotate scene by angle degrees around axis
+         * 
+         * @function $3Dmol.GLViewer#rotate
+         * @param {number}
+         *            [angle] - Angle, in degrees, to rotate by.
+         * @param {string}
+         *            [angle] - Axis ("x", "y", or "z") to rotate around.
+         *            Default "y"
+         * 
+         */
+        this.rotate = function(angle, axis) {
+            if (typeof (axis) === "undefined") {
+                axis = "y";
+            }
+            var i = 0, j = 0, k = 0;
+            var rangle = Math.PI * angle / 180.0;
+            var s = Math.sin(rangle / 2.0);
+            var c = Math.cos(rangle / 2.0);
+            if (axis == "x")
+                i = s;
+            if (axis == "y")
+                j = s;
+            if (axis == "z")
+                k = s;
+
+            var q = new $3Dmol.Quaternion(i, j, k, c).normalize();
+            rotationGroup.quaternion.multiply(q);
+            show();
+            return this;
+        };
+
+        /** Returns an array representing the current viewpoint.
+         * Translation, zoom, and rotation quaternion. 
+         * @function $3Dmol.GLViewer#getView
+         * @returns {Array.<number>} arg
+         *  */
+        this.getView = function() {
+            if (!modelGroup)
+                return [ 0, 0, 0, 0, 0, 0, 0, 1 ];
+            var pos = modelGroup.position;
+            var q = rotationGroup.quaternion;
+            return [ pos.x, pos.y, pos.z, rotationGroup.position.z, q.x, q.y,
+                    q.z, q.w ];
+        };
+
+        /** Sets the view to the specified translation, zoom, and rotation.
+         * 
+         * @function $3Dmol.GLViewer#setView
+         * @param {Array.<number>} arg Array formatted identically to the return value of getView */
+        this.setView = function(arg, nolink) {
+
+            if (arg === undefined
+                    || !(arg instanceof Array || arg.length !== 8))
+                return this;
+
+            if (!modelGroup || !rotationGroup)
+                return this;
+            modelGroup.position.x = arg[0];
+            modelGroup.position.y = arg[1];
+            modelGroup.position.z = arg[2];
+            rotationGroup.position.z = arg[3];
+            rotationGroup.quaternion.x = arg[4];
+            rotationGroup.quaternion.y = arg[5];
+            rotationGroup.quaternion.z = arg[6];
+            rotationGroup.quaternion.w = arg[7];
+            if(typeof(arg[8]) != "undefined") {
+                rotationGroup.position.x = arg[8];
+                rotationGroup.position.y = arg[9];
+            }
+            show(nolink);
+            return this;
+        };
+
+        // apply styles, models, etc in viewer
+        /**
+         * Render current state of viewer, after 
+         * adding/removing models, applying styles, etc.
+         * 
+         * @function $3Dmol.GLViewer#render
+         */
+        this.render = function() {
+
+            updateClickables(); //must render for clickable styles to take effect
+            var time1 = new Date();
+            var view = this.getView();
+            
+            var i, n;
+            var exts = renderer.supportedExtensions();
+            for (i = 0; i < models.length; i++) {
+                if (models[i]) {
+                    models[i].globj(modelGroup, exts);
+                }
+            }
+
+            for (i = 0; i < shapes.length; i++) {
+                if (shapes[i]) {
+                    shapes[i].globj(modelGroup, exts);
+                }
+            }
+            
+            for (i in surfaces) { // this is an object with possible holes
+                if(!surfaces.hasOwnProperty(i)) continue;
+                var surfArr = surfaces[i];
+                for (n = 0; n < surfArr.length; n++) {
+                    if (surfArr.hasOwnProperty(n)) {
+                        var geo = surfArr[n].geo;
+                        // async surface generation can cause
+                        // the geometry to be webgl initialized before it is fully
+                        // formed; force various recalculations until full surface
+                        // is
+                        // available
+                        if (!surfArr[n].finished) {
+                            geo.verticesNeedUpdate = true;
+                            geo.elementsNeedUpdate = true;
+                            geo.normalsNeedUpdate = true;
+                            geo.colorsNeedUpdate = true;
+                            geo.buffersNeedUpdate = true;
+                            geo.boundingSphere = null;
+
+                            if (surfArr[n].done)
+                                surfArr[n].finished = true;
+
+                            // remove partially rendered surface
+                            if (surfArr[n].lastGL)
+                                modelGroup.remove(surfArr[n].lastGL);
+
+                            // create new surface
+                            var smesh = null;
+
+                            if(surfArr[n].mat instanceof $3Dmol.LineBasicMaterial) {
+                                //special case line meshes
+                                smesh = new $3Dmol.Line(geo, surfArr[n].mat);
+                            }
+                            else {
+                                smesh = new $3Dmol.Mesh(geo, surfArr[n].mat);
+                            }
+                            if(surfArr[n].mat.transparent && surfArr[n].mat.opacity == 0) {
+                                //don't bother with hidden surfaces
+                                smesh.visible = false;
+                            } else {
+                                smesh.visible = true;
+                            }
+                            if (surfArr[n].symmetries.length > 1 || 
+                            (surfArr[n].symmetries.length == 1 && 
+                            !(surfArr[n].symmetries[n].isIdentity()))) {
+                                var j;
+                                var tmeshes = new $3Dmol.Object3D(); //transformed meshes
+                                for (j = 0; j < surfArr[n].symmetries.length; j++) {
+                                    var tmesh = smesh.clone();
+                                    tmesh.matrix = surfArr[n].symmetries[j];
+                                    tmesh.matrixAutoUpdate = false;
+                                    tmeshes.add(tmesh);
+                                }
+                                surfArr[n].lastGL = tmeshes;
+                                modelGroup.add(tmeshes);
+                            }
+                            else {
+                                surfArr[n].lastGL = smesh;
+                                modelGroup.add(smesh);
+                            }
+                        } // else final surface already there
+                    }
+                }
+            }
+            
+            this.setView(view); // Calls show() => renderer render
+            var time2 = new Date();
+            //console.log("render time: " + (time2 - time1));
+            return this;
+        };
+
+        /**
+         * 
+         * @param {AtomSelectionSpec}
+         *            sel
+         * @return {AtomSpec[]}
+         */
+        function getAtomsFromSel(sel) {
+            var atoms = [];
+            if (typeof (sel) === "undefined")
+                sel = {};
+
+            var ms = [];
+            var i;
+
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+
+            for (i = 0; i < ms.length; i++) {
+                atoms = atoms.concat(ms[i].selectedAtoms(sel));
+            }
+
+            return atoms;
+        }
+
+        /**
+         * 
+         * @param {AtomSpec}
+         *            atom
+         * @param {AtomSpec}
+         *            sel
+         * @return {boolean}
+         */
+        function atomIsSelected(atom, sel) {
+            if (typeof (sel) === "undefined")
+                sel = {};
+
+            var ms = [];
+            var i;
+
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+
+            for (i = 0; i < ms.length; i++) {
+                if (ms[i].atomIsSelected(atom, sel))
+                    return true;
+            }
+
+            return false;
+        }
+
+        
+        /** return list of atoms selected by sel
+         * 
+         * @function $3Dmol.GLViewer#selectedAtoms
+         * @param {AtomSelectionSpec} sel
+         * @return {Array.<Object>}
+         */
+        this.selectedAtoms = function(sel) {
+            return getAtomsFromSel(sel);
+        };
+        
+        /**
+         * Return pdb output of selected atoms (if atoms from pdb input)
+         * 
+         * @function $3Dmol.GLViewer#pdbData  
+         * @param {Object=} [sel] - Selection specification specifying model and atom properties to select.  Default: all atoms in viewer
+         * @return {string} PDB string of selected atoms
+         */
+        this.pdbData = function(sel) {
+            var atoms = getAtomsFromSel(sel);
+            var ret = "";
+            for (var i = 0, n = atoms.length; i < n; ++i) {
+                ret += atoms[i].pdbline + "\n";
+            }
+            return ret;
+        };
+
+        /**
+         * Zoom current view by a constant factor
+         * 
+         * @function $3Dmol.GLViewer#zoom
+         * @param {number}
+         *            [factor] - Magnification factor. Values greater than 1
+         *            will zoom in, less than one will zoom out. Default 2.
+         * 
+         */
+        this.zoom = function(factor) {
+            var factor = factor || 2;
+            var scale = (CAMERA_Z - rotationGroup.position.z) / factor;
+            rotationGroup.position.z = CAMERA_Z - scale;
+            show();
+            return this;
+        };
+        
+        /**
+         * Translate current view by x,y screen coordinates
+         * This pans the camera rather than translating the model.
+         * 
+         * @function $3Dmol.GLViewer#translate
+         * @param {number} x
+         * @param {number} y
+         * 
+         */
+        this.translate = function(x, y) {
+            
+            var dx = x/WIDTH;
+            var dy = y/HEIGHT;
+            var v = new $3Dmol.Vector3(0,0,-CAMERA_Z);
+
+            projector.projectVector(v, camera);
+            v.x -= dx;
+            v.y -= dy;
+            projector.unprojectVector(v, camera);
+            v.z = 0;            
+            lookingAt.add(v);
+            camera.lookAt(lookingAt);
+            show();
+            return this;
+        };
+        
+
+        /**
+         * Zoom to center of atom selection
+         * 
+         * @function $3Dmol.GLViewer#zoomTo
+         * @param {Object}
+         *            [sel] - Selection specification specifying model and atom
+         *            properties to select. Default: all atoms in viewer
+         * @example // Assuming we have created a model of a protein with
+         *          multiple chains (e.g. from a PDB file), focus on atoms in
+         *          chain B glviewer.zoomTo({chain: 'B'});
+         *  // Focus on centroid of all atoms of all models in this
+         * viewer glviewer.zoomTo(); // (equivalent to glviewer.zoomTo({}) )
+         */
+        this.zoomTo = function(sel) {
+            var allatoms, alltmp;
+            sel = sel || {};
+            var atoms = getAtomsFromSel(sel);
+            var tmp = $3Dmol.getExtent(atoms);
+
+            if($.isEmptyObject(sel)) {
+                //include shapes when zooming to full scene
+                //TODO: figure out a good way to specify shapes as part of a selection
+                $.each(shapes, function(i, shape) {
+                	if(shape && shape.boundingSphere && shape.boundingSphere.center)
+                	    var c = shape.boundingSphere.center;
+                	    var r = shape.boundingSphere.radius;
+                	    if(r > 0) {
+                	        //make sure full shape is visible
+                            atoms.push(new $3Dmol.Vector3(c.x+r,c.y,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x-r,c.y,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y+r,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y-r,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y,c.z+r));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y,c.z-r));
+                	    } else {
+                            atoms.push(c);
+                	    }
+                });
+                tmp = $3Dmol.getExtent(atoms);
+                allatoms = atoms;
+                alltmp = tmp;
+
+            }
+            else {
+                allatoms = getAtomsFromSel({});
+                alltmp = $3Dmol.getExtent(allatoms);
+            }
+
+            // use selection for center
+            var center = new $3Dmol.Vector3(tmp[2][0], tmp[2][1], tmp[2][2]);
+            modelGroup.position = center.clone().multiplyScalar(-1);
+            // but all for bounding box
+            var x = alltmp[1][0] - alltmp[0][0], y = alltmp[1][1]
+                    - alltmp[0][1], z = alltmp[1][2] - alltmp[0][2];
+
+            var maxD = Math.sqrt(x * x + y * y + z * z);
+            if (maxD < 5)
+                maxD = 5;
+
+            // use full bounding box for slab/fog
+            slabNear = -maxD / 1.9;
+            slabFar = maxD / 2;
+
+            // for zoom, use selection box
+            x = tmp[1][0] - tmp[0][0];
+            y = tmp[1][1] - tmp[0][1];
+            z = tmp[1][2] - tmp[0][2];
+            maxD = Math.sqrt(x * x + y * y + z * z);
+            if (maxD < 5)
+                maxD = 5;
+            
+            //find the farthest atom from center to get max distance needed for view
+            var maxDsq = 25;
+            for (var i = 0; i < atoms.length; i++) {
+                if(atoms[i]) {
+                    var dsq = center.distanceToSquared(atoms[i]);
+                    if(dsq > maxDsq)
+                        maxDsq = dsq;
+                }
+            }
+            
+            var maxD = Math.sqrt(maxDsq)*2;
+
+            rotationGroup.position.z = -(maxD * 0.5
+                    / Math.tan(Math.PI / 180.0 * camera.fov / 2) - CAMERA_Z);
+            show();
+            
+            return this;
+        };
+        
+        /**
+         * Set slab of view (contents outside of slab are clipped). M
+         * Must call render to update.
+         * 
+         * @function $3Dmol.GLViewer#setSlab
+         * @param {near}
+         * @param {far}
+         */
+        this.setSlab = function(near, far) {
+            slabNear = near;
+            slabFar = far;
+        };
+        
+        /**
+         * Get slab of view (contents outside of slab are clipped).
+         * 
+         * @function $3Dmol.GLViewer#setSlab
+         * @return {Object} near/far
+         */
+        this.getSlab = function(sel) {
+            return {near: slabNear, far: slabFar};
+        };
+                
+        /**
+         * Add label to viewer
+         * 
+         * @function $3Dmol.GLViewer#addLabel
+         * @param {string}
+         *            text - Label text
+         * @param {Object}
+         *            data - Label style specification
+         * @return {$3Dmol.Label}
+         * 
+         * @example
+         *  // Assuming glviewer contains a model representing a protein, label
+         * all alpha carbons with their residue name
+         *  // Select all alpha carbons (have property atom : "CA") from last
+         * model added var atoms =
+         * glviewer.getModel().selectedAtoms({atom:"CA"}); var labels = [];
+         * 
+         * for (var a in atoms) { var atom = atoms[a];
+         *  // Create label at alpha carbon's position displaying atom's residue
+         * and residue number var labelText = atom.resname + " " + atom.resi;
+         * 
+         * var l = glviewer.createLabel(labelText, {fontSize: 12, position: {x:
+         * atom.x, y: atom.y, z: atom.z});
+         * 
+         * labels.push(l); }
+
+         *  // Render labels glviewer.render();
+         */
+        this.addLabel = function(text, data) {
+            var label = new $3Dmol.Label(text, data);
+            label.setContext();
+            modelGroup.add(label.sprite);
+            labels.push(label);
+            show();
+            return label;
+        };
+        
+        /** Add residue labels.  This will generate one label per a
+         * residue within the selected atoms.  The label will be at the
+         * centroid of the atoms and styled according to the passed style.
+         * The label text will be [resn][resi]
+         * 
+         * @param {Object} sel
+         * @param {Object} style
+         */
+        this.addResLabels = function(sel, style) {
+            applyToModels("addResLabels", sel, this, style);
+            return this;
+        }
+
+        /**
+         * Remove label from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeLabel
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * 
+         * @example // Remove labels created in [addLabel example]{@link $3Dmol.GLViewer#addLabel}
+         * 
+         * for (var i = 0; i < labels.length; i++) {
+         * glviewer.removeLabel(label); }
+         * 
+         * glviewer.render();
+         */
+        this.removeLabel = function(label) {
+            //todo: don't do the linear search
+            for(var i = 0; i < labels.length; i++) {
+                if(labels[i] == label) {
+                    labels.splice(i,1);
+                    label.dispose();
+                    modelGroup.remove(label.sprite);
+                    break;
+                }
+            }
+            return this;
+        };
+
+        /**
+         * Remove all labels from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeAllLabels
+         */
+        this.removeAllLabels = function() {
+            for (var i = 0; i < labels.length; i++) {
+                modelGroup.remove(labels[i].sprite);
+            }
+            labels.splice(0,labels.length); //don't overwrite in case linked
+            return this;
+        };
+        
+        // Modify label style
+        /**
+         * Modify existing label's style
+         * 
+         * @function $3Dmol.GLViewer#setLabelStyle
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * @param {Object}
+         *            stylespec - Label style specification
+         * @return {$3Dmol.Label}
+         */
+        this.setLabelStyle = function(label, stylespec) {
+            modelGroup.remove(label.sprite);
+            label.dispose();
+            label.stylespec = stylespec;
+            label.setContext();
+            modelGroup.add(label.sprite);
+            show();
+            return label;
+
+        };
+
+        // Change label text
+        /**
+         * Modify existing label's text
+         * 
+         * @function $3Dmol.GLViewer#setLabelText
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * @param {String}
+         *            text - Label text
+         * @return {$3Dmol.Label}
+         */
+        this.setLabelText = function(label, text) {
+            modelGroup.remove(label.sprite);
+            label.dispose();
+            label.text = text;
+            label.setContext();
+            modelGroup.add(label.sprite);
+            show();
+            return label;
+
+        };
+
+        /**
+         * Add shape object to viewer 
+         * @see {@link $3Dmol.GLShape}
+         * 
+         * @function $3Dmol.GLViewer#addShape
+         * @param {ShapeSpec} shapeSpec - style specification for label
+         * @return {$3Dmol.GLShape}
+         */
+        this.addShape = function(shapeSpec) {
+            shapeSpec = shapeSpec || {};
+            var shape = new $3Dmol.GLShape(shapeSpec);
+            shape.shapePosition = shapes.length;
+            shapes.push(shape);
+
+            return shape;
+
+        };
+
+        /**
+         * Remove shape object from viewer
+         *
+         * @function $3Dmol.GLViewer#removeShape
+         * @param {$3Dmol.GLShape} shape - Reference to shape object to remove
+         */
+        this.removeShape = function(shape) {
+            if (!shape)
+                return this;
+            shape.removegl(modelGroup);
+            delete shapes[shape.shapePosition];
+            // clear off back of model array
+            while (shapes.length > 0
+                    && typeof (shapes[shapes.length - 1]) === "undefined")
+                shapes.pop();
+            return this;
+        };
+        
+        /**
+         * Remove all shape objects from viewer
+         * @function $3Dmol.GLViewer#removeAllShapes
+         */
+        this.removeAllShapes = function() {
+            for (var i = 0; i < shapes.length; i++) {
+                var shape = shapes[i];
+                shape.removegl(modelGroup);
+            }
+            shapes.splice(0,shapes.length);
+            return this;
+        }
+
+        /**
+         * Create and add sphere shape. This method provides a shorthand 
+         * way to create a spherical shape object
+         * 
+         * @function $3Dmol.GLViewer#addSphere
+         * @param {SphereSpec} spec - Sphere shape style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addSphere = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addSphere(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Create and add arrow shape
+         * 
+         * @function $3Dmol.GLViewer#addArrow
+         * @param {ArrowSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addArrow = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addArrow(spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Create and add cylinder shape
+         * 
+         * @function $3Dmol.GLViewer#addCylinder
+         * @param {CylinderSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCylinder = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addCylinder(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Create and add line shape
+         * 
+         * @function $3Dmol.GLViewer#addLine
+         * @param {LineSpec} spec - Style specification, can specify dashed, dashLength, and gapLength
+         * @return {$3Dmol.GLShape}
+         */
+        this.addLine = function(spec) {
+            spec = spec || {};
+            spec.wireframe = true;
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            if (spec.dashed)
+                s = addLineDashed(spec, s);
+            else
+                s.addLine(spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        
+        /**
+         * Create and add unit cell
+         *
+         * @function $3Dmol.GLViewer#addUnitCell
+         * @param {GLModel} Model with unit cell information (e.g., pdb derived).
+         * @return {$3Dmol.GLShape}  Line shape delineating unit cell.
+         */
+        this.addUnitCell = function(model) {
+
+            var s = new $3Dmol.GLShape({'wireframe' : true});
+            s.shapePosition = shapes.length;
+            var data = model.getCrystData();
+            if (data) {
+                var a = data.a, b = data.b, c = data.c, alpha = data.alpha, beta = data.beta, gamma = data.gamma;
+                alpha = alpha * Math.PI/180.0;
+                beta = beta * Math.PI/180.0;
+                gamma = gamma * Math.PI/180.0;
+            
+                var u, v, w;
+            
+                u = Math.cos(beta);
+                v = (Math.cos(alpha) - Math.cos(beta)*Math.cos(gamma))/Math.sin(gamma);
+                w = Math.sqrt(Math.max(0, 1-u*u-v*v));
+            
+                var matrix = new $3Dmol.Matrix4(a, b*Math.cos(gamma), c*u, 0, 
+                                                0, b*Math.sin(gamma), c*v, 0,
+                                                0, 0,                 c*w, 0,
+                                                0, 0,                 0,   1); 
+         
+                var points = [  new $3Dmol.Vector3(0, 0, 0),
+                                new $3Dmol.Vector3(1, 0, 0),
+                                new $3Dmol.Vector3(0, 1, 0),
+                                new $3Dmol.Vector3(0, 0, 1),
+                                new $3Dmol.Vector3(1, 1, 0),
+                                new $3Dmol.Vector3(0, 1, 1),
+                                new $3Dmol.Vector3(1, 0, 1),
+                                new $3Dmol.Vector3(1, 1, 1)  ];
+                            
+                for (var i = 0; i < points.length; i++) {
+                    points[i] = points[i].applyMatrix4(matrix);
+                }
+            
+                s.addLine({start: points[0], end: points[1]});
+                s.addLine({start: points[0], end: points[2]});
+                s.addLine({start: points[1], end: points[4]});
+                s.addLine({start: points[2], end: points[4]});
+            
+                s.addLine({start: points[0], end: points[3]});
+                s.addLine({start: points[3], end: points[5]});
+                s.addLine({start: points[2], end: points[5]});
+            
+                s.addLine({start: points[1], end: points[6]});
+                s.addLine({start: points[4], end: points[7]});
+                s.addLine({start: points[6], end: points[7]});
+            
+                s.addLine({start: points[3], end: points[6]});
+                s.addLine({start: points[5], end: points[7]});
+            }
+            
+            shapes.push(s);
+            return s;
+        };
+
+        function addLineDashed(spec, s) {
+            spec.dashLength = spec.dashLength || 0.5;
+            spec.gapLength = spec.gapLength || 0.5;
+            spec.start = spec.start || {};
+            spec.end = spec.end || {};
+            
+            var p1 = new $3Dmol.Vector3(spec.start.x || 0,
+        			spec.start.y || 0, spec.start.z || 0)
+        	var p2 = new $3Dmol.Vector3(spec.end.x,
+        			spec.end.y || 0, spec.end.z || 0);
+        			
+            var dir = new $3Dmol.Vector3();
+            var dash = new $3Dmol.Vector3();
+            var gap = new $3Dmol.Vector3();
+            var length, dashAmt, gapAmt;
+            var temp = p1.clone();
+            var drawn = 0;
+
+            dir.subVectors(p2, p1);
+            length = dir.length();
+            dir.normalize();
+            dash = dir.clone();
+            gap = dir.clone();
+            dash.multiplyScalar(spec.dashLength);
+            gap.multiplyScalar(spec.gapLength);
+            dashAmt = dash.length();
+            gapAmt = gap.length();
+
+            while (drawn < length) {
+                if ((drawn + dashAmt) > length) { 
+                    spec.start = p1;
+                    spec.end = p2;
+                    s.addLine(spec);
+                    break;
+                }
+                temp.addVectors(p1, dash); 
+                spec.start = p1;
+                spec.end = temp;
+                s.addLine(spec);
+                p1 = temp.clone();
+                drawn += dashAmt;
+
+                temp.addVectors(p1, gap);
+                p1 = temp.clone();   
+                drawn += gapAmt;
+            }
+        			
+        	return s;
+        }
+
+        /**
+         * Add custom shape component from user supplied function
+         * 
+         * @function $3Dmol.GLViewer#addCustom
+         * @param {CustomSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCustom = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addCustom(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Construct isosurface from volumetric data in gaussian cube format
+         * @deprecated
+         * @function $3Dmol.GLViewer#addVolumetricData
+         * @param {String} data - Input file contents 
+         * @param {String} format - Input file format (currently only supports "cube")
+         * @param {IsoSurfaceSpec} spec - Shape style specification
+         * @return {$3Dmol.GLShape}
+         * 
+         * @example
+         * viewer.addVolumetricData(data, "cube", {isoval: 0.01, color: "blue", opacity: 0.95});              
+         * viewer.addVolumetricData(data, "cube", {isoval: -0.01, color: "red", opacity: 0.95}); 
+         */
+        this.addVolumetricData = function(data, format, spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addVolumetricData(data, format, spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Construct isosurface from volumetric data
+         * @function $3Dmol.GLViewer#addIsosurface
+         * @param {$3Dmol.VolumeData} data - volumetric data
+         * @param {IsoSurfaceSpec} spec - Shape style specification
+         * @return {$3Dmol.GLShape}
+         * 
+         * @example
+         * var data = new $3Dmol.VolumeData(str,"cube");
+         * viewer.addIsosurface(data, {isoval: 0.01, color: "blue", opacity: 0.95});              
+         * viewer.addIsosurface(data, {isoval: -0.01, color: "red", opacity: 0.95}); 
+         */
+        this.addIsosurface = function(data,  spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addIsosurface(data, spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Sets the atomlists of all models in the viewer to specified frame
+         * Sets to last frame if framenum out of range
+         * 
+         * @function $3Dmol.GLViewer#setFrame
+         * @param {number} framenum - each model in viewer has their atoms set to this index in frames list
+         */
+        this.setFrame = function(framenum) {
+            for (var i = 0; i < models.length; i++) {
+                models[i].setFrame(framenum);
+            }
+            return this;
+        };
+        
+        /**
+         * Returns the number of frames that the model with the most frames in the viewer has
+         * 
+         * @function $3Dmol.GLViewer#getFrames
+         * @return {number}
+         */
+        this.getFrames = function() {
+            var mostFrames = 0;
+            var modelNum = 0;
+            for (var i = 0; i < models.length; i++) {
+                if (models[i].getFrames().length > mostFrames) {
+                    modelNum = i;
+                    mostFrames = models[i].getFrames().length;
+                }
+            }
+            return mostFrames;
+        };
+        
+
+        /**
+         * Animate all models in viewer from their respective frames
+         * @function $3Dmol.GLViewer#animate
+         * @param {Object} options - can specify interval (speed of animation), loop (direction
+         * of looping, 'backward', 'forward' or 'backAndForth') and reps (numer of repetitions, 0 indicates infinite loop)
+         *      
+         * @example
+         * viewer.addModelAsFrames(data, "pdb");
+         * viewer.animate({interval: 75, loop: "backward", reps: 30});
+         */
+        this.animate = function(options) {
+            animated = true;
+            var interval = 100;
+            var loop = "forward";
+            var reps = 0;
+            options = options || {};
+            if (options.interval) {
+                interval = options.interval;
+            }
+            if (options.loop) {
+                loop = options.loop;
+            }
+            if (options.reps) {
+                reps = options.reps;
+            }
+            var mostFrames = this.getFrames();
+            var that = this;
+            var currFrame = 0;
+            var inc = 1;
+            var displayCount = 0;
+            var displayMax = mostFrames * reps;
+            var display = function(direction) {
+                if (direction == "forward") {
+                    that.setFrame(currFrame);
+                    currFrame = (currFrame + inc) % mostFrames;
+                }
+                else if (direction == "backward") {
+                    that.setFrame((mostFrames-1) - currFrame);
+                    currFrame = (currFrame + inc) % mostFrames;
+                }
+                else { //back and forth
+                    that.setFrame(currFrame);
+                    currFrame += inc;
+                    inc *= (((currFrame % (mostFrames-1)) == 0) ? -1 : 1);
+                }
+                that.render();
+                if (++displayCount == displayMax || !that.isAnimated()) {
+                    clearInterval(intervalID);
+                }
+            };
+            var intervalID = setInterval( function() { display(loop); }, interval);
+            return this;
+        };
+        
+        /**
+         * Stop animation of all models in viewer
+         * @function $3Dmol.GLViewer#stopAnimate
+         */
+        this.stopAnimate = function() {
+            animated = false;
+            return this;
+        };
+        
+        /**
+         * Return true if viewer is currently being animated, false otherwise
+         * @function $3Dmol.GLViewer#isAnimated
+         * @return {boolean}
+         */
+        this.isAnimated = function() {
+            return animated;
+        };
+        
+
+        /**
+         * Create and add model to viewer, given molecular data and its format 
+         * (pdb, sdf, xyz, or mol2)
+         * 
+         * @function $3Dmol.GLViewer#addModel
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addModel = function(data, format, options) {
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+
+            return m;
+        };
+        
+        /**
+         * Given multimodel file and its format, add atom data to the viewer as separate models
+         * and return list of these models
+         * 
+         * @function $3Dmol.GLViewer#addModels
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {Array<$3Dmol.GLModel>}
+         */
+        this.addModels = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.frames = true;
+
+            var modelatoms = $3Dmol.GLModel.parseMolData(data, format, options);
+
+            for (var i = 0; i < modelatoms.length; i++) {
+                var newModel = new $3Dmol.GLModel(models.length, defaultcolors);
+                newModel.setAtomDefaults(modelatoms[i]);
+                newModel.addFrame(modelatoms[i]);
+                newModel.setFrame(0);
+                newModel.setModelData(modelatoms.modelData[i]);
+                newModel.setDontDuplicateAtoms(!options.duplicateAssemblyAtoms);
+                models.push(newModel);
+            }
+            
+            return models;
+        };
+        
+        /**
+         * Create and add model to viewer. Given multimodel file and its format, 
+         * different atomlists are stored in model's frame
+         * property and model's atoms are set to the 0th frame
+         * 
+         * @function $3Dmol.GLViewer#addModelsAsFrames
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addModelsAsFrames = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.frames = true;
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+
+            return m;
+        };
+        
+        /**
+         * Create and add model to viewer. Given multimodel file and its format,
+         * all atoms are added to one model
+         * 
+         * @function $3Dmol.GLViewer#addAsOneMolecule
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addAsOneMolecule = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.onemol = true;
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+            
+            return m;
+        };
+        
+
+        /**
+         * Delete specified model from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeModel
+         * @param {$3Dmol.GLModel} model
+         */
+        this.removeModel = function(model) {
+            if (!model)
+                return;
+            model.removegl(modelGroup);
+            delete models[model.getID()];
+            // clear off back of model array
+            while (models.length > 0
+                    && typeof (models[models.length - 1]) === "undefined")
+                models.pop();
+            return this;
+        };
+
+        /** 
+         * Delete all existing models
+         * @function $3Dmol.GLViewer#removeAllModels
+         */
+        this.removeAllModels = function() {
+            for (var i = 0; i < models.length; i++) {
+                var model = models[i];
+                model.removegl(modelGroup);
+
+            }
+            models.splice(0,models.length); //don't simply overwrite array in case linked
+            return this;
+        };
+
+        /**
+         * Export one or all of the loaded models into ChemDoodle compatible JSON.
+         * @function $3Dmol.GLViewer#exportJSON
+         * @param {boolean} includeStyles - Whether or not to include style information.
+         * @param {number} modelID - Optional parameter for which model to export. If left out, export all of them.
+         * @return {string}
+         */
+        this.exportJSON = function(includeStyles, modelID) {
+            var object = {};
+            if (modelID === undefined) {
+                object.m = models.map(function(model) {
+                    return model.toCDObject(includeStyles);
+                });
+            } else {
+                object.m = [ model[modelID].toCDObject() ];
+            }
+            return JSON.stringify(object);
+        }
+
+        /**
+         * Create a new model from atoms specified by sel.
+         * If extract, removes selected atoms from existing models 
+         * 
+         * @function $3Dmol.GLViewer#createModelFrom
+         * @param {Object} sel - Atom selection specification
+         * @param {boolean=} extract - If true, remove selected atoms from existing models
+         * @return {$3Dmol.GLModel}
+         */
+        this.createModelFrom = function(sel, extract) {
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            for (var i = 0; i < models.length; i++) {
+                if (models[i]) {
+                    var atoms = models[i].selectedAtoms(sel);
+                    m.addAtoms(atoms);
+                    if (extract)
+                        models[i].removeAtoms(atoms);
+                }
+            }
+            models.push(m);
+            return m;
+        };
+
+        function applyToModels(func, sel, value1, value2) {
+            
+            //apply func to all models that are selected by sel with value1 and 2
+            var ms = []
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+            
+            
+            for (var i = 0; i < ms.length; i++) {
+                if (ms[i]) {
+                    ms[i][func](sel, value1, value2);
+                }
+            }
+        }
+
+        /**
+         * Set style properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#setStyle
+         * @param {AtomSelectionSpec} sel - Atom selection specification
+         * @param {AtomStyleSpec} style - Style spec to apply to specified atoms
+         * 
+         * @example
+         * viewer.setStyle({}, {stick:{}}); //set all atoms to stick
+         * viewer.setStyle({chain: 'B'}, {cartoon: {color: 'spectrum'}}); //set chain B to rainbow cartoon
+         */
+        this.setStyle = function(sel, style) {
+            if(typeof(style) === 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            
+            applyToModels("setStyle", sel, style, false);
+            return this;
+        };
+
+        /**
+         * Add style properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#addStyle
+         * @param {AtomSelectionSpec} sel - Atom selection specification
+         * @param {AtomStyleSpec} style - style spec to add to specified atoms
+         */
+        this.addStyle = function(sel, style) {
+            if(typeof(style) === 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            applyToModels("setStyle", sel, style, true);
+            return this;
+        };
+
+        /**
+         * Set click-handling properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#setClickable
+         * @param {AtomSelectionSpec} sel - atom selection to apply clickable settings to
+         * @param {boolean} clickable - whether click-handling is enabled for the selection
+         * @param {function} callback - function called when an atom in the selection is clicked
+         * 
+         * @example
+         * viewer.setClickable({}, false); // disable click-handling for entire viewer
+         * viewer.setClickable({chain: 'B'}, true, function(){ console.log(this.elem); }); // chain B prints the clicked element to console
+         */
+        this.setClickable = function(sel, clickable, callback) {
+            applyToModels("setClickable", sel, clickable, callback);
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#setColorByProperty
+         * @param {AtomSelectionSpec} sel
+         * @param {type} prop
+         * @param {type} scheme
+         */
+        this.setColorByProperty = function(sel, prop, scheme) {
+            applyToModels("setColorByProperty", sel, prop, scheme);
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#setColorByElement
+         * @param {AtomSelectionSpec} sel
+         * @param {type} colors
+         */
+        this.setColorByElement = function(sel, colors) {
+            applyToModels("setColorByElement", sel, colors);
+            return this;
+        };
+
+        /**
+         * 
+         * @param {AtomSpec[]} atomlist
+         * @param {Array}
+         *            extent
+         * @return {Array}
+         */
+        var getAtomsWithin = function(atomlist, extent) {
+            var ret = [];
+
+            for (var i = 0; i < atomlist.length; i++) {
+                var atom = atomlist[i];
+                if (typeof (atom) == "undefined")
+                    continue;
+
+                if (atom.x < extent[0][0] || atom.x > extent[1][0])
+                    continue;
+                if (atom.y < extent[0][1] || atom.y > extent[1][1])
+                    continue;
+                if (atom.z < extent[0][2] || atom.z > extent[1][2])
+                    continue;
+                ret.push(i);
+            }
+            return ret;
+        };
+
+        // return volume of extent
+        var volume = function(extent) {
+            var w = extent[1][0] - extent[0][0];
+            var h = extent[1][1] - extent[0][1];
+            var d = extent[1][2] - extent[0][2];
+            return w * h * d;
+        }; // volume
+        /*
+         * Break up bounding box/atoms into smaller pieces so we can parallelize
+         * with webworkers and also limit the size of the working memory Returns
+         * a list of bounding boxes with the corresponding atoms. These extents
+         * are expanded by 4 angstroms on each side.
+         */
+        /**
+         * 
+         * @param {Array}
+         *            extent
+         * @param {AtomSpec[]} atomlist
+         * @param {AtomSpec[]} atomstoshow
+         * @return {Array}
+         */
+        var carveUpExtent = function(extent, atomlist, atomstoshow) {
+            var ret = [];
+
+            var copyExtent = function(extent) {
+                // copy just the dimensions
+                var ret = [];
+                ret[0] = [ extent[0][0], extent[0][1], extent[0][2] ];
+                ret[1] = [ extent[1][0], extent[1][1], extent[1][2] ];
+                return ret;
+            }; // copyExtent
+            var splitExtentR = function(extent) {
+                // recursively split until volume is below maxVol
+                if (volume(extent) < maxVolume) {
+                    return [ extent ];
+                } else {
+                    // find longest edge
+                    var w = extent[1][0] - extent[0][0];
+                    var h = extent[1][1] - extent[0][1];
+                    var d = extent[1][2] - extent[0][2];
+
+                    var index;
+
+                    if (w > h && w > d) {
+                        index = 0;
+                    } else if (h > w && h > d) {
+                        index = 1;
+                    } else {
+                        index = 2;
+                    }
+
+                    // create two halves, splitting at index
+                    var a = copyExtent(extent);
+                    var b = copyExtent(extent);
+                    var mid = (extent[1][index] - extent[0][index]) / 2
+                            + extent[0][index];
+                    a[1][index] = mid;
+                    b[0][index] = mid;
+
+                    var alist = splitExtentR(a);
+                    var blist = splitExtentR(b);
+                    return alist.concat(blist);
+                }
+            }; // splitExtentR
+
+            // divide up extent
+            var splits = splitExtentR(extent);
+            // now compute atoms within expanded (this could be more efficient)
+            var off = 6; // enough for water and 2*r, also depends on scale
+            // factor
+            for (var i = 0, n = splits.length; i < n; i++) {
+                var e = copyExtent(splits[i]);
+                e[0][0] -= off;
+                e[0][1] -= off;
+                e[0][2] -= off;
+                e[1][0] += off;
+                e[1][1] += off;
+                e[1][2] += off;
+
+                var atoms = getAtomsWithin(atomlist, e);
+                var toshow = getAtomsWithin(atomstoshow, splits[i]);
+
+                // ultimately, divide up by atom for best meshing
+                ret.push({
+                    extent : splits[i],
+                    atoms : atoms,
+                    toshow : toshow
+                });
+            }
+
+            return ret;
+        };
+
+        // create a mesh defined from the passed vertices and faces and material
+        // Just create a single geometry chunk - broken up whether sync or not
+        /**
+         * 
+         * @param {AtomSpec[]} atoms
+         * @param {{vertices:number,faces:number}}
+         *            VandF
+         * @param {$3Dmol.MeshLambertMaterial}
+         *            mat
+         * @return {$3Dmol.Mesh}
+         */
+        var generateSurfaceMesh = function(atoms, VandF, mat) {
+            var geo = new $3Dmol.Geometry(true);
+            // Only one group per call to generate surface mesh (addSurface
+            // should split up mesh render)
+            var geoGroup = geo.updateGeoGroup(0);
+
+            // set colors for vertices
+            var colors = [];
+            for (i = 0, il = atoms.length; i < il; i++) {
+                var atom = atoms[i];
+                if (atom) {
+                    if (typeof (atom.surfaceColor) != "undefined") {
+                        colors[i] = atom.surfaceColor;
+                    } else if (atom.color) // map from atom
+                        colors[i] = $3Dmol.CC.color(atom.color);
+                }
+            }
+            
+            var vertexArray = geoGroup.vertexArray;
+
+            // reconstruct vertices and faces
+            var v = VandF['vertices'];
+            var offset;
+            var i, il;
+            for (i = 0, il = v.length; i < il; i++) {
+                offset = geoGroup.vertices * 3;
+                vertexArray[offset] = v[i].x;
+                vertexArray[offset + 1] = v[i].y;
+                vertexArray[offset + 2] = v[i].z;
+                geoGroup.vertices++;                
+            }
+
+            //set colorArray of there are per-atom colors
+            var colorArray = geoGroup.colorArray;
+            
+            if(mat.voldata && mat.volscheme) {
+                //convert volumetric data into colors
+                var scheme = mat.volscheme;
+                var voldata = mat.voldata;
+                var range = scheme.range() || [-1,1];
+                for (i = 0, il = v.length; i < il; i++) {
+                    var val = voldata.getVal(v[i].x,v[i].y,v[i].z);
+                    var col =  $3Dmol.CC.color(scheme.valueToHex(val, range));
+                    var offset = i * 3;
+                    colorArray[offset] = col.r;
+                    colorArray[offset + 1] = col.g;
+                    colorArray[offset + 2] = col.b;
+                }
+            }
+            else if(colors.length > 0) { //have atom colors
+                for (i = 0, il = v.length; i < il; i++) {
+                    var A = v[i].atomid;
+                    var offsetA = i * 3;
+
+                    colorArray[offsetA] = colors[A].r;
+                    colorArray[offsetA + 1] = colors[A].g;
+                    colorArray[offsetA + 2] = colors[A].b;
+                }
+            }
+            
+            var faces = VandF['faces'];
+            geoGroup.faceidx = faces.length;// *3;
+            geo.initTypedArrays();
+
+            var verts = geoGroup.vertexArray;
+            var normalArray = geoGroup.normalArray;
+            var vA, vB, vC, norm;
+
+            // Setup colors, faces, and normals
+            for (i = 0, il = faces.length; i < il; i += 3) {
+
+                // var a = faces[i].a, b = faces[i].b, c = faces[i].c;
+                var a = faces[i], b = faces[i + 1], c = faces[i + 2];
+                var A = v[a]['atomid'];
+                var B = v[b]['atomid'];
+                var C = v[c]['atomid'];
+
+                var offsetA = a * 3, offsetB = b * 3, offsetC = c * 3;
+
+                // setup Normals
+                // todo - calculate normals in parallel code
+                vA = new $3Dmol.Vector3(verts[offsetA], verts[offsetA + 1],
+                        verts[offsetA + 2]);
+                vB = new $3Dmol.Vector3(verts[offsetB], verts[offsetB + 1],
+                        verts[offsetB + 2]);
+                vC = new $3Dmol.Vector3(verts[offsetC], verts[offsetC + 1],
+                        verts[offsetC + 2]);
+
+                vC.subVectors(vC, vB);
+                vA.subVectors(vA, vB);
+                vC.cross(vA);
+
+                // face normal
+                norm = vC;
+                norm.normalize();
+
+                normalArray[offsetA] += norm.x;
+                normalArray[offsetB] += norm.x;
+                normalArray[offsetC] += norm.x;
+                normalArray[offsetA + 1] += norm.y;
+                normalArray[offsetB + 1] += norm.y;
+                normalArray[offsetC + 1] += norm.y;
+                normalArray[offsetA + 2] += norm.z;
+                normalArray[offsetB + 2] += norm.z;
+                normalArray[offsetC + 2] += norm.z;
+
+            }
+            geoGroup.faceArray = new Uint16Array(faces);
+            var mesh = new $3Dmol.Mesh(geo, mat);
+            mesh.doubleSided = true;        
+            return mesh;
+        };
+
+        // do same thing as worker in main thread
+        /**
+         * 
+         * @param {$3Dmol.SurfaceType}
+         *            type
+         * @param {Array}
+         *            expandedExtent
+         * @param {Array}
+         *            extendedAtoms
+         * @param {Array}
+         *            atomsToShow
+         * @param {AtomSpec[]} atoms
+         * @param {number}
+         *            vol
+         * @return {Object}
+         */
+        var generateMeshSyncHelper = function(type, expandedExtent,
+                extendedAtoms, atomsToShow, atoms, vol) {
+            var time = new Date();
+            var ps = new $3Dmol.ProteinSurface();
+            ps.initparm(expandedExtent, (type === 1) ? false : true, vol);
+
+            var time2 = new Date();
+            //console.log("initialize " + (time2 - time) + "ms");
+
+            ps.fillvoxels(atoms, extendedAtoms);
+
+            var time3 = new Date();
+            //console.log("fillvoxels " + (time3 - time2) + "  " + (time3 - time) + "ms");
+
+            ps.buildboundary();
+
+            if (type == $3Dmol.SurfaceType.SES) {
+                ps.fastdistancemap();
+                ps.boundingatom(false);
+                ps.fillvoxelswaals(atoms, extendedAtoms);
+            }
+
+            var time4 = new Date();
+            //console.log("buildboundaryetc " + (time4 - time3) + "  " + (time4 - time) + "ms");
+
+            ps.marchingcube(type);
+
+            var time5 = new Date();
+            //console.log("marching cube " + (time5 - time4) + "  "+ (time5 - time) + "ms");
+
+            return ps.getFacesAndVertices(atomsToShow);
+        };
+
+        /**
+         * 
+         * @param {matSpec}
+         *            style
+         * @return {$3Dmol.MeshLambertMaterial}
+         */
+        function getMatWithStyle(style) {
+            var mat = new $3Dmol.MeshLambertMaterial();
+            mat.vertexColors = $3Dmol.VertexColors;
+
+            for ( var prop in style) {
+                if (prop === "color" || prop === "map") {
+                    // ignore
+                } else if (style.hasOwnProperty(prop))
+                    mat[prop] = style[prop];
+            }
+            if (style.opacity !== undefined) {
+                if (style.opacity === 1)
+                    mat.transparent = false;
+                else
+                    mat.transparent = true;
+            }
+
+            return mat;
+        }
+
+        
+        /**
+         * Adds an explicit mesh as a surface object.
+         * 
+         * @param {$3Dmol.Mesh}
+         *            mesh
+         * @param {Object}
+         *            style
+         * @returns {Number} surfid
+         */
+        this.addMesh = function(mesh) {
+            var surfobj = {
+                geo : mesh.geometry,
+                mat : mesh.material,
+                done : true,
+                finished : false //the rendered finishes surfaces when they are done
+            };
+            var surfid = nextSurfID();
+            surfaces[surfid] = surfobj;
+            return surfid;
+        }
+
+        //return a shallow copy of list l, e.g., for atoms so we can
+        //ignore superficial changes (ie surfacecolor, position) that happen
+        //while we're surface building
+        var shallowCopy = function(l) {
+            var ret = [];
+            $.each(l, function(k,v) {
+                ret[k] = $.extend({},v);
+            });
+            return ret;
+        }
+        /**
+         * Add surface representation to atoms
+         *  @function $3Dmol.GLViewer#addSurface
+         * @param {$3Dmol.SurfaceType} type - Surface type
+         * @param {SurfaceStyleSpec} style - optional style specification for surface material (e.g. for different coloring scheme, etc)
+         * @param {AtomSelectionSpec} atomsel - Show surface for atoms in this selection
+         * @param {AtomSelectionSpec} allsel - Use atoms in this selection to calculate surface; may be larger group than 'atomsel' 
+         * @param {AtomSelectionSpec} focus - Optionally begin rendering surface specified atoms
+         * 
+         * @return {number} surfid - Identifying number for this surface
+         */
+        this.addSurface = function(type, style, atomsel, allsel, focus) {
+            // type 1: VDW 3: SAS 4: MS 2: SES
+            // if sync is true, does all work in main thread, otherwise uses
+            // workers
+            // with workers, must ensure group is the actual modelgroup since
+            // surface
+            // will get added asynchronously
+            // all atoms in atomlist are used to compute surfaces, but only the
+            // surfaces
+            // of atomsToShow are displayed (e.g., for showing cavities)
+            // if focusSele is specified, will start rending surface around the
+            // atoms specified by this selection
+            var atomlist = null, focusSele = null;
+            //TODO: currently generating a shallow copy to avoid problems when atoms are chagned
+            //during surface generation - come up with a better solution
+            var atomsToShow = shallowCopy(getAtomsFromSel(atomsel));
+            if(!allsel) {
+                atomlist = atomsToShow;
+            }
+            else {
+                atomlist = shallowCopy(getAtomsFromSel(allsel));
+            }
+            
+            var symmetries = false;
+            var n;
+            for (n = 0; n < models.length; n++) { 
+                if(models[n]) {
+                    var symMatrices = models[n].getSymmetries();
+                    if (symMatrices.length > 1 || (symMatrices.length == 1 && !(symMatrices[0].isIdentity()))) {
+                        symmetries = true;
+                        break;
+                    }
+                }
+            }
+
+            var addSurfaceHelper = function addSurfaceHelper(surfobj, atomlist, atomsToShow) {
+            
+                if(!focus) {
+                    focusSele = atomsToShow;
+                } else {
+                    focusSele = shallowCopy(getAtomsFromSel(focus));
+                }
+
+                var atom;
+                var time = new Date();
+                var extent = $3Dmol.getExtent(atomsToShow, true);
+
+                var i, il;
+                if (style['map'] && style['map']['prop']) {
+                    // map color space using already set atom properties
+                    /** @type {AtomSpec} */
+                    var prop = style['map']['prop'];
+                    /** @type {Gradient} */
+                    var scheme = style['map']['scheme'] || style['map']['gradient'] || new $3Dmol.Gradient.RWB();
+                    var range = scheme.range();
+                    if (!range) {
+                        range = $3Dmol.getPropertyRange(atomsToShow, prop);
+                    }
+                    style.colorscheme = {prop: prop, gradient: scheme};
+
+                }
+                
+                //cache surface color on each atom
+                for (i = 0, il = atomlist.length; i < il; i++) {
+                    atom = atomlist[i];
+                    atom.surfaceColor = $3Dmol.getColorFromStyle(atom, style);
+                }                
+
+                var totalVol = volume(extent); // used to scale resolution
+                var extents = carveUpExtent(extent, atomlist, atomsToShow);
+
+                if (focusSele && focusSele.length && focusSele.length > 0) {
+                    var seleExtent = $3Dmol.getExtent(focusSele, true);
+                    // sort by how close to center of seleExtent
+                    var sortFunc = function(a, b) {
+                        var distSq = function(ex, sele) {
+                            // distance from e (which has no center of mass) and
+                            // sele which does
+                            var e = ex.extent;
+                            var x = e[1][0] - e[0][0];
+                            var y = e[1][1] - e[0][1];
+                            var z = e[1][2] - e[0][2];
+                            var dx = (x - sele[2][0]);
+                            dx *= dx;
+                            var dy = (y - sele[2][1]);
+                            dy *= dy;
+                            var dz = (z - sele[2][2]);
+                            dz *= dz;
+
+                            return dx + dy + dz;
+                        };
+                        var d1 = distSq(a, seleExtent);
+                        var d2 = distSq(b, seleExtent);
+                        return d1 - d2;
+                    };
+                    extents.sort(sortFunc);
+                }
+
+                //console.log("Extents " + extents.length + "  "+ (+new Date() - time) + "ms");
+
+
+                var reducedAtoms = [];
+                // to reduce amount data transfered, just pass x,y,z,serial and elem
+                for (i = 0, il = atomlist.length; i < il; i++) {
+                    atom = atomlist[i];
+                    reducedAtoms[i] = {
+                        x : atom.x,
+                        y : atom.y,
+                        z : atom.z,
+                        serial : i,
+                        elem : atom.elem
+                    };
+                }
+
+                var sync = !!($3Dmol.syncSurface);
+                if (sync) { // don't use worker, still break up for memory purposes
+
+                    // to keep the browser from locking up, call through setTimeout
+                    var callSyncHelper = function callSyncHelper(i) {
+                        if (i >= extents.length)
+                            return;
+
+                        var VandF = generateMeshSyncHelper(type, extents[i].extent,
+                                extents[i].atoms, extents[i].toshow, reducedAtoms,
+                                totalVol);
+                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
+                        $3Dmol.mergeGeos(surfobj.geo, mesh);
+                        _viewer.render();
+
+                        setTimeout(callSyncHelper, 1, i + 1);
+                    }
+
+                    setTimeout(callSyncHelper, 1, 0);
+
+                    // TODO: Asynchronously generate geometryGroups (not separate
+                    // meshes) and merge them into a single geometry
+                } else { // use worker
+
+                    var workers = [];
+                    if (type < 0)
+                        type = 0; // negative reserved for atom data
+                    for (i = 0, il = numWorkers; i < il; i++) {
+                        // var w = new Worker('3Dmol/SurfaceWorker.js');
+                        var w = new Worker($3Dmol.SurfaceWorker);
+                        workers.push(w);
+                        w.postMessage({
+                            'type' : -1,
+                            'atoms' : reducedAtoms,
+                            'volume' : totalVol
+                        });
+                    }
+                    var cnt = 0;
+
+                    var rfunction = function(event) {
+                        var VandFs = $3Dmol.splitMesh({vertexArr:event.data.vertices,
+							                           faceArr:event.data.faces});
+					    for(var i=0,vl=VandFs.length;i<vl;i++){
+                            var VandF={vertices:VandFs[i].vertexArr,
+								       faces:VandFs[i].faceArr};
+                            var mesh = generateSurfaceMesh(atomlist, VandF, mat);
+                            $3Dmol.mergeGeos(surfobj.geo, mesh);
+                            _viewer.render();
+						}
+
+                    //    console.log("async mesh generation " + (+new Date() - time) + "ms");
+                        cnt++;
+                        if (cnt == extents.length)
+                            surfobj.done = true;
+                    };
+
+                    var efunction = function(event) {
+                        console.log(event.message + " (" + event.filename + ":" + event.lineno + ")");
+                    };
+
+                    for (i = 0; i < extents.length; i++) {
+                        var worker = workers[i % workers.length];
+                        worker.onmessage = rfunction;
+
+                        worker.onerror = efunction;
+
+                        worker.postMessage({
+                            'type' : type,
+                            'expandedExtent' : extents[i].extent,
+                            'extendedAtoms' : extents[i].atoms,
+                            'atomsToShow' : extents[i].toshow
+                        });
+                    }
+                }
+
+                // NOTE: This is misleading if 'async' mesh generation - returns
+                // immediately
+                //console.log("full mesh generation " + (+new Date() - time) + "ms");
+            }
+            
+            style = style || {};
+            var mat = getMatWithStyle(style);
+            var surfobj = [];
+            
+            if (symmetries) { //do preprocessing
+                var modelsAtomList = {};
+                var modelsAtomsToShow = {};
+                for (n = 0; n < models.length; n++) {
+                    modelsAtomList[n] = [];
+                    modelsAtomsToShow[n] = [];
+                }
+                for (n = 0; n < atomlist.length; n++) {
+                    modelsAtomList[atomlist[n].model].push(atomlist[n]);
+                }
+                for (n = 0; n < atomsToShow.length; n++) {
+                    modelsAtomsToShow[atomsToShow[n].model].push(atomsToShow[n]);
+                }
+                for (n = 0; n < models.length; n++) {
+                    surfobj.push({
+                        geo : new $3Dmol.Geometry(true),
+                        mat : mat,
+                        done : false,
+                        finished : false,
+                        symmetries : models[n].getSymmetries()
+                    // also webgl initialized
+                    });
+                    addSurfaceHelper(surfobj[n], modelsAtomList[n], modelsAtomsToShow[n]);
+                }
+            }
+            else {
+                surfobj.push({
+                    geo : new $3Dmol.Geometry(true),
+                    mat : mat,
+                    done : false,
+                    finished : false,
+                    symmetries : [new $3Dmol.Matrix4()]
+                });
+                addSurfaceHelper(surfobj[surfobj.length-1], atomlist, atomsToShow);
+            } 
+            var surfid = nextSurfID();
+            surfaces[surfid] = surfobj;
+            
+            return surfid;
+
+        };
+
+        /**
+         * Set the surface material to something else, must render change
+         * 
+         * @param {number} surf - Surface ID to apply changes to
+         * @param {matSpec} style - new material style specification
+         */ 
+        this.setSurfaceMaterialStyle = function(surf, style) {
+            if (surfaces[surf]) {
+                surfArr = surfaces[surf];
+                for (var i = 0; i < surfArr.length; i++) {
+                    surfArr[i].mat = getMatWithStyle(style);
+                    surfArr[i].mat.side = $3Dmol.FrontSide;
+                    surfArr[i].finished = false; // trigger redraw
+                }
+            }
+            return this;
+        };
+
+        /**
+         * Remove surface with given ID
+         * 
+         * @param {number} surf - surface id
+         */
+        this.removeSurface = function(surf) {
+            var surfArr = surfaces[surf];
+            for (var i = 0; i < surfArr.length; i++) {
+                if (surfArr[i] && surfArr[i].lastGL) {
+                    if (surfArr[i].geo !== undefined)
+                        surfArr[i].geo.dispose();
+                    if (surfArr[i].mat !== undefined)
+                        surfArr[i].mat.dispose();
+                    modelGroup.remove(surfArr[i].lastGL); // remove from scene
+                }
+            }
+            delete surfaces[surf];
+            show();
+            return this;
+        };
+        
+        /** Remove all surfaces.
+         * @function $3Dmol.GLViewer#removeAllSurfaces */
+        this.removeAllSurfaces = function() {
+            for (n in  surfaces) {
+                if(!surfaces.hasOwnProperty(n)) continue;
+                var surfArr = surfaces[n];
+                for(var i = 0; i < surfArr.length; i++) {
+                    if (surfArr[i] && surfArr[i].lastGL) {
+                        if (surfArr[i].geo !== undefined)
+                            surfArr[i].geo.dispose();
+                        if (surfArr[i].mat !== undefined)
+                            surfArr[i].mat.dispose();
+                        modelGroup.remove(surfArr[i].lastGL); // remove from scene
+                    }
+                }
+                delete surfaces[n];
+            }
+            show();
+            return this;
+        };
+
+        /** return Jmol moveto command to position this scene */
+        this.jmolMoveTo = function() {
+            var pos = modelGroup.position;
+            // center on same position
+            var ret = "center { " + (-pos.x) + " " + (-pos.y) + " " + (-pos.z)
+                    + " }; ";
+            // apply rotation
+            var q = rotationGroup.quaternion;
+            ret += "moveto .5 quaternion { " + q.x + " " + q.y + " " + q.z
+                    + " " + q.w + " };";
+            // zoom is tricky.. maybe i would be best to let callee zoom on
+            // selection?
+            // can either do a bunch of math, or maybe zoom to the center with a
+            // fixed
+            // but reasonable percentage
+
+            return ret;
+        };
+
+        /** Clear scene of all objects 
+         * @function $3Dmol.GLViewer#clear
+         * */
+        this.clear = function() {
+            this.removeAllSurfaces();
+            this.removeAllModels();
+            this.removeAllLabels();
+            this.removeAllShapes();
+            show();
+            return this;
+        };
+
+        // props is a list of objects that select certain atoms and enumerate
+        // properties for those atoms
+        /**
+         * @function $3Dmol.GLViewer#mapAtomProperties
+         * Add specified properties to all atoms matching input argument
+         * @function $3Dmol.GLViewer#mapAtomProperties
+         * @param {Object} props, either array of atom selectors with associated props, or function that takes atom and sets its properties
+         * @param {AtomSelectionSpec} sel
+         */
+        this.mapAtomProperties = function(props, sel) {
+            sel = sel || {};
+            var atoms = getAtomsFromSel(sel);
+            
+            if(typeof(props) == "function") {
+                for (var a = 0, numa = atoms.length; a < numa; a++) {
+                    var atom = atoms[a];
+                    props(atom);
+                }
+            }
+            else {
+                for (var a = 0, numa = atoms.length; a < numa; a++) {
+                    var atom = atoms[a];
+                    for (var i = 0, n = props.length; i < n; i++) {
+                        var prop = props[i];
+                        if (prop.props) {
+                            for ( var p in prop.props) {
+                                if (prop.props.hasOwnProperty(p)) {
+                                    // check the atom
+                                    if (atomIsSelected(atom, prop)) {
+                                        if (!atom.properties)
+                                            atom.properties = {};
+                                        atom.properties[p] = prop.props[p];
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#linkViewer
+         * Synchronize this view matrix of this viewer to the passed viewer.
+         * When the viewpoint of this viewer changes, the other viewer will
+         * be set to this viewer's view.
+         * @function $3Dmol.GLViewer#linkViewer
+         */
+        this.linkViewer = function(otherviewer) {
+           linkedViewers.push(otherviewer);
+           return this;
+        };
+        
+
+        try {
+            if (typeof (callback) === "function")
+                callback(this);
+        } catch (e) {
+            // errors in callback shouldn't invalidate the viewer
+            console.log("error with glviewer callback: " + e);
+        }
+    }
+
+    return GLViewer;
+
+})();
+
+$3Dmol['glmolViewer'] = $3Dmol.GLViewer;
+//color scheme mappings
+var $3Dmol = $3Dmol || {};
+
+/** Color mapping gradiens
+ * @interface
+ * @param {number} min
+ * @param {number} max
+ */
+$3Dmol.Gradient = function(min, max) {};
+
+/**
+ * Map value to hex color
+ * @param {number} val
+ * @param {number} range
+ * @returns {number}
+ */
+$3Dmol.Gradient.valueToHex = function(val, range) {};
+//return range used for color mapping, null if none set
+$3Dmol.Gradient.range = function() {};
+
+
+
+/**
+ * Color scheme red to white to blue, for charges
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.RWB = function(min, max,mid) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+        
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val; //reverse if necessary
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(val === undefined)
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var middle = (hi+lo)/2;
+        if(typeof(mid) != 'undefined')
+            middle = mid; //allow user to specify midpoint
+        var scale, color;
+        
+        //scale bottom from red to white
+        if(val <= middle) {
+            scale = Math.floor(255*Math.sqrt((val-lo)/(middle-lo)));
+            color = 0xff0000 + 0x100*scale + scale;
+            return color;
+        }
+        else { //form white to blue
+            scale = Math.floor(255*Math.sqrt((1-(val-middle)/(hi-middle))));
+            color =  0x10000*scale+0x100*scale+0xff;
+            return color;
+        }
+    };
+    
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+
+/**
+ * rainbow gradient, but without purple to match jmol
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.ROYGB = function(min, max) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+    
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val;
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(typeof(val) == "undefined")
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var mid = (lo+hi)/2;
+        var q1 = (lo+mid)/2;
+        var q3 = (mid+hi)/2;
+        
+        var scale, color;
+        
+        if(val < q1) { //scale green up, red up, blue down
+            scale = Math.floor(255*Math.sqrt((val-lo)/(q1-lo)));
+            color = 0xff0000 + 0x100*scale + 0;
+            return color;
+        }
+        else if(val < mid) { //scale red down, green up, blue down
+            scale = Math.floor(255*Math.sqrt((1-(val-q1)/(mid-q1))));
+            color =  0x010000*scale+0xff00+0x0;
+            return color;
+        }
+        else if(val < q3) { //scale blue up, red down, green up
+            scale = Math.floor(255*Math.sqrt((val-mid)/(q3-mid)));
+            color = 0x000000 + 0xff00 + 0x1*scale;
+            return color;
+        }
+        else { //scale green down, blue up, red down
+            scale = Math.floor(255*Math.sqrt((1-(val-q3)/(hi-q3))));
+            color =  0x000000+0x0100*scale+0xff;
+            return color;
+        }        
+    };
+   
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+
+/**
+ * rainbow gradient with constant saturation, all the way to purple!
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.Sinebow = function(min, max) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val;
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(typeof(val) == "undefined")
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var scale = (val-lo)/(hi-lo);
+        var h = (5*scale/6.0+0.5);
+        var r = Math.sin(Math.PI*h);
+        r *= r*255;
+        var g = Math.sin(Math.PI*(h+1/3.0));
+        g *= g*255;
+        var b = Math.sin(Math.PI*(h+2/3.0));
+        b *= b*255;
+        
+        return 0x10000*Math.floor(r)+0x100*Math.floor(b)+0x1*Math.floor(g);
+    };
+    
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+//Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
+
+$3Dmol.LabelCount = 0;
+
+/**
+ * Renderable labels
+ * @constructor $3Dmol.Label
+ * @param {string} tag - Label text
+ * @param {LabelSpec} parameters Label style and font specifications
+ */
+$3Dmol.Label = function(text, parameters) {
+
+    this.id = $3Dmol.LabelCount++;
+    this.stylespec = parameters || {};
+
+    this.canvas = document.createElement('canvas');
+    //todo: implement resizing canvas..
+    this.canvas.width = 134;
+    this.canvas.height = 35;
+    this.context = this.canvas.getContext('2d');
+    this.sprite = new $3Dmol.Sprite();
+    this.text = text;
+
+};
+
+$3Dmol.Label.prototype = {
+
+    constructor : $3Dmol.Label,
+
+    getStyle : function () { return this.stylespec; }, 
+    
+    setContext : function() {
+        // function for drawing rounded rectangles - for Label drawing
+        var roundRect = function(ctx, x, y, w, h, r, drawBorder) {
+
+            ctx.beginPath();
+            ctx.moveTo(x + r, y);
+            ctx.lineTo(x + w - r, y);
+            ctx.quadraticCurveTo(x + w, y, x + w, y + r);
+            ctx.lineTo(x + w, y + h - r);
+            ctx.quadraticCurveTo(x + w, y + h, x + w - r, y + h);
+            ctx.lineTo(x + r, y + h);
+            ctx.quadraticCurveTo(x, y + h, x, y + h - r);
+            ctx.lineTo(x, y + r);
+            ctx.quadraticCurveTo(x, y, x + r, y);
+            ctx.closePath();
+            ctx.fill();
+            if(drawBorder)
+                ctx.stroke();
+
+        };
+        
+        //do all the checks to figure out what color is desired
+        var getColor = function(style, stylealpha, init) {
+            var ret = init;
+            if(typeof(style) != 'undefined') {
+                //convet regular colors
+                 if(style instanceof $3Dmol.Color) 
+                     ret = style.scaled();
+                 else //hex or name
+                    ret = $3Dmol.CC.color(style).scaled();                    
+            }
+            if(typeof(stylealpha) != 'undefined') {
+                ret.a = parseFloat(stylealpha);
+            }
+            return ret;
+        }
+
+        /**
+         * Label type specification
+         * @typedef LabelSpec
+         * @struct
+         * @prop {string} font - font name, default sans-serif
+         * @prop {number} fontSize - height of text, default 18
+         * @prop {ColorSpec} fontColor - font color, default white
+         * @prop {number} fontOpacity - font opacity, default 1
+         * @prop {number} borderThickness - line width of border around label, default 0
+         * @prop {ColorSpec} borderColor - color of border, default backgroundColor
+         * @prop {string} borderOpacity - color of border
+         * @prop {ColorSpec} backgroundColor - color of background, default black
+         * @prop {string} backgroundOpacity - opacity of background, default 1
+         * @prop {Object} position - x,y,z coordinates for label
+         * @prop {boolean} inFront - always put labels in from of model
+         * @prop {boolean} showBackground - show background rounded rectangle, default true
+         */
+        return function() {
+            
+            var style = this.stylespec;
+            var useScreen =  typeof(style.useScreen) == "undefined" ? false : style.useScreen;
+            
+            var showBackground = style.showBackground;
+            if(showBackground === '0' || showBackground === 'false') showBackground = false;
+            if(typeof(showBackground) == "undefined") showBackground = true; //default
+            var font = style.font ? style.font : "sans-serif";
+
+            var fontSize = parseInt(style.fontSize) ? parseInt(style.fontSize) : 18;
+
+            var fontColor = getColor(style.fontColor, style.fontOpacity,
+                     {
+                        r : 255,
+                        g : 255,
+                        b : 255,
+                        a : 1.0
+                    });
+
+            var padding = style.padding ? style.padding : 4;
+            var borderThickness = style.borderThickness ? style.borderThickness
+                    : 0;
+    
+            var backgroundColor = getColor(style.backgroundColor, style.backgroundOpacity, 
+                     {
+                        r : 0,
+                        g : 0,
+                        b : 0,
+                        a : 1.0
+                    });
+                    
+            var borderColor = getColor(style.borderColor, style.borderOpacity, backgroundColor);
+
+                    
+            var position = style.position ? style.position
+                    : {
+                        x : -10,
+                        y : 1,
+                        z : 1
+                    };
+                    
+            // Should labels always be in front of model?
+            var inFront = (style.inFront !== undefined) ? style.inFront    : true;
+            if(inFront === 'false' || inFront === '0') inFront = false;
+
+            // clear canvas
+
+            var spriteAlignment = style.alignment || $3Dmol.SpriteAlignment.topLeft;
+
+            var bold = "";
+            if(style.bold)
+                bold = "bold ";
+            this.context.font = bold+fontSize + "px  " + font;
+
+            var metrics = this.context.measureText(this.text);
+            var textWidth = metrics.width;
+            
+            if(!showBackground) borderThickness = 0;
+        
+            var width = textWidth+2.5*borderThickness +2*padding;
+            var height = fontSize*1.25+2*borderThickness+2*padding;            // 1.25 is extra height factor for text below baseline: g,j,p,q.
+
+            
+            if(style.backgroundImage) {
+                var img = style.backgroundImage;
+                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
+                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
+                if(w > width) width = w;
+                if(h > height) height = h;
+            }
+
+            this.canvas.width = width;
+            this.canvas.height = height;
+            this.context.clearRect(0, 0, this.canvas.width, this.canvas.height);
+
+            var bold = "";
+            if(style.bold)
+                bold = "bold ";
+            this.context.font = bold+fontSize + "px  " + font;
+
+            // background color
+            this.context.fillStyle = "rgba(" + backgroundColor.r + ","
+                    + backgroundColor.g + "," + backgroundColor.b
+                    + "," + backgroundColor.a + ")";
+            // border color
+            this.context.strokeStyle = "rgba(" + borderColor.r + ","
+                    + borderColor.g + "," + borderColor.b + ","
+                    + borderColor.a + ")";
+
+            this.context.lineWidth = borderThickness;
+            if(showBackground) {
+                roundRect(this.context, borderThickness,borderThickness , width-2*borderThickness,height-2*borderThickness, 6, borderThickness > 0);
+            }
+            
+            if(style.backgroundImage) {
+                var img = style.backgroundImage;
+                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
+                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
+                this.context.drawImage(img,0,0, w, h);
+            }
+            
+
+            // text color
+            this.context.fillStyle = "rgba(" + fontColor.r + ","
+                    + fontColor.g + "," + fontColor.b + ","
+                    + fontColor.a + ")";
+            
+            this.context.fillText(this.text, borderThickness+padding,
+                    fontSize + borderThickness+padding, textWidth);
+
+            // canvas contents will be used for a texture
+            var texture = new $3Dmol.Texture(this.canvas);
+            texture.needsUpdate = true;
+            this.sprite.material = new $3Dmol.SpriteMaterial({
+                map : texture,
+                useScreenCoordinates : useScreen,
+                alignment : spriteAlignment,
+                depthTest : !inFront
+            });
+
+            this.sprite.scale.set(1,1,1);
+
+            this.sprite.position.set(position.x, position.y, position.z);
+        };
+
+    }(),
+
+    // clean up material and texture
+    dispose : function() {
+
+        if (this.sprite.material.map !== undefined)
+            this.sprite.material.map.dispose();
+        if (this.sprite.material !== undefined)
+            this.sprite.material.dispose();
+    }
+
+};
+
+$3Dmol = $3Dmol || {};
+//Encapsulate marching cube algorithm for isosurface generation
+// (currently used by protein surface rendering and generic volumetric data reading)
+$3Dmol.MarchingCubeInitializer = function() {
+    
+    //Marching cube algorithm - assume data has been pre-treated so isovalue is 0 
+    // (i.e. select points greater than 0)
+    //origin -  vector of origin of volumetric data (default is (0,0,0))
+    // nX, nY, nZ - specifies number of voxels in each dimension
+    // scale - cube diagonal unit vector scale (3Dmol vector) (specifying distance between data points); diagonal of cube
+    // - default is 1 - assumes unit cube (1,1,1) diag)
+    // fulltable - if true, use full marching cubes and tritables - else use trimmed table (e.g. surf render)
+    // voxel - if true, draws with a blocky voxel style (default false)
+    // verts, faces - vertex and face arrays to fill up
+    
+    //to match with protein surface...
+    var ISDONE = 2;
+    var my = {};
+    
+    my.march = function(data, verts, faces, spec) {
+
+        var fulltable = !!(spec.fulltable);
+        var origin = (spec.hasOwnProperty('origin') && spec.origin.hasOwnProperty('x')) ? spec.origin : {x:0, y:0, z:0};
+        var voxel = !!(spec.voxel);
+        
+        var nX = spec.nX || 0;
+        var nY = spec.nY || 0;
+        var nZ = spec.nZ || 0;
+        
+        var scale = spec.scale || 1.0;
+        var unitCube = null;
+        if(spec.unitCube) {
+            unitCube = spec.unitCube;
+        } else {
+            unitCube = {x:scale,y:scale,z:scale};
+        }
+        
+        //keep track of calculated vertices to avoid repeats
+        var vertnums = new Int32Array(nX*nY*nZ);
+        
+        var i, il;
+        
+        for (i = 0, il = vertnums.length; i < il; ++i)
+            vertnums[i] = -1;
+
+        // create (or retrieve) a vertex at the appropriate point for
+        // the edge (p1,p2)
+        
+        var getVertex = function(i, j, k, code, p1, p2) {
+            var pt = {x: origin.x, y: origin.y, z: origin.z};
+            var val1 = !!(code & (1 << p1));
+            var val2 = !!(code & (1 << p2));
+             
+            // p1 if they are the same or if !val1
+            var p = p1;
+            if (!val1 && val2)
+                p = p2;
+            
+            // adjust i,j,k by p
+            if (p & 1)
+                k++;
+            if (p & 2)
+                j++;
+            if (p & 4)
+                i++;
+    
+            pt.x += unitCube.x*i;
+            pt.y += unitCube.y*j;
+            pt.z += unitCube.z*k;
+    
+            var index = ((nY * i) + j) * nZ + k;
+            
+            //Have to add option to do voxels
+            if (!voxel) {
+            
+                if (vertnums[index] < 0) // not created yet
+                {
+                    vertnums[index] = verts.length;
+                    verts.push( pt );
+                }
+                return vertnums[index];
+            
+            }
+            
+            else {
+                verts.push(pt);
+                return verts.length - 1;
+            }
+            
+        };
+            
+        var intersects = new Int32Array(12);
+        
+        var etable = (fulltable) ? edgeTable2 : edgeTable;
+        var tritable = (fulltable) ? triTable2 : triTable;
+                
+        //Run marching cubes algorithm
+        for (i = 0; i < nX-1; ++i) {
+            
+            for (var j = 0; j < nY-1; ++j){
+                
+                for (var k = 0; k < nZ-1; ++k){
+                    
+                    var code = 0;
+                    
+                    for (var p = 0; p < 8; ++p) {
+                        var index = ((nY * (i + ((p & 4) >> 2))) + j + ((p & 2) >> 1)) *
+                                        nZ + k + (p & 1);
+
+                        //TODO: Need to fix vpBits in protein surface for this to work
+                        var val = !!(data[index] & ISDONE);
+                        //var val = !!(data[index] > 0);   
+                        
+                        code |= val << p;                        
+                    }
+                    
+                    if (code === 0 || code === 255)
+                        continue;
+                    
+                    var ecode = etable[code];
+                    
+                    if (ecode === 0)
+                        continue;
+                        
+                    var ttable = tritable[code];                        
+                    
+                    if (ecode & 1)
+                        intersects[0] = getVertex(i, j, k, code, 0, 1);
+                    if (ecode & 2)
+                        intersects[1] = getVertex(i, j, k, code, 1, 3);
+                    if (ecode & 4)
+                        intersects[2] = getVertex(i, j, k, code, 3, 2);
+                    if (ecode & 8)
+                        intersects[3] = getVertex(i, j, k, code, 2, 0);
+                    if (ecode & 16)
+                        intersects[4] = getVertex(i, j, k, code, 4, 5);
+                    if (ecode & 32)
+                        intersects[5] = getVertex(i, j, k, code, 5, 7);
+                    if (ecode & 64)
+                        intersects[6] = getVertex(i, j, k, code, 7, 6);
+                    if (ecode & 128)
+                        intersects[7] = getVertex(i, j, k, code, 6, 4);
+                    if (ecode & 256)
+                        intersects[8] = getVertex(i, j, k, code, 0, 4);
+                    if (ecode & 512)
+                        intersects[9] = getVertex(i, j, k, code, 1, 5);
+                    if (ecode & 1024)
+                        intersects[10] = getVertex(i, j, k, code, 3, 7);
+                    if (ecode & 2048)
+                        intersects[11] = getVertex(i, j, k, code, 2, 6);       
+
+                    for (var t = 0; t < ttable.length; t += 3) {
+                        
+                        var a = intersects[ttable[t]],
+                            b = intersects[ttable[t+1]],
+                            c = intersects[ttable[t+2]];         
+                                           
+                        if (voxel && t >= 3) {
+                            verts.push(verts[a]); a = verts.length - 1;
+                            verts.push(verts[b]); b = verts.length - 1;
+                            verts.push(verts[c]); c = verts.length - 1;
+                        }
+
+                        
+                        faces.push(a); faces.push(b); faces.push(c);                               
+                    }              
+                    
+                }
+                
+            }
+            
+        }
+             
+        
+    };
+
+    my.laplacianSmooth = function(numiter, verts, faces) {
+            var tps = new Array(verts.length);
+            var i, il, j, jl, k, kl;
+            for (i = 0, il = verts.length; i < il; i++)
+                    tps[i] = {
+                        x : 0,
+                        y : 0,
+                        z : 0
+                    };
+            var vertdeg = new Array(20);
+            var flagvert;
+            for (i = 0; i < 20; i++)
+                    vertdeg[i] = new Array(verts.length);
+            for (i = 0, il = verts.length; i < il; i++)
+                    vertdeg[0][i] = 0;
+            for (i = 0, il = faces.length / 3; i < il; i++) {
+                var aoffset = i*3, boffset = i*3 + 1, coffset = i*3 + 2;
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
+                    if (faces[boffset] == vertdeg[j + 1][faces[aoffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[aoffset]]++;
+                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[boffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
+                    if (faces[coffset] == vertdeg[j + 1][faces[aoffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[aoffset]]++;
+                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[coffset];
+                }
+                // b
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
+                    if (faces[aoffset] == vertdeg[j + 1][faces[boffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[boffset]]++;
+                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[aoffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
+                    if (faces[coffset] == vertdeg[j + 1][faces[boffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[boffset]]++;
+                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[coffset];
+                }
+                // c
+                flagvert = true;
+                for (j = 0; j < vertdeg[0][faces[coffset]]; j++) {
+                    if (faces[aoffset] == vertdeg[j + 1][faces[coffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[coffset]]++;
+                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[aoffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[coffset]]; j < jl; j++) {
+                    if (faces[boffset] == vertdeg[j + 1][faces[coffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[coffset]]++;
+                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[boffset];
+                }
+            }
+
+            var wt = 1.00;
+            var wt2 = 0.50;
+            var ssign;
+            var scaleFactor = 1;
+            var outwt = 0.75 / (scaleFactor + 3.5); // area-preserving
+            for (k = 0; k < numiter; k++) {
+                    for (i = 0, il = verts.length; i < il; i++) {
+                            if (vertdeg[0][i] < 3) {
+                                    tps[i].x = verts[i].x;
+                                    tps[i].y = verts[i].y;
+                                    tps[i].z = verts[i].z;
+                            } else if (vertdeg[0][i] == 3 || vertdeg[0][i] == 4) {
+                                    tps[i].x = 0;
+                                    tps[i].y = 0;
+                                    tps[i].z = 0;
+                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
+                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
+                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
+                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
+                                    }
+                                    tps[i].x += wt2 * verts[i].x;
+                                    tps[i].y += wt2 * verts[i].y;
+                                    tps[i].z += wt2 * verts[i].z;
+                                    tps[i].x /= wt2 + vertdeg[0][i];
+                                    tps[i].y /= wt2 + vertdeg[0][i];
+                                    tps[i].z /= wt2 + vertdeg[0][i];
+                            } else {
+                                    tps[i].x = 0;
+                                    tps[i].y = 0;
+                                    tps[i].z = 0;
+                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
+                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
+                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
+                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
+                                    }
+                                    tps[i].x += wt * verts[i].x;
+                                    tps[i].y += wt * verts[i].y;
+                                    tps[i].z += wt * verts[i].z;
+                                    tps[i].x /= wt + vertdeg[0][i];
+                                    tps[i].y /= wt + vertdeg[0][i];
+                                    tps[i].z /= wt + vertdeg[0][i];
+                            }
+                    }
+                    for (i = 0, il = verts.length; i < il; i++) {
+                            verts[i].x = tps[i].x;
+                            verts[i].y = tps[i].y;
+                            verts[i].z = tps[i].z;
+                    }
+                    /*
+                     * computenorm(); for (var i = 0; i < vertnumber; i++) { if
+                     * (verts[i].inout) ssign = 1; else ssign = -1; verts[i].x += ssign *
+                     * outwt * verts[i].pn.x; verts[i].y += ssign * outwt *
+                     * verts[i].pn.y; verts[i].z += ssign * outwt * verts[i].pn.z; }
+                     */
+            }
+    };
+
+
+    /*
+     * These tables are based off those by Paul Bourke and Geoffrey Heller:
+     * http://paulbourke.net/geometry/polygonise/
+     * http://paulbourke.net/geometry/polygonise/table2.txt
+     * 
+     * However, they have been substantially modified to reflect a more 
+     * sensible corner numbering scheme and the discrete nature of our voxel data
+     * (resulting in fewer faces).
+     */
+    my.edgeTable = [ 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
+            0xb00, 0x0, 0x0, 0x0, 0x700, 0x0, 0xd00, 0xe00, 0xf00, 0x0, 0x0, 0x0,
+            0x8a, 0x0, 0x15, 0x0, 0x86, 0x0, 0x0, 0x0, 0x28c, 0x0, 0x813, 0xf19,
+            0xe10, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x0, 0x0, 0x126, 0x0, 0x0, 0x15, 0x1c,
+            0x0, 0xf23, 0x419, 0xd20, 0x0, 0xa8, 0xa2, 0xaa, 0x0, 0x285, 0x9ab,
+            0x8a2, 0x0, 0x2af, 0x125, 0xac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x0, 0x0,
+            0x0, 0x0, 0x0, 0x45, 0x0, 0x384, 0x0, 0x0, 0x0, 0x700, 0x8a, 0x83,
+            0x648, 0x780, 0x0, 0x51, 0x0, 0x81a, 0x54, 0x55, 0x54, 0x56, 0x0, 0x51,
+            0x0, 0xe5c, 0x14a, 0x451, 0x759, 0x650, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x45,
+            0x0, 0x1f6, 0x0, 0x0, 0x15, 0xdfc, 0x8a, 0x7f3, 0x4f9, 0x5f0, 0xb00,
+            0x68, 0x921, 0x6a, 0x348, 0x245, 0x16f, 0x66, 0xb00, 0xe6f, 0xd65,
+            0xc6c, 0x76a, 0x663, 0x569, 0x460, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
+            0xf46, 0x0, 0x0, 0x45, 0x24c, 0x2a, 0x823, 0x29, 0xb40, 0x0, 0x0, 0x0,
+            0x6ba, 0x0, 0x8f5, 0xfff, 0xef6, 0x0, 0xff, 0x2f5, 0x2fc, 0x9ea, 0x8f3,
+            0xbf9, 0xaf0, 0x0, 0x0, 0x51, 0x152, 0x0, 0xf55, 0x45f, 0xd56, 0x54,
+            0x357, 0x55, 0x154, 0x852, 0xb53, 0x59, 0x950, 0x700, 0x2c8, 0xc2,
+            0x48a, 0xfc4, 0xec5, 0xdcf, 0xcc6, 0x2c4, 0x2cf, 0xc5, 0xcc, 0xbca,
+            0xac3, 0x9c9, 0x8c0, 0x0, 0x0, 0x0, 0x0, 0xa8, 0x1a4, 0xa8, 0x7a6,
+            0xa2, 0xa2, 0x2a4, 0xbac, 0xaa, 0xa3, 0x2a8, 0x3a0, 0xd00, 0xc18,
+            0xd00, 0xe3a, 0x34, 0x35, 0x73f, 0x636, 0x924, 0x83f, 0xb35, 0xa3c,
+            0x12a, 0x33, 0x339, 0x230, 0xe00, 0xe00, 0xc12, 0xd9a, 0x684, 0x795,
+            0x49f, 0x596, 0x92, 0xb9f, 0x815, 0x99c, 0x9a, 0x393, 0x99, 0x190,
+            0xf00, 0xe08, 0xd01, 0xc0a, 0x704, 0x605, 0x50f, 0x406, 0xb02, 0xa0f,
+            0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
+    
+    var edgeTable = new Uint32Array(my.edgeTable);
+    
+    var triTable = my.triTable = [ [], [], [], [], [], [], [], [ 11, 9, 8 ], [], [], [],
+            [ 8, 10, 9 ], [], [ 10, 8, 11 ], [ 9, 11, 10 ],
+            [ 8, 10, 9, 8, 11, 10 ], [], [], [], [ 1, 7, 3 ], [], [ 4, 2, 0 ], [],
+            [ 2, 1, 7 ], [], [], [], [ 2, 7, 3, 2, 9, 7 ], [],
+            [ 1, 4, 11, 1, 0, 4 ], [ 3, 8, 0, 11, 9, 4, 11, 10, 9 ],
+            [ 4, 11, 9, 11, 10, 9 ], [], [], [], [ 5, 3, 1 ], [], [], [],
+            [ 2, 5, 8, 2, 1, 5 ], [], [], [ 2, 4, 0 ], [ 3, 2, 4 ], [],
+            [ 0, 9, 1, 8, 10, 5, 8, 11, 10 ], [ 3, 4, 0, 3, 10, 4 ],
+            [ 5, 8, 10, 8, 11, 10 ], [], [ 3, 5, 7 ], [ 7, 1, 5 ],
+            [ 1, 7, 3, 1, 5, 7 ], [], [ 9, 2, 0, 9, 7, 2 ],
+            [ 0, 3, 8, 1, 7, 11, 1, 5, 7 ], [ 11, 1, 7, 1, 5, 7 ], [],
+            [ 9, 1, 0, 5, 3, 2, 5, 7, 3 ], [ 8, 2, 5, 8, 0, 2 ],
+            [ 2, 5, 3, 5, 7, 3 ], [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
+            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
+            [ 11, 5, 7, 11, 10, 5 ], [], [], [], [], [], [ 0, 6, 2 ], [],
+            [ 7, 2, 9, 7, 9, 8 ], [], [], [], [ 8, 10, 9 ], [ 7, 1, 3 ],
+            [ 7, 1, 0 ], [ 6, 9, 3, 6, 10, 9 ], [ 7, 10, 8, 10, 9, 8 ], [],
+            [ 6, 0, 4 ], [], [ 11, 1, 4, 11, 3, 1 ], [ 2, 4, 6 ],
+            [ 2, 0, 4, 2, 4, 6 ], [ 2, 4, 6 ], [ 1, 4, 2, 4, 6, 2 ], [],
+            [ 6, 0, 4 ], [], [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ], [ 8, 6, 1, 8, 1, 3 ],
+            [ 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
+            [ 10, 4, 6, 10, 9, 4 ], [], [], [], [ 5, 3, 1 ], [], [ 0, 6, 2 ], [],
+            [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ], [], [], [ 2, 4, 0 ],
+            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ], [ 7, 1, 3 ],
+            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
+            [ 10, 5, 6, 4, 8, 7 ], [ 9, 11, 8 ], [ 3, 5, 6 ],
+            [ 0, 5, 11, 0, 11, 8 ], [ 6, 3, 5, 3, 1, 5 ], [ 3, 9, 6, 3, 8, 9 ],
+            [ 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
+            [ 1, 6, 2, 1, 5, 6 ], [ 9, 11, 8 ], [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ],
+            [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ], [ 3, 2, 11, 10, 5, 6 ],
+            [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ], [ 0, 9, 1, 5, 6, 10 ],
+            [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ], [], [], [], [], [], [], [],
+            [ 1, 10, 2, 9, 11, 6, 9, 8, 11 ], [], [], [ 6, 0, 2 ],
+            [ 3, 6, 9, 3, 2, 6 ], [ 3, 5, 1 ], [ 0, 5, 1, 0, 11, 5 ], [ 0, 3, 5 ],
+            [ 6, 9, 11, 9, 8, 11 ], [], [], [], [ 4, 5, 9, 7, 1, 10, 7, 3, 1 ], [],
+            [ 11, 6, 7, 2, 4, 5, 2, 0, 4 ],
+            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
+            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [],
+            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ], [ 9, 4, 5, 0, 6, 7, 0, 2, 6 ],
+            [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ], [ 6, 7, 11, 5, 3, 8, 5, 1, 3 ],
+            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
+            [ 9, 4, 5, 7, 11, 6 ], [], [], [ 0, 6, 4 ], [ 8, 6, 4, 8, 1, 6 ], [],
+            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
+            [ 10, 2, 1, 6, 0, 3, 6, 4, 0 ], [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ],
+            [ 4, 2, 6 ], [ 1, 0, 9, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
+            [ 8, 2, 4, 2, 6, 4 ], [ 11, 4, 1, 11, 6, 4 ],
+            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 3, 6, 0, 6, 4, 0 ],
+            [ 8, 6, 4, 8, 11, 6 ], [ 10, 8, 9 ], [ 6, 3, 9, 6, 7, 3 ], [ 6, 7, 1 ],
+            [ 10, 7, 1, 7, 3, 1 ], [ 7, 11, 6, 8, 10, 2, 8, 9, 10 ],
+            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
+            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2 ],
+            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 7, 0, 6, 0, 2, 6 ],
+            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
+            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ], [], [], [],
+            [], [ 5, 3, 7 ], [ 8, 5, 2, 8, 7, 5 ], [ 5, 3, 7 ],
+            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 1, 7, 5 ], [ 1, 7, 5 ],
+            [ 9, 2, 7, 9, 7, 5 ], [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ],
+            [ 1, 3, 7, 1, 7, 5 ], [ 0, 7, 1, 7, 5, 1 ], [ 9, 3, 5, 3, 7, 5 ],
+            [ 9, 7, 5, 9, 8, 7 ], [ 8, 10, 11 ], [ 3, 4, 10, 3, 10, 11 ],
+            [ 8, 10, 11 ], [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ], [ 2, 4, 5 ],
+            [ 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
+            [ 2, 1, 10, 9, 4, 5 ], [ 2, 8, 5, 2, 11, 8 ],
+            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
+            [ 11, 3, 2, 9, 4, 5 ], [ 8, 5, 3, 5, 1, 3 ], [ 5, 0, 4, 5, 1, 0 ],
+            [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ], [ 11, 9, 10 ], [ 11, 9, 10 ],
+            [ 1, 11, 4, 1, 10, 11 ], [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
+            [ 2, 7, 9, 2, 9, 10 ], [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ],
+            [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ], [ 10, 2, 1, 8, 7, 4 ], [ 1, 7, 4 ],
+            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 11, 4, 2, 4, 0, 2 ],
+            [ 2, 11, 3, 7, 4, 8 ], [ 4, 1, 7, 1, 3, 7 ], [ 1, 0, 9, 8, 7, 4 ],
+            [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ], [ 8, 9, 10, 8, 10, 11 ],
+            [ 3, 9, 11, 9, 10, 11 ], [ 0, 10, 8, 10, 11, 8 ],
+            [ 10, 3, 1, 10, 11, 3 ], [ 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
+            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 1, 11, 9, 11, 8, 9 ],
+            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
+            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
+     
+    var edgeTable2 = [ 0x0, 0x109, 0x203, 0x30a, 0x80c, 0x905, 0xa0f,
+            0xb06, 0x406, 0x50f, 0x605, 0x70c, 0xc0a, 0xd03, 0xe09, 0xf00, 0x190,
+            0x99, 0x393, 0x29a, 0x99c, 0x895, 0xb9f, 0xa96, 0x596, 0x49f, 0x795,
+            0x69c, 0xd9a, 0xc93, 0xf99, 0xe90, 0x230, 0x339, 0x33, 0x13a, 0xa3c,
+            0xb35, 0x83f, 0x936, 0x636, 0x73f, 0x435, 0x53c, 0xe3a, 0xf33, 0xc39,
+            0xd30, 0x3a0, 0x2a9, 0x1a3, 0xaa, 0xbac, 0xaa5, 0x9af, 0x8a6, 0x7a6,
+            0x6af, 0x5a5, 0x4ac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x8c0, 0x9c9, 0xac3,
+            0xbca, 0xcc, 0x1c5, 0x2cf, 0x3c6, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x4ca,
+            0x5c3, 0x6c9, 0x7c0, 0x950, 0x859, 0xb53, 0xa5a, 0x15c, 0x55, 0x35f,
+            0x256, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x55a, 0x453, 0x759, 0x650, 0xaf0,
+            0xbf9, 0x8f3, 0x9fa, 0x2fc, 0x3f5, 0xff, 0x1f6, 0xef6, 0xfff, 0xcf5,
+            0xdfc, 0x6fa, 0x7f3, 0x4f9, 0x5f0, 0xb60, 0xa69, 0x963, 0x86a, 0x36c,
+            0x265, 0x16f, 0x66, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x76a, 0x663, 0x569,
+            0x460, 0x460, 0x569, 0x663, 0x76a, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x66,
+            0x16f, 0x265, 0x36c, 0x86a, 0x963, 0xa69, 0xb60, 0x5f0, 0x4f9, 0x7f3,
+            0x6fa, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x1f6, 0xff, 0x3f5, 0x2fc, 0x9fa,
+            0x8f3, 0xbf9, 0xaf0, 0x650, 0x759, 0x453, 0x55a, 0xe5c, 0xf55, 0xc5f,
+            0xd56, 0x256, 0x35f, 0x55, 0x15c, 0xa5a, 0xb53, 0x859, 0x950, 0x7c0,
+            0x6c9, 0x5c3, 0x4ca, 0xfcc, 0xec5, 0xdcf, 0xcc6, 0x3c6, 0x2cf, 0x1c5,
+            0xcc, 0xbca, 0xac3, 0x9c9, 0x8c0, 0xca0, 0xda9, 0xea3, 0xfaa, 0x4ac,
+            0x5a5, 0x6af, 0x7a6, 0x8a6, 0x9af, 0xaa5, 0xbac, 0xaa, 0x1a3, 0x2a9,
+            0x3a0, 0xd30, 0xc39, 0xf33, 0xe3a, 0x53c, 0x435, 0x73f, 0x636, 0x936,
+            0x83f, 0xb35, 0xa3c, 0x13a, 0x33, 0x339, 0x230, 0xe90, 0xf99, 0xc93,
+            0xd9a, 0x69c, 0x795, 0x49f, 0x596, 0xa96, 0xb9f, 0x895, 0x99c, 0x29a,
+            0x393, 0x99, 0x190, 0xf00, 0xe09, 0xd03, 0xc0a, 0x70c, 0x605, 0x50f,
+            0x406, 0xb06, 0xa0f, 0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
+     
+    var triTable2 = [ [], [ 8, 3, 0 ], [ 9, 0, 1 ], [ 8, 3, 1, 8, 1, 9 ],
+            [ 11, 2, 3 ], [ 11, 2, 0, 11, 0, 8 ], [ 11, 2, 3, 0, 1, 9 ],
+            [ 2, 1, 11, 1, 9, 11, 11, 9, 8 ], [ 10, 1, 2 ], [ 8, 3, 0, 1, 2, 10 ],
+            [ 9, 0, 2, 9, 2, 10 ], [ 3, 2, 8, 2, 10, 8, 8, 10, 9 ],
+            [ 10, 1, 3, 10, 3, 11 ], [ 1, 0, 10, 0, 8, 10, 10, 8, 11 ],
+            [ 0, 3, 9, 3, 11, 9, 9, 11, 10 ], [ 8, 10, 9, 8, 11, 10 ], [ 8, 4, 7 ],
+            [ 3, 0, 4, 3, 4, 7 ], [ 1, 9, 0, 8, 4, 7 ],
+            [ 9, 4, 1, 4, 7, 1, 1, 7, 3 ], [ 2, 3, 11, 7, 8, 4 ],
+            [ 7, 11, 4, 11, 2, 4, 4, 2, 0 ], [ 3, 11, 2, 4, 7, 8, 9, 0, 1 ],
+            [ 2, 7, 11, 2, 1, 7, 1, 4, 7, 1, 9, 4 ], [ 10, 1, 2, 8, 4, 7 ],
+            [ 2, 10, 1, 0, 4, 7, 0, 7, 3 ], [ 4, 7, 8, 0, 2, 10, 0, 10, 9 ],
+            [ 2, 7, 3, 2, 9, 7, 7, 9, 4, 2, 10, 9 ],
+            [ 8, 4, 7, 11, 10, 1, 11, 1, 3 ],
+            [ 11, 4, 7, 1, 4, 11, 1, 11, 10, 1, 0, 4 ],
+            [ 3, 8, 0, 7, 11, 4, 11, 9, 4, 11, 10, 9 ],
+            [ 7, 11, 4, 4, 11, 9, 11, 10, 9 ], [ 9, 5, 4 ], [ 3, 0, 8, 4, 9, 5 ],
+            [ 5, 4, 0, 5, 0, 1 ], [ 4, 8, 5, 8, 3, 5, 5, 3, 1 ],
+            [ 11, 2, 3, 9, 5, 4 ], [ 9, 5, 4, 8, 11, 2, 8, 2, 0 ],
+            [ 3, 11, 2, 1, 5, 4, 1, 4, 0 ],
+            [ 8, 5, 4, 2, 5, 8, 2, 8, 11, 2, 1, 5 ], [ 2, 10, 1, 9, 5, 4 ],
+            [ 0, 8, 3, 5, 4, 9, 10, 1, 2 ], [ 10, 5, 2, 5, 4, 2, 2, 4, 0 ],
+            [ 3, 4, 8, 3, 2, 4, 2, 5, 4, 2, 10, 5 ],
+            [ 5, 4, 9, 1, 3, 11, 1, 11, 10 ],
+            [ 0, 9, 1, 4, 8, 5, 8, 10, 5, 8, 11, 10 ],
+            [ 3, 4, 0, 3, 10, 4, 4, 10, 5, 3, 11, 10 ],
+            [ 4, 8, 5, 5, 8, 10, 8, 11, 10 ], [ 9, 5, 7, 9, 7, 8 ],
+            [ 0, 9, 3, 9, 5, 3, 3, 5, 7 ], [ 8, 0, 7, 0, 1, 7, 7, 1, 5 ],
+            [ 1, 7, 3, 1, 5, 7 ], [ 11, 2, 3, 8, 9, 5, 8, 5, 7 ],
+            [ 9, 2, 0, 9, 7, 2, 2, 7, 11, 9, 5, 7 ],
+            [ 0, 3, 8, 2, 1, 11, 1, 7, 11, 1, 5, 7 ],
+            [ 2, 1, 11, 11, 1, 7, 1, 5, 7 ], [ 1, 2, 10, 5, 7, 8, 5, 8, 9 ],
+            [ 9, 1, 0, 10, 5, 2, 5, 3, 2, 5, 7, 3 ],
+            [ 5, 2, 10, 8, 2, 5, 8, 5, 7, 8, 0, 2 ],
+            [ 10, 5, 2, 2, 5, 3, 5, 7, 3 ],
+            [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
+            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
+            [ 11, 5, 7, 11, 10, 5 ], [ 11, 7, 6 ], [ 0, 8, 3, 11, 7, 6 ],
+            [ 9, 0, 1, 11, 7, 6 ], [ 7, 6, 11, 3, 1, 9, 3, 9, 8 ],
+            [ 2, 3, 7, 2, 7, 6 ], [ 8, 7, 0, 7, 6, 0, 0, 6, 2 ],
+            [ 1, 9, 0, 3, 7, 6, 3, 6, 2 ], [ 7, 6, 2, 7, 2, 9, 2, 1, 9, 7, 9, 8 ],
+            [ 1, 2, 10, 6, 11, 7 ], [ 2, 10, 1, 7, 6, 11, 8, 3, 0 ],
+            [ 11, 7, 6, 10, 9, 0, 10, 0, 2 ],
+            [ 7, 6, 11, 3, 2, 8, 8, 2, 10, 8, 10, 9 ],
+            [ 6, 10, 7, 10, 1, 7, 7, 1, 3 ],
+            [ 6, 10, 1, 6, 1, 7, 7, 1, 0, 7, 0, 8 ],
+            [ 9, 0, 3, 6, 9, 3, 6, 10, 9, 6, 3, 7 ],
+            [ 6, 10, 7, 7, 10, 8, 10, 9, 8 ], [ 8, 4, 6, 8, 6, 11 ],
+            [ 11, 3, 6, 3, 0, 6, 6, 0, 4 ], [ 0, 1, 9, 4, 6, 11, 4, 11, 8 ],
+            [ 1, 9, 4, 11, 1, 4, 11, 3, 1, 11, 4, 6 ],
+            [ 3, 8, 2, 8, 4, 2, 2, 4, 6 ], [ 2, 0, 4, 2, 4, 6 ],
+            [ 1, 9, 0, 3, 8, 2, 2, 8, 4, 2, 4, 6 ], [ 9, 4, 1, 1, 4, 2, 4, 6, 2 ],
+            [ 10, 1, 2, 11, 8, 4, 11, 4, 6 ],
+            [ 10, 1, 2, 11, 3, 6, 6, 3, 0, 6, 0, 4 ],
+            [ 0, 2, 10, 0, 10, 9, 4, 11, 8, 4, 6, 11 ],
+            [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ],
+            [ 8, 4, 6, 8, 6, 1, 6, 10, 1, 8, 1, 3 ],
+            [ 1, 0, 10, 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
+            [ 10, 4, 6, 10, 9, 4 ], [ 9, 5, 4, 7, 6, 11 ],
+            [ 4, 9, 5, 3, 0, 8, 11, 7, 6 ], [ 6, 11, 7, 4, 0, 1, 4, 1, 5 ],
+            [ 6, 11, 7, 4, 8, 5, 5, 8, 3, 5, 3, 1 ], [ 4, 9, 5, 6, 2, 3, 6, 3, 7 ],
+            [ 9, 5, 4, 8, 7, 0, 0, 7, 6, 0, 6, 2 ],
+            [ 4, 0, 1, 4, 1, 5, 6, 3, 7, 6, 2, 3 ], [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ],
+            [ 6, 11, 7, 1, 2, 10, 9, 5, 4 ],
+            [ 11, 7, 6, 8, 3, 0, 1, 2, 10, 9, 5, 4 ],
+            [ 11, 7, 6, 10, 5, 2, 2, 5, 4, 2, 4, 0 ],
+            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ],
+            [ 4, 9, 5, 6, 10, 7, 7, 10, 1, 7, 1, 3 ],
+            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
+            [ 10, 5, 6, 4, 8, 7 ], [ 5, 6, 9, 6, 11, 9, 9, 11, 8 ],
+            [ 0, 9, 5, 0, 5, 3, 3, 5, 6, 3, 6, 11 ],
+            [ 0, 1, 5, 0, 5, 11, 5, 6, 11, 0, 11, 8 ],
+            [ 11, 3, 6, 6, 3, 5, 3, 1, 5 ], [ 9, 5, 6, 3, 9, 6, 3, 8, 9, 3, 6, 2 ],
+            [ 5, 6, 9, 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
+            [ 1, 6, 2, 1, 5, 6 ], [ 1, 2, 10, 5, 6, 9, 9, 6, 11, 9, 11, 8 ],
+            [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ], [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ],
+            [ 3, 2, 11, 10, 5, 6 ], [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ],
+            [ 0, 9, 1, 5, 6, 10 ], [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ],
+            [ 10, 6, 5 ], [ 8, 3, 0, 10, 6, 5 ], [ 0, 1, 9, 5, 10, 6 ],
+            [ 10, 6, 5, 9, 8, 3, 9, 3, 1 ], [ 3, 11, 2, 10, 6, 5 ],
+            [ 6, 5, 10, 2, 0, 8, 2, 8, 11 ], [ 1, 9, 0, 6, 5, 10, 11, 2, 3 ],
+            [ 1, 10, 2, 5, 9, 6, 9, 11, 6, 9, 8, 11 ], [ 1, 2, 6, 1, 6, 5 ],
+            [ 0, 8, 3, 2, 6, 5, 2, 5, 1 ], [ 5, 9, 6, 9, 0, 6, 6, 0, 2 ],
+            [ 9, 6, 5, 3, 6, 9, 3, 9, 8, 3, 2, 6 ], [ 11, 6, 3, 6, 5, 3, 3, 5, 1 ],
+            [ 0, 5, 1, 0, 11, 5, 5, 11, 6, 0, 8, 11 ],
+            [ 0, 5, 9, 0, 3, 5, 3, 6, 5, 3, 11, 6 ],
+            [ 5, 9, 6, 6, 9, 11, 9, 8, 11 ], [ 10, 6, 5, 4, 7, 8 ],
+            [ 5, 10, 6, 7, 3, 0, 7, 0, 4 ], [ 5, 10, 6, 0, 1, 9, 8, 4, 7 ],
+            [ 4, 5, 9, 6, 7, 10, 7, 1, 10, 7, 3, 1 ],
+            [ 7, 8, 4, 2, 3, 11, 10, 6, 5 ],
+            [ 11, 6, 7, 10, 2, 5, 2, 4, 5, 2, 0, 4 ],
+            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
+            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [ 7, 8, 4, 5, 1, 2, 5, 2, 6 ],
+            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ],
+            [ 9, 4, 5, 8, 0, 7, 0, 6, 7, 0, 2, 6 ], [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ],
+            [ 6, 7, 11, 4, 5, 8, 5, 3, 8, 5, 1, 3 ],
+            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
+            [ 9, 4, 5, 7, 11, 6 ], [ 10, 6, 4, 10, 4, 9 ],
+            [ 8, 3, 0, 9, 10, 6, 9, 6, 4 ], [ 1, 10, 0, 10, 6, 0, 0, 6, 4 ],
+            [ 8, 6, 4, 8, 1, 6, 6, 1, 10, 8, 3, 1 ],
+            [ 2, 3, 11, 6, 4, 9, 6, 9, 10 ],
+            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
+            [ 10, 2, 1, 11, 6, 3, 6, 0, 3, 6, 4, 0 ],
+            [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ], [ 9, 1, 4, 1, 2, 4, 4, 2, 6 ],
+            [ 1, 0, 9, 3, 2, 8, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
+            [ 3, 2, 8, 8, 2, 4, 2, 6, 4 ],
+            [ 1, 4, 9, 11, 4, 1, 11, 1, 3, 11, 6, 4 ],
+            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 11, 6, 3, 3, 6, 0, 6, 4, 0 ],
+            [ 8, 6, 4, 8, 11, 6 ], [ 6, 7, 10, 7, 8, 10, 10, 8, 9 ],
+            [ 9, 3, 0, 6, 3, 9, 6, 9, 10, 6, 7, 3 ],
+            [ 6, 1, 10, 6, 7, 1, 7, 0, 1, 7, 8, 0 ],
+            [ 6, 7, 10, 10, 7, 1, 7, 3, 1 ],
+            [ 7, 11, 6, 3, 8, 2, 8, 10, 2, 8, 9, 10 ],
+            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
+            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2, 2, 9, 1, 7, 8, 9 ],
+            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 8, 0, 7, 7, 0, 6, 0, 2, 6 ],
+            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
+            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ],
+            [ 11, 7, 5, 11, 5, 10 ], [ 3, 0, 8, 7, 5, 10, 7, 10, 11 ],
+            [ 9, 0, 1, 10, 11, 7, 10, 7, 5 ],
+            [ 3, 1, 9, 3, 9, 8, 7, 10, 11, 7, 5, 10 ],
+            [ 10, 2, 5, 2, 3, 5, 5, 3, 7 ],
+            [ 5, 10, 2, 8, 5, 2, 8, 7, 5, 8, 2, 0 ],
+            [ 9, 0, 1, 10, 2, 5, 5, 2, 3, 5, 3, 7 ],
+            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 2, 11, 1, 11, 7, 1, 1, 7, 5 ],
+            [ 0, 8, 3, 2, 11, 1, 1, 11, 7, 1, 7, 5 ],
+            [ 9, 0, 2, 9, 2, 7, 2, 11, 7, 9, 7, 5 ],
+            [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ], [ 1, 3, 7, 1, 7, 5 ],
+            [ 8, 7, 0, 0, 7, 1, 7, 5, 1 ], [ 0, 3, 9, 9, 3, 5, 3, 7, 5 ],
+            [ 9, 7, 5, 9, 8, 7 ], [ 4, 5, 8, 5, 10, 8, 8, 10, 11 ],
+            [ 3, 0, 4, 3, 4, 10, 4, 5, 10, 3, 10, 11 ],
+            [ 0, 1, 9, 4, 5, 8, 8, 5, 10, 8, 10, 11 ],
+            [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ],
+            [ 3, 8, 4, 3, 4, 2, 2, 4, 5, 2, 5, 10 ],
+            [ 10, 2, 5, 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
+            [ 2, 1, 10, 9, 4, 5 ], [ 8, 4, 5, 2, 8, 5, 2, 11, 8, 2, 5, 1 ],
+            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
+            [ 11, 3, 2, 9, 4, 5 ], [ 4, 5, 8, 8, 5, 3, 5, 1, 3 ],
+            [ 5, 0, 4, 5, 1, 0 ], [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ],
+            [ 7, 4, 11, 4, 9, 11, 11, 9, 10 ],
+            [ 3, 0, 8, 7, 4, 11, 11, 4, 9, 11, 9, 10 ],
+            [ 11, 7, 4, 1, 11, 4, 1, 10, 11, 1, 4, 0 ],
+            [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
+            [ 2, 3, 7, 2, 7, 9, 7, 4, 9, 2, 9, 10 ],
+            [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ], [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ],
+            [ 10, 2, 1, 8, 7, 4 ], [ 2, 11, 7, 2, 7, 1, 1, 7, 4, 1, 4, 9 ],
+            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 7, 4, 11, 11, 4, 2, 4, 0, 2 ],
+            [ 2, 11, 3, 7, 4, 8 ], [ 9, 1, 4, 4, 1, 7, 1, 3, 7 ],
+            [ 1, 0, 9, 8, 7, 4 ], [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ],
+            [ 8, 9, 10, 8, 10, 11 ], [ 0, 9, 3, 3, 9, 11, 9, 10, 11 ],
+            [ 1, 10, 0, 0, 10, 8, 10, 11, 8 ], [ 10, 3, 1, 10, 11, 3 ],
+            [ 3, 8, 2, 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
+            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 2, 11, 1, 1, 11, 9, 11, 8, 9 ],
+            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
+            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
             
-            var showBackground = style.showBackground;
-            if(showBackground === '0' || showBackground === 'false') showBackground = false;
-            if(typeof(showBackground) == "undefined") showBackground = true; //default
-            var font = style.font ? style.font : "sans-serif";
-
-            var fontSize = parseInt(style.fontSize) ? parseInt(style.fontSize) : 18;
+            return my;
+};
 
-            var fontColor = getColor(style.fontColor, style.fontOpacity,
-                     {
-                        r : 255,
-                        g : 255,
-                        b : 255,
-                        a : 1.0
-                    });
+//each webworker needs its own marching cube object
+$3Dmol.MarchingCube  = $3Dmol.MarchingCubeInitializer();    
 
-            var padding = style.padding ? style.padding : 4;
-            var borderThickness = style.borderThickness ? style.borderThickness
-                    : 0;
-    
-            var backgroundColor = getColor(style.backgroundColor, style.backgroundOpacity, 
-                     {
-                        r : 0,
-                        g : 0,
-                        b : 0,
-                        a : 1.0
-                    });
-                    
-            var borderColor = getColor(style.borderColor, style.borderOpacity, backgroundColor);
 
-                    
-            var position = style.position ? style.position
-                    : {
-                        x : -10,
-                        y : 1,
-                        z : 1
-                    };
-                    
-            // Should labels always be in front of model?
-            var inFront = (style.inFront !== undefined) ? style.inFront    : true;
-            if(inFront === 'false' || inFront === '0') inFront = false;
 
-            // clear canvas
+/**
+ * $3Dmol.Parsers stores functions for parsing molecular data. They all take a string of molecular data
+ * and options. The default behavior is to only read the first model in the case of multimodel files, and
+ * all parsers return a list of atom list(s)
+ * 
+ * $3Dmol.Parsers.<ext> corresponds to the parsers for files with extension ext
+ */
+$3Dmol.Parsers = (function() {
+    var parsers = {};
 
-            var spriteAlignment = style.alignment || $3Dmol.SpriteAlignment.topLeft;
+    /**
+     * @param {AtomSpec[]}
+     *            atomsarray
+     */
+    var assignBonds = function(atoms) {
+        // assign bonds - yuck, can't count on connect records
 
-            var bold = "";
-            if(style.bold)
-                bold = "bold ";
-            this.context.font = bold+fontSize + "px  " + font;
+        for (var i = 0, n = atoms.length; i < n; i++) {
+            // Don't reindex if atoms are already indexed
+            if (!atoms[i].index)
+                atoms[i].index = i;
+        }
 
-            var metrics = this.context.measureText(this.text);
-            var textWidth = metrics.width;
-            
-            if(!showBackground) borderThickness = 0;
-        
-            var width = textWidth+2.5*borderThickness +2*padding;
-            var height = fontSize*1.25+2*borderThickness+2*padding;            // 1.25 is extra height factor for text below baseline: g,j,p,q.
+        var grid = {};
+        var MAX_BOND_LENGTH = 4.95; // (largest bond length, Cs) 2.25 * 2 * 1.1 (fudge factor)
 
-            
-            if(style.backgroundImage) {
-                var img = style.backgroundImage;
-                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
-                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
-                if(w > width) width = w;
-                if(h > height) height = h;
+        for (var index = 0; index < atoms.length; index++) {
+            var atom = atoms[index];
+            var x = Math.floor(atom.x / MAX_BOND_LENGTH);
+            var y = Math.floor(atom.y / MAX_BOND_LENGTH);
+            var z = Math.floor(atom.z / MAX_BOND_LENGTH);
+            if (!grid[x]) {
+                grid[x] = {};
             }
-
-            this.canvas.width = width;
-            this.canvas.height = height;
-            this.context.clearRect(0, 0, this.canvas.width, this.canvas.height);
-
-            var bold = "";
-            if(style.bold)
-                bold = "bold ";
-            this.context.font = bold+fontSize + "px  " + font;
-
-            // background color
-            this.context.fillStyle = "rgba(" + backgroundColor.r + ","
-                    + backgroundColor.g + "," + backgroundColor.b
-                    + "," + backgroundColor.a + ")";
-            // border color
-            this.context.strokeStyle = "rgba(" + borderColor.r + ","
-                    + borderColor.g + "," + borderColor.b + ","
-                    + borderColor.a + ")";
-
-            this.context.lineWidth = borderThickness;
-            if(showBackground) {
-                roundRect(this.context, borderThickness,borderThickness , width-2*borderThickness,height-2*borderThickness, 6, borderThickness > 0);
+            if (!grid[x][y]) {
+                grid[x][y] = {};
             }
-            
-            if(style.backgroundImage) {
-                var img = style.backgroundImage;
-                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
-                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
-                this.context.drawImage(img,0,0, w, h);
+            if (!grid[x][y][z]) {
+                grid[x][y][z] = [];
             }
-            
-
-            // text color
-            this.context.fillStyle = "rgba(" + fontColor.r + ","
-                    + fontColor.g + "," + fontColor.b + ","
-                    + fontColor.a + ")";
-            
-            this.context.fillText(this.text, borderThickness+padding,
-                    fontSize + borderThickness+padding, textWidth);
-
-            // canvas contents will be used for a texture
-            var texture = new $3Dmol.Texture(this.canvas);
-            texture.needsUpdate = true;
-            this.sprite.material = new $3Dmol.SpriteMaterial({
-                map : texture,
-                useScreenCoordinates : useScreen,
-                alignment : spriteAlignment,
-                depthTest : !inFront
-            });
-
-            this.sprite.scale.set(1,1,1);
-
-            this.sprite.position.set(position.x, position.y, position.z);
-        };
 
-    }(),
+            grid[x][y][z].push(atom);
+        }
 
-    // clean up material and texture
-    dispose : function() {
+        var findConnections = function(points, otherPoints) {
+            for (var i = 0; i < points.length; i++) {
+                var atom1 = points[i];
+                for (var j = 0; j < otherPoints.length; j++) {
+                    var atom2 = otherPoints[j];
+
+                    if (areConnected(atom1, atom2)) {
+                        if (atom1.bonds.indexOf(atom2.index) == -1) {
+                            atom1.bonds.push(atom2.index);
+                            atom1.bondOrder.push(1);
+                            atom2.bonds.push(atom1.index);
+                            atom2.bondOrder.push(1);
+                        }
+                    }
+                }
+            }
+        }
 
-        if (this.sprite.material.map !== undefined)
-            this.sprite.material.map.dispose();
-        if (this.sprite.material !== undefined)
-            this.sprite.material.dispose();
-    }
 
-};
+        /*const*/ var OFFSETS = [
+            {x: 0, y: 0, z: 1},
+            {x: 0, y: 1, z:-1},
+            {x: 0, y: 1, z: 0},
+            {x: 0, y: 1, z: 1},
+            {x: 1, y:-1, z:-1},
+            {x: 1, y:-1, z: 0},
+            {x: 1, y:-1, z: 1},
+            {x: 1, y: 0, z:-1},
+            {x: 1, y: 0, z: 0},
+            {x: 1, y: 0, z: 1},
+            {x: 1, y: 1, z:-1},
+            {x: 1, y: 1, z: 0},
+            {x: 1, y: 1, z: 1}
+        ];
+        for (var x in grid) {
+            x = parseInt(x);
+            for (var y in grid[x]) {
+                y = parseInt(y);
+                for (var z in grid[x][y]) {
+                    z = parseInt(z);
+                    var points = grid[x][y][z];
+
+                    for (var i = 0; i < points.length; i++) {
+                        var atom1 = points[i];
+                        for (var j = i + 1; j < points.length; j++) {
+                            var atom2 = points[j];
+                            if (areConnected(atom1, atom2)) {
+                                if (atom1.bonds.indexOf(atom2.index) == -1) {
+                                    atom1.bonds.push(atom2.index);
+                                    atom1.bondOrder.push(1);
+                                    atom2.bonds.push(atom1.index);
+                                    atom2.bondOrder.push(1);
+                                }
+                            }
+                        }
+                    }
 
-/**
- * $3Dmol.Parsers stores functions for parsing molecular data.
- * The all take an atom list (which gets filled out) and a string.
- * 
- * $3Dmol.Parsers.<ext> corresponds to the parsers for files with extension ext
- */
-$3Dmol.Parsers = (function() {
-    var parsers = {};
-    
-     /** @param {AtomSpec[]} atomsarray */
-    var assignBonds = function(atomsarray) {
-        // assign bonds - yuck, can't count on connect records
-        var atoms = atomsarray.slice(0);
-        var i, j, n;
-        for (i = 0, n = atomsarray.length; i < n; i++)
-        {
-            //Don't reindex if atoms are already indexed 
-            if (!atomsarray[i].index)
-                atomsarray[i].index = i;
-        }
-        
-        atoms.sort(function(a, b) {
-            return a.z - b.z;
-        });
-        for (i = 0, n = atoms.length; i < n; i++) {
-            var ai = atoms[i];
+                    for (var o = 0; o < OFFSETS.length; o++) {
+                        var offset = OFFSETS[o];
+                        if (!grid[x+offset.x]
+                            || !grid[x+offset.x][y+offset.y]
+                            || !grid[x+offset.x][y+offset.y][z+offset.z]) continue;
 
-            for (j = i + 1; j < n; j++) {
-                var aj = atoms[j];
-                if (aj.z - ai.z > 1.9) // can't be connected
-                    break;
-                if (areConnected(ai, aj)) {
-                    if (ai.bonds.indexOf(aj.index) == -1) {
-                        // only add if not already there
-                        ai.bonds.push(aj.index);
-                        ai.bondOrder.push(1);
-                        aj.bonds.push(ai.index);
-                        aj.bondOrder.push(1);
+                        var otherPoints = grid[x + offset.x][y + offset.y][z + offset.z];
+                        findConnections(points, otherPoints);
                     }
                 }
             }
         }
     };
-    
+
     // this is optimized for proteins where it is assumed connected
     // atoms are on the same or next residue
-    /** @param {AtomSpec[]} atomsarray */
+    /**
+     * @param {AtomSpec[]}
+     *            atomsarray
+     */
     var assignPDBBonds = function(atomsarray) {
         // assign bonds - yuck, can't count on connect records
         var protatoms = [];
-        var hetatoms = [];        
+        var hetatoms = [];
         var i, n;
         for (i = 0, n = atomsarray.length; i < n; i++) {
             var atom = atomsarray[i];
             atom.index = i;
-            if(atom.hetflag)
+            if (atom.hetflag)
                 hetatoms.push(atom);
             else
                 protatoms.push(atom);
         }
 
         assignBonds(hetatoms);
-        
+
         // sort by resid
         protatoms.sort(function(a, b) {
-            if(a.chain != b.chain)
+            if (a.chain != b.chain)
                 return a.chain < b.chain ? -1 : 1;
             return a.resi - b.resi;
         });
-        
-        //for identifying connected residues
+
+        // for identifying connected residues
         var currentResi = -1;
         var reschain = -1;
         var lastResConnected;
-        
+
         for (i = 0, n = protatoms.length; i < n; i++) {
             var ai = protatoms[i];
-            
+
             if (ai.resi !== currentResi) {
                 currentResi = ai.resi;
                 if (!lastResConnected)
                     reschain++;
-                    
+
                 lastResConnected = false;
             }
-            
+
             ai.reschain = reschain;
 
-            for ( var j = i + 1; j < protatoms.length; j++) {
+            for (var j = i + 1; j < protatoms.length; j++) {
                 var aj = protatoms[j];
-                if(aj.chain != ai.chain)
+                if (aj.chain != ai.chain)
                     break;
                 if (aj.resi - ai.resi > 1) // can't be connected
                     break;
@@ -14430,14 +20232,14 @@ $3Dmol.Parsers = (function() {
                         aj.bonds.push(ai.index);
                         aj.bondOrder.push(1);
                     }
-                    
-                    if (ai.resi !== aj.resi) 
-                        lastResConnected = true;                   
-                        
+
+                    if (ai.resi !== aj.resi)
+                        lastResConnected = true;
+
                 }
             }
         }
-        
+
     };
 
     // this will identify all hydrogen bonds between backbone
@@ -14455,7 +20257,7 @@ $3Dmol.Parsers = (function() {
             if (!atom.hetflag && (atom.atom === "N" || atom.atom === "O")) {
                 atoms.push(atom);
                 atom.hbondOther = null;
-                atom.hbondDistanceSq = Number.POSITIVE_INFINITY;                
+                atom.hbondDistanceSq = Number.POSITIVE_INFINITY;
             }
         }
 
@@ -14471,692 +20273,895 @@ $3Dmol.Parsers = (function() {
                 if (zdiff > maxlength) // can't be connected
                     break;
                 if (aj.atom == ai.atom)
-                    continue; //can't be connected, but later might be    
+                    continue; // can't be connected, but later might be
                 var ydiff = Math.abs(aj.y - ai.y);
-                if( ydiff > maxlength)
+                if (ydiff > maxlength)
                     continue;
                 var xdiff = Math.abs(aj.x - ai.x);
-                if(xdiff > maxlength)
+                if (xdiff > maxlength)
                     continue;
-                var dist = xdiff*xdiff+ydiff*ydiff+zdiff*zdiff;
-                if (dist >  maxlengthSq)
+                var dist = xdiff * xdiff + ydiff * ydiff + zdiff * zdiff;
+                if (dist > maxlengthSq)
                     continue;
 
-                if(aj.chain == ai.chain && Math.abs(aj.resi - ai.resi) < 4)
-                    continue; //ignore bonds between too close residues
-                //select closest hbond
+                if (aj.chain == ai.chain && Math.abs(aj.resi - ai.resi) < 4)
+                    continue; // ignore bonds between too close residues
+                // select closest hbond
                 if (dist < ai.hbondDistanceSq) {
                     ai.hbondOther = aj;
                     ai.hbondDistanceSq = dist;
                 }
-                if(dist < aj.hbondDistanceSq) {
+                if (dist < aj.hbondDistanceSq) {
                     aj.hbondOther = ai;
                     aj.hbondDistanceSq = dist;
                 }
             }
         }
-    };
+    };
+
+    var computeSecondaryStructure = function(atomsarray) {
+        assignBackboneHBonds(atomsarray);
+
+        // compute, per residue, what the secondary structure is
+        var chres = {}; // lookup by chain and resid
+        var i, il, c, r;
+        var atom, val;
+
+        //identify helices first
+        for (i = 0, il = atomsarray.length; i < il; i++) {
+            atom = atomsarray[i];
+
+            if (typeof (chres[atom.chain]) === "undefined")
+                chres[atom.chain] = [];
+            
+            if (isFinite(atom.hbondDistanceSq)) {
+                var other = atom.hbondOther;
+                if (typeof (chres[other.chain]) === "undefined")
+                    chres[other.chain] = [];
+                
+                if (Math.abs(other.resi - atom.resi) === 4) {
+                    // helix
+                    chres[atom.chain][atom.resi] = 'h';
+                } 
+            }
+        }
+        
+        // plug gaps in helices
+        for (c in chres) {
+            for (r = 1; r < chres[c].length - 1; r++) {
+                var valbefore = chres[c][r - 1];
+                var valafter = chres[c][r + 1];
+                val = chres[c][r];
+                if (valbefore == 'h' && valbefore == valafter && val != valbefore) {
+                    chres[c][r] = valbefore;
+                }
+            }
+        }
+        
+        //now potential sheets - but only if mate not part of helix
+        for (i = 0, il = atomsarray.length; i < il; i++) {
+            atom = atomsarray[i];
 
-    var computeSecondaryStructure = function(atomsarray) {
-        assignBackboneHBonds(atomsarray);
+            if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] != 'h' && atom.ss != 'h') {
+                chres[atom.chain][atom.resi] = 'maybesheet';
+            }
+        }
         
-        // compute, per residue, what the secondary structure is
-        var chres = {}; // lookup by chain and resid
-        var i, il, c, r;
-        var atom, val;
         
+        //sheets must bond to other sheets
         for (i = 0, il = atomsarray.length; i < il; i++) {
             atom = atomsarray[i];
-            
-            if (typeof(chres[atom.chain]) === "undefined")
-                chres[atom.chain] = [];
-            
-            if (isFinite(atom.hbondDistanceSq)) {
+
+            if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] == 'maybesheet') {
                 var other = atom.hbondOther;
-                if (Math.abs(other.resi - atom.resi) === 4) { 
-                    // helix
-                    chres[atom.chain][atom.resi] = 'h';
-                }
-                else { // otherwise assume sheet
+                var otherval = chres[other.chain][other.resi];
+                if (otherval == 'maybesheet' || otherval == 's') {
+                    // true sheet
                     chres[atom.chain][atom.resi] = 's';
+                    chres[other.chain][other.resi] = 's';
                 }
             }
         }
         
-        // plug gaps and remove singletons
+        // plug gaps in sheets and remove singletons
         for (c in chres) {
-            for (r = 1; r < chres[c].length-1; r++) {
-                var valbefore = chres[c][r-1];
-                var valafter = chres[c][r+1];
+            for (r = 1; r < chres[c].length - 1; r++) {
+                var valbefore = chres[c][r - 1];
+                var valafter = chres[c][r + 1];
                 val = chres[c][r];
-                if(valbefore == valafter && val != valbefore) {
+                if (valbefore == 's' && valbefore == valafter && val != valbefore) {
                     chres[c][r] = valbefore;
                 }
             }
             for (r = 0; r < chres[c].length; r++) {
                 val = chres[c][r];
                 if (val == 'h' || val == 's') {
-                    if (chres[c][r-1] != val && chres[c][r+1] != val)
+                    if (chres[c][r - 1] != val && chres[c][r + 1] != val)
                         delete chres[c][r];
                 }
             }
         }
+
         
         // assign to all atoms in residue, keep track of start
         var curres = null;
         for (i = 0, il = atomsarray.length; i < il; i++) {
             atom = atomsarray[i];
             val = chres[atom.chain][atom.resi];
-            if(typeof(val) == "undefined")
+            if (typeof (val) == "undefined" || val == 'maybesheet')
                 continue;
             atom.ss = val;
-            if(chres[atom.chain][atom.resi-1] != val)
+            if (chres[atom.chain][atom.resi - 1] != val)
                 atom.ssbegin = true;
-            if(chres[atom.chain][atom.resi+1] != val)
+            if (chres[atom.chain][atom.resi + 1] != val)
                 atom.ssend = true;
         }
     };
-    
+
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.cube = parsers.CUBE  = function(atoms, str, options) {
-        var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
-        
+    parsers.cube = parsers.CUBE = function(str, options) {
+        var atoms = [[]];
+        var lines = str.replace(/^\s+/, "").split(/\n\r|\r+/);
+
         if (lines.length < 6)
-            return;
-            
-        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");       
-          
-        var natoms = Math.abs(parseFloat(lineArr[0]));        
-        
+            return atoms;
+
+        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                " ");
+
+        var natoms = Math.abs(parseFloat(lineArr[0]));
+
         lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-        
-        //might have to convert from bohr units to angstroms
+
+        // might have to convert from bohr units to angstroms
         var convFactor = (parseFloat(lineArr[0]) > 0) ? 0.529177 : 1;
-        
-        //Extract atom portion; send to new GLModel...
+
+        // Extract atom portion; send to new GLModel...
         lines = lines.splice(6, natoms);
-       
-        var start = atoms.length;
+
+        var start = atoms[atoms.length-1].length;
         var end = start + lines.length;
-        
+
         for (var i = start; i < end; ++i) {
             var atom = {};
             atom.serial = i;
             var line = lines[i - start];
             var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
                     " ");
-            
-            if (tokens[0] == 6) 
+
+            if (tokens[0] == 6)
                 atom.elem = "C";
-                        
-            else if (tokens[0] == 1) 
+
+            else if (tokens[0] == 1)
                 atom.elem = "H";
-            
+
             else if (tokens[0] == 8)
                 atom.elem = "O";
-                
+
             else if (tokens[0] == 17)
-                atom.elem = "CL";
-                
+                atom.elem = "Cl";
+
             atom.x = parseFloat(tokens[2]) * convFactor;
             atom.y = parseFloat(tokens[3]) * convFactor;
             atom.z = parseFloat(tokens[4]) * convFactor;
-            
+
             atom.hetflag = true;
             atom.bonds = [];
             atom.bondOrder = [];
             atom.properties = {};
-            atoms.push(atom);
-            
-        }   
-        
-        assignBonds(atoms);
-        
-        return true; 
+            atoms[atoms.length-1].push(atom);
+
+        }
+        for (var i = 0; i < atoms.length; i++)
+            assignBonds(atoms[i]);
+
+        return atoms;
     };
-        
-    // read an XYZ file from str and put the result in atoms
+
+    // read an XYZ file from str and return result
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.xyz = parsers.XYZ = function(atoms, str, options) {
+    parsers.xyz = parsers.XYZ = function(str, options) {
+        
+        var atoms = [[]];
+        var lines = str.split(/\r?\n|\r/);
+        while (lines.length > 0) {
+            if (lines.length < 3)
+                break;
+            var atomCount = parseInt(lines[0]);
+            if (isNaN(atomCount) || atomCount <= 0)
+                break;
+            if (lines.length < atomCount + 2)
+                break;
+            var offset = 2;
+            var start = atoms[atoms.length-1].length;
+            var end = start + atomCount;
+            for (var i = start; i < end; i++) {
+                var line = lines[offset++];
+                var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                        " ");
+                var atom = {};
+                atom.serial = i;
+                var elem = tokens[0];
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                atom.x = parseFloat(tokens[1]);
+                atom.y = parseFloat(tokens[2]);
+                atom.z = parseFloat(tokens[3]);
+                atom.hetflag = true;
+                atom.bonds = [];
+                atom.bondOrder = [];
+                atom.properties = {};
+                atoms[atoms.length-1][i] = atom;
+                if (tokens.length >= 7) {
+                    atom.dx = parseFloat(tokens[4]);
+                    atom.dy = parseFloat(tokens[5]);
+                    atom.dz = parseFloat(tokens[6]);
+                }
+            }
 
-        var lines = str.split("\n");
-        if (lines.length < 3)
-            return;
-        var atomCount = parseInt(lines[0].substr(0, 3));
-        if (isNaN(atomCount) || atomCount <= 0)
-            return;
-        if (lines.length < atomCount + 2)
-            return;
-        var offset = 2;
-        var start = atoms.length;
-        var end = start + atomCount;
-        for ( var i = start; i < end; i++) {
-            var line = lines[offset++];
-            var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
-                    " ");
-            var atom = {};
-            atom.serial = i;
-            atom.atom = atom.elem = tokens[0];
-            atom.x = parseFloat(tokens[1]);
-            atom.y = parseFloat(tokens[2]);
-            atom.z = parseFloat(tokens[3]);
-            atom.hetflag = true;
-            atom.bonds = [];
-            atom.bondOrder = [];
-            atom.properties = {};
-            atoms[i] = atom;
+            if (options.multimodel) {
+                atoms.push([]);
+                lines.splice(0, offset);
+            }
+            else {
+                break;
+            }
+        }
+        
+        for (var i = 0; i < atoms.length; i++) {
+            assignBonds(atoms[i]);
+        }
+        
+        if (options.onemol) {
+            var temp = atoms;
+            atoms = [];
+            atoms.push(temp[0]);
+            for (var i = 1; i < temp.length; i++) {
+                var offset = atoms[0].length;
+                for (var j = 0; j < temp[i].length; j++) {
+                    var a = temp[i][j];
+                    for (var k = 0; k < a.bonds.length; k++) {
+                        a.bonds[k] = a.bonds[k] + offset;
+                    }
+                    a.index = atoms[0].length;
+                    a.serial = atoms[0].length;
+                    atoms[0].push(a);
+                }
+            }
         }
-        assignBonds(atoms);
 
-        return true;
+         return atoms;
     };
 
     // put atoms specified in sdf fromat in str into atoms
     // adds to atoms, does not replace
-    /** 
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+    /**
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.sdf = parsers.SDF = function(atoms, str, options) {
+    parsers.sdf = parsers.SDF = function(str, options) {
 
+        var atoms = [[]];
         var noH = false;
-        if(typeof options.keepH !== "undefined") 
+        if (typeof options.keepH !== "undefined")
             noH = !options.keepH;
-        var lines = str.split("\n");
-        if (lines.length < 4)
-            return;
-        var atomCount = parseInt(lines[3].substr(0, 3));
-        if (isNaN(atomCount) || atomCount <= 0)
-            return;
-        var bondCount = parseInt(lines[3].substr(3, 3));
-        var offset = 4;
-        if (lines.length < 4 + atomCount + bondCount)
-            return;
+        var lines = str.split(/\r?\n|\r/);
         
-        // serial is atom's index in file; index is atoms index in 'atoms'
-        var serialToIndex = [];
-        var start = atoms.length;
-        var end = start + atomCount;
-        var i, line;
-        for (i = start; i < end; i++) {
-            line = lines[offset];
-            offset++;
-            var atom = {};
-            atom.atom = atom.elem = line.substr(31, 3).replace(/ /g, "");
+        while(lines.length > 0) { 
+            if (lines.length < 4)
+                break;
+            var atomCount = parseInt(lines[3].substr(0, 3));
+            if (isNaN(atomCount) || atomCount <= 0)
+                break;
+            var bondCount = parseInt(lines[3].substr(3, 3));
+            var offset = 4;
+            if (lines.length < 4 + atomCount + bondCount)
+                break;
 
-            if (atom.elem != 'H' || !noH) {
-                atom.serial = i;
-                serialToIndex[i] = atoms.length;
-                atom.x = parseFloat(line.substr(0, 10));
-                atom.y = parseFloat(line.substr(10, 10));
-                atom.z = parseFloat(line.substr(20, 10));
-                atom.hetflag = true;
-                atom.bonds = [];
-                atom.bondOrder = [];
-                atom.properties = {};
-                atoms.push(atom);
+            // serial is atom's index in file; index is atoms index in 'atoms'
+            var serialToIndex = [];
+            var start = atoms[atoms.length-1].length;
+            var end = start + atomCount;
+            var i, line;
+            for (i = start; i < end; i++,offset++) {
+                line = lines[offset];
+                var atom = {};
+                var elem = line.substr(31, 3).replace(/ /g, "");
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+
+                if (atom.elem != 'H' || !noH) {
+                    atom.serial = i;
+                    serialToIndex[i] = atoms[atoms.length-1].length;
+                    atom.x = parseFloat(line.substr(0, 10));
+                    atom.y = parseFloat(line.substr(10, 10));
+                    atom.z = parseFloat(line.substr(20, 10));
+                    atom.hetflag = true;
+                    atom.bonds = [];
+                    atom.bondOrder = [];
+                    atom.properties = {};
+                    atom.index = atoms[atoms.length-1].length;
+                    atoms[atoms.length-1].push(atom);
+                }
             }
-        }
-        
-        for (i = 0; i < bondCount; i++) {
-            line = lines[offset];
-            offset++;
-            var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
-            var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
-            var order = parseInt(line.substr(6, 3));      
-            if(typeof(from) != 'undefined' && typeof(to) != 'undefined') {
-                atoms[from].bonds.push(to);
-                atoms[from].bondOrder.push(order);
-                atoms[to].bonds.push(from);
-                atoms[to].bondOrder.push(order);
+
+            for (i = 0; i < bondCount; i++,offset++) {
+                line = lines[offset];
+                var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
+                var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
+                var order = parseInt(line.substr(6, 3));
+                if (typeof (from) != 'undefined' && typeof (to) != 'undefined') {
+                    atoms[atoms.length-1][from].bonds.push(to);
+                    atoms[atoms.length-1][from].bondOrder.push(order);
+                    atoms[atoms.length-1][to].bonds.push(from);
+                    atoms[atoms.length-1][to].bondOrder.push(order);
+                }
+            }
+            if (options.multimodel) {
+                if (!options.onemol)
+                    atoms.push([]);
+                while (lines[offset] != "$$$$")
+                    offset++
+                lines.splice(0, ++offset);
+            }
+            else {
+                break;
             }
         }
 
-        return true;
+        return atoms;
     };
 
+    // This parses the ChemDoodle json file format. Although this is registered
+    // for the json file extension, other chemical json file formats exist that
+    // this can not parse. Check which one you have and do not assume that
+    // .json can be parsed
+    parsers.cdjson = parsers.json = function(str, options) {
+        var atoms = [[]];
+        if (typeof str === "string") { // Str is usually automatically parsed by JQuery
+            str = JSON.parse(str);
+        }
+        var molecules = str.m;
+        var atomsInFile = molecules[0].a; // Assumes there is at least one
+        var bondsInFile = molecules[0].b; // molecule and ignores any more
+                                          // Ignores any shapes
+        var styles = molecules[0].s;
+        var parseStyle = options !== undefined && options.parseStyle !== undefined ? options.parseStyle : styles !== undefined;
+        
+        var offset = atoms[atoms.length-1].length; // When adding atoms their index will be
+                                   // Offset by the number of existing atoms
+        
+        for (var i = 0; i < atomsInFile.length; i++) {
+            var currentAtom = atomsInFile[i];
+            var atom = {};
+            atom.id = currentAtom.i; // Probably won't exist. Doesn't seem to
+                                     // break anything.
+            atom.x = currentAtom.x;
+            atom.y = currentAtom.y;
+            atom.z = currentAtom.z || 0; // Default value if file is 2D
+
+            atom.bonds = [];
+            atom.bondOrder = [];
+            
+            var elem = currentAtom.l || 'C';
+            atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+
+            atom.serial = atoms[atoms.length-1].length;
+            if (parseStyle) {
+                atom.style = styles[currentAtom.s || 0];
+            }
+            atoms[atoms.length-1].push(atom);
+        }
+        for (var i = 0; i < bondsInFile.length; i++) {
+            var currentBond = bondsInFile[i];
+            var beginIndex = currentBond.b + offset;
+            var endIndex = currentBond.e + offset;
+            var bondOrder = currentBond.o || 1;
+            
+            var firstAtom = atoms[atoms.length-1][beginIndex];
+            var secondAtom = atoms[atoms.length-1][endIndex];
+
+            firstAtom.bonds.push(endIndex);
+            firstAtom.bondOrder.push(bondOrder);
+            secondAtom.bonds.push(beginIndex);
+            secondAtom.bondOrder.push(bondOrder);
+        }
+        return atoms;
+    }
+
     // puts atoms specified in mmCIF fromat in str into atoms
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.mcif = parsers.cif = function(atoms, str, options) {
+    parsers.mcif = parsers.cif = function(str, options) {
+        var atoms = [];
+        var noAssembly = !options.doAssembly; // don't assemble by default
+        var copyMatrix = !options.duplicateAssemblyAtoms;
+        var modelData = atoms.modelData = [];
 
-        //Used to handle quotes correctly
+        // Used to handle quotes correctly
         function splitRespectingQuotes(string, separator) {
             var sections = [];
             var sectionStart = 0;
             var sectionEnd = 0;
             while (sectionEnd < string.length) {
-                while (string.substr(sectionEnd, separator.length) !== separator && sectionEnd < string.length) {
-                    //currently does not support escaping quotes
+                while (string.substr(sectionEnd, separator.length) !== separator
+                        && sectionEnd < string.length) {
+                    // currently does not support escaping quotes
                     if (string[sectionEnd] === "'") {
                         sectionEnd++;
-                        while (sectionEnd < string.length && string[sectionEnd] !== "'") {
+                        while (sectionEnd < string.length
+                                && string[sectionEnd] !== "'") {
                             sectionEnd++;
                         }
-                    }
-                    else if (string[sectionEnd] === '"') {
+                    } else if (string[sectionEnd] === '"') {
                         sectionEnd++;
-                        while (sectionEnd < string.length && string[sectionEnd] !== '"') {
+                        while (sectionEnd < string.length
+                                && string[sectionEnd] !== '"') {
                             sectionEnd++;
                         }
                     }
                     sectionEnd++;
-                    
+
                 }
-                sections.push(string.substr(sectionStart, sectionEnd - sectionStart));
+                sections.push(string.substr(sectionStart, sectionEnd
+                        - sectionStart));
                 sectionStart = sectionEnd = sectionEnd + separator.length;
             }
             return sections;
         }
 
-        //Parser puts all of the data in the file in an object
-        //uses getDataItem() to get an array for the category and data item given
-        //The possible categories and data items in each category are defined in
-        //the mmCIF specification
-        function getDataItem(categoryName, dataItemName) {
-            if (! (categoryName in mmCIF)) {
-                mmCIF[categoryName] = {};
-            }
-            var category = mmCIF[categoryName];
-            if (! (dataItemName in category)) {
-                category[dataItemName] = [];
-            }
-            var dataItem = category[dataItemName];
-            return dataItem;
-        }
 
-        var lines = str.split("\n");
-        //Filter text to remove comments, trailing spaces, and empty lines
+        var lines = str.split(/\r?\n|\r/);
+        // Filter text to remove comments, trailing spaces, and empty lines
         var linesFiltered = [];
         var trimDisabled = false;
         for (var lineNum = 0; lineNum < lines.length; lineNum++) {
-            //first remove comments
-            //incorrect if #'s are allowed in strings
-            //comments might only be allowed at beginning of line, not sure
+            // first remove comments
+            // incorrect if #'s are allowed in strings
+            // comments might only be allowed at beginning of line, not sure
             var line = lines[lineNum].split('#')[0];
 
-            //inside data blocks, the string must be left verbatim
-            //datablocks are started with a ';' at the beginning of a line
-            //and ended with a ';' on its own line.
+            // inside data blocks, the string must be left verbatim
+            // datablocks are started with a ';' at the beginning of a line
+            // and ended with a ';' on its own line.
             if (trimDisabled) {
                 if (line[0] === ';') {
                     trimDisabled = false;
                 }
-            }
-            else {
+            } else {
                 if (line[0] === ';') {
                     trimDisabled = true;
                 }
             }
 
-            if (trimDisabled) {
+            if (trimDisabled || line !== "") {
+                if (!trimDisabled) {
+                    line = line.trim();
+                    if (line[0] === '_') {
+                        // Replace dot separating category from data item with underscore. Dots aren't guarenteed, to makes
+                        // files consistent.
+                        var dot = line.split(/\s/)[0].indexOf('.');
+                        if (dot > -1) {
+                            line[dot] = '_';
+                            line = line.substr(0,dot) + '_' + line.substr(dot + 1)
+                        }
+                    }
+                }
                 linesFiltered.push(line);
             }
-            else if (line !== "") {
-                linesFiltered.push(line.trim());
-            }
         }
 
-        //Process the lines and puts all of the data into an object.
-        var mmCIF = {};
         var lineNum = 0;
         while (lineNum < linesFiltered.length) {
-            if (linesFiltered[lineNum][0] === undefined) {
+            while (! linesFiltered[lineNum].startsWith("data_") ||
+                   linesFiltered[lineNum] === "data_global") {
                 lineNum++;
             }
-            else if (linesFiltered[lineNum][0] === '_') {
-                var categoryName = (linesFiltered[lineNum].split('.')[0]).toLowerCase();
-                var dataItemName = (linesFiltered[lineNum].split('.')[1].split(/\s/)[0]).toLowerCase();
-                var dataItem = getDataItem(categoryName, dataItemName);
-                
+            lineNum++;
 
-                //if nothing left on the line go to the next one
-                var restOfLine = linesFiltered[lineNum].substr(linesFiltered[lineNum].indexOf(dataItemName) + dataItemName.length);
-                if (restOfLine === "") {
+            // Process the lines and puts all of the data into an object.
+            var mmCIF = {};
+            while (lineNum < linesFiltered.length &&
+                   ! linesFiltered[lineNum].startsWith("data_")) {
+                if (linesFiltered[lineNum][0] === undefined) {
                     lineNum++;
-                    if (linesFiltered[lineNum][0] === ';') {
-                        var dataBlock = linesFiltered[lineNum].substr(1);
+                } else if (linesFiltered[lineNum][0] === '_') {
+                    var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
+                    var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
+
+                    // if nothing left on the line go to the next one
+                    var restOfLine = linesFiltered[lineNum]
+                        .substr(linesFiltered[lineNum].indexOf(dataItemName)
+                                + dataItemName.length);
+                    if (restOfLine === "") {
                         lineNum++;
-                        while (linesFiltered[lineNum] !== ';') {
-                            dataBlock = dataBlock + '\n' + linesFiltered[lineNum];
+                        if (linesFiltered[lineNum][0] === ';') {
+                            var dataBlock = linesFiltered[lineNum].substr(1);
                             lineNum++;
+                            while (linesFiltered[lineNum] !== ';') {
+                                dataBlock = dataBlock + '\n'
+                                            + linesFiltered[lineNum];
+                                lineNum++;
+                            }
+                            dataItem.push(dataBlock);
+                        } else {
+                            dataItem.push(linesFiltered[lineNum]);
                         }
-                        dataItem.push(dataBlock);
+                    } else {
+                        dataItem.push(restOfLine.trim());
                     }
-                    else {
-                        dataItem.push(linesFiltered[lineNum]);
+                    lineNum++;
+                } else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
+                    lineNum++;
+                    var dataItems = [];
+                    while (linesFiltered[lineNum] === ""
+                           || linesFiltered[lineNum][0] === '_') {
+                        if (linesFiltered[lineNum] !== "") {
+                            var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
+                            var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
+                            dataItems.push(dataItem);
+                        }
+                        lineNum++;
                     }
+
+                    var currentDataItem = 0;
+                    while (lineNum < linesFiltered.length
+                           && linesFiltered[lineNum][0] !== '_'
+                           && !linesFiltered[lineNum].startsWith("loop_")
+                           && !linesFiltered[lineNum].startsWith("data_")) {
+                        var line = splitRespectingQuotes(linesFiltered[lineNum], " ");
+                        for (var field = 0; field < line.length; field++) {
+                            if (line[field] !== "") {
+                                dataItems[currentDataItem].push(line[field]);
+                                currentDataItem = (currentDataItem + 1) % dataItems.length;
+                            }
+                        }
+                        lineNum++;
+                    }
+                } else {
+                    lineNum++;
+                }
+            }
+
+            modelData.push({symmetries:[]});
+
+            // Pulls atom information out of the data
+            atoms.push([]);
+            var currentIndex = 0;
+            var atomCount = mmCIF._atom_site_id !== undefined ? mmCIF._atom_site_id.length
+                : mmCIF._atom_site_label.length;
+            function sqr(n) {
+                return n*n;
+            }
+            var conversionMatrix;
+            if (mmCIF._cell_length_a !== undefined) {
+                var a = parseFloat(mmCIF._cell_length_a);
+                var b = parseFloat(mmCIF._cell_length_b);
+                var c = parseFloat(mmCIF._cell_length_c);
+                var alpha_deg = parseFloat(mmCIF._cell_angle_alpha) || 90;
+                var beta_deg = parseFloat(mmCIF._cell_angle_beta) || 90;
+                var gamma_deg = parseFloat(mmCIF._cell_angle_gamma) || 90;
+                var alpha = alpha_deg * Math.PI / 180;
+                var beta = beta_deg * Math.PI / 180;
+                var gamma = gamma_deg * Math.PI / 180;
+                var cos_alpha = Math.cos(alpha);
+                var cos_beta = Math.cos(beta);
+                var cos_gamma = Math.cos(gamma);
+                var sin_gamma = Math.sin(gamma);
+                conversionMatrix = [
+                    [a, b*cos_gamma, c*cos_beta],
+                    [0, b*sin_gamma, c*(cos_alpha-cos_beta*cos_gamma)/sin_gamma],
+                    [0, 0, c*Math.sqrt(1-sqr(cos_alpha)-sqr(cos_beta)-sqr(cos_gamma)+2*cos_alpha*cos_beta*cos_gamma)/sin_gamma]
+                ];
+                modelData[modelData.length-1].cryst = {'a' : a, 'b' : b, 'c' : c, 'alpha' : alpha_deg, 'beta' : beta_deg, 'gamma' : gamma_deg};
+            }
+            function fractionalToCartesian(a, b, c) {
+                var x = conversionMatrix[0][0]*a + conversionMatrix[0][1]*b + conversionMatrix[0][2]*c;
+                var y = conversionMatrix[1][0]*a + conversionMatrix[1][1]*b + conversionMatrix[1][2]*c;
+                var z = conversionMatrix[2][0]*a + conversionMatrix[2][1]*b + conversionMatrix[2][2]*c;
+                return {x:x, y:y, z:z};
+            }
+            for (var i = 0; i < atomCount; i++) {
+                if (mmCIF._atom_site_group_pdb !== undefined && mmCIF._atom_site_group_pdb[i] === "TER")
+                    continue;
+                var atom = {};
+                if (mmCIF._atom_site_cartn_x !== undefined) {
+                    atom.x = parseFloat(mmCIF._atom_site_cartn_x[i]);
+                    atom.y = parseFloat(mmCIF._atom_site_cartn_y[i]);
+                    atom.z = parseFloat(mmCIF._atom_site_cartn_z[i]);
                 }
                 else {
-                    dataItem.push(restOfLine.trim());
+                    var coords = fractionalToCartesian(
+                        parseFloat(mmCIF._atom_site_fract_x[i]),
+                        parseFloat(mmCIF._atom_site_fract_y[i]),
+                        parseFloat(mmCIF._atom_site_fract_z[i]));
+                    atom.x = coords.x;
+                    atom.y = coords.y;
+                    atom.z = coords.z;
                 }
-                lineNum++;
+                atom.chain = mmCIF._atom_site_auth_asym_id ? mmCIF._atom_site_auth_asym_id[i] : undefined;
+                atom.resi = mmCIF._atom_site_auth_seq_id ? parseInt(mmCIF._atom_site_auth_seq_id[i]) : undefined;
+                atom.resn = mmCIF._atom_site_auth_comp_id ? mmCIF._atom_site_auth_comp_id[i].trim() : undefined;
+                atom.atom = mmCIF._atom_site_auth_atom_id ? mmCIF._atom_site_auth_atom_id[i].replace(/"/gm,'')  : undefined; //"primed" names are in quotes
+                atom.hetflag = !mmCIF._atom_site_group_pdb || mmCIF._atom_site_group_pdb[i] === "HETA" || mmCIF._atom_site_group_pdb[i] === "HETATM";
+                var elem = mmCIF._atom_site_type_symbol[i];
+                atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                atom.bonds = [];
+                atom.ss = 'c';
+                atom.serial = i;
+                atom.bondOrder = [];
+                atom.properties = {};
+                atoms[atoms.length-1].push(atom);
             }
-            else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
-                lineNum++;
-                var dataItems = [];
-                var dataItemNames = []
-                while (linesFiltered[lineNum] === "" || linesFiltered[lineNum][0] === '_') {
-                    if (linesFiltered[lineNum] !== "") {
-                        var categoryName = (linesFiltered[lineNum].split('.')[0]).toLowerCase();
-                        var dataItemName = (linesFiltered[lineNum].split('.')[1].split(/\s/)[0]).toLowerCase();
-                        var dataItem = getDataItem(categoryName, dataItemName);
-                        dataItems.push(dataItem);
-                        dataItemNames.push(dataItemName);
-                    }
-                    lineNum++;
-                }
 
-                var currentDataItem = 0;
-                while (lineNum < linesFiltered.length && linesFiltered[lineNum][0] !== '_' && linesFiltered[lineNum].substr(0,5) !== "loop_") {
-                    var line = splitRespectingQuotes(linesFiltered[lineNum], " ");
-                    for (var field = 0; field < line.length; field++) {
-                        if (line[field] !== "") {
-                            dataItems[currentDataItem].push(line[field]);
-                            currentDataItem = (currentDataItem + 1) % dataItems.length;
+            if (mmCIF._pdbx_struct_oper_list_id !== undefined && !noAssembly) {
+                for (var i = 0; i < mmCIF._pdbx_struct_oper_list_id.length; i++) {
+                    var matrix11 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][1]'][i]);
+                    var matrix12 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][2]'][i]);
+                    var matrix13 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][3]'][i]);
+                    var vector1 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[1]'][i]);
+                    var matrix21 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][1]'][i]);
+                    var matrix22 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][2]'][i]);
+                    var matrix23 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][3]'][i]);
+                    var vector2 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[2]'][i]);
+                    var matrix31 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][1]'][i]);
+                    var matrix32 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][2]'][i]);
+                    var matrix33 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][3]'][i]);
+                    var vector3 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[3]'][i]);
+
+                    var matrix = new $3Dmol.Matrix4(matrix11, matrix12, matrix13, vector1,
+                                                    matrix21, matrix22, matrix23, vector2,
+                                                    matrix31, matrix32, matrix33, vector3);
+                    modelData[modelData.length-1].symmetries.push(matrix);
+                }
+                for (var i = 0; i < atoms.length; i++) {
+                    processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[i]);
+                }
+            }
+            function parseTerm(term){
+                var negative = term.match('-');
+                term = term.replace(/[-xyz]/g, "");
+                var fractionParts = term.split('/');
+
+                var numerator, denominator;
+                if (fractionParts[1] === undefined) {
+                    denominator = 1;
+                }
+                else {
+                    denominator = parseInt(fractionParts[1]);
+                }
+                if (fractionParts[0] === "") {
+                    numerator = 1;
+                }
+                else {
+                    numerator = parseInt(fractionParts[0]);
+                }
+                return numerator / denominator * (negative ? -1 : 1);
+            }
+            if (mmCIF._symmetry_equiv_pos_as_xyz !== undefined) {
+                for (var sym = 0; sym < mmCIF._symmetry_equiv_pos_as_xyz.length; sym++) {
+                    var transform = mmCIF._symmetry_equiv_pos_as_xyz[sym].replace(/["' ]/g,"");
+                    var componentStrings = transform.split(',').map(
+                        function(val){
+                            return val.replace(/-/g,"+-");
+                        });
+                    var matrix = new $3Dmol.Matrix4(0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,1);
+                    for (var coord = 0; coord < 3; coord++) {
+                        var terms = componentStrings[coord].split('+');
+                        var constant = 0, xTerm = 0, yTerm = 0, zTerm = 0;
+                        for (var t = 0; t < terms.length; t++) {
+                            var term = terms[t];
+                            if (term === "")
+                                continue;
+                            var coefficient = parseTerm(term);
+                            if (term.match('x')) {
+                                matrix.elements[coord + 0] = coefficient;
+                            }
+                            else if (term.match('y')) {
+                                matrix.elements[coord + 4] = coefficient;
+                            }
+                            else if (term.match('z')) {
+                                matrix.elements[coord + 8] = coefficient;
+                            }
+                            else {
+                                matrix.elements[coord + 12] = coefficient;
+                            }
                         }
                     }
-                    lineNum++;
+                    var conversionMatrix4 = new $3Dmol.Matrix4(
+                        conversionMatrix[0][0], conversionMatrix[0][1], conversionMatrix[0][2], 0,
+                        conversionMatrix[1][0], conversionMatrix[1][1], conversionMatrix[1][2], 0,
+                        conversionMatrix[2][0], conversionMatrix[2][1], conversionMatrix[2][2], 0);
+                    var conversionInverse = (new $3Dmol.Matrix4()).getInverse(conversionMatrix4, true);
+                    matrix = (new $3Dmol.Matrix4()).multiplyMatrices(matrix, conversionInverse);
+                    matrix = (new $3Dmol.Matrix4()).multiplyMatrices(conversionMatrix4, matrix);
+                    modelData[modelData.length-1].symmetries.push(matrix);
                 }
             }
-            else {
-                lineNum++;
-            }
+        }
+        for (var i = 0; i < atoms.length; i++) {
+            assignBonds(atoms[i]);
+            computeSecondaryStructure(atoms[i]);
+            processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[i]);
         }
 
-        //Pulls atom information out of the data
-        var atomsPreBonds = {};
-        for (var i = 0; i < mmCIF._atom_site.id.length; i++) {
-        if (mmCIF._atom_site.group_pdb[i] === "TER") continue;
-            var atom = {};
-            atom.id = parseFloat(mmCIF._atom_site.id[i]);
-            atom.x = parseFloat(mmCIF._atom_site.cartn_x[i]);
-            atom.y = parseFloat(mmCIF._atom_site.cartn_y[i]);
-            atom.z = parseFloat(mmCIF._atom_site.cartn_z[i]);
-            atom.hetflag = mmCIF._atom_site.group_pdb[i] === "HETA";
-            atom.elem = mmCIF._atom_site.type_symbol[i];
-            atom.bonds = [];
-            atom.bondOrder = [];
-            atom.properties = {};
-            atomsPreBonds[atom.id] = atom;
-        }
-        var atomsIndexed = [];
-        var currentIndex = 0;
-        for (var id in atomsPreBonds) {
-            var atom = atomsPreBonds[id];
-            atom.index = currentIndex;
-            atomsIndexed[currentIndex] = atom;
-            currentIndex++;
-        }
-
-        //create a hash table of the atoms using label and sequence as keys
-        var atomHashTable = {};
-        for (var i = 0; i < mmCIF._atom_site.id.length; i++) {
-            var label_alt = mmCIF._atom_site.label_alt_id[i];
-            if (label_alt === undefined) {
-                label_alt = '.';
-            }
-            var label_asym = mmCIF._atom_site.label_asym_id[i];
-            if (label_asym === undefined) {
-                label_asym = '.';
-            }
-            var label_atom = mmCIF._atom_site.label_atom_id[i];
-            if (label_atom === undefined) {
-                label_atom = '.';
-            }
-            var label_seq = mmCIF._atom_site.label_seq_id[i];
-            if (label_seq === undefined) {
-                label_seq = '.';
-            }
-            var id = mmCIF._atom_site.id[i]; //If file is sorted, id will be i+1
-
-            if (atomHashTable[label_alt] === undefined) {
-                atomHashTable[label_alt] = {};
-            }
-            if (atomHashTable[label_alt][label_asym] === undefined) {
-                atomHashTable[label_alt][label_asym] = {};
-            }
-            if (atomHashTable[label_alt][label_asym][label_atom] === undefined) {
-                atomHashTable[label_alt][label_asym][label_atom] = {};
-            }
-        
-            atomHashTable[label_alt][label_asym][label_atom][label_seq] = id;
-        }
-
-        for (var i = 0; i < mmCIF._struct_conn.id.length; i++) {
-	        var offset = atoms.length;
-	        
-	        var alt = (mmCIF._struct_conn.ptnr1_label_alt_id || [])[i];
-	        if (alt === undefined) {
-	            alt = ".";
-	        }
-	        var asym = (mmCIF._struct_conn.ptnr1_label_asym_id || [])[i];
-	        if (asym === undefined) {
-	            asym = ".";
-	        }
-	        var atom = (mmCIF._struct_conn.ptnr1_label_atom_id || [])[i];
-	        if (atom === undefined) {
-	            atom = ".";
-	        }
-	        var seq = (mmCIF._struct_conn.ptnr1_label_seq_id || [])[i];
-	        if (seq === undefined) {
-	            seq = ".";
-	        }
-	        
-            var id1 = atomHashTable[alt][asym][atom][seq];
-            //if (atomsPreBonds[id1] === undefined) continue;
-            var index1 = atomsPreBonds[id1].index;
-            
-            var alt = (mmCIF._struct_conn.ptnr2_label_alt_id || [])[i];
-	    if (alt === undefined) {
-	        alt = ".";
-	    }
-	    var asym = (mmCIF._struct_conn.ptnr2_label_asym_id || [])[i];
-	    if (asym === undefined) {
-	        asym = ".";
-	    }
-	    var atom = (mmCIF._struct_conn.ptnr2_label_atom_id || [])[i];
-	    if (atom === undefined) {
-	        atom = ".";
-	    }
-	    var seq = (mmCIF._struct_conn.ptnr2_label_seq_id || [])[i];
-	    if (seq === undefined) {
-	        seq = ".";
-	    }
-
-            var id2 = atomHashTable[mmCIF._struct_conn.ptnr2_label_alt_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_asym_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_atom_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_seq_id[i]];
-            if (atomsPreBonds[id2] === undefined) continue;
-            var index2 = atomsPreBonds[id2].index;
-
-            atomsPreBonds[id1].bonds.push(index2 + offset);
-            atomsPreBonds[id1].bondOrder.push(1);
-            atomsPreBonds[id2].bonds.push(index1 + offset);
-            atomsPreBonds[id2].bondOrder.push(1);
-            console.log("connected " + index1 + " and " + index2);
-        }
-
-        //atoms = atoms.concat(atomsPreBonds);
-        for (var i = 0; i < atomsIndexed.length; i++) {
-            delete atomsIndexed[i].index;
-            atoms.push(atomsIndexed[i]);
-        }
-
-        assignBonds(atoms);
-	
-    	var matrices = [];
-    	if (mmCIF._pdbx_struct_oper_list !== undefined) {    // transformations may not exist.
-            for (var i = 0; i < mmCIF._pdbx_struct_oper_list.id.length; i++) {
-           	var matrix11 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][1]']);
-           	var matrix12 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][2]']);
-           	var matrix13 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][3]']);
-           	var vector1  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[1]'   ]);
-           	var matrix21 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][1]']);
-           	var matrix22 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][2]']);
-           	var matrix23 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][3]']);
-           	var vector2  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[2]'   ]);
-           	var matrix31 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][1]']);
-           	var matrix32 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][2]']);
-           	var matrix33 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][3]']);
-           	var vector3  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[3]'   ]);
-           	
-    	        var matrix = new $3Dmol.Matrix4(
-    	                matrix11, matrix12, matrix13, vector1,
-    	                matrix21, matrix22, matrix23, vector2,
-    	                matrix31, matrix32, matrix33, vector3
-    	        );
-    	        matrices.push(matrix);
-    	    }
-    	}
+        return atoms;
     }
 
     // parse SYBYL mol2 file from string - assumed to only contain one molecule
     // tag
-    // TODO: Figure out how to handle multi molecule files (for SDF, too)
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options - keepH (do not strip hydrogens)
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.mol2 = parsers.MOL2 = function(atoms, str, options) {
-        
+    parsers.mol2 = parsers.MOL2 = function(str, options) {
+
+        var atoms = [[]];
         var noH = false;
-        if(typeof options.keepH !== "undefined") 
+        if (typeof options.keepH !== "undefined")
             noH = !options.keepH;
-        
-        // Note: these regex's work, though they don't match '<TRIPOS>'
-        // correctly - something to do with angle brackets
-        var mol_pos = str.search(/@<TRIPOS>MOLECULE/);
-        var atom_pos = str.search(/@<TRIPOS>ATOM/);
-        
-        // Assuming both Molecule and Atom sections exist
-        if (mol_pos == -1 || atom_pos == -1)
-            return;
-        
-        // serial is atom's index in file; index is atoms index in 'atoms'
-        var serialToIndex = [];
-        
 
         // assert (mol_pos < atom_pos), "Unexpected formatting of mol2 file
         // (expected 'molecule' section before 'atom' section)";
-        
 
-        var lines = str.substr(mol_pos, str.length).split("\n");
-        var tokens = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-        var natoms = parseInt(tokens[0]);
-        var nbonds = 0;
-        
-        if (tokens.length > 1)
-            nbonds = parseInt(tokens[1]); 
-        
-        var offset = 4;
-        var i;
-        // Continue until 'Atom' section
-        for (i = 3; i < lines.length; i++)
-        {
-            if (lines[i] == "@<TRIPOS>ATOM")
-            {
-                offset = i+1;
-                break;
-            }
-        }
-        
-        var start = atoms.length;
-        var end = start + natoms;
-        var line;
-        // Process ATOMS
-        for (i = start; i < end; i++) {
-            line = lines[offset++];
-            tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-            var atom = {};
-            //get element
-            atom.atom = atom.elem = tokens[5].split('.')[0];
-            if (atom.elem == 'H' && noH) {
-                //ignore
-            }
-            else {
-                // 'index' is this atom's index in 'atoms'; 'serial' is this atom's
-                // serial id in mol2 file
-                var index = atoms.length;
-                var serial = parseInt(tokens[0]);
-                atom.serial = serial;
-                // atom.serial = i;
-                
-                atom.x = parseFloat(tokens[2]);
-                atom.y = parseFloat(tokens[3]);
-                atom.z = parseFloat(tokens[4]);
-                atom.atom = tokens[5];
-                var charge = parseFloat(tokens[8]);
-                
-                atom.bonds = [];
-                atom.bondOrder = [];
-                atom.properties = {'charge': charge, 'partialCharge': charge};
-                serialToIndex[serial] = index;
-                
-                atoms.push(atom);
-            }
-        }
+        var lines = str.substr(mol_pos, str.length).split(/\r?\n|\r/);
         
-        // Process BONDS
-        var bonds_found = false;
-        while (offset < lines.length)
-        {
-            if (lines[offset++] == "@<TRIPOS>BOND")
-            {
-                bonds_found = true;
-                break;            
-            }        
-        }
+        while(lines.length > 0) { 
         
-        if (bonds_found && nbonds)
-        {
-            for (i = 0; i < nbonds; i++)
-            {
+            // Note: these regex's work, though they don't match '<TRIPOS>'
+            // correctly - something to do with angle brackets
+            var mol_pos = str.search(/@<TRIPOS>MOLECULE/);
+            var atom_pos = str.search(/@<TRIPOS>ATOM/);
+
+            // Assuming both Molecule and Atom sections exist
+            if (mol_pos == -1 || atom_pos == -1)
+                break;
+        
+            // serial is atom's index in file; index is atoms index in 'atoms'
+            var serialToIndex = []; 
+            var tokens = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                    " ");
+            var natoms = parseInt(tokens[0]);
+            var nbonds = 0;
+
+            if (tokens.length > 1)
+                nbonds = parseInt(tokens[1]);
+
+            var offset = 4;
+            var i;
+            // Continue until 'Atom' section
+            for (i = 3; i < lines.length; i++) {
+                if (lines[i] == "@<TRIPOS>ATOM") {
+                    offset = i + 1;
+                    break;
+                }
+            }
+        
+            var start = atoms[atoms.length-1].length;
+            var end = start + natoms;
+            var line;
+            // Process ATOMS
+            for (i = start; i < end; i++) {
                 line = lines[offset++];
+                tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+                var atom = {};
+                // get element
+                var elem = tokens[5].split('.')[0];
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                if (atom.elem == 'H' && noH) {
+                    // ignore
+                } else {
+                    // 'index' is this atom's index in 'atoms'; 'serial' is this
+                    // atom's
+                    // serial id in mol2 file
+                    var index = atoms[atoms.length-1].length;
+                    var serial = parseInt(tokens[0]);
+                    atom.serial = serial;
+                    // atom.serial = i;
+
+                    atom.x = parseFloat(tokens[2]);
+                    atom.y = parseFloat(tokens[3]);
+                    atom.z = parseFloat(tokens[4]);
+                    atom.atom = tokens[5];
+                    var charge = parseFloat(tokens[8]);
+                    
+                    atom.index = index;
+                    atom.bonds = [];
+                    atom.bondOrder = [];
+                    atom.properties = {
+                        'charge' : charge,
+                        'partialCharge' : charge
+                    };
+                    serialToIndex[serial] = index;
+
+                    atoms[atoms.length-1].push(atom);
+                }
+            }
 
-                tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
+            // Process BONDS
+            var bonds_found = false;
+            while (offset < lines.length) {
+                if (lines[offset++] == "@<TRIPOS>BOND") {
+                    bonds_found = true;
+                    break;
+                }
+            }
+
+            if (bonds_found && nbonds) {
+                for (i = 0; i < nbonds; i++) {
+                    line = lines[offset++];
+
+                    tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
                             " ");
-                var from = parseInt(tokens[1]);
-                fromAtom = atoms[serialToIndex[from]];
-                var to = parseInt(tokens[2]);
-                toAtom = atoms[serialToIndex[to]];              
-                    
-                // Won't be able to read aromatic bonds correctly...
-                var order = parseInt(tokens[3]);
-                if (isNaN(order))
-                    order = 1;
-                
-                if (fromAtom !== undefined && toAtom !== undefined){
-                    fromAtom.bonds.push(serialToIndex[to]);
-                    fromAtom.bondOrder.push(order);
-                    toAtom.bonds.push(serialToIndex[from]);
-                    toAtom.bondOrder.push(order);
-                }    
+                    var from = parseInt(tokens[1]);
+                    fromAtom = atoms[atoms.length-1][serialToIndex[from]];
+                    var to = parseInt(tokens[2]);
+                    toAtom = atoms[atoms.length-1][serialToIndex[to]];
 
-                
+                    // Won't be able to read aromatic bonds correctly...
+                    var order = parseInt(tokens[3]);
+                    if (isNaN(order))
+                        order = 1;
 
+                    if (fromAtom !== undefined && toAtom !== undefined) {
+                        fromAtom.bonds.push(serialToIndex[to]);
+                        fromAtom.bondOrder.push(order);
+                        toAtom.bonds.push(serialToIndex[from]);
+                        toAtom.bondOrder.push(order);
+                    }
+
+                }
+            }
+            if (options.multimodel) {
+                if (!options.onemol)
+                    atoms.push([])
+                lines.splice(0, offset);
+                str = lines.join("\n"); //update for str.search
+                continue;
+            }
+            else {
+                break;
             }
         }
-        
-        return true;
-        
+        return atoms;
+
     };
-    
 
+    var bondTable = {
+            H :0.37,                                                                                                                                He:0.32,
+            Li:1.34,Be:0.90,                                                                                B :0.82,C :0.77,N :0.75,O :0.73,F :0.71,Ne:0.69,
+            Na:1.54,Mg:1.30,                                                                                Al:1.18,Si:1.11,P :1.06,S :1.02,Cl:0.99,Ar:0.97,
+            K :1.96,Ca:1.74,Sc:1.44,Ti:1.56,V :1.25,/* Cr */Mn:1.39,Fe:1.25,Co:1.26,Ni:1.21,Cu:1.38,Zn:1.31,Ga:1.26,Ge:1.22,/* As */Se:1.16,Br:1.14,Kr:1.10,
+            Rb:2.11,Sr:1.92,Y :1.62,Zr:1.48,Nb:1.37,Mo:1.45,Tc:1.56,Ru:1.26,Rh:1.35,Pd:1.31,Ag:1.53,Cd:1.48,In:1.44,Sn:1.41,Sb:1.38,Te:1.35,I :1.33,Xe:1.30,
+            Cs:2.25,Ba:1.98,Lu:1.60,Hf:1.50,Ta:1.38,W :1.46,Re:1.59,Os:1.44,Ir:1.37,Pt:1.28,Au:1.44,Hg:1.49,Tl:1.48,Pb:1.47,Bi:1.46,/* Po *//* At */Rn:1.45,
+
+            // None of the boottom row or any of the Lanthanides have bond lengths
+    }
+    var bondLength = function(elem) {
+        return bondTable[elem] || 1.6;
+    }
     // return true if atom1 and atom2 are probably bonded to each other
     // based on distance alone
     var areConnected = function(atom1, atom2) {
-        var maxsq = 3.6;
+        var maxsq = bondLength(atom1.elem) + bondLength(atom2.elem);
+        maxsq += 0.25;// fudge factor, especially important for md frames, also see 1i3d
+        maxsq *= maxsq;
 
         var xdiff = atom1.x - atom2.x;
         xdiff *= xdiff;
@@ -15175,35 +21180,83 @@ $3Dmol.Parsers = (function() {
 
         if (isNaN(distSquared))
             return false;
-        if (distSquared < 0.5)
+        else if (distSquared < 0.5)
             return false; // maybe duplicate position.
-
-        if (distSquared > 1.3 && (atom1.elem == 'H' || atom2.elem == 'H' || atom1.elem == 'D' || atom2.elem == 'D'))
+        else if (distSquared > maxsq)
             return false;
-        if (distSquared < 3.6 && (atom1.elem == 'S' || atom2.elem == 'S'))
+        else
             return true;
-        if (distSquared > 2.78)
-            return false;
-        return true;
     };
-    
+
+    //adds symmetry info to either duplicate and rotate/translate biological unit later or add extra atoms now
+    var processSymmetries = function(copyMatrices, copyMatrix, atoms) {
+        var end = atoms.length;
+        var offset = end;
+        var t, l, n;
+        if (!copyMatrix) { // do full assembly
+            for (t = 0; t < copyMatrices.length; t++) {
+                if (!copyMatrices[t].isIdentity()) {
+                    var xyz = new $3Dmol.Vector3();
+                    for (n = 0; n < end; n++) {
+                        var bondsArr = [];
+                        for (l = 0; l < atoms[n].bonds.length; l++) {
+                            bondsArr.push(atoms[n].bonds[l] + offset);
+                        }
+                        xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
+                        xyz.applyMatrix4(copyMatrices[t]);
+                        var newAtom = {};
+                        for (var i in atoms[n]) {
+                            newAtom[i] = atoms[n][i];
+                        }
+                        newAtom.x = xyz.x;
+                        newAtom.y = xyz.y;
+                        newAtom.z = xyz.z;
+                        newAtom.bonds = bondsArr;
+                        atoms.push(newAtom);
+                    }
+                    offset = atoms.length;
+                }
+            }
+        }
+        else if(copyMatrices.length > 1) {
+            for (t = 0; t < atoms.length; t++) {
+                var symmetries = [];
+                for (l = 0; l < copyMatrices.length; l++) {
+                    if (!copyMatrices[l].isIdentity()) {
+                        var newXYZ = new $3Dmol.Vector3();
+                        newXYZ.set(atoms[t].x, atoms[t].y, atoms[t].z);
+                        newXYZ.applyMatrix4(copyMatrices[l]);
+                        symmetries.push(newXYZ);
+                    }
+                }
+                atoms[t].symmetries = symmetries;
+            }
+        }
+    }
+
+
     // parse pdb file from str and create atoms
-    //if computeStruct is true will always perform secondary structure analysis,
-    //otherwise only do analysis of SHEET/HELIX comments are missing
+    // if computeStruct is true will always perform secondary structure
+    // analysis,
+    // otherwise only do analysis of SHEET/HELIX comments are missing
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options - keepH (do not strip hydrogens), noSecondaryStructure (do not compute ss)
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options - keepH (do not strip hydrogens), noSecondaryStructure
+     *            (do not compute ss)
      */
-    parsers.pdb = parsers.PDB = parsers.pdbqt = parsers.PDBQT = function(atoms, str, options, copyMatrices) {
+    parsers.pdb = parsers.PDB = parsers.pdbqt = parsers.PDBQT = function(str, options) {
 
+        var atoms = [[]];
         var atoms_cnt = 0;
         var noH = !options.keepH; // suppress hydrogens by default
         var computeStruct = !options.noSecondaryStructure;
-        var noAssembly = !options.doAssembly; //don't assemble by default
-        var copyMatrix = !options.duplicateAssemblyAtoms; //if not specified, default to copyMatrix true
-        var allMatrices = [];
-        var start = atoms.length;
+        var noAssembly = !options.doAssembly; // don't assemble by default
+        var copyMatrix = !options.duplicateAssemblyAtoms; //default true
+        var modelData = atoms.modelData = [{symmetries:[]}];
+
+        var start = atoms[atoms.length-1].length;
         var atom;
         var protein = {
             sheet : [],
@@ -15212,20 +21265,35 @@ $3Dmol.Parsers = (function() {
 
         var hasStruct = false;
         var serialToIndex = []; // map from pdb serial to index in atoms
-        var lines = str.split("\n");
+        var lines = str.split(/\r?\n|\r/);
         var i, j, k, line;
+        var seenbonds = {}; //sometimes connect records are duplicated as an unofficial means of relaying bond orders
         for (i = 0; i < lines.length; i++) {
             line = lines[i].replace(/^\s*/, ''); // remove indent
             var recordName = line.substr(0, 6);
             var startChain, startResi, endChain, endResi;
-            if (recordName == 'ATOM  ' || recordName == 'HETATM') {
+            
+            if(recordName.indexOf("END") == 0) {
+                if (options.multimodel) {
+                    if (!options.onemol) {
+                        atoms.push([]);
+                        modelData.push({symmetries:[]});
+                    }
+                    continue;
+                }
+                else {
+                    break;
+                }
+            }
+
+            else if (recordName == 'ATOM  ' || recordName == 'HETATM') {
                 var resn, chain, resi, icode, x, y, z, hetflag, elem, serial, altLoc, b;
                 altLoc = line.substr(16, 1);
                 if (altLoc != ' ' && altLoc != 'A')
                     continue; // FIXME: ad hoc
                 serial = parseInt(line.substr(6, 5));
                 atom = line.substr(12, 4).replace(/ /g, "");
-                resn = line.substr(17, 3);
+                resn = line.substr(17, 3).replace(/ /g, "");
                 chain = line.substr(21, 1);
                 resi = parseInt(line.substr(22, 4));
                 icode = line.substr(26, 1);
@@ -15234,17 +21302,32 @@ $3Dmol.Parsers = (function() {
                 z = parseFloat(line.substr(46, 8));
                 b = parseFloat(line.substr(60, 8));
                 elem = line.substr(76, 2).replace(/ /g, "");
-                if (elem === '') { // for some incorrect PDB files
+                if (elem === '' || typeof(bondTable[elem]) === 'undefined') { // for some incorrect PDB files
                     elem = line.substr(12, 2).replace(/ /g, "");
+                    if(elem.length > 0 && elem[0] == 'H' && elem != 'Hg') {
+                        elem = 'H'; //workaround weird hydrogen names from MD, note mercury must use lowercase
+                    }
+                    if(elem.length > 1) {
+                        elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();   
+                        if(typeof(bondTable[elem]) === 'undefined') {
+                            //not a known element, probably should just use first letter
+                            elem = elem[0];
+                        } else if(line[0] == 'A' && elem == 'Ca') { //alpha carbon, not calcium
+                            elem = "C";
+                        }
+                    }
+                } else {
+                    elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();                    
                 }
-                if((elem == 'H' || elem == 'HH' || elem == 'HD') && noH)
+
+                if(elem == 'H' && noH)
                     continue;
                 if (line[0] == 'H')
                     hetflag = true;
                 else
                     hetflag = false;
-                serialToIndex[serial] = atoms.length;
-                atoms.push({
+                serialToIndex[serial] = atoms[atoms.length-1].length;
+                atoms[atoms.length-1].push({
                     'resn' : resn,
                     'x' : x,
                     'y' : y,
@@ -15254,10 +21337,10 @@ $3Dmol.Parsers = (function() {
                     'chain' : chain,
                     'resi' : resi,
                     'icode' : icode,
-                    'rescode': resi + (icode != ' ' ? "^"+icode: ""), // combo
-                                                                        // resi
-                                                                        // and
-                                                                        // icode
+                    'rescode' : resi + (icode != ' ' ? "^" + icode : ""), // combo
+                    // resi
+                    // and
+                    // icode
                     'serial' : serial,
                     'atom' : atom,
                     'bonds' : [],
@@ -15280,16 +21363,33 @@ $3Dmol.Parsers = (function() {
                 // also
                 // described in CONECT. But what about 2JYT???
                 var from = parseInt(line.substr(6, 5));
-                var fromAtom = atoms[serialToIndex[from]];
+                var fromindex = serialToIndex[from];
+                var fromAtom = atoms[atoms.length-1][fromindex];
                 for (j = 0; j < 4; j++) {
                     var to = parseInt(line.substr([ 11, 16, 21, 26 ][j], 5));
-                    var toAtom = atoms[serialToIndex[to]];
+                    var toindex = serialToIndex[to];
+                    var toAtom = atoms[atoms.length-1][toindex];
                     if (fromAtom !== undefined && toAtom !== undefined) {
-                        //minimal cleanup here - pymol likes to output duplicated conect records
-                        var toindex = serialToIndex[to];
-                        if(fromAtom.bonds[fromAtom.bonds.length-1] != toindex) {
-                            fromAtom.bonds.push(toindex);
-                            fromAtom.bondOrder.push(1);
+                        // duplicated conect records indicate bond order
+                        if(!seenbonds[ [fromindex,toindex] ]) {
+                            seenbonds[ [fromindex,toindex] ] = 1;
+                            if (fromAtom.bonds.length == 0 || fromAtom.bonds[fromAtom.bonds.length - 1] != toindex) {
+                                fromAtom.bonds.push(toindex);
+                                fromAtom.bondOrder.push(1);
+                            }
+                        } else { //update bond order
+                            seenbonds[ [fromindex,toindex] ] += 1;
+                            
+                            for(var bi = 0; bi < fromAtom.bonds.length; bi++) {
+                                if(fromAtom.bonds[bi] == toindex) {
+                                    var newbo = seenbonds[ [fromindex,toindex] ];
+                                    if(newbo >= 4) { //aromatic
+                                        fromAtom.bondOrder[bi] = 1;
+                                    } else {
+                                        fromAtom.bondOrder[bi] = newbo;
+                                    }
+                                }
+                            }
                         }
                     }
                 }
@@ -15301,20 +21401,28 @@ $3Dmol.Parsers = (function() {
                 endResi = parseInt(line.substr(33, 4));
                 protein.helix
                         .push([ startChain, startResi, endChain, endResi ]);
-            } else if ((!noAssembly) && (recordName == 'REMARK') && (line.substr(13, 5) == 'BIOMT')) {
+            } else if ((!noAssembly) && (recordName == 'REMARK')
+                    && (line.substr(13, 5) == 'BIOMT')) {
                 var n;
-                var matrix = new $3Dmol.Matrix4();
+                var matrix = new $3Dmol.Matrix4(); 
                 for (n = 1; n <= 3; n++) {
                     line = lines[i].replace(/^\s*/, '');
-                    if (parseInt(line.substr(18, 1)) == n) { //check for all three lines by matching # @ end of "BIOMT" to n
-                        matrix.elements[(n-1)] = parseFloat(line.substr(23, 10));
-                        matrix.elements[(n-1)+4] = parseFloat(line.substr(33, 10));
-                        matrix.elements[(n-1)+8] = parseFloat(line.substr(43, 10));
-                        matrix.elements[(n-1)+12] = parseFloat(line.substr(53));
+                    if (parseInt(line.substr(18, 1)) == n) { // check for all
+                                                                // three lines
+                                                                // by matching #
+                                                                // @ end of
+                                                                // "BIOMT" to n
+                        matrix.elements[(n - 1)] = parseFloat(line.substr(23,
+                                10));
+                        matrix.elements[(n - 1) + 4] = parseFloat(line.substr(
+                                33, 10));
+                        matrix.elements[(n - 1) + 8] = parseFloat(line.substr(
+                                43, 10));
+                        matrix.elements[(n - 1) + 12] = parseFloat(line
+                                .substr(53));
                         i++;
-                    }
-                    else {
-                        while(line.substr(13, 5) == 'BIOMT') { //increase "i" until you leave the REMARKs
+                    } else {
+                        while (line.substr(13, 5) == 'BIOMT') {
                             i++;
                             line = lines[i].replace(/^\s*/, '');
                         }
@@ -15324,173 +21432,145 @@ $3Dmol.Parsers = (function() {
                 matrix.elements[7] = 0;
                 matrix.elements[11] = 0;
                 matrix.elements[15] = 1;
-                allMatrices.push(matrix);
-                copyMatrices.push(matrix);
-                
-                i--; //set i back
+                modelData[modelData.length-1].symmetries.push(matrix);
+                i--; // set i back
+            } else if (recordName == 'CRYST1') {
+                var a, b, c, alpha, beta, gamma;
+                a = parseFloat(line.substr(7, 8));
+                b = parseFloat(line.substr(16, 8));
+                c = parseFloat(line.substr(25, 8));
+                alpha = parseFloat(line.substr(34, 6));
+                beta = parseFloat(line.substr(41, 6));
+                gamma = parseFloat(line.substr(48, 6));
+                modelData[modelData.length-1].cryst = {'a' : a, 'b' : b, 'c' : c, 'alpha' : alpha, 'beta' : beta, 'gamma' : gamma};
             }
-
         }
 
         var starttime = (new Date()).getTime();
-        // assign bonds - yuck, can't count on connect records
-        assignPDBBonds(atoms);
-        //console.log("bond connecting " + ((new Date()).getTime() - starttime));
-        
-        var end = atoms.length;
-        var offset = end;
-        var t, l, n;
-        if(!copyMatrix) { //do full assembly
-            for (t = 0; t < allMatrices.length; t++) {
-                if (!allMatrices[t].isIdentity()) {
-                    var xyz = new $3Dmol.Vector3();
-                    for (n = 0; n < end; n++) {
-                        var bondsArr = [];
-                        for (l = 0; l < atoms[n].bonds.length; l++) {
-                            bondsArr.push(atoms[n].bonds[l] + offset);
-                        }
-                        xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
-                        xyz.applyMatrix4(allMatrices[t]);
-                        atoms.push({
-                            'resn' : atoms[n].resn,
-                            'x' : xyz.x,
-                            'y' : xyz.y,
-                            'z' : xyz.z,
-                            'elem' : atoms[n].elem,
-                            'hetflag' : atoms[n].hetflag,
-                            'chain' : atoms[n].chain,
-                            'resi' : atoms[n].resi,
-                            'icode' : atoms[n].icode,
-                            'rescode': atoms[n].rescode,
-                            'serial' : atoms[n].serial,
-                            'atom' : atoms[n].atom,
-                            'bonds' : bondsArr,
-                            'ss' : atoms[n].ss,
-                            'bondOrder' : atoms[n].bondOrder,
-                            'properties' : atoms[n].properties,
-                            'b' : atoms[n].b,
-                            'pdbline' : atoms[n].pdbline,
-                        });
-                    }
-                    offset = atoms.length;
-                }
-            }
-        }
-        //ELSE give all atoms a pointer to their symmetries 
-        else {
-            for (t = 0; t < atoms.length; t++) {
-                var symmetries = [];
-                for (l = 0; l < copyMatrices.length; l++) {
-                    if (!copyMatrices[l].isIdentity()) {
-                        var newXYZ = new $3Dmol.Vector3();
-                        newXYZ.set(atoms[t].x, atoms[t].y, atoms[t].z);
-                        newXYZ.applyMatrix4(copyMatrices[l]);
-                        symmetries.push(newXYZ);
-                    }
-                }
-                atoms[t].symmetries = symmetries;
-            }
-        }
-                
         
-        if(computeStruct || !hasStruct) {
-            starttime = (new Date()).getTime();
-            computeSecondaryStructure(atoms);
-            //console.log("secondary structure " + ((new Date()).getTime() - starttime));
-        }
+        for (var n = 0; n < atoms.length; n++) {
+            // assign bonds - yuck, can't count on connect records
+            assignPDBBonds(atoms[n]);
+            // console.log("bond connecting " + ((new Date()).getTime() -
+            // starttime));
         
-        // Assign secondary structures from pdb file
-        for (i = start; i < atoms.length; i++) {
-            atom = atoms[i];
-            if (atom === undefined)
-                continue;
+            if (!noAssembly)
+                processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[n]);
 
-            var found = false;
-            // MEMO: Can start chain and end chain differ?
-            for (j = 0; j < protein.sheet.length; j++) {
-                if (atom.chain != protein.sheet[j][0])
-                    continue;
-                if (atom.resi < protein.sheet[j][1])
-                    continue;
-                if (atom.resi > protein.sheet[j][3])
-                    continue;
-                atom.ss = 's';
-                if (atom.resi == protein.sheet[j][1])
-                    atom.ssbegin = true;
-                if (atom.resi == protein.sheet[j][3])
-                    atom.ssend = true;
-            }
-            for (j = 0; j < protein.helix.length; j++) {
-                if (atom.chain != protein.helix[j][0])
-                    continue;
-                if (atom.resi < protein.helix[j][1])
-                    continue;
-                if (atom.resi > protein.helix[j][3])
+            if (computeStruct || !hasStruct) {
+                starttime = (new Date()).getTime();
+                computeSecondaryStructure(atoms[n]);
+                // console.log("secondary structure " + ((new Date()).getTime() -
+                // starttime));
+            }
+
+            // Assign secondary structures from pdb file
+            for (i = start; i < atoms[n].length; i++) {
+                atom = atoms[n][i];
+                if (atom === undefined)
                     continue;
-                atom.ss = 'h';
-                if (atom.resi == protein.helix[j][1])
-                    atom.ssbegin = true;
-                else if (atom.resi == protein.helix[j][3])
-                    atom.ssend = true;
+
+                var found = false;
+                // MEMO: Can start chain and end chain differ?
+                for (j = 0; j < protein.sheet.length; j++) {
+                    if (atom.chain != protein.sheet[j][0])
+                        continue;
+                    if (atom.resi < protein.sheet[j][1])
+                        continue;
+                    if (atom.resi > protein.sheet[j][3])
+                        continue;
+                    atom.ss = 's';
+                    if (atom.resi == protein.sheet[j][1])
+                        atom.ssbegin = true;
+                    if (atom.resi == protein.sheet[j][3])
+                        atom.ssend = true;
+                }
+                for (j = 0; j < protein.helix.length; j++) {
+                    if (atom.chain != protein.helix[j][0])
+                        continue;
+                    if (atom.resi < protein.helix[j][1])
+                        continue;
+                    if (atom.resi > protein.helix[j][3])
+                        continue;
+                    atom.ss = 'h';
+                    if (atom.resi == protein.helix[j][1])
+                        atom.ssbegin = true;
+                    else if (atom.resi == protein.helix[j][3])
+                        atom.ssend = true;
+                }
             }
         }
-        return true;
-    };
-
         
-    /** Parse a pqr file from str and create atoms.  A pqr file is assumed
-     * to be a whitespace delimited PDB with charge and radius fields.
+        return atoms;
+    };
 
-     * 
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options -  noSecondaryStructure (do not compute ss)
+    /**
+     * Parse a pqr file from str and create atoms. A pqr file is assumed to be a
+     * whitespace delimited PDB with charge and radius fields.
+     *
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options - noSecondaryStructure (do not compute ss)
      */
-    parsers.pqr = parsers.PQR = function(atoms, str, options) {
+    parsers.pqr = parsers.PQR = function(str, options) {
 
+        var atoms = [[]];
         var atoms_cnt = 0;
-        var start = atoms.length;
+        var start = atoms[atoms.length-1].length;
         var atom;
         var computeStruct = !options.noSecondaryStructure;
 
         var serialToIndex = []; // map from pdb serial to index in atoms
-        var lines = str.split("\n");
+        var lines = str.split(/\r?\n|\r/);
         var i, j, k, line;
         for (i = 0; i < lines.length; i++) {
             line = lines[i].replace(/^\s*/, ''); // remove indent
             var recordName = line.substr(0, 6);
             var startChain, startResi, endChain, endResi;
-            if (recordName == 'ATOM  ' || recordName == 'HETATM') {
-                    //I would have liked to split based solely on whitespace, but
-                //it seems that there is no guarantee that all the fields will
-                //be filled out (e.g. the chain) so this doesn't work
+            
+            if (recordName.indexOf("END") == 0) {
+                if (options.multimodel) {
+                    if (!options.onemol)
+                        atoms.push([]);
+                    continue;
+                }
+                else {
+                    break;
+                }
+            }
+            else if (recordName == 'ATOM  ' || recordName == 'HETATM') {
+                // I would have liked to split based solely on whitespace, but
+                // it seems that there is no guarantee that all the fields will
+                // be filled out (e.g. the chain) so this doesn't work
                 var serial = parseInt(line.substr(6, 5));
                 var atom = line.substr(12, 4).replace(/ /g, "");
                 var resn = line.substr(17, 3);
                 var chain = line.substr(21, 1);
                 var resi = parseInt(line.substr(22, 4));
-                //however let's split the coordinates, charge and radius by whitespace
-                //to support extra precision
+                // however let's split the coordinates, charge and radius by
+                // whitespace
+                // to support extra precision
                 var vals = line.substr(30).trim().split(/\s+/);
                 var x = parseFloat(vals[0]);
                 var y = parseFloat(vals[1]);
                 var z = parseFloat(vals[2]);
                 var charge = parseFloat(vals[3]);
                 var radius = parseFloat(vals[4]);
-                
+
                 var elem = atom[0];
-                if(atom.length > 1 && atom[1].toUpperCase() != atom[1]) {
-                    //slight hack - identify two character elements by the
-                    //second character in the atom name being lowercase
-                    elem = atom.substr(0,2);
+                if (atom.length > 1 && atom[1].toUpperCase() != atom[1]) {
+                    // slight hack - identify two character elements by the
+                    // second character in the atom name being lowercase
+                    elem = atom.substr(0, 2);
                 }
 
                 if (line[0] == 'H')
                     hetflag = true;
                 else
                     hetflag = false;
-                serialToIndex[serial] = atoms.length;
-                atoms.push({
+                serialToIndex[serial] = atoms[atoms.length-1].length;
+                atoms[atoms.length-1].push({
                     'resn' : resn,
                     'x' : x,
                     'y' : y,
@@ -15504,7 +21584,11 @@ $3Dmol.Parsers = (function() {
                     'bonds' : [],
                     'ss' : 'c',
                     'bondOrder' : [],
-                    'properties' : {'charge': charge, 'partialCharge': charge, 'radius': radius},
+                    'properties' : {
+                        'charge' : charge,
+                        'partialCharge' : charge,
+                        'radius' : radius
+                    },
                     'pdbline' : line
                 });
             } else if (recordName == 'CONECT') {
@@ -15512,10 +21596,10 @@ $3Dmol.Parsers = (function() {
                 // also
                 // described in CONECT. But what about 2JYT???
                 var from = parseInt(line.substr(6, 5));
-                var fromAtom = atoms[serialToIndex[from]];
+                var fromAtom = atoms[atoms.length-1][serialToIndex[from]];
                 for (j = 0; j < 4; j++) {
                     var to = parseInt(line.substr([ 11, 16, 21, 26 ][j], 5));
-                    var toAtom = atoms[serialToIndex[to]];
+                    var toAtom = atoms[atoms.length-1][serialToIndex[to]];
                     if (fromAtom !== undefined && toAtom !== undefined) {
                         fromAtom.bonds.push(serialToIndex[to]);
                         fromAtom.bondOrder.push(1);
@@ -15525,15 +21609,15 @@ $3Dmol.Parsers = (function() {
         }
 
         // assign bonds - yuck, can't count on connect records
-        assignPDBBonds(atoms);
-        if(computeStruct)
-            computeSecondaryStructure(atoms);
+        for (var i = 0; i < atoms.length; i++) {
+            assignPDBBonds(atoms[i]);
+            if (computeStruct)
+                computeSecondaryStructure(atoms[i]);
+        }
         
-        return true;
+        return atoms;
     };
 
-    
-    
     return parsers;
 })();
 var $3Dmol = $3Dmol || {};
@@ -15727,7 +21811,7 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  * @typedef ViewerSpec
  * @prop {Object} defaultcolors - map of elements to colors
  * @prop {boolean} nomouse - if true, disable handling of mouse events
- * @prop {string} backgroundColor - color of background
+ * @prop {ColorSpec} backgroundColor - color of background
  */
 
 /**
@@ -15737,8 +21821,8 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  * @prop {number} x - Atom's x coordinate
  * @prop {number} y - Atom's y coordinate
  * @prop {number} z - Atom's z coordinate
- * @prop {number} color - Atom's color, as hex code
- * @prop {number} surfaceColor - Hex code for color to be used for surface patch over this atom
+ * @prop {ColorSpec} color - Atom's color, as hex code or built-in color string
+ * @prop {ColorSpec} surfaceColor - Hex code for color to be used for surface patch over this atom
  * @prop {string} elem - Element abbreviation (e.g. 'H', 'Ca', etc)
  * @prop {boolean} hetflag - Set to true if atom is a heteroatom
  * @prop {string} chain - Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)
@@ -15808,9 +21892,11 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 /** 
  * @typedef SurfaceStyleSpec
  * @prop {number} opacity - sets the transparency: 0 to hide, 1 for fully opaque
- * @prop {string} colorscheme - element based coloring
- * @prop {string} color - fixed coloring, overrides colorscheme
- * @prop {Object} map - specifies a numeric atom property (prop) and color mapping (scheme) such as {@link $3Dmol.Gradient.RWB}
+ * @prop {ColorschemeSpec} colorscheme - element based coloring
+ * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+ * @prop {$3Dmol.VolumeData} voldata - volumetric data for vertex coloring
+ * @prop {$3Dmol.Gradient} volscheme - coloring scheme for mapping volumetric data to vertex color
+ * @prop {Object} map - specifies a numeric atom property (prop) and color mapping (scheme) such as {@link $3Dmol.Gradient.RWB}.  Deprecated, use colorscheme instead.
  * 
  * @example
  * viewer.addSurface($3Dmol.SurfaceType.MS, {map:{prop:'partialCharge',scheme:new $3Dmol.Gradient.RWB(-.6,.6)}, opacity:0.85});
@@ -15818,14 +21904,15 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  */
 
 /** 
- * Volumetric data style specification
- * @typedef VolSpec
+ * Isosurface style specification
+ * @typedef IsoSurfaceSpec
  * @prop {number} isoval - specifies the isovalue to draw surface at
  * @propr {boolean} voxel - if true uses voxel style rendering
- * @prop {string} color - solid color
- * @prop {number} alpha - transparency
+ * @prop {ColorSpec} color - solid color
+ * @prop {number} opacity - transparency, between 0 and 1
  * @prop {boolean} wireframe - draw as wireframe, not surface
  * @prop {number} linewidth - width of line for wireframe rendering
+ * @prop {number} smoothness - amount to smooth surface (default 1)
  * @prop {boolean} clickable - if true, user can click on object to trigger callback
  * @prop {function} callback - function to call on click 
  */
@@ -15833,7 +21920,7 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 /** 
  * GLShape style specification
  * @typedef ShapeSpec
- * @prop {string} color - solid color
+ * @prop {ColorSpec} color - solid color
  * @prop {number} alpha - transparency
  * @prop {boolean} wireframe - draw as wireframe, not surface
  * @prop {number} linewidth - width of line for wireframe rendering
@@ -15843,9 +21930,13 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 
 
 /**
- * Specification for adding custom shape
+ * Specification for adding custom shape. Extends {@link ShapeSpec}.
  * @typedef CustomShapeSpec
  * @augments ShapeSpec
+ * @prop {Array.<$3Dmol.Vector3>} vertexArr - List of vertex positions
+ * @prop {Array.<$3Dmol.Vector3>} normalArr - List of normal vectors for each vertex
+ * @prop {Array.<number>} faceArr - List of triangles to build the custom shape. Each triangle is defined by the indices of 3 vertices in vertexArr, so the array length should be 3 times the number of faces.
+ * @prop {ColorSpec | Array.<ColorSpec>} color - Either a single color for the whole object or an array specifying the color at each vertex.
  */
 
 /**
@@ -15887,3 +21978,251 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  */
 
 });
+/**
+ * $3Dmol.VolumeData stores volumetric data. This includes file parsing
+ * functionality.
+ * 
+ * @class
+ * @param {string} str - volumetric data
+ * @param {string} format - format of supplied data (cube)
+ */
+$3Dmol.VolumeData = function(str, format) {
+
+    this.unit = {
+        x : 1,
+        y : 1,
+        z : 1
+    }; // scale of each voxel
+    this.origin = {
+        x : 0,
+        y : 0,
+        z : 0
+    }; // origin (bottom "left", not center)
+    this.size = {
+        x : 0,
+        y : 0,
+        z : 0
+    }; // number of voxels in each direction
+    this.data = new Float32Array([]); // actual floating point data, arranged
+                                        // x->y->z
+
+    format = format.toLowerCase();
+    if (this[format]) {
+        this[format](str);
+    }
+};
+
+/**
+ * @function $3Dmol.VolumeData.getVal
+ * @param {number} x,y,z - the coordinates
+ * @returns - value closest to provided coordinate; zero if coordinate invalid
+ */
+$3Dmol.VolumeData.prototype.getVal = function(x,y,z) {
+    x -= this.origin.x;
+    y -= this.origin.y;
+    z -= this.origin.z;
+    
+    x /= this.unit.x;
+    y /= this.unit.y;
+    z /= this.unit.z;
+    
+    x = Math.round(x);
+    y = Math.round(y);
+    z = Math.round(z);
+    
+    if(x < 0 || x >= this.size.x) return 0;
+    if(y < 0 || y >= this.size.y) return 0;
+    if(z < 0 || z >= this.size.z) return 0;
+    
+    return this.data[x*this.size.y*this.size.z + y*this.size.z + z];
+};
+
+// parse cube data
+$3Dmol.VolumeData.prototype.cube = function(str) {
+    var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
+
+    if (lines.length < 6)
+        return;
+
+    var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+
+    var atomsnum = parseFloat(lineArr[0]); //includes sign, which indicates presence of oribital line in header
+    var natoms = Math.abs(atomsnum);
+
+    var origin = this.origin = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]));
+
+    lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+
+    // might have to convert from bohr units to angstroms
+    // there is a great deal of confusion here:
+    // n>0 means angstroms: http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm
+    // n<0 means angstroms: http://paulbourke.net/dataformats/cube/
+    // always assume bohr: openbabel source code
+    // always assume angstrom: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
+    // we are going to go with n<0 means angstrom - note this is just the first n
+    var convFactor = (lineArr[0] > 0) ? 0.529177 : 1;
+    origin.multiplyScalar(convFactor);
+
+    var nX = Math.abs(lineArr[0]);
+    var xVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+    var nY = Math.abs(lineArr[0]);
+    var yVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+    var nZ = Math.abs(lineArr[0]);
+    var zVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    this.size = {x:nX, y:nY, z:nZ};
+    this.unit = new $3Dmol.Vector3(xVec.x, yVec.y, zVec.z);
+    
+    if (xVec.y != 0 || xVec.z != 0 || yVec.x != 0 || yVec.z != 0 || zVec.x != 0
+            || zVec.y != 0)
+        console
+                .log("Warning: Cube file is not axis aligned.  This isn't going to look right.");   
+    var headerlines = 6;
+    if(atomsnum < 0) headerlines++; //see: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
+    var raw = lines.splice(natoms + headerlines).join(" ");
+    raw = raw.replace(/^\s+/,'');
+    raw = raw.split(/[\s\r]+/);
+    this.data = new Float32Array(raw);
+
+};
+
+//parse cp4 files
+$3Dmol.VolumeData.prototype.ccp4 = function(bin) {
+
+    // http://www.ccp4.ac.uk/html/maplib.html#description
+        
+        var header = {};
+
+        var intView = new Int32Array( bin, 0, 56 );
+        var floatView = new Float32Array( bin, 0, 56 );
+
+           //# of columns (fastest changing),rows, sections (slowest changing)
+        header.NX = intView[ 0 ];
+        header.NY = intView[ 1 ];
+        header.NZ = intView[ 2 ];
+
+        // mode
+        //  0 image : signed 8-bit bytes range -128 to 127
+        //  1 image : 16-bit halfwords
+        //  2 image : 32-bit reals
+        //  3 transform : complex 16-bit integers
+        //  4 transform : complex 32-bit reals
+        //  6 image : unsigned 16-bit range 0 to 65535
+        // 16 image: unsigned char * 3 (for rgb data, non-standard)
+        header.MODE = intView[ 3 ];
+
+        //position of first column, first row, and first section (voxel grid units)
+        header.NCSTART = intView[ 4 ];
+        header.NRSTART = intView[ 5 ];
+        header.NSSTART = intView[ 6 ];
+
+        //intervals per unit cell repeat along X,Y Z
+        header.MX = Math.abs(intView[ 7 ]);
+        header.MY = Math.abs(intView[ 8 ]);
+        header.MZ = Math.abs(intView[ 9 ]);
+
+       //Map lengths along X,Y,Z in Ångstroms
+        header.xlen =  floatView[ 10 ]; 
+        header.ylen = floatView[ 11 ];  
+        header.zlen = floatView[ 12 ];  
+
+        //single voxel lengths
+        xVox = header.xlen / header.NX; 
+        yVox = header.ylen / header.NY; 
+        zVox = header.zlen / header.NZ;
+
+        // cell angle
+        header.alpha = floatView[ 13 ];
+        header.beta  = floatView[ 14 ];
+        header.gamma = floatView[ 15 ];
+
+        //relationship of X,Y,Z axes to columns, rows, sections
+        header.MAPC = intView[ 16 ];
+        switch (header.MAPC){
+            case 1: header.NXSTART = header.NCSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NCSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NCSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+        header.MAPR = intView[ 17 ];
+        switch (header.MAPR){
+            case 1: header.NXSTART = header.NRSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NRSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NRSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+        header.MAPS = intView[ 18 ];
+         switch (header.MAPS){
+            case 1: header.NXSTART = header.NSSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NSSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NSSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+
+        //Origin Position
+        this.origin = new $3Dmol.Vector3(header.NXSTART, header.NYSTART, header.NZSTART);
+
+        //Minimum, maximum, average density
+        header.DMIN  = floatView[ 19 ];
+        header.DMAX  = floatView[ 20 ];
+        header.DMEAN = floatView[ 21 ];
+
+        // space group number 0 or 1 (default=0)
+        header.ISPG = intView[ 22 ];
+
+        // number of bytes used for symmetry data (0 or 80)
+        header.NSYMBT = intView[23];
+
+        // machine stamp
+        header.ARMS = floatView[54];
+
+        this.size = {x:header.MX, y:header.MY, z:header.MZ};
+        this.unit = new $3Dmol.Vector3(xVox, yVox, zVox ); 
+        var byteData = new Int8Array(bin); 
+        this.data = new Float32Array(bin, 1024 + header.NSYMBT);
+          
+};
+//Hackish way to create webworker (independent of $3Dmol namespace) within minified file
+$3Dmol.workerString = function(){
+
+    self.onmessage = function(oEvent) {
+        var obj = oEvent.data;
+        var type = obj.type;
+        if (type < 0) // sending atom data, initialize
+        {
+            self.atomData = obj.atoms;
+            self.volume = obj.volume;
+            self.ps = new ProteinSurface();
+        } else {
+            var ps = self.ps;
+            ps.initparm(obj.expandedExtent, (type == 1) ? false : true, self.volume);
+            ps.fillvoxels(self.atomData, obj.extendedAtoms);
+            ps.buildboundary();
+            if (type === 4 || type === 2) {
+                ps.fastdistancemap();
+                ps.boundingatom(false);
+                ps.fillvoxelswaals(self.atomData, obj.extendedAtoms);    
+            }        
+            ps.marchingcube(type);
+            var VandF = ps.getFacesAndVertices(obj.atomsToShow);
+            self.postMessage(VandF);
+        }
+    };
+    
+}.toString().replace(/(^.*?\{|\}$)/g, "");
+
+$3Dmol.workerString += "; var ProteinSurface=" + $3Dmol.ProteinSurface.toString().replace(/\$3Dmol.MarchingCube./g, "MarchingCube.");
+$3Dmol.workerString += ",MarchingCube=("+$3Dmol.MarchingCubeInitializer.toString() +")();";
+
+$3Dmol.SurfaceWorker = window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type: 'text/javascript'}));
+
+$3Dmol['workerString'] = $3Dmol.workerString;
+$3Dmol['SurfaceWorker'] = $3Dmol.SurfaceWorker;
diff --git a/release/3Dmol.js b/release/3Dmol.js
index 03833417b..47b31c5e0 100644
--- a/release/3Dmol.js
+++ b/release/3Dmol.js
@@ -1,90 +1,82 @@
 /*!
- * jQuery JavaScript Library v1.9.1
+ * jQuery JavaScript Library v1.11.3
  * http://jquery.com/
  *
  * Includes Sizzle.js
  * http://sizzlejs.com/
  *
- * Copyright 2005, 2012 jQuery Foundation, Inc. and other contributors
+ * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors
  * Released under the MIT license
  * http://jquery.org/license
  *
- * Date: 2013-2-4
+ * Date: 2015-04-28T16:19Z
  */
-(function( window, undefined ) {
+
+(function( global, factory ) {
+
+	if ( typeof module === "object" && typeof module.exports === "object" ) {
+		// For CommonJS and CommonJS-like environments where a proper window is present,
+		// execute the factory and get jQuery
+		// For environments that do not inherently posses a window with a document
+		// (such as Node.js), expose a jQuery-making factory as module.exports
+		// This accentuates the need for the creation of a real window
+		// e.g. var jQuery = require("jquery")(window);
+		// See ticket #14549 for more info
+		module.exports = global.document ?
+			factory( global, true ) :
+			function( w ) {
+				if ( !w.document ) {
+					throw new Error( "jQuery requires a window with a document" );
+				}
+				return factory( w );
+			};
+	} else {
+		factory( global );
+	}
+
+// Pass this if window is not defined yet
+}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
 
 // Can't do this because several apps including ASP.NET trace
 // the stack via arguments.caller.callee and Firefox dies if
 // you try to trace through "use strict" call chains. (#13335)
 // Support: Firefox 18+
-//"use strict";
-var
-	// The deferred used on DOM ready
-	readyList,
+//
 
-	// A central reference to the root jQuery(document)
-	rootjQuery,
+var deletedIds = [];
 
-	// Support: IE<9
-	// For `typeof node.method` instead of `node.method !== undefined`
-	core_strundefined = typeof undefined,
+var slice = deletedIds.slice;
 
-	// Use the correct document accordingly with window argument (sandbox)
-	document = window.document,
-	location = window.location,
+var concat = deletedIds.concat;
 
-	// Map over jQuery in case of overwrite
-	_jQuery = window.jQuery,
+var push = deletedIds.push;
 
-	// Map over the $ in case of overwrite
-	_$ = window.$,
+var indexOf = deletedIds.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
 
-	// [[Class]] -> type pairs
-	class2type = {},
+var hasOwn = class2type.hasOwnProperty;
 
-	// List of deleted data cache ids, so we can reuse them
-	core_deletedIds = [],
+var support = {};
 
-	core_version = "1.9.1",
 
-	// Save a reference to some core methods
-	core_concat = core_deletedIds.concat,
-	core_push = core_deletedIds.push,
-	core_slice = core_deletedIds.slice,
-	core_indexOf = core_deletedIds.indexOf,
-	core_toString = class2type.toString,
-	core_hasOwn = class2type.hasOwnProperty,
-	core_trim = core_version.trim,
+
+var
+	version = "1.11.3",
 
 	// Define a local copy of jQuery
 	jQuery = function( selector, context ) {
 		// The jQuery object is actually just the init constructor 'enhanced'
-		return new jQuery.fn.init( selector, context, rootjQuery );
+		// Need init if jQuery is called (just allow error to be thrown if not included)
+		return new jQuery.fn.init( selector, context );
 	},
 
-	// Used for matching numbers
-	core_pnum = /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,
-
-	// Used for splitting on whitespace
-	core_rnotwhite = /\S+/g,
-
-	// Make sure we trim BOM and NBSP (here's looking at you, Safari 5.0 and IE)
+	// Support: Android<4.1, IE<9
+	// Make sure we trim BOM and NBSP
 	rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
 
-	// A simple way to check for HTML strings
-	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
-	// Strict HTML recognition (#11290: must start with <)
-	rquickExpr = /^(?:(<[\w\W]+>)[^>]*|#([\w-]*))$/,
-
-	// Match a standalone tag
-	rsingleTag = /^<(\w+)\s*\/?>(?:<\/\1>|)$/,
-
-	// JSON RegExp
-	rvalidchars = /^[\],:{}\s]*$/,
-	rvalidbraces = /(?:^|:|,)(?:\s*\[)+/g,
-	rvalidescape = /\\(?:["\\\/bfnrt]|u[\da-fA-F]{4})/g,
-	rvalidtokens = /"[^"\\\r\n]*"|true|false|null|-?(?:\d+\.|)\d+(?:[eE][+-]?\d+|)/g,
-
 	// Matches dashed string for camelizing
 	rmsPrefix = /^-ms-/,
 	rdashAlpha = /-([\da-z])/gi,
@@ -92,134 +84,13 @@ var
 	// Used by jQuery.camelCase as callback to replace()
 	fcamelCase = function( all, letter ) {
 		return letter.toUpperCase();
-	},
-
-	// The ready event handler
-	completed = function( event ) {
-
-		// readyState === "complete" is good enough for us to call the dom ready in oldIE
-		if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
-			detach();
-			jQuery.ready();
-		}
-	},
-	// Clean-up method for dom ready events
-	detach = function() {
-		if ( document.addEventListener ) {
-			document.removeEventListener( "DOMContentLoaded", completed, false );
-			window.removeEventListener( "load", completed, false );
-
-		} else {
-			document.detachEvent( "onreadystatechange", completed );
-			window.detachEvent( "onload", completed );
-		}
 	};
 
 jQuery.fn = jQuery.prototype = {
 	// The current version of jQuery being used
-	jquery: core_version,
+	jquery: version,
 
 	constructor: jQuery,
-	init: function( selector, context, rootjQuery ) {
-		var match, elem;
-
-		// HANDLE: $(""), $(null), $(undefined), $(false)
-		if ( !selector ) {
-			return this;
-		}
-
-		// Handle HTML strings
-		if ( typeof selector === "string" ) {
-			if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
-				// Assume that strings that start and end with <> are HTML and skip the regex check
-				match = [ null, selector, null ];
-
-			} else {
-				match = rquickExpr.exec( selector );
-			}
-
-			// Match html or make sure no context is specified for #id
-			if ( match && (match[1] || !context) ) {
-
-				// HANDLE: $(html) -> $(array)
-				if ( match[1] ) {
-					context = context instanceof jQuery ? context[0] : context;
-
-					// scripts is true for back-compat
-					jQuery.merge( this, jQuery.parseHTML(
-						match[1],
-						context && context.nodeType ? context.ownerDocument || context : document,
-						true
-					) );
-
-					// HANDLE: $(html, props)
-					if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
-						for ( match in context ) {
-							// Properties of context are called as methods if possible
-							if ( jQuery.isFunction( this[ match ] ) ) {
-								this[ match ]( context[ match ] );
-
-							// ...and otherwise set as attributes
-							} else {
-								this.attr( match, context[ match ] );
-							}
-						}
-					}
-
-					return this;
-
-				// HANDLE: $(#id)
-				} else {
-					elem = document.getElementById( match[2] );
-
-					// Check parentNode to catch when Blackberry 4.6 returns
-					// nodes that are no longer in the document #6963
-					if ( elem && elem.parentNode ) {
-						// Handle the case where IE and Opera return items
-						// by name instead of ID
-						if ( elem.id !== match[2] ) {
-							return rootjQuery.find( selector );
-						}
-
-						// Otherwise, we inject the element directly into the jQuery object
-						this.length = 1;
-						this[0] = elem;
-					}
-
-					this.context = document;
-					this.selector = selector;
-					return this;
-				}
-
-			// HANDLE: $(expr, $(...))
-			} else if ( !context || context.jquery ) {
-				return ( context || rootjQuery ).find( selector );
-
-			// HANDLE: $(expr, context)
-			// (which is just equivalent to: $(context).find(expr)
-			} else {
-				return this.constructor( context ).find( selector );
-			}
-
-		// HANDLE: $(DOMElement)
-		} else if ( selector.nodeType ) {
-			this.context = this[0] = selector;
-			this.length = 1;
-			return this;
-
-		// HANDLE: $(function)
-		// Shortcut for document ready
-		} else if ( jQuery.isFunction( selector ) ) {
-			return rootjQuery.ready( selector );
-		}
-
-		if ( selector.selector !== undefined ) {
-			this.selector = selector.selector;
-			this.context = selector.context;
-		}
-
-		return jQuery.makeArray( selector, this );
-	},
 
 	// Start with an empty selector
 	selector: "",
@@ -227,25 +98,20 @@ jQuery.fn = jQuery.prototype = {
 	// The default length of a jQuery object is 0
 	length: 0,
 
-	// The number of elements contained in the matched element set
-	size: function() {
-		return this.length;
-	},
-
 	toArray: function() {
-		return core_slice.call( this );
+		return slice.call( this );
 	},
 
 	// Get the Nth element in the matched element set OR
 	// Get the whole matched element set as a clean array
 	get: function( num ) {
-		return num == null ?
+		return num != null ?
 
-			// Return a 'clean' array
-			this.toArray() :
+			// Return just the one element from the set
+			( num < 0 ? this[ num + this.length ] : this[ num ] ) :
 
-			// Return just the object
-			( num < 0 ? this[ this.length + num ] : this[ num ] );
+			// Return all the elements in a clean array
+			slice.call( this );
 	},
 
 	// Take an array of elements and push it onto the stack
@@ -270,15 +136,14 @@ jQuery.fn = jQuery.prototype = {
 		return jQuery.each( this, callback, args );
 	},
 
-	ready: function( fn ) {
-		// Add the callback
-		jQuery.ready.promise().done( fn );
-
-		return this;
+	map: function( callback ) {
+		return this.pushStack( jQuery.map(this, function( elem, i ) {
+			return callback.call( elem, i, elem );
+		}));
 	},
 
 	slice: function() {
-		return this.pushStack( core_slice.apply( this, arguments ) );
+		return this.pushStack( slice.apply( this, arguments ) );
 	},
 
 	first: function() {
@@ -295,26 +160,17 @@ jQuery.fn = jQuery.prototype = {
 		return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] );
 	},
 
-	map: function( callback ) {
-		return this.pushStack( jQuery.map(this, function( elem, i ) {
-			return callback.call( elem, i, elem );
-		}));
-	},
-
 	end: function() {
 		return this.prevObject || this.constructor(null);
 	},
 
 	// For internal use only.
 	// Behaves like an Array's method, not like a jQuery method.
-	push: core_push,
-	sort: [].sort,
-	splice: [].splice
+	push: push,
+	sort: deletedIds.sort,
+	splice: deletedIds.splice
 };
 
-// Give the init function the jQuery prototype for later instantiation
-jQuery.fn.init.prototype = jQuery.fn;
-
 jQuery.extend = jQuery.fn.extend = function() {
 	var src, copyIsArray, copy, name, options, clone,
 		target = arguments[0] || {},
@@ -325,9 +181,10 @@ jQuery.extend = jQuery.fn.extend = function() {
 	// Handle a deep copy situation
 	if ( typeof target === "boolean" ) {
 		deep = target;
-		target = arguments[1] || {};
+
 		// skip the boolean and the target
-		i = 2;
+		target = arguments[ i ] || {};
+		i++;
 	}
 
 	// Handle case when target is a string or something (possible in deep copy)
@@ -336,9 +193,9 @@ jQuery.extend = jQuery.fn.extend = function() {
 	}
 
 	// extend jQuery itself if only one argument is passed
-	if ( length === i ) {
+	if ( i === length ) {
 		target = this;
-		--i;
+		i--;
 	}
 
 	for ( ; i < length; i++ ) {
@@ -380,63 +237,17 @@ jQuery.extend = jQuery.fn.extend = function() {
 };
 
 jQuery.extend({
-	noConflict: function( deep ) {
-		if ( window.$ === jQuery ) {
-			window.$ = _$;
-		}
-
-		if ( deep && window.jQuery === jQuery ) {
-			window.jQuery = _jQuery;
-		}
-
-		return jQuery;
-	},
-
-	// Is the DOM ready to be used? Set to true once it occurs.
-	isReady: false,
+	// Unique for each copy of jQuery on the page
+	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
 
-	// A counter to track how many items to wait for before
-	// the ready event fires. See #6781
-	readyWait: 1,
+	// Assume jQuery is ready without the ready module
+	isReady: true,
 
-	// Hold (or release) the ready event
-	holdReady: function( hold ) {
-		if ( hold ) {
-			jQuery.readyWait++;
-		} else {
-			jQuery.ready( true );
-		}
+	error: function( msg ) {
+		throw new Error( msg );
 	},
 
-	// Handle when the DOM is ready
-	ready: function( wait ) {
-
-		// Abort if there are pending holds or we're already ready
-		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
-			return;
-		}
-
-		// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
-		if ( !document.body ) {
-			return setTimeout( jQuery.ready );
-		}
-
-		// Remember that the DOM is ready
-		jQuery.isReady = true;
-
-		// If a normal DOM Ready event fired, decrement, and wait if need be
-		if ( wait !== true && --jQuery.readyWait > 0 ) {
-			return;
-		}
-
-		// If there are functions bound, to execute
-		readyList.resolveWith( document, [ jQuery ] );
-
-		// Trigger any bound ready events
-		if ( jQuery.fn.trigger ) {
-			jQuery( document ).trigger("ready").off("ready");
-		}
-	},
+	noop: function() {},
 
 	// See test/unit/core.js for details concerning isFunction.
 	// Since version 1.3, DOM methods and functions like alert
@@ -450,23 +261,29 @@ jQuery.extend({
 	},
 
 	isWindow: function( obj ) {
+		/* jshint eqeqeq: false */
 		return obj != null && obj == obj.window;
 	},
 
 	isNumeric: function( obj ) {
-		return !isNaN( parseFloat(obj) ) && isFinite( obj );
+		// parseFloat NaNs numeric-cast false positives (null|true|false|"")
+		// ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+		// subtraction forces infinities to NaN
+		// adding 1 corrects loss of precision from parseFloat (#15100)
+		return !jQuery.isArray( obj ) && (obj - parseFloat( obj ) + 1) >= 0;
 	},
 
-	type: function( obj ) {
-		if ( obj == null ) {
-			return String( obj );
+	isEmptyObject: function( obj ) {
+		var name;
+		for ( name in obj ) {
+			return false;
 		}
-		return typeof obj === "object" || typeof obj === "function" ?
-			class2type[ core_toString.call(obj) ] || "object" :
-			typeof obj;
+		return true;
 	},
 
 	isPlainObject: function( obj ) {
+		var key;
+
 		// Must be an Object.
 		// Because of IE, we also have to check the presence of the constructor property.
 		// Make sure that DOM nodes and window objects don't pass through, as well
@@ -477,8 +294,8 @@ jQuery.extend({
 		try {
 			// Not own constructor property must be Object
 			if ( obj.constructor &&
-				!core_hasOwn.call(obj, "constructor") &&
-				!core_hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
+				!hasOwn.call(obj, "constructor") &&
+				!hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
 				return false;
 			}
 		} catch ( e ) {
@@ -486,134 +303,53 @@ jQuery.extend({
 			return false;
 		}
 
+		// Support: IE<9
+		// Handle iteration over inherited properties before own properties.
+		if ( support.ownLast ) {
+			for ( key in obj ) {
+				return hasOwn.call( obj, key );
+			}
+		}
+
 		// Own properties are enumerated firstly, so to speed up,
 		// if last one is own, then all properties are own.
-
-		var key;
 		for ( key in obj ) {}
 
-		return key === undefined || core_hasOwn.call( obj, key );
+		return key === undefined || hasOwn.call( obj, key );
 	},
 
-	isEmptyObject: function( obj ) {
-		var name;
-		for ( name in obj ) {
-			return false;
+	type: function( obj ) {
+		if ( obj == null ) {
+			return obj + "";
 		}
-		return true;
-	},
-
-	error: function( msg ) {
-		throw new Error( msg );
+		return typeof obj === "object" || typeof obj === "function" ?
+			class2type[ toString.call(obj) ] || "object" :
+			typeof obj;
 	},
 
-	// data: string of html
-	// context (optional): If specified, the fragment will be created in this context, defaults to document
-	// keepScripts (optional): If true, will include scripts passed in the html string
-	parseHTML: function( data, context, keepScripts ) {
-		if ( !data || typeof data !== "string" ) {
-			return null;
-		}
-		if ( typeof context === "boolean" ) {
-			keepScripts = context;
-			context = false;
-		}
-		context = context || document;
-
-		var parsed = rsingleTag.exec( data ),
-			scripts = !keepScripts && [];
-
-		// Single tag
-		if ( parsed ) {
-			return [ context.createElement( parsed[1] ) ];
+	// Evaluates a script in a global context
+	// Workarounds based on findings by Jim Driscoll
+	// http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
+	globalEval: function( data ) {
+		if ( data && jQuery.trim( data ) ) {
+			// We use execScript on Internet Explorer
+			// We use an anonymous function so that context is window
+			// rather than jQuery in Firefox
+			( window.execScript || function( data ) {
+				window[ "eval" ].call( window, data );
+			} )( data );
 		}
+	},
 
-		parsed = jQuery.buildFragment( [ data ], context, scripts );
-		if ( scripts ) {
-			jQuery( scripts ).remove();
-		}
-		return jQuery.merge( [], parsed.childNodes );
+	// Convert dashed to camelCase; used by the css and data modules
+	// Microsoft forgot to hump their vendor prefix (#9572)
+	camelCase: function( string ) {
+		return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
 	},
 
-	parseJSON: function( data ) {
-		// Attempt to parse using the native JSON parser first
-		if ( window.JSON && window.JSON.parse ) {
-			return window.JSON.parse( data );
-		}
-
-		if ( data === null ) {
-			return data;
-		}
-
-		if ( typeof data === "string" ) {
-
-			// Make sure leading/trailing whitespace is removed (IE can't handle it)
-			data = jQuery.trim( data );
-
-			if ( data ) {
-				// Make sure the incoming data is actual JSON
-				// Logic borrowed from http://json.org/json2.js
-				if ( rvalidchars.test( data.replace( rvalidescape, "@" )
-					.replace( rvalidtokens, "]" )
-					.replace( rvalidbraces, "")) ) {
-
-					return ( new Function( "return " + data ) )();
-				}
-			}
-		}
-
-		jQuery.error( "Invalid JSON: " + data );
-	},
-
-	// Cross-browser xml parsing
-	parseXML: function( data ) {
-		var xml, tmp;
-		if ( !data || typeof data !== "string" ) {
-			return null;
-		}
-		try {
-			if ( window.DOMParser ) { // Standard
-				tmp = new DOMParser();
-				xml = tmp.parseFromString( data , "text/xml" );
-			} else { // IE
-				xml = new ActiveXObject( "Microsoft.XMLDOM" );
-				xml.async = "false";
-				xml.loadXML( data );
-			}
-		} catch( e ) {
-			xml = undefined;
-		}
-		if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
-			jQuery.error( "Invalid XML: " + data );
-		}
-		return xml;
-	},
-
-	noop: function() {},
-
-	// Evaluates a script in a global context
-	// Workarounds based on findings by Jim Driscoll
-	// http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
-	globalEval: function( data ) {
-		if ( data && jQuery.trim( data ) ) {
-			// We use execScript on Internet Explorer
-			// We use an anonymous function so that context is window
-			// rather than jQuery in Firefox
-			( window.execScript || function( data ) {
-				window[ "eval" ].call( window, data );
-			} )( data );
-		}
-	},
-
-	// Convert dashed to camelCase; used by the css and data modules
-	// Microsoft forgot to hump their vendor prefix (#9572)
-	camelCase: function( string ) {
-		return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
-	},
-
-	nodeName: function( elem, name ) {
-		return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
-	},
+	nodeName: function( elem, name ) {
+		return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+	},
 
 	// args is for internal usage only
 	each: function( obj, callback, args ) {
@@ -665,20 +401,12 @@ jQuery.extend({
 		return obj;
 	},
 
-	// Use native String.trim function wherever possible
-	trim: core_trim && !core_trim.call("\uFEFF\xA0") ?
-		function( text ) {
-			return text == null ?
-				"" :
-				core_trim.call( text );
-		} :
-
-		// Otherwise use our own trimming functionality
-		function( text ) {
-			return text == null ?
-				"" :
-				( text + "" ).replace( rtrim, "" );
-		},
+	// Support: Android<4.1, IE<9
+	trim: function( text ) {
+		return text == null ?
+			"" :
+			( text + "" ).replace( rtrim, "" );
+	},
 
 	// results is for internal usage only
 	makeArray: function( arr, results ) {
@@ -691,7 +419,7 @@ jQuery.extend({
 					[ arr ] : arr
 				);
 			} else {
-				core_push.call( ret, arr );
+				push.call( ret, arr );
 			}
 		}
 
@@ -702,8 +430,8 @@ jQuery.extend({
 		var len;
 
 		if ( arr ) {
-			if ( core_indexOf ) {
-				return core_indexOf.call( arr, elem, i );
+			if ( indexOf ) {
+				return indexOf.call( arr, elem, i );
 			}
 
 			len = arr.length;
@@ -721,15 +449,17 @@ jQuery.extend({
 	},
 
 	merge: function( first, second ) {
-		var l = second.length,
-			i = first.length,
-			j = 0;
+		var len = +second.length,
+			j = 0,
+			i = first.length;
 
-		if ( typeof l === "number" ) {
-			for ( ; j < l; j++ ) {
-				first[ i++ ] = second[ j ];
-			}
-		} else {
+		while ( j < len ) {
+			first[ i++ ] = second[ j++ ];
+		}
+
+		// Support: IE<9
+		// Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists)
+		if ( len !== len ) {
 			while ( second[j] !== undefined ) {
 				first[ i++ ] = second[ j++ ];
 			}
@@ -740,23 +470,23 @@ jQuery.extend({
 		return first;
 	},
 
-	grep: function( elems, callback, inv ) {
-		var retVal,
-			ret = [],
+	grep: function( elems, callback, invert ) {
+		var callbackInverse,
+			matches = [],
 			i = 0,
-			length = elems.length;
-		inv = !!inv;
+			length = elems.length,
+			callbackExpect = !invert;
 
 		// Go through the array, only saving the items
 		// that pass the validator function
 		for ( ; i < length; i++ ) {
-			retVal = !!callback( elems[ i ], i );
-			if ( inv !== retVal ) {
-				ret.push( elems[ i ] );
+			callbackInverse = !callback( elems[ i ], i );
+			if ( callbackInverse !== callbackExpect ) {
+				matches.push( elems[ i ] );
 			}
 		}
 
-		return ret;
+		return matches;
 	},
 
 	// arg is for internal usage only
@@ -767,13 +497,13 @@ jQuery.extend({
 			isArray = isArraylike( elems ),
 			ret = [];
 
-		// Go through the array, translating each of the items to their
+		// Go through the array, translating each of the items to their new values
 		if ( isArray ) {
 			for ( ; i < length; i++ ) {
 				value = callback( elems[ i ], i, arg );
 
 				if ( value != null ) {
-					ret[ ret.length ] = value;
+					ret.push( value );
 				}
 			}
 
@@ -783,13 +513,13 @@ jQuery.extend({
 				value = callback( elems[ i ], i, arg );
 
 				if ( value != null ) {
-					ret[ ret.length ] = value;
+					ret.push( value );
 				}
 			}
 		}
 
 		// Flatten any nested arrays
-		return core_concat.apply( [], ret );
+		return concat.apply( [], ret );
 	},
 
 	// A global GUID counter for objects
@@ -813,9 +543,9 @@ jQuery.extend({
 		}
 
 		// Simulated bind
-		args = core_slice.call( arguments, 2 );
+		args = slice.call( arguments, 2 );
 		proxy = function() {
-			return fn.apply( context || this, args.concat( core_slice.call( arguments ) ) );
+			return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
 		};
 
 		// Set the guid of unique handler to the same of original handler, so it can be removed
@@ -824,5389 +554,4845 @@ jQuery.extend({
 		return proxy;
 	},
 
-	// Multifunctional method to get and set values of a collection
-	// The value/s can optionally be executed if it's a function
-	access: function( elems, fn, key, value, chainable, emptyGet, raw ) {
-		var i = 0,
-			length = elems.length,
-			bulk = key == null;
+	now: function() {
+		return +( new Date() );
+	},
 
-		// Sets many values
-		if ( jQuery.type( key ) === "object" ) {
-			chainable = true;
-			for ( i in key ) {
-				jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
-			}
+	// jQuery.support is not used in Core but other projects attach their
+	// properties to it so it needs to exist.
+	support: support
+});
 
-		// Sets one value
-		} else if ( value !== undefined ) {
-			chainable = true;
+// Populate the class2type map
+jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
+	class2type[ "[object " + name + "]" ] = name.toLowerCase();
+});
 
-			if ( !jQuery.isFunction( value ) ) {
-				raw = true;
-			}
+function isArraylike( obj ) {
 
-			if ( bulk ) {
-				// Bulk operations run against the entire set
-				if ( raw ) {
-					fn.call( elems, value );
-					fn = null;
+	// Support: iOS 8.2 (not reproducible in simulator)
+	// `in` check used to prevent JIT error (gh-2145)
+	// hasOwn isn't used here due to false negatives
+	// regarding Nodelist length in IE
+	var length = "length" in obj && obj.length,
+		type = jQuery.type( obj );
 
-				// ...except when executing function values
-				} else {
-					bulk = fn;
-					fn = function( elem, key, value ) {
-						return bulk.call( jQuery( elem ), value );
-					};
-				}
-			}
+	if ( type === "function" || jQuery.isWindow( obj ) ) {
+		return false;
+	}
 
-			if ( fn ) {
-				for ( ; i < length; i++ ) {
-					fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
-				}
-			}
+	if ( obj.nodeType === 1 && length ) {
+		return true;
+	}
+
+	return type === "array" || length === 0 ||
+		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
+}
+var Sizzle =
+/*!
+ * Sizzle CSS Selector Engine v2.2.0-pre
+ * http://sizzlejs.com/
+ *
+ * Copyright 2008, 2014 jQuery Foundation, Inc. and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2014-12-16
+ */
+(function( window ) {
+
+var i,
+	support,
+	Expr,
+	getText,
+	isXML,
+	tokenize,
+	compile,
+	select,
+	outermostContext,
+	sortInput,
+	hasDuplicate,
+
+	// Local document vars
+	setDocument,
+	document,
+	docElem,
+	documentIsHTML,
+	rbuggyQSA,
+	rbuggyMatches,
+	matches,
+	contains,
+
+	// Instance-specific data
+	expando = "sizzle" + 1 * new Date(),
+	preferredDoc = window.document,
+	dirruns = 0,
+	done = 0,
+	classCache = createCache(),
+	tokenCache = createCache(),
+	compilerCache = createCache(),
+	sortOrder = function( a, b ) {
+		if ( a === b ) {
+			hasDuplicate = true;
 		}
+		return 0;
+	},
 
-		return chainable ?
-			elems :
+	// General-purpose constants
+	MAX_NEGATIVE = 1 << 31,
 
-			// Gets
-			bulk ?
-				fn.call( elems ) :
-				length ? fn( elems[0], key ) : emptyGet;
+	// Instance methods
+	hasOwn = ({}).hasOwnProperty,
+	arr = [],
+	pop = arr.pop,
+	push_native = arr.push,
+	push = arr.push,
+	slice = arr.slice,
+	// Use a stripped-down indexOf as it's faster than native
+	// http://jsperf.com/thor-indexof-vs-for/5
+	indexOf = function( list, elem ) {
+		var i = 0,
+			len = list.length;
+		for ( ; i < len; i++ ) {
+			if ( list[i] === elem ) {
+				return i;
+			}
+		}
+		return -1;
 	},
 
-	now: function() {
-		return ( new Date() ).getTime();
-	}
-});
+	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
 
-jQuery.ready.promise = function( obj ) {
-	if ( !readyList ) {
+	// Regular expressions
 
-		readyList = jQuery.Deferred();
+	// Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
+	whitespace = "[\\x20\\t\\r\\n\\f]",
+	// http://www.w3.org/TR/css3-syntax/#characters
+	characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
 
-		// Catch cases where $(document).ready() is called after the browser event has already occurred.
-		// we once tried to use readyState "interactive" here, but it caused issues like the one
-		// discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
-		if ( document.readyState === "complete" ) {
-			// Handle it asynchronously to allow scripts the opportunity to delay ready
-			setTimeout( jQuery.ready );
+	// Loosely modeled on CSS identifier characters
+	// An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
+	// Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+	identifier = characterEncoding.replace( "w", "w#" ),
 
-		// Standards-based browsers support DOMContentLoaded
-		} else if ( document.addEventListener ) {
-			// Use the handy event callback
-			document.addEventListener( "DOMContentLoaded", completed, false );
+	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
+	attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace +
+		// Operator (capture 2)
+		"*([*^$|!~]?=)" + whitespace +
+		// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
+		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
+		"*\\]",
+
+	pseudos = ":(" + characterEncoding + ")(?:\\((" +
+		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
+		// 1. quoted (capture 3; capture 4 or capture 5)
+		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
+		// 2. simple (capture 6)
+		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
+		// 3. anything else (capture 2)
+		".*" +
+		")\\)|)",
 
-			// A fallback to window.onload, that will always work
-			window.addEventListener( "load", completed, false );
+	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+	rwhitespace = new RegExp( whitespace + "+", "g" ),
+	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
 
-		// If IE event model is used
-		} else {
-			// Ensure firing before onload, maybe late but safe also for iframes
-			document.attachEvent( "onreadystatechange", completed );
+	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
 
-			// A fallback to window.onload, that will always work
-			window.attachEvent( "onload", completed );
+	rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
 
-			// If IE and not a frame
-			// continually check to see if the document is ready
-			var top = false;
+	rpseudo = new RegExp( pseudos ),
+	ridentifier = new RegExp( "^" + identifier + "$" ),
 
-			try {
-				top = window.frameElement == null && document.documentElement;
-			} catch(e) {}
+	matchExpr = {
+		"ID": new RegExp( "^#(" + characterEncoding + ")" ),
+		"CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
+		"TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
+		"ATTR": new RegExp( "^" + attributes ),
+		"PSEUDO": new RegExp( "^" + pseudos ),
+		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
+			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
+		// For use in libraries implementing .is()
+		// We use this for POS matching in `select`
+		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
+			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+	},
 
-			if ( top && top.doScroll ) {
-				(function doScrollCheck() {
-					if ( !jQuery.isReady ) {
+	rinputs = /^(?:input|select|textarea|button)$/i,
+	rheader = /^h\d$/i,
 
-						try {
-							// Use the trick by Diego Perini
-							// http://javascript.nwbox.com/IEContentLoaded/
-							top.doScroll("left");
-						} catch(e) {
-							return setTimeout( doScrollCheck, 50 );
-						}
+	rnative = /^[^{]+\{\s*\[native \w/,
 
-						// detach all dom ready events
-						detach();
+	// Easily-parseable/retrievable ID or TAG or CLASS selectors
+	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
 
-						// and execute any waiting functions
-						jQuery.ready();
-					}
-				})();
-			}
-		}
-	}
-	return readyList.promise( obj );
-};
+	rsibling = /[+~]/,
+	rescape = /'|\\/g,
 
-// Populate the class2type map
-jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
-	class2type[ "[object " + name + "]" ] = name.toLowerCase();
-});
+	// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+	runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
+	funescape = function( _, escaped, escapedWhitespace ) {
+		var high = "0x" + escaped - 0x10000;
+		// NaN means non-codepoint
+		// Support: Firefox<24
+		// Workaround erroneous numeric interpretation of +"0x"
+		return high !== high || escapedWhitespace ?
+			escaped :
+			high < 0 ?
+				// BMP codepoint
+				String.fromCharCode( high + 0x10000 ) :
+				// Supplemental Plane codepoint (surrogate pair)
+				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
+	},
 
-function isArraylike( obj ) {
-	var length = obj.length,
-		type = jQuery.type( obj );
+	// Used for iframes
+	// See setDocument()
+	// Removing the function wrapper causes a "Permission Denied"
+	// error in IE
+	unloadHandler = function() {
+		setDocument();
+	};
 
-	if ( jQuery.isWindow( obj ) ) {
-		return false;
-	}
+// Optimize for push.apply( _, NodeList )
+try {
+	push.apply(
+		(arr = slice.call( preferredDoc.childNodes )),
+		preferredDoc.childNodes
+	);
+	// Support: Android<4.0
+	// Detect silently failing push.apply
+	arr[ preferredDoc.childNodes.length ].nodeType;
+} catch ( e ) {
+	push = { apply: arr.length ?
 
-	if ( obj.nodeType === 1 && length ) {
-		return true;
-	}
+		// Leverage slice if possible
+		function( target, els ) {
+			push_native.apply( target, slice.call(els) );
+		} :
 
-	return type === "array" || type !== "function" &&
-		( length === 0 ||
-		typeof length === "number" && length > 0 && ( length - 1 ) in obj );
+		// Support: IE<9
+		// Otherwise append directly
+		function( target, els ) {
+			var j = target.length,
+				i = 0;
+			// Can't trust NodeList.length
+			while ( (target[j++] = els[i++]) ) {}
+			target.length = j - 1;
+		}
+	};
 }
 
-// All jQuery objects should point back to these
-rootjQuery = jQuery(document);
-// String to Object options format cache
-var optionsCache = {};
+function Sizzle( selector, context, results, seed ) {
+	var match, elem, m, nodeType,
+		// QSA vars
+		i, groups, old, nid, newContext, newSelector;
 
-// Convert String-formatted options into Object-formatted ones and store in cache
-function createOptions( options ) {
-	var object = optionsCache[ options ] = {};
-	jQuery.each( options.match( core_rnotwhite ) || [], function( _, flag ) {
-		object[ flag ] = true;
-	});
-	return object;
-}
+	if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+		setDocument( context );
+	}
 
-/*
- * Create a callback list using the following parameters:
- *
- *	options: an optional list of space-separated options that will change how
- *			the callback list behaves or a more traditional option object
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible options:
- *
- *	once:			will ensure the callback list can only be fired once (like a Deferred)
- *
- *	memory:			will keep track of previous values and will call any callback added
- *					after the list has been fired right away with the latest "memorized"
- *					values (like a Deferred)
- *
- *	unique:			will ensure a callback can only be added once (no duplicate in the list)
- *
- *	stopOnFalse:	interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( options ) {
+	context = context || document;
+	results = results || [];
+	nodeType = context.nodeType;
 
-	// Convert options from String-formatted to Object-formatted if needed
-	// (we check in cache first)
-	options = typeof options === "string" ?
-		( optionsCache[ options ] || createOptions( options ) ) :
-		jQuery.extend( {}, options );
+	if ( typeof selector !== "string" || !selector ||
+		nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
 
-	var // Flag to know if list is currently firing
-		firing,
-		// Last fire value (for non-forgettable lists)
-		memory,
-		// Flag to know if list was already fired
-		fired,
-		// End of the loop when firing
-		firingLength,
-		// Index of currently firing callback (modified by remove if needed)
-		firingIndex,
-		// First callback to fire (used internally by add and fireWith)
-		firingStart,
-		// Actual callback list
-		list = [],
-		// Stack of fire calls for repeatable lists
-		stack = !options.once && [],
-		// Fire callbacks
-		fire = function( data ) {
-			memory = options.memory && data;
-			fired = true;
-			firingIndex = firingStart || 0;
-			firingStart = 0;
-			firingLength = list.length;
-			firing = true;
-			for ( ; list && firingIndex < firingLength; firingIndex++ ) {
-				if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
-					memory = false; // To prevent further calls using add
-					break;
-				}
-			}
-			firing = false;
-			if ( list ) {
-				if ( stack ) {
-					if ( stack.length ) {
-						fire( stack.shift() );
+		return results;
+	}
+
+	if ( !seed && documentIsHTML ) {
+
+		// Try to shortcut find operations when possible (e.g., not under DocumentFragment)
+		if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
+			// Speed-up: Sizzle("#ID")
+			if ( (m = match[1]) ) {
+				if ( nodeType === 9 ) {
+					elem = context.getElementById( m );
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document (jQuery #6963)
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE, Opera, and Webkit return items
+						// by name instead of ID
+						if ( elem.id === m ) {
+							results.push( elem );
+							return results;
+						}
+					} else {
+						return results;
 					}
-				} else if ( memory ) {
-					list = [];
 				} else {
-					self.disable();
-				}
-			}
-		},
-		// Actual Callbacks object
-		self = {
-			// Add a callback or a collection of callbacks to the list
-			add: function() {
-				if ( list ) {
-					// First, we save the current length
-					var start = list.length;
-					(function add( args ) {
-						jQuery.each( args, function( _, arg ) {
-							var type = jQuery.type( arg );
-							if ( type === "function" ) {
-								if ( !options.unique || !self.has( arg ) ) {
-									list.push( arg );
-								}
-							} else if ( arg && arg.length && type !== "string" ) {
-								// Inspect recursively
-								add( arg );
-							}
-						});
-					})( arguments );
-					// Do we need to add the callbacks to the
-					// current firing batch?
-					if ( firing ) {
-						firingLength = list.length;
-					// With memory, if we're not firing then
-					// we should call right away
-					} else if ( memory ) {
-						firingStart = start;
-						fire( memory );
+					// Context is not a document
+					if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
+						contains( context, elem ) && elem.id === m ) {
+						results.push( elem );
+						return results;
 					}
 				}
-				return this;
-			},
-			// Remove a callback from the list
-			remove: function() {
-				if ( list ) {
-					jQuery.each( arguments, function( _, arg ) {
-						var index;
-						while( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
-							list.splice( index, 1 );
-							// Handle firing indexes
-							if ( firing ) {
-								if ( index <= firingLength ) {
-									firingLength--;
-								}
-								if ( index <= firingIndex ) {
-									firingIndex--;
-								}
-							}
-						}
-					});
+
+			// Speed-up: Sizzle("TAG")
+			} else if ( match[2] ) {
+				push.apply( results, context.getElementsByTagName( selector ) );
+				return results;
+
+			// Speed-up: Sizzle(".CLASS")
+			} else if ( (m = match[3]) && support.getElementsByClassName ) {
+				push.apply( results, context.getElementsByClassName( m ) );
+				return results;
+			}
+		}
+
+		// QSA path
+		if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
+			nid = old = expando;
+			newContext = context;
+			newSelector = nodeType !== 1 && selector;
+
+			// qSA works strangely on Element-rooted queries
+			// We can work around this by specifying an extra ID on the root
+			// and working up from there (Thanks to Andrew Dupont for the technique)
+			// IE 8 doesn't work on object elements
+			if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
+				groups = tokenize( selector );
+
+				if ( (old = context.getAttribute("id")) ) {
+					nid = old.replace( rescape, "\\$&" );
+				} else {
+					context.setAttribute( "id", nid );
 				}
-				return this;
-			},
-			// Check if a given callback is in the list.
-			// If no argument is given, return whether or not list has callbacks attached.
-			has: function( fn ) {
-				return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
-			},
-			// Remove all callbacks from the list
-			empty: function() {
-				list = [];
-				return this;
-			},
-			// Have the list do nothing anymore
-			disable: function() {
-				list = stack = memory = undefined;
-				return this;
-			},
-			// Is it disabled?
-			disabled: function() {
-				return !list;
-			},
-			// Lock the list in its current state
-			lock: function() {
-				stack = undefined;
-				if ( !memory ) {
-					self.disable();
+				nid = "[id='" + nid + "'] ";
+
+				i = groups.length;
+				while ( i-- ) {
+					groups[i] = nid + toSelector( groups[i] );
 				}
-				return this;
-			},
-			// Is it locked?
-			locked: function() {
-				return !stack;
-			},
-			// Call all callbacks with the given context and arguments
-			fireWith: function( context, args ) {
-				args = args || [];
-				args = [ context, args.slice ? args.slice() : args ];
-				if ( list && ( !fired || stack ) ) {
-					if ( firing ) {
-						stack.push( args );
-					} else {
-						fire( args );
+				newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context;
+				newSelector = groups.join(",");
+			}
+
+			if ( newSelector ) {
+				try {
+					push.apply( results,
+						newContext.querySelectorAll( newSelector )
+					);
+					return results;
+				} catch(qsaError) {
+				} finally {
+					if ( !old ) {
+						context.removeAttribute("id");
 					}
 				}
-				return this;
-			},
-			// Call all the callbacks with the given arguments
-			fire: function() {
-				self.fireWith( this, arguments );
-				return this;
-			},
-			// To know if the callbacks have already been called at least once
-			fired: function() {
-				return !!fired;
 			}
-		};
+		}
+	}
 
-	return self;
-};
-jQuery.extend({
+	// All others
+	return select( selector.replace( rtrim, "$1" ), context, results, seed );
+}
 
-	Deferred: function( func ) {
-		var tuples = [
-				// action, add listener, listener list, final state
-				[ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
-				[ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
-				[ "notify", "progress", jQuery.Callbacks("memory") ]
-			],
-			state = "pending",
-			promise = {
-				state: function() {
-					return state;
-				},
-				always: function() {
-					deferred.done( arguments ).fail( arguments );
-					return this;
-				},
-				then: function( /* fnDone, fnFail, fnProgress */ ) {
-					var fns = arguments;
-					return jQuery.Deferred(function( newDefer ) {
-						jQuery.each( tuples, function( i, tuple ) {
-							var action = tuple[ 0 ],
-								fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
-							// deferred[ done | fail | progress ] for forwarding actions to newDefer
-							deferred[ tuple[1] ](function() {
-								var returned = fn && fn.apply( this, arguments );
-								if ( returned && jQuery.isFunction( returned.promise ) ) {
-									returned.promise()
-										.done( newDefer.resolve )
-										.fail( newDefer.reject )
-										.progress( newDefer.notify );
-								} else {
-									newDefer[ action + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
-								}
-							});
-						});
-						fns = null;
-					}).promise();
-				},
-				// Get a promise for this deferred
-				// If obj is provided, the promise aspect is added to the object
-				promise: function( obj ) {
-					return obj != null ? jQuery.extend( obj, promise ) : promise;
-				}
-			},
-			deferred = {};
-
-		// Keep pipe for back-compat
-		promise.pipe = promise.then;
-
-		// Add list-specific methods
-		jQuery.each( tuples, function( i, tuple ) {
-			var list = tuple[ 2 ],
-				stateString = tuple[ 3 ];
-
-			// promise[ done | fail | progress ] = list.add
-			promise[ tuple[1] ] = list.add;
-
-			// Handle state
-			if ( stateString ) {
-				list.add(function() {
-					// state = [ resolved | rejected ]
-					state = stateString;
-
-				// [ reject_list | resolve_list ].disable; progress_list.lock
-				}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
-			}
-
-			// deferred[ resolve | reject | notify ]
-			deferred[ tuple[0] ] = function() {
-				deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
-				return this;
-			};
-			deferred[ tuple[0] + "With" ] = list.fireWith;
-		});
-
-		// Make the deferred a promise
-		promise.promise( deferred );
+/**
+ * Create key-value caches of limited size
+ * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
+ *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
+ *	deleting the oldest entry
+ */
+function createCache() {
+	var keys = [];
 
-		// Call given func if any
-		if ( func ) {
-			func.call( deferred, deferred );
+	function cache( key, value ) {
+		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
+		if ( keys.push( key + " " ) > Expr.cacheLength ) {
+			// Only keep the most recent entries
+			delete cache[ keys.shift() ];
 		}
+		return (cache[ key + " " ] = value);
+	}
+	return cache;
+}
 
-		// All done!
-		return deferred;
-	},
-
-	// Deferred helper
-	when: function( subordinate /* , ..., subordinateN */ ) {
-		var i = 0,
-			resolveValues = core_slice.call( arguments ),
-			length = resolveValues.length,
-
-			// the count of uncompleted subordinates
-			remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
-
-			// the master Deferred. If resolveValues consist of only a single Deferred, just use that.
-			deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
-
-			// Update function for both resolve and progress values
-			updateFunc = function( i, contexts, values ) {
-				return function( value ) {
-					contexts[ i ] = this;
-					values[ i ] = arguments.length > 1 ? core_slice.call( arguments ) : value;
-					if( values === progressValues ) {
-						deferred.notifyWith( contexts, values );
-					} else if ( !( --remaining ) ) {
-						deferred.resolveWith( contexts, values );
-					}
-				};
-			},
+/**
+ * Mark a function for special use by Sizzle
+ * @param {Function} fn The function to mark
+ */
+function markFunction( fn ) {
+	fn[ expando ] = true;
+	return fn;
+}
 
-			progressValues, progressContexts, resolveContexts;
+/**
+ * Support testing using an element
+ * @param {Function} fn Passed the created div and expects a boolean result
+ */
+function assert( fn ) {
+	var div = document.createElement("div");
 
-		// add listeners to Deferred subordinates; treat others as resolved
-		if ( length > 1 ) {
-			progressValues = new Array( length );
-			progressContexts = new Array( length );
-			resolveContexts = new Array( length );
-			for ( ; i < length; i++ ) {
-				if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
-					resolveValues[ i ].promise()
-						.done( updateFunc( i, resolveContexts, resolveValues ) )
-						.fail( deferred.reject )
-						.progress( updateFunc( i, progressContexts, progressValues ) );
-				} else {
-					--remaining;
-				}
-			}
+	try {
+		return !!fn( div );
+	} catch (e) {
+		return false;
+	} finally {
+		// Remove from its parent by default
+		if ( div.parentNode ) {
+			div.parentNode.removeChild( div );
 		}
+		// release memory in IE
+		div = null;
+	}
+}
 
-		// if we're not waiting on anything, resolve the master
-		if ( !remaining ) {
-			deferred.resolveWith( resolveContexts, resolveValues );
-		}
+/**
+ * Adds the same handler for all of the specified attrs
+ * @param {String} attrs Pipe-separated list of attributes
+ * @param {Function} handler The method that will be applied
+ */
+function addHandle( attrs, handler ) {
+	var arr = attrs.split("|"),
+		i = attrs.length;
 
-		return deferred.promise();
+	while ( i-- ) {
+		Expr.attrHandle[ arr[i] ] = handler;
 	}
-});
-jQuery.support = (function() {
-
-	var support, all, a,
-		input, select, fragment,
-		opt, eventName, isSupported, i,
-		div = document.createElement("div");
+}
 
-	// Setup
-	div.setAttribute( "className", "t" );
-	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+/**
+ * Checks document order of two siblings
+ * @param {Element} a
+ * @param {Element} b
+ * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
+ */
+function siblingCheck( a, b ) {
+	var cur = b && a,
+		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
+			( ~b.sourceIndex || MAX_NEGATIVE ) -
+			( ~a.sourceIndex || MAX_NEGATIVE );
 
-	// Support tests won't run in some limited or non-browser environments
-	all = div.getElementsByTagName("*");
-	a = div.getElementsByTagName("a")[ 0 ];
-	if ( !all || !a || !all.length ) {
-		return {};
+	// Use IE sourceIndex if available on both nodes
+	if ( diff ) {
+		return diff;
 	}
 
-	// First batch of tests
-	select = document.createElement("select");
-	opt = select.appendChild( document.createElement("option") );
-	input = div.getElementsByTagName("input")[ 0 ];
+	// Check if b follows a
+	if ( cur ) {
+		while ( (cur = cur.nextSibling) ) {
+			if ( cur === b ) {
+				return -1;
+			}
+		}
+	}
 
-	a.style.cssText = "top:1px;float:left;opacity:.5";
-	support = {
-		// Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
-		getSetAttribute: div.className !== "t",
+	return a ? 1 : -1;
+}
 
-		// IE strips leading whitespace when .innerHTML is used
-		leadingWhitespace: div.firstChild.nodeType === 3,
+/**
+ * Returns a function to use in pseudos for input types
+ * @param {String} type
+ */
+function createInputPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return name === "input" && elem.type === type;
+	};
+}
 
-		// Make sure that tbody elements aren't automatically inserted
-		// IE will insert them into empty tables
-		tbody: !div.getElementsByTagName("tbody").length,
+/**
+ * Returns a function to use in pseudos for buttons
+ * @param {String} type
+ */
+function createButtonPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return (name === "input" || name === "button") && elem.type === type;
+	};
+}
 
-		// Make sure that link elements get serialized correctly by innerHTML
-		// This requires a wrapper element in IE
-		htmlSerialize: !!div.getElementsByTagName("link").length,
+/**
+ * Returns a function to use in pseudos for positionals
+ * @param {Function} fn
+ */
+function createPositionalPseudo( fn ) {
+	return markFunction(function( argument ) {
+		argument = +argument;
+		return markFunction(function( seed, matches ) {
+			var j,
+				matchIndexes = fn( [], seed.length, argument ),
+				i = matchIndexes.length;
 
-		// Get the style information from getAttribute
-		// (IE uses .cssText instead)
-		style: /top/.test( a.getAttribute("style") ),
+			// Match elements found at the specified indexes
+			while ( i-- ) {
+				if ( seed[ (j = matchIndexes[i]) ] ) {
+					seed[j] = !(matches[j] = seed[j]);
+				}
+			}
+		});
+	});
+}
 
-		// Make sure that URLs aren't manipulated
-		// (IE normalizes it by default)
-		hrefNormalized: a.getAttribute("href") === "/a",
+/**
+ * Checks a node for validity as a Sizzle context
+ * @param {Element|Object=} context
+ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
+ */
+function testContext( context ) {
+	return context && typeof context.getElementsByTagName !== "undefined" && context;
+}
 
-		// Make sure that element opacity exists
-		// (IE uses filter instead)
-		// Use a regex to work around a WebKit issue. See #5145
-		opacity: /^0.5/.test( a.style.opacity ),
+// Expose support vars for convenience
+support = Sizzle.support = {};
 
-		// Verify style float existence
-		// (IE uses styleFloat instead of cssFloat)
-		cssFloat: !!a.style.cssFloat,
+/**
+ * Detects XML nodes
+ * @param {Element|Object} elem An element or a document
+ * @returns {Boolean} True iff elem is a non-HTML XML node
+ */
+isXML = Sizzle.isXML = function( elem ) {
+	// documentElement is verified for cases where it doesn't yet exist
+	// (such as loading iframes in IE - #4833)
+	var documentElement = elem && (elem.ownerDocument || elem).documentElement;
+	return documentElement ? documentElement.nodeName !== "HTML" : false;
+};
 
-		// Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
-		checkOn: !!input.value,
+/**
+ * Sets document-related variables once based on the current document
+ * @param {Element|Object} [doc] An element or document object to use to set the document
+ * @returns {Object} Returns the current document
+ */
+setDocument = Sizzle.setDocument = function( node ) {
+	var hasCompare, parent,
+		doc = node ? node.ownerDocument || node : preferredDoc;
 
-		// Make sure that a selected-by-default option has a working selected property.
-		// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
-		optSelected: opt.selected,
+	// If no document and documentElement is available, return
+	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
+		return document;
+	}
 
-		// Tests for enctype support on a form (#6743)
-		enctype: !!document.createElement("form").enctype,
+	// Set our document
+	document = doc;
+	docElem = doc.documentElement;
+	parent = doc.defaultView;
+
+	// Support: IE>8
+	// If iframe document is assigned to "document" variable and if iframe has been reloaded,
+	// IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936
+	// IE6-8 do not support the defaultView property so parent will be undefined
+	if ( parent && parent !== parent.top ) {
+		// IE11 does not have attachEvent, so all must suffer
+		if ( parent.addEventListener ) {
+			parent.addEventListener( "unload", unloadHandler, false );
+		} else if ( parent.attachEvent ) {
+			parent.attachEvent( "onunload", unloadHandler );
+		}
+	}
 
-		// Makes sure cloning an html5 element does not cause problems
-		// Where outerHTML is undefined, this still works
-		html5Clone: document.createElement("nav").cloneNode( true ).outerHTML !== "<:nav></:nav>",
+	/* Support tests
+	---------------------------------------------------------------------- */
+	documentIsHTML = !isXML( doc );
 
-		// jQuery.support.boxModel DEPRECATED in 1.8 since we don't support Quirks Mode
-		boxModel: document.compatMode === "CSS1Compat",
+	/* Attributes
+	---------------------------------------------------------------------- */
 
-		// Will be defined later
-		deleteExpando: true,
-		noCloneEvent: true,
-		inlineBlockNeedsLayout: false,
-		shrinkWrapBlocks: false,
-		reliableMarginRight: true,
-		boxSizingReliable: true,
-		pixelPosition: false
-	};
+	// Support: IE<8
+	// Verify that getAttribute really returns attributes and not properties
+	// (excepting IE8 booleans)
+	support.attributes = assert(function( div ) {
+		div.className = "i";
+		return !div.getAttribute("className");
+	});
 
-	// Make sure checked status is properly cloned
-	input.checked = true;
-	support.noCloneChecked = input.cloneNode( true ).checked;
+	/* getElement(s)By*
+	---------------------------------------------------------------------- */
 
-	// Make sure that the options inside disabled selects aren't marked as disabled
-	// (WebKit marks them as disabled)
-	select.disabled = true;
-	support.optDisabled = !opt.disabled;
+	// Check if getElementsByTagName("*") returns only elements
+	support.getElementsByTagName = assert(function( div ) {
+		div.appendChild( doc.createComment("") );
+		return !div.getElementsByTagName("*").length;
+	});
 
 	// Support: IE<9
-	try {
-		delete div.test;
-	} catch( e ) {
-		support.deleteExpando = false;
-	}
+	support.getElementsByClassName = rnative.test( doc.getElementsByClassName );
 
-	// Check if we can trust getAttribute("value")
-	input = document.createElement("input");
-	input.setAttribute( "value", "" );
-	support.input = input.getAttribute( "value" ) === "";
-
-	// Check if an input maintains its value after becoming a radio
-	input.value = "t";
-	input.setAttribute( "type", "radio" );
-	support.radioValue = input.value === "t";
-
-	// #11217 - WebKit loses check when the name is after the checked attribute
-	input.setAttribute( "checked", "t" );
-	input.setAttribute( "name", "t" );
-
-	fragment = document.createDocumentFragment();
-	fragment.appendChild( input );
-
-	// Check if a disconnected checkbox will retain its checked
-	// value of true after appended to the DOM (IE6/7)
-	support.appendChecked = input.checked;
-
-	// WebKit doesn't clone checked state correctly in fragments
-	support.checkClone = fragment.cloneNode( true ).cloneNode( true ).lastChild.checked;
+	// Support: IE<10
+	// Check if getElementById returns elements by name
+	// The broken getElementById methods don't pick up programatically-set names,
+	// so use a roundabout getElementsByName test
+	support.getById = assert(function( div ) {
+		docElem.appendChild( div ).id = expando;
+		return !doc.getElementsByName || !doc.getElementsByName( expando ).length;
+	});
 
-	// Support: IE<9
-	// Opera does not clone events (and typeof div.attachEvent === undefined).
-	// IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
-	if ( div.attachEvent ) {
-		div.attachEvent( "onclick", function() {
-			support.noCloneEvent = false;
-		});
+	// ID find and filter
+	if ( support.getById ) {
+		Expr.find["ID"] = function( id, context ) {
+			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+				var m = context.getElementById( id );
+				// Check parentNode to catch when Blackberry 4.6 returns
+				// nodes that are no longer in the document #6963
+				return m && m.parentNode ? [ m ] : [];
+			}
+		};
+		Expr.filter["ID"] = function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				return elem.getAttribute("id") === attrId;
+			};
+		};
+	} else {
+		// Support: IE6/7
+		// getElementById is not reliable as a find shortcut
+		delete Expr.find["ID"];
 
-		div.cloneNode( true ).click();
+		Expr.filter["ID"] =  function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id");
+				return node && node.value === attrId;
+			};
+		};
 	}
 
-	// Support: IE<9 (lack submit/change bubble), Firefox 17+ (lack focusin event)
-	// Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP), test/csp.php
-	for ( i in { submit: true, change: true, focusin: true }) {
-		div.setAttribute( eventName = "on" + i, "t" );
+	// Tag
+	Expr.find["TAG"] = support.getElementsByTagName ?
+		function( tag, context ) {
+			if ( typeof context.getElementsByTagName !== "undefined" ) {
+				return context.getElementsByTagName( tag );
 
-		support[ i + "Bubbles" ] = eventName in window || div.attributes[ eventName ].expando === false;
-	}
+			// DocumentFragment nodes don't have gEBTN
+			} else if ( support.qsa ) {
+				return context.querySelectorAll( tag );
+			}
+		} :
 
-	div.style.backgroundClip = "content-box";
-	div.cloneNode( true ).style.backgroundClip = "";
-	support.clearCloneStyle = div.style.backgroundClip === "content-box";
+		function( tag, context ) {
+			var elem,
+				tmp = [],
+				i = 0,
+				// By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
+				results = context.getElementsByTagName( tag );
+
+			// Filter out possible comments
+			if ( tag === "*" ) {
+				while ( (elem = results[i++]) ) {
+					if ( elem.nodeType === 1 ) {
+						tmp.push( elem );
+					}
+				}
 
-	// Run tests that need a body at doc ready
-	jQuery(function() {
-		var container, marginDiv, tds,
-			divReset = "padding:0;margin:0;border:0;display:block;box-sizing:content-box;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;",
-			body = document.getElementsByTagName("body")[0];
+				return tmp;
+			}
+			return results;
+		};
 
-		if ( !body ) {
-			// Return for frameset docs that don't have a body
-			return;
+	// Class
+	Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
+		if ( documentIsHTML ) {
+			return context.getElementsByClassName( className );
 		}
+	};
 
-		container = document.createElement("div");
-		container.style.cssText = "border:0;width:0;height:0;position:absolute;top:0;left:-9999px;margin-top:1px";
-
-		body.appendChild( container ).appendChild( div );
+	/* QSA/matchesSelector
+	---------------------------------------------------------------------- */
 
-		// Support: IE8
-		// Check if table cells still have offsetWidth/Height when they are set
-		// to display:none and there are still other visible table cells in a
-		// table row; if so, offsetWidth/Height are not reliable for use when
-		// determining if an element has been hidden directly using
-		// display:none (it is still safe to use offsets if a parent element is
-		// hidden; don safety goggles and see bug #4512 for more information).
-		div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
-		tds = div.getElementsByTagName("td");
-		tds[ 0 ].style.cssText = "padding:0;margin:0;border:0;display:none";
-		isSupported = ( tds[ 0 ].offsetHeight === 0 );
+	// QSA and matchesSelector support
 
-		tds[ 0 ].style.display = "";
-		tds[ 1 ].style.display = "none";
+	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+	rbuggyMatches = [];
 
-		// Support: IE8
-		// Check if empty table cells still have offsetWidth/Height
-		support.reliableHiddenOffsets = isSupported && ( tds[ 0 ].offsetHeight === 0 );
+	// qSa(:focus) reports false when true (Chrome 21)
+	// We allow this because of a bug in IE8/9 that throws an error
+	// whenever `document.activeElement` is accessed on an iframe
+	// So, we allow :focus to pass through QSA all the time to avoid the IE error
+	// See http://bugs.jquery.com/ticket/13378
+	rbuggyQSA = [];
 
-		// Check box-sizing and margin behavior
-		div.innerHTML = "";
-		div.style.cssText = "box-sizing:border-box;-moz-box-sizing:border-box;-webkit-box-sizing:border-box;padding:1px;border:1px;display:block;width:4px;margin-top:1%;position:absolute;top:1%;";
-		support.boxSizing = ( div.offsetWidth === 4 );
-		support.doesNotIncludeMarginInBodyOffset = ( body.offsetTop !== 1 );
+	if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) {
+		// Build QSA regex
+		// Regex strategy adopted from Diego Perini
+		assert(function( div ) {
+			// Select is set to empty string on purpose
+			// This is to test IE's treatment of not explicitly
+			// setting a boolean content attribute,
+			// since its presence should be enough
+			// http://bugs.jquery.com/ticket/12359
+			docElem.appendChild( div ).innerHTML = "<a id='" + expando + "'></a>" +
+				"<select id='" + expando + "-\f]' msallowcapture=''>" +
+				"<option selected=''></option></select>";
+
+			// Support: IE8, Opera 11-12.16
+			// Nothing should be selected when empty strings follow ^= or $= or *=
+			// The test attribute must be unknown in Opera but "safe" for WinRT
+			// http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+			if ( div.querySelectorAll("[msallowcapture^='']").length ) {
+				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
+			}
 
-		// Use window.getComputedStyle because jsdom on node.js will break without it.
-		if ( window.getComputedStyle ) {
-			support.pixelPosition = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
-			support.boxSizingReliable = ( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
+			// Support: IE8
+			// Boolean attributes and "value" are not treated correctly
+			if ( !div.querySelectorAll("[selected]").length ) {
+				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
+			}
 
-			// Check if div with explicit width and no margin-right incorrectly
-			// gets computed margin-right based on width of container. (#3333)
-			// Fails in WebKit before Feb 2011 nightlies
-			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
-			marginDiv = div.appendChild( document.createElement("div") );
-			marginDiv.style.cssText = div.style.cssText = divReset;
-			marginDiv.style.marginRight = marginDiv.style.width = "0";
-			div.style.width = "1px";
+			// Support: Chrome<29, Android<4.2+, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.7+
+			if ( !div.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
+				rbuggyQSA.push("~=");
+			}
 
-			support.reliableMarginRight =
-				!parseFloat( ( window.getComputedStyle( marginDiv, null ) || {} ).marginRight );
-		}
+			// Webkit/Opera - :checked should return selected option elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":checked").length ) {
+				rbuggyQSA.push(":checked");
+			}
 
-		if ( typeof div.style.zoom !== core_strundefined ) {
-			// Support: IE<8
-			// Check if natively block-level elements act like inline-block
-			// elements when setting their display to 'inline' and giving
-			// them layout
-			div.innerHTML = "";
-			div.style.cssText = divReset + "width:1px;padding:1px;display:inline;zoom:1";
-			support.inlineBlockNeedsLayout = ( div.offsetWidth === 3 );
-
-			// Support: IE6
-			// Check if elements with layout shrink-wrap their children
-			div.style.display = "block";
-			div.innerHTML = "<div></div>";
-			div.firstChild.style.width = "5px";
-			support.shrinkWrapBlocks = ( div.offsetWidth !== 3 );
-
-			if ( support.inlineBlockNeedsLayout ) {
-				// Prevent IE 6 from affecting layout for positioned elements #11048
-				// Prevent IE from shrinking the body in IE 7 mode #12869
-				// Support: IE<8
-				body.style.zoom = 1;
+			// Support: Safari 8+, iOS 8+
+			// https://bugs.webkit.org/show_bug.cgi?id=136851
+			// In-page `selector#id sibing-combinator selector` fails
+			if ( !div.querySelectorAll( "a#" + expando + "+*" ).length ) {
+				rbuggyQSA.push(".#.+[+~]");
 			}
-		}
+		});
 
-		body.removeChild( container );
+		assert(function( div ) {
+			// Support: Windows 8 Native Apps
+			// The type and name attributes are restricted during .innerHTML assignment
+			var input = doc.createElement("input");
+			input.setAttribute( "type", "hidden" );
+			div.appendChild( input ).setAttribute( "name", "D" );
+
+			// Support: IE8
+			// Enforce case-sensitivity of name attribute
+			if ( div.querySelectorAll("[name=d]").length ) {
+				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
+			}
 
-		// Null elements to avoid leaks in IE
-		container = div = tds = marginDiv = null;
-	});
+			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":enabled").length ) {
+				rbuggyQSA.push( ":enabled", ":disabled" );
+			}
 
-	// Null elements to avoid leaks in IE
-	all = select = fragment = opt = a = input = null;
+			// Opera 10-11 does not throw on post-comma invalid pseudos
+			div.querySelectorAll("*,:x");
+			rbuggyQSA.push(",.*:");
+		});
+	}
 
-	return support;
-})();
+	if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
+		docElem.webkitMatchesSelector ||
+		docElem.mozMatchesSelector ||
+		docElem.oMatchesSelector ||
+		docElem.msMatchesSelector) )) ) {
 
-var rbrace = /(?:\{[\s\S]*\}|\[[\s\S]*\])$/,
-	rmultiDash = /([A-Z])/g;
+		assert(function( div ) {
+			// Check to see if it's possible to do matchesSelector
+			// on a disconnected node (IE 9)
+			support.disconnectedMatch = matches.call( div, "div" );
 
-function internalData( elem, name, data, pvt /* Internal Use Only */ ){
-	if ( !jQuery.acceptData( elem ) ) {
-		return;
+			// This should fail with an exception
+			// Gecko does not error, returns false instead
+			matches.call( div, "[s!='']:x" );
+			rbuggyMatches.push( "!=", pseudos );
+		});
 	}
 
-	var thisCache, ret,
-		internalKey = jQuery.expando,
-		getByName = typeof name === "string",
+	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
+	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
 
-		// We have to handle DOM nodes and JS objects differently because IE6-7
-		// can't GC object references properly across the DOM-JS boundary
-		isNode = elem.nodeType,
+	/* Contains
+	---------------------------------------------------------------------- */
+	hasCompare = rnative.test( docElem.compareDocumentPosition );
 
-		// Only DOM nodes need the global jQuery cache; JS object data is
-		// attached directly to the object so GC can occur automatically
-		cache = isNode ? jQuery.cache : elem,
+	// Element contains another
+	// Purposefully does not implement inclusive descendent
+	// As in, an element does not contain itself
+	contains = hasCompare || rnative.test( docElem.contains ) ?
+		function( a, b ) {
+			var adown = a.nodeType === 9 ? a.documentElement : a,
+				bup = b && b.parentNode;
+			return a === bup || !!( bup && bup.nodeType === 1 && (
+				adown.contains ?
+					adown.contains( bup ) :
+					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
+			));
+		} :
+		function( a, b ) {
+			if ( b ) {
+				while ( (b = b.parentNode) ) {
+					if ( b === a ) {
+						return true;
+					}
+				}
+			}
+			return false;
+		};
 
-		// Only defining an ID for JS objects if its cache already exists allows
-		// the code to shortcut on the same path as a DOM node with no cache
-		id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
+	/* Sorting
+	---------------------------------------------------------------------- */
 
-	// Avoid doing any more work than we need to when trying to get data on an
-	// object that has no data at all
-	if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && getByName && data === undefined ) {
-		return;
-	}
+	// Document order sorting
+	sortOrder = hasCompare ?
+	function( a, b ) {
 
-	if ( !id ) {
-		// Only DOM nodes need a new unique ID for each element since their data
-		// ends up in the global cache
-		if ( isNode ) {
-			elem[ internalKey ] = id = core_deletedIds.pop() || jQuery.guid++;
-		} else {
-			id = internalKey;
+		// Flag for duplicate removal
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
 		}
-	}
-
-	if ( !cache[ id ] ) {
-		cache[ id ] = {};
 
-		// Avoids exposing jQuery metadata on plain JS objects when the object
-		// is serialized using JSON.stringify
-		if ( !isNode ) {
-			cache[ id ].toJSON = jQuery.noop;
+		// Sort on method existence if only one input has compareDocumentPosition
+		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
+		if ( compare ) {
+			return compare;
 		}
-	}
 
-	// An object can be passed to jQuery.data instead of a key/value pair; this gets
-	// shallow copied over onto the existing cache
-	if ( typeof name === "object" || typeof name === "function" ) {
-		if ( pvt ) {
-			cache[ id ] = jQuery.extend( cache[ id ], name );
-		} else {
-			cache[ id ].data = jQuery.extend( cache[ id ].data, name );
-		}
-	}
+		// Calculate position if both inputs belong to the same document
+		compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
+			a.compareDocumentPosition( b ) :
 
-	thisCache = cache[ id ];
+			// Otherwise we know they are disconnected
+			1;
 
-	// jQuery data() is stored in a separate object inside the object's internal data
-	// cache in order to avoid key collisions between internal data and user-defined
-	// data.
-	if ( !pvt ) {
-		if ( !thisCache.data ) {
-			thisCache.data = {};
-		}
+		// Disconnected nodes
+		if ( compare & 1 ||
+			(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
 
-		thisCache = thisCache.data;
-	}
+			// Choose the first element that is related to our preferred document
+			if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+				return -1;
+			}
+			if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+				return 1;
+			}
 
-	if ( data !== undefined ) {
-		thisCache[ jQuery.camelCase( name ) ] = data;
-	}
+			// Maintain original order
+			return sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
+		}
 
-	// Check for both converted-to-camel and non-converted data property names
-	// If a data property was specified
-	if ( getByName ) {
+		return compare & 4 ? -1 : 1;
+	} :
+	function( a, b ) {
+		// Exit early if the nodes are identical
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
 
-		// First Try to find as-is property data
-		ret = thisCache[ name ];
+		var cur,
+			i = 0,
+			aup = a.parentNode,
+			bup = b.parentNode,
+			ap = [ a ],
+			bp = [ b ];
 
-		// Test for null|undefined property data
-		if ( ret == null ) {
+		// Parentless nodes are either documents or disconnected
+		if ( !aup || !bup ) {
+			return a === doc ? -1 :
+				b === doc ? 1 :
+				aup ? -1 :
+				bup ? 1 :
+				sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
 
-			// Try to find the camelCased property
-			ret = thisCache[ jQuery.camelCase( name ) ];
+		// If the nodes are siblings, we can do a quick check
+		} else if ( aup === bup ) {
+			return siblingCheck( a, b );
 		}
-	} else {
-		ret = thisCache;
-	}
-
-	return ret;
-}
-
-function internalRemoveData( elem, name, pvt ) {
-	if ( !jQuery.acceptData( elem ) ) {
-		return;
-	}
 
-	var i, l, thisCache,
-		isNode = elem.nodeType,
+		// Otherwise we need full lists of their ancestors for comparison
+		cur = a;
+		while ( (cur = cur.parentNode) ) {
+			ap.unshift( cur );
+		}
+		cur = b;
+		while ( (cur = cur.parentNode) ) {
+			bp.unshift( cur );
+		}
 
-		// See jQuery.data for more information
-		cache = isNode ? jQuery.cache : elem,
-		id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+		// Walk down the tree looking for a discrepancy
+		while ( ap[i] === bp[i] ) {
+			i++;
+		}
 
-	// If there is already no cache entry for this object, there is no
-	// purpose in continuing
-	if ( !cache[ id ] ) {
-		return;
-	}
+		return i ?
+			// Do a sibling check if the nodes have a common ancestor
+			siblingCheck( ap[i], bp[i] ) :
 
-	if ( name ) {
+			// Otherwise nodes in our document sort first
+			ap[i] === preferredDoc ? -1 :
+			bp[i] === preferredDoc ? 1 :
+			0;
+	};
 
-		thisCache = pvt ? cache[ id ] : cache[ id ].data;
+	return doc;
+};
 
-		if ( thisCache ) {
+Sizzle.matches = function( expr, elements ) {
+	return Sizzle( expr, null, null, elements );
+};
 
-			// Support array or space separated string names for data keys
-			if ( !jQuery.isArray( name ) ) {
+Sizzle.matchesSelector = function( elem, expr ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
 
-				// try the string as a key before any manipulation
-				if ( name in thisCache ) {
-					name = [ name ];
-				} else {
+	// Make sure that attribute selectors are quoted
+	expr = expr.replace( rattributeQuotes, "='$1']" );
 
-					// split the camel cased version by spaces unless a key with the spaces exists
-					name = jQuery.camelCase( name );
-					if ( name in thisCache ) {
-						name = [ name ];
-					} else {
-						name = name.split(" ");
-					}
-				}
-			} else {
-				// If "name" is an array of keys...
-				// When data is initially created, via ("key", "val") signature,
-				// keys will be converted to camelCase.
-				// Since there is no way to tell _how_ a key was added, remove
-				// both plain key and camelCase key. #12786
-				// This will only penalize the array argument path.
-				name = name.concat( jQuery.map( name, jQuery.camelCase ) );
-			}
+	if ( support.matchesSelector && documentIsHTML &&
+		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
+		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
 
-			for ( i = 0, l = name.length; i < l; i++ ) {
-				delete thisCache[ name[i] ];
-			}
+		try {
+			var ret = matches.call( elem, expr );
 
-			// If there is no data left in the cache, we want to continue
-			// and let the cache object itself get destroyed
-			if ( !( pvt ? isEmptyDataObject : jQuery.isEmptyObject )( thisCache ) ) {
-				return;
+			// IE 9's matchesSelector returns false on disconnected nodes
+			if ( ret || support.disconnectedMatch ||
+					// As well, disconnected nodes are said to be in a document
+					// fragment in IE 9
+					elem.document && elem.document.nodeType !== 11 ) {
+				return ret;
 			}
-		}
+		} catch (e) {}
 	}
 
-	// See jQuery.data for more information
-	if ( !pvt ) {
-		delete cache[ id ].data;
+	return Sizzle( expr, document, null, [ elem ] ).length > 0;
+};
 
-		// Don't destroy the parent cache unless the internal data object
-		// had been the only thing left in it
-		if ( !isEmptyDataObject( cache[ id ] ) ) {
-			return;
-		}
+Sizzle.contains = function( context, elem ) {
+	// Set document vars if needed
+	if ( ( context.ownerDocument || context ) !== document ) {
+		setDocument( context );
 	}
+	return contains( context, elem );
+};
 
-	// Destroy the cache
-	if ( isNode ) {
-		jQuery.cleanData( [ elem ], true );
-
-	// Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
-	} else if ( jQuery.support.deleteExpando || cache != cache.window ) {
-		delete cache[ id ];
-
-	// When all else fails, null
-	} else {
-		cache[ id ] = null;
+Sizzle.attr = function( elem, name ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
 	}
-}
 
-jQuery.extend({
-	cache: {},
+	var fn = Expr.attrHandle[ name.toLowerCase() ],
+		// Don't get fooled by Object.prototype properties (jQuery #13807)
+		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
+			fn( elem, name, !documentIsHTML ) :
+			undefined;
 
-	// Unique for each copy of jQuery on the page
-	// Non-digits removed to match rinlinejQuery
-	expando: "jQuery" + ( core_version + Math.random() ).replace( /\D/g, "" ),
+	return val !== undefined ?
+		val :
+		support.attributes || !documentIsHTML ?
+			elem.getAttribute( name ) :
+			(val = elem.getAttributeNode(name)) && val.specified ?
+				val.value :
+				null;
+};
 
-	// The following elements throw uncatchable exceptions if you
-	// attempt to add expando properties to them.
-	noData: {
-		"embed": true,
-		// Ban all objects except for Flash (which handle expandos)
-		"object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000",
-		"applet": true
-	},
+Sizzle.error = function( msg ) {
+	throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
 
-	hasData: function( elem ) {
-		elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
-		return !!elem && !isEmptyDataObject( elem );
-	},
+/**
+ * Document sorting and removing duplicates
+ * @param {ArrayLike} results
+ */
+Sizzle.uniqueSort = function( results ) {
+	var elem,
+		duplicates = [],
+		j = 0,
+		i = 0;
 
-	data: function( elem, name, data ) {
-		return internalData( elem, name, data );
-	},
+	// Unless we *know* we can detect duplicates, assume their presence
+	hasDuplicate = !support.detectDuplicates;
+	sortInput = !support.sortStable && results.slice( 0 );
+	results.sort( sortOrder );
 
-	removeData: function( elem, name ) {
-		return internalRemoveData( elem, name );
-	},
+	if ( hasDuplicate ) {
+		while ( (elem = results[i++]) ) {
+			if ( elem === results[ i ] ) {
+				j = duplicates.push( i );
+			}
+		}
+		while ( j-- ) {
+			results.splice( duplicates[ j ], 1 );
+		}
+	}
 
-	// For internal use only.
-	_data: function( elem, name, data ) {
-		return internalData( elem, name, data, true );
-	},
+	// Clear input after sorting to release objects
+	// See https://github.com/jquery/sizzle/pull/225
+	sortInput = null;
 
-	_removeData: function( elem, name ) {
-		return internalRemoveData( elem, name, true );
-	},
+	return results;
+};
 
-	// A method for determining if a DOM node can handle the data expando
-	acceptData: function( elem ) {
-		// Do not set data on non-element because it will not be cleared (#8335).
-		if ( elem.nodeType && elem.nodeType !== 1 && elem.nodeType !== 9 ) {
-			return false;
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+	var node,
+		ret = "",
+		i = 0,
+		nodeType = elem.nodeType;
+
+	if ( !nodeType ) {
+		// If no nodeType, this is expected to be an array
+		while ( (node = elem[i++]) ) {
+			// Do not traverse comment nodes
+			ret += getText( node );
+		}
+	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+		// Use textContent for elements
+		// innerText usage removed for consistency of new lines (jQuery #11153)
+		if ( typeof elem.textContent === "string" ) {
+			return elem.textContent;
+		} else {
+			// Traverse its children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				ret += getText( elem );
+			}
 		}
+	} else if ( nodeType === 3 || nodeType === 4 ) {
+		return elem.nodeValue;
+	}
+	// Do not include comment or processing instruction nodes
 
-		var noData = elem.nodeName && jQuery.noData[ elem.nodeName.toLowerCase() ];
+	return ret;
+};
 
-		// nodes accept data unless otherwise specified; rejection can be conditional
-		return !noData || noData !== true && elem.getAttribute("classid") === noData;
-	}
-});
+Expr = Sizzle.selectors = {
 
-jQuery.fn.extend({
-	data: function( key, value ) {
-		var attrs, name,
-			elem = this[0],
-			i = 0,
-			data = null;
+	// Can be adjusted by the user
+	cacheLength: 50,
 
-		// Gets all values
-		if ( key === undefined ) {
-			if ( this.length ) {
-				data = jQuery.data( elem );
+	createPseudo: markFunction,
 
-				if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
-					attrs = elem.attributes;
-					for ( ; i < attrs.length; i++ ) {
-						name = attrs[i].name;
+	match: matchExpr,
 
-						if ( !name.indexOf( "data-" ) ) {
-							name = jQuery.camelCase( name.slice(5) );
+	attrHandle: {},
 
-							dataAttr( elem, name, data[ name ] );
-						}
-					}
-					jQuery._data( elem, "parsedAttrs", true );
-				}
-			}
+	find: {},
 
-			return data;
-		}
+	relative: {
+		">": { dir: "parentNode", first: true },
+		" ": { dir: "parentNode" },
+		"+": { dir: "previousSibling", first: true },
+		"~": { dir: "previousSibling" }
+	},
 
-		// Sets multiple values
-		if ( typeof key === "object" ) {
-			return this.each(function() {
-				jQuery.data( this, key );
-			});
-		}
+	preFilter: {
+		"ATTR": function( match ) {
+			match[1] = match[1].replace( runescape, funescape );
 
-		return jQuery.access( this, function( value ) {
+			// Move the given value to match[3] whether quoted or unquoted
+			match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
 
-			if ( value === undefined ) {
-				// Try to fetch any internally stored data first
-				return elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : null;
+			if ( match[2] === "~=" ) {
+				match[3] = " " + match[3] + " ";
 			}
 
-			this.each(function() {
-				jQuery.data( this, key, value );
-			});
-		}, null, value, arguments.length > 1, null, true );
-	},
-
-	removeData: function( key ) {
-		return this.each(function() {
-			jQuery.removeData( this, key );
-		});
-	}
-});
+			return match.slice( 0, 4 );
+		},
 
-function dataAttr( elem, key, data ) {
-	// If nothing was found internally, try to fetch any
-	// data from the HTML5 data-* attribute
-	if ( data === undefined && elem.nodeType === 1 ) {
+		"CHILD": function( match ) {
+			/* matches from matchExpr["CHILD"]
+				1 type (only|nth|...)
+				2 what (child|of-type)
+				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+				4 xn-component of xn+y argument ([+-]?\d*n|)
+				5 sign of xn-component
+				6 x of xn-component
+				7 sign of y-component
+				8 y of y-component
+			*/
+			match[1] = match[1].toLowerCase();
 
-		var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
+			if ( match[1].slice( 0, 3 ) === "nth" ) {
+				// nth-* requires argument
+				if ( !match[3] ) {
+					Sizzle.error( match[0] );
+				}
 
-		data = elem.getAttribute( name );
+				// numeric x and y parameters for Expr.filter.CHILD
+				// remember that false/true cast respectively to 0/1
+				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
+				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
 
-		if ( typeof data === "string" ) {
-			try {
-				data = data === "true" ? true :
-					data === "false" ? false :
-					data === "null" ? null :
-					// Only convert to a number if it doesn't change the string
-					+data + "" === data ? +data :
-					rbrace.test( data ) ? jQuery.parseJSON( data ) :
-						data;
-			} catch( e ) {}
+			// other types prohibit arguments
+			} else if ( match[3] ) {
+				Sizzle.error( match[0] );
+			}
 
-			// Make sure we set the data so it isn't changed later
-			jQuery.data( elem, key, data );
+			return match;
+		},
 
-		} else {
-			data = undefined;
-		}
-	}
+		"PSEUDO": function( match ) {
+			var excess,
+				unquoted = !match[6] && match[2];
 
-	return data;
-}
+			if ( matchExpr["CHILD"].test( match[0] ) ) {
+				return null;
+			}
 
-// checks a cache object for emptiness
-function isEmptyDataObject( obj ) {
-	var name;
-	for ( name in obj ) {
+			// Accept quoted arguments as-is
+			if ( match[3] ) {
+				match[2] = match[4] || match[5] || "";
 
-		// if the public data object is empty, the private is still empty
-		if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
-			continue;
-		}
-		if ( name !== "toJSON" ) {
-			return false;
+			// Strip excess characters from unquoted arguments
+			} else if ( unquoted && rpseudo.test( unquoted ) &&
+				// Get excess from tokenize (recursively)
+				(excess = tokenize( unquoted, true )) &&
+				// advance to the next closing parenthesis
+				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+				// excess is a negative index
+				match[0] = match[0].slice( 0, excess );
+				match[2] = unquoted.slice( 0, excess );
+			}
+
+			// Return only captures needed by the pseudo filter method (type and argument)
+			return match.slice( 0, 3 );
 		}
-	}
+	},
 
-	return true;
-}
-jQuery.extend({
-	queue: function( elem, type, data ) {
-		var queue;
+	filter: {
 
-		if ( elem ) {
-			type = ( type || "fx" ) + "queue";
-			queue = jQuery._data( elem, type );
+		"TAG": function( nodeNameSelector ) {
+			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
+			return nodeNameSelector === "*" ?
+				function() { return true; } :
+				function( elem ) {
+					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+				};
+		},
 
-			// Speed up dequeue by getting out quickly if this is just a lookup
-			if ( data ) {
-				if ( !queue || jQuery.isArray(data) ) {
-					queue = jQuery._data( elem, type, jQuery.makeArray(data) );
-				} else {
-					queue.push( data );
+		"CLASS": function( className ) {
+			var pattern = classCache[ className + " " ];
+
+			return pattern ||
+				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+				classCache( className, function( elem ) {
+					return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
+				});
+		},
+
+		"ATTR": function( name, operator, check ) {
+			return function( elem ) {
+				var result = Sizzle.attr( elem, name );
+
+				if ( result == null ) {
+					return operator === "!=";
+				}
+				if ( !operator ) {
+					return true;
 				}
-			}
-			return queue || [];
-		}
-	},
 
-	dequeue: function( elem, type ) {
-		type = type || "fx";
+				result += "";
 
-		var queue = jQuery.queue( elem, type ),
-			startLength = queue.length,
-			fn = queue.shift(),
-			hooks = jQuery._queueHooks( elem, type ),
-			next = function() {
-				jQuery.dequeue( elem, type );
+				return operator === "=" ? result === check :
+					operator === "!=" ? result !== check :
+					operator === "^=" ? check && result.indexOf( check ) === 0 :
+					operator === "*=" ? check && result.indexOf( check ) > -1 :
+					operator === "$=" ? check && result.slice( -check.length ) === check :
+					operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
+					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
+					false;
 			};
+		},
 
-		// If the fx queue is dequeued, always remove the progress sentinel
-		if ( fn === "inprogress" ) {
-			fn = queue.shift();
-			startLength--;
-		}
+		"CHILD": function( type, what, argument, first, last ) {
+			var simple = type.slice( 0, 3 ) !== "nth",
+				forward = type.slice( -4 ) !== "last",
+				ofType = what === "of-type";
 
-		hooks.cur = fn;
-		if ( fn ) {
+			return first === 1 && last === 0 ?
 
-			// Add a progress sentinel to prevent the fx queue from being
-			// automatically dequeued
-			if ( type === "fx" ) {
-				queue.unshift( "inprogress" );
-			}
+				// Shortcut for :nth-*(n)
+				function( elem ) {
+					return !!elem.parentNode;
+				} :
 
-			// clear up the last queue stop function
-			delete hooks.stop;
-			fn.call( elem, next, hooks );
-		}
+				function( elem, context, xml ) {
+					var cache, outerCache, node, diff, nodeIndex, start,
+						dir = simple !== forward ? "nextSibling" : "previousSibling",
+						parent = elem.parentNode,
+						name = ofType && elem.nodeName.toLowerCase(),
+						useCache = !xml && !ofType;
 
-		if ( !startLength && hooks ) {
-			hooks.empty.fire();
-		}
-	},
+					if ( parent ) {
 
-	// not intended for public consumption - generates a queueHooks object, or returns the current one
-	_queueHooks: function( elem, type ) {
-		var key = type + "queueHooks";
-		return jQuery._data( elem, key ) || jQuery._data( elem, key, {
-			empty: jQuery.Callbacks("once memory").add(function() {
-				jQuery._removeData( elem, type + "queue" );
-				jQuery._removeData( elem, key );
-			})
-		});
-	}
-});
+						// :(first|last|only)-(child|of-type)
+						if ( simple ) {
+							while ( dir ) {
+								node = elem;
+								while ( (node = node[ dir ]) ) {
+									if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
+										return false;
+									}
+								}
+								// Reverse direction for :only-* (if we haven't yet done so)
+								start = dir = type === "only" && !start && "nextSibling";
+							}
+							return true;
+						}
 
-jQuery.fn.extend({
-	queue: function( type, data ) {
-		var setter = 2;
+						start = [ forward ? parent.firstChild : parent.lastChild ];
 
-		if ( typeof type !== "string" ) {
-			data = type;
-			type = "fx";
-			setter--;
-		}
+						// non-xml :nth-child(...) stores cache data on `parent`
+						if ( forward && useCache ) {
+							// Seek `elem` from a previously-cached index
+							outerCache = parent[ expando ] || (parent[ expando ] = {});
+							cache = outerCache[ type ] || [];
+							nodeIndex = cache[0] === dirruns && cache[1];
+							diff = cache[0] === dirruns && cache[2];
+							node = nodeIndex && parent.childNodes[ nodeIndex ];
 
-		if ( arguments.length < setter ) {
-			return jQuery.queue( this[0], type );
-		}
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
 
-		return data === undefined ?
-			this :
-			this.each(function() {
-				var queue = jQuery.queue( this, type, data );
+								// Fallback to seeking `elem` from the start
+								(diff = nodeIndex = 0) || start.pop()) ) {
 
-				// ensure a hooks for this queue
-				jQuery._queueHooks( this, type );
+								// When found, cache indexes on `parent` and break
+								if ( node.nodeType === 1 && ++diff && node === elem ) {
+									outerCache[ type ] = [ dirruns, nodeIndex, diff ];
+									break;
+								}
+							}
 
-				if ( type === "fx" && queue[0] !== "inprogress" ) {
-					jQuery.dequeue( this, type );
-				}
-			});
-	},
-	dequeue: function( type ) {
-		return this.each(function() {
-			jQuery.dequeue( this, type );
-		});
-	},
-	// Based off of the plugin by Clint Helfers, with permission.
-	// http://blindsignals.com/index.php/2009/07/jquery-delay/
-	delay: function( time, type ) {
-		time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
-		type = type || "fx";
+						// Use previously-cached element index if available
+						} else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
+							diff = cache[1];
 
-		return this.queue( type, function( next, hooks ) {
-			var timeout = setTimeout( next, time );
-			hooks.stop = function() {
-				clearTimeout( timeout );
-			};
-		});
-	},
-	clearQueue: function( type ) {
-		return this.queue( type || "fx", [] );
-	},
-	// Get a promise resolved when queues of a certain type
-	// are emptied (fx is the type by default)
-	promise: function( type, obj ) {
-		var tmp,
-			count = 1,
-			defer = jQuery.Deferred(),
-			elements = this,
-			i = this.length,
-			resolve = function() {
-				if ( !( --count ) ) {
-					defer.resolveWith( elements, [ elements ] );
-				}
-			};
-
-		if ( typeof type !== "string" ) {
-			obj = type;
-			type = undefined;
-		}
-		type = type || "fx";
+						// xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
+						} else {
+							// Use the same loop as above to seek `elem` from the start
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+								(diff = nodeIndex = 0) || start.pop()) ) {
 
-		while( i-- ) {
-			tmp = jQuery._data( elements[ i ], type + "queueHooks" );
-			if ( tmp && tmp.empty ) {
-				count++;
-				tmp.empty.add( resolve );
-			}
-		}
-		resolve();
-		return defer.promise( obj );
-	}
-});
-var nodeHook, boolHook,
-	rclass = /[\t\r\n]/g,
-	rreturn = /\r/g,
-	rfocusable = /^(?:input|select|textarea|button|object)$/i,
-	rclickable = /^(?:a|area)$/i,
-	rboolean = /^(?:checked|selected|autofocus|autoplay|async|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped)$/i,
-	ruseDefault = /^(?:checked|selected)$/i,
-	getSetAttribute = jQuery.support.getSetAttribute,
-	getSetInput = jQuery.support.input;
+								if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
+									// Cache the index of each encountered element
+									if ( useCache ) {
+										(node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
+									}
 
-jQuery.fn.extend({
-	attr: function( name, value ) {
-		return jQuery.access( this, jQuery.attr, name, value, arguments.length > 1 );
-	},
+									if ( node === elem ) {
+										break;
+									}
+								}
+							}
+						}
 
-	removeAttr: function( name ) {
-		return this.each(function() {
-			jQuery.removeAttr( this, name );
-		});
-	},
+						// Incorporate the offset, then check against cycle size
+						diff -= last;
+						return diff === first || ( diff % first === 0 && diff / first >= 0 );
+					}
+				};
+		},
 
-	prop: function( name, value ) {
-		return jQuery.access( this, jQuery.prop, name, value, arguments.length > 1 );
-	},
+		"PSEUDO": function( pseudo, argument ) {
+			// pseudo-class names are case-insensitive
+			// http://www.w3.org/TR/selectors/#pseudo-classes
+			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+			// Remember that setFilters inherits from pseudos
+			var args,
+				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+					Sizzle.error( "unsupported pseudo: " + pseudo );
 
-	removeProp: function( name ) {
-		name = jQuery.propFix[ name ] || name;
-		return this.each(function() {
-			// try/catch handles cases where IE balks (such as removing a property on window)
-			try {
-				this[ name ] = undefined;
-				delete this[ name ];
-			} catch( e ) {}
-		});
-	},
+			// The user may use createPseudo to indicate that
+			// arguments are needed to create the filter function
+			// just as Sizzle does
+			if ( fn[ expando ] ) {
+				return fn( argument );
+			}
 
-	addClass: function( value ) {
-		var classes, elem, cur, clazz, j,
-			i = 0,
-			len = this.length,
-			proceed = typeof value === "string" && value;
+			// But maintain support for old signatures
+			if ( fn.length > 1 ) {
+				args = [ pseudo, pseudo, "", argument ];
+				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+					markFunction(function( seed, matches ) {
+						var idx,
+							matched = fn( seed, argument ),
+							i = matched.length;
+						while ( i-- ) {
+							idx = indexOf( seed, matched[i] );
+							seed[ idx ] = !( matches[ idx ] = matched[i] );
+						}
+					}) :
+					function( elem ) {
+						return fn( elem, 0, args );
+					};
+			}
 
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( j ) {
-				jQuery( this ).addClass( value.call( this, j, this.className ) );
-			});
+			return fn;
 		}
+	},
 
-		if ( proceed ) {
-			// The disjunction here is for better compressibility (see removeClass)
-			classes = ( value || "" ).match( core_rnotwhite ) || [];
+	pseudos: {
+		// Potentially complex pseudos
+		"not": markFunction(function( selector ) {
+			// Trim the selector passed to compile
+			// to avoid treating leading and trailing
+			// spaces as combinators
+			var input = [],
+				results = [],
+				matcher = compile( selector.replace( rtrim, "$1" ) );
 
-			for ( ; i < len; i++ ) {
-				elem = this[ i ];
-				cur = elem.nodeType === 1 && ( elem.className ?
-					( " " + elem.className + " " ).replace( rclass, " " ) :
-					" "
-				);
+			return matcher[ expando ] ?
+				markFunction(function( seed, matches, context, xml ) {
+					var elem,
+						unmatched = matcher( seed, null, xml, [] ),
+						i = seed.length;
 
-				if ( cur ) {
-					j = 0;
-					while ( (clazz = classes[j++]) ) {
-						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
-							cur += clazz + " ";
+					// Match elements unmatched by `matcher`
+					while ( i-- ) {
+						if ( (elem = unmatched[i]) ) {
+							seed[i] = !(matches[i] = elem);
 						}
 					}
-					elem.className = jQuery.trim( cur );
-
-				}
-			}
-		}
-
-		return this;
-	},
-
-	removeClass: function( value ) {
-		var classes, elem, cur, clazz, j,
-			i = 0,
-			len = this.length,
-			proceed = arguments.length === 0 || typeof value === "string" && value;
+				}) :
+				function( elem, context, xml ) {
+					input[0] = elem;
+					matcher( input, null, xml, results );
+					// Don't keep the element (issue #299)
+					input[0] = null;
+					return !results.pop();
+				};
+		}),
 
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( j ) {
-				jQuery( this ).removeClass( value.call( this, j, this.className ) );
-			});
-		}
-		if ( proceed ) {
-			classes = ( value || "" ).match( core_rnotwhite ) || [];
+		"has": markFunction(function( selector ) {
+			return function( elem ) {
+				return Sizzle( selector, elem ).length > 0;
+			};
+		}),
 
-			for ( ; i < len; i++ ) {
-				elem = this[ i ];
-				// This expression is here for better compressibility (see addClass)
-				cur = elem.nodeType === 1 && ( elem.className ?
-					( " " + elem.className + " " ).replace( rclass, " " ) :
-					""
-				);
+		"contains": markFunction(function( text ) {
+			text = text.replace( runescape, funescape );
+			return function( elem ) {
+				return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
+			};
+		}),
 
-				if ( cur ) {
-					j = 0;
-					while ( (clazz = classes[j++]) ) {
-						// Remove *all* instances
-						while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
-							cur = cur.replace( " " + clazz + " ", " " );
-						}
-					}
-					elem.className = value ? jQuery.trim( cur ) : "";
-				}
+		// "Whether an element is represented by a :lang() selector
+		// is based solely on the element's language value
+		// being equal to the identifier C,
+		// or beginning with the identifier C immediately followed by "-".
+		// The matching of C against the element's language value is performed case-insensitively.
+		// The identifier C does not have to be a valid language name."
+		// http://www.w3.org/TR/selectors/#lang-pseudo
+		"lang": markFunction( function( lang ) {
+			// lang value must be a valid identifier
+			if ( !ridentifier.test(lang || "") ) {
+				Sizzle.error( "unsupported lang: " + lang );
 			}
-		}
+			lang = lang.replace( runescape, funescape ).toLowerCase();
+			return function( elem ) {
+				var elemLang;
+				do {
+					if ( (elemLang = documentIsHTML ?
+						elem.lang :
+						elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
 
-		return this;
-	},
+						elemLang = elemLang.toLowerCase();
+						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
+					}
+				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
+				return false;
+			};
+		}),
 
-	toggleClass: function( value, stateVal ) {
-		var type = typeof value,
-			isBool = typeof stateVal === "boolean";
+		// Miscellaneous
+		"target": function( elem ) {
+			var hash = window.location && window.location.hash;
+			return hash && hash.slice( 1 ) === elem.id;
+		},
 
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( i ) {
-				jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
-			});
-		}
+		"root": function( elem ) {
+			return elem === docElem;
+		},
 
-		return this.each(function() {
-			if ( type === "string" ) {
-				// toggle individual class names
-				var className,
-					i = 0,
-					self = jQuery( this ),
-					state = stateVal,
-					classNames = value.match( core_rnotwhite ) || [];
+		"focus": function( elem ) {
+			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+		},
 
-				while ( (className = classNames[ i++ ]) ) {
-					// check each className given, space separated list
-					state = isBool ? state : !self.hasClass( className );
-					self[ state ? "addClass" : "removeClass" ]( className );
-				}
+		// Boolean properties
+		"enabled": function( elem ) {
+			return elem.disabled === false;
+		},
 
-			// Toggle whole class name
-			} else if ( type === core_strundefined || type === "boolean" ) {
-				if ( this.className ) {
-					// store className if set
-					jQuery._data( this, "__className__", this.className );
-				}
+		"disabled": function( elem ) {
+			return elem.disabled === true;
+		},
 
-				// If the element has a class name or if we're passed "false",
-				// then remove the whole classname (if there was one, the above saved it).
-				// Otherwise bring back whatever was previously saved (if anything),
-				// falling back to the empty string if nothing was stored.
-				this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+		"checked": function( elem ) {
+			// In CSS3, :checked should return both checked and selected elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			var nodeName = elem.nodeName.toLowerCase();
+			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+		},
+
+		"selected": function( elem ) {
+			// Accessing this property makes selected-by-default
+			// options in Safari work properly
+			if ( elem.parentNode ) {
+				elem.parentNode.selectedIndex;
 			}
-		});
-	},
 
-	hasClass: function( selector ) {
-		var className = " " + selector + " ",
-			i = 0,
-			l = this.length;
-		for ( ; i < l; i++ ) {
-			if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
-				return true;
+			return elem.selected === true;
+		},
+
+		// Contents
+		"empty": function( elem ) {
+			// http://www.w3.org/TR/selectors/#empty-pseudo
+			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
+			//   but not by others (comment: 8; processing instruction: 7; etc.)
+			// nodeType < 6 works because attributes (2) do not appear as children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				if ( elem.nodeType < 6 ) {
+					return false;
+				}
 			}
-		}
+			return true;
+		},
 
-		return false;
-	},
+		"parent": function( elem ) {
+			return !Expr.pseudos["empty"]( elem );
+		},
 
-	val: function( value ) {
-		var ret, hooks, isFunction,
-			elem = this[0];
+		// Element/input types
+		"header": function( elem ) {
+			return rheader.test( elem.nodeName );
+		},
 
-		if ( !arguments.length ) {
-			if ( elem ) {
-				hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+		"input": function( elem ) {
+			return rinputs.test( elem.nodeName );
+		},
 
-				if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
-					return ret;
-				}
+		"button": function( elem ) {
+			var name = elem.nodeName.toLowerCase();
+			return name === "input" && elem.type === "button" || name === "button";
+		},
 
-				ret = elem.value;
+		"text": function( elem ) {
+			var attr;
+			return elem.nodeName.toLowerCase() === "input" &&
+				elem.type === "text" &&
 
-				return typeof ret === "string" ?
-					// handle most common string cases
-					ret.replace(rreturn, "") :
-					// handle cases where value is null/undef or number
-					ret == null ? "" : ret;
-			}
+				// Support: IE<8
+				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
+				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
+		},
 
-			return;
-		}
+		// Position-in-collection
+		"first": createPositionalPseudo(function() {
+			return [ 0 ];
+		}),
 
-		isFunction = jQuery.isFunction( value );
+		"last": createPositionalPseudo(function( matchIndexes, length ) {
+			return [ length - 1 ];
+		}),
 
-		return this.each(function( i ) {
-			var val,
-				self = jQuery(this);
+		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			return [ argument < 0 ? argument + length : argument ];
+		}),
 
-			if ( this.nodeType !== 1 ) {
-				return;
+		"even": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 0;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
 			}
+			return matchIndexes;
+		}),
 
-			if ( isFunction ) {
-				val = value.call( this, i, self.val() );
-			} else {
-				val = value;
+		"odd": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 1;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
 			}
+			return matchIndexes;
+		}),
 
-			// Treat null/undefined as ""; convert numbers to string
-			if ( val == null ) {
-				val = "";
-			} else if ( typeof val === "number" ) {
-				val += "";
-			} else if ( jQuery.isArray( val ) ) {
-				val = jQuery.map(val, function ( value ) {
-					return value == null ? "" : value + "";
-				});
+		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; --i >= 0; ) {
+				matchIndexes.push( i );
 			}
+			return matchIndexes;
+		}),
 
-			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
-			// If set returns undefined, fall back to normal setting
-			if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
-				this.value = val;
+		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; ++i < length; ) {
+				matchIndexes.push( i );
 			}
-		});
+			return matchIndexes;
+		})
 	}
-});
-
-jQuery.extend({
-	valHooks: {
-		option: {
-			get: function( elem ) {
-				// attributes.value is undefined in Blackberry 4.7 but
-				// uses .value. See #6932
-				var val = elem.attributes.value;
-				return !val || val.specified ? elem.value : elem.text;
-			}
-		},
-		select: {
-			get: function( elem ) {
-				var value, option,
-					options = elem.options,
-					index = elem.selectedIndex,
-					one = elem.type === "select-one" || index < 0,
-					values = one ? null : [],
-					max = one ? index + 1 : options.length,
-					i = index < 0 ?
-						max :
-						one ? index : 0;
-
-				// Loop through all the selected options
-				for ( ; i < max; i++ ) {
-					option = options[ i ];
+};
 
-					// oldIE doesn't update selected after form reset (#2551)
-					if ( ( option.selected || i === index ) &&
-							// Don't return options that are disabled or in a disabled optgroup
-							( jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
-							( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
 
-						// Get the specific value for the option
-						value = jQuery( option ).val();
+// Add button/input type pseudos
+for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
+	Expr.pseudos[ i ] = createInputPseudo( i );
+}
+for ( i in { submit: true, reset: true } ) {
+	Expr.pseudos[ i ] = createButtonPseudo( i );
+}
 
-						// We don't need an array for one selects
-						if ( one ) {
-							return value;
-						}
+// Easy API for creating new setFilters
+function setFilters() {}
+setFilters.prototype = Expr.filters = Expr.pseudos;
+Expr.setFilters = new setFilters();
 
-						// Multi-Selects return an array
-						values.push( value );
-					}
-				}
+tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
+	var matched, match, tokens, type,
+		soFar, groups, preFilters,
+		cached = tokenCache[ selector + " " ];
 
-				return values;
-			},
+	if ( cached ) {
+		return parseOnly ? 0 : cached.slice( 0 );
+	}
 
-			set: function( elem, value ) {
-				var values = jQuery.makeArray( value );
+	soFar = selector;
+	groups = [];
+	preFilters = Expr.preFilter;
 
-				jQuery(elem).find("option").each(function() {
-					this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0;
-				});
+	while ( soFar ) {
 
-				if ( !values.length ) {
-					elem.selectedIndex = -1;
-				}
-				return values;
+		// Comma and first run
+		if ( !matched || (match = rcomma.exec( soFar )) ) {
+			if ( match ) {
+				// Don't consume trailing commas as valid
+				soFar = soFar.slice( match[0].length ) || soFar;
 			}
+			groups.push( (tokens = []) );
 		}
-	},
 
-	attr: function( elem, name, value ) {
-		var hooks, notxml, ret,
-			nType = elem.nodeType;
+		matched = false;
 
-		// don't get/set attributes on text, comment and attribute nodes
-		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
-			return;
+		// Combinators
+		if ( (match = rcombinators.exec( soFar )) ) {
+			matched = match.shift();
+			tokens.push({
+				value: matched,
+				// Cast descendant combinators to space
+				type: match[0].replace( rtrim, " " )
+			});
+			soFar = soFar.slice( matched.length );
 		}
 
-		// Fallback to prop when attributes are not supported
-		if ( typeof elem.getAttribute === core_strundefined ) {
-			return jQuery.prop( elem, name, value );
+		// Filters
+		for ( type in Expr.filter ) {
+			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+				(match = preFilters[ type ]( match ))) ) {
+				matched = match.shift();
+				tokens.push({
+					value: matched,
+					type: type,
+					matches: match
+				});
+				soFar = soFar.slice( matched.length );
+			}
 		}
 
-		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
-
-		// All attributes are lowercase
-		// Grab necessary hook if one is defined
-		if ( notxml ) {
-			name = name.toLowerCase();
-			hooks = jQuery.attrHooks[ name ] || ( rboolean.test( name ) ? boolHook : nodeHook );
+		if ( !matched ) {
+			break;
 		}
+	}
 
-		if ( value !== undefined ) {
-
-			if ( value === null ) {
-				jQuery.removeAttr( elem, name );
-
-			} else if ( hooks && notxml && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
-				return ret;
+	// Return the length of the invalid excess
+	// if we're just parsing
+	// Otherwise, throw an error or return tokens
+	return parseOnly ?
+		soFar.length :
+		soFar ?
+			Sizzle.error( selector ) :
+			// Cache the tokens
+			tokenCache( selector, groups ).slice( 0 );
+};
 
-			} else {
-				elem.setAttribute( name, value + "" );
-				return value;
-			}
-
-		} else if ( hooks && notxml && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
-			return ret;
+function toSelector( tokens ) {
+	var i = 0,
+		len = tokens.length,
+		selector = "";
+	for ( ; i < len; i++ ) {
+		selector += tokens[i].value;
+	}
+	return selector;
+}
 
-		} else {
+function addCombinator( matcher, combinator, base ) {
+	var dir = combinator.dir,
+		checkNonElements = base && dir === "parentNode",
+		doneName = done++;
 
-			// In IE9+, Flash objects don't have .getAttribute (#12945)
-			// Support: IE9+
-			if ( typeof elem.getAttribute !== core_strundefined ) {
-				ret =  elem.getAttribute( name );
+	return combinator.first ?
+		// Check against closest ancestor/preceding element
+		function( elem, context, xml ) {
+			while ( (elem = elem[ dir ]) ) {
+				if ( elem.nodeType === 1 || checkNonElements ) {
+					return matcher( elem, context, xml );
+				}
 			}
+		} :
 
-			// Non-existent attributes return null, we normalize to undefined
-			return ret == null ?
-				undefined :
-				ret;
-		}
-	},
+		// Check against all ancestor/preceding elements
+		function( elem, context, xml ) {
+			var oldCache, outerCache,
+				newCache = [ dirruns, doneName ];
 
-	removeAttr: function( elem, value ) {
-		var name, propName,
-			i = 0,
-			attrNames = value && value.match( core_rnotwhite );
+			// We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
+			if ( xml ) {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						if ( matcher( elem, context, xml ) ) {
+							return true;
+						}
+					}
+				}
+			} else {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						outerCache = elem[ expando ] || (elem[ expando ] = {});
+						if ( (oldCache = outerCache[ dir ]) &&
+							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
 
-		if ( attrNames && elem.nodeType === 1 ) {
-			while ( (name = attrNames[i++]) ) {
-				propName = jQuery.propFix[ name ] || name;
+							// Assign to newCache so results back-propagate to previous elements
+							return (newCache[ 2 ] = oldCache[ 2 ]);
+						} else {
+							// Reuse newcache so results back-propagate to previous elements
+							outerCache[ dir ] = newCache;
 
-				// Boolean attributes get special treatment (#10870)
-				if ( rboolean.test( name ) ) {
-					// Set corresponding property to false for boolean attributes
-					// Also clear defaultChecked/defaultSelected (if appropriate) for IE<8
-					if ( !getSetAttribute && ruseDefault.test( name ) ) {
-						elem[ jQuery.camelCase( "default-" + name ) ] =
-							elem[ propName ] = false;
-					} else {
-						elem[ propName ] = false;
+							// A match means we're done; a fail means we have to keep checking
+							if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
+								return true;
+							}
+						}
 					}
-
-				// See #9699 for explanation of this approach (setting first, then removal)
-				} else {
-					jQuery.attr( elem, name, "" );
 				}
-
-				elem.removeAttribute( getSetAttribute ? name : propName );
 			}
-		}
-	},
+		};
+}
 
-	attrHooks: {
-		type: {
-			set: function( elem, value ) {
-				if ( !jQuery.support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
-					// Setting the type on a radio button after the value resets the value in IE6-9
-					// Reset value to default in case type is set after value during creation
-					var val = elem.value;
-					elem.setAttribute( "type", value );
-					if ( val ) {
-						elem.value = val;
-					}
-					return value;
+function elementMatcher( matchers ) {
+	return matchers.length > 1 ?
+		function( elem, context, xml ) {
+			var i = matchers.length;
+			while ( i-- ) {
+				if ( !matchers[i]( elem, context, xml ) ) {
+					return false;
 				}
 			}
-		}
-	},
+			return true;
+		} :
+		matchers[0];
+}
 
-	propFix: {
-		tabindex: "tabIndex",
-		readonly: "readOnly",
-		"for": "htmlFor",
-		"class": "className",
-		maxlength: "maxLength",
-		cellspacing: "cellSpacing",
-		cellpadding: "cellPadding",
-		rowspan: "rowSpan",
-		colspan: "colSpan",
-		usemap: "useMap",
-		frameborder: "frameBorder",
-		contenteditable: "contentEditable"
-	},
+function multipleContexts( selector, contexts, results ) {
+	var i = 0,
+		len = contexts.length;
+	for ( ; i < len; i++ ) {
+		Sizzle( selector, contexts[i], results );
+	}
+	return results;
+}
 
-	prop: function( elem, name, value ) {
-		var ret, hooks, notxml,
-			nType = elem.nodeType;
+function condense( unmatched, map, filter, context, xml ) {
+	var elem,
+		newUnmatched = [],
+		i = 0,
+		len = unmatched.length,
+		mapped = map != null;
 
-		// don't get/set properties on text, comment and attribute nodes
-		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
-			return;
+	for ( ; i < len; i++ ) {
+		if ( (elem = unmatched[i]) ) {
+			if ( !filter || filter( elem, context, xml ) ) {
+				newUnmatched.push( elem );
+				if ( mapped ) {
+					map.push( i );
+				}
+			}
 		}
+	}
 
-		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+	return newUnmatched;
+}
 
-		if ( notxml ) {
-			// Fix name and attach hooks
-			name = jQuery.propFix[ name ] || name;
-			hooks = jQuery.propHooks[ name ];
-		}
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+	if ( postFilter && !postFilter[ expando ] ) {
+		postFilter = setMatcher( postFilter );
+	}
+	if ( postFinder && !postFinder[ expando ] ) {
+		postFinder = setMatcher( postFinder, postSelector );
+	}
+	return markFunction(function( seed, results, context, xml ) {
+		var temp, i, elem,
+			preMap = [],
+			postMap = [],
+			preexisting = results.length,
 
-		if ( value !== undefined ) {
-			if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
-				return ret;
+			// Get initial elements from seed or context
+			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
 
-			} else {
-				return ( elem[ name ] = value );
-			}
+			// Prefilter to get matcher input, preserving a map for seed-results synchronization
+			matcherIn = preFilter && ( seed || !selector ) ?
+				condense( elems, preMap, preFilter, context, xml ) :
+				elems,
 
-		} else {
-			if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
-				return ret;
+			matcherOut = matcher ?
+				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
 
-			} else {
-				return elem[ name ];
-			}
-		}
-	},
+					// ...intermediate processing is necessary
+					[] :
 
-	propHooks: {
-		tabIndex: {
-			get: function( elem ) {
-				// elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
-				// http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
-				var attributeNode = elem.getAttributeNode("tabindex");
+					// ...otherwise use results directly
+					results :
+				matcherIn;
 
-				return attributeNode && attributeNode.specified ?
-					parseInt( attributeNode.value, 10 ) :
-					rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
-						0 :
-						undefined;
-			}
+		// Find primary matches
+		if ( matcher ) {
+			matcher( matcherIn, matcherOut, context, xml );
 		}
-	}
-});
 
-// Hook for boolean attributes
-boolHook = {
-	get: function( elem, name ) {
-		var
-			// Use .prop to determine if this attribute is understood as boolean
-			prop = jQuery.prop( elem, name ),
-
-			// Fetch it accordingly
-			attr = typeof prop === "boolean" && elem.getAttribute( name ),
-			detail = typeof prop === "boolean" ?
-
-				getSetInput && getSetAttribute ?
-					attr != null :
-					// oldIE fabricates an empty string for missing boolean attributes
-					// and conflates checked/selected into attroperties
-					ruseDefault.test( name ) ?
-						elem[ jQuery.camelCase( "default-" + name ) ] :
-						!!attr :
-
-				// fetch an attribute node for properties not recognized as boolean
-				elem.getAttributeNode( name );
-
-		return detail && detail.value !== false ?
-			name.toLowerCase() :
-			undefined;
-	},
-	set: function( elem, value, name ) {
-		if ( value === false ) {
-			// Remove boolean attributes when set to false
-			jQuery.removeAttr( elem, name );
-		} else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
-			// IE<8 needs the *property* name
-			elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
+		// Apply postFilter
+		if ( postFilter ) {
+			temp = condense( matcherOut, postMap );
+			postFilter( temp, [], context, xml );
 
-		// Use defaultChecked and defaultSelected for oldIE
-		} else {
-			elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
+			// Un-match failing elements by moving them back to matcherIn
+			i = temp.length;
+			while ( i-- ) {
+				if ( (elem = temp[i]) ) {
+					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+				}
+			}
 		}
 
-		return name;
-	}
-};
+		if ( seed ) {
+			if ( postFinder || preFilter ) {
+				if ( postFinder ) {
+					// Get the final matcherOut by condensing this intermediate into postFinder contexts
+					temp = [];
+					i = matcherOut.length;
+					while ( i-- ) {
+						if ( (elem = matcherOut[i]) ) {
+							// Restore matcherIn since elem is not yet a final match
+							temp.push( (matcherIn[i] = elem) );
+						}
+					}
+					postFinder( null, (matcherOut = []), temp, xml );
+				}
 
-// fix oldIE value attroperty
-if ( !getSetInput || !getSetAttribute ) {
-	jQuery.attrHooks.value = {
-		get: function( elem, name ) {
-			var ret = elem.getAttributeNode( name );
-			return jQuery.nodeName( elem, "input" ) ?
+				// Move matched elements from seed to results to keep them synchronized
+				i = matcherOut.length;
+				while ( i-- ) {
+					if ( (elem = matcherOut[i]) &&
+						(temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
 
-				// Ignore the value *property* by using defaultValue
-				elem.defaultValue :
+						seed[temp] = !(results[temp] = elem);
+					}
+				}
+			}
 
-				ret && ret.specified ? ret.value : undefined;
-		},
-		set: function( elem, value, name ) {
-			if ( jQuery.nodeName( elem, "input" ) ) {
-				// Does not return so that setAttribute is also used
-				elem.defaultValue = value;
+		// Add elements to results, through postFinder if defined
+		} else {
+			matcherOut = condense(
+				matcherOut === results ?
+					matcherOut.splice( preexisting, matcherOut.length ) :
+					matcherOut
+			);
+			if ( postFinder ) {
+				postFinder( null, results, matcherOut, xml );
 			} else {
-				// Use nodeHook if defined (#1954); otherwise setAttribute is fine
-				return nodeHook && nodeHook.set( elem, value, name );
+				push.apply( results, matcherOut );
 			}
 		}
-	};
+	});
 }
 
-// IE6/7 do not support getting/setting some attributes with get/setAttribute
-if ( !getSetAttribute ) {
+function matcherFromTokens( tokens ) {
+	var checkContext, matcher, j,
+		len = tokens.length,
+		leadingRelative = Expr.relative[ tokens[0].type ],
+		implicitRelative = leadingRelative || Expr.relative[" "],
+		i = leadingRelative ? 1 : 0,
 
-	// Use this for any attribute in IE6/7
-	// This fixes almost every IE6/7 issue
-	nodeHook = jQuery.valHooks.button = {
-		get: function( elem, name ) {
-			var ret = elem.getAttributeNode( name );
-			return ret && ( name === "id" || name === "name" || name === "coords" ? ret.value !== "" : ret.specified ) ?
-				ret.value :
-				undefined;
-		},
-		set: function( elem, value, name ) {
-			// Set the existing or create a new attribute node
-			var ret = elem.getAttributeNode( name );
-			if ( !ret ) {
-				elem.setAttributeNode(
-					(ret = elem.ownerDocument.createAttribute( name ))
+		// The foundational matcher ensures that elements are reachable from top-level context(s)
+		matchContext = addCombinator( function( elem ) {
+			return elem === checkContext;
+		}, implicitRelative, true ),
+		matchAnyContext = addCombinator( function( elem ) {
+			return indexOf( checkContext, elem ) > -1;
+		}, implicitRelative, true ),
+		matchers = [ function( elem, context, xml ) {
+			var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+				(checkContext = context).nodeType ?
+					matchContext( elem, context, xml ) :
+					matchAnyContext( elem, context, xml ) );
+			// Avoid hanging onto element (issue #299)
+			checkContext = null;
+			return ret;
+		} ];
+
+	for ( ; i < len; i++ ) {
+		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
+		} else {
+			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+			// Return special upon seeing a positional matcher
+			if ( matcher[ expando ] ) {
+				// Find the next relative operator (if any) for proper handling
+				j = ++i;
+				for ( ; j < len; j++ ) {
+					if ( Expr.relative[ tokens[j].type ] ) {
+						break;
+					}
+				}
+				return setMatcher(
+					i > 1 && elementMatcher( matchers ),
+					i > 1 && toSelector(
+						// If the preceding token was a descendant combinator, insert an implicit any-element `*`
+						tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
+					).replace( rtrim, "$1" ),
+					matcher,
+					i < j && matcherFromTokens( tokens.slice( i, j ) ),
+					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+					j < len && toSelector( tokens )
 				);
 			}
+			matchers.push( matcher );
+		}
+	}
 
-			ret.value = value += "";
+	return elementMatcher( matchers );
+}
 
-			// Break association with cloned elements by also using setAttribute (#9646)
-			return name === "value" || value === elem.getAttribute( name ) ?
-				value :
-				undefined;
-		}
-	};
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+	var bySet = setMatchers.length > 0,
+		byElement = elementMatchers.length > 0,
+		superMatcher = function( seed, context, xml, results, outermost ) {
+			var elem, j, matcher,
+				matchedCount = 0,
+				i = "0",
+				unmatched = seed && [],
+				setMatched = [],
+				contextBackup = outermostContext,
+				// We must always have either seed elements or outermost context
+				elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
+				// Use integer dirruns iff this is the outermost matcher
+				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
+				len = elems.length;
 
-	// Set contenteditable to false on removals(#10429)
-	// Setting to empty string throws an error as an invalid value
-	jQuery.attrHooks.contenteditable = {
-		get: nodeHook.get,
-		set: function( elem, value, name ) {
-			nodeHook.set( elem, value === "" ? false : value, name );
-		}
-	};
+			if ( outermost ) {
+				outermostContext = context !== document && context;
+			}
 
-	// Set width and height to auto instead of 0 on empty string( Bug #8150 )
-	// This is for removals
-	jQuery.each([ "width", "height" ], function( i, name ) {
-		jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
-			set: function( elem, value ) {
-				if ( value === "" ) {
-					elem.setAttribute( name, "auto" );
-					return value;
+			// Add elements passing elementMatchers directly to results
+			// Keep `i` a string if there are no elements so `matchedCount` will be "00" below
+			// Support: IE<9, Safari
+			// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
+			for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
+				if ( byElement && elem ) {
+					j = 0;
+					while ( (matcher = elementMatchers[j++]) ) {
+						if ( matcher( elem, context, xml ) ) {
+							results.push( elem );
+							break;
+						}
+					}
+					if ( outermost ) {
+						dirruns = dirrunsUnique;
+					}
 				}
-			}
-		});
-	});
-}
 
+				// Track unmatched elements for set filters
+				if ( bySet ) {
+					// They will have gone through all possible matchers
+					if ( (elem = !matcher && elem) ) {
+						matchedCount--;
+					}
 
-// Some attributes require a special call on IE
-// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !jQuery.support.hrefNormalized ) {
-	jQuery.each([ "href", "src", "width", "height" ], function( i, name ) {
-		jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
-			get: function( elem ) {
-				var ret = elem.getAttribute( name, 2 );
-				return ret == null ? undefined : ret;
+					// Lengthen the array for every element, matched or not
+					if ( seed ) {
+						unmatched.push( elem );
+					}
+				}
 			}
-		});
-	});
 
-	// href/src property should get the full normalized URL (#10299/#12915)
-	jQuery.each([ "href", "src" ], function( i, name ) {
-		jQuery.propHooks[ name ] = {
-			get: function( elem ) {
-				return elem.getAttribute( name, 4 );
-			}
-		};
-	});
-}
+			// Apply set filters to unmatched elements
+			matchedCount += i;
+			if ( bySet && i !== matchedCount ) {
+				j = 0;
+				while ( (matcher = setMatchers[j++]) ) {
+					matcher( unmatched, setMatched, context, xml );
+				}
 
-if ( !jQuery.support.style ) {
-	jQuery.attrHooks.style = {
-		get: function( elem ) {
-			// Return undefined in the case of empty string
-			// Note: IE uppercases css property names, but if we were to .toLowerCase()
-			// .cssText, that would destroy case senstitivity in URL's, like in "background"
-			return elem.style.cssText || undefined;
-		},
-		set: function( elem, value ) {
-			return ( elem.style.cssText = value + "" );
-		}
-	};
-}
+				if ( seed ) {
+					// Reintegrate element matches to eliminate the need for sorting
+					if ( matchedCount > 0 ) {
+						while ( i-- ) {
+							if ( !(unmatched[i] || setMatched[i]) ) {
+								setMatched[i] = pop.call( results );
+							}
+						}
+					}
 
-// Safari mis-reports the default selected property of an option
-// Accessing the parent's selectedIndex property fixes it
-if ( !jQuery.support.optSelected ) {
-	jQuery.propHooks.selected = jQuery.extend( jQuery.propHooks.selected, {
-		get: function( elem ) {
-			var parent = elem.parentNode;
+					// Discard index placeholder values to get only actual matches
+					setMatched = condense( setMatched );
+				}
 
-			if ( parent ) {
-				parent.selectedIndex;
+				// Add matches to results
+				push.apply( results, setMatched );
 
-				// Make sure that it also works with optgroups, see #5701
-				if ( parent.parentNode ) {
-					parent.parentNode.selectedIndex;
+				// Seedless set matches succeeding multiple successful matchers stipulate sorting
+				if ( outermost && !seed && setMatched.length > 0 &&
+					( matchedCount + setMatchers.length ) > 1 ) {
+
+					Sizzle.uniqueSort( results );
 				}
 			}
-			return null;
-		}
-	});
-}
-
-// IE6/7 call enctype encoding
-if ( !jQuery.support.enctype ) {
-	jQuery.propFix.enctype = "encoding";
-}
 
-// Radios and checkboxes getter/setter
-if ( !jQuery.support.checkOn ) {
-	jQuery.each([ "radio", "checkbox" ], function() {
-		jQuery.valHooks[ this ] = {
-			get: function( elem ) {
-				// Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified
-				return elem.getAttribute("value") === null ? "on" : elem.value;
+			// Override manipulation of globals by nested matchers
+			if ( outermost ) {
+				dirruns = dirrunsUnique;
+				outermostContext = contextBackup;
 			}
+
+			return unmatched;
 		};
-	});
+
+	return bySet ?
+		markFunction( superMatcher ) :
+		superMatcher;
 }
-jQuery.each([ "radio", "checkbox" ], function() {
-	jQuery.valHooks[ this ] = jQuery.extend( jQuery.valHooks[ this ], {
-		set: function( elem, value ) {
-			if ( jQuery.isArray( value ) ) {
-				return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
+
+compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
+	var i,
+		setMatchers = [],
+		elementMatchers = [],
+		cached = compilerCache[ selector + " " ];
+
+	if ( !cached ) {
+		// Generate a function of recursive functions that can be used to check each element
+		if ( !match ) {
+			match = tokenize( selector );
+		}
+		i = match.length;
+		while ( i-- ) {
+			cached = matcherFromTokens( match[i] );
+			if ( cached[ expando ] ) {
+				setMatchers.push( cached );
+			} else {
+				elementMatchers.push( cached );
 			}
 		}
-	});
-});
-var rformElems = /^(?:input|select|textarea)$/i,
-	rkeyEvent = /^key/,
-	rmouseEvent = /^(?:mouse|contextmenu)|click/,
-	rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
-	rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
 
-function returnTrue() {
-	return true;
-}
+		// Cache the compiled function
+		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
 
-function returnFalse() {
-	return false;
-}
+		// Save selector and tokenization
+		cached.selector = selector;
+	}
+	return cached;
+};
 
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
+/**
+ * A low-level selection function that works with Sizzle's compiled
+ *  selector functions
+ * @param {String|Function} selector A selector or a pre-compiled
+ *  selector function built with Sizzle.compile
+ * @param {Element} context
+ * @param {Array} [results]
+ * @param {Array} [seed] A set of elements to match against
  */
-jQuery.event = {
+select = Sizzle.select = function( selector, context, results, seed ) {
+	var i, tokens, token, type, find,
+		compiled = typeof selector === "function" && selector,
+		match = !seed && tokenize( (selector = compiled.selector || selector) );
 
-	global: {},
+	results = results || [];
 
-	add: function( elem, types, handler, data, selector ) {
-		var tmp, events, t, handleObjIn,
-			special, eventHandle, handleObj,
-			handlers, type, namespaces, origType,
-			elemData = jQuery._data( elem );
+	// Try to minimize operations if there is no seed and only one group
+	if ( match.length === 1 ) {
 
-		// Don't attach events to noData or text/comment nodes (but allow plain objects)
-		if ( !elemData ) {
-			return;
+		// Take a shortcut and set the context if the root selector is an ID
+		tokens = match[0] = match[0].slice( 0 );
+		if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+				support.getById && context.nodeType === 9 && documentIsHTML &&
+				Expr.relative[ tokens[1].type ] ) {
+
+			context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
+			if ( !context ) {
+				return results;
+
+			// Precompiled matchers will still verify ancestry, so step up a level
+			} else if ( compiled ) {
+				context = context.parentNode;
+			}
+
+			selector = selector.slice( tokens.shift().value.length );
 		}
 
-		// Caller can pass in an object of custom data in lieu of the handler
-		if ( handler.handler ) {
-			handleObjIn = handler;
-			handler = handleObjIn.handler;
-			selector = handleObjIn.selector;
+		// Fetch a seed set for right-to-left matching
+		i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
+		while ( i-- ) {
+			token = tokens[i];
+
+			// Abort if we hit a combinator
+			if ( Expr.relative[ (type = token.type) ] ) {
+				break;
+			}
+			if ( (find = Expr.find[ type ]) ) {
+				// Search, expanding context for leading sibling combinators
+				if ( (seed = find(
+					token.matches[0].replace( runescape, funescape ),
+					rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
+				)) ) {
+
+					// If seed is empty or no tokens remain, we can return early
+					tokens.splice( i, 1 );
+					selector = seed.length && toSelector( tokens );
+					if ( !selector ) {
+						push.apply( results, seed );
+						return results;
+					}
+
+					break;
+				}
+			}
 		}
+	}
 
-		// Make sure that the handler has a unique ID, used to find/remove it later
-		if ( !handler.guid ) {
-			handler.guid = jQuery.guid++;
+	// Compile and execute a filtering function if one is not provided
+	// Provide `match` to avoid retokenization if we modified the selector above
+	( compiled || compile( selector, match ) )(
+		seed,
+		context,
+		!documentIsHTML,
+		results,
+		rsibling.test( selector ) && testContext( context.parentNode ) || context
+	);
+	return results;
+};
+
+// One-time assignments
+
+// Sort stability
+support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
+
+// Support: Chrome 14-35+
+// Always assume duplicates if they aren't passed to the comparison function
+support.detectDuplicates = !!hasDuplicate;
+
+// Initialize against the default document
+setDocument();
+
+// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
+// Detached nodes confoundingly follow *each other*
+support.sortDetached = assert(function( div1 ) {
+	// Should return 1, but returns 4 (following)
+	return div1.compareDocumentPosition( document.createElement("div") ) & 1;
+});
+
+// Support: IE<8
+// Prevent attribute/property "interpolation"
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( div ) {
+	div.innerHTML = "<a href='#'></a>";
+	return div.firstChild.getAttribute("href") === "#" ;
+}) ) {
+	addHandle( "type|href|height|width", function( elem, name, isXML ) {
+		if ( !isXML ) {
+			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
 		}
+	});
+}
 
-		// Init the element's event structure and main handler, if this is the first
-		if ( !(events = elemData.events) ) {
-			events = elemData.events = {};
+// Support: IE<9
+// Use defaultValue in place of getAttribute("value")
+if ( !support.attributes || !assert(function( div ) {
+	div.innerHTML = "<input/>";
+	div.firstChild.setAttribute( "value", "" );
+	return div.firstChild.getAttribute( "value" ) === "";
+}) ) {
+	addHandle( "value", function( elem, name, isXML ) {
+		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
+			return elem.defaultValue;
 		}
-		if ( !(eventHandle = elemData.handle) ) {
-			eventHandle = elemData.handle = function( e ) {
-				// Discard the second event of a jQuery.event.trigger() and
-				// when an event is called after a page has unloaded
-				return typeof jQuery !== core_strundefined && (!e || jQuery.event.triggered !== e.type) ?
-					jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
-					undefined;
-			};
-			// Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
-			eventHandle.elem = elem;
+	});
+}
+
+// Support: IE<9
+// Use getAttributeNode to fetch booleans when getAttribute lies
+if ( !assert(function( div ) {
+	return div.getAttribute("disabled") == null;
+}) ) {
+	addHandle( booleans, function( elem, name, isXML ) {
+		var val;
+		if ( !isXML ) {
+			return elem[ name ] === true ? name.toLowerCase() :
+					(val = elem.getAttributeNode( name )) && val.specified ?
+					val.value :
+				null;
 		}
+	});
+}
 
-		// Handle multiple events separated by a space
-		// jQuery(...).bind("mouseover mouseout", fn);
-		types = ( types || "" ).match( core_rnotwhite ) || [""];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[t] ) || [];
-			type = origType = tmp[1];
-			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+return Sizzle;
 
-			// If event changes its type, use the special event handlers for the changed type
-			special = jQuery.event.special[ type ] || {};
+})( window );
 
-			// If selector defined, determine special event api type, otherwise given type
-			type = ( selector ? special.delegateType : special.bindType ) || type;
 
-			// Update special based on newly reset type
-			special = jQuery.event.special[ type ] || {};
 
-			// handleObj is passed to all event handlers
-			handleObj = jQuery.extend({
-				type: type,
-				origType: origType,
-				data: data,
-				handler: handler,
-				guid: handler.guid,
-				selector: selector,
-				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
-				namespace: namespaces.join(".")
-			}, handleObjIn );
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+jQuery.expr[":"] = jQuery.expr.pseudos;
+jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
 
-			// Init the event handler queue if we're the first
-			if ( !(handlers = events[ type ]) ) {
-				handlers = events[ type ] = [];
-				handlers.delegateCount = 0;
 
-				// Only use addEventListener/attachEvent if the special events handler returns false
-				if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
-					// Bind the global event handler to the element
-					if ( elem.addEventListener ) {
-						elem.addEventListener( type, eventHandle, false );
 
-					} else if ( elem.attachEvent ) {
-						elem.attachEvent( "on" + type, eventHandle );
-					}
-				}
-			}
+var rneedsContext = jQuery.expr.match.needsContext;
 
-			if ( special.add ) {
-				special.add.call( elem, handleObj );
+var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/);
 
-				if ( !handleObj.handler.guid ) {
-					handleObj.handler.guid = handler.guid;
-				}
-			}
 
-			// Add to the element's handler list, delegates in front
-			if ( selector ) {
-				handlers.splice( handlers.delegateCount++, 0, handleObj );
-			} else {
-				handlers.push( handleObj );
-			}
 
-			// Keep track of which events have ever been used, for event optimization
-			jQuery.event.global[ type ] = true;
-		}
+var risSimple = /^.[^:#\[\.,]*$/;
 
-		// Nullify elem to prevent memory leaks in IE
-		elem = null;
-	},
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+	if ( jQuery.isFunction( qualifier ) ) {
+		return jQuery.grep( elements, function( elem, i ) {
+			/* jshint -W018 */
+			return !!qualifier.call( elem, i, elem ) !== not;
+		});
 
-	// Detach an event or set of events from an element
-	remove: function( elem, types, handler, selector, mappedTypes ) {
-		var j, handleObj, tmp,
-			origCount, t, events,
-			special, handlers, type,
-			namespaces, origType,
-			elemData = jQuery.hasData( elem ) && jQuery._data( elem );
+	}
 
-		if ( !elemData || !(events = elemData.events) ) {
-			return;
+	if ( qualifier.nodeType ) {
+		return jQuery.grep( elements, function( elem ) {
+			return ( elem === qualifier ) !== not;
+		});
+
+	}
+
+	if ( typeof qualifier === "string" ) {
+		if ( risSimple.test( qualifier ) ) {
+			return jQuery.filter( qualifier, elements, not );
 		}
 
-		// Once for each type.namespace in types; type may be omitted
-		types = ( types || "" ).match( core_rnotwhite ) || [""];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[t] ) || [];
-			type = origType = tmp[1];
-			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+		qualifier = jQuery.filter( qualifier, elements );
+	}
 
-			// Unbind all events (on this namespace, if provided) for the element
-			if ( !type ) {
-				for ( type in events ) {
-					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
-				}
-				continue;
-			}
+	return jQuery.grep( elements, function( elem ) {
+		return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not;
+	});
+}
 
-			special = jQuery.event.special[ type ] || {};
-			type = ( selector ? special.delegateType : special.bindType ) || type;
-			handlers = events[ type ] || [];
-			tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
+jQuery.filter = function( expr, elems, not ) {
+	var elem = elems[ 0 ];
 
-			// Remove matching events
-			origCount = j = handlers.length;
-			while ( j-- ) {
-				handleObj = handlers[ j ];
+	if ( not ) {
+		expr = ":not(" + expr + ")";
+	}
 
-				if ( ( mappedTypes || origType === handleObj.origType ) &&
-					( !handler || handler.guid === handleObj.guid ) &&
-					( !tmp || tmp.test( handleObj.namespace ) ) &&
-					( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
-					handlers.splice( j, 1 );
+	return elems.length === 1 && elem.nodeType === 1 ?
+		jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :
+		jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+			return elem.nodeType === 1;
+		}));
+};
 
-					if ( handleObj.selector ) {
-						handlers.delegateCount--;
-					}
-					if ( special.remove ) {
-						special.remove.call( elem, handleObj );
-					}
-				}
-			}
+jQuery.fn.extend({
+	find: function( selector ) {
+		var i,
+			ret = [],
+			self = this,
+			len = self.length;
 
-			// Remove generic event handler if we removed something and no more handlers exist
-			// (avoids potential for endless recursion during removal of special event handlers)
-			if ( origCount && !handlers.length ) {
-				if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
-					jQuery.removeEvent( elem, type, elemData.handle );
+		if ( typeof selector !== "string" ) {
+			return this.pushStack( jQuery( selector ).filter(function() {
+				for ( i = 0; i < len; i++ ) {
+					if ( jQuery.contains( self[ i ], this ) ) {
+						return true;
+					}
 				}
-
-				delete events[ type ];
-			}
+			}) );
 		}
 
-		// Remove the expando if it's no longer used
-		if ( jQuery.isEmptyObject( events ) ) {
-			delete elemData.handle;
-
-			// removeData also checks for emptiness and clears the expando if empty
-			// so use it instead of delete
-			jQuery._removeData( elem, "events" );
+		for ( i = 0; i < len; i++ ) {
+			jQuery.find( selector, self[ i ], ret );
 		}
+
+		// Needed because $( selector, context ) becomes $( context ).find( selector )
+		ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
+		ret.selector = this.selector ? this.selector + " " + selector : selector;
+		return ret;
+	},
+	filter: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], false) );
+	},
+	not: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], true) );
 	},
+	is: function( selector ) {
+		return !!winnow(
+			this,
+
+			// If this is a positional/relative selector, check membership in the returned set
+			// so $("p:first").is("p:last") won't return true for a doc with two "p".
+			typeof selector === "string" && rneedsContext.test( selector ) ?
+				jQuery( selector ) :
+				selector || [],
+			false
+		).length;
+	}
+});
 
-	trigger: function( event, data, elem, onlyHandlers ) {
-		var handle, ontype, cur,
-			bubbleType, special, tmp, i,
-			eventPath = [ elem || document ],
-			type = core_hasOwn.call( event, "type" ) ? event.type : event,
-			namespaces = core_hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
 
-		cur = tmp = elem = elem || document;
+// Initialize a jQuery object
 
-		// Don't do events on text and comment nodes
-		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
-			return;
-		}
 
-		// focus/blur morphs to focusin/out; ensure we're not firing them right now
-		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
-			return;
-		}
+// A central reference to the root jQuery(document)
+var rootjQuery,
 
-		if ( type.indexOf(".") >= 0 ) {
-			// Namespaced trigger; create a regexp to match event type in handle()
-			namespaces = type.split(".");
-			type = namespaces.shift();
-			namespaces.sort();
-		}
-		ontype = type.indexOf(":") < 0 && "on" + type;
+	// Use the correct document accordingly with window argument (sandbox)
+	document = window.document,
 
-		// Caller can pass in a jQuery.Event object, Object, or just an event type string
-		event = event[ jQuery.expando ] ?
-			event :
-			new jQuery.Event( type, typeof event === "object" && event );
+	// A simple way to check for HTML strings
+	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+	// Strict HTML recognition (#11290: must start with <)
+	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,
 
-		event.isTrigger = true;
-		event.namespace = namespaces.join(".");
-		event.namespace_re = event.namespace ?
-			new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
-			null;
+	init = jQuery.fn.init = function( selector, context ) {
+		var match, elem;
 
-		// Clean up the event in case it is being reused
-		event.result = undefined;
-		if ( !event.target ) {
-			event.target = elem;
+		// HANDLE: $(""), $(null), $(undefined), $(false)
+		if ( !selector ) {
+			return this;
 		}
 
-		// Clone any incoming data and prepend the event, creating the handler arg list
-		data = data == null ?
-			[ event ] :
-			jQuery.makeArray( data, [ event ] );
-
-		// Allow special events to draw outside the lines
-		special = jQuery.event.special[ type ] || {};
-		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
-			return;
-		}
-
-		// Determine event propagation path in advance, per W3C events spec (#9951)
-		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
-		if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
-
-			bubbleType = special.delegateType || type;
-			if ( !rfocusMorph.test( bubbleType + type ) ) {
-				cur = cur.parentNode;
-			}
-			for ( ; cur; cur = cur.parentNode ) {
-				eventPath.push( cur );
-				tmp = cur;
-			}
+		// Handle HTML strings
+		if ( typeof selector === "string" ) {
+			if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
+				// Assume that strings that start and end with <> are HTML and skip the regex check
+				match = [ null, selector, null ];
 
-			// Only add window if we got to document (e.g., not plain obj or detached DOM)
-			if ( tmp === (elem.ownerDocument || document) ) {
-				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+			} else {
+				match = rquickExpr.exec( selector );
 			}
-		}
-
-		// Fire handlers on the event path
-		i = 0;
-		while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
 
-			event.type = i > 1 ?
-				bubbleType :
-				special.bindType || type;
+			// Match html or make sure no context is specified for #id
+			if ( match && (match[1] || !context) ) {
 
-			// jQuery handler
-			handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
-			if ( handle ) {
-				handle.apply( cur, data );
-			}
+				// HANDLE: $(html) -> $(array)
+				if ( match[1] ) {
+					context = context instanceof jQuery ? context[0] : context;
 
-			// Native handler
-			handle = ontype && cur[ ontype ];
-			if ( handle && jQuery.acceptData( cur ) && handle.apply && handle.apply( cur, data ) === false ) {
-				event.preventDefault();
-			}
-		}
-		event.type = type;
+					// scripts is true for back-compat
+					// Intentionally let the error be thrown if parseHTML is not present
+					jQuery.merge( this, jQuery.parseHTML(
+						match[1],
+						context && context.nodeType ? context.ownerDocument || context : document,
+						true
+					) );
 
-		// If nobody prevented the default action, do it now
-		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+					// HANDLE: $(html, props)
+					if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
+						for ( match in context ) {
+							// Properties of context are called as methods if possible
+							if ( jQuery.isFunction( this[ match ] ) ) {
+								this[ match ]( context[ match ] );
 
-			if ( (!special._default || special._default.apply( elem.ownerDocument, data ) === false) &&
-				!(type === "click" && jQuery.nodeName( elem, "a" )) && jQuery.acceptData( elem ) ) {
+							// ...and otherwise set as attributes
+							} else {
+								this.attr( match, context[ match ] );
+							}
+						}
+					}
 
-				// Call a native DOM method on the target with the same name name as the event.
-				// Can't use an .isFunction() check here because IE6/7 fails that test.
-				// Don't do default actions on window, that's where global variables be (#6170)
-				if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
+					return this;
 
-					// Don't re-trigger an onFOO event when we call its FOO() method
-					tmp = elem[ ontype ];
+				// HANDLE: $(#id)
+				} else {
+					elem = document.getElementById( match[2] );
 
-					if ( tmp ) {
-						elem[ ontype ] = null;
-					}
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document #6963
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE and Opera return items
+						// by name instead of ID
+						if ( elem.id !== match[2] ) {
+							return rootjQuery.find( selector );
+						}
 
-					// Prevent re-triggering of the same event, since we already bubbled it above
-					jQuery.event.triggered = type;
-					try {
-						elem[ type ]();
-					} catch ( e ) {
-						// IE<9 dies on focus/blur to hidden element (#1486,#12518)
-						// only reproducible on winXP IE8 native, not IE9 in IE8 mode
+						// Otherwise, we inject the element directly into the jQuery object
+						this.length = 1;
+						this[0] = elem;
 					}
-					jQuery.event.triggered = undefined;
 
-					if ( tmp ) {
-						elem[ ontype ] = tmp;
-					}
+					this.context = document;
+					this.selector = selector;
+					return this;
 				}
-			}
-		}
-
-		return event.result;
-	},
 
-	dispatch: function( event ) {
+			// HANDLE: $(expr, $(...))
+			} else if ( !context || context.jquery ) {
+				return ( context || rootjQuery ).find( selector );
 
-		// Make a writable jQuery.Event from the native event object
-		event = jQuery.event.fix( event );
+			// HANDLE: $(expr, context)
+			// (which is just equivalent to: $(context).find(expr)
+			} else {
+				return this.constructor( context ).find( selector );
+			}
 
-		var i, ret, handleObj, matched, j,
-			handlerQueue = [],
-			args = core_slice.call( arguments ),
-			handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
-			special = jQuery.event.special[ event.type ] || {};
+		// HANDLE: $(DOMElement)
+		} else if ( selector.nodeType ) {
+			this.context = this[0] = selector;
+			this.length = 1;
+			return this;
 
-		// Use the fix-ed jQuery.Event rather than the (read-only) native event
-		args[0] = event;
-		event.delegateTarget = this;
+		// HANDLE: $(function)
+		// Shortcut for document ready
+		} else if ( jQuery.isFunction( selector ) ) {
+			return typeof rootjQuery.ready !== "undefined" ?
+				rootjQuery.ready( selector ) :
+				// Execute immediately if ready is not present
+				selector( jQuery );
+		}
 
-		// Call the preDispatch hook for the mapped type, and let it bail if desired
-		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
-			return;
+		if ( selector.selector !== undefined ) {
+			this.selector = selector.selector;
+			this.context = selector.context;
 		}
 
-		// Determine handlers
-		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
+		return jQuery.makeArray( selector, this );
+	};
 
-		// Run delegates first; they may want to stop propagation beneath us
-		i = 0;
-		while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
-			event.currentTarget = matched.elem;
+// Give the init function the jQuery prototype for later instantiation
+init.prototype = jQuery.fn;
 
-			j = 0;
-			while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
+// Initialize central reference
+rootjQuery = jQuery( document );
 
-				// Triggered event must either 1) have no namespace, or
-				// 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
-				if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
 
-					event.handleObj = handleObj;
-					event.data = handleObj.data;
+var rparentsprev = /^(?:parents|prev(?:Until|All))/,
+	// methods guaranteed to produce a unique set when starting from a unique set
+	guaranteedUnique = {
+		children: true,
+		contents: true,
+		next: true,
+		prev: true
+	};
 
-					ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
-							.apply( matched.elem, args );
+jQuery.extend({
+	dir: function( elem, dir, until ) {
+		var matched = [],
+			cur = elem[ dir ];
 
-					if ( ret !== undefined ) {
-						if ( (event.result = ret) === false ) {
-							event.preventDefault();
-							event.stopPropagation();
-						}
-					}
-				}
+		while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
+			if ( cur.nodeType === 1 ) {
+				matched.push( cur );
 			}
+			cur = cur[dir];
 		}
-
-		// Call the postDispatch hook for the mapped type
-		if ( special.postDispatch ) {
-			special.postDispatch.call( this, event );
-		}
-
-		return event.result;
+		return matched;
 	},
 
-	handlers: function( event, handlers ) {
-		var sel, handleObj, matches, i,
-			handlerQueue = [],
-			delegateCount = handlers.delegateCount,
-			cur = event.target;
-
-		// Find delegate handlers
-		// Black-hole SVG <use> instance trees (#13180)
-		// Avoid non-left-click bubbling in Firefox (#3861)
-		if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
+	sibling: function( n, elem ) {
+		var r = [];
 
-			for ( ; cur != this; cur = cur.parentNode || this ) {
+		for ( ; n; n = n.nextSibling ) {
+			if ( n.nodeType === 1 && n !== elem ) {
+				r.push( n );
+			}
+		}
 
-				// Don't check non-elements (#13208)
-				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
-				if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
-					matches = [];
-					for ( i = 0; i < delegateCount; i++ ) {
-						handleObj = handlers[ i ];
+		return r;
+	}
+});
 
-						// Don't conflict with Object.prototype properties (#13203)
-						sel = handleObj.selector + " ";
+jQuery.fn.extend({
+	has: function( target ) {
+		var i,
+			targets = jQuery( target, this ),
+			len = targets.length;
 
-						if ( matches[ sel ] === undefined ) {
-							matches[ sel ] = handleObj.needsContext ?
-								jQuery( sel, this ).index( cur ) >= 0 :
-								jQuery.find( sel, this, null, [ cur ] ).length;
-						}
-						if ( matches[ sel ] ) {
-							matches.push( handleObj );
-						}
-					}
-					if ( matches.length ) {
-						handlerQueue.push({ elem: cur, handlers: matches });
-					}
+		return this.filter(function() {
+			for ( i = 0; i < len; i++ ) {
+				if ( jQuery.contains( this, targets[i] ) ) {
+					return true;
 				}
 			}
-		}
-
-		// Add the remaining (directly-bound) handlers
-		if ( delegateCount < handlers.length ) {
-			handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
-		}
-
-		return handlerQueue;
+		});
 	},
 
-	fix: function( event ) {
-		if ( event[ jQuery.expando ] ) {
-			return event;
-		}
+	closest: function( selectors, context ) {
+		var cur,
+			i = 0,
+			l = this.length,
+			matched = [],
+			pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
+				jQuery( selectors, context || this.context ) :
+				0;
 
-		// Create a writable copy of the event object and normalize some properties
-		var i, prop, copy,
-			type = event.type,
-			originalEvent = event,
-			fixHook = this.fixHooks[ type ];
+		for ( ; i < l; i++ ) {
+			for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) {
+				// Always skip document fragments
+				if ( cur.nodeType < 11 && (pos ?
+					pos.index(cur) > -1 :
 
-		if ( !fixHook ) {
-			this.fixHooks[ type ] = fixHook =
-				rmouseEvent.test( type ) ? this.mouseHooks :
-				rkeyEvent.test( type ) ? this.keyHooks :
-				{};
+					// Don't pass non-elements to Sizzle
+					cur.nodeType === 1 &&
+						jQuery.find.matchesSelector(cur, selectors)) ) {
+
+					matched.push( cur );
+					break;
+				}
+			}
 		}
-		copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
 
-		event = new jQuery.Event( originalEvent );
+		return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched );
+	},
 
-		i = copy.length;
-		while ( i-- ) {
-			prop = copy[ i ];
-			event[ prop ] = originalEvent[ prop ];
-		}
+	// Determine the position of an element within
+	// the matched set of elements
+	index: function( elem ) {
 
-		// Support: IE<9
-		// Fix target property (#1925)
-		if ( !event.target ) {
-			event.target = originalEvent.srcElement || document;
+		// No argument, return index in parent
+		if ( !elem ) {
+			return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
 		}
 
-		// Support: Chrome 23+, Safari?
-		// Target should not be a text node (#504, #13143)
-		if ( event.target.nodeType === 3 ) {
-			event.target = event.target.parentNode;
+		// index in selector
+		if ( typeof elem === "string" ) {
+			return jQuery.inArray( this[0], jQuery( elem ) );
 		}
 
-		// Support: IE<9
-		// For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
-		event.metaKey = !!event.metaKey;
-
-		return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
+		// Locate the position of the desired element
+		return jQuery.inArray(
+			// If it receives a jQuery object, the first element is used
+			elem.jquery ? elem[0] : elem, this );
 	},
 
-	// Includes some event props shared by KeyEvent and MouseEvent
-	props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
-
-	fixHooks: {},
-
-	keyHooks: {
-		props: "char charCode key keyCode".split(" "),
-		filter: function( event, original ) {
-
-			// Add which for key events
-			if ( event.which == null ) {
-				event.which = original.charCode != null ? original.charCode : original.keyCode;
-			}
-
-			return event;
-		}
+	add: function( selector, context ) {
+		return this.pushStack(
+			jQuery.unique(
+				jQuery.merge( this.get(), jQuery( selector, context ) )
+			)
+		);
 	},
 
-	mouseHooks: {
-		props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
-		filter: function( event, original ) {
-			var body, eventDoc, doc,
-				button = original.button,
-				fromElement = original.fromElement;
-
-			// Calculate pageX/Y if missing and clientX/Y available
-			if ( event.pageX == null && original.clientX != null ) {
-				eventDoc = event.target.ownerDocument || document;
-				doc = eventDoc.documentElement;
-				body = eventDoc.body;
-
-				event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
-				event.pageY = original.clientY + ( doc && doc.scrollTop  || body && body.scrollTop  || 0 ) - ( doc && doc.clientTop  || body && body.clientTop  || 0 );
-			}
+	addBack: function( selector ) {
+		return this.add( selector == null ?
+			this.prevObject : this.prevObject.filter(selector)
+		);
+	}
+});
 
-			// Add relatedTarget, if necessary
-			if ( !event.relatedTarget && fromElement ) {
-				event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
-			}
+function sibling( cur, dir ) {
+	do {
+		cur = cur[ dir ];
+	} while ( cur && cur.nodeType !== 1 );
 
-			// Add which for click: 1 === left; 2 === middle; 3 === right
-			// Note: button is not normalized, so don't use it
-			if ( !event.which && button !== undefined ) {
-				event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
-			}
+	return cur;
+}
 
-			return event;
-		}
+jQuery.each({
+	parent: function( elem ) {
+		var parent = elem.parentNode;
+		return parent && parent.nodeType !== 11 ? parent : null;
 	},
-
-	special: {
-		load: {
-			// Prevent triggered image.load events from bubbling to window.load
-			noBubble: true
-		},
-		click: {
-			// For checkbox, fire native event so checked state will be right
-			trigger: function() {
-				if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
-					this.click();
-					return false;
-				}
-			}
-		},
-		focus: {
-			// Fire native event if possible so blur/focus sequence is correct
-			trigger: function() {
-				if ( this !== document.activeElement && this.focus ) {
-					try {
-						this.focus();
-						return false;
-					} catch ( e ) {
-						// Support: IE<9
-						// If we error on focus to hidden element (#1486, #12518),
-						// let .trigger() run the handlers
-					}
-				}
-			},
-			delegateType: "focusin"
-		},
-		blur: {
-			trigger: function() {
-				if ( this === document.activeElement && this.blur ) {
-					this.blur();
-					return false;
-				}
-			},
-			delegateType: "focusout"
-		},
-
-		beforeunload: {
-			postDispatch: function( event ) {
-
-				// Even when returnValue equals to undefined Firefox will still show alert
-				if ( event.result !== undefined ) {
-					event.originalEvent.returnValue = event.result;
-				}
-			}
-		}
+	parents: function( elem ) {
+		return jQuery.dir( elem, "parentNode" );
 	},
-
-	simulate: function( type, elem, event, bubble ) {
-		// Piggyback on a donor event to simulate a different one.
-		// Fake originalEvent to avoid donor's stopPropagation, but if the
-		// simulated event prevents default then we do the same on the donor.
-		var e = jQuery.extend(
-			new jQuery.Event(),
-			event,
-			{ type: type,
-				isSimulated: true,
-				originalEvent: {}
-			}
-		);
-		if ( bubble ) {
-			jQuery.event.trigger( e, null, elem );
-		} else {
-			jQuery.event.dispatch.call( elem, e );
-		}
-		if ( e.isDefaultPrevented() ) {
-			event.preventDefault();
-		}
+	parentsUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "parentNode", until );
+	},
+	next: function( elem ) {
+		return sibling( elem, "nextSibling" );
+	},
+	prev: function( elem ) {
+		return sibling( elem, "previousSibling" );
+	},
+	nextAll: function( elem ) {
+		return jQuery.dir( elem, "nextSibling" );
+	},
+	prevAll: function( elem ) {
+		return jQuery.dir( elem, "previousSibling" );
+	},
+	nextUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "nextSibling", until );
+	},
+	prevUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "previousSibling", until );
+	},
+	siblings: function( elem ) {
+		return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
+	},
+	children: function( elem ) {
+		return jQuery.sibling( elem.firstChild );
+	},
+	contents: function( elem ) {
+		return jQuery.nodeName( elem, "iframe" ) ?
+			elem.contentDocument || elem.contentWindow.document :
+			jQuery.merge( [], elem.childNodes );
 	}
-};
+}, function( name, fn ) {
+	jQuery.fn[ name ] = function( until, selector ) {
+		var ret = jQuery.map( this, fn, until );
 
-jQuery.removeEvent = document.removeEventListener ?
-	function( elem, type, handle ) {
-		if ( elem.removeEventListener ) {
-			elem.removeEventListener( type, handle, false );
+		if ( name.slice( -5 ) !== "Until" ) {
+			selector = until;
 		}
-	} :
-	function( elem, type, handle ) {
-		var name = "on" + type;
 
-		if ( elem.detachEvent ) {
+		if ( selector && typeof selector === "string" ) {
+			ret = jQuery.filter( selector, ret );
+		}
 
-			// #8545, #7054, preventing memory leaks for custom events in IE6-8
-			// detachEvent needed property on element, by name of that event, to properly expose it to GC
-			if ( typeof elem[ name ] === core_strundefined ) {
-				elem[ name ] = null;
+		if ( this.length > 1 ) {
+			// Remove duplicates
+			if ( !guaranteedUnique[ name ] ) {
+				ret = jQuery.unique( ret );
 			}
 
-			elem.detachEvent( name, handle );
+			// Reverse order for parents* and prev-derivatives
+			if ( rparentsprev.test( name ) ) {
+				ret = ret.reverse();
+			}
 		}
-	};
 
-jQuery.Event = function( src, props ) {
-	// Allow instantiation without the 'new' keyword
-	if ( !(this instanceof jQuery.Event) ) {
-		return new jQuery.Event( src, props );
-	}
+		return this.pushStack( ret );
+	};
+});
+var rnotwhite = (/\S+/g);
 
-	// Event object
-	if ( src && src.type ) {
-		this.originalEvent = src;
-		this.type = src.type;
 
-		// Events bubbling up the document may have been marked as prevented
-		// by a handler lower down the tree; reflect the correct value.
-		this.isDefaultPrevented = ( src.defaultPrevented || src.returnValue === false ||
-			src.getPreventDefault && src.getPreventDefault() ) ? returnTrue : returnFalse;
 
-	// Event type
-	} else {
-		this.type = src;
-	}
-
-	// Put explicitly provided properties onto the event object
-	if ( props ) {
-		jQuery.extend( this, props );
-	}
-
-	// Create a timestamp if incoming event doesn't have one
-	this.timeStamp = src && src.timeStamp || jQuery.now();
-
-	// Mark it as fixed
-	this[ jQuery.expando ] = true;
-};
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
-	isDefaultPrevented: returnFalse,
-	isPropagationStopped: returnFalse,
-	isImmediatePropagationStopped: returnFalse,
-
-	preventDefault: function() {
-		var e = this.originalEvent;
-
-		this.isDefaultPrevented = returnTrue;
-		if ( !e ) {
-			return;
-		}
-
-		// If preventDefault exists, run it on the original event
-		if ( e.preventDefault ) {
-			e.preventDefault();
-
-		// Support: IE
-		// Otherwise set the returnValue property of the original event to false
-		} else {
-			e.returnValue = false;
-		}
-	},
-	stopPropagation: function() {
-		var e = this.originalEvent;
-
-		this.isPropagationStopped = returnTrue;
-		if ( !e ) {
-			return;
-		}
-		// If stopPropagation exists, run it on the original event
-		if ( e.stopPropagation ) {
-			e.stopPropagation();
-		}
-
-		// Support: IE
-		// Set the cancelBubble property of the original event to true
-		e.cancelBubble = true;
-	},
-	stopImmediatePropagation: function() {
-		this.isImmediatePropagationStopped = returnTrue;
-		this.stopPropagation();
-	}
-};
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-jQuery.each({
-	mouseenter: "mouseover",
-	mouseleave: "mouseout"
-}, function( orig, fix ) {
-	jQuery.event.special[ orig ] = {
-		delegateType: fix,
-		bindType: fix,
-
-		handle: function( event ) {
-			var ret,
-				target = this,
-				related = event.relatedTarget,
-				handleObj = event.handleObj;
-
-			// For mousenter/leave call the handler if related is outside the target.
-			// NB: No relatedTarget if the mouse left/entered the browser window
-			if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
-				event.type = handleObj.origType;
-				ret = handleObj.handler.apply( this, arguments );
-				event.type = fix;
-			}
-			return ret;
-		}
-	};
-});
-
-// IE submit delegation
-if ( !jQuery.support.submitBubbles ) {
-
-	jQuery.event.special.submit = {
-		setup: function() {
-			// Only need this for delegated form submit events
-			if ( jQuery.nodeName( this, "form" ) ) {
-				return false;
-			}
-
-			// Lazy-add a submit handler when a descendant form may potentially be submitted
-			jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
-				// Node name check avoids a VML-related crash in IE (#9807)
-				var elem = e.target,
-					form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
-				if ( form && !jQuery._data( form, "submitBubbles" ) ) {
-					jQuery.event.add( form, "submit._submit", function( event ) {
-						event._submit_bubble = true;
-					});
-					jQuery._data( form, "submitBubbles", true );
-				}
-			});
-			// return undefined since we don't need an event listener
-		},
-
-		postDispatch: function( event ) {
-			// If form was submitted by the user, bubble the event up the tree
-			if ( event._submit_bubble ) {
-				delete event._submit_bubble;
-				if ( this.parentNode && !event.isTrigger ) {
-					jQuery.event.simulate( "submit", this.parentNode, event, true );
-				}
-			}
-		},
-
-		teardown: function() {
-			// Only need this for delegated form submit events
-			if ( jQuery.nodeName( this, "form" ) ) {
-				return false;
-			}
+// String to Object options format cache
+var optionsCache = {};
 
-			// Remove delegated handlers; cleanData eventually reaps submit handlers attached above
-			jQuery.event.remove( this, "._submit" );
-		}
-	};
+// Convert String-formatted options into Object-formatted ones and store in cache
+function createOptions( options ) {
+	var object = optionsCache[ options ] = {};
+	jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {
+		object[ flag ] = true;
+	});
+	return object;
 }
 
-// IE change delegation and checkbox/radio fix
-if ( !jQuery.support.changeBubbles ) {
-
-	jQuery.event.special.change = {
+/*
+ * Create a callback list using the following parameters:
+ *
+ *	options: an optional list of space-separated options that will change how
+ *			the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ *	once:			will ensure the callback list can only be fired once (like a Deferred)
+ *
+ *	memory:			will keep track of previous values and will call any callback added
+ *					after the list has been fired right away with the latest "memorized"
+ *					values (like a Deferred)
+ *
+ *	unique:			will ensure a callback can only be added once (no duplicate in the list)
+ *
+ *	stopOnFalse:	interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
 
-		setup: function() {
+	// Convert options from String-formatted to Object-formatted if needed
+	// (we check in cache first)
+	options = typeof options === "string" ?
+		( optionsCache[ options ] || createOptions( options ) ) :
+		jQuery.extend( {}, options );
 
-			if ( rformElems.test( this.nodeName ) ) {
-				// IE doesn't fire change on a check/radio until blur; trigger it on click
-				// after a propertychange. Eat the blur-change in special.change.handle.
-				// This still fires onchange a second time for check/radio after blur.
-				if ( this.type === "checkbox" || this.type === "radio" ) {
-					jQuery.event.add( this, "propertychange._change", function( event ) {
-						if ( event.originalEvent.propertyName === "checked" ) {
-							this._just_changed = true;
-						}
-					});
-					jQuery.event.add( this, "click._change", function( event ) {
-						if ( this._just_changed && !event.isTrigger ) {
-							this._just_changed = false;
-						}
-						// Allow triggered, simulated change events (#11500)
-						jQuery.event.simulate( "change", this, event, true );
-					});
+	var // Flag to know if list is currently firing
+		firing,
+		// Last fire value (for non-forgettable lists)
+		memory,
+		// Flag to know if list was already fired
+		fired,
+		// End of the loop when firing
+		firingLength,
+		// Index of currently firing callback (modified by remove if needed)
+		firingIndex,
+		// First callback to fire (used internally by add and fireWith)
+		firingStart,
+		// Actual callback list
+		list = [],
+		// Stack of fire calls for repeatable lists
+		stack = !options.once && [],
+		// Fire callbacks
+		fire = function( data ) {
+			memory = options.memory && data;
+			fired = true;
+			firingIndex = firingStart || 0;
+			firingStart = 0;
+			firingLength = list.length;
+			firing = true;
+			for ( ; list && firingIndex < firingLength; firingIndex++ ) {
+				if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
+					memory = false; // To prevent further calls using add
+					break;
 				}
-				return false;
 			}
-			// Delegated event; lazy-add a change handler on descendant inputs
-			jQuery.event.add( this, "beforeactivate._change", function( e ) {
-				var elem = e.target;
-
-				if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
-					jQuery.event.add( elem, "change._change", function( event ) {
-						if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
-							jQuery.event.simulate( "change", this.parentNode, event, true );
-						}
-					});
-					jQuery._data( elem, "changeBubbles", true );
+			firing = false;
+			if ( list ) {
+				if ( stack ) {
+					if ( stack.length ) {
+						fire( stack.shift() );
+					}
+				} else if ( memory ) {
+					list = [];
+				} else {
+					self.disable();
 				}
-			});
-		},
-
-		handle: function( event ) {
-			var elem = event.target;
-
-			// Swallow native change events from checkbox/radio, we already triggered them above
-			if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
-				return event.handleObj.handler.apply( this, arguments );
 			}
 		},
-
-		teardown: function() {
-			jQuery.event.remove( this, "._change" );
-
-			return !rformElems.test( this.nodeName );
-		}
-	};
-}
-
-// Create "bubbling" focus and blur events
-if ( !jQuery.support.focusinBubbles ) {
-	jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
-		// Attach a single capturing handler while someone wants focusin/focusout
-		var attaches = 0,
-			handler = function( event ) {
-				jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
-			};
-
-		jQuery.event.special[ fix ] = {
-			setup: function() {
-				if ( attaches++ === 0 ) {
-					document.addEventListener( orig, handler, true );
+		// Actual Callbacks object
+		self = {
+			// Add a callback or a collection of callbacks to the list
+			add: function() {
+				if ( list ) {
+					// First, we save the current length
+					var start = list.length;
+					(function add( args ) {
+						jQuery.each( args, function( _, arg ) {
+							var type = jQuery.type( arg );
+							if ( type === "function" ) {
+								if ( !options.unique || !self.has( arg ) ) {
+									list.push( arg );
+								}
+							} else if ( arg && arg.length && type !== "string" ) {
+								// Inspect recursively
+								add( arg );
+							}
+						});
+					})( arguments );
+					// Do we need to add the callbacks to the
+					// current firing batch?
+					if ( firing ) {
+						firingLength = list.length;
+					// With memory, if we're not firing then
+					// we should call right away
+					} else if ( memory ) {
+						firingStart = start;
+						fire( memory );
+					}
 				}
+				return this;
 			},
-			teardown: function() {
-				if ( --attaches === 0 ) {
-					document.removeEventListener( orig, handler, true );
+			// Remove a callback from the list
+			remove: function() {
+				if ( list ) {
+					jQuery.each( arguments, function( _, arg ) {
+						var index;
+						while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+							list.splice( index, 1 );
+							// Handle firing indexes
+							if ( firing ) {
+								if ( index <= firingLength ) {
+									firingLength--;
+								}
+								if ( index <= firingIndex ) {
+									firingIndex--;
+								}
+							}
+						}
+					});
+				}
+				return this;
+			},
+			// Check if a given callback is in the list.
+			// If no argument is given, return whether or not list has callbacks attached.
+			has: function( fn ) {
+				return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
+			},
+			// Remove all callbacks from the list
+			empty: function() {
+				list = [];
+				firingLength = 0;
+				return this;
+			},
+			// Have the list do nothing anymore
+			disable: function() {
+				list = stack = memory = undefined;
+				return this;
+			},
+			// Is it disabled?
+			disabled: function() {
+				return !list;
+			},
+			// Lock the list in its current state
+			lock: function() {
+				stack = undefined;
+				if ( !memory ) {
+					self.disable();
+				}
+				return this;
+			},
+			// Is it locked?
+			locked: function() {
+				return !stack;
+			},
+			// Call all callbacks with the given context and arguments
+			fireWith: function( context, args ) {
+				if ( list && ( !fired || stack ) ) {
+					args = args || [];
+					args = [ context, args.slice ? args.slice() : args ];
+					if ( firing ) {
+						stack.push( args );
+					} else {
+						fire( args );
+					}
 				}
+				return this;
+			},
+			// Call all the callbacks with the given arguments
+			fire: function() {
+				self.fireWith( this, arguments );
+				return this;
+			},
+			// To know if the callbacks have already been called at least once
+			fired: function() {
+				return !!fired;
 			}
 		};
-	});
-}
 
-jQuery.fn.extend({
+	return self;
+};
 
-	on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
-		var type, origFn;
 
-		// Types can be a map of types/handlers
-		if ( typeof types === "object" ) {
-			// ( types-Object, selector, data )
-			if ( typeof selector !== "string" ) {
-				// ( types-Object, data )
-				data = data || selector;
-				selector = undefined;
-			}
-			for ( type in types ) {
-				this.on( type, selector, data, types[ type ], one );
-			}
-			return this;
-		}
+jQuery.extend({
 
-		if ( data == null && fn == null ) {
-			// ( types, fn )
-			fn = selector;
-			data = selector = undefined;
-		} else if ( fn == null ) {
-			if ( typeof selector === "string" ) {
-				// ( types, selector, fn )
-				fn = data;
-				data = undefined;
-			} else {
-				// ( types, data, fn )
-				fn = data;
-				data = selector;
-				selector = undefined;
+	Deferred: function( func ) {
+		var tuples = [
+				// action, add listener, listener list, final state
+				[ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
+				[ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
+				[ "notify", "progress", jQuery.Callbacks("memory") ]
+			],
+			state = "pending",
+			promise = {
+				state: function() {
+					return state;
+				},
+				always: function() {
+					deferred.done( arguments ).fail( arguments );
+					return this;
+				},
+				then: function( /* fnDone, fnFail, fnProgress */ ) {
+					var fns = arguments;
+					return jQuery.Deferred(function( newDefer ) {
+						jQuery.each( tuples, function( i, tuple ) {
+							var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
+							// deferred[ done | fail | progress ] for forwarding actions to newDefer
+							deferred[ tuple[1] ](function() {
+								var returned = fn && fn.apply( this, arguments );
+								if ( returned && jQuery.isFunction( returned.promise ) ) {
+									returned.promise()
+										.done( newDefer.resolve )
+										.fail( newDefer.reject )
+										.progress( newDefer.notify );
+								} else {
+									newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
+								}
+							});
+						});
+						fns = null;
+					}).promise();
+				},
+				// Get a promise for this deferred
+				// If obj is provided, the promise aspect is added to the object
+				promise: function( obj ) {
+					return obj != null ? jQuery.extend( obj, promise ) : promise;
+				}
+			},
+			deferred = {};
+
+		// Keep pipe for back-compat
+		promise.pipe = promise.then;
+
+		// Add list-specific methods
+		jQuery.each( tuples, function( i, tuple ) {
+			var list = tuple[ 2 ],
+				stateString = tuple[ 3 ];
+
+			// promise[ done | fail | progress ] = list.add
+			promise[ tuple[1] ] = list.add;
+
+			// Handle state
+			if ( stateString ) {
+				list.add(function() {
+					// state = [ resolved | rejected ]
+					state = stateString;
+
+				// [ reject_list | resolve_list ].disable; progress_list.lock
+				}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
 			}
-		}
-		if ( fn === false ) {
-			fn = returnFalse;
-		} else if ( !fn ) {
-			return this;
-		}
 
-		if ( one === 1 ) {
-			origFn = fn;
-			fn = function( event ) {
-				// Can use an empty set, since event contains the info
-				jQuery().off( event );
-				return origFn.apply( this, arguments );
+			// deferred[ resolve | reject | notify ]
+			deferred[ tuple[0] ] = function() {
+				deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
+				return this;
 			};
-			// Use same guid so caller can remove using origFn
-			fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
-		}
-		return this.each( function() {
-			jQuery.event.add( this, types, fn, data, selector );
+			deferred[ tuple[0] + "With" ] = list.fireWith;
 		});
-	},
-	one: function( types, selector, data, fn ) {
-		return this.on( types, selector, data, fn, 1 );
-	},
-	off: function( types, selector, fn ) {
-		var handleObj, type;
-		if ( types && types.preventDefault && types.handleObj ) {
-			// ( event )  dispatched jQuery.Event
-			handleObj = types.handleObj;
-			jQuery( types.delegateTarget ).off(
-				handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
-				handleObj.selector,
-				handleObj.handler
-			);
-			return this;
+
+		// Make the deferred a promise
+		promise.promise( deferred );
+
+		// Call given func if any
+		if ( func ) {
+			func.call( deferred, deferred );
 		}
-		if ( typeof types === "object" ) {
-			// ( types-object [, selector] )
-			for ( type in types ) {
-				this.off( type, selector, types[ type ] );
-			}
-			return this;
-		}
-		if ( selector === false || typeof selector === "function" ) {
-			// ( types [, fn] )
-			fn = selector;
-			selector = undefined;
-		}
-		if ( fn === false ) {
-			fn = returnFalse;
-		}
-		return this.each(function() {
-			jQuery.event.remove( this, types, fn, selector );
-		});
-	},
 
-	bind: function( types, data, fn ) {
-		return this.on( types, null, data, fn );
-	},
-	unbind: function( types, fn ) {
-		return this.off( types, null, fn );
+		// All done!
+		return deferred;
 	},
 
-	delegate: function( selector, types, data, fn ) {
-		return this.on( types, selector, data, fn );
-	},
-	undelegate: function( selector, types, fn ) {
-		// ( namespace ) or ( selector, types [, fn] )
-		return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
-	},
+	// Deferred helper
+	when: function( subordinate /* , ..., subordinateN */ ) {
+		var i = 0,
+			resolveValues = slice.call( arguments ),
+			length = resolveValues.length,
 
-	trigger: function( type, data ) {
-		return this.each(function() {
-			jQuery.event.trigger( type, data, this );
-		});
-	},
-	triggerHandler: function( type, data ) {
-		var elem = this[0];
-		if ( elem ) {
-			return jQuery.event.trigger( type, data, elem, true );
-		}
-	}
-});
-/*!
- * Sizzle CSS Selector Engine
- * Copyright 2012 jQuery Foundation and other contributors
- * Released under the MIT license
- * http://sizzlejs.com/
- */
-(function( window, undefined ) {
+			// the count of uncompleted subordinates
+			remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
 
-var i,
-	cachedruns,
-	Expr,
-	getText,
-	isXML,
-	compile,
-	hasDuplicate,
-	outermostContext,
+			// the master Deferred. If resolveValues consist of only a single Deferred, just use that.
+			deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
 
-	// Local document vars
-	setDocument,
-	document,
-	docElem,
-	documentIsXML,
-	rbuggyQSA,
-	rbuggyMatches,
-	matches,
-	contains,
-	sortOrder,
+			// Update function for both resolve and progress values
+			updateFunc = function( i, contexts, values ) {
+				return function( value ) {
+					contexts[ i ] = this;
+					values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+					if ( values === progressValues ) {
+						deferred.notifyWith( contexts, values );
 
-	// Instance-specific data
-	expando = "sizzle" + -(new Date()),
-	preferredDoc = window.document,
-	support = {},
-	dirruns = 0,
-	done = 0,
-	classCache = createCache(),
-	tokenCache = createCache(),
-	compilerCache = createCache(),
+					} else if ( !(--remaining) ) {
+						deferred.resolveWith( contexts, values );
+					}
+				};
+			},
 
-	// General-purpose constants
-	strundefined = typeof undefined,
-	MAX_NEGATIVE = 1 << 31,
+			progressValues, progressContexts, resolveContexts;
 
-	// Array methods
-	arr = [],
-	pop = arr.pop,
-	push = arr.push,
-	slice = arr.slice,
-	// Use a stripped-down indexOf if we can't use a native one
-	indexOf = arr.indexOf || function( elem ) {
-		var i = 0,
-			len = this.length;
-		for ( ; i < len; i++ ) {
-			if ( this[i] === elem ) {
-				return i;
+		// add listeners to Deferred subordinates; treat others as resolved
+		if ( length > 1 ) {
+			progressValues = new Array( length );
+			progressContexts = new Array( length );
+			resolveContexts = new Array( length );
+			for ( ; i < length; i++ ) {
+				if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
+					resolveValues[ i ].promise()
+						.done( updateFunc( i, resolveContexts, resolveValues ) )
+						.fail( deferred.reject )
+						.progress( updateFunc( i, progressContexts, progressValues ) );
+				} else {
+					--remaining;
+				}
 			}
 		}
-		return -1;
-	},
 
+		// if we're not waiting on anything, resolve the master
+		if ( !remaining ) {
+			deferred.resolveWith( resolveContexts, resolveValues );
+		}
 
-	// Regular expressions
+		return deferred.promise();
+	}
+});
 
-	// Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
-	whitespace = "[\\x20\\t\\r\\n\\f]",
-	// http://www.w3.org/TR/css3-syntax/#characters
-	characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
 
-	// Loosely modeled on CSS identifier characters
-	// An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
-	// Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
-	identifier = characterEncoding.replace( "w", "w#" ),
+// The deferred used on DOM ready
+var readyList;
 
-	// Acceptable operators http://www.w3.org/TR/selectors/#attribute-selectors
-	operators = "([*^$|!~]?=)",
-	attributes = "\\[" + whitespace + "*(" + characterEncoding + ")" + whitespace +
-		"*(?:" + operators + whitespace + "*(?:(['\"])((?:\\\\.|[^\\\\])*?)\\3|(" + identifier + ")|)|)" + whitespace + "*\\]",
+jQuery.fn.ready = function( fn ) {
+	// Add the callback
+	jQuery.ready.promise().done( fn );
 
-	// Prefer arguments quoted,
-	//   then not containing pseudos/brackets,
-	//   then attribute selectors/non-parenthetical expressions,
-	//   then anything else
-	// These preferences are here to reduce the number of selectors
-	//   needing tokenize in the PSEUDO preFilter
-	pseudos = ":(" + characterEncoding + ")(?:\\(((['\"])((?:\\\\.|[^\\\\])*?)\\3|((?:\\\\.|[^\\\\()[\\]]|" + attributes.replace( 3, 8 ) + ")*)|.*)\\)|)",
+	return this;
+};
 
-	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
-	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+jQuery.extend({
+	// Is the DOM ready to be used? Set to true once it occurs.
+	isReady: false,
 
-	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
-	rcombinators = new RegExp( "^" + whitespace + "*([\\x20\\t\\r\\n\\f>+~])" + whitespace + "*" ),
-	rpseudo = new RegExp( pseudos ),
-	ridentifier = new RegExp( "^" + identifier + "$" ),
+	// A counter to track how many items to wait for before
+	// the ready event fires. See #6781
+	readyWait: 1,
 
-	matchExpr = {
-		"ID": new RegExp( "^#(" + characterEncoding + ")" ),
-		"CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
-		"NAME": new RegExp( "^\\[name=['\"]?(" + characterEncoding + ")['\"]?\\]" ),
-		"TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
-		"ATTR": new RegExp( "^" + attributes ),
-		"PSEUDO": new RegExp( "^" + pseudos ),
-		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
-			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
-			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
-		// For use in libraries implementing .is()
-		// We use this for POS matching in `select`
-		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
-			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+	// Hold (or release) the ready event
+	holdReady: function( hold ) {
+		if ( hold ) {
+			jQuery.readyWait++;
+		} else {
+			jQuery.ready( true );
+		}
 	},
 
-	rsibling = /[\x20\t\r\n\f]*[+~]/,
-
-	rnative = /^[^{]+\{\s*\[native code/,
-
-	// Easily-parseable/retrievable ID or TAG or CLASS selectors
-	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
+	// Handle when the DOM is ready
+	ready: function( wait ) {
 
-	rinputs = /^(?:input|select|textarea|button)$/i,
-	rheader = /^h\d$/i,
+		// Abort if there are pending holds or we're already ready
+		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+			return;
+		}
 
-	rescape = /'|\\/g,
-	rattributeQuotes = /\=[\x20\t\r\n\f]*([^'"\]]*)[\x20\t\r\n\f]*\]/g,
+		// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
+		if ( !document.body ) {
+			return setTimeout( jQuery.ready );
+		}
 
-	// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
-	runescape = /\\([\da-fA-F]{1,6}[\x20\t\r\n\f]?|.)/g,
-	funescape = function( _, escaped ) {
-		var high = "0x" + escaped - 0x10000;
-		// NaN means non-codepoint
-		return high !== high ?
-			escaped :
-			// BMP codepoint
-			high < 0 ?
-				String.fromCharCode( high + 0x10000 ) :
-				// Supplemental Plane codepoint (surrogate pair)
-				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
-	};
+		// Remember that the DOM is ready
+		jQuery.isReady = true;
 
-// Use a stripped-down slice if we can't use a native one
-try {
-	slice.call( preferredDoc.documentElement.childNodes, 0 )[0].nodeType;
-} catch ( e ) {
-	slice = function( i ) {
-		var elem,
-			results = [];
-		while ( (elem = this[i++]) ) {
-			results.push( elem );
+		// If a normal DOM Ready event fired, decrement, and wait if need be
+		if ( wait !== true && --jQuery.readyWait > 0 ) {
+			return;
 		}
-		return results;
-	};
-}
-
-/**
- * For feature detection
- * @param {Function} fn The function to test for native support
- */
-function isNative( fn ) {
-	return rnative.test( fn + "" );
-}
 
-/**
- * Create key-value caches of limited size
- * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
- *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
- *	deleting the oldest entry
- */
-function createCache() {
-	var cache,
-		keys = [];
+		// If there are functions bound, to execute
+		readyList.resolveWith( document, [ jQuery ] );
 
-	return (cache = function( key, value ) {
-		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
-		if ( keys.push( key += " " ) > Expr.cacheLength ) {
-			// Only keep the most recent entries
-			delete cache[ keys.shift() ];
+		// Trigger any bound ready events
+		if ( jQuery.fn.triggerHandler ) {
+			jQuery( document ).triggerHandler( "ready" );
+			jQuery( document ).off( "ready" );
 		}
-		return (cache[ key ] = value);
-	});
-}
+	}
+});
 
 /**
- * Mark a function for special use by Sizzle
- * @param {Function} fn The function to mark
+ * Clean-up method for dom ready events
  */
-function markFunction( fn ) {
-	fn[ expando ] = true;
-	return fn;
+function detach() {
+	if ( document.addEventListener ) {
+		document.removeEventListener( "DOMContentLoaded", completed, false );
+		window.removeEventListener( "load", completed, false );
+
+	} else {
+		document.detachEvent( "onreadystatechange", completed );
+		window.detachEvent( "onload", completed );
+	}
 }
 
 /**
- * Support testing using an element
- * @param {Function} fn Passed the created div and expects a boolean result
+ * The ready event handler and self cleanup method
  */
-function assert( fn ) {
-	var div = document.createElement("div");
-
-	try {
-		return fn( div );
-	} catch (e) {
-		return false;
-	} finally {
-		// release memory in IE
-		div = null;
+function completed() {
+	// readyState === "complete" is good enough for us to call the dom ready in oldIE
+	if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
+		detach();
+		jQuery.ready();
 	}
 }
 
-function Sizzle( selector, context, results, seed ) {
-	var match, elem, m, nodeType,
-		// QSA vars
-		i, groups, old, nid, newContext, newSelector;
+jQuery.ready.promise = function( obj ) {
+	if ( !readyList ) {
 
-	if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
-		setDocument( context );
-	}
+		readyList = jQuery.Deferred();
 
-	context = context || document;
-	results = results || [];
+		// Catch cases where $(document).ready() is called after the browser event has already occurred.
+		// we once tried to use readyState "interactive" here, but it caused issues like the one
+		// discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
+		if ( document.readyState === "complete" ) {
+			// Handle it asynchronously to allow scripts the opportunity to delay ready
+			setTimeout( jQuery.ready );
 
-	if ( !selector || typeof selector !== "string" ) {
-		return results;
-	}
-
-	if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) {
-		return [];
-	}
+		// Standards-based browsers support DOMContentLoaded
+		} else if ( document.addEventListener ) {
+			// Use the handy event callback
+			document.addEventListener( "DOMContentLoaded", completed, false );
 
-	if ( !documentIsXML && !seed ) {
+			// A fallback to window.onload, that will always work
+			window.addEventListener( "load", completed, false );
 
-		// Shortcuts
-		if ( (match = rquickExpr.exec( selector )) ) {
-			// Speed-up: Sizzle("#ID")
-			if ( (m = match[1]) ) {
-				if ( nodeType === 9 ) {
-					elem = context.getElementById( m );
-					// Check parentNode to catch when Blackberry 4.6 returns
-					// nodes that are no longer in the document #6963
-					if ( elem && elem.parentNode ) {
-						// Handle the case where IE, Opera, and Webkit return items
-						// by name instead of ID
-						if ( elem.id === m ) {
-							results.push( elem );
-							return results;
-						}
-					} else {
-						return results;
-					}
-				} else {
-					// Context is not a document
-					if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
-						contains( context, elem ) && elem.id === m ) {
-						results.push( elem );
-						return results;
-					}
-				}
+		// If IE event model is used
+		} else {
+			// Ensure firing before onload, maybe late but safe also for iframes
+			document.attachEvent( "onreadystatechange", completed );
 
-			// Speed-up: Sizzle("TAG")
-			} else if ( match[2] ) {
-				push.apply( results, slice.call(context.getElementsByTagName( selector ), 0) );
-				return results;
+			// A fallback to window.onload, that will always work
+			window.attachEvent( "onload", completed );
 
-			// Speed-up: Sizzle(".CLASS")
-			} else if ( (m = match[3]) && support.getByClassName && context.getElementsByClassName ) {
-				push.apply( results, slice.call(context.getElementsByClassName( m ), 0) );
-				return results;
-			}
-		}
+			// If IE and not a frame
+			// continually check to see if the document is ready
+			var top = false;
 
-		// QSA path
-		if ( support.qsa && !rbuggyQSA.test(selector) ) {
-			old = true;
-			nid = expando;
-			newContext = context;
-			newSelector = nodeType === 9 && selector;
+			try {
+				top = window.frameElement == null && document.documentElement;
+			} catch(e) {}
 
-			// qSA works strangely on Element-rooted queries
-			// We can work around this by specifying an extra ID on the root
-			// and working up from there (Thanks to Andrew Dupont for the technique)
-			// IE 8 doesn't work on object elements
-			if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
-				groups = tokenize( selector );
+			if ( top && top.doScroll ) {
+				(function doScrollCheck() {
+					if ( !jQuery.isReady ) {
 
-				if ( (old = context.getAttribute("id")) ) {
-					nid = old.replace( rescape, "\\$&" );
-				} else {
-					context.setAttribute( "id", nid );
-				}
-				nid = "[id='" + nid + "'] ";
+						try {
+							// Use the trick by Diego Perini
+							// http://javascript.nwbox.com/IEContentLoaded/
+							top.doScroll("left");
+						} catch(e) {
+							return setTimeout( doScrollCheck, 50 );
+						}
 
-				i = groups.length;
-				while ( i-- ) {
-					groups[i] = nid + toSelector( groups[i] );
-				}
-				newContext = rsibling.test( selector ) && context.parentNode || context;
-				newSelector = groups.join(",");
-			}
+						// detach all dom ready events
+						detach();
 
-			if ( newSelector ) {
-				try {
-					push.apply( results, slice.call( newContext.querySelectorAll(
-						newSelector
-					), 0 ) );
-					return results;
-				} catch(qsaError) {
-				} finally {
-					if ( !old ) {
-						context.removeAttribute("id");
+						// and execute any waiting functions
+						jQuery.ready();
 					}
-				}
+				})();
 			}
 		}
 	}
+	return readyList.promise( obj );
+};
 
-	// All others
-	return select( selector.replace( rtrim, "$1" ), context, results, seed );
-}
 
-/**
- * Detect xml
- * @param {Element|Object} elem An element or a document
- */
-isXML = Sizzle.isXML = function( elem ) {
-	// documentElement is verified for cases where it doesn't yet exist
-	// (such as loading iframes in IE - #4833)
-	var documentElement = elem && (elem.ownerDocument || elem).documentElement;
-	return documentElement ? documentElement.nodeName !== "HTML" : false;
-};
+var strundefined = typeof undefined;
 
-/**
- * Sets document-related variables once based on the current document
- * @param {Element|Object} [doc] An element or document object to use to set the document
- * @returns {Object} Returns the current document
- */
-setDocument = Sizzle.setDocument = function( node ) {
-	var doc = node ? node.ownerDocument || node : preferredDoc;
 
-	// If no document and documentElement is available, return
-	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
-		return document;
-	}
 
-	// Set our document
-	document = doc;
-	docElem = doc.documentElement;
+// Support: IE<9
+// Iteration over object's inherited properties before its own
+var i;
+for ( i in jQuery( support ) ) {
+	break;
+}
+support.ownLast = i !== "0";
 
-	// Support tests
-	documentIsXML = isXML( doc );
+// Note: most support tests are defined in their respective modules.
+// false until the test is run
+support.inlineBlockNeedsLayout = false;
 
-	// Check if getElementsByTagName("*") returns only elements
-	support.tagNameNoComments = assert(function( div ) {
-		div.appendChild( doc.createComment("") );
-		return !div.getElementsByTagName("*").length;
-	});
+// Execute ASAP in case we need to set body.style.zoom
+jQuery(function() {
+	// Minified: var a,b,c,d
+	var val, div, body, container;
 
-	// Check if attributes should be retrieved by attribute nodes
-	support.attributes = assert(function( div ) {
-		div.innerHTML = "<select></select>";
-		var type = typeof div.lastChild.getAttribute("multiple");
-		// IE8 returns a string for some attributes even when not present
-		return type !== "boolean" && type !== "string";
-	});
+	body = document.getElementsByTagName( "body" )[ 0 ];
+	if ( !body || !body.style ) {
+		// Return for frameset docs that don't have a body
+		return;
+	}
 
-	// Check if getElementsByClassName can be trusted
-	support.getByClassName = assert(function( div ) {
-		// Opera can't find a second classname (in 9.6)
-		div.innerHTML = "<div class='hidden e'></div><div class='hidden'></div>";
-		if ( !div.getElementsByClassName || !div.getElementsByClassName("e").length ) {
-			return false;
+	// Setup
+	div = document.createElement( "div" );
+	container = document.createElement( "div" );
+	container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+	body.appendChild( container ).appendChild( div );
+
+	if ( typeof div.style.zoom !== strundefined ) {
+		// Support: IE<8
+		// Check if natively block-level elements act like inline-block
+		// elements when setting their display to 'inline' and giving
+		// them layout
+		div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1";
+
+		support.inlineBlockNeedsLayout = val = div.offsetWidth === 3;
+		if ( val ) {
+			// Prevent IE 6 from affecting layout for positioned elements #11048
+			// Prevent IE from shrinking the body in IE 7 mode #12869
+			// Support: IE<8
+			body.style.zoom = 1;
 		}
+	}
 
-		// Safari 3.2 caches class attributes and doesn't catch changes
-		div.lastChild.className = "e";
-		return div.getElementsByClassName("e").length === 2;
-	});
-
-	// Check if getElementById returns elements by name
-	// Check if getElementsByName privileges form controls or returns elements by ID
-	support.getByName = assert(function( div ) {
-		// Inject content
-		div.id = expando + 0;
-		div.innerHTML = "<a name='" + expando + "'></a><div name='" + expando + "'></div>";
-		docElem.insertBefore( div, docElem.firstChild );
-
-		// Test
-		var pass = doc.getElementsByName &&
-			// buggy browsers will return fewer than the correct 2
-			doc.getElementsByName( expando ).length === 2 +
-			// buggy browsers will return more than the correct 0
-			doc.getElementsByName( expando + 0 ).length;
-		support.getIdNotName = !doc.getElementById( expando );
-
-		// Cleanup
-		docElem.removeChild( div );
-
-		return pass;
-	});
+	body.removeChild( container );
+});
 
-	// IE6/7 return modified attributes
-	Expr.attrHandle = assert(function( div ) {
-		div.innerHTML = "<a href='#'></a>";
-		return div.firstChild && typeof div.firstChild.getAttribute !== strundefined &&
-			div.firstChild.getAttribute("href") === "#";
-	}) ?
-		{} :
-		{
-			"href": function( elem ) {
-				return elem.getAttribute( "href", 2 );
-			},
-			"type": function( elem ) {
-				return elem.getAttribute("type");
-			}
-		};
 
-	// ID find and filter
-	if ( support.getIdNotName ) {
-		Expr.find["ID"] = function( id, context ) {
-			if ( typeof context.getElementById !== strundefined && !documentIsXML ) {
-				var m = context.getElementById( id );
-				// Check parentNode to catch when Blackberry 4.6 returns
-				// nodes that are no longer in the document #6963
-				return m && m.parentNode ? [m] : [];
-			}
-		};
-		Expr.filter["ID"] = function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				return elem.getAttribute("id") === attrId;
-			};
-		};
-	} else {
-		Expr.find["ID"] = function( id, context ) {
-			if ( typeof context.getElementById !== strundefined && !documentIsXML ) {
-				var m = context.getElementById( id );
 
-				return m ?
-					m.id === id || typeof m.getAttributeNode !== strundefined && m.getAttributeNode("id").value === id ?
-						[m] :
-						undefined :
-					[];
-			}
-		};
-		Expr.filter["ID"] =  function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id");
-				return node && node.value === attrId;
-			};
-		};
-	}
 
-	// Tag
-	Expr.find["TAG"] = support.tagNameNoComments ?
-		function( tag, context ) {
-			if ( typeof context.getElementsByTagName !== strundefined ) {
-				return context.getElementsByTagName( tag );
-			}
-		} :
-		function( tag, context ) {
-			var elem,
-				tmp = [],
-				i = 0,
-				results = context.getElementsByTagName( tag );
+(function() {
+	var div = document.createElement( "div" );
 
-			// Filter out possible comments
-			if ( tag === "*" ) {
-				while ( (elem = results[i++]) ) {
-					if ( elem.nodeType === 1 ) {
-						tmp.push( elem );
-					}
-				}
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
 
-				return tmp;
-			}
-			return results;
-		};
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
 
-	// Name
-	Expr.find["NAME"] = support.getByName && function( tag, context ) {
-		if ( typeof context.getElementsByName !== strundefined ) {
-			return context.getElementsByName( name );
-		}
-	};
 
-	// Class
-	Expr.find["CLASS"] = support.getByClassName && function( className, context ) {
-		if ( typeof context.getElementsByClassName !== strundefined && !documentIsXML ) {
-			return context.getElementsByClassName( className );
-		}
-	};
+/**
+ * Determines whether an object can have data
+ */
+jQuery.acceptData = function( elem ) {
+	var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ],
+		nodeType = +elem.nodeType || 1;
 
-	// QSA and matchesSelector support
+	// Do not set data on non-element DOM nodes because it will not be cleared (#8335).
+	return nodeType !== 1 && nodeType !== 9 ?
+		false :
 
-	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
-	rbuggyMatches = [];
+		// Nodes accept data unless otherwise specified; rejection can be conditional
+		!noData || noData !== true && elem.getAttribute("classid") === noData;
+};
 
-	// qSa(:focus) reports false when true (Chrome 21),
-	// no need to also add to buggyMatches since matches checks buggyQSA
-	// A support test would require too much code (would include document ready)
-	rbuggyQSA = [ ":focus" ];
 
-	if ( (support.qsa = isNative(doc.querySelectorAll)) ) {
-		// Build QSA regex
-		// Regex strategy adopted from Diego Perini
-		assert(function( div ) {
-			// Select is set to empty string on purpose
-			// This is to test IE's treatment of not explictly
-			// setting a boolean content attribute,
-			// since its presence should be enough
-			// http://bugs.jquery.com/ticket/12359
-			div.innerHTML = "<select><option selected=''></option></select>";
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+	rmultiDash = /([A-Z])/g;
 
-			// IE8 - Some boolean attributes are not treated correctly
-			if ( !div.querySelectorAll("[selected]").length ) {
-				rbuggyQSA.push( "\\[" + whitespace + "*(?:checked|disabled|ismap|multiple|readonly|selected|value)" );
-			}
+function dataAttr( elem, key, data ) {
+	// If nothing was found internally, try to fetch any
+	// data from the HTML5 data-* attribute
+	if ( data === undefined && elem.nodeType === 1 ) {
 
-			// Webkit/Opera - :checked should return selected option elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			// IE8 throws error here and will not see later tests
-			if ( !div.querySelectorAll(":checked").length ) {
-				rbuggyQSA.push(":checked");
-			}
-		});
+		var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
 
-		assert(function( div ) {
+		data = elem.getAttribute( name );
 
-			// Opera 10-12/IE8 - ^= $= *= and empty values
-			// Should not select anything
-			div.innerHTML = "<input type='hidden' i=''/>";
-			if ( div.querySelectorAll("[i^='']").length ) {
-				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:\"\"|'')" );
-			}
+		if ( typeof data === "string" ) {
+			try {
+				data = data === "true" ? true :
+					data === "false" ? false :
+					data === "null" ? null :
+					// Only convert to a number if it doesn't change the string
+					+data + "" === data ? +data :
+					rbrace.test( data ) ? jQuery.parseJSON( data ) :
+					data;
+			} catch( e ) {}
 
-			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
-			// IE8 throws error here and will not see later tests
-			if ( !div.querySelectorAll(":enabled").length ) {
-				rbuggyQSA.push( ":enabled", ":disabled" );
-			}
+			// Make sure we set the data so it isn't changed later
+			jQuery.data( elem, key, data );
 
-			// Opera 10-11 does not throw on post-comma invalid pseudos
-			div.querySelectorAll("*,:x");
-			rbuggyQSA.push(",.*:");
-		});
+		} else {
+			data = undefined;
+		}
 	}
 
-	if ( (support.matchesSelector = isNative( (matches = docElem.matchesSelector ||
-		docElem.mozMatchesSelector ||
-		docElem.webkitMatchesSelector ||
-		docElem.oMatchesSelector ||
-		docElem.msMatchesSelector) )) ) {
+	return data;
+}
 
-		assert(function( div ) {
-			// Check to see if it's possible to do matchesSelector
-			// on a disconnected node (IE 9)
-			support.disconnectedMatch = matches.call( div, "div" );
+// checks a cache object for emptiness
+function isEmptyDataObject( obj ) {
+	var name;
+	for ( name in obj ) {
 
-			// This should fail with an exception
-			// Gecko does not error, returns false instead
-			matches.call( div, "[s!='']:x" );
-			rbuggyMatches.push( "!=", pseudos );
-		});
+		// if the public data object is empty, the private is still empty
+		if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
+			continue;
+		}
+		if ( name !== "toJSON" ) {
+			return false;
+		}
 	}
 
-	rbuggyQSA = new RegExp( rbuggyQSA.join("|") );
-	rbuggyMatches = new RegExp( rbuggyMatches.join("|") );
-
-	// Element contains another
-	// Purposefully does not implement inclusive descendent
-	// As in, an element does not contain itself
-	contains = isNative(docElem.contains) || docElem.compareDocumentPosition ?
-		function( a, b ) {
-			var adown = a.nodeType === 9 ? a.documentElement : a,
-				bup = b && b.parentNode;
-			return a === bup || !!( bup && bup.nodeType === 1 && (
-				adown.contains ?
-					adown.contains( bup ) :
-					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
-			));
-		} :
-		function( a, b ) {
-			if ( b ) {
-				while ( (b = b.parentNode) ) {
-					if ( b === a ) {
-						return true;
-					}
-				}
-			}
-			return false;
-		};
+	return true;
+}
 
-	// Document order sorting
-	sortOrder = docElem.compareDocumentPosition ?
-	function( a, b ) {
-		var compare;
+function internalData( elem, name, data, pvt /* Internal Use Only */ ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
+	}
 
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
-		}
+	var ret, thisCache,
+		internalKey = jQuery.expando,
 
-		if ( (compare = b.compareDocumentPosition && a.compareDocumentPosition && a.compareDocumentPosition( b )) ) {
-			if ( compare & 1 || a.parentNode && a.parentNode.nodeType === 11 ) {
-				if ( a === doc || contains( preferredDoc, a ) ) {
-					return -1;
-				}
-				if ( b === doc || contains( preferredDoc, b ) ) {
-					return 1;
-				}
-				return 0;
-			}
-			return compare & 4 ? -1 : 1;
-		}
+		// We have to handle DOM nodes and JS objects differently because IE6-7
+		// can't GC object references properly across the DOM-JS boundary
+		isNode = elem.nodeType,
 
-		return a.compareDocumentPosition ? -1 : 1;
-	} :
-	function( a, b ) {
-		var cur,
-			i = 0,
-			aup = a.parentNode,
-			bup = b.parentNode,
-			ap = [ a ],
-			bp = [ b ];
+		// Only DOM nodes need the global jQuery cache; JS object data is
+		// attached directly to the object so GC can occur automatically
+		cache = isNode ? jQuery.cache : elem,
 
-		// Exit early if the nodes are identical
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
+		// Only defining an ID for JS objects if its cache already exists allows
+		// the code to shortcut on the same path as a DOM node with no cache
+		id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
 
-		// Parentless nodes are either documents or disconnected
-		} else if ( !aup || !bup ) {
-			return a === doc ? -1 :
-				b === doc ? 1 :
-				aup ? -1 :
-				bup ? 1 :
-				0;
+	// Avoid doing any more work than we need to when trying to get data on an
+	// object that has no data at all
+	if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) {
+		return;
+	}
 
-		// If the nodes are siblings, we can do a quick check
-		} else if ( aup === bup ) {
-			return siblingCheck( a, b );
+	if ( !id ) {
+		// Only DOM nodes need a new unique ID for each element since their data
+		// ends up in the global cache
+		if ( isNode ) {
+			id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++;
+		} else {
+			id = internalKey;
 		}
+	}
 
-		// Otherwise we need full lists of their ancestors for comparison
-		cur = a;
-		while ( (cur = cur.parentNode) ) {
-			ap.unshift( cur );
-		}
-		cur = b;
-		while ( (cur = cur.parentNode) ) {
-			bp.unshift( cur );
+	if ( !cache[ id ] ) {
+		// Avoid exposing jQuery metadata on plain JS objects when the object
+		// is serialized using JSON.stringify
+		cache[ id ] = isNode ? {} : { toJSON: jQuery.noop };
+	}
+
+	// An object can be passed to jQuery.data instead of a key/value pair; this gets
+	// shallow copied over onto the existing cache
+	if ( typeof name === "object" || typeof name === "function" ) {
+		if ( pvt ) {
+			cache[ id ] = jQuery.extend( cache[ id ], name );
+		} else {
+			cache[ id ].data = jQuery.extend( cache[ id ].data, name );
 		}
+	}
 
-		// Walk down the tree looking for a discrepancy
-		while ( ap[i] === bp[i] ) {
-			i++;
+	thisCache = cache[ id ];
+
+	// jQuery data() is stored in a separate object inside the object's internal data
+	// cache in order to avoid key collisions between internal data and user-defined
+	// data.
+	if ( !pvt ) {
+		if ( !thisCache.data ) {
+			thisCache.data = {};
 		}
 
-		return i ?
-			// Do a sibling check if the nodes have a common ancestor
-			siblingCheck( ap[i], bp[i] ) :
+		thisCache = thisCache.data;
+	}
 
-			// Otherwise nodes in our document sort first
-			ap[i] === preferredDoc ? -1 :
-			bp[i] === preferredDoc ? 1 :
-			0;
-	};
+	if ( data !== undefined ) {
+		thisCache[ jQuery.camelCase( name ) ] = data;
+	}
 
-	// Always assume the presence of duplicates if sort doesn't
-	// pass them to our comparison function (as in Google Chrome).
-	hasDuplicate = false;
-	[0, 0].sort( sortOrder );
-	support.detectDuplicates = hasDuplicate;
+	// Check for both converted-to-camel and non-converted data property names
+	// If a data property was specified
+	if ( typeof name === "string" ) {
 
-	return document;
-};
+		// First Try to find as-is property data
+		ret = thisCache[ name ];
 
-Sizzle.matches = function( expr, elements ) {
-	return Sizzle( expr, null, null, elements );
-};
+		// Test for null|undefined property data
+		if ( ret == null ) {
 
-Sizzle.matchesSelector = function( elem, expr ) {
-	// Set document vars if needed
-	if ( ( elem.ownerDocument || elem ) !== document ) {
-		setDocument( elem );
+			// Try to find the camelCased property
+			ret = thisCache[ jQuery.camelCase( name ) ];
+		}
+	} else {
+		ret = thisCache;
 	}
 
-	// Make sure that attribute selectors are quoted
-	expr = expr.replace( rattributeQuotes, "='$1']" );
-
-	// rbuggyQSA always contains :focus, so no need for an existence check
-	if ( support.matchesSelector && !documentIsXML && (!rbuggyMatches || !rbuggyMatches.test(expr)) && !rbuggyQSA.test(expr) ) {
-		try {
-			var ret = matches.call( elem, expr );
+	return ret;
+}
 
-			// IE 9's matchesSelector returns false on disconnected nodes
-			if ( ret || support.disconnectedMatch ||
-					// As well, disconnected nodes are said to be in a document
-					// fragment in IE 9
-					elem.document && elem.document.nodeType !== 11 ) {
-				return ret;
-			}
-		} catch(e) {}
+function internalRemoveData( elem, name, pvt ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
 	}
 
-	return Sizzle( expr, document, null, [elem] ).length > 0;
-};
+	var thisCache, i,
+		isNode = elem.nodeType,
 
-Sizzle.contains = function( context, elem ) {
-	// Set document vars if needed
-	if ( ( context.ownerDocument || context ) !== document ) {
-		setDocument( context );
+		// See jQuery.data for more information
+		cache = isNode ? jQuery.cache : elem,
+		id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+
+	// If there is already no cache entry for this object, there is no
+	// purpose in continuing
+	if ( !cache[ id ] ) {
+		return;
 	}
-	return contains( context, elem );
-};
 
-Sizzle.attr = function( elem, name ) {
-	var val;
+	if ( name ) {
 
-	// Set document vars if needed
-	if ( ( elem.ownerDocument || elem ) !== document ) {
-		setDocument( elem );
-	}
+		thisCache = pvt ? cache[ id ] : cache[ id ].data;
 
-	if ( !documentIsXML ) {
-		name = name.toLowerCase();
-	}
-	if ( (val = Expr.attrHandle[ name ]) ) {
-		return val( elem );
-	}
-	if ( documentIsXML || support.attributes ) {
-		return elem.getAttribute( name );
-	}
-	return ( (val = elem.getAttributeNode( name )) || elem.getAttribute( name ) ) && elem[ name ] === true ?
-		name :
-		val && val.specified ? val.value : null;
-};
+		if ( thisCache ) {
 
-Sizzle.error = function( msg ) {
-	throw new Error( "Syntax error, unrecognized expression: " + msg );
-};
+			// Support array or space separated string names for data keys
+			if ( !jQuery.isArray( name ) ) {
 
-// Document sorting and removing duplicates
-Sizzle.uniqueSort = function( results ) {
-	var elem,
-		duplicates = [],
-		i = 1,
-		j = 0;
+				// try the string as a key before any manipulation
+				if ( name in thisCache ) {
+					name = [ name ];
+				} else {
 
-	// Unless we *know* we can detect duplicates, assume their presence
-	hasDuplicate = !support.detectDuplicates;
-	results.sort( sortOrder );
+					// split the camel cased version by spaces unless a key with the spaces exists
+					name = jQuery.camelCase( name );
+					if ( name in thisCache ) {
+						name = [ name ];
+					} else {
+						name = name.split(" ");
+					}
+				}
+			} else {
+				// If "name" is an array of keys...
+				// When data is initially created, via ("key", "val") signature,
+				// keys will be converted to camelCase.
+				// Since there is no way to tell _how_ a key was added, remove
+				// both plain key and camelCase key. #12786
+				// This will only penalize the array argument path.
+				name = name.concat( jQuery.map( name, jQuery.camelCase ) );
+			}
 
-	if ( hasDuplicate ) {
-		for ( ; (elem = results[i]); i++ ) {
-			if ( elem === results[ i - 1 ] ) {
-				j = duplicates.push( i );
+			i = name.length;
+			while ( i-- ) {
+				delete thisCache[ name[i] ];
 			}
-		}
-		while ( j-- ) {
-			results.splice( duplicates[ j ], 1 );
-		}
-	}
 
-	return results;
-};
-
-function siblingCheck( a, b ) {
-	var cur = b && a,
-		diff = cur && ( ~b.sourceIndex || MAX_NEGATIVE ) - ( ~a.sourceIndex || MAX_NEGATIVE );
-
-	// Use IE sourceIndex if available on both nodes
-	if ( diff ) {
-		return diff;
-	}
-
-	// Check if b follows a
-	if ( cur ) {
-		while ( (cur = cur.nextSibling) ) {
-			if ( cur === b ) {
-				return -1;
+			// If there is no data left in the cache, we want to continue
+			// and let the cache object itself get destroyed
+			if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) {
+				return;
 			}
 		}
 	}
 
-	return a ? 1 : -1;
-}
+	// See jQuery.data for more information
+	if ( !pvt ) {
+		delete cache[ id ].data;
 
-// Returns a function to use in pseudos for input types
-function createInputPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return name === "input" && elem.type === type;
-	};
-}
+		// Don't destroy the parent cache unless the internal data object
+		// had been the only thing left in it
+		if ( !isEmptyDataObject( cache[ id ] ) ) {
+			return;
+		}
+	}
 
-// Returns a function to use in pseudos for buttons
-function createButtonPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return (name === "input" || name === "button") && elem.type === type;
-	};
-}
+	// Destroy the cache
+	if ( isNode ) {
+		jQuery.cleanData( [ elem ], true );
 
-// Returns a function to use in pseudos for positionals
-function createPositionalPseudo( fn ) {
-	return markFunction(function( argument ) {
-		argument = +argument;
-		return markFunction(function( seed, matches ) {
-			var j,
-				matchIndexes = fn( [], seed.length, argument ),
-				i = matchIndexes.length;
+	// Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
+	/* jshint eqeqeq: false */
+	} else if ( support.deleteExpando || cache != cache.window ) {
+		/* jshint eqeqeq: true */
+		delete cache[ id ];
 
-			// Match elements found at the specified indexes
-			while ( i-- ) {
-				if ( seed[ (j = matchIndexes[i]) ] ) {
-					seed[j] = !(matches[j] = seed[j]);
-				}
-			}
-		});
-	});
+	// When all else fails, null
+	} else {
+		cache[ id ] = null;
+	}
 }
 
-/**
- * Utility function for retrieving the text value of an array of DOM nodes
- * @param {Array|Element} elem
- */
-getText = Sizzle.getText = function( elem ) {
-	var node,
-		ret = "",
-		i = 0,
-		nodeType = elem.nodeType;
+jQuery.extend({
+	cache: {},
 
-	if ( !nodeType ) {
-		// If no nodeType, this is expected to be an array
-		for ( ; (node = elem[i]); i++ ) {
-			// Do not traverse comment nodes
-			ret += getText( node );
-		}
-	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
-		// Use textContent for elements
-		// innerText usage removed for consistency of new lines (see #11153)
-		if ( typeof elem.textContent === "string" ) {
-			return elem.textContent;
-		} else {
-			// Traverse its children
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				ret += getText( elem );
-			}
-		}
-	} else if ( nodeType === 3 || nodeType === 4 ) {
-		return elem.nodeValue;
-	}
-	// Do not include comment or processing instruction nodes
+	// The following elements (space-suffixed to avoid Object.prototype collisions)
+	// throw uncatchable exceptions if you attempt to set expando properties
+	noData: {
+		"applet ": true,
+		"embed ": true,
+		// ...but Flash objects (which have this classid) *can* handle expandos
+		"object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
+	},
 
-	return ret;
-};
+	hasData: function( elem ) {
+		elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
+		return !!elem && !isEmptyDataObject( elem );
+	},
 
-Expr = Sizzle.selectors = {
+	data: function( elem, name, data ) {
+		return internalData( elem, name, data );
+	},
 
-	// Can be adjusted by the user
-	cacheLength: 50,
+	removeData: function( elem, name ) {
+		return internalRemoveData( elem, name );
+	},
 
-	createPseudo: markFunction,
+	// For internal use only.
+	_data: function( elem, name, data ) {
+		return internalData( elem, name, data, true );
+	},
 
-	match: matchExpr,
+	_removeData: function( elem, name ) {
+		return internalRemoveData( elem, name, true );
+	}
+});
 
-	find: {},
+jQuery.fn.extend({
+	data: function( key, value ) {
+		var i, name, data,
+			elem = this[0],
+			attrs = elem && elem.attributes;
 
-	relative: {
-		">": { dir: "parentNode", first: true },
-		" ": { dir: "parentNode" },
-		"+": { dir: "previousSibling", first: true },
-		"~": { dir: "previousSibling" }
-	},
+		// Special expections of .data basically thwart jQuery.access,
+		// so implement the relevant behavior ourselves
 
-	preFilter: {
-		"ATTR": function( match ) {
-			match[1] = match[1].replace( runescape, funescape );
+		// Gets all values
+		if ( key === undefined ) {
+			if ( this.length ) {
+				data = jQuery.data( elem );
 
-			// Move the given value to match[3] whether quoted or unquoted
-			match[3] = ( match[4] || match[5] || "" ).replace( runescape, funescape );
+				if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
+					i = attrs.length;
+					while ( i-- ) {
 
-			if ( match[2] === "~=" ) {
-				match[3] = " " + match[3] + " ";
+						// Support: IE11+
+						// The attrs elements can be null (#14894)
+						if ( attrs[ i ] ) {
+							name = attrs[ i ].name;
+							if ( name.indexOf( "data-" ) === 0 ) {
+								name = jQuery.camelCase( name.slice(5) );
+								dataAttr( elem, name, data[ name ] );
+							}
+						}
+					}
+					jQuery._data( elem, "parsedAttrs", true );
+				}
 			}
 
-			return match.slice( 0, 4 );
-		},
-
-		"CHILD": function( match ) {
-			/* matches from matchExpr["CHILD"]
-				1 type (only|nth|...)
-				2 what (child|of-type)
-				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
-				4 xn-component of xn+y argument ([+-]?\d*n|)
-				5 sign of xn-component
-				6 x of xn-component
-				7 sign of y-component
-				8 y of y-component
-			*/
-			match[1] = match[1].toLowerCase();
+			return data;
+		}
 
-			if ( match[1].slice( 0, 3 ) === "nth" ) {
-				// nth-* requires argument
-				if ( !match[3] ) {
-					Sizzle.error( match[0] );
-				}
+		// Sets multiple values
+		if ( typeof key === "object" ) {
+			return this.each(function() {
+				jQuery.data( this, key );
+			});
+		}
 
-				// numeric x and y parameters for Expr.filter.CHILD
-				// remember that false/true cast respectively to 0/1
-				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
-				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
+		return arguments.length > 1 ?
 
-			// other types prohibit arguments
-			} else if ( match[3] ) {
-				Sizzle.error( match[0] );
-			}
+			// Sets one value
+			this.each(function() {
+				jQuery.data( this, key, value );
+			}) :
 
-			return match;
-		},
+			// Gets one value
+			// Try to fetch any internally stored data first
+			elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined;
+	},
 
-		"PSEUDO": function( match ) {
-			var excess,
-				unquoted = !match[5] && match[2];
+	removeData: function( key ) {
+		return this.each(function() {
+			jQuery.removeData( this, key );
+		});
+	}
+});
 
-			if ( matchExpr["CHILD"].test( match[0] ) ) {
-				return null;
-			}
 
-			// Accept quoted arguments as-is
-			if ( match[4] ) {
-				match[2] = match[4];
+jQuery.extend({
+	queue: function( elem, type, data ) {
+		var queue;
 
-			// Strip excess characters from unquoted arguments
-			} else if ( unquoted && rpseudo.test( unquoted ) &&
-				// Get excess from tokenize (recursively)
-				(excess = tokenize( unquoted, true )) &&
-				// advance to the next closing parenthesis
-				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+		if ( elem ) {
+			type = ( type || "fx" ) + "queue";
+			queue = jQuery._data( elem, type );
 
-				// excess is a negative index
-				match[0] = match[0].slice( 0, excess );
-				match[2] = unquoted.slice( 0, excess );
+			// Speed up dequeue by getting out quickly if this is just a lookup
+			if ( data ) {
+				if ( !queue || jQuery.isArray(data) ) {
+					queue = jQuery._data( elem, type, jQuery.makeArray(data) );
+				} else {
+					queue.push( data );
+				}
 			}
-
-			// Return only captures needed by the pseudo filter method (type and argument)
-			return match.slice( 0, 3 );
+			return queue || [];
 		}
 	},
 
-	filter: {
-
-		"TAG": function( nodeName ) {
-			if ( nodeName === "*" ) {
-				return function() { return true; };
-			}
+	dequeue: function( elem, type ) {
+		type = type || "fx";
 
-			nodeName = nodeName.replace( runescape, funescape ).toLowerCase();
-			return function( elem ) {
-				return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+		var queue = jQuery.queue( elem, type ),
+			startLength = queue.length,
+			fn = queue.shift(),
+			hooks = jQuery._queueHooks( elem, type ),
+			next = function() {
+				jQuery.dequeue( elem, type );
 			};
-		},
 
-		"CLASS": function( className ) {
-			var pattern = classCache[ className + " " ];
+		// If the fx queue is dequeued, always remove the progress sentinel
+		if ( fn === "inprogress" ) {
+			fn = queue.shift();
+			startLength--;
+		}
 
-			return pattern ||
-				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
-				classCache( className, function( elem ) {
-					return pattern.test( elem.className || (typeof elem.getAttribute !== strundefined && elem.getAttribute("class")) || "" );
-				});
-		},
+		if ( fn ) {
 
-		"ATTR": function( name, operator, check ) {
-			return function( elem ) {
-				var result = Sizzle.attr( elem, name );
+			// Add a progress sentinel to prevent the fx queue from being
+			// automatically dequeued
+			if ( type === "fx" ) {
+				queue.unshift( "inprogress" );
+			}
 
-				if ( result == null ) {
-					return operator === "!=";
-				}
-				if ( !operator ) {
-					return true;
-				}
+			// clear up the last queue stop function
+			delete hooks.stop;
+			fn.call( elem, next, hooks );
+		}
 
-				result += "";
+		if ( !startLength && hooks ) {
+			hooks.empty.fire();
+		}
+	},
 
-				return operator === "=" ? result === check :
-					operator === "!=" ? result !== check :
-					operator === "^=" ? check && result.indexOf( check ) === 0 :
-					operator === "*=" ? check && result.indexOf( check ) > -1 :
-					operator === "$=" ? check && result.slice( -check.length ) === check :
-					operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 :
-					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
-					false;
-			};
-		},
+	// not intended for public consumption - generates a queueHooks object, or returns the current one
+	_queueHooks: function( elem, type ) {
+		var key = type + "queueHooks";
+		return jQuery._data( elem, key ) || jQuery._data( elem, key, {
+			empty: jQuery.Callbacks("once memory").add(function() {
+				jQuery._removeData( elem, type + "queue" );
+				jQuery._removeData( elem, key );
+			})
+		});
+	}
+});
 
-		"CHILD": function( type, what, argument, first, last ) {
-			var simple = type.slice( 0, 3 ) !== "nth",
-				forward = type.slice( -4 ) !== "last",
-				ofType = what === "of-type";
+jQuery.fn.extend({
+	queue: function( type, data ) {
+		var setter = 2;
 
-			return first === 1 && last === 0 ?
+		if ( typeof type !== "string" ) {
+			data = type;
+			type = "fx";
+			setter--;
+		}
 
-				// Shortcut for :nth-*(n)
-				function( elem ) {
-					return !!elem.parentNode;
-				} :
+		if ( arguments.length < setter ) {
+			return jQuery.queue( this[0], type );
+		}
 
-				function( elem, context, xml ) {
-					var cache, outerCache, node, diff, nodeIndex, start,
-						dir = simple !== forward ? "nextSibling" : "previousSibling",
-						parent = elem.parentNode,
-						name = ofType && elem.nodeName.toLowerCase(),
-						useCache = !xml && !ofType;
+		return data === undefined ?
+			this :
+			this.each(function() {
+				var queue = jQuery.queue( this, type, data );
 
-					if ( parent ) {
+				// ensure a hooks for this queue
+				jQuery._queueHooks( this, type );
 
-						// :(first|last|only)-(child|of-type)
-						if ( simple ) {
-							while ( dir ) {
-								node = elem;
-								while ( (node = node[ dir ]) ) {
-									if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
-										return false;
-									}
-								}
-								// Reverse direction for :only-* (if we haven't yet done so)
-								start = dir = type === "only" && !start && "nextSibling";
-							}
-							return true;
-						}
+				if ( type === "fx" && queue[0] !== "inprogress" ) {
+					jQuery.dequeue( this, type );
+				}
+			});
+	},
+	dequeue: function( type ) {
+		return this.each(function() {
+			jQuery.dequeue( this, type );
+		});
+	},
+	clearQueue: function( type ) {
+		return this.queue( type || "fx", [] );
+	},
+	// Get a promise resolved when queues of a certain type
+	// are emptied (fx is the type by default)
+	promise: function( type, obj ) {
+		var tmp,
+			count = 1,
+			defer = jQuery.Deferred(),
+			elements = this,
+			i = this.length,
+			resolve = function() {
+				if ( !( --count ) ) {
+					defer.resolveWith( elements, [ elements ] );
+				}
+			};
 
-						start = [ forward ? parent.firstChild : parent.lastChild ];
+		if ( typeof type !== "string" ) {
+			obj = type;
+			type = undefined;
+		}
+		type = type || "fx";
 
-						// non-xml :nth-child(...) stores cache data on `parent`
-						if ( forward && useCache ) {
-							// Seek `elem` from a previously-cached index
-							outerCache = parent[ expando ] || (parent[ expando ] = {});
-							cache = outerCache[ type ] || [];
-							nodeIndex = cache[0] === dirruns && cache[1];
-							diff = cache[0] === dirruns && cache[2];
-							node = nodeIndex && parent.childNodes[ nodeIndex ];
+		while ( i-- ) {
+			tmp = jQuery._data( elements[ i ], type + "queueHooks" );
+			if ( tmp && tmp.empty ) {
+				count++;
+				tmp.empty.add( resolve );
+			}
+		}
+		resolve();
+		return defer.promise( obj );
+	}
+});
+var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source;
 
-							while ( (node = ++nodeIndex && node && node[ dir ] ||
+var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
 
-								// Fallback to seeking `elem` from the start
-								(diff = nodeIndex = 0) || start.pop()) ) {
+var isHidden = function( elem, el ) {
+		// isHidden might be called from jQuery#filter function;
+		// in that case, element will be second argument
+		elem = el || elem;
+		return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
+	};
 
-								// When found, cache indexes on `parent` and break
-								if ( node.nodeType === 1 && ++diff && node === elem ) {
-									outerCache[ type ] = [ dirruns, nodeIndex, diff ];
-									break;
-								}
-							}
 
-						// Use previously-cached element index if available
-						} else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
-							diff = cache[1];
 
-						// xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
-						} else {
-							// Use the same loop as above to seek `elem` from the start
-							while ( (node = ++nodeIndex && node && node[ dir ] ||
-								(diff = nodeIndex = 0) || start.pop()) ) {
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+	var i = 0,
+		length = elems.length,
+		bulk = key == null;
 
-								if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
-									// Cache the index of each encountered element
-									if ( useCache ) {
-										(node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
-									}
+	// Sets many values
+	if ( jQuery.type( key ) === "object" ) {
+		chainable = true;
+		for ( i in key ) {
+			jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
+		}
 
-									if ( node === elem ) {
-										break;
-									}
-								}
-							}
-						}
+	// Sets one value
+	} else if ( value !== undefined ) {
+		chainable = true;
 
-						// Incorporate the offset, then check against cycle size
-						diff -= last;
-						return diff === first || ( diff % first === 0 && diff / first >= 0 );
-					}
-				};
-		},
+		if ( !jQuery.isFunction( value ) ) {
+			raw = true;
+		}
 
-		"PSEUDO": function( pseudo, argument ) {
-			// pseudo-class names are case-insensitive
-			// http://www.w3.org/TR/selectors/#pseudo-classes
-			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
-			// Remember that setFilters inherits from pseudos
-			var args,
-				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
-					Sizzle.error( "unsupported pseudo: " + pseudo );
+		if ( bulk ) {
+			// Bulk operations run against the entire set
+			if ( raw ) {
+				fn.call( elems, value );
+				fn = null;
 
-			// The user may use createPseudo to indicate that
-			// arguments are needed to create the filter function
-			// just as Sizzle does
-			if ( fn[ expando ] ) {
-				return fn( argument );
+			// ...except when executing function values
+			} else {
+				bulk = fn;
+				fn = function( elem, key, value ) {
+					return bulk.call( jQuery( elem ), value );
+				};
 			}
+		}
 
-			// But maintain support for old signatures
-			if ( fn.length > 1 ) {
-				args = [ pseudo, pseudo, "", argument ];
-				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
-					markFunction(function( seed, matches ) {
-						var idx,
-							matched = fn( seed, argument ),
-							i = matched.length;
-						while ( i-- ) {
-							idx = indexOf.call( seed, matched[i] );
-							seed[ idx ] = !( matches[ idx ] = matched[i] );
-						}
-					}) :
-					function( elem ) {
-						return fn( elem, 0, args );
-					};
+		if ( fn ) {
+			for ( ; i < length; i++ ) {
+				fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
 			}
-
-			return fn;
 		}
-	},
+	}
 
-	pseudos: {
-		// Potentially complex pseudos
-		"not": markFunction(function( selector ) {
-			// Trim the selector passed to compile
-			// to avoid treating leading and trailing
-			// spaces as combinators
-			var input = [],
-				results = [],
-				matcher = compile( selector.replace( rtrim, "$1" ) );
+	return chainable ?
+		elems :
 
-			return matcher[ expando ] ?
-				markFunction(function( seed, matches, context, xml ) {
-					var elem,
-						unmatched = matcher( seed, null, xml, [] ),
-						i = seed.length;
+		// Gets
+		bulk ?
+			fn.call( elems ) :
+			length ? fn( elems[0], key ) : emptyGet;
+};
+var rcheckableType = (/^(?:checkbox|radio)$/i);
 
-					// Match elements unmatched by `matcher`
-					while ( i-- ) {
-						if ( (elem = unmatched[i]) ) {
-							seed[i] = !(matches[i] = elem);
-						}
-					}
-				}) :
-				function( elem, context, xml ) {
-					input[0] = elem;
-					matcher( input, null, xml, results );
-					return !results.pop();
-				};
-		}),
 
-		"has": markFunction(function( selector ) {
-			return function( elem ) {
-				return Sizzle( selector, elem ).length > 0;
-			};
-		}),
 
-		"contains": markFunction(function( text ) {
-			return function( elem ) {
-				return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
-			};
-		}),
+(function() {
+	// Minified: var a,b,c
+	var input = document.createElement( "input" ),
+		div = document.createElement( "div" ),
+		fragment = document.createDocumentFragment();
 
-		// "Whether an element is represented by a :lang() selector
-		// is based solely on the element's language value
-		// being equal to the identifier C,
-		// or beginning with the identifier C immediately followed by "-".
-		// The matching of C against the element's language value is performed case-insensitively.
-		// The identifier C does not have to be a valid language name."
-		// http://www.w3.org/TR/selectors/#lang-pseudo
-		"lang": markFunction( function( lang ) {
-			// lang value must be a valid identifider
-			if ( !ridentifier.test(lang || "") ) {
-				Sizzle.error( "unsupported lang: " + lang );
-			}
-			lang = lang.replace( runescape, funescape ).toLowerCase();
-			return function( elem ) {
-				var elemLang;
-				do {
-					if ( (elemLang = documentIsXML ?
-						elem.getAttribute("xml:lang") || elem.getAttribute("lang") :
-						elem.lang) ) {
-
-						elemLang = elemLang.toLowerCase();
-						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
-					}
-				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
-				return false;
-			};
-		}),
-
-		// Miscellaneous
-		"target": function( elem ) {
-			var hash = window.location && window.location.hash;
-			return hash && hash.slice( 1 ) === elem.id;
-		},
-
-		"root": function( elem ) {
-			return elem === docElem;
-		},
+	// Setup
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
 
-		"focus": function( elem ) {
-			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
-		},
+	// IE strips leading whitespace when .innerHTML is used
+	support.leadingWhitespace = div.firstChild.nodeType === 3;
 
-		// Boolean properties
-		"enabled": function( elem ) {
-			return elem.disabled === false;
-		},
+	// Make sure that tbody elements aren't automatically inserted
+	// IE will insert them into empty tables
+	support.tbody = !div.getElementsByTagName( "tbody" ).length;
 
-		"disabled": function( elem ) {
-			return elem.disabled === true;
-		},
+	// Make sure that link elements get serialized correctly by innerHTML
+	// This requires a wrapper element in IE
+	support.htmlSerialize = !!div.getElementsByTagName( "link" ).length;
 
-		"checked": function( elem ) {
-			// In CSS3, :checked should return both checked and selected elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			var nodeName = elem.nodeName.toLowerCase();
-			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
-		},
+	// Makes sure cloning an html5 element does not cause problems
+	// Where outerHTML is undefined, this still works
+	support.html5Clone =
+		document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>";
 
-		"selected": function( elem ) {
-			// Accessing this property makes selected-by-default
-			// options in Safari work properly
-			if ( elem.parentNode ) {
-				elem.parentNode.selectedIndex;
-			}
+	// Check if a disconnected checkbox will retain its checked
+	// value of true after appended to the DOM (IE6/7)
+	input.type = "checkbox";
+	input.checked = true;
+	fragment.appendChild( input );
+	support.appendChecked = input.checked;
 
-			return elem.selected === true;
-		},
+	// Make sure textarea (and checkbox) defaultValue is properly cloned
+	// Support: IE6-IE11+
+	div.innerHTML = "<textarea>x</textarea>";
+	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
 
-		// Contents
-		"empty": function( elem ) {
-			// http://www.w3.org/TR/selectors/#empty-pseudo
-			// :empty is only affected by element nodes and content nodes(including text(3), cdata(4)),
-			//   not comment, processing instructions, or others
-			// Thanks to Diego Perini for the nodeName shortcut
-			//   Greater than "@" means alpha characters (specifically not starting with "#" or "?")
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				if ( elem.nodeName > "@" || elem.nodeType === 3 || elem.nodeType === 4 ) {
-					return false;
-				}
-			}
-			return true;
-		},
+	// #11217 - WebKit loses check when the name is after the checked attribute
+	fragment.appendChild( div );
+	div.innerHTML = "<input type='radio' checked='checked' name='t'/>";
 
-		"parent": function( elem ) {
-			return !Expr.pseudos["empty"]( elem );
-		},
+	// Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3
+	// old WebKit doesn't clone checked state correctly in fragments
+	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
 
-		// Element/input types
-		"header": function( elem ) {
-			return rheader.test( elem.nodeName );
-		},
+	// Support: IE<9
+	// Opera does not clone events (and typeof div.attachEvent === undefined).
+	// IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
+	support.noCloneEvent = true;
+	if ( div.attachEvent ) {
+		div.attachEvent( "onclick", function() {
+			support.noCloneEvent = false;
+		});
 
-		"input": function( elem ) {
-			return rinputs.test( elem.nodeName );
-		},
+		div.cloneNode( true ).click();
+	}
 
-		"button": function( elem ) {
-			var name = elem.nodeName.toLowerCase();
-			return name === "input" && elem.type === "button" || name === "button";
-		},
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
+})();
 
-		"text": function( elem ) {
-			var attr;
-			// IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc)
-			// use getAttribute instead to test this case
-			return elem.nodeName.toLowerCase() === "input" &&
-				elem.type === "text" &&
-				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === elem.type );
-		},
 
-		// Position-in-collection
-		"first": createPositionalPseudo(function() {
-			return [ 0 ];
-		}),
+(function() {
+	var i, eventName,
+		div = document.createElement( "div" );
 
-		"last": createPositionalPseudo(function( matchIndexes, length ) {
-			return [ length - 1 ];
-		}),
+	// Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event)
+	for ( i in { submit: true, change: true, focusin: true }) {
+		eventName = "on" + i;
 
-		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			return [ argument < 0 ? argument + length : argument ];
-		}),
+		if ( !(support[ i + "Bubbles" ] = eventName in window) ) {
+			// Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP)
+			div.setAttribute( eventName, "t" );
+			support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false;
+		}
+	}
 
-		"even": createPositionalPseudo(function( matchIndexes, length ) {
-			var i = 0;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
 
-		"odd": createPositionalPseudo(function( matchIndexes, length ) {
-			var i = 1;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
 
-		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			var i = argument < 0 ? argument + length : argument;
-			for ( ; --i >= 0; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
+var rformElems = /^(?:input|select|textarea)$/i,
+	rkeyEvent = /^key/,
+	rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/,
+	rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+	rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
 
-		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			var i = argument < 0 ? argument + length : argument;
-			for ( ; ++i < length; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		})
-	}
-};
+function returnTrue() {
+	return true;
+}
 
-// Add button/input type pseudos
-for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
-	Expr.pseudos[ i ] = createInputPseudo( i );
+function returnFalse() {
+	return false;
 }
-for ( i in { submit: true, reset: true } ) {
-	Expr.pseudos[ i ] = createButtonPseudo( i );
+
+function safeActiveElement() {
+	try {
+		return document.activeElement;
+	} catch ( err ) { }
 }
 
-function tokenize( selector, parseOnly ) {
-	var matched, match, tokens, type,
-		soFar, groups, preFilters,
-		cached = tokenCache[ selector + " " ];
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
 
-	if ( cached ) {
-		return parseOnly ? 0 : cached.slice( 0 );
-	}
+	global: {},
 
-	soFar = selector;
-	groups = [];
-	preFilters = Expr.preFilter;
+	add: function( elem, types, handler, data, selector ) {
+		var tmp, events, t, handleObjIn,
+			special, eventHandle, handleObj,
+			handlers, type, namespaces, origType,
+			elemData = jQuery._data( elem );
 
-	while ( soFar ) {
+		// Don't attach events to noData or text/comment nodes (but allow plain objects)
+		if ( !elemData ) {
+			return;
+		}
 
-		// Comma and first run
-		if ( !matched || (match = rcomma.exec( soFar )) ) {
-			if ( match ) {
-				// Don't consume trailing commas as valid
-				soFar = soFar.slice( match[0].length ) || soFar;
-			}
-			groups.push( tokens = [] );
+		// Caller can pass in an object of custom data in lieu of the handler
+		if ( handler.handler ) {
+			handleObjIn = handler;
+			handler = handleObjIn.handler;
+			selector = handleObjIn.selector;
 		}
 
-		matched = false;
+		// Make sure that the handler has a unique ID, used to find/remove it later
+		if ( !handler.guid ) {
+			handler.guid = jQuery.guid++;
+		}
 
-		// Combinators
-		if ( (match = rcombinators.exec( soFar )) ) {
-			matched = match.shift();
-			tokens.push( {
-				value: matched,
-				// Cast descendant combinators to space
-				type: match[0].replace( rtrim, " " )
-			} );
-			soFar = soFar.slice( matched.length );
+		// Init the element's event structure and main handler, if this is the first
+		if ( !(events = elemData.events) ) {
+			events = elemData.events = {};
+		}
+		if ( !(eventHandle = elemData.handle) ) {
+			eventHandle = elemData.handle = function( e ) {
+				// Discard the second event of a jQuery.event.trigger() and
+				// when an event is called after a page has unloaded
+				return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ?
+					jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
+					undefined;
+			};
+			// Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
+			eventHandle.elem = elem;
 		}
 
-		// Filters
-		for ( type in Expr.filter ) {
-			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
-				(match = preFilters[ type ]( match ))) ) {
-				matched = match.shift();
-				tokens.push( {
-					value: matched,
-					type: type,
-					matches: match
-				} );
-				soFar = soFar.slice( matched.length );
+		// Handle multiple events separated by a space
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+
+			// There *must* be a type, no attaching namespace-only handlers
+			if ( !type ) {
+				continue;
 			}
-		}
 
-		if ( !matched ) {
-			break;
-		}
-	}
+			// If event changes its type, use the special event handlers for the changed type
+			special = jQuery.event.special[ type ] || {};
 
-	// Return the length of the invalid excess
-	// if we're just parsing
-	// Otherwise, throw an error or return tokens
-	return parseOnly ?
-		soFar.length :
-		soFar ?
-			Sizzle.error( selector ) :
-			// Cache the tokens
-			tokenCache( selector, groups ).slice( 0 );
-}
+			// If selector defined, determine special event api type, otherwise given type
+			type = ( selector ? special.delegateType : special.bindType ) || type;
 
-function toSelector( tokens ) {
-	var i = 0,
-		len = tokens.length,
-		selector = "";
-	for ( ; i < len; i++ ) {
-		selector += tokens[i].value;
-	}
-	return selector;
-}
+			// Update special based on newly reset type
+			special = jQuery.event.special[ type ] || {};
 
-function addCombinator( matcher, combinator, base ) {
-	var dir = combinator.dir,
-		checkNonElements = base && dir === "parentNode",
-		doneName = done++;
+			// handleObj is passed to all event handlers
+			handleObj = jQuery.extend({
+				type: type,
+				origType: origType,
+				data: data,
+				handler: handler,
+				guid: handler.guid,
+				selector: selector,
+				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+				namespace: namespaces.join(".")
+			}, handleObjIn );
 
-	return combinator.first ?
-		// Check against closest ancestor/preceding element
-		function( elem, context, xml ) {
-			while ( (elem = elem[ dir ]) ) {
-				if ( elem.nodeType === 1 || checkNonElements ) {
-					return matcher( elem, context, xml );
-				}
-			}
-		} :
+			// Init the event handler queue if we're the first
+			if ( !(handlers = events[ type ]) ) {
+				handlers = events[ type ] = [];
+				handlers.delegateCount = 0;
 
-		// Check against all ancestor/preceding elements
-		function( elem, context, xml ) {
-			var data, cache, outerCache,
-				dirkey = dirruns + " " + doneName;
+				// Only use addEventListener/attachEvent if the special events handler returns false
+				if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+					// Bind the global event handler to the element
+					if ( elem.addEventListener ) {
+						elem.addEventListener( type, eventHandle, false );
 
-			// We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
-			if ( xml ) {
-				while ( (elem = elem[ dir ]) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						if ( matcher( elem, context, xml ) ) {
-							return true;
-						}
-					}
-				}
-			} else {
-				while ( (elem = elem[ dir ]) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						outerCache = elem[ expando ] || (elem[ expando ] = {});
-						if ( (cache = outerCache[ dir ]) && cache[0] === dirkey ) {
-							if ( (data = cache[1]) === true || data === cachedruns ) {
-								return data === true;
-							}
-						} else {
-							cache = outerCache[ dir ] = [ dirkey ];
-							cache[1] = matcher( elem, context, xml ) || cachedruns;
-							if ( cache[1] === true ) {
-								return true;
-							}
-						}
+					} else if ( elem.attachEvent ) {
+						elem.attachEvent( "on" + type, eventHandle );
 					}
 				}
 			}
-		};
-}
-
-function elementMatcher( matchers ) {
-	return matchers.length > 1 ?
-		function( elem, context, xml ) {
-			var i = matchers.length;
-			while ( i-- ) {
-				if ( !matchers[i]( elem, context, xml ) ) {
-					return false;
-				}
-			}
-			return true;
-		} :
-		matchers[0];
-}
 
-function condense( unmatched, map, filter, context, xml ) {
-	var elem,
-		newUnmatched = [],
-		i = 0,
-		len = unmatched.length,
-		mapped = map != null;
+			if ( special.add ) {
+				special.add.call( elem, handleObj );
 
-	for ( ; i < len; i++ ) {
-		if ( (elem = unmatched[i]) ) {
-			if ( !filter || filter( elem, context, xml ) ) {
-				newUnmatched.push( elem );
-				if ( mapped ) {
-					map.push( i );
+				if ( !handleObj.handler.guid ) {
+					handleObj.handler.guid = handler.guid;
 				}
 			}
-		}
-	}
-
-	return newUnmatched;
-}
-
-function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
-	if ( postFilter && !postFilter[ expando ] ) {
-		postFilter = setMatcher( postFilter );
-	}
-	if ( postFinder && !postFinder[ expando ] ) {
-		postFinder = setMatcher( postFinder, postSelector );
-	}
-	return markFunction(function( seed, results, context, xml ) {
-		var temp, i, elem,
-			preMap = [],
-			postMap = [],
-			preexisting = results.length,
-
-			// Get initial elements from seed or context
-			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
 
-			// Prefilter to get matcher input, preserving a map for seed-results synchronization
-			matcherIn = preFilter && ( seed || !selector ) ?
-				condense( elems, preMap, preFilter, context, xml ) :
-				elems,
+			// Add to the element's handler list, delegates in front
+			if ( selector ) {
+				handlers.splice( handlers.delegateCount++, 0, handleObj );
+			} else {
+				handlers.push( handleObj );
+			}
 
-			matcherOut = matcher ?
-				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
-				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+			// Keep track of which events have ever been used, for event optimization
+			jQuery.event.global[ type ] = true;
+		}
 
-					// ...intermediate processing is necessary
-					[] :
+		// Nullify elem to prevent memory leaks in IE
+		elem = null;
+	},
 
-					// ...otherwise use results directly
-					results :
-				matcherIn;
+	// Detach an event or set of events from an element
+	remove: function( elem, types, handler, selector, mappedTypes ) {
+		var j, handleObj, tmp,
+			origCount, t, events,
+			special, handlers, type,
+			namespaces, origType,
+			elemData = jQuery.hasData( elem ) && jQuery._data( elem );
 
-		// Find primary matches
-		if ( matcher ) {
-			matcher( matcherIn, matcherOut, context, xml );
+		if ( !elemData || !(events = elemData.events) ) {
+			return;
 		}
 
-		// Apply postFilter
-		if ( postFilter ) {
-			temp = condense( matcherOut, postMap );
-			postFilter( temp, [], context, xml );
+		// Once for each type.namespace in types; type may be omitted
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
 
-			// Un-match failing elements by moving them back to matcherIn
-			i = temp.length;
-			while ( i-- ) {
-				if ( (elem = temp[i]) ) {
-					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+			// Unbind all events (on this namespace, if provided) for the element
+			if ( !type ) {
+				for ( type in events ) {
+					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
 				}
+				continue;
 			}
-		}
 
-		if ( seed ) {
-			if ( postFinder || preFilter ) {
-				if ( postFinder ) {
-					// Get the final matcherOut by condensing this intermediate into postFinder contexts
-					temp = [];
-					i = matcherOut.length;
-					while ( i-- ) {
-						if ( (elem = matcherOut[i]) ) {
-							// Restore matcherIn since elem is not yet a final match
-							temp.push( (matcherIn[i] = elem) );
-						}
-					}
-					postFinder( null, (matcherOut = []), temp, xml );
-				}
+			special = jQuery.event.special[ type ] || {};
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+			handlers = events[ type ] || [];
+			tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
 
-				// Move matched elements from seed to results to keep them synchronized
-				i = matcherOut.length;
-				while ( i-- ) {
-					if ( (elem = matcherOut[i]) &&
-						(temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) {
+			// Remove matching events
+			origCount = j = handlers.length;
+			while ( j-- ) {
+				handleObj = handlers[ j ];
 
-						seed[temp] = !(results[temp] = elem);
+				if ( ( mappedTypes || origType === handleObj.origType ) &&
+					( !handler || handler.guid === handleObj.guid ) &&
+					( !tmp || tmp.test( handleObj.namespace ) ) &&
+					( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
+					handlers.splice( j, 1 );
+
+					if ( handleObj.selector ) {
+						handlers.delegateCount--;
+					}
+					if ( special.remove ) {
+						special.remove.call( elem, handleObj );
 					}
 				}
 			}
 
-		// Add elements to results, through postFinder if defined
-		} else {
-			matcherOut = condense(
-				matcherOut === results ?
-					matcherOut.splice( preexisting, matcherOut.length ) :
-					matcherOut
-			);
-			if ( postFinder ) {
-				postFinder( null, results, matcherOut, xml );
-			} else {
-				push.apply( results, matcherOut );
+			// Remove generic event handler if we removed something and no more handlers exist
+			// (avoids potential for endless recursion during removal of special event handlers)
+			if ( origCount && !handlers.length ) {
+				if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+					jQuery.removeEvent( elem, type, elemData.handle );
+				}
+
+				delete events[ type ];
 			}
 		}
-	});
-}
 
-function matcherFromTokens( tokens ) {
-	var checkContext, matcher, j,
-		len = tokens.length,
-		leadingRelative = Expr.relative[ tokens[0].type ],
-		implicitRelative = leadingRelative || Expr.relative[" "],
-		i = leadingRelative ? 1 : 0,
+		// Remove the expando if it's no longer used
+		if ( jQuery.isEmptyObject( events ) ) {
+			delete elemData.handle;
 
-		// The foundational matcher ensures that elements are reachable from top-level context(s)
-		matchContext = addCombinator( function( elem ) {
-			return elem === checkContext;
-		}, implicitRelative, true ),
-		matchAnyContext = addCombinator( function( elem ) {
-			return indexOf.call( checkContext, elem ) > -1;
-		}, implicitRelative, true ),
-		matchers = [ function( elem, context, xml ) {
-			return ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
-				(checkContext = context).nodeType ?
-					matchContext( elem, context, xml ) :
-					matchAnyContext( elem, context, xml ) );
-		} ];
-
-	for ( ; i < len; i++ ) {
-		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
-			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
-		} else {
-			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
-
-			// Return special upon seeing a positional matcher
-			if ( matcher[ expando ] ) {
-				// Find the next relative operator (if any) for proper handling
-				j = ++i;
-				for ( ; j < len; j++ ) {
-					if ( Expr.relative[ tokens[j].type ] ) {
-						break;
-					}
-				}
-				return setMatcher(
-					i > 1 && elementMatcher( matchers ),
-					i > 1 && toSelector( tokens.slice( 0, i - 1 ) ).replace( rtrim, "$1" ),
-					matcher,
-					i < j && matcherFromTokens( tokens.slice( i, j ) ),
-					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
-					j < len && toSelector( tokens )
-				);
-			}
-			matchers.push( matcher );
+			// removeData also checks for emptiness and clears the expando if empty
+			// so use it instead of delete
+			jQuery._removeData( elem, "events" );
 		}
-	}
+	},
 
-	return elementMatcher( matchers );
-}
+	trigger: function( event, data, elem, onlyHandlers ) {
+		var handle, ontype, cur,
+			bubbleType, special, tmp, i,
+			eventPath = [ elem || document ],
+			type = hasOwn.call( event, "type" ) ? event.type : event,
+			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
 
-function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
-	// A counter to specify which element is currently being matched
-	var matcherCachedRuns = 0,
-		bySet = setMatchers.length > 0,
-		byElement = elementMatchers.length > 0,
-		superMatcher = function( seed, context, xml, results, expandContext ) {
-			var elem, j, matcher,
-				setMatched = [],
-				matchedCount = 0,
-				i = "0",
-				unmatched = seed && [],
-				outermost = expandContext != null,
-				contextBackup = outermostContext,
-				// We must always have either seed elements or context
-				elems = seed || byElement && Expr.find["TAG"]( "*", expandContext && context.parentNode || context ),
-				// Use integer dirruns iff this is the outermost matcher
-				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1);
+		cur = tmp = elem = elem || document;
 
-			if ( outermost ) {
-				outermostContext = context !== document && context;
-				cachedruns = matcherCachedRuns;
-			}
+		// Don't do events on text and comment nodes
+		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+			return;
+		}
 
-			// Add elements passing elementMatchers directly to results
-			// Keep `i` a string if there are no elements so `matchedCount` will be "00" below
-			for ( ; (elem = elems[i]) != null; i++ ) {
-				if ( byElement && elem ) {
-					j = 0;
-					while ( (matcher = elementMatchers[j++]) ) {
-						if ( matcher( elem, context, xml ) ) {
-							results.push( elem );
-							break;
-						}
-					}
-					if ( outermost ) {
-						dirruns = dirrunsUnique;
-						cachedruns = ++matcherCachedRuns;
-					}
-				}
+		// focus/blur morphs to focusin/out; ensure we're not firing them right now
+		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+			return;
+		}
 
-				// Track unmatched elements for set filters
-				if ( bySet ) {
-					// They will have gone through all possible matchers
-					if ( (elem = !matcher && elem) ) {
-						matchedCount--;
-					}
+		if ( type.indexOf(".") >= 0 ) {
+			// Namespaced trigger; create a regexp to match event type in handle()
+			namespaces = type.split(".");
+			type = namespaces.shift();
+			namespaces.sort();
+		}
+		ontype = type.indexOf(":") < 0 && "on" + type;
 
-					// Lengthen the array for every element, matched or not
-					if ( seed ) {
-						unmatched.push( elem );
-					}
-				}
-			}
+		// Caller can pass in a jQuery.Event object, Object, or just an event type string
+		event = event[ jQuery.expando ] ?
+			event :
+			new jQuery.Event( type, typeof event === "object" && event );
 
-			// Apply set filters to unmatched elements
-			matchedCount += i;
-			if ( bySet && i !== matchedCount ) {
-				j = 0;
-				while ( (matcher = setMatchers[j++]) ) {
-					matcher( unmatched, setMatched, context, xml );
-				}
+		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+		event.isTrigger = onlyHandlers ? 2 : 3;
+		event.namespace = namespaces.join(".");
+		event.namespace_re = event.namespace ?
+			new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
+			null;
 
-				if ( seed ) {
-					// Reintegrate element matches to eliminate the need for sorting
-					if ( matchedCount > 0 ) {
-						while ( i-- ) {
-							if ( !(unmatched[i] || setMatched[i]) ) {
-								setMatched[i] = pop.call( results );
-							}
-						}
-					}
+		// Clean up the event in case it is being reused
+		event.result = undefined;
+		if ( !event.target ) {
+			event.target = elem;
+		}
 
-					// Discard index placeholder values to get only actual matches
-					setMatched = condense( setMatched );
-				}
+		// Clone any incoming data and prepend the event, creating the handler arg list
+		data = data == null ?
+			[ event ] :
+			jQuery.makeArray( data, [ event ] );
 
-				// Add matches to results
-				push.apply( results, setMatched );
+		// Allow special events to draw outside the lines
+		special = jQuery.event.special[ type ] || {};
+		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+			return;
+		}
 
-				// Seedless set matches succeeding multiple successful matchers stipulate sorting
-				if ( outermost && !seed && setMatched.length > 0 &&
-					( matchedCount + setMatchers.length ) > 1 ) {
+		// Determine event propagation path in advance, per W3C events spec (#9951)
+		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+		if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
 
-					Sizzle.uniqueSort( results );
-				}
+			bubbleType = special.delegateType || type;
+			if ( !rfocusMorph.test( bubbleType + type ) ) {
+				cur = cur.parentNode;
+			}
+			for ( ; cur; cur = cur.parentNode ) {
+				eventPath.push( cur );
+				tmp = cur;
 			}
 
-			// Override manipulation of globals by nested matchers
-			if ( outermost ) {
-				dirruns = dirrunsUnique;
-				outermostContext = contextBackup;
+			// Only add window if we got to document (e.g., not plain obj or detached DOM)
+			if ( tmp === (elem.ownerDocument || document) ) {
+				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
 			}
+		}
 
-			return unmatched;
-		};
+		// Fire handlers on the event path
+		i = 0;
+		while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
 
-	return bySet ?
-		markFunction( superMatcher ) :
-		superMatcher;
-}
+			event.type = i > 1 ?
+				bubbleType :
+				special.bindType || type;
 
-compile = Sizzle.compile = function( selector, group /* Internal Use Only */ ) {
-	var i,
-		setMatchers = [],
-		elementMatchers = [],
-		cached = compilerCache[ selector + " " ];
+			// jQuery handler
+			handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
+			if ( handle ) {
+				handle.apply( cur, data );
+			}
 
-	if ( !cached ) {
-		// Generate a function of recursive functions that can be used to check each element
-		if ( !group ) {
-			group = tokenize( selector );
-		}
-		i = group.length;
-		while ( i-- ) {
-			cached = matcherFromTokens( group[i] );
-			if ( cached[ expando ] ) {
-				setMatchers.push( cached );
-			} else {
-				elementMatchers.push( cached );
+			// Native handler
+			handle = ontype && cur[ ontype ];
+			if ( handle && handle.apply && jQuery.acceptData( cur ) ) {
+				event.result = handle.apply( cur, data );
+				if ( event.result === false ) {
+					event.preventDefault();
+				}
 			}
 		}
+		event.type = type;
 
-		// Cache the compiled function
-		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
-	}
-	return cached;
-};
-
-function multipleContexts( selector, contexts, results ) {
-	var i = 0,
-		len = contexts.length;
-	for ( ; i < len; i++ ) {
-		Sizzle( selector, contexts[i], results );
-	}
-	return results;
-}
-
-function select( selector, context, results, seed ) {
-	var i, tokens, token, type, find,
-		match = tokenize( selector );
-
-	if ( !seed ) {
-		// Try to minimize operations if there is only one group
-		if ( match.length === 1 ) {
+		// If nobody prevented the default action, do it now
+		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
 
-			// Take a shortcut and set the context if the root selector is an ID
-			tokens = match[0] = match[0].slice( 0 );
-			if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
-					context.nodeType === 9 && !documentIsXML &&
-					Expr.relative[ tokens[1].type ] ) {
+			if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) &&
+				jQuery.acceptData( elem ) ) {
 
-				context = Expr.find["ID"]( token.matches[0].replace( runescape, funescape ), context )[0];
-				if ( !context ) {
-					return results;
-				}
+				// Call a native DOM method on the target with the same name name as the event.
+				// Can't use an .isFunction() check here because IE6/7 fails that test.
+				// Don't do default actions on window, that's where global variables be (#6170)
+				if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
 
-				selector = selector.slice( tokens.shift().value.length );
-			}
+					// Don't re-trigger an onFOO event when we call its FOO() method
+					tmp = elem[ ontype ];
 
-			// Fetch a seed set for right-to-left matching
-			i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
-			while ( i-- ) {
-				token = tokens[i];
+					if ( tmp ) {
+						elem[ ontype ] = null;
+					}
 
-				// Abort if we hit a combinator
-				if ( Expr.relative[ (type = token.type) ] ) {
-					break;
-				}
-				if ( (find = Expr.find[ type ]) ) {
-					// Search, expanding context for leading sibling combinators
-					if ( (seed = find(
-						token.matches[0].replace( runescape, funescape ),
-						rsibling.test( tokens[0].type ) && context.parentNode || context
-					)) ) {
-
-						// If seed is empty or no tokens remain, we can return early
-						tokens.splice( i, 1 );
-						selector = seed.length && toSelector( tokens );
-						if ( !selector ) {
-							push.apply( results, slice.call( seed, 0 ) );
-							return results;
-						}
+					// Prevent re-triggering of the same event, since we already bubbled it above
+					jQuery.event.triggered = type;
+					try {
+						elem[ type ]();
+					} catch ( e ) {
+						// IE<9 dies on focus/blur to hidden element (#1486,#12518)
+						// only reproducible on winXP IE8 native, not IE9 in IE8 mode
+					}
+					jQuery.event.triggered = undefined;
 
-						break;
+					if ( tmp ) {
+						elem[ ontype ] = tmp;
 					}
 				}
 			}
 		}
-	}
 
-	// Compile and execute a filtering function
-	// Provide `match` to avoid retokenization if we modified the selector above
-	compile( selector, match )(
-		seed,
-		context,
-		documentIsXML,
-		results,
-		rsibling.test( selector )
-	);
-	return results;
-}
+		return event.result;
+	},
 
-// Deprecated
-Expr.pseudos["nth"] = Expr.pseudos["eq"];
+	dispatch: function( event ) {
 
-// Easy API for creating new setFilters
-function setFilters() {}
-Expr.filters = setFilters.prototype = Expr.pseudos;
-Expr.setFilters = new setFilters();
+		// Make a writable jQuery.Event from the native event object
+		event = jQuery.event.fix( event );
 
-// Initialize with the default document
-setDocument();
+		var i, ret, handleObj, matched, j,
+			handlerQueue = [],
+			args = slice.call( arguments ),
+			handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
+			special = jQuery.event.special[ event.type ] || {};
 
-// Override sizzle attribute retrieval
-Sizzle.attr = jQuery.attr;
-jQuery.find = Sizzle;
-jQuery.expr = Sizzle.selectors;
-jQuery.expr[":"] = jQuery.expr.pseudos;
-jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = Sizzle.getText;
-jQuery.isXMLDoc = Sizzle.isXML;
-jQuery.contains = Sizzle.contains;
+		// Use the fix-ed jQuery.Event rather than the (read-only) native event
+		args[0] = event;
+		event.delegateTarget = this;
 
+		// Call the preDispatch hook for the mapped type, and let it bail if desired
+		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+			return;
+		}
 
-})( window );
-var runtil = /Until$/,
-	rparentsprev = /^(?:parents|prev(?:Until|All))/,
-	isSimple = /^.[^:#\[\.,]*$/,
-	rneedsContext = jQuery.expr.match.needsContext,
-	// methods guaranteed to produce a unique set when starting from a unique set
-	guaranteedUnique = {
-		children: true,
-		contents: true,
-		next: true,
-		prev: true
-	};
+		// Determine handlers
+		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
 
-jQuery.fn.extend({
-	find: function( selector ) {
-		var i, ret, self,
-			len = this.length;
+		// Run delegates first; they may want to stop propagation beneath us
+		i = 0;
+		while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
+			event.currentTarget = matched.elem;
 
-		if ( typeof selector !== "string" ) {
-			self = this;
-			return this.pushStack( jQuery( selector ).filter(function() {
-				for ( i = 0; i < len; i++ ) {
-					if ( jQuery.contains( self[ i ], this ) ) {
-						return true;
+			j = 0;
+			while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
+
+				// Triggered event must either 1) have no namespace, or
+				// 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
+				if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
+
+					event.handleObj = handleObj;
+					event.data = handleObj.data;
+
+					ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
+							.apply( matched.elem, args );
+
+					if ( ret !== undefined ) {
+						if ( (event.result = ret) === false ) {
+							event.preventDefault();
+							event.stopPropagation();
+						}
 					}
 				}
-			}) );
+			}
 		}
 
-		ret = [];
-		for ( i = 0; i < len; i++ ) {
-			jQuery.find( selector, this[ i ], ret );
+		// Call the postDispatch hook for the mapped type
+		if ( special.postDispatch ) {
+			special.postDispatch.call( this, event );
 		}
 
-		// Needed because $( selector, context ) becomes $( context ).find( selector )
-		ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
-		ret.selector = ( this.selector ? this.selector + " " : "" ) + selector;
-		return ret;
+		return event.result;
 	},
 
-	has: function( target ) {
-		var i,
-			targets = jQuery( target, this ),
-			len = targets.length;
+	handlers: function( event, handlers ) {
+		var sel, handleObj, matches, i,
+			handlerQueue = [],
+			delegateCount = handlers.delegateCount,
+			cur = event.target;
 
-		return this.filter(function() {
-			for ( i = 0; i < len; i++ ) {
-				if ( jQuery.contains( this, targets[i] ) ) {
-					return true;
+		// Find delegate handlers
+		// Black-hole SVG <use> instance trees (#13180)
+		// Avoid non-left-click bubbling in Firefox (#3861)
+		if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
+
+			/* jshint eqeqeq: false */
+			for ( ; cur != this; cur = cur.parentNode || this ) {
+				/* jshint eqeqeq: true */
+
+				// Don't check non-elements (#13208)
+				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
+				if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
+					matches = [];
+					for ( i = 0; i < delegateCount; i++ ) {
+						handleObj = handlers[ i ];
+
+						// Don't conflict with Object.prototype properties (#13203)
+						sel = handleObj.selector + " ";
+
+						if ( matches[ sel ] === undefined ) {
+							matches[ sel ] = handleObj.needsContext ?
+								jQuery( sel, this ).index( cur ) >= 0 :
+								jQuery.find( sel, this, null, [ cur ] ).length;
+						}
+						if ( matches[ sel ] ) {
+							matches.push( handleObj );
+						}
+					}
+					if ( matches.length ) {
+						handlerQueue.push({ elem: cur, handlers: matches });
+					}
 				}
 			}
-		});
-	},
-
-	not: function( selector ) {
-		return this.pushStack( winnow(this, selector, false) );
-	},
+		}
 
-	filter: function( selector ) {
-		return this.pushStack( winnow(this, selector, true) );
-	},
+		// Add the remaining (directly-bound) handlers
+		if ( delegateCount < handlers.length ) {
+			handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
+		}
 
-	is: function( selector ) {
-		return !!selector && (
-			typeof selector === "string" ?
-				// If this is a positional/relative selector, check membership in the returned set
-				// so $("p:first").is("p:last") won't return true for a doc with two "p".
-				rneedsContext.test( selector ) ?
-					jQuery( selector, this.context ).index( this[0] ) >= 0 :
-					jQuery.filter( selector, this ).length > 0 :
-				this.filter( selector ).length > 0 );
+		return handlerQueue;
 	},
 
-	closest: function( selectors, context ) {
-		var cur,
-			i = 0,
-			l = this.length,
-			ret = [],
-			pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
-				jQuery( selectors, context || this.context ) :
-				0;
+	fix: function( event ) {
+		if ( event[ jQuery.expando ] ) {
+			return event;
+		}
 
-		for ( ; i < l; i++ ) {
-			cur = this[i];
+		// Create a writable copy of the event object and normalize some properties
+		var i, prop, copy,
+			type = event.type,
+			originalEvent = event,
+			fixHook = this.fixHooks[ type ];
 
-			while ( cur && cur.ownerDocument && cur !== context && cur.nodeType !== 11 ) {
-				if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) {
-					ret.push( cur );
-					break;
-				}
-				cur = cur.parentNode;
-			}
+		if ( !fixHook ) {
+			this.fixHooks[ type ] = fixHook =
+				rmouseEvent.test( type ) ? this.mouseHooks :
+				rkeyEvent.test( type ) ? this.keyHooks :
+				{};
 		}
+		copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
 
-		return this.pushStack( ret.length > 1 ? jQuery.unique( ret ) : ret );
-	},
+		event = new jQuery.Event( originalEvent );
 
-	// Determine the position of an element within
-	// the matched set of elements
-	index: function( elem ) {
+		i = copy.length;
+		while ( i-- ) {
+			prop = copy[ i ];
+			event[ prop ] = originalEvent[ prop ];
+		}
 
-		// No argument, return index in parent
-		if ( !elem ) {
-			return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
+		// Support: IE<9
+		// Fix target property (#1925)
+		if ( !event.target ) {
+			event.target = originalEvent.srcElement || document;
 		}
 
-		// index in selector
-		if ( typeof elem === "string" ) {
-			return jQuery.inArray( this[0], jQuery( elem ) );
+		// Support: Chrome 23+, Safari?
+		// Target should not be a text node (#504, #13143)
+		if ( event.target.nodeType === 3 ) {
+			event.target = event.target.parentNode;
 		}
 
-		// Locate the position of the desired element
-		return jQuery.inArray(
-			// If it receives a jQuery object, the first element is used
-			elem.jquery ? elem[0] : elem, this );
+		// Support: IE<9
+		// For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
+		event.metaKey = !!event.metaKey;
+
+		return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
 	},
 
-	add: function( selector, context ) {
-		var set = typeof selector === "string" ?
-				jQuery( selector, context ) :
-				jQuery.makeArray( selector && selector.nodeType ? [ selector ] : selector ),
-			all = jQuery.merge( this.get(), set );
+	// Includes some event props shared by KeyEvent and MouseEvent
+	props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
+
+	fixHooks: {},
+
+	keyHooks: {
+		props: "char charCode key keyCode".split(" "),
+		filter: function( event, original ) {
 
-		return this.pushStack( jQuery.unique(all) );
+			// Add which for key events
+			if ( event.which == null ) {
+				event.which = original.charCode != null ? original.charCode : original.keyCode;
+			}
+
+			return event;
+		}
 	},
 
-	addBack: function( selector ) {
-		return this.add( selector == null ?
-			this.prevObject : this.prevObject.filter(selector)
-		);
-	}
-});
+	mouseHooks: {
+		props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
+		filter: function( event, original ) {
+			var body, eventDoc, doc,
+				button = original.button,
+				fromElement = original.fromElement;
 
-jQuery.fn.andSelf = jQuery.fn.addBack;
+			// Calculate pageX/Y if missing and clientX/Y available
+			if ( event.pageX == null && original.clientX != null ) {
+				eventDoc = event.target.ownerDocument || document;
+				doc = eventDoc.documentElement;
+				body = eventDoc.body;
 
-function sibling( cur, dir ) {
-	do {
-		cur = cur[ dir ];
-	} while ( cur && cur.nodeType !== 1 );
+				event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
+				event.pageY = original.clientY + ( doc && doc.scrollTop  || body && body.scrollTop  || 0 ) - ( doc && doc.clientTop  || body && body.clientTop  || 0 );
+			}
 
-	return cur;
-}
+			// Add relatedTarget, if necessary
+			if ( !event.relatedTarget && fromElement ) {
+				event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
+			}
 
-jQuery.each({
-	parent: function( elem ) {
-		var parent = elem.parentNode;
-		return parent && parent.nodeType !== 11 ? parent : null;
-	},
-	parents: function( elem ) {
-		return jQuery.dir( elem, "parentNode" );
-	},
-	parentsUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "parentNode", until );
+			// Add which for click: 1 === left; 2 === middle; 3 === right
+			// Note: button is not normalized, so don't use it
+			if ( !event.which && button !== undefined ) {
+				event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
+			}
+
+			return event;
+		}
 	},
-	next: function( elem ) {
-		return sibling( elem, "nextSibling" );
-	},
-	prev: function( elem ) {
-		return sibling( elem, "previousSibling" );
-	},
-	nextAll: function( elem ) {
-		return jQuery.dir( elem, "nextSibling" );
-	},
-	prevAll: function( elem ) {
-		return jQuery.dir( elem, "previousSibling" );
-	},
-	nextUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "nextSibling", until );
-	},
-	prevUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "previousSibling", until );
-	},
-	siblings: function( elem ) {
-		return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
-	},
-	children: function( elem ) {
-		return jQuery.sibling( elem.firstChild );
-	},
-	contents: function( elem ) {
-		return jQuery.nodeName( elem, "iframe" ) ?
-			elem.contentDocument || elem.contentWindow.document :
-			jQuery.merge( [], elem.childNodes );
-	}
-}, function( name, fn ) {
-	jQuery.fn[ name ] = function( until, selector ) {
-		var ret = jQuery.map( this, fn, until );
 
-		if ( !runtil.test( name ) ) {
-			selector = until;
-		}
+	special: {
+		load: {
+			// Prevent triggered image.load events from bubbling to window.load
+			noBubble: true
+		},
+		focus: {
+			// Fire native event if possible so blur/focus sequence is correct
+			trigger: function() {
+				if ( this !== safeActiveElement() && this.focus ) {
+					try {
+						this.focus();
+						return false;
+					} catch ( e ) {
+						// Support: IE<9
+						// If we error on focus to hidden element (#1486, #12518),
+						// let .trigger() run the handlers
+					}
+				}
+			},
+			delegateType: "focusin"
+		},
+		blur: {
+			trigger: function() {
+				if ( this === safeActiveElement() && this.blur ) {
+					this.blur();
+					return false;
+				}
+			},
+			delegateType: "focusout"
+		},
+		click: {
+			// For checkbox, fire native event so checked state will be right
+			trigger: function() {
+				if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
+					this.click();
+					return false;
+				}
+			},
 
-		if ( selector && typeof selector === "string" ) {
-			ret = jQuery.filter( selector, ret );
-		}
+			// For cross-browser consistency, don't fire native .click() on links
+			_default: function( event ) {
+				return jQuery.nodeName( event.target, "a" );
+			}
+		},
 
-		ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret;
+		beforeunload: {
+			postDispatch: function( event ) {
 
-		if ( this.length > 1 && rparentsprev.test( name ) ) {
-			ret = ret.reverse();
+				// Support: Firefox 20+
+				// Firefox doesn't alert if the returnValue field is not set.
+				if ( event.result !== undefined && event.originalEvent ) {
+					event.originalEvent.returnValue = event.result;
+				}
+			}
 		}
+	},
 
-		return this.pushStack( ret );
-	};
-});
-
-jQuery.extend({
-	filter: function( expr, elems, not ) {
-		if ( not ) {
-			expr = ":not(" + expr + ")";
+	simulate: function( type, elem, event, bubble ) {
+		// Piggyback on a donor event to simulate a different one.
+		// Fake originalEvent to avoid donor's stopPropagation, but if the
+		// simulated event prevents default then we do the same on the donor.
+		var e = jQuery.extend(
+			new jQuery.Event(),
+			event,
+			{
+				type: type,
+				isSimulated: true,
+				originalEvent: {}
+			}
+		);
+		if ( bubble ) {
+			jQuery.event.trigger( e, null, elem );
+		} else {
+			jQuery.event.dispatch.call( elem, e );
+		}
+		if ( e.isDefaultPrevented() ) {
+			event.preventDefault();
 		}
+	}
+};
 
-		return elems.length === 1 ?
-			jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] :
-			jQuery.find.matches(expr, elems);
-	},
+jQuery.removeEvent = document.removeEventListener ?
+	function( elem, type, handle ) {
+		if ( elem.removeEventListener ) {
+			elem.removeEventListener( type, handle, false );
+		}
+	} :
+	function( elem, type, handle ) {
+		var name = "on" + type;
 
-	dir: function( elem, dir, until ) {
-		var matched = [],
-			cur = elem[ dir ];
+		if ( elem.detachEvent ) {
 
-		while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
-			if ( cur.nodeType === 1 ) {
-				matched.push( cur );
+			// #8545, #7054, preventing memory leaks for custom events in IE6-8
+			// detachEvent needed property on element, by name of that event, to properly expose it to GC
+			if ( typeof elem[ name ] === strundefined ) {
+				elem[ name ] = null;
 			}
-			cur = cur[dir];
+
+			elem.detachEvent( name, handle );
 		}
-		return matched;
-	},
+	};
 
-	sibling: function( n, elem ) {
-		var r = [];
+jQuery.Event = function( src, props ) {
+	// Allow instantiation without the 'new' keyword
+	if ( !(this instanceof jQuery.Event) ) {
+		return new jQuery.Event( src, props );
+	}
 
-		for ( ; n; n = n.nextSibling ) {
-			if ( n.nodeType === 1 && n !== elem ) {
-				r.push( n );
-			}
-		}
+	// Event object
+	if ( src && src.type ) {
+		this.originalEvent = src;
+		this.type = src.type;
 
-		return r;
+		// Events bubbling up the document may have been marked as prevented
+		// by a handler lower down the tree; reflect the correct value.
+		this.isDefaultPrevented = src.defaultPrevented ||
+				src.defaultPrevented === undefined &&
+				// Support: IE < 9, Android < 4.0
+				src.returnValue === false ?
+			returnTrue :
+			returnFalse;
+
+	// Event type
+	} else {
+		this.type = src;
 	}
-});
 
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, keep ) {
+	// Put explicitly provided properties onto the event object
+	if ( props ) {
+		jQuery.extend( this, props );
+	}
 
-	// Can't pass null or undefined to indexOf in Firefox 4
-	// Set to 0 to skip string check
-	qualifier = qualifier || 0;
+	// Create a timestamp if incoming event doesn't have one
+	this.timeStamp = src && src.timeStamp || jQuery.now();
 
-	if ( jQuery.isFunction( qualifier ) ) {
-		return jQuery.grep(elements, function( elem, i ) {
-			var retVal = !!qualifier.call( elem, i, elem );
-			return retVal === keep;
-		});
+	// Mark it as fixed
+	this[ jQuery.expando ] = true;
+};
 
-	} else if ( qualifier.nodeType ) {
-		return jQuery.grep(elements, function( elem ) {
-			return ( elem === qualifier ) === keep;
-		});
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+	isDefaultPrevented: returnFalse,
+	isPropagationStopped: returnFalse,
+	isImmediatePropagationStopped: returnFalse,
 
-	} else if ( typeof qualifier === "string" ) {
-		var filtered = jQuery.grep(elements, function( elem ) {
-			return elem.nodeType === 1;
-		});
+	preventDefault: function() {
+		var e = this.originalEvent;
 
-		if ( isSimple.test( qualifier ) ) {
-			return jQuery.filter(qualifier, filtered, !keep);
-		} else {
-			qualifier = jQuery.filter( qualifier, filtered );
+		this.isDefaultPrevented = returnTrue;
+		if ( !e ) {
+			return;
 		}
-	}
 
-	return jQuery.grep(elements, function( elem ) {
-		return ( jQuery.inArray( elem, qualifier ) >= 0 ) === keep;
-	});
-}
-function createSafeFragment( document ) {
-	var list = nodeNames.split( "|" ),
-		safeFrag = document.createDocumentFragment();
+		// If preventDefault exists, run it on the original event
+		if ( e.preventDefault ) {
+			e.preventDefault();
 
-	if ( safeFrag.createElement ) {
-		while ( list.length ) {
-			safeFrag.createElement(
-				list.pop()
-			);
+		// Support: IE
+		// Otherwise set the returnValue property of the original event to false
+		} else {
+			e.returnValue = false;
 		}
-	}
-	return safeFrag;
-}
-
-var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
-		"header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
-	rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
-	rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
-	rleadingWhitespace = /^\s+/,
-	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
-	rtagName = /<([\w:]+)/,
-	rtbody = /<tbody/i,
-	rhtml = /<|&#?\w+;/,
-	rnoInnerhtml = /<(?:script|style|link)/i,
-	manipulation_rcheckableType = /^(?:checkbox|radio)$/i,
-	// checked="checked" or checked
-	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
-	rscriptType = /^$|\/(?:java|ecma)script/i,
-	rscriptTypeMasked = /^true\/(.*)/,
-	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
+	},
+	stopPropagation: function() {
+		var e = this.originalEvent;
 
-	// We have to close these tags to support XHTML (#13200)
-	wrapMap = {
-		option: [ 1, "<select multiple='multiple'>", "</select>" ],
-		legend: [ 1, "<fieldset>", "</fieldset>" ],
-		area: [ 1, "<map>", "</map>" ],
-		param: [ 1, "<object>", "</object>" ],
-		thead: [ 1, "<table>", "</table>" ],
-		tr: [ 2, "<table><tbody>", "</tbody></table>" ],
-		col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
-		td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+		this.isPropagationStopped = returnTrue;
+		if ( !e ) {
+			return;
+		}
+		// If stopPropagation exists, run it on the original event
+		if ( e.stopPropagation ) {
+			e.stopPropagation();
+		}
 
-		// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
-		// unless wrapped in a div with non-breaking characters in front of it.
-		_default: jQuery.support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>"  ]
+		// Support: IE
+		// Set the cancelBubble property of the original event to true
+		e.cancelBubble = true;
 	},
-	safeFragment = createSafeFragment( document ),
-	fragmentDiv = safeFragment.appendChild( document.createElement("div") );
+	stopImmediatePropagation: function() {
+		var e = this.originalEvent;
 
-wrapMap.optgroup = wrapMap.option;
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
+		this.isImmediatePropagationStopped = returnTrue;
 
-jQuery.fn.extend({
-	text: function( value ) {
-		return jQuery.access( this, function( value ) {
-			return value === undefined ?
-				jQuery.text( this ) :
-				this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
-		}, null, value, arguments.length );
-	},
-
-	wrapAll: function( html ) {
-		if ( jQuery.isFunction( html ) ) {
-			return this.each(function(i) {
-				jQuery(this).wrapAll( html.call(this, i) );
-			});
+		if ( e && e.stopImmediatePropagation ) {
+			e.stopImmediatePropagation();
 		}
 
-		if ( this[0] ) {
-			// The elements to wrap the target around
-			var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
+		this.stopPropagation();
+	}
+};
 
-			if ( this[0].parentNode ) {
-				wrap.insertBefore( this[0] );
+// Create mouseenter/leave events using mouseover/out and event-time checks
+jQuery.each({
+	mouseenter: "mouseover",
+	mouseleave: "mouseout",
+	pointerenter: "pointerover",
+	pointerleave: "pointerout"
+}, function( orig, fix ) {
+	jQuery.event.special[ orig ] = {
+		delegateType: fix,
+		bindType: fix,
+
+		handle: function( event ) {
+			var ret,
+				target = this,
+				related = event.relatedTarget,
+				handleObj = event.handleObj;
+
+			// For mousenter/leave call the handler if related is outside the target.
+			// NB: No relatedTarget if the mouse left/entered the browser window
+			if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
+				event.type = handleObj.origType;
+				ret = handleObj.handler.apply( this, arguments );
+				event.type = fix;
 			}
+			return ret;
+		}
+	};
+});
 
-			wrap.map(function() {
-				var elem = this;
+// IE submit delegation
+if ( !support.submitBubbles ) {
 
-				while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
-					elem = elem.firstChild;
+	jQuery.event.special.submit = {
+		setup: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
+
+			// Lazy-add a submit handler when a descendant form may potentially be submitted
+			jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
+				// Node name check avoids a VML-related crash in IE (#9807)
+				var elem = e.target,
+					form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
+				if ( form && !jQuery._data( form, "submitBubbles" ) ) {
+					jQuery.event.add( form, "submit._submit", function( event ) {
+						event._submit_bubble = true;
+					});
+					jQuery._data( form, "submitBubbles", true );
 				}
+			});
+			// return undefined since we don't need an event listener
+		},
 
-				return elem;
-			}).append( this );
-		}
+		postDispatch: function( event ) {
+			// If form was submitted by the user, bubble the event up the tree
+			if ( event._submit_bubble ) {
+				delete event._submit_bubble;
+				if ( this.parentNode && !event.isTrigger ) {
+					jQuery.event.simulate( "submit", this.parentNode, event, true );
+				}
+			}
+		},
 
-		return this;
-	},
+		teardown: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
 
-	wrapInner: function( html ) {
-		if ( jQuery.isFunction( html ) ) {
-			return this.each(function(i) {
-				jQuery(this).wrapInner( html.call(this, i) );
-			});
+			// Remove delegated handlers; cleanData eventually reaps submit handlers attached above
+			jQuery.event.remove( this, "._submit" );
 		}
+	};
+}
 
-		return this.each(function() {
-			var self = jQuery( this ),
-				contents = self.contents();
+// IE change delegation and checkbox/radio fix
+if ( !support.changeBubbles ) {
 
-			if ( contents.length ) {
-				contents.wrapAll( html );
+	jQuery.event.special.change = {
 
-			} else {
-				self.append( html );
+		setup: function() {
+
+			if ( rformElems.test( this.nodeName ) ) {
+				// IE doesn't fire change on a check/radio until blur; trigger it on click
+				// after a propertychange. Eat the blur-change in special.change.handle.
+				// This still fires onchange a second time for check/radio after blur.
+				if ( this.type === "checkbox" || this.type === "radio" ) {
+					jQuery.event.add( this, "propertychange._change", function( event ) {
+						if ( event.originalEvent.propertyName === "checked" ) {
+							this._just_changed = true;
+						}
+					});
+					jQuery.event.add( this, "click._change", function( event ) {
+						if ( this._just_changed && !event.isTrigger ) {
+							this._just_changed = false;
+						}
+						// Allow triggered, simulated change events (#11500)
+						jQuery.event.simulate( "change", this, event, true );
+					});
+				}
+				return false;
 			}
-		});
-	},
+			// Delegated event; lazy-add a change handler on descendant inputs
+			jQuery.event.add( this, "beforeactivate._change", function( e ) {
+				var elem = e.target;
 
-	wrap: function( html ) {
-		var isFunction = jQuery.isFunction( html );
+				if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
+					jQuery.event.add( elem, "change._change", function( event ) {
+						if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
+							jQuery.event.simulate( "change", this.parentNode, event, true );
+						}
+					});
+					jQuery._data( elem, "changeBubbles", true );
+				}
+			});
+		},
 
-		return this.each(function(i) {
-			jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
-		});
-	},
+		handle: function( event ) {
+			var elem = event.target;
 
-	unwrap: function() {
-		return this.parent().each(function() {
-			if ( !jQuery.nodeName( this, "body" ) ) {
-				jQuery( this ).replaceWith( this.childNodes );
+			// Swallow native change events from checkbox/radio, we already triggered them above
+			if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
+				return event.handleObj.handler.apply( this, arguments );
 			}
-		}).end();
-	},
+		},
 
-	append: function() {
-		return this.domManip(arguments, true, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				this.appendChild( elem );
-			}
-		});
-	},
+		teardown: function() {
+			jQuery.event.remove( this, "._change" );
 
-	prepend: function() {
-		return this.domManip(arguments, true, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				this.insertBefore( elem, this.firstChild );
-			}
-		});
-	},
+			return !rformElems.test( this.nodeName );
+		}
+	};
+}
 
-	before: function() {
-		return this.domManip( arguments, false, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this );
-			}
-		});
-	},
+// Create "bubbling" focus and blur events
+if ( !support.focusinBubbles ) {
+	jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
 
-	after: function() {
-		return this.domManip( arguments, false, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this.nextSibling );
-			}
-		});
-	},
+		// Attach a single capturing handler on the document while someone wants focusin/focusout
+		var handler = function( event ) {
+				jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
+			};
 
-	// keepData is for internal use only--do not document
-	remove: function( selector, keepData ) {
-		var elem,
-			i = 0;
+		jQuery.event.special[ fix ] = {
+			setup: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix );
 
-		for ( ; (elem = this[i]) != null; i++ ) {
-			if ( !selector || jQuery.filter( selector, [ elem ] ).length > 0 ) {
-				if ( !keepData && elem.nodeType === 1 ) {
-					jQuery.cleanData( getAll( elem ) );
+				if ( !attaches ) {
+					doc.addEventListener( orig, handler, true );
 				}
+				jQuery._data( doc, fix, ( attaches || 0 ) + 1 );
+			},
+			teardown: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix ) - 1;
 
-				if ( elem.parentNode ) {
-					if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
-						setGlobalEval( getAll( elem, "script" ) );
-					}
-					elem.parentNode.removeChild( elem );
+				if ( !attaches ) {
+					doc.removeEventListener( orig, handler, true );
+					jQuery._removeData( doc, fix );
+				} else {
+					jQuery._data( doc, fix, attaches );
 				}
 			}
-		}
+		};
+	});
+}
 
-		return this;
-	},
+jQuery.fn.extend({
 
-	empty: function() {
-		var elem,
-			i = 0;
+	on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
+		var type, origFn;
 
-		for ( ; (elem = this[i]) != null; i++ ) {
-			// Remove element nodes and prevent memory leaks
-			if ( elem.nodeType === 1 ) {
-				jQuery.cleanData( getAll( elem, false ) );
+		// Types can be a map of types/handlers
+		if ( typeof types === "object" ) {
+			// ( types-Object, selector, data )
+			if ( typeof selector !== "string" ) {
+				// ( types-Object, data )
+				data = data || selector;
+				selector = undefined;
 			}
-
-			// Remove any remaining nodes
-			while ( elem.firstChild ) {
-				elem.removeChild( elem.firstChild );
+			for ( type in types ) {
+				this.on( type, selector, data, types[ type ], one );
 			}
+			return this;
+		}
 
-			// If this is a select, ensure that it displays empty (#12336)
-			// Support: IE<9
-			if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
-				elem.options.length = 0;
+		if ( data == null && fn == null ) {
+			// ( types, fn )
+			fn = selector;
+			data = selector = undefined;
+		} else if ( fn == null ) {
+			if ( typeof selector === "string" ) {
+				// ( types, selector, fn )
+				fn = data;
+				data = undefined;
+			} else {
+				// ( types, data, fn )
+				fn = data;
+				data = selector;
+				selector = undefined;
 			}
 		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		} else if ( !fn ) {
+			return this;
+		}
 
-		return this;
-	},
-
-	clone: function( dataAndEvents, deepDataAndEvents ) {
-		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
-		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
-		return this.map( function () {
-			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+		if ( one === 1 ) {
+			origFn = fn;
+			fn = function( event ) {
+				// Can use an empty set, since event contains the info
+				jQuery().off( event );
+				return origFn.apply( this, arguments );
+			};
+			// Use same guid so caller can remove using origFn
+			fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+		}
+		return this.each( function() {
+			jQuery.event.add( this, types, fn, data, selector );
 		});
 	},
-
-	html: function( value ) {
-		return jQuery.access( this, function( value ) {
-			var elem = this[0] || {},
-				i = 0,
-				l = this.length;
-
-			if ( value === undefined ) {
-				return elem.nodeType === 1 ?
-					elem.innerHTML.replace( rinlinejQuery, "" ) :
-					undefined;
-			}
-
-			// See if we can take a shortcut and just use innerHTML
-			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
-				( jQuery.support.htmlSerialize || !rnoshimcache.test( value )  ) &&
-				( jQuery.support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
-				!wrapMap[ ( rtagName.exec( value ) || ["", ""] )[1].toLowerCase() ] ) {
-
-				value = value.replace( rxhtmlTag, "<$1></$2>" );
-
-				try {
-					for (; i < l; i++ ) {
-						// Remove element nodes and prevent memory leaks
-						elem = this[i] || {};
-						if ( elem.nodeType === 1 ) {
-							jQuery.cleanData( getAll( elem, false ) );
-							elem.innerHTML = value;
-						}
-					}
-
-					elem = 0;
-
-				// If using innerHTML throws an exception, use the fallback method
-				} catch(e) {}
-			}
-
-			if ( elem ) {
-				this.empty().append( value );
-			}
-		}, null, value, arguments.length );
+	one: function( types, selector, data, fn ) {
+		return this.on( types, selector, data, fn, 1 );
 	},
-
-	replaceWith: function( value ) {
-		var isFunc = jQuery.isFunction( value );
-
-		// Make sure that the elements are removed from the DOM before they are inserted
-		// this can help fix replacing a parent with child elements
-		if ( !isFunc && typeof value !== "string" ) {
-			value = jQuery( value ).not( this ).detach();
+	off: function( types, selector, fn ) {
+		var handleObj, type;
+		if ( types && types.preventDefault && types.handleObj ) {
+			// ( event )  dispatched jQuery.Event
+			handleObj = types.handleObj;
+			jQuery( types.delegateTarget ).off(
+				handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
+				handleObj.selector,
+				handleObj.handler
+			);
+			return this;
 		}
-
-		return this.domManip( [ value ], true, function( elem ) {
-			var next = this.nextSibling,
-				parent = this.parentNode;
-
-			if ( parent ) {
-				jQuery( this ).remove();
-				parent.insertBefore( elem, next );
+		if ( typeof types === "object" ) {
+			// ( types-object [, selector] )
+			for ( type in types ) {
+				this.off( type, selector, types[ type ] );
 			}
+			return this;
+		}
+		if ( selector === false || typeof selector === "function" ) {
+			// ( types [, fn] )
+			fn = selector;
+			selector = undefined;
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		}
+		return this.each(function() {
+			jQuery.event.remove( this, types, fn, selector );
 		});
 	},
 
-	detach: function( selector ) {
-		return this.remove( selector, true );
+	trigger: function( type, data ) {
+		return this.each(function() {
+			jQuery.event.trigger( type, data, this );
+		});
 	},
-
-	domManip: function( args, table, callback ) {
-
-		// Flatten any nested arrays
-		args = core_concat.apply( [], args );
-
-		var first, node, hasScripts,
-			scripts, doc, fragment,
-			i = 0,
-			l = this.length,
-			set = this,
-			iNoClone = l - 1,
-			value = args[0],
-			isFunction = jQuery.isFunction( value );
-
-		// We can't cloneNode fragments that contain checked, in WebKit
-		if ( isFunction || !( l <= 1 || typeof value !== "string" || jQuery.support.checkClone || !rchecked.test( value ) ) ) {
-			return this.each(function( index ) {
-				var self = set.eq( index );
-				if ( isFunction ) {
-					args[0] = value.call( this, index, table ? self.html() : undefined );
-				}
-				self.domManip( args, table, callback );
-			});
+	triggerHandler: function( type, data ) {
+		var elem = this[0];
+		if ( elem ) {
+			return jQuery.event.trigger( type, data, elem, true );
 		}
+	}
+});
 
-		if ( l ) {
-			fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
-			first = fragment.firstChild;
-
-			if ( fragment.childNodes.length === 1 ) {
-				fragment = first;
-			}
-
-			if ( first ) {
-				table = table && jQuery.nodeName( first, "tr" );
-				scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
-				hasScripts = scripts.length;
-
-				// Use the original fragment for the last item instead of the first because it can end up
-				// being emptied incorrectly in certain situations (#8070).
-				for ( ; i < l; i++ ) {
-					node = fragment;
 
-					if ( i !== iNoClone ) {
-						node = jQuery.clone( node, true, true );
+function createSafeFragment( document ) {
+	var list = nodeNames.split( "|" ),
+		safeFrag = document.createDocumentFragment();
 
-						// Keep references to cloned scripts for later restoration
-						if ( hasScripts ) {
-							jQuery.merge( scripts, getAll( node, "script" ) );
-						}
-					}
+	if ( safeFrag.createElement ) {
+		while ( list.length ) {
+			safeFrag.createElement(
+				list.pop()
+			);
+		}
+	}
+	return safeFrag;
+}
 
-					callback.call(
-						table && jQuery.nodeName( this[i], "table" ) ?
-							findOrAppend( this[i], "tbody" ) :
-							this[i],
-						node,
-						i
-					);
-				}
+var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
+		"header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
+	rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
+	rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
+	rleadingWhitespace = /^\s+/,
+	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
+	rtagName = /<([\w:]+)/,
+	rtbody = /<tbody/i,
+	rhtml = /<|&#?\w+;/,
+	rnoInnerhtml = /<(?:script|style|link)/i,
+	// checked="checked" or checked
+	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+	rscriptType = /^$|\/(?:java|ecma)script/i,
+	rscriptTypeMasked = /^true\/(.*)/,
+	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
 
-				if ( hasScripts ) {
-					doc = scripts[ scripts.length - 1 ].ownerDocument;
+	// We have to close these tags to support XHTML (#13200)
+	wrapMap = {
+		option: [ 1, "<select multiple='multiple'>", "</select>" ],
+		legend: [ 1, "<fieldset>", "</fieldset>" ],
+		area: [ 1, "<map>", "</map>" ],
+		param: [ 1, "<object>", "</object>" ],
+		thead: [ 1, "<table>", "</table>" ],
+		tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+		col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
+		td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
 
-					// Reenable scripts
-					jQuery.map( scripts, restoreScript );
+		// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
+		// unless wrapped in a div with non-breaking characters in front of it.
+		_default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>"  ]
+	},
+	safeFragment = createSafeFragment( document ),
+	fragmentDiv = safeFragment.appendChild( document.createElement("div") );
 
-					// Evaluate executable scripts on first document insertion
-					for ( i = 0; i < hasScripts; i++ ) {
-						node = scripts[ i ];
-						if ( rscriptType.test( node.type || "" ) &&
-							!jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
+wrapMap.optgroup = wrapMap.option;
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
 
-							if ( node.src ) {
-								// Hope ajax is available...
-								jQuery.ajax({
-									url: node.src,
-									type: "GET",
-									dataType: "script",
-									async: false,
-									global: false,
-									"throws": true
-								});
-							} else {
-								jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
-							}
-						}
-					}
-				}
+function getAll( context, tag ) {
+	var elems, elem,
+		i = 0,
+		found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) :
+			typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) :
+			undefined;
 
-				// Fix #11809: Avoid leaking memory
-				fragment = first = null;
+	if ( !found ) {
+		for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
+			if ( !tag || jQuery.nodeName( elem, tag ) ) {
+				found.push( elem );
+			} else {
+				jQuery.merge( found, getAll( elem, tag ) );
 			}
 		}
+	}
 
-		return this;
+	return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
+		jQuery.merge( [ context ], found ) :
+		found;
+}
+
+// Used in buildFragment, fixes the defaultChecked property
+function fixDefaultChecked( elem ) {
+	if ( rcheckableType.test( elem.type ) ) {
+		elem.defaultChecked = elem.checked;
 	}
-});
+}
+
+// Support: IE<8
+// Manipulating tables requires a tbody
+function manipulationTarget( elem, content ) {
+	return jQuery.nodeName( elem, "table" ) &&
+		jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ?
 
-function findOrAppend( elem, tag ) {
-	return elem.getElementsByTagName( tag )[0] || elem.appendChild( elem.ownerDocument.createElement( tag ) );
+		elem.getElementsByTagName("tbody")[0] ||
+			elem.appendChild( elem.ownerDocument.createElement("tbody") ) :
+		elem;
 }
 
 // Replace/restore the type attribute of script elements for safe DOM manipulation
 function disableScript( elem ) {
-	var attr = elem.getAttributeNode("type");
-	elem.type = ( attr && attr.specified ) + "/" + elem.type;
+	elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type;
 	return elem;
 }
 function restoreScript( elem ) {
@@ -6267,7 +5453,7 @@ function fixCloneNodeIssues( src, dest ) {
 	nodeName = dest.nodeName.toLowerCase();
 
 	// IE6-8 copies events bound via attachEvent when using cloneNode.
-	if ( !jQuery.support.noCloneEvent && dest[ jQuery.expando ] ) {
+	if ( !support.noCloneEvent && dest[ jQuery.expando ] ) {
 		data = jQuery._data( dest );
 
 		for ( e in data.events ) {
@@ -6294,11 +5480,11 @@ function fixCloneNodeIssues( src, dest ) {
 		// element in IE9, the outerHTML strategy above is not sufficient.
 		// If the src has innerHTML and the destination does not,
 		// copy the src.innerHTML into the dest.innerHTML. #10324
-		if ( jQuery.support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
+		if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
 			dest.innerHTML = src.innerHTML;
 		}
 
-	} else if ( nodeName === "input" && manipulation_rcheckableType.test( src.type ) ) {
+	} else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
 		// IE6-8 fails to persist the checked state of a cloned checkbox
 		// or radio button. Worse, IE6-7 fail to give the cloned element
 		// a checked appearance if the defaultChecked value isn't also set
@@ -6323,76 +5509,21 @@ function fixCloneNodeIssues( src, dest ) {
 	}
 }
 
-jQuery.each({
-	appendTo: "append",
-	prependTo: "prepend",
-	insertBefore: "before",
-	insertAfter: "after",
-	replaceAll: "replaceWith"
-}, function( name, original ) {
-	jQuery.fn[ name ] = function( selector ) {
-		var elems,
-			i = 0,
-			ret = [],
-			insert = jQuery( selector ),
-			last = insert.length - 1;
+jQuery.extend({
+	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+		var destElements, node, clone, i, srcElements,
+			inPage = jQuery.contains( elem.ownerDocument, elem );
 
-		for ( ; i <= last; i++ ) {
-			elems = i === last ? this : this.clone(true);
-			jQuery( insert[i] )[ original ]( elems );
+		if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
+			clone = elem.cloneNode( true );
 
-			// Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
-			core_push.apply( ret, elems.get() );
+		// IE<=8 does not properly clone detached, unknown element nodes
+		} else {
+			fragmentDiv.innerHTML = elem.outerHTML;
+			fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
 		}
 
-		return this.pushStack( ret );
-	};
-});
-
-function getAll( context, tag ) {
-	var elems, elem,
-		i = 0,
-		found = typeof context.getElementsByTagName !== core_strundefined ? context.getElementsByTagName( tag || "*" ) :
-			typeof context.querySelectorAll !== core_strundefined ? context.querySelectorAll( tag || "*" ) :
-			undefined;
-
-	if ( !found ) {
-		for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
-			if ( !tag || jQuery.nodeName( elem, tag ) ) {
-				found.push( elem );
-			} else {
-				jQuery.merge( found, getAll( elem, tag ) );
-			}
-		}
-	}
-
-	return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
-		jQuery.merge( [ context ], found ) :
-		found;
-}
-
-// Used in buildFragment, fixes the defaultChecked property
-function fixDefaultChecked( elem ) {
-	if ( manipulation_rcheckableType.test( elem.type ) ) {
-		elem.defaultChecked = elem.checked;
-	}
-}
-
-jQuery.extend({
-	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
-		var destElements, node, clone, i, srcElements,
-			inPage = jQuery.contains( elem.ownerDocument, elem );
-
-		if ( jQuery.support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
-			clone = elem.cloneNode( true );
-
-		// IE<=8 does not properly clone detached, unknown element nodes
-		} else {
-			fragmentDiv.innerHTML = elem.outerHTML;
-			fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
-		}
-
-		if ( (!jQuery.support.noCloneEvent || !jQuery.support.noCloneChecked) &&
+		if ( (!support.noCloneEvent || !support.noCloneChecked) &&
 				(elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
 
 			// We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2
@@ -6463,7 +5594,7 @@ jQuery.extend({
 					tmp = tmp || safe.appendChild( context.createElement("div") );
 
 					// Deserialize a standard representation
-					tag = ( rtagName.exec( elem ) || ["", ""] )[1].toLowerCase();
+					tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase();
 					wrap = wrapMap[ tag ] || wrapMap._default;
 
 					tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2];
@@ -6475,12 +5606,12 @@ jQuery.extend({
 					}
 
 					// Manually add leading whitespace removed by IE
-					if ( !jQuery.support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
+					if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
 						nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) );
 					}
 
 					// Remove IE's autoinserted <tbody> from table fragments
-					if ( !jQuery.support.tbody ) {
+					if ( !support.tbody ) {
 
 						// String was a <table>, *may* have spurious <tbody>
 						elem = tag === "table" && !rtbody.test( elem ) ?
@@ -6522,7 +5653,7 @@ jQuery.extend({
 
 		// Reset defaultChecked for any radios and checkboxes
 		// about to be appended to the DOM in IE 6/7 (#8060)
-		if ( !jQuery.support.appendChecked ) {
+		if ( !support.appendChecked ) {
 			jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked );
 		}
 
@@ -6566,11 +5697,10 @@ jQuery.extend({
 			i = 0,
 			internalKey = jQuery.expando,
 			cache = jQuery.cache,
-			deleteExpando = jQuery.support.deleteExpando,
+			deleteExpando = support.deleteExpando,
 			special = jQuery.event.special;
 
 		for ( ; (elem = elems[i]) != null; i++ ) {
-
 			if ( acceptData || jQuery.acceptData( elem ) ) {
 
 				id = elem[ internalKey ];
@@ -6600,340 +5730,439 @@ jQuery.extend({
 						if ( deleteExpando ) {
 							delete elem[ internalKey ];
 
-						} else if ( typeof elem.removeAttribute !== core_strundefined ) {
+						} else if ( typeof elem.removeAttribute !== strundefined ) {
 							elem.removeAttribute( internalKey );
 
 						} else {
 							elem[ internalKey ] = null;
 						}
 
-						core_deletedIds.push( id );
+						deletedIds.push( id );
 					}
 				}
 			}
 		}
 	}
 });
-var iframe, getStyles, curCSS,
-	ralpha = /alpha\([^)]*\)/i,
-	ropacity = /opacity\s*=\s*([^)]*)/,
-	rposition = /^(top|right|bottom|left)$/,
-	// swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
-	// see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
-	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
-	rmargin = /^margin/,
-	rnumsplit = new RegExp( "^(" + core_pnum + ")(.*)$", "i" ),
-	rnumnonpx = new RegExp( "^(" + core_pnum + ")(?!px)[a-z%]+$", "i" ),
-	rrelNum = new RegExp( "^([+-])=(" + core_pnum + ")", "i" ),
-	elemdisplay = { BODY: "block" },
 
-	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
-	cssNormalTransform = {
-		letterSpacing: 0,
-		fontWeight: 400
+jQuery.fn.extend({
+	text: function( value ) {
+		return access( this, function( value ) {
+			return value === undefined ?
+				jQuery.text( this ) :
+				this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
+		}, null, value, arguments.length );
 	},
 
-	cssExpand = [ "Top", "Right", "Bottom", "Left" ],
-	cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
-
-// return a css property mapped to a potentially vendor prefixed property
-function vendorPropName( style, name ) {
+	append: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.appendChild( elem );
+			}
+		});
+	},
 
-	// shortcut for names that are not vendor prefixed
-	if ( name in style ) {
-		return name;
-	}
+	prepend: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.insertBefore( elem, target.firstChild );
+			}
+		});
+	},
 
-	// check for vendor prefixed names
-	var capName = name.charAt(0).toUpperCase() + name.slice(1),
-		origName = name,
-		i = cssPrefixes.length;
+	before: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this );
+			}
+		});
+	},
 
-	while ( i-- ) {
-		name = cssPrefixes[ i ] + capName;
-		if ( name in style ) {
-			return name;
-		}
-	}
+	after: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this.nextSibling );
+			}
+		});
+	},
 
-	return origName;
-}
+	remove: function( selector, keepData /* Internal Use Only */ ) {
+		var elem,
+			elems = selector ? jQuery.filter( selector, this ) : this,
+			i = 0;
 
-function isHidden( elem, el ) {
-	// isHidden might be called from jQuery#filter function;
-	// in that case, element will be second argument
-	elem = el || elem;
-	return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
-}
+		for ( ; (elem = elems[i]) != null; i++ ) {
 
-function showHide( elements, show ) {
-	var display, elem, hidden,
-		values = [],
-		index = 0,
-		length = elements.length;
+			if ( !keepData && elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem ) );
+			}
 
-	for ( ; index < length; index++ ) {
-		elem = elements[ index ];
-		if ( !elem.style ) {
-			continue;
+			if ( elem.parentNode ) {
+				if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
+					setGlobalEval( getAll( elem, "script" ) );
+				}
+				elem.parentNode.removeChild( elem );
+			}
 		}
 
-		values[ index ] = jQuery._data( elem, "olddisplay" );
-		display = elem.style.display;
-		if ( show ) {
-			// Reset the inline display of this element to learn if it is
-			// being hidden by cascaded rules or not
-			if ( !values[ index ] && display === "none" ) {
-				elem.style.display = "";
-			}
+		return this;
+	},
 
-			// Set elements which have been overridden with display: none
-			// in a stylesheet to whatever the default browser style is
-			// for such an element
-			if ( elem.style.display === "" && isHidden( elem ) ) {
-				values[ index ] = jQuery._data( elem, "olddisplay", css_defaultDisplay(elem.nodeName) );
+	empty: function() {
+		var elem,
+			i = 0;
+
+		for ( ; (elem = this[i]) != null; i++ ) {
+			// Remove element nodes and prevent memory leaks
+			if ( elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem, false ) );
 			}
-		} else {
 
-			if ( !values[ index ] ) {
-				hidden = isHidden( elem );
+			// Remove any remaining nodes
+			while ( elem.firstChild ) {
+				elem.removeChild( elem.firstChild );
+			}
 
-				if ( display && display !== "none" || !hidden ) {
-					jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
-				}
+			// If this is a select, ensure that it displays empty (#12336)
+			// Support: IE<9
+			if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
+				elem.options.length = 0;
 			}
 		}
-	}
 
-	// Set the display of most of the elements in a second loop
-	// to avoid the constant reflow
-	for ( index = 0; index < length; index++ ) {
-		elem = elements[ index ];
-		if ( !elem.style ) {
-			continue;
-		}
-		if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
-			elem.style.display = show ? values[ index ] || "" : "none";
-		}
-	}
+		return this;
+	},
 
-	return elements;
-}
+	clone: function( dataAndEvents, deepDataAndEvents ) {
+		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
 
-jQuery.fn.extend({
-	css: function( name, value ) {
-		return jQuery.access( this, function( elem, name, value ) {
-			var len, styles,
-				map = {},
-				i = 0;
+		return this.map(function() {
+			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+		});
+	},
 
-			if ( jQuery.isArray( name ) ) {
-				styles = getStyles( elem );
-				len = name.length;
+	html: function( value ) {
+		return access( this, function( value ) {
+			var elem = this[ 0 ] || {},
+				i = 0,
+				l = this.length;
 
-				for ( ; i < len; i++ ) {
-					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
-				}
+			if ( value === undefined ) {
+				return elem.nodeType === 1 ?
+					elem.innerHTML.replace( rinlinejQuery, "" ) :
+					undefined;
+			}
 
-				return map;
+			// See if we can take a shortcut and just use innerHTML
+			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+				( support.htmlSerialize || !rnoshimcache.test( value )  ) &&
+				( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
+				!wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) {
+
+				value = value.replace( rxhtmlTag, "<$1></$2>" );
+
+				try {
+					for (; i < l; i++ ) {
+						// Remove element nodes and prevent memory leaks
+						elem = this[i] || {};
+						if ( elem.nodeType === 1 ) {
+							jQuery.cleanData( getAll( elem, false ) );
+							elem.innerHTML = value;
+						}
+					}
+
+					elem = 0;
+
+				// If using innerHTML throws an exception, use the fallback method
+				} catch(e) {}
 			}
 
-			return value !== undefined ?
-				jQuery.style( elem, name, value ) :
-				jQuery.css( elem, name );
-		}, name, value, arguments.length > 1 );
-	},
-	show: function() {
-		return showHide( this, true );
-	},
-	hide: function() {
-		return showHide( this );
+			if ( elem ) {
+				this.empty().append( value );
+			}
+		}, null, value, arguments.length );
 	},
-	toggle: function( state ) {
-		var bool = typeof state === "boolean";
 
-		return this.each(function() {
-			if ( bool ? state : isHidden( this ) ) {
-				jQuery( this ).show();
-			} else {
-				jQuery( this ).hide();
+	replaceWith: function() {
+		var arg = arguments[ 0 ];
+
+		// Make the changes, replacing each context element with the new content
+		this.domManip( arguments, function( elem ) {
+			arg = this.parentNode;
+
+			jQuery.cleanData( getAll( this ) );
+
+			if ( arg ) {
+				arg.replaceChild( elem, this );
 			}
 		});
-	}
-});
 
-jQuery.extend({
-	// Add in style property hooks for overriding the default
-	// behavior of getting and setting a style property
-	cssHooks: {
-		opacity: {
-			get: function( elem, computed ) {
-				if ( computed ) {
-					// We should always get a number back from opacity
-					var ret = curCSS( elem, "opacity" );
-					return ret === "" ? "1" : ret;
-				}
-			}
-		}
+		// Force removal if there was no new content (e.g., from empty arguments)
+		return arg && (arg.length || arg.nodeType) ? this : this.remove();
 	},
 
-	// Exclude the following css properties to add px
-	cssNumber: {
-		"columnCount": true,
-		"fillOpacity": true,
-		"fontWeight": true,
-		"lineHeight": true,
-		"opacity": true,
-		"orphans": true,
-		"widows": true,
-		"zIndex": true,
-		"zoom": true
-	},
-
-	// Add in properties whose names you wish to fix before
-	// setting or getting the value
-	cssProps: {
-		// normalize float css property
-		"float": jQuery.support.cssFloat ? "cssFloat" : "styleFloat"
+	detach: function( selector ) {
+		return this.remove( selector, true );
 	},
 
-	// Get and set the style property on a DOM Node
-	style: function( elem, name, value, extra ) {
-		// Don't set styles on text and comment nodes
-		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
-			return;
-		}
+	domManip: function( args, callback ) {
 
-		// Make sure that we're working with the right name
-		var ret, type, hooks,
-			origName = jQuery.camelCase( name ),
-			style = elem.style;
+		// Flatten any nested arrays
+		args = concat.apply( [], args );
 
-		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
+		var first, node, hasScripts,
+			scripts, doc, fragment,
+			i = 0,
+			l = this.length,
+			set = this,
+			iNoClone = l - 1,
+			value = args[0],
+			isFunction = jQuery.isFunction( value );
 
-		// gets hook for the prefixed version
-		// followed by the unprefixed version
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+		// We can't cloneNode fragments that contain checked, in WebKit
+		if ( isFunction ||
+				( l > 1 && typeof value === "string" &&
+					!support.checkClone && rchecked.test( value ) ) ) {
+			return this.each(function( index ) {
+				var self = set.eq( index );
+				if ( isFunction ) {
+					args[0] = value.call( this, index, self.html() );
+				}
+				self.domManip( args, callback );
+			});
+		}
 
-		// Check if we're setting a value
-		if ( value !== undefined ) {
-			type = typeof value;
+		if ( l ) {
+			fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
+			first = fragment.firstChild;
 
-			// convert relative number strings (+= or -=) to relative numbers. #7345
-			if ( type === "string" && (ret = rrelNum.exec( value )) ) {
-				value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
-				// Fixes bug #9237
-				type = "number";
+			if ( fragment.childNodes.length === 1 ) {
+				fragment = first;
 			}
 
-			// Make sure that NaN and null values aren't set. See: #7116
-			if ( value == null || type === "number" && isNaN( value ) ) {
-				return;
-			}
+			if ( first ) {
+				scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+				hasScripts = scripts.length;
 
-			// If a number was passed in, add 'px' to the (except for certain CSS properties)
-			if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
-				value += "px";
-			}
+				// Use the original fragment for the last item instead of the first because it can end up
+				// being emptied incorrectly in certain situations (#8070).
+				for ( ; i < l; i++ ) {
+					node = fragment;
 
-			// Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
-			// but it would mean to define eight (for every problematic property) identical functions
-			if ( !jQuery.support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
-				style[ name ] = "inherit";
-			}
+					if ( i !== iNoClone ) {
+						node = jQuery.clone( node, true, true );
 
-			// If a hook was provided, use that value, otherwise just set the specified value
-			if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+						// Keep references to cloned scripts for later restoration
+						if ( hasScripts ) {
+							jQuery.merge( scripts, getAll( node, "script" ) );
+						}
+					}
 
-				// Wrapped to prevent IE from throwing errors when 'invalid' values are provided
-				// Fixes bug #5509
-				try {
-					style[ name ] = value;
-				} catch(e) {}
-			}
+					callback.call( this[i], node, i );
+				}
 
-		} else {
-			// If a hook was provided get the non-computed value from there
-			if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
-				return ret;
-			}
+				if ( hasScripts ) {
+					doc = scripts[ scripts.length - 1 ].ownerDocument;
 
-			// Otherwise just get the value from the style object
-			return style[ name ];
+					// Reenable scripts
+					jQuery.map( scripts, restoreScript );
+
+					// Evaluate executable scripts on first document insertion
+					for ( i = 0; i < hasScripts; i++ ) {
+						node = scripts[ i ];
+						if ( rscriptType.test( node.type || "" ) &&
+							!jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
+
+							if ( node.src ) {
+								// Optional AJAX dependency, but won't run scripts if not present
+								if ( jQuery._evalUrl ) {
+									jQuery._evalUrl( node.src );
+								}
+							} else {
+								jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
+							}
+						}
+					}
+				}
+
+				// Fix #11809: Avoid leaking memory
+				fragment = first = null;
+			}
 		}
-	},
 
-	css: function( elem, name, extra, styles ) {
-		var num, val, hooks,
-			origName = jQuery.camelCase( name );
+		return this;
+	}
+});
 
-		// Make sure that we're working with the right name
-		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+jQuery.each({
+	appendTo: "append",
+	prependTo: "prepend",
+	insertBefore: "before",
+	insertAfter: "after",
+	replaceAll: "replaceWith"
+}, function( name, original ) {
+	jQuery.fn[ name ] = function( selector ) {
+		var elems,
+			i = 0,
+			ret = [],
+			insert = jQuery( selector ),
+			last = insert.length - 1;
 
-		// gets hook for the prefixed version
-		// followed by the unprefixed version
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+		for ( ; i <= last; i++ ) {
+			elems = i === last ? this : this.clone(true);
+			jQuery( insert[i] )[ original ]( elems );
 
-		// If a hook was provided get the computed value from there
-		if ( hooks && "get" in hooks ) {
-			val = hooks.get( elem, true, extra );
+			// Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
+			push.apply( ret, elems.get() );
 		}
 
-		// Otherwise, if a way to get the computed value exists, use that
-		if ( val === undefined ) {
-			val = curCSS( elem, name, styles );
-		}
+		return this.pushStack( ret );
+	};
+});
 
-		//convert "normal" to computed value
-		if ( val === "normal" && name in cssNormalTransform ) {
-			val = cssNormalTransform[ name ];
+
+var iframe,
+	elemdisplay = {};
+
+/**
+ * Retrieve the actual display of a element
+ * @param {String} name nodeName of the element
+ * @param {Object} doc Document object
+ */
+// Called only from within defaultDisplay
+function actualDisplay( name, doc ) {
+	var style,
+		elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
+
+		// getDefaultComputedStyle might be reliably used only on attached element
+		display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ?
+
+			// Use of this method is a temporary fix (more like optmization) until something better comes along,
+			// since it was removed from specification and supported only in FF
+			style.display : jQuery.css( elem[ 0 ], "display" );
+
+	// We don't have any data stored on the element,
+	// so use "detach" method as fast way to get rid of the element
+	elem.detach();
+
+	return display;
+}
+
+/**
+ * Try to determine the default display value of an element
+ * @param {String} nodeName
+ */
+function defaultDisplay( nodeName ) {
+	var doc = document,
+		display = elemdisplay[ nodeName ];
+
+	if ( !display ) {
+		display = actualDisplay( nodeName, doc );
+
+		// If the simple way fails, read from inside an iframe
+		if ( display === "none" || !display ) {
+
+			// Use the already-created iframe if possible
+			iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement );
+
+			// Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
+			doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document;
+
+			// Support: IE
+			doc.write();
+			doc.close();
+
+			display = actualDisplay( nodeName, doc );
+			iframe.detach();
 		}
 
-		// Return, converting to number if forced or a qualifier was provided and val looks numeric
-		if ( extra === "" || extra ) {
-			num = parseFloat( val );
-			return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
+		// Store the correct default display
+		elemdisplay[ nodeName ] = display;
+	}
+
+	return display;
+}
+
+
+(function() {
+	var shrinkWrapBlocksVal;
+
+	support.shrinkWrapBlocks = function() {
+		if ( shrinkWrapBlocksVal != null ) {
+			return shrinkWrapBlocksVal;
 		}
-		return val;
-	},
 
-	// A method for quickly swapping in/out CSS properties to get correct calculations
-	swap: function( elem, options, callback, args ) {
-		var ret, name,
-			old = {};
+		// Will be changed later if needed.
+		shrinkWrapBlocksVal = false;
 
-		// Remember the old values, and insert the new ones
-		for ( name in options ) {
-			old[ name ] = elem.style[ name ];
-			elem.style[ name ] = options[ name ];
+		// Minified: var b,c,d
+		var div, body, container;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
 		}
 
-		ret = callback.apply( elem, args || [] );
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
 
-		// Revert the old values
-		for ( name in options ) {
-			elem.style[ name ] = old[ name ];
+		// Support: IE6
+		// Check if elements with layout shrink-wrap their children
+		if ( typeof div.style.zoom !== strundefined ) {
+			// Reset CSS: box-sizing; display; margin; border
+			div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;" +
+				"padding:1px;width:1px;zoom:1";
+			div.appendChild( document.createElement( "div" ) ).style.width = "5px";
+			shrinkWrapBlocksVal = div.offsetWidth !== 3;
 		}
 
-		return ret;
-	}
-});
+		body.removeChild( container );
+
+		return shrinkWrapBlocksVal;
+	};
+
+})();
+var rmargin = (/^margin/);
+
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
+
+
+
+var getStyles, curCSS,
+	rposition = /^(top|right|bottom|left)$/;
 
-// NOTE: we've included the "window" in window.getComputedStyle
-// because jsdom on node.js will break without it.
 if ( window.getComputedStyle ) {
 	getStyles = function( elem ) {
+		// Support: IE<=11+, Firefox<=30+ (#15098, #14150)
+		// IE throws on elements created in popups
+		// FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
+		if ( elem.ownerDocument.defaultView.opener ) {
+			return elem.ownerDocument.defaultView.getComputedStyle( elem, null );
+		}
+
 		return window.getComputedStyle( elem, null );
 	};
 
-	curCSS = function( elem, name, _computed ) {
-		var width, minWidth, maxWidth,
-			computed = _computed || getStyles( elem ),
-
-			// getPropertyValue is only needed for .css('filter') in IE9, see #12537
-			ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined,
+	curCSS = function( elem, name, computed ) {
+		var width, minWidth, maxWidth, ret,
 			style = elem.style;
 
+		computed = computed || getStyles( elem );
+
+		// getPropertyValue is only needed for .css('filter') in IE9, see #12537
+		ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined;
+
 		if ( computed ) {
 
 			if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
@@ -6962,19 +6191,24 @@ if ( window.getComputedStyle ) {
 			}
 		}
 
-		return ret;
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "";
 	};
 } else if ( document.documentElement.currentStyle ) {
 	getStyles = function( elem ) {
 		return elem.currentStyle;
 	};
 
-	curCSS = function( elem, name, _computed ) {
-		var left, rs, rsLeft,
-			computed = _computed || getStyles( elem ),
-			ret = computed ? computed[ name ] : undefined,
+	curCSS = function( elem, name, computed ) {
+		var left, rs, rsLeft, ret,
 			style = elem.style;
 
+		computed = computed || getStyles( elem );
+		ret = computed ? computed[ name ] : undefined;
+
 		// Avoid setting ret to empty string here
 		// so we don't default to auto
 		if ( ret == null && style && style[ name ] ) {
@@ -7009,46 +6243,340 @@ if ( window.getComputedStyle ) {
 			}
 		}
 
-		return ret === "" ? "auto" : ret;
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "" || "auto";
 	};
 }
 
-function setPositiveNumber( elem, value, subtract ) {
-	var matches = rnumsplit.exec( value );
-	return matches ?
-		// Guard against undefined "subtract", e.g., when used as in cssHooks
-		Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
-		value;
-}
 
-function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
-	var i = extra === ( isBorderBox ? "border" : "content" ) ?
-		// If we already have the right measurement, avoid augmentation
-		4 :
-		// Otherwise initialize for horizontal or vertical properties
-		name === "width" ? 1 : 0,
 
-		val = 0;
 
-	for ( ; i < 4; i += 2 ) {
-		// both box models exclude margin, so add it if we want it
-		if ( extra === "margin" ) {
-			val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
-		}
+function addGetHookIf( conditionFn, hookFn ) {
+	// Define the hook, we'll check on the first run if it's really needed.
+	return {
+		get: function() {
+			var condition = conditionFn();
 
-		if ( isBorderBox ) {
-			// border-box includes padding, so remove it if we want content
-			if ( extra === "content" ) {
-				val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+			if ( condition == null ) {
+				// The test was not ready at this point; screw the hook this time
+				// but check again when needed next time.
+				return;
 			}
 
-			// at this point, extra isn't border nor margin, so remove border
-			if ( extra !== "margin" ) {
-				val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			if ( condition ) {
+				// Hook not needed (or it's not possible to use it due to missing dependency),
+				// remove it.
+				// Since there are no other hooks for marginRight, remove the whole object.
+				delete this.get;
+				return;
 			}
-		} else {
-			// at this point, extra isn't content, so add padding
-			val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+
+			// Hook needed; redefine it so that the support test is not executed again.
+
+			return (this.get = hookFn).apply( this, arguments );
+		}
+	};
+}
+
+
+(function() {
+	// Minified: var b,c,d,e,f,g, h,i
+	var div, style, a, pixelPositionVal, boxSizingReliableVal,
+		reliableHiddenOffsetsVal, reliableMarginRightVal;
+
+	// Setup
+	div = document.createElement( "div" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName( "a" )[ 0 ];
+	style = a && a.style;
+
+	// Finish early in limited (non-browser) environments
+	if ( !style ) {
+		return;
+	}
+
+	style.cssText = "float:left;opacity:.5";
+
+	// Support: IE<9
+	// Make sure that element opacity exists (as opposed to filter)
+	support.opacity = style.opacity === "0.5";
+
+	// Verify style float existence
+	// (IE uses styleFloat instead of cssFloat)
+	support.cssFloat = !!style.cssFloat;
+
+	div.style.backgroundClip = "content-box";
+	div.cloneNode( true ).style.backgroundClip = "";
+	support.clearCloneStyle = div.style.backgroundClip === "content-box";
+
+	// Support: Firefox<29, Android 2.3
+	// Vendor-prefix box-sizing
+	support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" ||
+		style.WebkitBoxSizing === "";
+
+	jQuery.extend(support, {
+		reliableHiddenOffsets: function() {
+			if ( reliableHiddenOffsetsVal == null ) {
+				computeStyleTests();
+			}
+			return reliableHiddenOffsetsVal;
+		},
+
+		boxSizingReliable: function() {
+			if ( boxSizingReliableVal == null ) {
+				computeStyleTests();
+			}
+			return boxSizingReliableVal;
+		},
+
+		pixelPosition: function() {
+			if ( pixelPositionVal == null ) {
+				computeStyleTests();
+			}
+			return pixelPositionVal;
+		},
+
+		// Support: Android 2.3
+		reliableMarginRight: function() {
+			if ( reliableMarginRightVal == null ) {
+				computeStyleTests();
+			}
+			return reliableMarginRightVal;
+		}
+	});
+
+	function computeStyleTests() {
+		// Minified: var b,c,d,j
+		var div, body, container, contents;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
+		}
+
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
+
+		div.style.cssText =
+			// Support: Firefox<29, Android 2.3
+			// Vendor-prefix box-sizing
+			"-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" +
+			"box-sizing:border-box;display:block;margin-top:1%;top:1%;" +
+			"border:1px;padding:1px;width:4px;position:absolute";
+
+		// Support: IE<9
+		// Assume reasonable values in the absence of getComputedStyle
+		pixelPositionVal = boxSizingReliableVal = false;
+		reliableMarginRightVal = true;
+
+		// Check for getComputedStyle so that this code is not run in IE<9.
+		if ( window.getComputedStyle ) {
+			pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
+			boxSizingReliableVal =
+				( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
+
+			// Support: Android 2.3
+			// Div with explicit width and no margin-right incorrectly
+			// gets computed margin-right based on width of container (#3333)
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			contents = div.appendChild( document.createElement( "div" ) );
+
+			// Reset CSS: box-sizing; display; margin; border; padding
+			contents.style.cssText = div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;padding:0";
+			contents.style.marginRight = contents.style.width = "0";
+			div.style.width = "1px";
+
+			reliableMarginRightVal =
+				!parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight );
+
+			div.removeChild( contents );
+		}
+
+		// Support: IE8
+		// Check if table cells still have offsetWidth/Height when they are set
+		// to display:none and there are still other visible table cells in a
+		// table row; if so, offsetWidth/Height are not reliable for use when
+		// determining if an element has been hidden directly using
+		// display:none (it is still safe to use offsets if a parent element is
+		// hidden; don safety goggles and see bug #4512 for more information).
+		div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
+		contents = div.getElementsByTagName( "td" );
+		contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
+		reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		if ( reliableHiddenOffsetsVal ) {
+			contents[ 0 ].style.display = "";
+			contents[ 1 ].style.display = "none";
+			reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		}
+
+		body.removeChild( container );
+	}
+
+})();
+
+
+// A method for quickly swapping in/out CSS properties to get correct calculations.
+jQuery.swap = function( elem, options, callback, args ) {
+	var ret, name,
+		old = {};
+
+	// Remember the old values, and insert the new ones
+	for ( name in options ) {
+		old[ name ] = elem.style[ name ];
+		elem.style[ name ] = options[ name ];
+	}
+
+	ret = callback.apply( elem, args || [] );
+
+	// Revert the old values
+	for ( name in options ) {
+		elem.style[ name ] = old[ name ];
+	}
+
+	return ret;
+};
+
+
+var
+		ralpha = /alpha\([^)]*\)/i,
+	ropacity = /opacity\s*=\s*([^)]*)/,
+
+	// swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
+	// see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+	rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ),
+	rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ),
+
+	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+	cssNormalTransform = {
+		letterSpacing: "0",
+		fontWeight: "400"
+	},
+
+	cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
+
+
+// return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( style, name ) {
+
+	// shortcut for names that are not vendor prefixed
+	if ( name in style ) {
+		return name;
+	}
+
+	// check for vendor prefixed names
+	var capName = name.charAt(0).toUpperCase() + name.slice(1),
+		origName = name,
+		i = cssPrefixes.length;
+
+	while ( i-- ) {
+		name = cssPrefixes[ i ] + capName;
+		if ( name in style ) {
+			return name;
+		}
+	}
+
+	return origName;
+}
+
+function showHide( elements, show ) {
+	var display, elem, hidden,
+		values = [],
+		index = 0,
+		length = elements.length;
+
+	for ( ; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+
+		values[ index ] = jQuery._data( elem, "olddisplay" );
+		display = elem.style.display;
+		if ( show ) {
+			// Reset the inline display of this element to learn if it is
+			// being hidden by cascaded rules or not
+			if ( !values[ index ] && display === "none" ) {
+				elem.style.display = "";
+			}
+
+			// Set elements which have been overridden with display: none
+			// in a stylesheet to whatever the default browser style is
+			// for such an element
+			if ( elem.style.display === "" && isHidden( elem ) ) {
+				values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
+			}
+		} else {
+			hidden = isHidden( elem );
+
+			if ( display && display !== "none" || !hidden ) {
+				jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
+			}
+		}
+	}
+
+	// Set the display of most of the elements in a second loop
+	// to avoid the constant reflow
+	for ( index = 0; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+		if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
+			elem.style.display = show ? values[ index ] || "" : "none";
+		}
+	}
+
+	return elements;
+}
+
+function setPositiveNumber( elem, value, subtract ) {
+	var matches = rnumsplit.exec( value );
+	return matches ?
+		// Guard against undefined "subtract", e.g., when used as in cssHooks
+		Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
+		value;
+}
+
+function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
+	var i = extra === ( isBorderBox ? "border" : "content" ) ?
+		// If we already have the right measurement, avoid augmentation
+		4 :
+		// Otherwise initialize for horizontal or vertical properties
+		name === "width" ? 1 : 0,
+
+		val = 0;
+
+	for ( ; i < 4; i += 2 ) {
+		// both box models exclude margin, so add it if we want it
+		if ( extra === "margin" ) {
+			val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
+		}
+
+		if ( isBorderBox ) {
+			// border-box includes padding, so remove it if we want content
+			if ( extra === "content" ) {
+				val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+			}
+
+			// at this point, extra isn't border nor margin, so remove border
+			if ( extra !== "margin" ) {
+				val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		} else {
+			// at this point, extra isn't content, so add padding
+			val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
 
 			// at this point, extra isn't content nor padding, so add border
 			if ( extra !== "padding" ) {
@@ -7066,7 +6594,7 @@ function getWidthOrHeight( elem, name, extra ) {
 	var valueIsBorderBox = true,
 		val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
 		styles = getStyles( elem ),
-		isBorderBox = jQuery.support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
+		isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
 
 	// some non-html elements return undefined for offsetWidth, so check for null/undefined
 	// svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
@@ -7085,7 +6613,7 @@ function getWidthOrHeight( elem, name, extra ) {
 
 		// we need the check for style in case a browser which returns unreliable values
 		// for getComputedStyle silently falls back to the reliable elem.style
-		valueIsBorderBox = isBorderBox && ( jQuery.support.boxSizingReliable || val === elem.style[ name ] );
+		valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] );
 
 		// Normalize "", auto, and prepare for extra
 		val = parseFloat( val ) || 0;
@@ -7103,45 +6631,144 @@ function getWidthOrHeight( elem, name, extra ) {
 	) + "px";
 }
 
-// Try to determine the default display value of an element
-function css_defaultDisplay( nodeName ) {
-	var doc = document,
-		display = elemdisplay[ nodeName ];
-
-	if ( !display ) {
-		display = actualDisplay( nodeName, doc );
+jQuery.extend({
+	// Add in style property hooks for overriding the default
+	// behavior of getting and setting a style property
+	cssHooks: {
+		opacity: {
+			get: function( elem, computed ) {
+				if ( computed ) {
+					// We should always get a number back from opacity
+					var ret = curCSS( elem, "opacity" );
+					return ret === "" ? "1" : ret;
+				}
+			}
+		}
+	},
 
-		// If the simple way fails, read from inside an iframe
-		if ( display === "none" || !display ) {
-			// Use the already-created iframe if possible
-			iframe = ( iframe ||
-				jQuery("<iframe frameborder='0' width='0' height='0'/>")
-				.css( "cssText", "display:block !important" )
-			).appendTo( doc.documentElement );
+	// Don't automatically add "px" to these possibly-unitless properties
+	cssNumber: {
+		"columnCount": true,
+		"fillOpacity": true,
+		"flexGrow": true,
+		"flexShrink": true,
+		"fontWeight": true,
+		"lineHeight": true,
+		"opacity": true,
+		"order": true,
+		"orphans": true,
+		"widows": true,
+		"zIndex": true,
+		"zoom": true
+	},
 
-			// Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
-			doc = ( iframe[0].contentWindow || iframe[0].contentDocument ).document;
-			doc.write("<!doctype html><html><body>");
-			doc.close();
+	// Add in properties whose names you wish to fix before
+	// setting or getting the value
+	cssProps: {
+		// normalize float css property
+		"float": support.cssFloat ? "cssFloat" : "styleFloat"
+	},
 
-			display = actualDisplay( nodeName, doc );
-			iframe.detach();
+	// Get and set the style property on a DOM Node
+	style: function( elem, name, value, extra ) {
+		// Don't set styles on text and comment nodes
+		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+			return;
 		}
 
-		// Store the correct default display
-		elemdisplay[ nodeName ] = display;
-	}
+		// Make sure that we're working with the right name
+		var ret, type, hooks,
+			origName = jQuery.camelCase( name ),
+			style = elem.style;
 
-	return display;
-}
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
 
-// Called ONLY from within css_defaultDisplay
-function actualDisplay( name, doc ) {
-	var elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
-		display = jQuery.css( elem[0], "display" );
-	elem.remove();
-	return display;
-}
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// Check if we're setting a value
+		if ( value !== undefined ) {
+			type = typeof value;
+
+			// convert relative number strings (+= or -=) to relative numbers. #7345
+			if ( type === "string" && (ret = rrelNum.exec( value )) ) {
+				value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
+				// Fixes bug #9237
+				type = "number";
+			}
+
+			// Make sure that null and NaN values aren't set. See: #7116
+			if ( value == null || value !== value ) {
+				return;
+			}
+
+			// If a number was passed in, add 'px' to the (except for certain CSS properties)
+			if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
+				value += "px";
+			}
+
+			// Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
+			// but it would mean to define eight (for every problematic property) identical functions
+			if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
+				style[ name ] = "inherit";
+			}
+
+			// If a hook was provided, use that value, otherwise just set the specified value
+			if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+
+				// Support: IE
+				// Swallow errors from 'invalid' CSS values (#5509)
+				try {
+					style[ name ] = value;
+				} catch(e) {}
+			}
+
+		} else {
+			// If a hook was provided get the non-computed value from there
+			if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+				return ret;
+			}
+
+			// Otherwise just get the value from the style object
+			return style[ name ];
+		}
+	},
+
+	css: function( elem, name, extra, styles ) {
+		var num, val, hooks,
+			origName = jQuery.camelCase( name );
+
+		// Make sure that we're working with the right name
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// If a hook was provided get the computed value from there
+		if ( hooks && "get" in hooks ) {
+			val = hooks.get( elem, true, extra );
+		}
+
+		// Otherwise, if a way to get the computed value exists, use that
+		if ( val === undefined ) {
+			val = curCSS( elem, name, styles );
+		}
+
+		//convert "normal" to computed value
+		if ( val === "normal" && name in cssNormalTransform ) {
+			val = cssNormalTransform[ name ];
+		}
+
+		// Return, converting to number if forced or a qualifier was provided and val looks numeric
+		if ( extra === "" || extra ) {
+			num = parseFloat( val );
+			return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
+		}
+		return val;
+	}
+});
 
 jQuery.each([ "height", "width" ], function( i, name ) {
 	jQuery.cssHooks[ name ] = {
@@ -7149,7 +6776,7 @@ jQuery.each([ "height", "width" ], function( i, name ) {
 			if ( computed ) {
 				// certain elements can have dimension info if we invisibly show them
 				// however, it must have a current display style that would benefit from this
-				return elem.offsetWidth === 0 && rdisplayswap.test( jQuery.css( elem, "display" ) ) ?
+				return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ?
 					jQuery.swap( elem, cssShow, function() {
 						return getWidthOrHeight( elem, name, extra );
 					}) :
@@ -7164,7 +6791,7 @@ jQuery.each([ "height", "width" ], function( i, name ) {
 					elem,
 					name,
 					extra,
-					jQuery.support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+					support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
 					styles
 				) : 0
 			);
@@ -7172,7 +6799,7 @@ jQuery.each([ "height", "width" ], function( i, name ) {
 	};
 });
 
-if ( !jQuery.support.opacity ) {
+if ( !support.opacity ) {
 	jQuery.cssHooks.opacity = {
 		get: function( elem, computed ) {
 			// IE uses filters for opacity
@@ -7216,55 +6843,16 @@ if ( !jQuery.support.opacity ) {
 	};
 }
 
-// These hooks cannot be added until DOM ready because the support test
-// for it is not run until after DOM ready
-jQuery(function() {
-	if ( !jQuery.support.reliableMarginRight ) {
-		jQuery.cssHooks.marginRight = {
-			get: function( elem, computed ) {
-				if ( computed ) {
-					// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
-					// Work around by temporarily setting element display to inline-block
-					return jQuery.swap( elem, { "display": "inline-block" },
-						curCSS, [ elem, "marginRight" ] );
-				}
-			}
-		};
-	}
-
-	// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
-	// getComputedStyle returns percent when specified for top/left/bottom/right
-	// rather than make the css module depend on the offset module, we just check for it here
-	if ( !jQuery.support.pixelPosition && jQuery.fn.position ) {
-		jQuery.each( [ "top", "left" ], function( i, prop ) {
-			jQuery.cssHooks[ prop ] = {
-				get: function( elem, computed ) {
-					if ( computed ) {
-						computed = curCSS( elem, prop );
-						// if curCSS returns percentage, fallback to offset
-						return rnumnonpx.test( computed ) ?
-							jQuery( elem ).position()[ prop ] + "px" :
-							computed;
-					}
-				}
-			};
-		});
+jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight,
+	function( elem, computed ) {
+		if ( computed ) {
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			// Work around by temporarily setting element display to inline-block
+			return jQuery.swap( elem, { "display": "inline-block" },
+				curCSS, [ elem, "marginRight" ] );
+		}
 	}
-
-});
-
-if ( jQuery.expr && jQuery.expr.filters ) {
-	jQuery.expr.filters.hidden = function( elem ) {
-		// Support: Opera <= 12.12
-		// Opera reports offsetWidths and offsetHeights less than zero on some elements
-		return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
-			(!jQuery.support.reliableHiddenOffsets && ((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
-	};
-
-	jQuery.expr.filters.visible = function( elem ) {
-		return !jQuery.expr.filters.hidden( elem );
-	};
-}
+);
 
 // These hooks are used by animate to expand properties
 jQuery.each({
@@ -7293,16729 +6881,23697 @@ jQuery.each({
 		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
 	}
 });
-var r20 = /%20/g,
-	rbracket = /\[\]$/,
-	rCRLF = /\r?\n/g,
-	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
-	rsubmittable = /^(?:input|select|textarea|keygen)/i;
 
 jQuery.fn.extend({
-	serialize: function() {
-		return jQuery.param( this.serializeArray() );
+	css: function( name, value ) {
+		return access( this, function( elem, name, value ) {
+			var styles, len,
+				map = {},
+				i = 0;
+
+			if ( jQuery.isArray( name ) ) {
+				styles = getStyles( elem );
+				len = name.length;
+
+				for ( ; i < len; i++ ) {
+					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
+				}
+
+				return map;
+			}
+
+			return value !== undefined ?
+				jQuery.style( elem, name, value ) :
+				jQuery.css( elem, name );
+		}, name, value, arguments.length > 1 );
 	},
-	serializeArray: function() {
-		return this.map(function(){
-			// Can add propHook for "elements" to filter or add form elements
-			var elements = jQuery.prop( this, "elements" );
-			return elements ? jQuery.makeArray( elements ) : this;
-		})
-		.filter(function(){
-			var type = this.type;
-			// Use .is(":disabled") so that fieldset[disabled] works
-			return this.name && !jQuery( this ).is( ":disabled" ) &&
-				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
-				( this.checked || !manipulation_rcheckableType.test( type ) );
-		})
-		.map(function( i, elem ){
-			var val = jQuery( this ).val();
+	show: function() {
+		return showHide( this, true );
+	},
+	hide: function() {
+		return showHide( this );
+	},
+	toggle: function( state ) {
+		if ( typeof state === "boolean" ) {
+			return state ? this.show() : this.hide();
+		}
 
-			return val == null ?
-				null :
-				jQuery.isArray( val ) ?
-					jQuery.map( val, function( val ){
-						return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-					}) :
-					{ name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-		}).get();
+		return this.each(function() {
+			if ( isHidden( this ) ) {
+				jQuery( this ).show();
+			} else {
+				jQuery( this ).hide();
+			}
+		});
 	}
 });
 
-//Serialize an array of form elements or a set of
-//key/values into a query string
-jQuery.param = function( a, traditional ) {
-	var prefix,
-		s = [],
-		add = function( key, value ) {
-			// If value is a function, invoke it and return its value
-			value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
-			s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
-		};
 
-	// Set traditional to true for jQuery <= 1.3.2 behavior.
-	if ( traditional === undefined ) {
-		traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
-	}
+function Tween( elem, options, prop, end, easing ) {
+	return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
 
-	// If an array was passed in, assume that it is an array of form elements.
-	if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
-		// Serialize the form elements
-		jQuery.each( a, function() {
-			add( this.name, this.value );
-		});
+Tween.prototype = {
+	constructor: Tween,
+	init: function( elem, options, prop, end, easing, unit ) {
+		this.elem = elem;
+		this.prop = prop;
+		this.easing = easing || "swing";
+		this.options = options;
+		this.start = this.now = this.cur();
+		this.end = end;
+		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+	},
+	cur: function() {
+		var hooks = Tween.propHooks[ this.prop ];
 
-	} else {
-		// If traditional, encode the "old" way (the way 1.3.2 or older
-		// did it), otherwise encode params recursively.
-		for ( prefix in a ) {
-			buildParams( prefix, a[ prefix ], traditional, add );
+		return hooks && hooks.get ?
+			hooks.get( this ) :
+			Tween.propHooks._default.get( this );
+	},
+	run: function( percent ) {
+		var eased,
+			hooks = Tween.propHooks[ this.prop ];
+
+		if ( this.options.duration ) {
+			this.pos = eased = jQuery.easing[ this.easing ](
+				percent, this.options.duration * percent, 0, 1, this.options.duration
+			);
+		} else {
+			this.pos = eased = percent;
 		}
-	}
+		this.now = ( this.end - this.start ) * eased + this.start;
 
-	// Return the resulting serialization
-	return s.join( "&" ).replace( r20, "+" );
+		if ( this.options.step ) {
+			this.options.step.call( this.elem, this.now, this );
+		}
+
+		if ( hooks && hooks.set ) {
+			hooks.set( this );
+		} else {
+			Tween.propHooks._default.set( this );
+		}
+		return this;
+	}
 };
 
-function buildParams( prefix, obj, traditional, add ) {
-	var name;
+Tween.prototype.init.prototype = Tween.prototype;
 
-	if ( jQuery.isArray( obj ) ) {
-		// Serialize array item.
-		jQuery.each( obj, function( i, v ) {
-			if ( traditional || rbracket.test( prefix ) ) {
-				// Treat each array item as a scalar.
-				add( prefix, v );
+Tween.propHooks = {
+	_default: {
+		get: function( tween ) {
+			var result;
 
-			} else {
-				// Item is non-scalar (array or object), encode its numeric index.
-				buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
+			if ( tween.elem[ tween.prop ] != null &&
+				(!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
+				return tween.elem[ tween.prop ];
 			}
-		});
 
-	} else if ( !traditional && jQuery.type( obj ) === "object" ) {
-		// Serialize object item.
-		for ( name in obj ) {
-			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+			// passing an empty string as a 3rd parameter to .css will automatically
+			// attempt a parseFloat and fallback to a string if the parse fails
+			// so, simple values such as "10px" are parsed to Float.
+			// complex values such as "rotate(1rad)" are returned as is.
+			result = jQuery.css( tween.elem, tween.prop, "" );
+			// Empty strings, null, undefined and "auto" are converted to 0.
+			return !result || result === "auto" ? 0 : result;
+		},
+		set: function( tween ) {
+			// use step hook for back compat - use cssHook if its there - use .style if its
+			// available and use plain properties where available
+			if ( jQuery.fx.step[ tween.prop ] ) {
+				jQuery.fx.step[ tween.prop ]( tween );
+			} else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
+				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+			} else {
+				tween.elem[ tween.prop ] = tween.now;
+			}
 		}
-
-	} else {
-		// Serialize scalar item.
-		add( prefix, obj );
 	}
-}
-jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
-	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
-	"change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
+};
 
-	// Handle event binding
-	jQuery.fn[ name ] = function( data, fn ) {
-		return arguments.length > 0 ?
-			this.on( name, null, data, fn ) :
-			this.trigger( name );
-	};
-});
+// Support: IE <=9
+// Panic based approach to setting things on disconnected nodes
 
-jQuery.fn.hover = function( fnOver, fnOut ) {
-	return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+	set: function( tween ) {
+		if ( tween.elem.nodeType && tween.elem.parentNode ) {
+			tween.elem[ tween.prop ] = tween.now;
+		}
+	}
 };
-var
-	// Document location
-	ajaxLocParts,
-	ajaxLocation,
-	ajax_nonce = jQuery.now(),
 
-	ajax_rquery = /\?/,
-	rhash = /#.*$/,
-	rts = /([?&])_=[^&]*/,
-	rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
-	// #7653, #8125, #8152: local protocol detection
-	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
-	rnoContent = /^(?:GET|HEAD)$/,
-	rprotocol = /^\/\//,
-	rurl = /^([\w.+-]+:)(?:\/\/([^\/?#:]*)(?::(\d+)|)|)/,
+jQuery.easing = {
+	linear: function( p ) {
+		return p;
+	},
+	swing: function( p ) {
+		return 0.5 - Math.cos( p * Math.PI ) / 2;
+	}
+};
 
-	// Keep a copy of the old load method
-	_load = jQuery.fn.load,
+jQuery.fx = Tween.prototype.init;
 
-	/* Prefilters
-	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
-	 * 2) These are called:
-	 *    - BEFORE asking for a transport
-	 *    - AFTER param serialization (s.data is a string if s.processData is true)
-	 * 3) key is the dataType
-	 * 4) the catchall symbol "*" can be used
-	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
-	 */
-	prefilters = {},
+// Back Compat <1.8 extension point
+jQuery.fx.step = {};
 
-	/* Transports bindings
-	 * 1) key is the dataType
-	 * 2) the catchall symbol "*" can be used
-	 * 3) selection will start with transport dataType and THEN go to "*" if needed
-	 */
-	transports = {},
 
-	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
-	allTypes = "*/".concat("*");
 
-// #8138, IE may throw an exception when accessing
-// a field from window.location if document.domain has been set
-try {
-	ajaxLocation = location.href;
-} catch( e ) {
-	// Use the href attribute of an A element
-	// since IE will modify it given document.location
-	ajaxLocation = document.createElement( "a" );
-	ajaxLocation.href = "";
-	ajaxLocation = ajaxLocation.href;
-}
 
-// Segment location into parts
-ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
+var
+	fxNow, timerId,
+	rfxtypes = /^(?:toggle|show|hide)$/,
+	rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ),
+	rrun = /queueHooks$/,
+	animationPrefilters = [ defaultPrefilter ],
+	tweeners = {
+		"*": [ function( prop, value ) {
+			var tween = this.createTween( prop, value ),
+				target = tween.cur(),
+				parts = rfxnum.exec( value ),
+				unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
 
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
+				// Starting value computation is required for potential unit mismatches
+				start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) &&
+					rfxnum.exec( jQuery.css( tween.elem, prop ) ),
+				scale = 1,
+				maxIterations = 20;
 
-	// dataTypeExpression is optional and defaults to "*"
-	return function( dataTypeExpression, func ) {
+			if ( start && start[ 3 ] !== unit ) {
+				// Trust units reported by jQuery.css
+				unit = unit || start[ 3 ];
 
-		if ( typeof dataTypeExpression !== "string" ) {
-			func = dataTypeExpression;
-			dataTypeExpression = "*";
-		}
+				// Make sure we update the tween properties later on
+				parts = parts || [];
 
-		var dataType,
-			i = 0,
-			dataTypes = dataTypeExpression.toLowerCase().match( core_rnotwhite ) || [];
+				// Iteratively approximate from a nonzero starting point
+				start = +target || 1;
 
-		if ( jQuery.isFunction( func ) ) {
-			// For each dataType in the dataTypeExpression
-			while ( (dataType = dataTypes[i++]) ) {
-				// Prepend if requested
-				if ( dataType[0] === "+" ) {
-					dataType = dataType.slice( 1 ) || "*";
-					(structure[ dataType ] = structure[ dataType ] || []).unshift( func );
+				do {
+					// If previous iteration zeroed out, double until we get *something*
+					// Use a string for doubling factor so we don't accidentally see scale as unchanged below
+					scale = scale || ".5";
 
-				// Otherwise append
-				} else {
-					(structure[ dataType ] = structure[ dataType ] || []).push( func );
-				}
+					// Adjust and apply
+					start = start / scale;
+					jQuery.style( tween.elem, prop, start + unit );
+
+				// Update scale, tolerating zero or NaN from tween.cur()
+				// And breaking the loop if scale is unchanged or perfect, or if we've just had enough
+				} while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
 			}
-		}
+
+			// Update tween properties
+			if ( parts ) {
+				start = tween.start = +start || +target || 0;
+				tween.unit = unit;
+				// If a +=/-= token was provided, we're doing a relative animation
+				tween.end = parts[ 1 ] ?
+					start + ( parts[ 1 ] + 1 ) * parts[ 2 ] :
+					+parts[ 2 ];
+			}
+
+			return tween;
+		} ]
 	};
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+	setTimeout(function() {
+		fxNow = undefined;
+	});
+	return ( fxNow = jQuery.now() );
 }
 
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+	var which,
+		attrs = { height: type },
+		i = 0;
 
-	var inspected = {},
-		seekingTransport = ( structure === transports );
+	// if we include width, step value is 1 to do all cssExpand values,
+	// if we don't include width, step value is 2 to skip over Left and Right
+	includeWidth = includeWidth ? 1 : 0;
+	for ( ; i < 4 ; i += 2 - includeWidth ) {
+		which = cssExpand[ i ];
+		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+	}
 
-	function inspect( dataType ) {
-		var selected;
-		inspected[ dataType ] = true;
-		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
-			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
-			if( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
-				options.dataTypes.unshift( dataTypeOrTransport );
-				inspect( dataTypeOrTransport );
-				return false;
-			} else if ( seekingTransport ) {
-				return !( selected = dataTypeOrTransport );
-			}
-		});
-		return selected;
+	if ( includeWidth ) {
+		attrs.opacity = attrs.width = type;
 	}
 
-	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+	return attrs;
 }
 
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
-	var deep, key,
-		flatOptions = jQuery.ajaxSettings.flatOptions || {};
+function createTween( value, prop, animation ) {
+	var tween,
+		collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
+		index = 0,
+		length = collection.length;
+	for ( ; index < length; index++ ) {
+		if ( (tween = collection[ index ].call( animation, prop, value )) ) {
 
-	for ( key in src ) {
-		if ( src[ key ] !== undefined ) {
-			( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
+			// we're done with this property
+			return tween;
 		}
 	}
-	if ( deep ) {
-		jQuery.extend( true, target, deep );
-	}
-
-	return target;
 }
 
-jQuery.fn.load = function( url, params, callback ) {
-	if ( typeof url !== "string" && _load ) {
-		return _load.apply( this, arguments );
-	}
+function defaultPrefilter( elem, props, opts ) {
+	/* jshint validthis: true */
+	var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay,
+		anim = this,
+		orig = {},
+		style = elem.style,
+		hidden = elem.nodeType && isHidden( elem ),
+		dataShow = jQuery._data( elem, "fxshow" );
 
-	var selector, response, type,
-		self = this,
-		off = url.indexOf(" ");
+	// handle queue: false promises
+	if ( !opts.queue ) {
+		hooks = jQuery._queueHooks( elem, "fx" );
+		if ( hooks.unqueued == null ) {
+			hooks.unqueued = 0;
+			oldfire = hooks.empty.fire;
+			hooks.empty.fire = function() {
+				if ( !hooks.unqueued ) {
+					oldfire();
+				}
+			};
+		}
+		hooks.unqueued++;
 
-	if ( off >= 0 ) {
-		selector = url.slice( off, url.length );
-		url = url.slice( 0, off );
+		anim.always(function() {
+			// doing this makes sure that the complete handler will be called
+			// before this completes
+			anim.always(function() {
+				hooks.unqueued--;
+				if ( !jQuery.queue( elem, "fx" ).length ) {
+					hooks.empty.fire();
+				}
+			});
+		});
 	}
 
-	// If it's a function
-	if ( jQuery.isFunction( params ) ) {
-
-		// We assume that it's the callback
-		callback = params;
-		params = undefined;
-
-	// Otherwise, build a param string
-	} else if ( params && typeof params === "object" ) {
-		type = "POST";
-	}
+	// height/width overflow pass
+	if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
+		// Make sure that nothing sneaks out
+		// Record all 3 overflow attributes because IE does not
+		// change the overflow attribute when overflowX and
+		// overflowY are set to the same value
+		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
 
-	// If we have elements to modify, make the request
-	if ( self.length > 0 ) {
-		jQuery.ajax({
-			url: url,
+		// Set display property to inline-block for height/width
+		// animations on inline elements that are having width/height animated
+		display = jQuery.css( elem, "display" );
 
-			// if "type" variable is undefined, then "GET" method will be used
-			type: type,
-			dataType: "html",
-			data: params
-		}).done(function( responseText ) {
+		// Test default display if display is currently "none"
+		checkDisplay = display === "none" ?
+			jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display;
 
-			// Save response for use in complete callback
-			response = arguments;
+		if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) {
 
-			self.html( selector ?
-
-				// If a selector was specified, locate the right elements in a dummy div
-				// Exclude scripts to avoid IE 'Permission Denied' errors
-				jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
-
-				// Otherwise use the full result
-				responseText );
+			// inline-level elements accept inline-block;
+			// block-level elements need to be inline with layout
+			if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) {
+				style.display = "inline-block";
+			} else {
+				style.zoom = 1;
+			}
+		}
+	}
 
-		}).complete( callback && function( jqXHR, status ) {
-			self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
-		});
+	if ( opts.overflow ) {
+		style.overflow = "hidden";
+		if ( !support.shrinkWrapBlocks() ) {
+			anim.always(function() {
+				style.overflow = opts.overflow[ 0 ];
+				style.overflowX = opts.overflow[ 1 ];
+				style.overflowY = opts.overflow[ 2 ];
+			});
+		}
 	}
 
-	return this;
-};
+	// show/hide pass
+	for ( prop in props ) {
+		value = props[ prop ];
+		if ( rfxtypes.exec( value ) ) {
+			delete props[ prop ];
+			toggle = toggle || value === "toggle";
+			if ( value === ( hidden ? "hide" : "show" ) ) {
 
-// Attach a bunch of functions for handling common AJAX events
-jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ){
-	jQuery.fn[ type ] = function( fn ){
-		return this.on( type, fn );
-	};
-});
+				// If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden
+				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
+					hidden = true;
+				} else {
+					continue;
+				}
+			}
+			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
 
-jQuery.each( [ "get", "post" ], function( i, method ) {
-	jQuery[ method ] = function( url, data, callback, type ) {
-		// shift arguments if data argument was omitted
-		if ( jQuery.isFunction( data ) ) {
-			type = type || callback;
-			callback = data;
-			data = undefined;
+		// Any non-fx value stops us from restoring the original display value
+		} else {
+			display = undefined;
 		}
+	}
 
-		return jQuery.ajax({
-			url: url,
-			type: method,
-			dataType: type,
-			data: data,
-			success: callback
-		});
-	};
-});
+	if ( !jQuery.isEmptyObject( orig ) ) {
+		if ( dataShow ) {
+			if ( "hidden" in dataShow ) {
+				hidden = dataShow.hidden;
+			}
+		} else {
+			dataShow = jQuery._data( elem, "fxshow", {} );
+		}
 
-jQuery.extend({
+		// store state if its toggle - enables .stop().toggle() to "reverse"
+		if ( toggle ) {
+			dataShow.hidden = !hidden;
+		}
+		if ( hidden ) {
+			jQuery( elem ).show();
+		} else {
+			anim.done(function() {
+				jQuery( elem ).hide();
+			});
+		}
+		anim.done(function() {
+			var prop;
+			jQuery._removeData( elem, "fxshow" );
+			for ( prop in orig ) {
+				jQuery.style( elem, prop, orig[ prop ] );
+			}
+		});
+		for ( prop in orig ) {
+			tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
 
-	// Counter for holding the number of active queries
-	active: 0,
+			if ( !( prop in dataShow ) ) {
+				dataShow[ prop ] = tween.start;
+				if ( hidden ) {
+					tween.end = tween.start;
+					tween.start = prop === "width" || prop === "height" ? 1 : 0;
+				}
+			}
+		}
 
-	// Last-Modified header cache for next request
-	lastModified: {},
-	etag: {},
+	// If this is a noop like .hide().hide(), restore an overwritten display value
+	} else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) {
+		style.display = display;
+	}
+}
 
-	ajaxSettings: {
-		url: ajaxLocation,
-		type: "GET",
-		isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
-		global: true,
-		processData: true,
-		async: true,
-		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
-		/*
-		timeout: 0,
-		data: null,
-		dataType: null,
-		username: null,
-		password: null,
-		cache: null,
-		throws: false,
-		traditional: false,
-		headers: {},
-		*/
+function propFilter( props, specialEasing ) {
+	var index, name, easing, value, hooks;
 
-		accepts: {
-			"*": allTypes,
-			text: "text/plain",
-			html: "text/html",
-			xml: "application/xml, text/xml",
-			json: "application/json, text/javascript"
-		},
+	// camelCase, specialEasing and expand cssHook pass
+	for ( index in props ) {
+		name = jQuery.camelCase( index );
+		easing = specialEasing[ name ];
+		value = props[ index ];
+		if ( jQuery.isArray( value ) ) {
+			easing = value[ 1 ];
+			value = props[ index ] = value[ 0 ];
+		}
 
-		contents: {
-			xml: /xml/,
-			html: /html/,
-			json: /json/
-		},
+		if ( index !== name ) {
+			props[ name ] = value;
+			delete props[ index ];
+		}
 
-		responseFields: {
-			xml: "responseXML",
-			text: "responseText"
-		},
+		hooks = jQuery.cssHooks[ name ];
+		if ( hooks && "expand" in hooks ) {
+			value = hooks.expand( value );
+			delete props[ name ];
 
-		// Data converters
-		// Keys separate source (or catchall "*") and destination types with a single space
-		converters: {
+			// not quite $.extend, this wont overwrite keys already present.
+			// also - reusing 'index' from above because we have the correct "name"
+			for ( index in value ) {
+				if ( !( index in props ) ) {
+					props[ index ] = value[ index ];
+					specialEasing[ index ] = easing;
+				}
+			}
+		} else {
+			specialEasing[ name ] = easing;
+		}
+	}
+}
 
-			// Convert anything to text
-			"* text": window.String,
+function Animation( elem, properties, options ) {
+	var result,
+		stopped,
+		index = 0,
+		length = animationPrefilters.length,
+		deferred = jQuery.Deferred().always( function() {
+			// don't match elem in the :animated selector
+			delete tick.elem;
+		}),
+		tick = function() {
+			if ( stopped ) {
+				return false;
+			}
+			var currentTime = fxNow || createFxNow(),
+				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+				// archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
+				temp = remaining / animation.duration || 0,
+				percent = 1 - temp,
+				index = 0,
+				length = animation.tweens.length;
 
-			// Text to html (true = no transformation)
-			"text html": true,
+			for ( ; index < length ; index++ ) {
+				animation.tweens[ index ].run( percent );
+			}
 
-			// Evaluate text as a json expression
-			"text json": jQuery.parseJSON,
+			deferred.notifyWith( elem, [ animation, percent, remaining ]);
 
-			// Parse text as xml
-			"text xml": jQuery.parseXML
+			if ( percent < 1 && length ) {
+				return remaining;
+			} else {
+				deferred.resolveWith( elem, [ animation ] );
+				return false;
+			}
 		},
+		animation = deferred.promise({
+			elem: elem,
+			props: jQuery.extend( {}, properties ),
+			opts: jQuery.extend( true, { specialEasing: {} }, options ),
+			originalProperties: properties,
+			originalOptions: options,
+			startTime: fxNow || createFxNow(),
+			duration: options.duration,
+			tweens: [],
+			createTween: function( prop, end ) {
+				var tween = jQuery.Tween( elem, animation.opts, prop, end,
+						animation.opts.specialEasing[ prop ] || animation.opts.easing );
+				animation.tweens.push( tween );
+				return tween;
+			},
+			stop: function( gotoEnd ) {
+				var index = 0,
+					// if we are going to the end, we want to run all the tweens
+					// otherwise we skip this part
+					length = gotoEnd ? animation.tweens.length : 0;
+				if ( stopped ) {
+					return this;
+				}
+				stopped = true;
+				for ( ; index < length ; index++ ) {
+					animation.tweens[ index ].run( 1 );
+				}
 
-		// For options that shouldn't be deep extended:
-		// you can add your own custom options here if
-		// and when you create one that shouldn't be
-		// deep extended (see ajaxExtend)
-		flatOptions: {
-			url: true,
-			context: true
-		}
-	},
-
-	// Creates a full fledged settings object into target
-	// with both ajaxSettings and settings fields.
-	// If target is omitted, writes into ajaxSettings.
-	ajaxSetup: function( target, settings ) {
-		return settings ?
+				// resolve when we played the last frame
+				// otherwise, reject
+				if ( gotoEnd ) {
+					deferred.resolveWith( elem, [ animation, gotoEnd ] );
+				} else {
+					deferred.rejectWith( elem, [ animation, gotoEnd ] );
+				}
+				return this;
+			}
+		}),
+		props = animation.props;
 
-			// Building a settings object
-			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
+	propFilter( props, animation.opts.specialEasing );
 
-			// Extending ajaxSettings
-			ajaxExtend( jQuery.ajaxSettings, target );
-	},
-
-	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
-	ajaxTransport: addToPrefiltersOrTransports( transports ),
-
-	// Main method
-	ajax: function( url, options ) {
-
-		// If url is an object, simulate pre-1.5 signature
-		if ( typeof url === "object" ) {
-			options = url;
-			url = undefined;
+	for ( ; index < length ; index++ ) {
+		result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
+		if ( result ) {
+			return result;
 		}
+	}
 
-		// Force options to be an object
-		options = options || {};
-
-		var // Cross-domain detection vars
-			parts,
-			// Loop variable
-			i,
-			// URL without anti-cache param
-			cacheURL,
-			// Response headers as string
-			responseHeadersString,
-			// timeout handle
-			timeoutTimer,
-
-			// To know if global events are to be dispatched
-			fireGlobals,
+	jQuery.map( props, createTween, animation );
 
-			transport,
-			// Response headers
-			responseHeaders,
-			// Create the final options object
-			s = jQuery.ajaxSetup( {}, options ),
-			// Callbacks context
-			callbackContext = s.context || s,
-			// Context for global events is callbackContext if it is a DOM node or jQuery collection
-			globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
-				jQuery( callbackContext ) :
-				jQuery.event,
-			// Deferreds
-			deferred = jQuery.Deferred(),
-			completeDeferred = jQuery.Callbacks("once memory"),
-			// Status-dependent callbacks
-			statusCode = s.statusCode || {},
-			// Headers (they are sent all at once)
-			requestHeaders = {},
-			requestHeadersNames = {},
-			// The jqXHR state
-			state = 0,
-			// Default abort message
-			strAbort = "canceled",
-			// Fake xhr
-			jqXHR = {
-				readyState: 0,
+	if ( jQuery.isFunction( animation.opts.start ) ) {
+		animation.opts.start.call( elem, animation );
+	}
 
-				// Builds headers hashtable if needed
-				getResponseHeader: function( key ) {
-					var match;
-					if ( state === 2 ) {
-						if ( !responseHeaders ) {
-							responseHeaders = {};
-							while ( (match = rheaders.exec( responseHeadersString )) ) {
-								responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
-							}
-						}
-						match = responseHeaders[ key.toLowerCase() ];
-					}
-					return match == null ? null : match;
-				},
+	jQuery.fx.timer(
+		jQuery.extend( tick, {
+			elem: elem,
+			anim: animation,
+			queue: animation.opts.queue
+		})
+	);
 
-				// Raw string
-				getAllResponseHeaders: function() {
-					return state === 2 ? responseHeadersString : null;
-				},
+	// attach callbacks from options
+	return animation.progress( animation.opts.progress )
+		.done( animation.opts.done, animation.opts.complete )
+		.fail( animation.opts.fail )
+		.always( animation.opts.always );
+}
 
-				// Caches the header
-				setRequestHeader: function( name, value ) {
-					var lname = name.toLowerCase();
-					if ( !state ) {
-						name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
-						requestHeaders[ name ] = value;
-					}
-					return this;
-				},
+jQuery.Animation = jQuery.extend( Animation, {
+	tweener: function( props, callback ) {
+		if ( jQuery.isFunction( props ) ) {
+			callback = props;
+			props = [ "*" ];
+		} else {
+			props = props.split(" ");
+		}
 
-				// Overrides response content-type header
-				overrideMimeType: function( type ) {
-					if ( !state ) {
-						s.mimeType = type;
-					}
-					return this;
-				},
+		var prop,
+			index = 0,
+			length = props.length;
 
-				// Status-dependent callbacks
-				statusCode: function( map ) {
-					var code;
-					if ( map ) {
-						if ( state < 2 ) {
-							for ( code in map ) {
-								// Lazy-add the new callback in a way that preserves old ones
-								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
-							}
-						} else {
-							// Execute the appropriate callbacks
-							jqXHR.always( map[ jqXHR.status ] );
-						}
-					}
-					return this;
-				},
+		for ( ; index < length ; index++ ) {
+			prop = props[ index ];
+			tweeners[ prop ] = tweeners[ prop ] || [];
+			tweeners[ prop ].unshift( callback );
+		}
+	},
 
-				// Cancel the request
-				abort: function( statusText ) {
-					var finalText = statusText || strAbort;
-					if ( transport ) {
-						transport.abort( finalText );
-					}
-					done( 0, finalText );
-					return this;
-				}
-			};
+	prefilter: function( callback, prepend ) {
+		if ( prepend ) {
+			animationPrefilters.unshift( callback );
+		} else {
+			animationPrefilters.push( callback );
+		}
+	}
+});
 
-		// Attach deferreds
-		deferred.promise( jqXHR ).complete = completeDeferred.add;
-		jqXHR.success = jqXHR.done;
-		jqXHR.error = jqXHR.fail;
+jQuery.speed = function( speed, easing, fn ) {
+	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+		complete: fn || !fn && easing ||
+			jQuery.isFunction( speed ) && speed,
+		duration: speed,
+		easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
+	};
 
-		// Remove hash character (#7531: and string promotion)
-		// Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
-		// Handle falsy url in the settings object (#10093: consistency with old signature)
-		// We also use the url parameter if available
-		s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
+	opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
+		opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
 
-		// Alias method option to type as per ticket #12004
-		s.type = options.method || options.type || s.method || s.type;
+	// normalize opt.queue - true/undefined/null -> "fx"
+	if ( opt.queue == null || opt.queue === true ) {
+		opt.queue = "fx";
+	}
 
-		// Extract dataTypes list
-		s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( core_rnotwhite ) || [""];
+	// Queueing
+	opt.old = opt.complete;
 
-		// A cross-domain request is in order when we have a protocol:host:port mismatch
-		if ( s.crossDomain == null ) {
-			parts = rurl.exec( s.url.toLowerCase() );
-			s.crossDomain = !!( parts &&
-				( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
-					( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) !=
-						( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? 80 : 443 ) ) )
-			);
+	opt.complete = function() {
+		if ( jQuery.isFunction( opt.old ) ) {
+			opt.old.call( this );
 		}
 
-		// Convert data if not already a string
-		if ( s.data && s.processData && typeof s.data !== "string" ) {
-			s.data = jQuery.param( s.data, s.traditional );
+		if ( opt.queue ) {
+			jQuery.dequeue( this, opt.queue );
 		}
+	};
 
-		// Apply prefilters
-		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
-		// If request was aborted inside a prefilter, stop there
-		if ( state === 2 ) {
-			return jqXHR;
-		}
+	return opt;
+};
 
-		// We can fire global events as of now if asked to
-		fireGlobals = s.global;
+jQuery.fn.extend({
+	fadeTo: function( speed, to, easing, callback ) {
 
-		// Watch for a new set of requests
-		if ( fireGlobals && jQuery.active++ === 0 ) {
-			jQuery.event.trigger("ajaxStart");
-		}
+		// show any hidden elements after setting opacity to 0
+		return this.filter( isHidden ).css( "opacity", 0 ).show()
 
-		// Uppercase the type
-		s.type = s.type.toUpperCase();
+			// animate to the value specified
+			.end().animate({ opacity: to }, speed, easing, callback );
+	},
+	animate: function( prop, speed, easing, callback ) {
+		var empty = jQuery.isEmptyObject( prop ),
+			optall = jQuery.speed( speed, easing, callback ),
+			doAnimation = function() {
+				// Operate on a copy of prop so per-property easing won't be lost
+				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
 
-		// Determine if request has content
-		s.hasContent = !rnoContent.test( s.type );
+				// Empty animations, or finishing resolves immediately
+				if ( empty || jQuery._data( this, "finish" ) ) {
+					anim.stop( true );
+				}
+			};
+			doAnimation.finish = doAnimation;
 
-		// Save the URL in case we're toying with the If-Modified-Since
-		// and/or If-None-Match header later on
-		cacheURL = s.url;
+		return empty || optall.queue === false ?
+			this.each( doAnimation ) :
+			this.queue( optall.queue, doAnimation );
+	},
+	stop: function( type, clearQueue, gotoEnd ) {
+		var stopQueue = function( hooks ) {
+			var stop = hooks.stop;
+			delete hooks.stop;
+			stop( gotoEnd );
+		};
 
-		// More options handling for requests with no content
-		if ( !s.hasContent ) {
+		if ( typeof type !== "string" ) {
+			gotoEnd = clearQueue;
+			clearQueue = type;
+			type = undefined;
+		}
+		if ( clearQueue && type !== false ) {
+			this.queue( type || "fx", [] );
+		}
 
-			// If data is available, append data to url
-			if ( s.data ) {
-				cacheURL = ( s.url += ( ajax_rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
-				// #9682: remove data so that it's not used in an eventual retry
-				delete s.data;
-			}
+		return this.each(function() {
+			var dequeue = true,
+				index = type != null && type + "queueHooks",
+				timers = jQuery.timers,
+				data = jQuery._data( this );
 
-			// Add anti-cache in url if needed
-			if ( s.cache === false ) {
-				s.url = rts.test( cacheURL ) ?
+			if ( index ) {
+				if ( data[ index ] && data[ index ].stop ) {
+					stopQueue( data[ index ] );
+				}
+			} else {
+				for ( index in data ) {
+					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+						stopQueue( data[ index ] );
+					}
+				}
+			}
 
-					// If there is already a '_' parameter, set its value
-					cacheURL.replace( rts, "$1_=" + ajax_nonce++ ) :
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
+					timers[ index ].anim.stop( gotoEnd );
+					dequeue = false;
+					timers.splice( index, 1 );
+				}
+			}
 
-					// Otherwise add one to the end
-					cacheURL + ( ajax_rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ajax_nonce++;
+			// start the next in the queue if the last step wasn't forced
+			// timers currently will call their complete callbacks, which will dequeue
+			// but only if they were gotoEnd
+			if ( dequeue || !gotoEnd ) {
+				jQuery.dequeue( this, type );
 			}
+		});
+	},
+	finish: function( type ) {
+		if ( type !== false ) {
+			type = type || "fx";
 		}
+		return this.each(function() {
+			var index,
+				data = jQuery._data( this ),
+				queue = data[ type + "queue" ],
+				hooks = data[ type + "queueHooks" ],
+				timers = jQuery.timers,
+				length = queue ? queue.length : 0;
 
-		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-		if ( s.ifModified ) {
-			if ( jQuery.lastModified[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+			// enable finishing flag on private data
+			data.finish = true;
+
+			// empty the queue first
+			jQuery.queue( this, type, [] );
+
+			if ( hooks && hooks.stop ) {
+				hooks.stop.call( this, true );
 			}
-			if ( jQuery.etag[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+
+			// look for any active animations, and finish them
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
+					timers[ index ].anim.stop( true );
+					timers.splice( index, 1 );
+				}
 			}
-		}
 
-		// Set the correct header, if data is being sent
-		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
-			jqXHR.setRequestHeader( "Content-Type", s.contentType );
-		}
+			// look for any animations in the old queue and finish them
+			for ( index = 0; index < length; index++ ) {
+				if ( queue[ index ] && queue[ index ].finish ) {
+					queue[ index ].finish.call( this );
+				}
+			}
 
-		// Set the Accepts header for the server, depending on the dataType
-		jqXHR.setRequestHeader(
-			"Accept",
-			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
-				s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
-				s.accepts[ "*" ]
-		);
+			// turn off finishing flag
+			delete data.finish;
+		});
+	}
+});
 
-		// Check for headers option
-		for ( i in s.headers ) {
-			jqXHR.setRequestHeader( i, s.headers[ i ] );
-		}
+jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
+	var cssFn = jQuery.fn[ name ];
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return speed == null || typeof speed === "boolean" ?
+			cssFn.apply( this, arguments ) :
+			this.animate( genFx( name, true ), speed, easing, callback );
+	};
+});
 
-		// Allow custom headers/mimetypes and early abort
-		if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
-			// Abort if not done already and return
-			return jqXHR.abort();
-		}
+// Generate shortcuts for custom animations
+jQuery.each({
+	slideDown: genFx("show"),
+	slideUp: genFx("hide"),
+	slideToggle: genFx("toggle"),
+	fadeIn: { opacity: "show" },
+	fadeOut: { opacity: "hide" },
+	fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return this.animate( props, speed, easing, callback );
+	};
+});
 
-		// aborting is no longer a cancellation
-		strAbort = "abort";
+jQuery.timers = [];
+jQuery.fx.tick = function() {
+	var timer,
+		timers = jQuery.timers,
+		i = 0;
 
-		// Install callbacks on deferreds
-		for ( i in { success: 1, error: 1, complete: 1 } ) {
-			jqXHR[ i ]( s[ i ] );
+	fxNow = jQuery.now();
+
+	for ( ; i < timers.length; i++ ) {
+		timer = timers[ i ];
+		// Checks the timer has not already been removed
+		if ( !timer() && timers[ i ] === timer ) {
+			timers.splice( i--, 1 );
 		}
+	}
 
-		// Get transport
-		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+	if ( !timers.length ) {
+		jQuery.fx.stop();
+	}
+	fxNow = undefined;
+};
 
-		// If no transport, we auto-abort
-		if ( !transport ) {
-			done( -1, "No Transport" );
-		} else {
-			jqXHR.readyState = 1;
+jQuery.fx.timer = function( timer ) {
+	jQuery.timers.push( timer );
+	if ( timer() ) {
+		jQuery.fx.start();
+	} else {
+		jQuery.timers.pop();
+	}
+};
 
-			// Send global event
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
-			}
-			// Timeout
-			if ( s.async && s.timeout > 0 ) {
-				timeoutTimer = setTimeout(function() {
-					jqXHR.abort("timeout");
-				}, s.timeout );
-			}
+jQuery.fx.interval = 13;
 
-			try {
-				state = 1;
-				transport.send( requestHeaders, done );
-			} catch ( e ) {
-				// Propagate exception as error if not done
-				if ( state < 2 ) {
-					done( -1, e );
-				// Simply rethrow otherwise
-				} else {
-					throw e;
-				}
-			}
-		}
+jQuery.fx.start = function() {
+	if ( !timerId ) {
+		timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
+	}
+};
 
-		// Callback for when everything is done
-		function done( status, nativeStatusText, responses, headers ) {
-			var isSuccess, success, error, response, modified,
-				statusText = nativeStatusText;
+jQuery.fx.stop = function() {
+	clearInterval( timerId );
+	timerId = null;
+};
 
-			// Called once
-			if ( state === 2 ) {
-				return;
-			}
+jQuery.fx.speeds = {
+	slow: 600,
+	fast: 200,
+	// Default speed
+	_default: 400
+};
 
-			// State is "done" now
-			state = 2;
 
-			// Clear timeout if it exists
-			if ( timeoutTimer ) {
-				clearTimeout( timeoutTimer );
-			}
+// Based off of the plugin by Clint Helfers, with permission.
+// http://blindsignals.com/index.php/2009/07/jquery-delay/
+jQuery.fn.delay = function( time, type ) {
+	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+	type = type || "fx";
 
-			// Dereference transport for early garbage collection
-			// (no matter how long the jqXHR object will be used)
-			transport = undefined;
+	return this.queue( type, function( next, hooks ) {
+		var timeout = setTimeout( next, time );
+		hooks.stop = function() {
+			clearTimeout( timeout );
+		};
+	});
+};
 
-			// Cache response headers
-			responseHeadersString = headers || "";
 
-			// Set readyState
-			jqXHR.readyState = status > 0 ? 4 : 0;
+(function() {
+	// Minified: var a,b,c,d,e
+	var input, div, select, a, opt;
 
-			// Get response data
-			if ( responses ) {
-				response = ajaxHandleResponses( s, jqXHR, responses );
-			}
+	// Setup
+	div = document.createElement( "div" );
+	div.setAttribute( "className", "t" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName("a")[ 0 ];
 
-			// If successful, handle type chaining
-			if ( status >= 200 && status < 300 || status === 304 ) {
+	// First batch of tests.
+	select = document.createElement("select");
+	opt = select.appendChild( document.createElement("option") );
+	input = div.getElementsByTagName("input")[ 0 ];
 
-				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-				if ( s.ifModified ) {
-					modified = jqXHR.getResponseHeader("Last-Modified");
-					if ( modified ) {
-						jQuery.lastModified[ cacheURL ] = modified;
-					}
-					modified = jqXHR.getResponseHeader("etag");
-					if ( modified ) {
-						jQuery.etag[ cacheURL ] = modified;
-					}
-				}
+	a.style.cssText = "top:1px";
 
-				// if no content
-				if ( status === 204 ) {
-					isSuccess = true;
-					statusText = "nocontent";
+	// Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
+	support.getSetAttribute = div.className !== "t";
 
-				// if not modified
-				} else if ( status === 304 ) {
-					isSuccess = true;
-					statusText = "notmodified";
-
-				// If we have data, let's convert it
-				} else {
-					isSuccess = ajaxConvert( s, response );
-					statusText = isSuccess.state;
-					success = isSuccess.data;
-					error = isSuccess.error;
-					isSuccess = !error;
-				}
-			} else {
-				// We extract error from statusText
-				// then normalize statusText and status for non-aborts
-				error = statusText;
-				if ( status || !statusText ) {
-					statusText = "error";
-					if ( status < 0 ) {
-						status = 0;
-					}
-				}
-			}
+	// Get the style information from getAttribute
+	// (IE uses .cssText instead)
+	support.style = /top/.test( a.getAttribute("style") );
 
-			// Set data for the fake xhr object
-			jqXHR.status = status;
-			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+	// Make sure that URLs aren't manipulated
+	// (IE normalizes it by default)
+	support.hrefNormalized = a.getAttribute("href") === "/a";
 
-			// Success/Error
-			if ( isSuccess ) {
-				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
-			} else {
-				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
-			}
+	// Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
+	support.checkOn = !!input.value;
 
-			// Status-dependent callbacks
-			jqXHR.statusCode( statusCode );
-			statusCode = undefined;
+	// Make sure that a selected-by-default option has a working selected property.
+	// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
+	support.optSelected = opt.selected;
 
-			if ( fireGlobals ) {
-				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
-					[ jqXHR, s, isSuccess ? success : error ] );
-			}
+	// Tests for enctype support on a form (#6743)
+	support.enctype = !!document.createElement("form").enctype;
 
-			// Complete
-			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+	// Make sure that the options inside disabled selects aren't marked as disabled
+	// (WebKit marks them as disabled)
+	select.disabled = true;
+	support.optDisabled = !opt.disabled;
 
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
-				// Handle the global AJAX counter
-				if ( !( --jQuery.active ) ) {
-					jQuery.event.trigger("ajaxStop");
-				}
-			}
-		}
+	// Support: IE8 only
+	// Check if we can trust getAttribute("value")
+	input = document.createElement( "input" );
+	input.setAttribute( "value", "" );
+	support.input = input.getAttribute( "value" ) === "";
 
-		return jqXHR;
-	},
+	// Check if an input maintains its value after becoming a radio
+	input.value = "t";
+	input.setAttribute( "type", "radio" );
+	support.radioValue = input.value === "t";
+})();
 
-	getScript: function( url, callback ) {
-		return jQuery.get( url, undefined, callback, "script" );
-	},
 
-	getJSON: function( url, data, callback ) {
-		return jQuery.get( url, data, callback, "json" );
-	}
-});
+var rreturn = /\r/g;
 
-/* Handles responses to an ajax request:
- * - sets all responseXXX fields accordingly
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-	var firstDataType, ct, finalDataType, type,
-		contents = s.contents,
-		dataTypes = s.dataTypes,
-		responseFields = s.responseFields;
+jQuery.fn.extend({
+	val: function( value ) {
+		var hooks, ret, isFunction,
+			elem = this[0];
 
-	// Fill responseXXX fields
-	for ( type in responseFields ) {
-		if ( type in responses ) {
-			jqXHR[ responseFields[type] ] = responses[ type ];
-		}
-	}
+		if ( !arguments.length ) {
+			if ( elem ) {
+				hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
 
-	// Remove auto dataType and get content-type in the process
-	while( dataTypes[ 0 ] === "*" ) {
-		dataTypes.shift();
-		if ( ct === undefined ) {
-			ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
-		}
-	}
+				if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
+					return ret;
+				}
 
-	// Check if we're dealing with a known content-type
-	if ( ct ) {
-		for ( type in contents ) {
-			if ( contents[ type ] && contents[ type ].test( ct ) ) {
-				dataTypes.unshift( type );
-				break;
-			}
-		}
-	}
+				ret = elem.value;
 
-	// Check to see if we have a response for the expected dataType
-	if ( dataTypes[ 0 ] in responses ) {
-		finalDataType = dataTypes[ 0 ];
-	} else {
-		// Try convertible dataTypes
-		for ( type in responses ) {
-			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
-				finalDataType = type;
-				break;
-			}
-			if ( !firstDataType ) {
-				firstDataType = type;
+				return typeof ret === "string" ?
+					// handle most common string cases
+					ret.replace(rreturn, "") :
+					// handle cases where value is null/undef or number
+					ret == null ? "" : ret;
 			}
-		}
-		// Or just use first one
-		finalDataType = finalDataType || firstDataType;
-	}
 
-	// If we found a dataType
-	// We add the dataType to the list if needed
-	// and return the corresponding response
-	if ( finalDataType ) {
-		if ( finalDataType !== dataTypes[ 0 ] ) {
-			dataTypes.unshift( finalDataType );
+			return;
 		}
-		return responses[ finalDataType ];
-	}
-}
 
-// Chain conversions given the request and the original response
-function ajaxConvert( s, response ) {
-	var conv2, current, conv, tmp,
-		converters = {},
-		i = 0,
-		// Work with a copy of dataTypes in case we need to modify it for conversion
-		dataTypes = s.dataTypes.slice(),
-		prev = dataTypes[ 0 ];
+		isFunction = jQuery.isFunction( value );
 
-	// Apply the dataFilter if provided
-	if ( s.dataFilter ) {
-		response = s.dataFilter( response, s.dataType );
-	}
+		return this.each(function( i ) {
+			var val;
 
-	// Create converters map with lowercased keys
-	if ( dataTypes[ 1 ] ) {
-		for ( conv in s.converters ) {
-			converters[ conv.toLowerCase() ] = s.converters[ conv ];
-		}
-	}
+			if ( this.nodeType !== 1 ) {
+				return;
+			}
 
-	// Convert to each sequential dataType, tolerating list modification
-	for ( ; (current = dataTypes[++i]); ) {
+			if ( isFunction ) {
+				val = value.call( this, i, jQuery( this ).val() );
+			} else {
+				val = value;
+			}
 
-		// There's only work to do if current dataType is non-auto
-		if ( current !== "*" ) {
+			// Treat null/undefined as ""; convert numbers to string
+			if ( val == null ) {
+				val = "";
+			} else if ( typeof val === "number" ) {
+				val += "";
+			} else if ( jQuery.isArray( val ) ) {
+				val = jQuery.map( val, function( value ) {
+					return value == null ? "" : value + "";
+				});
+			}
 
-			// Convert response if prev dataType is non-auto and differs from current
-			if ( prev !== "*" && prev !== current ) {
+			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
 
-				// Seek a direct converter
-				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+			// If set returns undefined, fall back to normal setting
+			if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
+				this.value = val;
+			}
+		});
+	}
+});
 
-				// If none found, seek a pair
-				if ( !conv ) {
-					for ( conv2 in converters ) {
+jQuery.extend({
+	valHooks: {
+		option: {
+			get: function( elem ) {
+				var val = jQuery.find.attr( elem, "value" );
+				return val != null ?
+					val :
+					// Support: IE10-11+
+					// option.text throws exceptions (#14686, #14858)
+					jQuery.trim( jQuery.text( elem ) );
+			}
+		},
+		select: {
+			get: function( elem ) {
+				var value, option,
+					options = elem.options,
+					index = elem.selectedIndex,
+					one = elem.type === "select-one" || index < 0,
+					values = one ? null : [],
+					max = one ? index + 1 : options.length,
+					i = index < 0 ?
+						max :
+						one ? index : 0;
 
-						// If conv2 outputs current
-						tmp = conv2.split(" ");
-						if ( tmp[ 1 ] === current ) {
+				// Loop through all the selected options
+				for ( ; i < max; i++ ) {
+					option = options[ i ];
 
-							// If prev can be converted to accepted input
-							conv = converters[ prev + " " + tmp[ 0 ] ] ||
-								converters[ "* " + tmp[ 0 ] ];
-							if ( conv ) {
-								// Condense equivalence converters
-								if ( conv === true ) {
-									conv = converters[ conv2 ];
+					// oldIE doesn't update selected after form reset (#2551)
+					if ( ( option.selected || i === index ) &&
+							// Don't return options that are disabled or in a disabled optgroup
+							( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
+							( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
 
-								// Otherwise, insert the intermediate dataType
-								} else if ( converters[ conv2 ] !== true ) {
-									current = tmp[ 0 ];
-									dataTypes.splice( i--, 0, current );
-								}
+						// Get the specific value for the option
+						value = jQuery( option ).val();
 
-								break;
-							}
+						// We don't need an array for one selects
+						if ( one ) {
+							return value;
 						}
+
+						// Multi-Selects return an array
+						values.push( value );
 					}
 				}
 
-				// Apply converter (if not an equivalence)
-				if ( conv !== true ) {
+				return values;
+			},
 
-					// Unless errors are allowed to bubble, catch and return them
-					if ( conv && s["throws"] ) {
-						response = conv( response );
-					} else {
+			set: function( elem, value ) {
+				var optionSet, option,
+					options = elem.options,
+					values = jQuery.makeArray( value ),
+					i = options.length;
+
+				while ( i-- ) {
+					option = options[ i ];
+
+					if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) {
+
+						// Support: IE6
+						// When new option element is added to select box we need to
+						// force reflow of newly added node in order to workaround delay
+						// of initialization properties
 						try {
-							response = conv( response );
-						} catch ( e ) {
-							return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+							option.selected = optionSet = true;
+
+						} catch ( _ ) {
+
+							// Will be executed only in IE6
+							option.scrollHeight;
 						}
+
+					} else {
+						option.selected = false;
 					}
 				}
+
+				// Force browsers to behave consistently when non-matching value is set
+				if ( !optionSet ) {
+					elem.selectedIndex = -1;
+				}
+
+				return options;
 			}
+		}
+	}
+});
 
-			// Update prev for next iteration
-			prev = current;
+// Radios and checkboxes getter/setter
+jQuery.each([ "radio", "checkbox" ], function() {
+	jQuery.valHooks[ this ] = {
+		set: function( elem, value ) {
+			if ( jQuery.isArray( value ) ) {
+				return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
+			}
 		}
+	};
+	if ( !support.checkOn ) {
+		jQuery.valHooks[ this ].get = function( elem ) {
+			// Support: Webkit
+			// "" is returned instead of "on" if a value isn't specified
+			return elem.getAttribute("value") === null ? "on" : elem.value;
+		};
 	}
+});
 
-	return { state: "success", data: response };
-}
-// Install script dataType
-jQuery.ajaxSetup({
-	accepts: {
-		script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
-	},
-	contents: {
-		script: /(?:java|ecma)script/
+
+
+
+var nodeHook, boolHook,
+	attrHandle = jQuery.expr.attrHandle,
+	ruseDefault = /^(?:checked|selected)$/i,
+	getSetAttribute = support.getSetAttribute,
+	getSetInput = support.input;
+
+jQuery.fn.extend({
+	attr: function( name, value ) {
+		return access( this, jQuery.attr, name, value, arguments.length > 1 );
 	},
-	converters: {
-		"text script": function( text ) {
-			jQuery.globalEval( text );
-			return text;
-		}
-	}
-});
 
-// Handle cache's special case and global
-jQuery.ajaxPrefilter( "script", function( s ) {
-	if ( s.cache === undefined ) {
-		s.cache = false;
-	}
-	if ( s.crossDomain ) {
-		s.type = "GET";
-		s.global = false;
+	removeAttr: function( name ) {
+		return this.each(function() {
+			jQuery.removeAttr( this, name );
+		});
 	}
 });
 
-// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function(s) {
-
-	// This transport only deals with cross domain requests
-	if ( s.crossDomain ) {
+jQuery.extend({
+	attr: function( elem, name, value ) {
+		var hooks, ret,
+			nType = elem.nodeType;
 
-		var script,
-			head = document.head || jQuery("head")[0] || document.documentElement;
+		// don't get/set attributes on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
 
-		return {
+		// Fallback to prop when attributes are not supported
+		if ( typeof elem.getAttribute === strundefined ) {
+			return jQuery.prop( elem, name, value );
+		}
 
-			send: function( _, callback ) {
+		// All attributes are lowercase
+		// Grab necessary hook if one is defined
+		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+			name = name.toLowerCase();
+			hooks = jQuery.attrHooks[ name ] ||
+				( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook );
+		}
 
-				script = document.createElement("script");
+		if ( value !== undefined ) {
 
-				script.async = true;
+			if ( value === null ) {
+				jQuery.removeAttr( elem, name );
 
-				if ( s.scriptCharset ) {
-					script.charset = s.scriptCharset;
-				}
+			} else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
+				return ret;
 
-				script.src = s.url;
+			} else {
+				elem.setAttribute( name, value + "" );
+				return value;
+			}
 
-				// Attach handlers for all browsers
-				script.onload = script.onreadystatechange = function( _, isAbort ) {
+		} else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
+			return ret;
 
-					if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
+		} else {
+			ret = jQuery.find.attr( elem, name );
 
-						// Handle memory leak in IE
-						script.onload = script.onreadystatechange = null;
+			// Non-existent attributes return null, we normalize to undefined
+			return ret == null ?
+				undefined :
+				ret;
+		}
+	},
 
-						// Remove the script
-						if ( script.parentNode ) {
-							script.parentNode.removeChild( script );
-						}
+	removeAttr: function( elem, value ) {
+		var name, propName,
+			i = 0,
+			attrNames = value && value.match( rnotwhite );
 
-						// Dereference the script
-						script = null;
+		if ( attrNames && elem.nodeType === 1 ) {
+			while ( (name = attrNames[i++]) ) {
+				propName = jQuery.propFix[ name ] || name;
 
-						// Callback if not abort
-						if ( !isAbort ) {
-							callback( 200, "success" );
-						}
+				// Boolean attributes get special treatment (#10870)
+				if ( jQuery.expr.match.bool.test( name ) ) {
+					// Set corresponding property to false
+					if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+						elem[ propName ] = false;
+					// Support: IE<9
+					// Also clear defaultChecked/defaultSelected (if appropriate)
+					} else {
+						elem[ jQuery.camelCase( "default-" + name ) ] =
+							elem[ propName ] = false;
 					}
-				};
-
-				// Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
-				// Use native DOM manipulation to avoid our domManip AJAX trickery
-				head.insertBefore( script, head.firstChild );
-			},
 
-			abort: function() {
-				if ( script ) {
-					script.onload( undefined, true );
+				// See #9699 for explanation of this approach (setting first, then removal)
+				} else {
+					jQuery.attr( elem, name, "" );
 				}
+
+				elem.removeAttribute( getSetAttribute ? name : propName );
 			}
-		};
-	}
-});
-var oldCallbacks = [],
-	rjsonp = /(=)\?(?=&|$)|\?\?/;
+		}
+	},
 
-// Default jsonp settings
-jQuery.ajaxSetup({
-	jsonp: "callback",
-	jsonpCallback: function() {
-		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( ajax_nonce++ ) );
-		this[ callback ] = true;
-		return callback;
+	attrHooks: {
+		type: {
+			set: function( elem, value ) {
+				if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
+					// Setting the type on a radio button after the value resets the value in IE6-9
+					// Reset value to default in case type is set after value during creation
+					var val = elem.value;
+					elem.setAttribute( "type", value );
+					if ( val ) {
+						elem.value = val;
+					}
+					return value;
+				}
+			}
+		}
 	}
 });
 
-// Detect, normalize options and install callbacks for jsonp requests
-jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
-
-	var callbackName, overwritten, responseContainer,
-		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
-			"url" :
-			typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
-		);
-
-	// Handle iff the expected data type is "jsonp" or we have a parameter to set
-	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
-
-		// Get callback name, remembering preexisting value associated with it
-		callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
-			s.jsonpCallback() :
-			s.jsonpCallback;
+// Hook for boolean attributes
+boolHook = {
+	set: function( elem, value, name ) {
+		if ( value === false ) {
+			// Remove boolean attributes when set to false
+			jQuery.removeAttr( elem, name );
+		} else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+			// IE<8 needs the *property* name
+			elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
 
-		// Insert callback into url or form data
-		if ( jsonProp ) {
-			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
-		} else if ( s.jsonp !== false ) {
-			s.url += ( ajax_rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+		// Use defaultChecked and defaultSelected for oldIE
+		} else {
+			elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
 		}
 
-		// Use data converter to retrieve json after script execution
-		s.converters["script json"] = function() {
-			if ( !responseContainer ) {
-				jQuery.error( callbackName + " was not called" );
+		return name;
+	}
+};
+
+// Retrieve booleans specially
+jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
+
+	var getter = attrHandle[ name ] || jQuery.find.attr;
+
+	attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ?
+		function( elem, name, isXML ) {
+			var ret, handle;
+			if ( !isXML ) {
+				// Avoid an infinite loop by temporarily removing this function from the getter
+				handle = attrHandle[ name ];
+				attrHandle[ name ] = ret;
+				ret = getter( elem, name, isXML ) != null ?
+					name.toLowerCase() :
+					null;
+				attrHandle[ name ] = handle;
+			}
+			return ret;
+		} :
+		function( elem, name, isXML ) {
+			if ( !isXML ) {
+				return elem[ jQuery.camelCase( "default-" + name ) ] ?
+					name.toLowerCase() :
+					null;
 			}
-			return responseContainer[ 0 ];
 		};
+});
 
-		// force json dataType
-		s.dataTypes[ 0 ] = "json";
+// fix oldIE attroperties
+if ( !getSetInput || !getSetAttribute ) {
+	jQuery.attrHooks.value = {
+		set: function( elem, value, name ) {
+			if ( jQuery.nodeName( elem, "input" ) ) {
+				// Does not return so that setAttribute is also used
+				elem.defaultValue = value;
+			} else {
+				// Use nodeHook if defined (#1954); otherwise setAttribute is fine
+				return nodeHook && nodeHook.set( elem, value, name );
+			}
+		}
+	};
+}
 
-		// Install callback
-		overwritten = window[ callbackName ];
-		window[ callbackName ] = function() {
-			responseContainer = arguments;
-		};
+// IE6/7 do not support getting/setting some attributes with get/setAttribute
+if ( !getSetAttribute ) {
 
-		// Clean-up function (fires after converters)
-		jqXHR.always(function() {
-			// Restore preexisting value
-			window[ callbackName ] = overwritten;
+	// Use this for any attribute in IE6/7
+	// This fixes almost every IE6/7 issue
+	nodeHook = {
+		set: function( elem, value, name ) {
+			// Set the existing or create a new attribute node
+			var ret = elem.getAttributeNode( name );
+			if ( !ret ) {
+				elem.setAttributeNode(
+					(ret = elem.ownerDocument.createAttribute( name ))
+				);
+			}
 
-			// Save back as free
-			if ( s[ callbackName ] ) {
-				// make sure that re-using the options doesn't screw things around
-				s.jsonpCallback = originalSettings.jsonpCallback;
+			ret.value = value += "";
 
-				// save the callback name for future use
-				oldCallbacks.push( callbackName );
+			// Break association with cloned elements by also using setAttribute (#9646)
+			if ( name === "value" || value === elem.getAttribute( name ) ) {
+				return value;
 			}
+		}
+	};
 
-			// Call if it was a function and we have a response
-			if ( responseContainer && jQuery.isFunction( overwritten ) ) {
-				overwritten( responseContainer[ 0 ] );
+	// Some attributes are constructed with empty-string values when not defined
+	attrHandle.id = attrHandle.name = attrHandle.coords =
+		function( elem, name, isXML ) {
+			var ret;
+			if ( !isXML ) {
+				return (ret = elem.getAttributeNode( name )) && ret.value !== "" ?
+					ret.value :
+					null;
 			}
+		};
 
-			responseContainer = overwritten = undefined;
-		});
+	// Fixing value retrieval on a button requires this module
+	jQuery.valHooks.button = {
+		get: function( elem, name ) {
+			var ret = elem.getAttributeNode( name );
+			if ( ret && ret.specified ) {
+				return ret.value;
+			}
+		},
+		set: nodeHook.set
+	};
 
-		// Delegate to script
-		return "script";
-	}
-});
-var xhrCallbacks, xhrSupported,
-	xhrId = 0,
-	// #5280: Internet Explorer will keep connections alive if we don't abort on unload
-	xhrOnUnloadAbort = window.ActiveXObject && function() {
-		// Abort all pending requests
-		var key;
-		for ( key in xhrCallbacks ) {
-			xhrCallbacks[ key ]( undefined, true );
+	// Set contenteditable to false on removals(#10429)
+	// Setting to empty string throws an error as an invalid value
+	jQuery.attrHooks.contenteditable = {
+		set: function( elem, value, name ) {
+			nodeHook.set( elem, value === "" ? false : value, name );
 		}
 	};
 
-// Functions to create xhrs
-function createStandardXHR() {
-	try {
-		return new window.XMLHttpRequest();
-	} catch( e ) {}
+	// Set width and height to auto instead of 0 on empty string( Bug #8150 )
+	// This is for removals
+	jQuery.each([ "width", "height" ], function( i, name ) {
+		jQuery.attrHooks[ name ] = {
+			set: function( elem, value ) {
+				if ( value === "" ) {
+					elem.setAttribute( name, "auto" );
+					return value;
+				}
+			}
+		};
+	});
 }
 
-function createActiveXHR() {
-	try {
-		return new window.ActiveXObject("Microsoft.XMLHTTP");
-	} catch( e ) {}
+if ( !support.style ) {
+	jQuery.attrHooks.style = {
+		get: function( elem ) {
+			// Return undefined in the case of empty string
+			// Note: IE uppercases css property names, but if we were to .toLowerCase()
+			// .cssText, that would destroy case senstitivity in URL's, like in "background"
+			return elem.style.cssText || undefined;
+		},
+		set: function( elem, value ) {
+			return ( elem.style.cssText = value + "" );
+		}
+	};
 }
 
-// Create the request object
-// (This is still attached to ajaxSettings for backward compatibility)
-jQuery.ajaxSettings.xhr = window.ActiveXObject ?
-	/* Microsoft failed to properly
-	 * implement the XMLHttpRequest in IE7 (can't request local files),
-	 * so we use the ActiveXObject when it is available
-	 * Additionally XMLHttpRequest can be disabled in IE7/IE8 so
-	 * we need a fallback.
-	 */
-	function() {
-		return !this.isLocal && createStandardXHR() || createActiveXHR();
-	} :
-	// For all other browsers, use the standard XMLHttpRequest object
-	createStandardXHR;
 
-// Determine support properties
-xhrSupported = jQuery.ajaxSettings.xhr();
-jQuery.support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-xhrSupported = jQuery.support.ajax = !!xhrSupported;
 
-// Create transport if the browser can provide an xhr
-if ( xhrSupported ) {
 
-	jQuery.ajaxTransport(function( s ) {
-		// Cross domain only allowed if supported through XMLHttpRequest
-		if ( !s.crossDomain || jQuery.support.cors ) {
+var rfocusable = /^(?:input|select|textarea|button|object)$/i,
+	rclickable = /^(?:a|area)$/i;
 
-			var callback;
+jQuery.fn.extend({
+	prop: function( name, value ) {
+		return access( this, jQuery.prop, name, value, arguments.length > 1 );
+	},
 
-			return {
-				send: function( headers, complete ) {
+	removeProp: function( name ) {
+		name = jQuery.propFix[ name ] || name;
+		return this.each(function() {
+			// try/catch handles cases where IE balks (such as removing a property on window)
+			try {
+				this[ name ] = undefined;
+				delete this[ name ];
+			} catch( e ) {}
+		});
+	}
+});
+
+jQuery.extend({
+	propFix: {
+		"for": "htmlFor",
+		"class": "className"
+	},
 
-					// Get a new xhr
-					var handle, i,
-						xhr = s.xhr();
+	prop: function( elem, name, value ) {
+		var ret, hooks, notxml,
+			nType = elem.nodeType;
 
-					// Open the socket
-					// Passing null username, generates a login popup on Opera (#2865)
-					if ( s.username ) {
-						xhr.open( s.type, s.url, s.async, s.username, s.password );
-					} else {
-						xhr.open( s.type, s.url, s.async );
-					}
+		// don't get/set properties on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
 
-					// Apply custom fields if provided
-					if ( s.xhrFields ) {
-						for ( i in s.xhrFields ) {
-							xhr[ i ] = s.xhrFields[ i ];
-						}
-					}
+		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
 
-					// Override mime type if needed
-					if ( s.mimeType && xhr.overrideMimeType ) {
-						xhr.overrideMimeType( s.mimeType );
-					}
+		if ( notxml ) {
+			// Fix name and attach hooks
+			name = jQuery.propFix[ name ] || name;
+			hooks = jQuery.propHooks[ name ];
+		}
 
-					// X-Requested-With header
-					// For cross-domain requests, seeing as conditions for a preflight are
-					// akin to a jigsaw puzzle, we simply never set it to be sure.
-					// (it can always be set on a per-request basis or even using ajaxSetup)
-					// For same-domain requests, won't change header if already provided.
-					if ( !s.crossDomain && !headers["X-Requested-With"] ) {
-						headers["X-Requested-With"] = "XMLHttpRequest";
-					}
+		if ( value !== undefined ) {
+			return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ?
+				ret :
+				( elem[ name ] = value );
 
-					// Need an extra try/catch for cross domain requests in Firefox 3
-					try {
-						for ( i in headers ) {
-							xhr.setRequestHeader( i, headers[ i ] );
-						}
-					} catch( err ) {}
+		} else {
+			return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ?
+				ret :
+				elem[ name ];
+		}
+	},
 
-					// Do send the request
-					// This may raise an exception which is actually
-					// handled in jQuery.ajax (so no try/catch here)
-					xhr.send( ( s.hasContent && s.data ) || null );
+	propHooks: {
+		tabIndex: {
+			get: function( elem ) {
+				// elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
+				// http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+				// Use proper attribute retrieval(#12072)
+				var tabindex = jQuery.find.attr( elem, "tabindex" );
 
-					// Listener
-					callback = function( _, isAbort ) {
-						var status, responseHeaders, statusText, responses;
+				return tabindex ?
+					parseInt( tabindex, 10 ) :
+					rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
+						0 :
+						-1;
+			}
+		}
+	}
+});
 
-						// Firefox throws exceptions when accessing properties
-						// of an xhr when a network error occurred
-						// http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0x80040111_(NS_ERROR_NOT_AVAILABLE)
-						try {
+// Some attributes require a special call on IE
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !support.hrefNormalized ) {
+	// href/src property should get the full normalized URL (#10299/#12915)
+	jQuery.each([ "href", "src" ], function( i, name ) {
+		jQuery.propHooks[ name ] = {
+			get: function( elem ) {
+				return elem.getAttribute( name, 4 );
+			}
+		};
+	});
+}
 
-							// Was never called and is aborted or complete
-							if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+// Support: Safari, IE9+
+// mis-reports the default selected property of an option
+// Accessing the parent's selectedIndex property fixes it
+if ( !support.optSelected ) {
+	jQuery.propHooks.selected = {
+		get: function( elem ) {
+			var parent = elem.parentNode;
 
-								// Only called once
-								callback = undefined;
+			if ( parent ) {
+				parent.selectedIndex;
 
-								// Do not keep as active anymore
-								if ( handle ) {
-									xhr.onreadystatechange = jQuery.noop;
-									if ( xhrOnUnloadAbort ) {
-										delete xhrCallbacks[ handle ];
-									}
-								}
+				// Make sure that it also works with optgroups, see #5701
+				if ( parent.parentNode ) {
+					parent.parentNode.selectedIndex;
+				}
+			}
+			return null;
+		}
+	};
+}
 
-								// If it's an abort
-								if ( isAbort ) {
-									// Abort it manually if needed
-									if ( xhr.readyState !== 4 ) {
-										xhr.abort();
-									}
-								} else {
-									responses = {};
-									status = xhr.status;
-									responseHeaders = xhr.getAllResponseHeaders();
-
-									// When requesting binary data, IE6-9 will throw an exception
-									// on any attempt to access responseText (#11426)
-									if ( typeof xhr.responseText === "string" ) {
-										responses.text = xhr.responseText;
-									}
+jQuery.each([
+	"tabIndex",
+	"readOnly",
+	"maxLength",
+	"cellSpacing",
+	"cellPadding",
+	"rowSpan",
+	"colSpan",
+	"useMap",
+	"frameBorder",
+	"contentEditable"
+], function() {
+	jQuery.propFix[ this.toLowerCase() ] = this;
+});
 
-									// Firefox throws an exception when accessing
-									// statusText for faulty cross-domain requests
-									try {
-										statusText = xhr.statusText;
-									} catch( e ) {
-										// We normalize with Webkit giving an empty statusText
-										statusText = "";
-									}
+// IE6/7 call enctype encoding
+if ( !support.enctype ) {
+	jQuery.propFix.enctype = "encoding";
+}
 
-									// Filter status for non standard behaviors
 
-									// If the request is local and we have data: assume a success
-									// (success with no data won't get notified, that's the best we
-									// can do given current implementations)
-									if ( !status && s.isLocal && !s.crossDomain ) {
-										status = responses.text ? 200 : 404;
-									// IE - #1450: sometimes returns 1223 when it should be 204
-									} else if ( status === 1223 ) {
-										status = 204;
-									}
-								}
-							}
-						} catch( firefoxAccessException ) {
-							if ( !isAbort ) {
-								complete( -1, firefoxAccessException );
-							}
-						}
 
-						// Call complete if needed
-						if ( responses ) {
-							complete( status, statusText, responses, responseHeaders );
-						}
-					};
 
-					if ( !s.async ) {
-						// if we're in sync mode we fire the callback
-						callback();
-					} else if ( xhr.readyState === 4 ) {
-						// (IE6 & IE7) if it's in cache and has been
-						// retrieved directly we need to fire the callback
-						setTimeout( callback );
-					} else {
-						handle = ++xhrId;
-						if ( xhrOnUnloadAbort ) {
-							// Create the active xhrs callbacks list if needed
-							// and attach the unload handler
-							if ( !xhrCallbacks ) {
-								xhrCallbacks = {};
-								jQuery( window ).unload( xhrOnUnloadAbort );
-							}
-							// Add to list of active xhrs callbacks
-							xhrCallbacks[ handle ] = callback;
+var rclass = /[\t\r\n\f]/g;
+
+jQuery.fn.extend({
+	addClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = typeof value === "string" && value;
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).addClass( value.call( this, j, this.className ) );
+			});
+		}
+
+		if ( proceed ) {
+			// The disjunction here is for better compressibility (see removeClass)
+			classes = ( value || "" ).match( rnotwhite ) || [];
+
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					" "
+				);
+
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
+							cur += clazz + " ";
 						}
-						xhr.onreadystatechange = callback;
 					}
-				},
 
-				abort: function() {
-					if ( callback ) {
-						callback( undefined, true );
+					// only assign if different to avoid unneeded rendering.
+					finalValue = jQuery.trim( cur );
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
 					}
 				}
-			};
-		}
-	});
-}
-var fxNow, timerId,
-	rfxtypes = /^(?:toggle|show|hide)$/,
-	rfxnum = new RegExp( "^(?:([+-])=|)(" + core_pnum + ")([a-z%]*)$", "i" ),
-	rrun = /queueHooks$/,
-	animationPrefilters = [ defaultPrefilter ],
-	tweeners = {
-		"*": [function( prop, value ) {
-			var end, unit,
-				tween = this.createTween( prop, value ),
-				parts = rfxnum.exec( value ),
-				target = tween.cur(),
-				start = +target || 0,
-				scale = 1,
-				maxIterations = 20;
-
-			if ( parts ) {
-				end = +parts[2];
-				unit = parts[3] || ( jQuery.cssNumber[ prop ] ? "" : "px" );
-
-				// We need to compute starting value
-				if ( unit !== "px" && start ) {
-					// Iteratively approximate from a nonzero starting point
-					// Prefer the current property, because this process will be trivial if it uses the same units
-					// Fallback to end or a simple constant
-					start = jQuery.css( tween.elem, prop, true ) || end || 1;
-
-					do {
-						// If previous iteration zeroed out, double until we get *something*
-						// Use a string for doubling factor so we don't accidentally see scale as unchanged below
-						scale = scale || ".5";
-
-						// Adjust and apply
-						start = start / scale;
-						jQuery.style( tween.elem, prop, start + unit );
-
-					// Update scale, tolerating zero or NaN from tween.cur()
-					// And breaking the loop if scale is unchanged or perfect, or if we've just had enough
-					} while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
-				}
-
-				tween.unit = unit;
-				tween.start = start;
-				// If a +=/-= token was provided, we're doing a relative animation
-				tween.end = parts[1] ? start + ( parts[1] + 1 ) * end : end;
 			}
-			return tween;
-		}]
-	};
+		}
 
-// Animations created synchronously will run synchronously
-function createFxNow() {
-	setTimeout(function() {
-		fxNow = undefined;
-	});
-	return ( fxNow = jQuery.now() );
-}
+		return this;
+	},
 
-function createTweens( animation, props ) {
-	jQuery.each( props, function( prop, value ) {
-		var collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
-			index = 0,
-			length = collection.length;
-		for ( ; index < length; index++ ) {
-			if ( collection[ index ].call( animation, prop, value ) ) {
+	removeClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = arguments.length === 0 || typeof value === "string" && value;
 
-				// we're done with this property
-				return;
-			}
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).removeClass( value.call( this, j, this.className ) );
+			});
 		}
-	});
-}
+		if ( proceed ) {
+			classes = ( value || "" ).match( rnotwhite ) || [];
 
-function Animation( elem, properties, options ) {
-	var result,
-		stopped,
-		index = 0,
-		length = animationPrefilters.length,
-		deferred = jQuery.Deferred().always( function() {
-			// don't match elem in the :animated selector
-			delete tick.elem;
-		}),
-		tick = function() {
-			if ( stopped ) {
-				return false;
-			}
-			var currentTime = fxNow || createFxNow(),
-				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
-				// archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
-				temp = remaining / animation.duration || 0,
-				percent = 1 - temp,
-				index = 0,
-				length = animation.tweens.length;
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				// This expression is here for better compressibility (see addClass)
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					""
+				);
 
-			for ( ; index < length ; index++ ) {
-				animation.tweens[ index ].run( percent );
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						// Remove *all* instances
+						while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
+							cur = cur.replace( " " + clazz + " ", " " );
+						}
+					}
+
+					// only assign if different to avoid unneeded rendering.
+					finalValue = value ? jQuery.trim( cur ) : "";
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
+					}
+				}
 			}
+		}
 
-			deferred.notifyWith( elem, [ animation, percent, remaining ]);
+		return this;
+	},
 
-			if ( percent < 1 && length ) {
-				return remaining;
-			} else {
-				deferred.resolveWith( elem, [ animation ] );
-				return false;
-			}
-		},
-		animation = deferred.promise({
-			elem: elem,
-			props: jQuery.extend( {}, properties ),
-			opts: jQuery.extend( true, { specialEasing: {} }, options ),
-			originalProperties: properties,
-			originalOptions: options,
-			startTime: fxNow || createFxNow(),
-			duration: options.duration,
-			tweens: [],
-			createTween: function( prop, end ) {
-				var tween = jQuery.Tween( elem, animation.opts, prop, end,
-						animation.opts.specialEasing[ prop ] || animation.opts.easing );
-				animation.tweens.push( tween );
-				return tween;
-			},
-			stop: function( gotoEnd ) {
-				var index = 0,
-					// if we are going to the end, we want to run all the tweens
-					// otherwise we skip this part
-					length = gotoEnd ? animation.tweens.length : 0;
-				if ( stopped ) {
-					return this;
-				}
-				stopped = true;
-				for ( ; index < length ; index++ ) {
-					animation.tweens[ index ].run( 1 );
+	toggleClass: function( value, stateVal ) {
+		var type = typeof value;
+
+		if ( typeof stateVal === "boolean" && type === "string" ) {
+			return stateVal ? this.addClass( value ) : this.removeClass( value );
+		}
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( i ) {
+				jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
+			});
+		}
+
+		return this.each(function() {
+			if ( type === "string" ) {
+				// toggle individual class names
+				var className,
+					i = 0,
+					self = jQuery( this ),
+					classNames = value.match( rnotwhite ) || [];
+
+				while ( (className = classNames[ i++ ]) ) {
+					// check each className given, space separated list
+					if ( self.hasClass( className ) ) {
+						self.removeClass( className );
+					} else {
+						self.addClass( className );
+					}
 				}
 
-				// resolve when we played the last frame
-				// otherwise, reject
-				if ( gotoEnd ) {
-					deferred.resolveWith( elem, [ animation, gotoEnd ] );
-				} else {
-					deferred.rejectWith( elem, [ animation, gotoEnd ] );
+			// Toggle whole class name
+			} else if ( type === strundefined || type === "boolean" ) {
+				if ( this.className ) {
+					// store className if set
+					jQuery._data( this, "__className__", this.className );
 				}
-				return this;
-			}
-		}),
-		props = animation.props;
 
-	propFilter( props, animation.opts.specialEasing );
+				// If the element has a class name or if we're passed "false",
+				// then remove the whole classname (if there was one, the above saved it).
+				// Otherwise bring back whatever was previously saved (if anything),
+				// falling back to the empty string if nothing was stored.
+				this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+			}
+		});
+	},
 
-	for ( ; index < length ; index++ ) {
-		result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
-		if ( result ) {
-			return result;
+	hasClass: function( selector ) {
+		var className = " " + selector + " ",
+			i = 0,
+			l = this.length;
+		for ( ; i < l; i++ ) {
+			if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
+				return true;
+			}
 		}
+
+		return false;
 	}
+});
 
-	createTweens( animation, props );
 
-	if ( jQuery.isFunction( animation.opts.start ) ) {
-		animation.opts.start.call( elem, animation );
-	}
 
-	jQuery.fx.timer(
-		jQuery.extend( tick, {
-			elem: elem,
-			anim: animation,
-			queue: animation.opts.queue
-		})
-	);
 
-	// attach callbacks from options
-	return animation.progress( animation.opts.progress )
-		.done( animation.opts.done, animation.opts.complete )
-		.fail( animation.opts.fail )
-		.always( animation.opts.always );
-}
+// Return jQuery for attributes-only inclusion
 
-function propFilter( props, specialEasing ) {
-	var value, name, index, easing, hooks;
 
-	// camelCase, specialEasing and expand cssHook pass
-	for ( index in props ) {
-		name = jQuery.camelCase( index );
-		easing = specialEasing[ name ];
-		value = props[ index ];
-		if ( jQuery.isArray( value ) ) {
-			easing = value[ 1 ];
-			value = props[ index ] = value[ 0 ];
-		}
+jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
+	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+	"change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
 
-		if ( index !== name ) {
-			props[ name ] = value;
-			delete props[ index ];
-		}
+	// Handle event binding
+	jQuery.fn[ name ] = function( data, fn ) {
+		return arguments.length > 0 ?
+			this.on( name, null, data, fn ) :
+			this.trigger( name );
+	};
+});
 
-		hooks = jQuery.cssHooks[ name ];
-		if ( hooks && "expand" in hooks ) {
-			value = hooks.expand( value );
-			delete props[ name ];
+jQuery.fn.extend({
+	hover: function( fnOver, fnOut ) {
+		return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+	},
 
-			// not quite $.extend, this wont overwrite keys already present.
-			// also - reusing 'index' from above because we have the correct "name"
-			for ( index in value ) {
-				if ( !( index in props ) ) {
-					props[ index ] = value[ index ];
-					specialEasing[ index ] = easing;
-				}
-			}
-		} else {
-			specialEasing[ name ] = easing;
-		}
+	bind: function( types, data, fn ) {
+		return this.on( types, null, data, fn );
+	},
+	unbind: function( types, fn ) {
+		return this.off( types, null, fn );
+	},
+
+	delegate: function( selector, types, data, fn ) {
+		return this.on( types, selector, data, fn );
+	},
+	undelegate: function( selector, types, fn ) {
+		// ( namespace ) or ( selector, types [, fn] )
+		return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
 	}
-}
+});
 
-jQuery.Animation = jQuery.extend( Animation, {
 
-	tweener: function( props, callback ) {
-		if ( jQuery.isFunction( props ) ) {
-			callback = props;
-			props = [ "*" ];
-		} else {
-			props = props.split(" ");
-		}
+var nonce = jQuery.now();
 
-		var prop,
-			index = 0,
-			length = props.length;
+var rquery = (/\?/);
 
-		for ( ; index < length ; index++ ) {
-			prop = props[ index ];
-			tweeners[ prop ] = tweeners[ prop ] || [];
-			tweeners[ prop ].unshift( callback );
-		}
-	},
 
-	prefilter: function( callback, prepend ) {
-		if ( prepend ) {
-			animationPrefilters.unshift( callback );
-		} else {
-			animationPrefilters.push( callback );
-		}
+
+var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;
+
+jQuery.parseJSON = function( data ) {
+	// Attempt to parse using the native JSON parser first
+	if ( window.JSON && window.JSON.parse ) {
+		// Support: Android 2.3
+		// Workaround failure to string-cast null input
+		return window.JSON.parse( data + "" );
 	}
-});
 
-function defaultPrefilter( elem, props, opts ) {
-	/*jshint validthis:true */
-	var prop, index, length,
-		value, dataShow, toggle,
-		tween, hooks, oldfire,
-		anim = this,
-		style = elem.style,
-		orig = {},
-		handled = [],
-		hidden = elem.nodeType && isHidden( elem );
+	var requireNonComma,
+		depth = null,
+		str = jQuery.trim( data + "" );
 
-	// handle queue: false promises
-	if ( !opts.queue ) {
-		hooks = jQuery._queueHooks( elem, "fx" );
-		if ( hooks.unqueued == null ) {
-			hooks.unqueued = 0;
-			oldfire = hooks.empty.fire;
-			hooks.empty.fire = function() {
-				if ( !hooks.unqueued ) {
-					oldfire();
-				}
-			};
+	// Guard against invalid (and possibly dangerous) input by ensuring that nothing remains
+	// after removing valid tokens
+	return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) {
+
+		// Force termination if we see a misplaced comma
+		if ( requireNonComma && comma ) {
+			depth = 0;
 		}
-		hooks.unqueued++;
 
-		anim.always(function() {
-			// doing this makes sure that the complete handler will be called
-			// before this completes
-			anim.always(function() {
-				hooks.unqueued--;
-				if ( !jQuery.queue( elem, "fx" ).length ) {
-					hooks.empty.fire();
-				}
-			});
-		});
-	}
+		// Perform no more replacements after returning to outermost depth
+		if ( depth === 0 ) {
+			return token;
+		}
 
-	// height/width overflow pass
-	if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
-		// Make sure that nothing sneaks out
-		// Record all 3 overflow attributes because IE does not
-		// change the overflow attribute when overflowX and
-		// overflowY are set to the same value
-		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+		// Commas must not follow "[", "{", or ","
+		requireNonComma = open || comma;
 
-		// Set display property to inline-block for height/width
-		// animations on inline elements that are having width/height animated
-		if ( jQuery.css( elem, "display" ) === "inline" &&
-				jQuery.css( elem, "float" ) === "none" ) {
+		// Determine new depth
+		// array/object open ("[" or "{"): depth += true - false (increment)
+		// array/object close ("]" or "}"): depth += false - true (decrement)
+		// other cases ("," or primitive): depth += true - true (numeric cast)
+		depth += !close - !open;
 
-			// inline-level elements accept inline-block;
-			// block-level elements need to be inline with layout
-			if ( !jQuery.support.inlineBlockNeedsLayout || css_defaultDisplay( elem.nodeName ) === "inline" ) {
-				style.display = "inline-block";
+		// Remove this token
+		return "";
+	}) ) ?
+		( Function( "return " + str ) )() :
+		jQuery.error( "Invalid JSON: " + data );
+};
 
-			} else {
-				style.zoom = 1;
-			}
-		}
-	}
 
-	if ( opts.overflow ) {
-		style.overflow = "hidden";
-		if ( !jQuery.support.shrinkWrapBlocks ) {
-			anim.always(function() {
-				style.overflow = opts.overflow[ 0 ];
-				style.overflowX = opts.overflow[ 1 ];
-				style.overflowY = opts.overflow[ 2 ];
-			});
+// Cross-browser xml parsing
+jQuery.parseXML = function( data ) {
+	var xml, tmp;
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	try {
+		if ( window.DOMParser ) { // Standard
+			tmp = new DOMParser();
+			xml = tmp.parseFromString( data, "text/xml" );
+		} else { // IE
+			xml = new ActiveXObject( "Microsoft.XMLDOM" );
+			xml.async = "false";
+			xml.loadXML( data );
 		}
+	} catch( e ) {
+		xml = undefined;
+	}
+	if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
+		jQuery.error( "Invalid XML: " + data );
 	}
+	return xml;
+};
 
 
-	// show/hide pass
-	for ( index in props ) {
-		value = props[ index ];
-		if ( rfxtypes.exec( value ) ) {
-			delete props[ index ];
-			toggle = toggle || value === "toggle";
-			if ( value === ( hidden ? "hide" : "show" ) ) {
-				continue;
-			}
-			handled.push( index );
-		}
-	}
+var
+	// Document location
+	ajaxLocParts,
+	ajaxLocation,
 
-	length = handled.length;
-	if ( length ) {
-		dataShow = jQuery._data( elem, "fxshow" ) || jQuery._data( elem, "fxshow", {} );
-		if ( "hidden" in dataShow ) {
-			hidden = dataShow.hidden;
-		}
+	rhash = /#.*$/,
+	rts = /([?&])_=[^&]*/,
+	rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
+	// #7653, #8125, #8152: local protocol detection
+	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
+	rnoContent = /^(?:GET|HEAD)$/,
+	rprotocol = /^\/\//,
+	rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,
 
-		// store state if its toggle - enables .stop().toggle() to "reverse"
-		if ( toggle ) {
-			dataShow.hidden = !hidden;
-		}
-		if ( hidden ) {
-			jQuery( elem ).show();
-		} else {
-			anim.done(function() {
-				jQuery( elem ).hide();
-			});
-		}
-		anim.done(function() {
-			var prop;
-			jQuery._removeData( elem, "fxshow" );
-			for ( prop in orig ) {
-				jQuery.style( elem, prop, orig[ prop ] );
-			}
-		});
-		for ( index = 0 ; index < length ; index++ ) {
-			prop = handled[ index ];
-			tween = anim.createTween( prop, hidden ? dataShow[ prop ] : 0 );
-			orig[ prop ] = dataShow[ prop ] || jQuery.style( elem, prop );
+	/* Prefilters
+	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+	 * 2) These are called:
+	 *    - BEFORE asking for a transport
+	 *    - AFTER param serialization (s.data is a string if s.processData is true)
+	 * 3) key is the dataType
+	 * 4) the catchall symbol "*" can be used
+	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+	 */
+	prefilters = {},
 
-			if ( !( prop in dataShow ) ) {
-				dataShow[ prop ] = tween.start;
-				if ( hidden ) {
-					tween.end = tween.start;
-					tween.start = prop === "width" || prop === "height" ? 1 : 0;
-				}
-			}
-		}
-	}
-}
+	/* Transports bindings
+	 * 1) key is the dataType
+	 * 2) the catchall symbol "*" can be used
+	 * 3) selection will start with transport dataType and THEN go to "*" if needed
+	 */
+	transports = {},
 
-function Tween( elem, options, prop, end, easing ) {
-	return new Tween.prototype.init( elem, options, prop, end, easing );
+	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+	allTypes = "*/".concat("*");
+
+// #8138, IE may throw an exception when accessing
+// a field from window.location if document.domain has been set
+try {
+	ajaxLocation = location.href;
+} catch( e ) {
+	// Use the href attribute of an A element
+	// since IE will modify it given document.location
+	ajaxLocation = document.createElement( "a" );
+	ajaxLocation.href = "";
+	ajaxLocation = ajaxLocation.href;
 }
-jQuery.Tween = Tween;
 
-Tween.prototype = {
-	constructor: Tween,
-	init: function( elem, options, prop, end, easing, unit ) {
-		this.elem = elem;
-		this.prop = prop;
-		this.easing = easing || "swing";
-		this.options = options;
-		this.start = this.now = this.cur();
-		this.end = end;
-		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
-	},
-	cur: function() {
-		var hooks = Tween.propHooks[ this.prop ];
+// Segment location into parts
+ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
 
-		return hooks && hooks.get ?
-			hooks.get( this ) :
-			Tween.propHooks._default.get( this );
-	},
-	run: function( percent ) {
-		var eased,
-			hooks = Tween.propHooks[ this.prop ];
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
 
-		if ( this.options.duration ) {
-			this.pos = eased = jQuery.easing[ this.easing ](
-				percent, this.options.duration * percent, 0, 1, this.options.duration
-			);
-		} else {
-			this.pos = eased = percent;
-		}
-		this.now = ( this.end - this.start ) * eased + this.start;
+	// dataTypeExpression is optional and defaults to "*"
+	return function( dataTypeExpression, func ) {
 
-		if ( this.options.step ) {
-			this.options.step.call( this.elem, this.now, this );
+		if ( typeof dataTypeExpression !== "string" ) {
+			func = dataTypeExpression;
+			dataTypeExpression = "*";
 		}
 
-		if ( hooks && hooks.set ) {
-			hooks.set( this );
-		} else {
-			Tween.propHooks._default.set( this );
+		var dataType,
+			i = 0,
+			dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || [];
+
+		if ( jQuery.isFunction( func ) ) {
+			// For each dataType in the dataTypeExpression
+			while ( (dataType = dataTypes[i++]) ) {
+				// Prepend if requested
+				if ( dataType.charAt( 0 ) === "+" ) {
+					dataType = dataType.slice( 1 ) || "*";
+					(structure[ dataType ] = structure[ dataType ] || []).unshift( func );
+
+				// Otherwise append
+				} else {
+					(structure[ dataType ] = structure[ dataType ] || []).push( func );
+				}
+			}
 		}
-		return this;
-	}
-};
+	};
+}
 
-Tween.prototype.init.prototype = Tween.prototype;
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
 
-Tween.propHooks = {
-	_default: {
-		get: function( tween ) {
-			var result;
+	var inspected = {},
+		seekingTransport = ( structure === transports );
 
-			if ( tween.elem[ tween.prop ] != null &&
-				(!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
-				return tween.elem[ tween.prop ];
+	function inspect( dataType ) {
+		var selected;
+		inspected[ dataType ] = true;
+		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
+			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
+			if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+				options.dataTypes.unshift( dataTypeOrTransport );
+				inspect( dataTypeOrTransport );
+				return false;
+			} else if ( seekingTransport ) {
+				return !( selected = dataTypeOrTransport );
 			}
+		});
+		return selected;
+	}
 
-			// passing an empty string as a 3rd parameter to .css will automatically
-			// attempt a parseFloat and fallback to a string if the parse fails
-			// so, simple values such as "10px" are parsed to Float.
-			// complex values such as "rotate(1rad)" are returned as is.
-			result = jQuery.css( tween.elem, tween.prop, "" );
-			// Empty strings, null, undefined and "auto" are converted to 0.
-			return !result || result === "auto" ? 0 : result;
-		},
-		set: function( tween ) {
-			// use step hook for back compat - use cssHook if its there - use .style if its
-			// available and use plain properties where available
-			if ( jQuery.fx.step[ tween.prop ] ) {
-				jQuery.fx.step[ tween.prop ]( tween );
-			} else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
-				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
-			} else {
-				tween.elem[ tween.prop ] = tween.now;
-			}
+	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+	var deep, key,
+		flatOptions = jQuery.ajaxSettings.flatOptions || {};
+
+	for ( key in src ) {
+		if ( src[ key ] !== undefined ) {
+			( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
 		}
 	}
-};
+	if ( deep ) {
+		jQuery.extend( true, target, deep );
+	}
 
-// Remove in 2.0 - this supports IE8's panic based approach
-// to setting things on disconnected nodes
+	return target;
+}
 
-Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
-	set: function( tween ) {
-		if ( tween.elem.nodeType && tween.elem.parentNode ) {
-			tween.elem[ tween.prop ] = tween.now;
+/* Handles responses to an ajax request:
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+	var firstDataType, ct, finalDataType, type,
+		contents = s.contents,
+		dataTypes = s.dataTypes;
+
+	// Remove auto dataType and get content-type in the process
+	while ( dataTypes[ 0 ] === "*" ) {
+		dataTypes.shift();
+		if ( ct === undefined ) {
+			ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
 		}
 	}
-};
 
-jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
-	var cssFn = jQuery.fn[ name ];
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return speed == null || typeof speed === "boolean" ?
-			cssFn.apply( this, arguments ) :
-			this.animate( genFx( name, true ), speed, easing, callback );
-	};
-});
-
-jQuery.fn.extend({
-	fadeTo: function( speed, to, easing, callback ) {
+	// Check if we're dealing with a known content-type
+	if ( ct ) {
+		for ( type in contents ) {
+			if ( contents[ type ] && contents[ type ].test( ct ) ) {
+				dataTypes.unshift( type );
+				break;
+			}
+		}
+	}
 
-		// show any hidden elements after setting opacity to 0
-		return this.filter( isHidden ).css( "opacity", 0 ).show()
+	// Check to see if we have a response for the expected dataType
+	if ( dataTypes[ 0 ] in responses ) {
+		finalDataType = dataTypes[ 0 ];
+	} else {
+		// Try convertible dataTypes
+		for ( type in responses ) {
+			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+				finalDataType = type;
+				break;
+			}
+			if ( !firstDataType ) {
+				firstDataType = type;
+			}
+		}
+		// Or just use first one
+		finalDataType = finalDataType || firstDataType;
+	}
 
-			// animate to the value specified
-			.end().animate({ opacity: to }, speed, easing, callback );
-	},
-	animate: function( prop, speed, easing, callback ) {
-		var empty = jQuery.isEmptyObject( prop ),
-			optall = jQuery.speed( speed, easing, callback ),
-			doAnimation = function() {
-				// Operate on a copy of prop so per-property easing won't be lost
-				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
-				doAnimation.finish = function() {
-					anim.stop( true );
-				};
-				// Empty animations, or finishing resolves immediately
-				if ( empty || jQuery._data( this, "finish" ) ) {
-					anim.stop( true );
-				}
-			};
-			doAnimation.finish = doAnimation;
+	// If we found a dataType
+	// We add the dataType to the list if needed
+	// and return the corresponding response
+	if ( finalDataType ) {
+		if ( finalDataType !== dataTypes[ 0 ] ) {
+			dataTypes.unshift( finalDataType );
+		}
+		return responses[ finalDataType ];
+	}
+}
 
-		return empty || optall.queue === false ?
-			this.each( doAnimation ) :
-			this.queue( optall.queue, doAnimation );
-	},
-	stop: function( type, clearQueue, gotoEnd ) {
-		var stopQueue = function( hooks ) {
-			var stop = hooks.stop;
-			delete hooks.stop;
-			stop( gotoEnd );
-		};
+/* Chain conversions given the request and the original response
+ * Also sets the responseXXX fields on the jqXHR instance
+ */
+function ajaxConvert( s, response, jqXHR, isSuccess ) {
+	var conv2, current, conv, tmp, prev,
+		converters = {},
+		// Work with a copy of dataTypes in case we need to modify it for conversion
+		dataTypes = s.dataTypes.slice();
 
-		if ( typeof type !== "string" ) {
-			gotoEnd = clearQueue;
-			clearQueue = type;
-			type = undefined;
-		}
-		if ( clearQueue && type !== false ) {
-			this.queue( type || "fx", [] );
+	// Create converters map with lowercased keys
+	if ( dataTypes[ 1 ] ) {
+		for ( conv in s.converters ) {
+			converters[ conv.toLowerCase() ] = s.converters[ conv ];
 		}
+	}
 
-		return this.each(function() {
-			var dequeue = true,
-				index = type != null && type + "queueHooks",
-				timers = jQuery.timers,
-				data = jQuery._data( this );
-
-			if ( index ) {
-				if ( data[ index ] && data[ index ].stop ) {
-					stopQueue( data[ index ] );
-				}
-			} else {
-				for ( index in data ) {
-					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
-						stopQueue( data[ index ] );
-					}
-				}
-			}
+	current = dataTypes.shift();
 
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
-					timers[ index ].anim.stop( gotoEnd );
-					dequeue = false;
-					timers.splice( index, 1 );
-				}
-			}
+	// Convert to each sequential dataType
+	while ( current ) {
 
-			// start the next in the queue if the last step wasn't forced
-			// timers currently will call their complete callbacks, which will dequeue
-			// but only if they were gotoEnd
-			if ( dequeue || !gotoEnd ) {
-				jQuery.dequeue( this, type );
-			}
-		});
-	},
-	finish: function( type ) {
-		if ( type !== false ) {
-			type = type || "fx";
+		if ( s.responseFields[ current ] ) {
+			jqXHR[ s.responseFields[ current ] ] = response;
 		}
-		return this.each(function() {
-			var index,
-				data = jQuery._data( this ),
-				queue = data[ type + "queue" ],
-				hooks = data[ type + "queueHooks" ],
-				timers = jQuery.timers,
-				length = queue ? queue.length : 0;
-
-			// enable finishing flag on private data
-			data.finish = true;
 
-			// empty the queue first
-			jQuery.queue( this, type, [] );
+		// Apply the dataFilter if provided
+		if ( !prev && isSuccess && s.dataFilter ) {
+			response = s.dataFilter( response, s.dataType );
+		}
 
-			if ( hooks && hooks.cur && hooks.cur.finish ) {
-				hooks.cur.finish.call( this );
-			}
+		prev = current;
+		current = dataTypes.shift();
 
-			// look for any active animations, and finish them
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
-					timers[ index ].anim.stop( true );
-					timers.splice( index, 1 );
-				}
-			}
+		if ( current ) {
 
-			// look for any animations in the old queue and finish them
-			for ( index = 0; index < length; index++ ) {
-				if ( queue[ index ] && queue[ index ].finish ) {
-					queue[ index ].finish.call( this );
-				}
-			}
+			// There's only work to do if current dataType is non-auto
+			if ( current === "*" ) {
 
-			// turn off finishing flag
-			delete data.finish;
-		});
-	}
-});
+				current = prev;
 
-// Generate parameters to create a standard animation
-function genFx( type, includeWidth ) {
-	var which,
-		attrs = { height: type },
-		i = 0;
+			// Convert response if prev dataType is non-auto and differs from current
+			} else if ( prev !== "*" && prev !== current ) {
 
-	// if we include width, step value is 1 to do all cssExpand values,
-	// if we don't include width, step value is 2 to skip over Left and Right
-	includeWidth = includeWidth? 1 : 0;
-	for( ; i < 4 ; i += 2 - includeWidth ) {
-		which = cssExpand[ i ];
-		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
-	}
+				// Seek a direct converter
+				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
 
-	if ( includeWidth ) {
-		attrs.opacity = attrs.width = type;
-	}
+				// If none found, seek a pair
+				if ( !conv ) {
+					for ( conv2 in converters ) {
 
-	return attrs;
-}
+						// If conv2 outputs current
+						tmp = conv2.split( " " );
+						if ( tmp[ 1 ] === current ) {
 
-// Generate shortcuts for custom animations
-jQuery.each({
-	slideDown: genFx("show"),
-	slideUp: genFx("hide"),
-	slideToggle: genFx("toggle"),
-	fadeIn: { opacity: "show" },
-	fadeOut: { opacity: "hide" },
-	fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return this.animate( props, speed, easing, callback );
-	};
-});
+							// If prev can be converted to accepted input
+							conv = converters[ prev + " " + tmp[ 0 ] ] ||
+								converters[ "* " + tmp[ 0 ] ];
+							if ( conv ) {
+								// Condense equivalence converters
+								if ( conv === true ) {
+									conv = converters[ conv2 ];
 
-jQuery.speed = function( speed, easing, fn ) {
-	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
-		complete: fn || !fn && easing ||
-			jQuery.isFunction( speed ) && speed,
-		duration: speed,
-		easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
-	};
+								// Otherwise, insert the intermediate dataType
+								} else if ( converters[ conv2 ] !== true ) {
+									current = tmp[ 0 ];
+									dataTypes.unshift( tmp[ 1 ] );
+								}
+								break;
+							}
+						}
+					}
+				}
 
-	opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
-		opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
+				// Apply converter (if not an equivalence)
+				if ( conv !== true ) {
 
-	// normalize opt.queue - true/undefined/null -> "fx"
-	if ( opt.queue == null || opt.queue === true ) {
-		opt.queue = "fx";
+					// Unless errors are allowed to bubble, catch and return them
+					if ( conv && s[ "throws" ] ) {
+						response = conv( response );
+					} else {
+						try {
+							response = conv( response );
+						} catch ( e ) {
+							return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+						}
+					}
+				}
+			}
+		}
 	}
 
-	// Queueing
-	opt.old = opt.complete;
+	return { state: "success", data: response };
+}
 
-	opt.complete = function() {
-		if ( jQuery.isFunction( opt.old ) ) {
-			opt.old.call( this );
-		}
+jQuery.extend({
 
-		if ( opt.queue ) {
-			jQuery.dequeue( this, opt.queue );
-		}
-	};
+	// Counter for holding the number of active queries
+	active: 0,
 
-	return opt;
-};
+	// Last-Modified header cache for next request
+	lastModified: {},
+	etag: {},
 
-jQuery.easing = {
-	linear: function( p ) {
-		return p;
-	},
-	swing: function( p ) {
-		return 0.5 - Math.cos( p*Math.PI ) / 2;
-	}
-};
-
-jQuery.timers = [];
-jQuery.fx = Tween.prototype.init;
-jQuery.fx.tick = function() {
-	var timer,
-		timers = jQuery.timers,
-		i = 0;
-
-	fxNow = jQuery.now();
-
-	for ( ; i < timers.length; i++ ) {
-		timer = timers[ i ];
-		// Checks the timer has not already been removed
-		if ( !timer() && timers[ i ] === timer ) {
-			timers.splice( i--, 1 );
-		}
-	}
-
-	if ( !timers.length ) {
-		jQuery.fx.stop();
-	}
-	fxNow = undefined;
-};
-
-jQuery.fx.timer = function( timer ) {
-	if ( timer() && jQuery.timers.push( timer ) ) {
-		jQuery.fx.start();
-	}
-};
-
-jQuery.fx.interval = 13;
+	ajaxSettings: {
+		url: ajaxLocation,
+		type: "GET",
+		isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
+		global: true,
+		processData: true,
+		async: true,
+		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+		/*
+		timeout: 0,
+		data: null,
+		dataType: null,
+		username: null,
+		password: null,
+		cache: null,
+		throws: false,
+		traditional: false,
+		headers: {},
+		*/
 
-jQuery.fx.start = function() {
-	if ( !timerId ) {
-		timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
-	}
-};
+		accepts: {
+			"*": allTypes,
+			text: "text/plain",
+			html: "text/html",
+			xml: "application/xml, text/xml",
+			json: "application/json, text/javascript"
+		},
 
-jQuery.fx.stop = function() {
-	clearInterval( timerId );
-	timerId = null;
-};
+		contents: {
+			xml: /xml/,
+			html: /html/,
+			json: /json/
+		},
 
-jQuery.fx.speeds = {
-	slow: 600,
-	fast: 200,
-	// Default speed
-	_default: 400
-};
+		responseFields: {
+			xml: "responseXML",
+			text: "responseText",
+			json: "responseJSON"
+		},
 
-// Back Compat <1.8 extension point
-jQuery.fx.step = {};
+		// Data converters
+		// Keys separate source (or catchall "*") and destination types with a single space
+		converters: {
 
-if ( jQuery.expr && jQuery.expr.filters ) {
-	jQuery.expr.filters.animated = function( elem ) {
-		return jQuery.grep(jQuery.timers, function( fn ) {
-			return elem === fn.elem;
-		}).length;
-	};
-}
-jQuery.fn.offset = function( options ) {
-	if ( arguments.length ) {
-		return options === undefined ?
-			this :
-			this.each(function( i ) {
-				jQuery.offset.setOffset( this, options, i );
-			});
-	}
+			// Convert anything to text
+			"* text": String,
 
-	var docElem, win,
-		box = { top: 0, left: 0 },
-		elem = this[ 0 ],
-		doc = elem && elem.ownerDocument;
+			// Text to html (true = no transformation)
+			"text html": true,
 
-	if ( !doc ) {
-		return;
-	}
+			// Evaluate text as a json expression
+			"text json": jQuery.parseJSON,
 
-	docElem = doc.documentElement;
+			// Parse text as xml
+			"text xml": jQuery.parseXML
+		},
 
-	// Make sure it's not a disconnected DOM node
-	if ( !jQuery.contains( docElem, elem ) ) {
-		return box;
-	}
+		// For options that shouldn't be deep extended:
+		// you can add your own custom options here if
+		// and when you create one that shouldn't be
+		// deep extended (see ajaxExtend)
+		flatOptions: {
+			url: true,
+			context: true
+		}
+	},
 
-	// If we don't have gBCR, just use 0,0 rather than error
-	// BlackBerry 5, iOS 3 (original iPhone)
-	if ( typeof elem.getBoundingClientRect !== core_strundefined ) {
-		box = elem.getBoundingClientRect();
-	}
-	win = getWindow( doc );
-	return {
-		top: box.top  + ( win.pageYOffset || docElem.scrollTop )  - ( docElem.clientTop  || 0 ),
-		left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
-	};
-};
+	// Creates a full fledged settings object into target
+	// with both ajaxSettings and settings fields.
+	// If target is omitted, writes into ajaxSettings.
+	ajaxSetup: function( target, settings ) {
+		return settings ?
 
-jQuery.offset = {
+			// Building a settings object
+			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
 
-	setOffset: function( elem, options, i ) {
-		var position = jQuery.css( elem, "position" );
+			// Extending ajaxSettings
+			ajaxExtend( jQuery.ajaxSettings, target );
+	},
 
-		// set position first, in-case top/left are set even on static elem
-		if ( position === "static" ) {
-			elem.style.position = "relative";
-		}
+	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+	ajaxTransport: addToPrefiltersOrTransports( transports ),
 
-		var curElem = jQuery( elem ),
-			curOffset = curElem.offset(),
-			curCSSTop = jQuery.css( elem, "top" ),
-			curCSSLeft = jQuery.css( elem, "left" ),
-			calculatePosition = ( position === "absolute" || position === "fixed" ) && jQuery.inArray("auto", [curCSSTop, curCSSLeft]) > -1,
-			props = {}, curPosition = {}, curTop, curLeft;
+	// Main method
+	ajax: function( url, options ) {
 
-		// need to be able to calculate position if either top or left is auto and position is either absolute or fixed
-		if ( calculatePosition ) {
-			curPosition = curElem.position();
-			curTop = curPosition.top;
-			curLeft = curPosition.left;
-		} else {
-			curTop = parseFloat( curCSSTop ) || 0;
-			curLeft = parseFloat( curCSSLeft ) || 0;
+		// If url is an object, simulate pre-1.5 signature
+		if ( typeof url === "object" ) {
+			options = url;
+			url = undefined;
 		}
 
-		if ( jQuery.isFunction( options ) ) {
-			options = options.call( elem, i, curOffset );
-		}
+		// Force options to be an object
+		options = options || {};
 
-		if ( options.top != null ) {
-			props.top = ( options.top - curOffset.top ) + curTop;
-		}
-		if ( options.left != null ) {
-			props.left = ( options.left - curOffset.left ) + curLeft;
-		}
+		var // Cross-domain detection vars
+			parts,
+			// Loop variable
+			i,
+			// URL without anti-cache param
+			cacheURL,
+			// Response headers as string
+			responseHeadersString,
+			// timeout handle
+			timeoutTimer,
 
-		if ( "using" in options ) {
-			options.using.call( elem, props );
-		} else {
-			curElem.css( props );
-		}
-	}
-};
+			// To know if global events are to be dispatched
+			fireGlobals,
 
+			transport,
+			// Response headers
+			responseHeaders,
+			// Create the final options object
+			s = jQuery.ajaxSetup( {}, options ),
+			// Callbacks context
+			callbackContext = s.context || s,
+			// Context for global events is callbackContext if it is a DOM node or jQuery collection
+			globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
+				jQuery( callbackContext ) :
+				jQuery.event,
+			// Deferreds
+			deferred = jQuery.Deferred(),
+			completeDeferred = jQuery.Callbacks("once memory"),
+			// Status-dependent callbacks
+			statusCode = s.statusCode || {},
+			// Headers (they are sent all at once)
+			requestHeaders = {},
+			requestHeadersNames = {},
+			// The jqXHR state
+			state = 0,
+			// Default abort message
+			strAbort = "canceled",
+			// Fake xhr
+			jqXHR = {
+				readyState: 0,
 
-jQuery.fn.extend({
+				// Builds headers hashtable if needed
+				getResponseHeader: function( key ) {
+					var match;
+					if ( state === 2 ) {
+						if ( !responseHeaders ) {
+							responseHeaders = {};
+							while ( (match = rheaders.exec( responseHeadersString )) ) {
+								responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+							}
+						}
+						match = responseHeaders[ key.toLowerCase() ];
+					}
+					return match == null ? null : match;
+				},
 
-	position: function() {
-		if ( !this[ 0 ] ) {
-			return;
-		}
+				// Raw string
+				getAllResponseHeaders: function() {
+					return state === 2 ? responseHeadersString : null;
+				},
 
-		var offsetParent, offset,
-			parentOffset = { top: 0, left: 0 },
-			elem = this[ 0 ];
+				// Caches the header
+				setRequestHeader: function( name, value ) {
+					var lname = name.toLowerCase();
+					if ( !state ) {
+						name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
+						requestHeaders[ name ] = value;
+					}
+					return this;
+				},
 
-		// fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is it's only offset parent
-		if ( jQuery.css( elem, "position" ) === "fixed" ) {
-			// we assume that getBoundingClientRect is available when computed position is fixed
-			offset = elem.getBoundingClientRect();
-		} else {
-			// Get *real* offsetParent
-			offsetParent = this.offsetParent();
+				// Overrides response content-type header
+				overrideMimeType: function( type ) {
+					if ( !state ) {
+						s.mimeType = type;
+					}
+					return this;
+				},
 
-			// Get correct offsets
-			offset = this.offset();
-			if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
-				parentOffset = offsetParent.offset();
-			}
-
-			// Add offsetParent borders
-			parentOffset.top  += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
-			parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
-		}
-
-		// Subtract parent offsets and element margins
-		// note: when an element has margin: auto the offsetLeft and marginLeft
-		// are the same in Safari causing offset.left to incorrectly be 0
-		return {
-			top:  offset.top  - parentOffset.top - jQuery.css( elem, "marginTop", true ),
-			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
-		};
-	},
+				// Status-dependent callbacks
+				statusCode: function( map ) {
+					var code;
+					if ( map ) {
+						if ( state < 2 ) {
+							for ( code in map ) {
+								// Lazy-add the new callback in a way that preserves old ones
+								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
+							}
+						} else {
+							// Execute the appropriate callbacks
+							jqXHR.always( map[ jqXHR.status ] );
+						}
+					}
+					return this;
+				},
 
-	offsetParent: function() {
-		return this.map(function() {
-			var offsetParent = this.offsetParent || document.documentElement;
-			while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position") === "static" ) ) {
-				offsetParent = offsetParent.offsetParent;
-			}
-			return offsetParent || document.documentElement;
-		});
-	}
-});
+				// Cancel the request
+				abort: function( statusText ) {
+					var finalText = statusText || strAbort;
+					if ( transport ) {
+						transport.abort( finalText );
+					}
+					done( 0, finalText );
+					return this;
+				}
+			};
 
+		// Attach deferreds
+		deferred.promise( jqXHR ).complete = completeDeferred.add;
+		jqXHR.success = jqXHR.done;
+		jqXHR.error = jqXHR.fail;
 
-// Create scrollLeft and scrollTop methods
-jQuery.each( {scrollLeft: "pageXOffset", scrollTop: "pageYOffset"}, function( method, prop ) {
-	var top = /Y/.test( prop );
+		// Remove hash character (#7531: and string promotion)
+		// Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+		// Handle falsy url in the settings object (#10093: consistency with old signature)
+		// We also use the url parameter if available
+		s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
 
-	jQuery.fn[ method ] = function( val ) {
-		return jQuery.access( this, function( elem, method, val ) {
-			var win = getWindow( elem );
+		// Alias method option to type as per ticket #12004
+		s.type = options.method || options.type || s.method || s.type;
 
-			if ( val === undefined ) {
-				return win ? (prop in win) ? win[ prop ] :
-					win.document.documentElement[ method ] :
-					elem[ method ];
-			}
+		// Extract dataTypes list
+		s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ];
 
-			if ( win ) {
-				win.scrollTo(
-					!top ? val : jQuery( win ).scrollLeft(),
-					top ? val : jQuery( win ).scrollTop()
-				);
+		// A cross-domain request is in order when we have a protocol:host:port mismatch
+		if ( s.crossDomain == null ) {
+			parts = rurl.exec( s.url.toLowerCase() );
+			s.crossDomain = !!( parts &&
+				( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
+					( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !==
+						( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) )
+			);
+		}
 
-			} else {
-				elem[ method ] = val;
-			}
-		}, method, val, arguments.length, null );
-	};
-});
+		// Convert data if not already a string
+		if ( s.data && s.processData && typeof s.data !== "string" ) {
+			s.data = jQuery.param( s.data, s.traditional );
+		}
 
-function getWindow( elem ) {
-	return jQuery.isWindow( elem ) ?
-		elem :
-		elem.nodeType === 9 ?
-			elem.defaultView || elem.parentWindow :
-			false;
-}
-// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
-jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
-	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
-		// margin is only for outerHeight, outerWidth
-		jQuery.fn[ funcName ] = function( margin, value ) {
-			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
-				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+		// Apply prefilters
+		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
 
-			return jQuery.access( this, function( elem, type, value ) {
-				var doc;
+		// If request was aborted inside a prefilter, stop there
+		if ( state === 2 ) {
+			return jqXHR;
+		}
 
-				if ( jQuery.isWindow( elem ) ) {
-					// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
-					// isn't a whole lot we can do. See pull request at this URL for discussion:
-					// https://github.com/jquery/jquery/pull/764
-					return elem.document.documentElement[ "client" + name ];
-				}
+		// We can fire global events as of now if asked to
+		// Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
+		fireGlobals = jQuery.event && s.global;
 
-				// Get document width or height
-				if ( elem.nodeType === 9 ) {
-					doc = elem.documentElement;
+		// Watch for a new set of requests
+		if ( fireGlobals && jQuery.active++ === 0 ) {
+			jQuery.event.trigger("ajaxStart");
+		}
 
-					// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
-					// unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
-					return Math.max(
-						elem.body[ "scroll" + name ], doc[ "scroll" + name ],
-						elem.body[ "offset" + name ], doc[ "offset" + name ],
-						doc[ "client" + name ]
-					);
-				}
+		// Uppercase the type
+		s.type = s.type.toUpperCase();
 
-				return value === undefined ?
-					// Get width or height on the element, requesting but not forcing parseFloat
-					jQuery.css( elem, type, extra ) :
+		// Determine if request has content
+		s.hasContent = !rnoContent.test( s.type );
 
-					// Set width or height on the element
-					jQuery.style( elem, type, value, extra );
-			}, type, chainable ? margin : undefined, chainable, null );
-		};
-	});
-});
-// Limit scope pollution from any deprecated API
-// (function() {
-
-// })();
-// Expose jQuery to the global object
-window.jQuery = window.$ = jQuery;
-
-// Expose jQuery as an AMD module, but only for AMD loaders that
-// understand the issues with loading multiple versions of jQuery
-// in a page that all might call define(). The loader will indicate
-// they have special allowances for multiple jQuery versions by
-// specifying define.amd.jQuery = true. Register as a named module,
-// since jQuery can be concatenated with other files that may use define,
-// but not use a proper concatenation script that understands anonymous
-// AMD modules. A named AMD is safest and most robust way to register.
-// Lowercase jquery is used because AMD module names are derived from
-// file names, and jQuery is normally delivered in a lowercase file name.
-// Do this after creating the global so that if an AMD module wants to call
-// noConflict to hide this version of jQuery, it will work.
-if ( typeof define === "function" && define.amd && define.amd.jQuery ) {
-	define( "jquery", [], function () { return jQuery; } );
-}
+		// Save the URL in case we're toying with the If-Modified-Since
+		// and/or If-None-Match header later on
+		cacheURL = s.url;
 
-})( window );
-/*
-* math-like functionality
-* quaternion, vector, matrix
-*/
+		// More options handling for requests with no content
+		if ( !s.hasContent ) {
 
-var $3Dmol = $3Dmol || {};
-$3Dmol.Math = {
+			// If data is available, append data to url
+			if ( s.data ) {
+				cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
+				// #9682: remove data so that it's not used in an eventual retry
+				delete s.data;
+			}
 
-    clamp : function(x, min, max) {
-        return Math.min( Math.max( x, min ), max );
-    },
+			// Add anti-cache in url if needed
+			if ( s.cache === false ) {
+				s.url = rts.test( cacheURL ) ?
 
-    degToRad : function() {
-       var degreeToRadiansFactor = Math.PI / 180;
-       
-       return function(deg) {
-           return deg * degreeToRadiansFactor;
-       };
-    
-    }()
-    
-};
+					// If there is already a '_' parameter, set its value
+					cacheURL.replace( rts, "$1_=" + nonce++ ) :
 
+					// Otherwise add one to the end
+					cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++;
+			}
+		}
 
-// Quaternion
-/** @constructor */
-$3Dmol.Quaternion = function(x, y, z, w) {
+		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+		if ( s.ifModified ) {
+			if ( jQuery.lastModified[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+			}
+			if ( jQuery.etag[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+			}
+		}
 
-    this.x = x || 0;
-    this.y = y || 0;
-    this.z = z || 0;
-    this.w = (w !== undefined) ? w : 1;
+		// Set the correct header, if data is being sent
+		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+			jqXHR.setRequestHeader( "Content-Type", s.contentType );
+		}
 
-};
+		// Set the Accepts header for the server, depending on the dataType
+		jqXHR.setRequestHeader(
+			"Accept",
+			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
+				s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+				s.accepts[ "*" ]
+		);
 
-$3Dmol.Quaternion.prototype = {
+		// Check for headers option
+		for ( i in s.headers ) {
+			jqXHR.setRequestHeader( i, s.headers[ i ] );
+		}
 
-    constructor : $3Dmol.Quaternion,
+		// Allow custom headers/mimetypes and early abort
+		if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
+			// Abort if not done already and return
+			return jqXHR.abort();
+		}
 
-    set : function(x, y, z, w) {
-        
-        this.x = x;
-        this.y = y;
-        this.z = z;
-        this.w = w;
+		// aborting is no longer a cancellation
+		strAbort = "abort";
 
-        return this;
-    },
+		// Install callbacks on deferreds
+		for ( i in { success: 1, error: 1, complete: 1 } ) {
+			jqXHR[ i ]( s[ i ] );
+		}
 
-    copy : function(q) {
-        
-        this.x = q.x;
-        this.y = q.y;
-        this.z = q.z;
-        this.w = q.w;
+		// Get transport
+		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
 
-        return this;
-    },
+		// If no transport, we auto-abort
+		if ( !transport ) {
+			done( -1, "No Transport" );
+		} else {
+			jqXHR.readyState = 1;
 
-    conjugate : function() {
-        
-        this.x *= -1;
-        this.y *= -1;
-        this.z *= -1;
+			// Send global event
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+			}
+			// Timeout
+			if ( s.async && s.timeout > 0 ) {
+				timeoutTimer = setTimeout(function() {
+					jqXHR.abort("timeout");
+				}, s.timeout );
+			}
 
-        return this;
-    },
+			try {
+				state = 1;
+				transport.send( requestHeaders, done );
+			} catch ( e ) {
+				// Propagate exception as error if not done
+				if ( state < 2 ) {
+					done( -1, e );
+				// Simply rethrow otherwise
+				} else {
+					throw e;
+				}
+			}
+		}
 
-    inverse : function() {
-        
-        return this.conjugate().normalize();
-    },
+		// Callback for when everything is done
+		function done( status, nativeStatusText, responses, headers ) {
+			var isSuccess, success, error, response, modified,
+				statusText = nativeStatusText;
 
-    length : function() {
-        
-        return Math.sqrt(this.x * this.x + this.y * this.y + this.z * this.z + this.w * this.w);
-    },
+			// Called once
+			if ( state === 2 ) {
+				return;
+			}
 
-    normalize : function() {
-        
-        var l = this.length();
+			// State is "done" now
+			state = 2;
 
-        if (l === 0) {
-            this.x = 0;
-            this.y = 0;
-            this.z = 0;
-            this.w = 1;
-        } else {
-            l = 1 / l;
+			// Clear timeout if it exists
+			if ( timeoutTimer ) {
+				clearTimeout( timeoutTimer );
+			}
 
-            this.x *= l;
-            this.y *= l;
-            this.z *= l;
-            this.w *= l;
-        }
+			// Dereference transport for early garbage collection
+			// (no matter how long the jqXHR object will be used)
+			transport = undefined;
 
-        return this;
+			// Cache response headers
+			responseHeadersString = headers || "";
 
-    },
+			// Set readyState
+			jqXHR.readyState = status > 0 ? 4 : 0;
 
-    multiply : function(q) {
-        
-        return this.multiplyQuaternions(this, q);
-    },
+			// Determine if successful
+			isSuccess = status >= 200 && status < 300 || status === 304;
 
-    multiplyQuaternions : function(a, b) {
+			// Get response data
+			if ( responses ) {
+				response = ajaxHandleResponses( s, jqXHR, responses );
+			}
 
-        var qax = a.x, qay = a.y, qaz = a.z, qaw = a.w;
-        var qbx = b.x, qby = b.y, qbz = b.z, qbw = b.w;
+			// Convert no matter what (that way responseXXX fields are always set)
+			response = ajaxConvert( s, response, jqXHR, isSuccess );
 
-        this.x = qax * qbw + qaw * qbx + qay * qbz - qaz * qby;
-        this.y = qay * qbw + qaw * qby + qaz * qbx - qax * qbz;
-        this.z = qaz * qbw + qaw * qbz + qax * qby - qay * qbx;
-        this.w = qaw * qbw - qax * qbx - qay * qby - qaz * qbz;
+			// If successful, handle type chaining
+			if ( isSuccess ) {
 
-    }
-};
+				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+				if ( s.ifModified ) {
+					modified = jqXHR.getResponseHeader("Last-Modified");
+					if ( modified ) {
+						jQuery.lastModified[ cacheURL ] = modified;
+					}
+					modified = jqXHR.getResponseHeader("etag");
+					if ( modified ) {
+						jQuery.etag[ cacheURL ] = modified;
+					}
+				}
 
-//A 2 Vector
-/** @constructor */
-$3Dmol.Vector2 = function(x, y) {
-    
-    this.x = x || 0.0;
-    this.y = y || 0.0;
-};
+				// if no content
+				if ( status === 204 || s.type === "HEAD" ) {
+					statusText = "nocontent";
 
-$3Dmol.Vector2.prototype = {
-    
-    constructor : $3Dmol.Vector2,
-   
-    set : function(x, y) {
-       
-        this.x = x;
-        this.y = y;
-       
-        return this;
-    },
-    
-    subVectors : function(a, b) {
-        
-      this.x = a.x - b.x;
-      this.y = a.y - b.y;
-      
-      return this;
-    },
-   
-    copy : function(v) {
-       
-        this.x = v.x;
-        this.y = v.y;
-       
-        return this;
-    },
-   
-    clone : function() {
-        
-        return new $3Dmol.Vector2(this.x, this.y);
-    }    
-   
-};
+				// if not modified
+				} else if ( status === 304 ) {
+					statusText = "notmodified";
 
-//A 3 Vector
+				// If we have data, let's convert it
+				} else {
+					statusText = response.state;
+					success = response.data;
+					error = response.error;
+					isSuccess = !error;
+				}
+			} else {
+				// We extract error from statusText
+				// then normalize statusText and status for non-aborts
+				error = statusText;
+				if ( status || !statusText ) {
+					statusText = "error";
+					if ( status < 0 ) {
+						status = 0;
+					}
+				}
+			}
 
-$3Dmol.Vector3 = function(x, y, z) {
-    this.x = x || 0.0;
-    this.y = y || 0.0;
-    this.z = z || 0.0;
+			// Set data for the fake xhr object
+			jqXHR.status = status;
+			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+			// Success/Error
+			if ( isSuccess ) {
+				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+			} else {
+				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+			}
+
+			// Status-dependent callbacks
+			jqXHR.statusCode( statusCode );
+			statusCode = undefined;
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
+					[ jqXHR, s, isSuccess ? success : error ] );
+			}
+
+			// Complete
+			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+				// Handle the global AJAX counter
+				if ( !( --jQuery.active ) ) {
+					jQuery.event.trigger("ajaxStop");
+				}
+			}
+		}
+
+		return jqXHR;
+	},
+
+	getJSON: function( url, data, callback ) {
+		return jQuery.get( url, data, callback, "json" );
+	},
+
+	getScript: function( url, callback ) {
+		return jQuery.get( url, undefined, callback, "script" );
+	}
+});
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+	jQuery[ method ] = function( url, data, callback, type ) {
+		// shift arguments if data argument was omitted
+		if ( jQuery.isFunction( data ) ) {
+			type = type || callback;
+			callback = data;
+			data = undefined;
+		}
+
+		return jQuery.ajax({
+			url: url,
+			type: method,
+			dataType: type,
+			data: data,
+			success: callback
+		});
+	};
+});
+
+
+jQuery._evalUrl = function( url ) {
+	return jQuery.ajax({
+		url: url,
+		type: "GET",
+		dataType: "script",
+		async: false,
+		global: false,
+		"throws": true
+	});
 };
-/** @this {$3Dmol.Vector3} */
-$3Dmol.Vector3.prototype =  {
-    
-    constructor : $3Dmol.Vector3,
-    
-    set : function(x, y, z) {
-        
-        this.x = x;
-        this.y = y;
-        this.z = z;
-        
-        return this;
-    },
-    
-    copy : function(v) {
-        
-        this.x = v.x;
-        this.y = v.y;
-        this.z = v.z;
-        
-        return this;  
-    },
-    
-    add : function(v) {
-        
-        this.x += v.x;
-        this.y += v.y;
-        this.z += v.z;  
-        
-        return this;
-    },
-    
-    addVectors : function(a, b) {
-        
-        this.x = a.x + b.x;
-        this.y = a.y + b.y;
-        this.z = a.z + b.z;
-        
-        return this;
-    },
-    
-    sub : function(v) {
-        
-        this.x -= v.x;
-        this.y -= v.y;
-        this.z -= v.z;
-        
-        return this;
-    },
-    
-    subVectors : function(a, b) {
-        
-        this.x = a.x - b.x;
-        this.y = a.y - b.y;
-        this.z = a.z - b.z;
-        
-        return this;
-    },
-    
-    multiplyScalar : function(s) {
-        
-        this.x *= s;
-        this.y *= s;
-        this.z *= s;
-        
-        return this;
-    },
-    
-    divideScalar : function(s) {
-        
-        if (s !== 0) {
-            this.x /= s;
-            this.y /= s;
-            this.z /= s;
-        }
-        
-        else {
-            this.x = 0;
-            this.y = 0;
-            this.z = 0;
-        }
-        
-        return this;
-    },
-    
-
-    distanceTo: function(v) {
-        return Math.sqrt(this.distanceToSquared(v));
-    },
 
-    distanceToSquared: function(v) {
-        var dx = this.x - v.x;
-        var dy = this.y - v.y;
-        var dz = this.z - v.z;
 
-        return dx * dx + dy * dy + dz * dz;
-    },
-    
-    applyMatrix4 : function(m) {
-    
-        var x = this.x, y = this.y, z = this.z;
-        
-        var e = m.elements;
-        
-        this.x = e[0]*x + e[4]*y + e[8]*z + e[12];
-        this.y = e[1]*x + e[5]*y + e[9]*z + e[13];
-        this.z = e[2]*x + e[6]*y + e[10]*z + e[14];
-        
-        return this;
-    },
-    
-    applyProjection : function(m) {
-        
-        //input: $3Dmol.Matrix4 projection matrix
-        
-        var x = this.x, y = this.y, z = this.z;
-        
-        var e = m.elements;
-        var d = ( e[3]*x + e[7]*y + e[11]*z + e[15]);
-        
-        this.x = (e[0]*x + e[4]*y + e[8]*z + e[12]) / d;
-        this.y = (e[1]*x + e[5]*y + e[9]*z + e[13]) / d;
-        this.z = (e[2]*x + e[6]*y + e[10]*z + e[14]) / d;
-        
-        return this;
-    },
-    
-    applyQuaternion : function(q) { 
-        
-        //save values
-        var x = this.x;
-        var y = this.y;
-        var z = this.z;
-        
-        var qx = q.x;
-        var qy = q.y;
-        var qz = q.z;
-        var qw = q.w;
-        
-        //compute this as
-        //t = 2 * cross(q.xyz, v)
-        //newv = v + q.w * t + cross(q.xyz, t)
-        //this from molecularmusings
-        //http://molecularmusings.wordpress.com/2013/05/24/a-faster-quaternion-vector-multiplication/
-        var t = {};
-        t.x = 2*(y * qz - z * qy);
-        t.y = 2*(z * qx - x * qz);
-        t.z = 2*(x * qy - y * qx);
-        
-        //cross t with q
-        var t2 = {};
-        t2.x = t.y * qz - t.z * qy;
-        t2.y = t.z * qx - t.x * qz;
-        t2.z = t.x * qy - t.y * qx;
-        
-        this.x = x + q.w*t.x + t2.x;
-        this.y = y + q.w*t.y + t2.y;
-        this.z = z + q.w*t.z + t2.z;
-        
-        return this;
-    },
-    
-    negate : function() {
-        
-        return this.multiplyScalar(-1);
-    },
-    
-    dot : function(v) {
-        
-        return this.x * v.x + this.y * v.y + this.z * v.z;
-    },
-    
-    length : function() {
-        
-        return Math.sqrt(this.x*this.x + this.y*this.y + this.z*this.z);
-    },
-    
-    lengthSq : function() {
-    
-        return (this.x*this.x + this.y*this.y + this.z*this.z);
-    },
-    
-    normalize : function() {
-        
-        return this.divideScalar( this.length() );
-    },
-    
-    cross : function (v) {
-        
-        var x = this.x, y = this.y, z = this.z;
-        
-        this.x = y * v.z - z * v.y;
-        this.y = z * v.x - x * v.z;
-        this.z = x * v.y - y * v.x;
-        
-        return this;
-    },
-    
-    crossVectors : function(a, b) {
-        
-        this.x = a.y * b.z - a.z * b.y;
-        this.y = a.z * b.x - a.x * b.z;
-        this.z = a.x * b.y - a.y * b.x;
-        
-        return this;
-    },
-    
-    getPositionFromMatrix : function(m) {
-        
-        this.x = m.elements[12];
-        this.y = m.elements[13];
-        this.z = m.elements[14];
-        
-        return this;
-    },
+jQuery.fn.extend({
+	wrapAll: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapAll( html.call(this, i) );
+			});
+		}
 
-    setEulerFromRotationMatrix : function (m, order) {
+		if ( this[0] ) {
+			// The elements to wrap the target around
+			var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
 
-        // assumes the upper 3x3 of m is a pure rotation matrix (i.e, unscaled)
+			if ( this[0].parentNode ) {
+				wrap.insertBefore( this[0] );
+			}
 
-        var te = m.elements;
-        var m11 = te[0], m12 = te[4], m13 = te[8];
-        var m21 = te[1], m22 = te[5], m23 = te[9];
-        var m31 = te[2], m32 = te[6], m33 = te[10];
+			wrap.map(function() {
+				var elem = this;
 
-        if ( order === undefined || order === 'XYZ' ) {
+				while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
+					elem = elem.firstChild;
+				}
 
-            this.y = Math.asin( $3Dmol.Math.clamp( m13, -1, 1 ) );
+				return elem;
+			}).append( this );
+		}
 
-            if ( Math.abs( m13 ) < 0.99999 ) {
+		return this;
+	},
 
-                this.x = Math.atan2( - m23, m33 );
-                this.z = Math.atan2( - m12, m11 );
+	wrapInner: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapInner( html.call(this, i) );
+			});
+		}
 
-            } else {
+		return this.each(function() {
+			var self = jQuery( this ),
+				contents = self.contents();
 
-                this.x = Math.atan2( m32, m22 );
-                this.z = 0;
+			if ( contents.length ) {
+				contents.wrapAll( html );
 
-            }
-        }
-        
-        else {
-            console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: " + order);
-        }
-        
-        return this;
+			} else {
+				self.append( html );
+			}
+		});
+	},
 
-    },
-    
-    clone : function() {
-        return new $3Dmol.Vector3(this.x, this.y, this.z);
-    }
-    
-};
-
-//Matrices
+	wrap: function( html ) {
+		var isFunction = jQuery.isFunction( html );
 
-//Matrix3
-/** @constructor */
-$3Dmol.Matrix3 = function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
-    
-    this.elements = new Float32Array(9);
-    
-    this.set(
-        (n11 !== undefined) ? n11 : 1, n12 || 0, n13 || 0,
-        n21 || 0, (n22 !== undefined) ? n22 : 1, n23 || 0,
-        n31 || 0, n32 || 0, (n33 !== undefined) ? n33 : 1
-    );
-    
-};
+		return this.each(function(i) {
+			jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
+		});
+	},
 
-$3Dmol.Matrix3.prototype = {
-    
-    constructor : $3Dmol.Matrix3,    
-   
-    set : function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
-        var te = this.elements;
-        
-        te[0] = n11; te[3] = n12; te[6] = n13;
-        te[1] = n21; te[4] = n22; te[7] = n23;
-        te[2] = n31; te[5] = n32; te[8] = n33;
-        
-        return this;
-    },
-    
-    identity : function() {   
-        this.set(
-            1,0,0,
-            0,1,0,
-            0,0,1
-        );
-        
-        return this;
-    },
-   
-    copy : function(m) {
-        var me = m.elements;
-       
-        this.set(
-            me[0], me[3], me[6],
-            me[1], me[4], me[7],
-            me[2], me[5], me[8]
-        );
-    },
-    
-    multiplyScalar: function ( s ) {
-        var te = this.elements;
+	unwrap: function() {
+		return this.parent().each(function() {
+			if ( !jQuery.nodeName( this, "body" ) ) {
+				jQuery( this ).replaceWith( this.childNodes );
+			}
+		}).end();
+	}
+});
 
-        te[0] *= s; te[3] *= s; te[6] *= s;
-        te[1] *= s; te[4] *= s; te[7] *= s;
-        te[2] *= s; te[5] *= s; te[8] *= s;
 
-        return this;
-    },
+jQuery.expr.filters.hidden = function( elem ) {
+	// Support: Opera <= 12.12
+	// Opera reports offsetWidths and offsetHeights less than zero on some elements
+	return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
+		(!support.reliableHiddenOffsets() &&
+			((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
+};
 
-    getInverse: function ( matrix, throwOnInvertible ) {
-        // input: Matrix4
+jQuery.expr.filters.visible = function( elem ) {
+	return !jQuery.expr.filters.hidden( elem );
+};
 
-        var me = matrix.elements;
-        var te = this.elements;
 
-        te[ 0 ] =   me[10] * me[5] - me[6] * me[9];
-        te[ 1 ] = - me[10] * me[1] + me[2] * me[9];
-        te[ 2 ] =   me[6] * me[1] - me[2] * me[5];
-        te[ 3 ] = - me[10] * me[4] + me[6] * me[8];
-        te[ 4 ] =   me[10] * me[0] - me[2] * me[8];
-        te[ 5 ] = - me[6] * me[0] + me[2] * me[4];
-        te[ 6 ] =   me[9] * me[4] - me[5] * me[8];
-        te[ 7 ] = - me[9] * me[0] + me[1] * me[8];
-        te[ 8 ] =   me[5] * me[0] - me[1] * me[4];
 
-        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 3 ] + me[ 2 ] * te[ 6 ];
 
-        // no inverse
+var r20 = /%20/g,
+	rbracket = /\[\]$/,
+	rCRLF = /\r?\n/g,
+	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+	rsubmittable = /^(?:input|select|textarea|keygen)/i;
 
-        if ( det === 0 ) {
+function buildParams( prefix, obj, traditional, add ) {
+	var name;
 
-            var msg = "Matrix3.getInverse(): can't invert matrix, determinant is 0";
+	if ( jQuery.isArray( obj ) ) {
+		// Serialize array item.
+		jQuery.each( obj, function( i, v ) {
+			if ( traditional || rbracket.test( prefix ) ) {
+				// Treat each array item as a scalar.
+				add( prefix, v );
 
-            if ( throwOnInvertible || false ) {
+			} else {
+				// Item is non-scalar (array or object), encode its numeric index.
+				buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
+			}
+		});
 
-                throw new Error( msg ); 
+	} else if ( !traditional && jQuery.type( obj ) === "object" ) {
+		// Serialize object item.
+		for ( name in obj ) {
+			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+		}
 
-            } else {
+	} else {
+		// Serialize scalar item.
+		add( prefix, obj );
+	}
+}
 
-                console.warn( msg );
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+	var prefix,
+		s = [],
+		add = function( key, value ) {
+			// If value is a function, invoke it and return its value
+			value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
+			s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
+		};
 
-            }
+	// Set traditional to true for jQuery <= 1.3.2 behavior.
+	if ( traditional === undefined ) {
+		traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
+	}
 
-            this.identity();
+	// If an array was passed in, assume that it is an array of form elements.
+	if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+		// Serialize the form elements
+		jQuery.each( a, function() {
+			add( this.name, this.value );
+		});
 
-            return this;
+	} else {
+		// If traditional, encode the "old" way (the way 1.3.2 or older
+		// did it), otherwise encode params recursively.
+		for ( prefix in a ) {
+			buildParams( prefix, a[ prefix ], traditional, add );
+		}
+	}
 
-        }
+	// Return the resulting serialization
+	return s.join( "&" ).replace( r20, "+" );
+};
 
-        this.multiplyScalar( 1.0 / det );
+jQuery.fn.extend({
+	serialize: function() {
+		return jQuery.param( this.serializeArray() );
+	},
+	serializeArray: function() {
+		return this.map(function() {
+			// Can add propHook for "elements" to filter or add form elements
+			var elements = jQuery.prop( this, "elements" );
+			return elements ? jQuery.makeArray( elements ) : this;
+		})
+		.filter(function() {
+			var type = this.type;
+			// Use .is(":disabled") so that fieldset[disabled] works
+			return this.name && !jQuery( this ).is( ":disabled" ) &&
+				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+				( this.checked || !rcheckableType.test( type ) );
+		})
+		.map(function( i, elem ) {
+			var val = jQuery( this ).val();
 
-        return this;
-    },
-    
-    transpose: function () {
-        var tmp, m = this.elements;
+			return val == null ?
+				null :
+				jQuery.isArray( val ) ?
+					jQuery.map( val, function( val ) {
+						return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+					}) :
+					{ name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+		}).get();
+	}
+});
 
-        tmp = m[1]; m[1] = m[3]; m[3] = tmp;
-        tmp = m[2]; m[2] = m[6]; m[6] = tmp;
-        tmp = m[5]; m[5] = m[7]; m[7] = tmp;
 
-        return this;
-    },
-    
-    clone: function () {
-        var te = this.elements;
+// Create the request object
+// (This is still attached to ajaxSettings for backward compatibility)
+jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ?
+	// Support: IE6+
+	function() {
 
-        return new $3Dmol.Matrix3(
+		// XHR cannot access local files, always use ActiveX for that case
+		return !this.isLocal &&
 
-            te[0], te[3], te[6],
-            te[1], te[4], te[7],
-            te[2], te[5], te[8]
+			// Support: IE7-8
+			// oldIE XHR does not support non-RFC2616 methods (#13240)
+			// See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx
+			// and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9
+			// Although this check for six methods instead of eight
+			// since IE also does not support "trace" and "connect"
+			/^(get|post|head|put|delete|options)$/i.test( this.type ) &&
 
-        );
-    }
-   
-};
+			createStandardXHR() || createActiveXHR();
+	} :
+	// For all other browsers, use the standard XMLHttpRequest object
+	createStandardXHR;
 
-//Matrix 4
-/** @constructor */
-$3Dmol.Matrix4 = function(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44) {
+var xhrId = 0,
+	xhrCallbacks = {},
+	xhrSupported = jQuery.ajaxSettings.xhr();
 
-    var te = this.elements = new Float32Array( 16 );
-    
-    te[0] = ( n11 !== undefined ) ? n11 : 1; te[4] = n12 || 0; te[8] = n13 || 0; te[12] = n14 || 0;
-    te[1] = n21 || 0; te[5] = ( n22 !== undefined ) ? n22 : 1; te[9] = n23 || 0; te[13] = n24 || 0;
-    te[2] = n31 || 0; te[6] = n32 || 0; te[10] = ( n33 !== undefined ) ? n33 : 1; te[14] = n34 || 0;
-    te[3] = n41 || 0; te[7] = n42 || 0; te[11] = n43 || 0; te[15] = ( n44 !== undefined ) ? n44 : 1;
+// Support: IE<10
+// Open requests must be manually aborted on unload (#5280)
+// See https://support.microsoft.com/kb/2856746 for more info
+if ( window.attachEvent ) {
+	window.attachEvent( "onunload", function() {
+		for ( var key in xhrCallbacks ) {
+			xhrCallbacks[ key ]( undefined, true );
+		}
+	});
+}
 
-};
+// Determine support properties
+support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+xhrSupported = support.ajax = !!xhrSupported;
 
-$3Dmol.Matrix4.prototype = {
+// Create transport if the browser can provide an xhr
+if ( xhrSupported ) {
 
-    constructor : $3Dmol.Matrix4,
+	jQuery.ajaxTransport(function( options ) {
+		// Cross domain only allowed if supported through XMLHttpRequest
+		if ( !options.crossDomain || support.cors ) {
 
-    set: function ( n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44 ) {
-        var te = this.elements;
+			var callback;
 
-        te[0] = n11; te[4] = n12; te[8] = n13; te[12] = n14;
-        te[1] = n21; te[5] = n22; te[9] = n23; te[13] = n24;
-        te[2] = n31; te[6] = n32; te[10] = n33; te[14] = n34;
-        te[3] = n41; te[7] = n42; te[11] = n43; te[15] = n44;
+			return {
+				send: function( headers, complete ) {
+					var i,
+						xhr = options.xhr(),
+						id = ++xhrId;
 
-        return this;
-    },
+					// Open the socket
+					xhr.open( options.type, options.url, options.async, options.username, options.password );
 
-    identity: function () {
-        this.set(
+					// Apply custom fields if provided
+					if ( options.xhrFields ) {
+						for ( i in options.xhrFields ) {
+							xhr[ i ] = options.xhrFields[ i ];
+						}
+					}
 
-            1, 0, 0, 0,
-            0, 1, 0, 0,
-            0, 0, 1, 0,
-            0, 0, 0, 1
+					// Override mime type if needed
+					if ( options.mimeType && xhr.overrideMimeType ) {
+						xhr.overrideMimeType( options.mimeType );
+					}
 
-        );
+					// X-Requested-With header
+					// For cross-domain requests, seeing as conditions for a preflight are
+					// akin to a jigsaw puzzle, we simply never set it to be sure.
+					// (it can always be set on a per-request basis or even using ajaxSetup)
+					// For same-domain requests, won't change header if already provided.
+					if ( !options.crossDomain && !headers["X-Requested-With"] ) {
+						headers["X-Requested-With"] = "XMLHttpRequest";
+					}
 
-        return this;
-    },
+					// Set headers
+					for ( i in headers ) {
+						// Support: IE<9
+						// IE's ActiveXObject throws a 'Type Mismatch' exception when setting
+						// request header to a null-value.
+						//
+						// To keep consistent with other XHR implementations, cast the value
+						// to string and ignore `undefined`.
+						if ( headers[ i ] !== undefined ) {
+							xhr.setRequestHeader( i, headers[ i ] + "" );
+						}
+					}
 
-    copy: function ( m ) {
-        var me = m.elements;
+					// Do send the request
+					// This may raise an exception which is actually
+					// handled in jQuery.ajax (so no try/catch here)
+					xhr.send( ( options.hasContent && options.data ) || null );
 
-        this.set(
+					// Listener
+					callback = function( _, isAbort ) {
+						var status, statusText, responses;
+
+						// Was never called and is aborted or complete
+						if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+							// Clean up
+							delete xhrCallbacks[ id ];
+							callback = undefined;
+							xhr.onreadystatechange = jQuery.noop;
+
+							// Abort manually if needed
+							if ( isAbort ) {
+								if ( xhr.readyState !== 4 ) {
+									xhr.abort();
+								}
+							} else {
+								responses = {};
+								status = xhr.status;
+
+								// Support: IE<10
+								// Accessing binary-data responseText throws an exception
+								// (#11426)
+								if ( typeof xhr.responseText === "string" ) {
+									responses.text = xhr.responseText;
+								}
 
-            me[0], me[4], me[8], me[12],
-            me[1], me[5], me[9], me[13],
-            me[2], me[6], me[10], me[14],
-            me[3], me[7], me[11], me[15]
+								// Firefox throws an exception when accessing
+								// statusText for faulty cross-domain requests
+								try {
+									statusText = xhr.statusText;
+								} catch( e ) {
+									// We normalize with Webkit giving an empty statusText
+									statusText = "";
+								}
 
-        );
+								// Filter status for non standard behaviors
 
-        return this;
-    },
+								// If the request is local and we have data: assume a success
+								// (success with no data won't get notified, that's the best we
+								// can do given current implementations)
+								if ( !status && options.isLocal && !options.crossDomain ) {
+									status = responses.text ? 200 : 404;
+								// IE - #1450: sometimes returns 1223 when it should be 204
+								} else if ( status === 1223 ) {
+									status = 204;
+								}
+							}
+						}
 
-    setRotationFromEuler: function ( v, order ) {
+						// Call complete if needed
+						if ( responses ) {
+							complete( status, statusText, responses, xhr.getAllResponseHeaders() );
+						}
+					};
 
-        var te = this.elements;
+					if ( !options.async ) {
+						// if we're in sync mode we fire the callback
+						callback();
+					} else if ( xhr.readyState === 4 ) {
+						// (IE6 & IE7) if it's in cache and has been
+						// retrieved directly we need to fire the callback
+						setTimeout( callback );
+					} else {
+						// Add to the list of active xhr callbacks
+						xhr.onreadystatechange = xhrCallbacks[ id ] = callback;
+					}
+				},
 
-        var x = v.x, y = v.y, z = v.z;
-        var a = Math.cos( x ), b = Math.sin( x );
-        var c = Math.cos( y ), d = Math.sin( y );
-        var e = Math.cos( z ), f = Math.sin( z );
+				abort: function() {
+					if ( callback ) {
+						callback( undefined, true );
+					}
+				}
+			};
+		}
+	});
+}
 
-        if ( order === undefined || order === 'XYZ' ) {
+// Functions to create xhrs
+function createStandardXHR() {
+	try {
+		return new window.XMLHttpRequest();
+	} catch( e ) {}
+}
 
-            var ae = a * e, af = a * f, be = b * e, bf = b * f;
+function createActiveXHR() {
+	try {
+		return new window.ActiveXObject( "Microsoft.XMLHTTP" );
+	} catch( e ) {}
+}
 
-            te[0] = c * e;
-            te[4] = - c * f;
-            te[8] = d;
 
-            te[1] = af + be * d;
-            te[5] = ae - bf * d;
-            te[9] = - b * c;
 
-            te[2] = bf - ae * d;
-            te[6] = be + af * d;
-            te[10] = a * c;
 
-        } 
-        
-        else
-            console.error("Error with matrix4 setRotationFromEuler. Order: " + order);
+// Install script dataType
+jQuery.ajaxSetup({
+	accepts: {
+		script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
+	},
+	contents: {
+		script: /(?:java|ecma)script/
+	},
+	converters: {
+		"text script": function( text ) {
+			jQuery.globalEval( text );
+			return text;
+		}
+	}
+});
 
-        return this;
+// Handle cache's special case and global
+jQuery.ajaxPrefilter( "script", function( s ) {
+	if ( s.cache === undefined ) {
+		s.cache = false;
+	}
+	if ( s.crossDomain ) {
+		s.type = "GET";
+		s.global = false;
+	}
+});
 
-    },
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function(s) {
 
-    setRotationFromQuaternion: function ( q ) {
-        var te = this.elements;
+	// This transport only deals with cross domain requests
+	if ( s.crossDomain ) {
 
-        var x = q.x, y = q.y, z = q.z, w = q.w;
-        var x2 = x + x, y2 = y + y, z2 = z + z;
-        var xx = x * x2, xy = x * y2, xz = x * z2;
-        var yy = y * y2, yz = y * z2, zz = z * z2;
-        var wx = w * x2, wy = w * y2, wz = w * z2;
+		var script,
+			head = document.head || jQuery("head")[0] || document.documentElement;
 
-        te[0] = 1 - ( yy + zz );
-        te[4] = xy - wz;
-        te[8] = xz + wy;
+		return {
 
-        te[1] = xy + wz;
-        te[5] = 1 - ( xx + zz );
-        te[9] = yz - wx;
+			send: function( _, callback ) {
 
-        te[2] = xz - wy;
-        te[6] = yz + wx;
-        te[10] = 1 - ( xx + yy );
+				script = document.createElement("script");
 
-        return this;
-    },
+				script.async = true;
 
-    lookAt: function() {
-        var x = new $3Dmol.Vector3();
-        var y = new $3Dmol.Vector3();
-        var z = new $3Dmol.Vector3();
+				if ( s.scriptCharset ) {
+					script.charset = s.scriptCharset;
+				}
 
-        return function ( eye, target, up ) {
+				script.src = s.url;
 
-            var te = this.elements;
+				// Attach handlers for all browsers
+				script.onload = script.onreadystatechange = function( _, isAbort ) {
 
-            z.subVectors( eye, target ).normalize();
+					if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
 
-            if ( z.length() === 0 ) {
+						// Handle memory leak in IE
+						script.onload = script.onreadystatechange = null;
 
-                z.z = 1;
+						// Remove the script
+						if ( script.parentNode ) {
+							script.parentNode.removeChild( script );
+						}
 
-            }
+						// Dereference the script
+						script = null;
 
-            x.crossVectors( up, z ).normalize();
+						// Callback if not abort
+						if ( !isAbort ) {
+							callback( 200, "success" );
+						}
+					}
+				};
 
-            if ( x.length() === 0 ) {
+				// Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
+				// Use native DOM manipulation to avoid our domManip AJAX trickery
+				head.insertBefore( script, head.firstChild );
+			},
 
-                z.x += 0.0001;
-                x.crossVectors( up, z ).normalize();
+			abort: function() {
+				if ( script ) {
+					script.onload( undefined, true );
+				}
+			}
+		};
+	}
+});
 
-            }
 
-            y.crossVectors( z, x );
 
 
-            te[0] = x.x; te[4] = y.x; te[8] = z.x;
-            te[1] = x.y; te[5] = y.y; te[9] = z.y;
-            te[2] = x.z; te[6] = y.z; te[10] = z.z;
+var oldCallbacks = [],
+	rjsonp = /(=)\?(?=&|$)|\?\?/;
 
-            return this;
-        };
+// Default jsonp settings
+jQuery.ajaxSetup({
+	jsonp: "callback",
+	jsonpCallback: function() {
+		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+		this[ callback ] = true;
+		return callback;
+	}
+});
 
-    }(),
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
 
-    multiplyMatrices: function ( a, b ) {
-        var ae = a.elements;
-        var be = b.elements;
-        var te = this.elements;
+	var callbackName, overwritten, responseContainer,
+		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
+			"url" :
+			typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
+		);
 
-        var a11 = ae[0], a12 = ae[4], a13 = ae[8], a14 = ae[12];
-        var a21 = ae[1], a22 = ae[5], a23 = ae[9], a24 = ae[13];
-        var a31 = ae[2], a32 = ae[6], a33 = ae[10], a34 = ae[14];
-        var a41 = ae[3], a42 = ae[7], a43 = ae[11], a44 = ae[15];
+	// Handle iff the expected data type is "jsonp" or we have a parameter to set
+	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
 
-        var b11 = be[0], b12 = be[4], b13 = be[8], b14 = be[12];
-        var b21 = be[1], b22 = be[5], b23 = be[9], b24 = be[13];
-        var b31 = be[2], b32 = be[6], b33 = be[10], b34 = be[14];
-        var b41 = be[3], b42 = be[7], b43 = be[11], b44 = be[15];
+		// Get callback name, remembering preexisting value associated with it
+		callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
+			s.jsonpCallback() :
+			s.jsonpCallback;
 
-        te[0] = a11 * b11 + a12 * b21 + a13 * b31 + a14 * b41;
-        te[4] = a11 * b12 + a12 * b22 + a13 * b32 + a14 * b42;
-        te[8] = a11 * b13 + a12 * b23 + a13 * b33 + a14 * b43;
-        te[12] = a11 * b14 + a12 * b24 + a13 * b34 + a14 * b44;
+		// Insert callback into url or form data
+		if ( jsonProp ) {
+			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
+		} else if ( s.jsonp !== false ) {
+			s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+		}
 
-        te[1] = a21 * b11 + a22 * b21 + a23 * b31 + a24 * b41;
-        te[5] = a21 * b12 + a22 * b22 + a23 * b32 + a24 * b42;
-        te[9] = a21 * b13 + a22 * b23 + a23 * b33 + a24 * b43;
-        te[13] = a21 * b14 + a22 * b24 + a23 * b34 + a24 * b44;
+		// Use data converter to retrieve json after script execution
+		s.converters["script json"] = function() {
+			if ( !responseContainer ) {
+				jQuery.error( callbackName + " was not called" );
+			}
+			return responseContainer[ 0 ];
+		};
 
-        te[2] = a31 * b11 + a32 * b21 + a33 * b31 + a34 * b41;
-        te[6] = a31 * b12 + a32 * b22 + a33 * b32 + a34 * b42;
-        te[10] = a31 * b13 + a32 * b23 + a33 * b33 + a34 * b43;
-        te[14] = a31 * b14 + a32 * b24 + a33 * b34 + a34 * b44;
+		// force json dataType
+		s.dataTypes[ 0 ] = "json";
 
-        te[3] = a41 * b11 + a42 * b21 + a43 * b31 + a44 * b41;
-        te[7] = a41 * b12 + a42 * b22 + a43 * b32 + a44 * b42;
-        te[11] = a41 * b13 + a42 * b23 + a43 * b33 + a44 * b43;
-        te[15] = a41 * b14 + a42 * b24 + a43 * b34 + a44 * b44;
+		// Install callback
+		overwritten = window[ callbackName ];
+		window[ callbackName ] = function() {
+			responseContainer = arguments;
+		};
 
-        return this;
-    },
-    
-    multiplyScalar: function ( s ) {
-        var te = this.elements;
-    
-        te[0] *= s; te[4] *= s; te[8] *= s; te[12] *= s;
-        te[1] *= s; te[5] *= s; te[9] *= s; te[13] *= s;
-        te[2] *= s; te[6] *= s; te[10] *= s; te[14] *= s;
-        te[3] *= s; te[7] *= s; te[11] *= s; te[15] *= s;
-    
-        return this;
-    },
-    
-    transpose: function () {
-        var te = this.elements;
-        var tmp;
+		// Clean-up function (fires after converters)
+		jqXHR.always(function() {
+			// Restore preexisting value
+			window[ callbackName ] = overwritten;
 
-        tmp = te[1]; te[1] = te[4]; te[4] = tmp;
-        tmp = te[2]; te[2] = te[8]; te[8] = tmp;
-        tmp = te[6]; te[6] = te[9]; te[9] = tmp;
+			// Save back as free
+			if ( s[ callbackName ] ) {
+				// make sure that re-using the options doesn't screw things around
+				s.jsonpCallback = originalSettings.jsonpCallback;
 
-        tmp = te[3]; te[3] = te[12]; te[12] = tmp;
-        tmp = te[7]; te[7] = te[13]; te[13] = tmp;
-        tmp = te[11]; te[11] = te[14]; te[14] = tmp;
+				// save the callback name for future use
+				oldCallbacks.push( callbackName );
+			}
 
-        return this;
-    },
+			// Call if it was a function and we have a response
+			if ( responseContainer && jQuery.isFunction( overwritten ) ) {
+				overwritten( responseContainer[ 0 ] );
+			}
 
-    getPosition: function() {
-        var v1 = new $3Dmol.Vector3();
+			responseContainer = overwritten = undefined;
+		});
 
-        return function () {
+		// Delegate to script
+		return "script";
+	}
+});
 
-            console.warn( 'DEPRECATED: Matrix4\'s .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.' );
 
-            var te = this.elements;
-            return v1.set( te[12], te[13], te[14] );
-        };
 
-    }(),
 
-    setPosition: function ( v ) {
-        var te = this.elements;
+// data: string of html
+// context (optional): If specified, the fragment will be created in this context, defaults to document
+// keepScripts (optional): If true, will include scripts passed in the html string
+jQuery.parseHTML = function( data, context, keepScripts ) {
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	if ( typeof context === "boolean" ) {
+		keepScripts = context;
+		context = false;
+	}
+	context = context || document;
 
-        te[12] = v.x;
-        te[13] = v.y;
-        te[14] = v.z;
+	var parsed = rsingleTag.exec( data ),
+		scripts = !keepScripts && [];
 
-        return this;
-    },
+	// Single tag
+	if ( parsed ) {
+		return [ context.createElement( parsed[1] ) ];
+	}
 
-    getInverse: function ( m, throwOnInvertible ) {
-        // based on http://www.euclideanspace.com/maths/algebra/matrix/functions/inverse/fourD/index.htm
-        var te = this.elements;
-        var me = m.elements;
+	parsed = jQuery.buildFragment( [ data ], context, scripts );
 
-        var n11 = me[0], n12 = me[4], n13 = me[8], n14 = me[12];
-        var n21 = me[1], n22 = me[5], n23 = me[9], n24 = me[13];
-        var n31 = me[2], n32 = me[6], n33 = me[10], n34 = me[14];
-        var n41 = me[3], n42 = me[7], n43 = me[11], n44 = me[15];
+	if ( scripts && scripts.length ) {
+		jQuery( scripts ).remove();
+	}
 
-        te[0] = n23*n34*n42 - n24*n33*n42 + n24*n32*n43 - n22*n34*n43 - n23*n32*n44 + n22*n33*n44;
-        te[4] = n14*n33*n42 - n13*n34*n42 - n14*n32*n43 + n12*n34*n43 + n13*n32*n44 - n12*n33*n44;
-        te[8] = n13*n24*n42 - n14*n23*n42 + n14*n22*n43 - n12*n24*n43 - n13*n22*n44 + n12*n23*n44;
-        te[12] = n14*n23*n32 - n13*n24*n32 - n14*n22*n33 + n12*n24*n33 + n13*n22*n34 - n12*n23*n34;
-        te[1] = n24*n33*n41 - n23*n34*n41 - n24*n31*n43 + n21*n34*n43 + n23*n31*n44 - n21*n33*n44;
-        te[5] = n13*n34*n41 - n14*n33*n41 + n14*n31*n43 - n11*n34*n43 - n13*n31*n44 + n11*n33*n44;
-        te[9] = n14*n23*n41 - n13*n24*n41 - n14*n21*n43 + n11*n24*n43 + n13*n21*n44 - n11*n23*n44;
-        te[13] = n13*n24*n31 - n14*n23*n31 + n14*n21*n33 - n11*n24*n33 - n13*n21*n34 + n11*n23*n34;
-        te[2] = n22*n34*n41 - n24*n32*n41 + n24*n31*n42 - n21*n34*n42 - n22*n31*n44 + n21*n32*n44;
-        te[6] = n14*n32*n41 - n12*n34*n41 - n14*n31*n42 + n11*n34*n42 + n12*n31*n44 - n11*n32*n44;
-        te[10] = n12*n24*n41 - n14*n22*n41 + n14*n21*n42 - n11*n24*n42 - n12*n21*n44 + n11*n22*n44;
-        te[14] = n14*n22*n31 - n12*n24*n31 - n14*n21*n32 + n11*n24*n32 + n12*n21*n34 - n11*n22*n34;
-        te[3] = n23*n32*n41 - n22*n33*n41 - n23*n31*n42 + n21*n33*n42 + n22*n31*n43 - n21*n32*n43;
-        te[7] = n12*n33*n41 - n13*n32*n41 + n13*n31*n42 - n11*n33*n42 - n12*n31*n43 + n11*n32*n43;
-        te[11] = n13*n22*n41 - n12*n23*n41 - n13*n21*n42 + n11*n23*n42 + n12*n21*n43 - n11*n22*n43;
-        te[15] = n12*n23*n31 - n13*n22*n31 + n13*n21*n32 - n11*n23*n32 - n12*n21*n33 + n11*n22*n33;
+	return jQuery.merge( [], parsed.childNodes );
+};
 
-        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 4 ] + me[ 2 ] * te[ 8 ] + me[ 3 ] * te[ 12 ];
 
-        if ( det === 0 ) {
+// Keep a copy of the old load method
+var _load = jQuery.fn.load;
 
-            var msg = "Matrix4.getInverse(): can't invert matrix, determinant is 0";
+/**
+ * Load a url into a page
+ */
+jQuery.fn.load = function( url, params, callback ) {
+	if ( typeof url !== "string" && _load ) {
+		return _load.apply( this, arguments );
+	}
 
-            if ( throwOnInvertible || false ) {
+	var selector, response, type,
+		self = this,
+		off = url.indexOf(" ");
 
-                throw new Error( msg ); 
+	if ( off >= 0 ) {
+		selector = jQuery.trim( url.slice( off, url.length ) );
+		url = url.slice( 0, off );
+	}
 
-            } else {
+	// If it's a function
+	if ( jQuery.isFunction( params ) ) {
 
-                console.warn( msg );
+		// We assume that it's the callback
+		callback = params;
+		params = undefined;
 
-            }
+	// Otherwise, build a param string
+	} else if ( params && typeof params === "object" ) {
+		type = "POST";
+	}
 
-            this.identity();
+	// If we have elements to modify, make the request
+	if ( self.length > 0 ) {
+		jQuery.ajax({
+			url: url,
 
-            return this;
-        }
+			// if "type" variable is undefined, then "GET" method will be used
+			type: type,
+			dataType: "html",
+			data: params
+		}).done(function( responseText ) {
 
-        this.multiplyScalar( 1 / det );
+			// Save response for use in complete callback
+			response = arguments;
 
-        return this;
-    },
+			self.html( selector ?
 
-    compose: function() {
-        var mRotation = new $3Dmol.Matrix4(),
-            mScale = new $3Dmol.Matrix4();
-        
-        return function ( translation, rotation, scale ) {
+				// If a selector was specified, locate the right elements in a dummy div
+				// Exclude scripts to avoid IE 'Permission Denied' errors
+				jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
 
-            var te = this.elements;
+				// Otherwise use the full result
+				responseText );
 
-            mRotation.identity();
-            mRotation.setRotationFromQuaternion( rotation );
+		}).complete( callback && function( jqXHR, status ) {
+			self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
+		});
+	}
 
-            mScale.makeScale( scale.x, scale.y, scale.z );
+	return this;
+};
 
-            this.multiplyMatrices( mRotation, mScale );
 
-            te[12] = translation.x;
-            te[13] = translation.y;
-            te[14] = translation.z;
 
-            return this;
 
-        };
-    }(),
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) {
+	jQuery.fn[ type ] = function( fn ) {
+		return this.on( type, fn );
+	};
+});
 
-    decompose: function() {
-        var x = new $3Dmol.Vector3(),
-            y = new $3Dmol.Vector3(),
-            z = new $3Dmol.Vector3(),
-            matrix = new $3Dmol.Matrix4();
 
-        return function ( translation, rotation, scale ) {
 
-            var te = this.elements;
 
-            // grab the axis vectors
-            x.set( te[0], te[1], te[2] );
-            y.set( te[4], te[5], te[6] );
-            z.set( te[8], te[9], te[10] );
+jQuery.expr.filters.animated = function( elem ) {
+	return jQuery.grep(jQuery.timers, function( fn ) {
+		return elem === fn.elem;
+	}).length;
+};
 
-            translation = ( translation instanceof $3Dmol.Vector3 ) ? translation : new $3Dmol.Vector3();
-            rotation = ( rotation instanceof $3Dmol.Quaternion ) ? rotation : new $3Dmol.Quaternion();
-            scale = ( scale instanceof $3Dmol.Vector3 ) ? scale : new $3Dmol.Vector3();
 
-            scale.x = x.length();
-            scale.y = y.length();
-            scale.z = z.length();
 
-            translation.x = te[12];
-            translation.y = te[13];
-            translation.z = te[14];
 
-            // scale the rotation part
 
-            matrix.copy( this );
+var docElem = window.document.documentElement;
 
-            matrix.elements[0] /= scale.x;
-            matrix.elements[1] /= scale.x;
-            matrix.elements[2] /= scale.x;
+/**
+ * Gets a window from an element
+ */
+function getWindow( elem ) {
+	return jQuery.isWindow( elem ) ?
+		elem :
+		elem.nodeType === 9 ?
+			elem.defaultView || elem.parentWindow :
+			false;
+}
 
-            matrix.elements[4] /= scale.y;
-            matrix.elements[5] /= scale.y;
-            matrix.elements[6] /= scale.y;
+jQuery.offset = {
+	setOffset: function( elem, options, i ) {
+		var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
+			position = jQuery.css( elem, "position" ),
+			curElem = jQuery( elem ),
+			props = {};
 
-            matrix.elements[8] /= scale.z;
-            matrix.elements[9] /= scale.z;
-            matrix.elements[10] /= scale.z;
+		// set position first, in-case top/left are set even on static elem
+		if ( position === "static" ) {
+			elem.style.position = "relative";
+		}
 
-            rotation.setFromRotationMatrix( matrix );
+		curOffset = curElem.offset();
+		curCSSTop = jQuery.css( elem, "top" );
+		curCSSLeft = jQuery.css( elem, "left" );
+		calculatePosition = ( position === "absolute" || position === "fixed" ) &&
+			jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1;
 
-            return [ translation, rotation, scale ];
+		// need to be able to calculate position if either top or left is auto and position is either absolute or fixed
+		if ( calculatePosition ) {
+			curPosition = curElem.position();
+			curTop = curPosition.top;
+			curLeft = curPosition.left;
+		} else {
+			curTop = parseFloat( curCSSTop ) || 0;
+			curLeft = parseFloat( curCSSLeft ) || 0;
+		}
 
-        };
-    }(),
+		if ( jQuery.isFunction( options ) ) {
+			options = options.call( elem, i, curOffset );
+		}
 
-    scale: function ( v ) {
-        var te = this.elements;
-        var x = v.x, y = v.y, z = v.z;
+		if ( options.top != null ) {
+			props.top = ( options.top - curOffset.top ) + curTop;
+		}
+		if ( options.left != null ) {
+			props.left = ( options.left - curOffset.left ) + curLeft;
+		}
 
-        te[0] *= x; te[4] *= y; te[8] *= z;
-        te[1] *= x; te[5] *= y; te[9] *= z;
-        te[2] *= x; te[6] *= y; te[10] *= z;
-        te[3] *= x; te[7] *= y; te[11] *= z;
+		if ( "using" in options ) {
+			options.using.call( elem, props );
+		} else {
+			curElem.css( props );
+		}
+	}
+};
 
-        return this;
-    },
-    
-    getMaxScaleOnAxis : function() {
-        
-        var te = this.elements;
-        
-        var scaleXSq = te[0] * te[0] + te[1] * te[1] + te[2] * te[2];
-        var scaleYSq = te[4] * te[4] + te[5] * te[5] + te[6] * te[6];
-        var scaleZSq = te[8] * te[8] + te[9] * te[9] + te[10] * te[10];
-        
-        return Math.sqrt(Math.max(scaleXSq, Math.max(scaleYSq, scaleZSq)));
-        
-    },
+jQuery.fn.extend({
+	offset: function( options ) {
+		if ( arguments.length ) {
+			return options === undefined ?
+				this :
+				this.each(function( i ) {
+					jQuery.offset.setOffset( this, options, i );
+				});
+		}
 
-    makeFrustum: function ( left, right, bottom, top, near, far ) {
-        var te = this.elements;
-        var x = 2 * near / ( right - left );
-        var y = 2 * near / ( top - bottom );
+		var docElem, win,
+			box = { top: 0, left: 0 },
+			elem = this[ 0 ],
+			doc = elem && elem.ownerDocument;
 
-        var a = ( right + left ) / ( right - left );
-        var b = ( top + bottom ) / ( top - bottom );
-        var c = - ( far + near ) / ( far - near );
-        var d = - 2 * far * near / ( far - near );
+		if ( !doc ) {
+			return;
+		}
 
-        te[0] = x;  te[4] = 0;  te[8] = a;  te[12] = 0;
-        te[1] = 0;  te[5] = y;  te[9] = b;  te[13] = 0;
-        te[2] = 0;  te[6] = 0;  te[10] = c; te[14] = d;
-        te[3] = 0;  te[7] = 0;  te[11] = - 1;   te[15] = 0;
+		docElem = doc.documentElement;
 
-        return this;
-    },
+		// Make sure it's not a disconnected DOM node
+		if ( !jQuery.contains( docElem, elem ) ) {
+			return box;
+		}
 
-    makePerspective: function ( fov, aspect, near, far ) {
-        var ymax = near * Math.tan( $3Dmol.Math.degToRad( fov * 0.5 ) );
-        var ymin = - ymax;
-        var xmin = ymin * aspect;
-        var xmax = ymax * aspect;
+		// If we don't have gBCR, just use 0,0 rather than error
+		// BlackBerry 5, iOS 3 (original iPhone)
+		if ( typeof elem.getBoundingClientRect !== strundefined ) {
+			box = elem.getBoundingClientRect();
+		}
+		win = getWindow( doc );
+		return {
+			top: box.top  + ( win.pageYOffset || docElem.scrollTop )  - ( docElem.clientTop  || 0 ),
+			left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
+		};
+	},
 
-        return this.makeFrustum( xmin, xmax, ymin, ymax, near, far );
-    },
-    
-    isEqual : function (m) {
-        var me = m.elements;
-        var te = this.elements;
-        
-        if (te[0] == me[0] && te[4] == me[4] && te[8] == me[8] && te[12] == me[12] &&
-            te[1] == me[1] && te[5] == me[5] && te[9] == me[9] && te[13] == me[13] &&
-            te[2] == me[2] && te[6] == me[6] && te[10] == me[10] && te[14] == me[14] &&
-            te[3] == me[3] && te[7] == me[7] && te[11] == me[11] && te[15] == me[15]) {
-            return true;
-        }
-        else {
-            return false;
-        }
-    },
+	position: function() {
+		if ( !this[ 0 ] ) {
+			return;
+		}
 
-    clone: function () {
-        var te = this.elements;
+		var offsetParent, offset,
+			parentOffset = { top: 0, left: 0 },
+			elem = this[ 0 ];
 
-        return new $3Dmol.Matrix4(
+		// fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent
+		if ( jQuery.css( elem, "position" ) === "fixed" ) {
+			// we assume that getBoundingClientRect is available when computed position is fixed
+			offset = elem.getBoundingClientRect();
+		} else {
+			// Get *real* offsetParent
+			offsetParent = this.offsetParent();
 
-            te[0], te[4], te[8], te[12],
-            te[1], te[5], te[9], te[13],
-            te[2], te[6], te[10], te[14],
-            te[3], te[7], te[11], te[15]
+			// Get correct offsets
+			offset = this.offset();
+			if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
+				parentOffset = offsetParent.offset();
+			}
 
-        );
-    },
-    
-    isIdentity: function () {
-        var te = this.elements;
-        
-        if (te[0] == 1 && te[4] == 0 && te[8] == 0 && te[12] == 0 &&
-            te[1] == 0 && te[5] == 1 && te[9] == 0 && te[13] == 0 &&
-            te[2] == 0 && te[6] == 0 && te[10] == 1 && te[14] == 0 &&
-            te[3] == 0 && te[7] == 0 && te[11] == 0 && te[15] == 1) {
-            return true;
-        }
-        else {
-            return false;
-        }
-    }
-    
+			// Add offsetParent borders
+			parentOffset.top  += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
+			parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
+		}
+
+		// Subtract parent offsets and element margins
+		// note: when an element has margin: auto the offsetLeft and marginLeft
+		// are the same in Safari causing offset.left to incorrectly be 0
+		return {
+			top:  offset.top  - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
+		};
+	},
+
+	offsetParent: function() {
+		return this.map(function() {
+			var offsetParent = this.offsetParent || docElem;
+
+			while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) {
+				offsetParent = offsetParent.offsetParent;
+			}
+			return offsetParent || docElem;
+		});
+	}
+});
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
+	var top = /Y/.test( prop );
+
+	jQuery.fn[ method ] = function( val ) {
+		return access( this, function( elem, method, val ) {
+			var win = getWindow( elem );
+
+			if ( val === undefined ) {
+				return win ? (prop in win) ? win[ prop ] :
+					win.document.documentElement[ method ] :
+					elem[ method ];
+			}
+
+			if ( win ) {
+				win.scrollTo(
+					!top ? val : jQuery( win ).scrollLeft(),
+					top ? val : jQuery( win ).scrollTop()
+				);
+
+			} else {
+				elem[ method ] = val;
+			}
+		}, method, val, arguments.length, null );
+	};
+});
+
+// Add the top/left cssHooks using jQuery.fn.position
+// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+// getComputedStyle returns percent when specified for top/left/bottom/right
+// rather than make the css module depend on the offset module, we just check for it here
+jQuery.each( [ "top", "left" ], function( i, prop ) {
+	jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
+		function( elem, computed ) {
+			if ( computed ) {
+				computed = curCSS( elem, prop );
+				// if curCSS returns percentage, fallback to offset
+				return rnumnonpx.test( computed ) ?
+					jQuery( elem ).position()[ prop ] + "px" :
+					computed;
+			}
+		}
+	);
+});
+
+
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
+		// margin is only for outerHeight, outerWidth
+		jQuery.fn[ funcName ] = function( margin, value ) {
+			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+			return access( this, function( elem, type, value ) {
+				var doc;
+
+				if ( jQuery.isWindow( elem ) ) {
+					// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
+					// isn't a whole lot we can do. See pull request at this URL for discussion:
+					// https://github.com/jquery/jquery/pull/764
+					return elem.document.documentElement[ "client" + name ];
+				}
+
+				// Get document width or height
+				if ( elem.nodeType === 9 ) {
+					doc = elem.documentElement;
+
+					// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
+					// unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
+					return Math.max(
+						elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+						elem.body[ "offset" + name ], doc[ "offset" + name ],
+						doc[ "client" + name ]
+					);
+				}
+
+				return value === undefined ?
+					// Get width or height on the element, requesting but not forcing parseFloat
+					jQuery.css( elem, type, extra ) :
+
+					// Set width or height on the element
+					jQuery.style( elem, type, value, extra );
+			}, type, chainable ? margin : undefined, chainable, null );
+		};
+	});
+});
+
+
+// The number of elements contained in the matched element set
+jQuery.fn.size = function() {
+	return this.length;
 };
-/** @constructor */
-$3Dmol.Ray = function(origin, direction) {
-    
-    this.origin = (origin !== undefined) ? 
-        origin : new $3Dmol.Vector3();
-        
-    this.direction = (direction !== undefined) ?
-        direction : new $3Dmol.Vector3();
-      
+
+jQuery.fn.andSelf = jQuery.fn.addBack;
+
+
+
+
+// Register as a named AMD module, since jQuery can be concatenated with other
+// files that may use define, but not via a proper concatenation script that
+// understands anonymous AMD modules. A named AMD is safest and most robust
+// way to register. Lowercase jquery is used because AMD module names are
+// derived from file names, and jQuery is normally delivered in a lowercase
+// file name. Do this after creating the global so that if an AMD module wants
+// to call noConflict to hide this version of jQuery, it will work.
+
+// Note that for maximum portability, libraries that are not jQuery should
+// declare themselves as anonymous modules, and avoid setting a global if an
+// AMD loader is present. jQuery is a special case. For more information, see
+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
+
+if ( typeof define === "function" && define.amd ) {
+	define( "jquery", [], function() {
+		return jQuery;
+	});
+}
+
+
+
+
+var
+	// Map over jQuery in case of overwrite
+	_jQuery = window.jQuery,
+
+	// Map over the $ in case of overwrite
+	_$ = window.$;
+
+jQuery.noConflict = function( deep ) {
+	if ( window.$ === jQuery ) {
+		window.$ = _$;
+	}
+
+	if ( deep && window.jQuery === jQuery ) {
+		window.jQuery = _jQuery;
+	}
+
+	return jQuery;
 };
 
-//TODO: Remove methods we don't need (intersectPlane ??)
-$3Dmol.Ray.prototype = {
-    
-    constructor : $3Dmol.Ray,
-     
-    set : function(origin, direction){
-        
-        this.origin.copy(origin);
-        this.direction.copy(direction);
-        
-        return this;
-    
-    },
-    
-    copy : function(ray) {
-        
-        this.origin.copy(ray.origin);
-        this.direction.copy(ray.direction);
-        
-        return this;
-        
-    },
-    
-    at : function(t, optionalTarget) {
-        
-        var result = optionalTarget || new $3Dmol.Vector3();
-        
-        return result.copy(this.direction).multiplyScalar(t).add(this.origin);
-        
-    },
-    
-    recast : function() {
-        
-        var v1 = new $3Dmol.Vector3();
-        
-        return function(t) {
-            this.origin.copy(this.at(t, v1));
-            
-            return this;
-        };
-        
-    }(),
-    
-    closestPointToPoint : function(point, optionalTarget) {
-        
-        var result = optionalTarget || new $3Dmol.Vector3();
-        result.subVectors(point, this.origin);
-        var directionDistance = result.dot(this.direction);
-        
-        //returns a point on this ray
-        return result.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
-        
-    },
-    
-    distanceToPoint : function() {
-        
-        var v1 = new $3Dmol.Vector3();
-        
-        return function(point) {
-            var directionDistance = v1.subVectors(point, this.origin).dot(this.direction);
-            v1.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
-            
-            return v1.distanceTo(point);
-        };
-        
-    }(),
-    
-    isIntersectionCylinder : function() {
-        
-    },
-    
-    isIntersectionSphere : function(sphere) {
-       
-       return (this.distanceToPoint(sphere.center) <= sphere.radius);
-          
-    },
-    
-    isIntersectionPlane : function(plane) {
-        
-        var denominator = plane.normal.dot(this.direction);
-        
-        //plane and ray are not perpendicular
-        if (denominator !== 0) 
-            return true;
-        
-        if (plane.distanceToPoint(this.origin) === 0) 
-            return true;
-        
-        return false;
-        
-    },
-    
-    distanceToPlane : function(plane) {
-       
-       var denominator = plane.normal.dot(this.direction);
-       if (denominator === 0) {
-           
-           //line is coplanar
-       if (plane.distanceToPoint(this.origin) === 0)
-           return 0;
-       
-       //ray is parallel
-           return undefined;
-       }
-       
-       var t = - (this.origin.dot(plane.normal) + plane.constant) / denominator;
-       
-       return t;
-       
-    },
-    
-    intersectPlane : function(plane, optionalTarget) {
-       
-       var t = this.distanceToPlane(plane);
-       
-       if (t === undefined)
-           return undefined;
-       
-       return this.at(t, optionalTarget);
-       
-    },
-    
-    applyMatrix4 : function(matrix4) {
-       
-       this.direction.add(this.origin).applyMatrix4(matrix4);
-       this.origin.applyMatrix4(matrix4);
-       this.direction.sub(this.origin);
-       
-       return this;
-       
-    },
-    
-    equals : function(ray) {
-       
-       return ray.origin.equals(this.origin) && ray.direction.equals(this.direction);
-       
-    },
-    
-    clone : function() {
-    
-       return new $3Dmol.Ray().copy(this);
-    
-    }
- 
-     
-};
+// Expose jQuery and $ identifiers, even in
+// AMD (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// and CommonJS for browser emulators (#13566)
+if ( typeof noGlobal === strundefined ) {
+	window.jQuery = window.$ = jQuery;
+}
 
-//Intersection sphere and box shapes.  
 
 
-//Intersection sphere for sphere, stick render
-/** @constructor */
-$3Dmol.Sphere = function(center, radius) {
 
-    this.center = (center !== undefined) ? 
-        center : new $3Dmol.Vector3();
-        
-    this.radius = (radius !== undefined) ?
-        radius : 0;
-        
-};
+return jQuery;
 
-$3Dmol.Sphere.prototype = {
-    
-    constructor : $3Dmol.Sphere,
-    
-    set : function(center, radius) {
-        
-        this.center.copy(center);
-        this.radius = radius;
-        
-        return this;
-        
-    },
-    
-    copy : function(sphere) {
-        
-        this.center.copy(sphere.center);
-        this.radius = sphere.radius;
-        
-        return this;
-        
-    },
-    
-    applyMatrix4 : function(matrix) {
-        
-        this.center.applyMatrix4(matrix);
-        this.radius = this.radius * matrix.getMaxScaleOnAxis();
-        
-        return this;
-        
-    },
-    
-    translate : function(offset) {
-        
-        this.center.add(offset);
-        
-        return this;
-        
-    },
-    
-    equals : function(sphere) {
-        
-        return sphere.center.equals(this.center) && (sphere.radius === this.radius);
-        
-    },
-       
-    clone : function() {
-        
-        return new $3Dmol.Sphere().copy(this);
-        
+}));
+/* pako 0.2.7 nodeca/pako */(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.pako = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
+'use strict';
+
+
+var TYPED_OK =  (typeof Uint8Array !== 'undefined') &&
+                (typeof Uint16Array !== 'undefined') &&
+                (typeof Int32Array !== 'undefined');
+
+
+exports.assign = function (obj /*from1, from2, from3, ...*/) {
+  var sources = Array.prototype.slice.call(arguments, 1);
+  while (sources.length) {
+    var source = sources.shift();
+    if (!source) { continue; }
+
+    if (typeof source !== 'object') {
+      throw new TypeError(source + 'must be non-object');
     }
 
+    for (var p in source) {
+      if (source.hasOwnProperty(p)) {
+        obj[p] = source[p];
+      }
+    }
+  }
+
+  return obj;
 };
 
 
-//Bounding cylinder for stick render  
-/** @constructor */
-$3Dmol.Cylinder = function(c1, c2, radius) {
+// reduce buffer size, avoiding mem copy
+exports.shrinkBuf = function (buf, size) {
+  if (buf.length === size) { return buf; }
+  if (buf.subarray) { return buf.subarray(0, size); }
+  buf.length = size;
+  return buf;
+};
 
-    this.c1 = (c1 !== undefined) ?
-        c1 : new $3Dmol.Vector3();
 
-    this.c2 = (c2 !== undefined) ?
-        c2 : new $3Dmol.Vector3();
-        
-    this.direction = new $3Dmol.Vector3().subVectors(this.c2, this.c1).normalize();
+var fnTyped = {
+  arraySet: function (dest, src, src_offs, len, dest_offs) {
+    if (src.subarray && dest.subarray) {
+      dest.set(src.subarray(src_offs, src_offs+len), dest_offs);
+      return;
+    }
+    // Fallback to ordinary array
+    for (var i=0; i<len; i++) {
+      dest[dest_offs + i] = src[src_offs + i];
+    }
+  },
+  // Join array of chunks to single array.
+  flattenChunks: function(chunks) {
+    var i, l, len, pos, chunk, result;
+
+    // calculate data length
+    len = 0;
+    for (i=0, l=chunks.length; i<l; i++) {
+      len += chunks[i].length;
+    }
 
-    this.radius = (radius !== undefined) ?
-        radius : 0;
-    
+    // join chunks
+    result = new Uint8Array(len);
+    pos = 0;
+    for (i=0, l=chunks.length; i<l; i++) {
+      chunk = chunks[i];
+      result.set(chunk, pos);
+      pos += chunk.length;
+    }
+
+    return result;
+  }
 };
 
-$3Dmol.Cylinder.prototype = {
+var fnUntyped = {
+  arraySet: function (dest, src, src_offs, len, dest_offs) {
+    for (var i=0; i<len; i++) {
+      dest[dest_offs + i] = src[src_offs + i];
+    }
+  },
+  // Join array of chunks to single array.
+  flattenChunks: function(chunks) {
+    return [].concat.apply([], chunks);
+  }
+};
 
-    constructor : $3Dmol.Cylinder,
 
-    copy : function(cylinder) {
+// Enable/Disable typed arrays use, for testing
+//
+exports.setTyped = function (on) {
+  if (on) {
+    exports.Buf8  = Uint8Array;
+    exports.Buf16 = Uint16Array;
+    exports.Buf32 = Int32Array;
+    exports.assign(exports, fnTyped);
+  } else {
+    exports.Buf8  = Array;
+    exports.Buf16 = Array;
+    exports.Buf32 = Array;
+    exports.assign(exports, fnUntyped);
+  }
+};
 
-        this.c1.copy(cylinder.c1);
-        this.c2.copy(cylinder.c2);
-        this.direction.copy(cylinder.direction);
-        this.radius = cylinder.radius;
+exports.setTyped(TYPED_OK);
 
-        return this;
+},{}],2:[function(require,module,exports){
+// String encode/decode helpers
+'use strict';
 
-    },
-    
-    lengthSq : function() {
-    
-        var vector = new $3Dmol.Vector3();
-        
-        return function(){
-            return vector.subVectors(this.c2, this.c1).lengthSq();
-        };
-        
-    }(),
 
-    applyMatrix4 : function(matrix) {
-        
-        this.direction.add(this.c1).applyMatrix4(matrix);
-        this.c1.applyMatrix4(matrix);
-        this.c2.applyMatrix4(matrix);
-        this.direction.sub(this.c1).normalize();
-        this.radius = this.radius * matrix.getMaxScaleOnAxis();
+var utils = require('./common');
+
+
+// Quick check if we can use fast array to bin string conversion
+//
+// - apply(Array) can fail on Android 2.2
+// - apply(Uint8Array) can fail on iOS 5.1 Safary
+//
+var STR_APPLY_OK = true;
+var STR_APPLY_UIA_OK = true;
+
+try { String.fromCharCode.apply(null, [0]); } catch(__) { STR_APPLY_OK = false; }
+try { String.fromCharCode.apply(null, new Uint8Array(1)); } catch(__) { STR_APPLY_UIA_OK = false; }
 
-        return this;
 
+// Table with utf8 lengths (calculated by first byte of sequence)
+// Note, that 5 & 6-byte values and some 4-byte values can not be represented in JS,
+// because max possible codepoint is 0x10ffff
+var _utf8len = new utils.Buf8(256);
+for (var q=0; q<256; q++) {
+  _utf8len[q] = (q >= 252 ? 6 : q >= 248 ? 5 : q >= 240 ? 4 : q >= 224 ? 3 : q >= 192 ? 2 : 1);
+}
+_utf8len[254]=_utf8len[254]=1; // Invalid sequence start
+
+
+// convert string to array (typed, when possible)
+exports.string2buf = function (str) {
+  var buf, c, c2, m_pos, i, str_len = str.length, buf_len = 0;
+
+  // count binary size
+  for (m_pos = 0; m_pos < str_len; m_pos++) {
+    c = str.charCodeAt(m_pos);
+    if ((c & 0xfc00) === 0xd800 && (m_pos+1 < str_len)) {
+      c2 = str.charCodeAt(m_pos+1);
+      if ((c2 & 0xfc00) === 0xdc00) {
+        c = 0x10000 + ((c - 0xd800) << 10) + (c2 - 0xdc00);
+        m_pos++;
+      }
+    }
+    buf_len += c < 0x80 ? 1 : c < 0x800 ? 2 : c < 0x10000 ? 3 : 4;
+  }
+
+  // allocate buffer
+  buf = new utils.Buf8(buf_len);
+
+  // convert
+  for (i=0, m_pos = 0; i < buf_len; m_pos++) {
+    c = str.charCodeAt(m_pos);
+    if ((c & 0xfc00) === 0xd800 && (m_pos+1 < str_len)) {
+      c2 = str.charCodeAt(m_pos+1);
+      if ((c2 & 0xfc00) === 0xdc00) {
+        c = 0x10000 + ((c - 0xd800) << 10) + (c2 - 0xdc00);
+        m_pos++;
+      }
     }
+    if (c < 0x80) {
+      /* one byte */
+      buf[i++] = c;
+    } else if (c < 0x800) {
+      /* two bytes */
+      buf[i++] = 0xC0 | (c >>> 6);
+      buf[i++] = 0x80 | (c & 0x3f);
+    } else if (c < 0x10000) {
+      /* three bytes */
+      buf[i++] = 0xE0 | (c >>> 12);
+      buf[i++] = 0x80 | (c >>> 6 & 0x3f);
+      buf[i++] = 0x80 | (c & 0x3f);
+    } else {
+      /* four bytes */
+      buf[i++] = 0xf0 | (c >>> 18);
+      buf[i++] = 0x80 | (c >>> 12 & 0x3f);
+      buf[i++] = 0x80 | (c >>> 6 & 0x3f);
+      buf[i++] = 0x80 | (c & 0x3f);
+    }
+  }
 
+  return buf;
 };
 
+// Helper (used in 2 places)
+function buf2binstring(buf, len) {
+  // use fallback for big arrays to avoid stack overflow
+  if (len < 65537) {
+    if ((buf.subarray && STR_APPLY_UIA_OK) || (!buf.subarray && STR_APPLY_OK)) {
+      return String.fromCharCode.apply(null, utils.shrinkBuf(buf, len));
+    }
+  }
 
-//plane specified by three points
-/** @constructor */
-$3Dmol.Triangle = function(a, b, c){
-   
-    this.a = (a !== undefined) ?
-        a : new $3Dmol.Vector3();
+  var result = '';
+  for (var i=0; i < len; i++) {
+    result += String.fromCharCode(buf[i]);
+  }
+  return result;
+}
 
-    this.b = (b !== undefined) ?
-        b : new $3Dmol.Vector3();
-    
-    this.c = (c !== undefined) ?
-        c : new $3Dmol.Vector3();   
-  
-};
 
-$3Dmol.Triangle.prototype = {
+// Convert byte array to binary string
+exports.buf2binstring = function(buf) {
+  return buf2binstring(buf, buf.length);
+};
 
-    constructor : $3Dmol.Triangle,
-    
-    copy : function(triangle) {
-        
-        this.a.copy(triangle.a);
-        this.b.copy(triangle.b);
-        this.c.copy(triangle.c);
-        
-        return this;
-        
-    },
-    
-    applyMatrix4 : function(matrix) {
-        
-        this.a.applyMatrix4(matrix);
-        this.b.applyMatrix4(matrix);
-        this.c.applyMatrix4(matrix);
-        
-        return this;
-        
-    },
-    
-    getNormal : function() {
-        
-        var v1 = new $3Dmol.Vector3();
-        
-        return function() {
-            
-            var norm = this.a.clone();
-            norm.sub(this.b);
-            v1.subVectors(this.c, this.b);
-            
-            norm.cross(v1);
-            norm.normalize();
-            
-            return norm;
-            
-        };
-        
-    }()
 
+// Convert binary string (typed, when possible)
+exports.binstring2buf = function(str) {
+  var buf = new utils.Buf8(str.length);
+  for (var i=0, len=buf.length; i < len; i++) {
+    buf[i] = str.charCodeAt(i);
+  }
+  return buf;
 };
 
 
-/* core Object3D
- * Base class for Scene, Camera, Geometry
- * Geometry class
- */
+// convert array to string
+exports.buf2string = function (buf, max) {
+  var i, out, c, c_len;
+  var len = max || buf.length;
 
-//Event Handling
-/** @this {$3Dmol.EventDispatcher} */
-$3Dmol.EventDispatcher = function() {
-  
-    var listeners = {};
-    
-    this.addEventListener = function(type, listener) {
-        if (listeners[type] === undefined)
-            listeners[type] = [];
-        
-        if (listeners[type].indexOf(listener) === -1)
-            listeners[type].push(listener);
-    };  
-    
-    this.removeEventListener = function(type, listener) {
-        
-        var index = listeners[type].indexOf(listener);
-        
-        if (index !== -1)
-            listeners[type].splice(index, 1);
-              
-    };
-    
-    this.dispatchEvent = function(event) {
-        
-        var listenerArray = listeners[event.type];
-        
-        if (listenerArray !== undefined) {
-            event.target = this;
-            
-            for (var i = 0, l = listenerArray.length; i < l; i++)
-                listenerArray[i].call(this, event);
-                
-        }
-            
-    };
-    
-};
+  // Reserve max possible length (2 words per char)
+  // NB: by unknown reasons, Array is significantly faster for
+  //     String.fromCharCode.apply than Uint16Array.
+  var utf16buf = new Array(len*2);
 
-$3Dmol.Color = function( color ){
-    
-    if ( arguments.length > 1) {
-            this.r = arguments[0] || 0.0;
-            this.g = arguments[1] || 0.0;
-            this.b = arguments[2] || 0.0;
+  for (out=0, i=0; i<len;) {
+    c = buf[i++];
+    // quick process ascii
+    if (c < 0x80) { utf16buf[out++] = c; continue; }
 
-            return this;
+    c_len = _utf8len[c];
+    // skip 5 & 6 byte codes
+    if (c_len > 4) { utf16buf[out++] = 0xfffd; i += c_len-1; continue; }
+
+    // apply mask on first byte
+    c &= c_len === 2 ? 0x1f : c_len === 3 ? 0x0f : 0x07;
+    // join the rest
+    while (c_len > 1 && i < len) {
+      c = (c << 6) | (buf[i++] & 0x3f);
+      c_len--;
     }
-    
-    return this.set(color);
-                
+
+    // terminated by end of string?
+    if (c_len > 1) { utf16buf[out++] = 0xfffd; continue; }
+
+    if (c < 0x10000) {
+      utf16buf[out++] = c;
+    } else {
+      c -= 0x10000;
+      utf16buf[out++] = 0xd800 | ((c >> 10) & 0x3ff);
+      utf16buf[out++] = 0xdc00 | (c & 0x3ff);
+    }
+  }
+
+  return buf2binstring(utf16buf, out);
 };
 
-$3Dmol.Color.prototype = {
-    
-    constructor: $3Dmol.Color,
-    
-    r: 0.0, g: 0.0, b: 0.0,
-    
-    set : function(val) {
-        
-            if (val instanceof $3Dmol.Color) 
-                return val.clone();
 
-            else if (typeof val === 'number')
-                this.setHex(val);
-    },
-    
-    setHex: function(hex) {
-        
-            hex = Math.floor(hex);
+// Calculate max possible position in utf8 buffer,
+// that will not break sequence. If that's not possible
+// - (very small limits) return max size as is.
+//
+// buf[] - utf8 bytes array
+// max   - length limit (mandatory);
+exports.utf8border = function(buf, max) {
+  var pos;
 
-            this.r = (hex >> 16 & 255) / 255;
-            this.g = (hex >> 8 & 255) / 255;
-            this.b = (hex & 255) / 255;                                                                                     
-        
-            return this;
-    },
-    
-    getHex: function() {
-        var R = Math.round(this.r*255);
-        var G = Math.round(this.g*255);
-        var B = Math.round(this.b*255);
-        return R<<16 | G << 8 | B;
-    },
-    
-    clone : function() {
-            return new $3Dmol.Color(this.r, this.g, this.b);
-    },
-        
-    copy : function(color) {
-        this.r = color.r;
-        this.g = color.g;
-        this.b = color.b;
-        
-        return this;
-    },
-    
-    //return object that represents color components from 0 to 255
-    scaled : function() {
-        var ret = {};
-        ret.r = Math.round(this.r*255);
-        ret.g = Math.round(this.g*255);
-        ret.b = Math.round(this.b*255);
-        ret.a = 1.0;
-        return ret;
-    }
-    
+  max = max || buf.length;
+  if (max > buf.length) { max = buf.length; }
+
+  // go back from last position, until start of sequence found
+  pos = max-1;
+  while (pos >= 0 && (buf[pos] & 0xC0) === 0x80) { pos--; }
+
+  // Fuckup - very small and broken sequence,
+  // return max, because we should return something anyway.
+  if (pos < 0) { return max; }
+
+  // If we came to start of buffer - that means vuffer is too small,
+  // return max too.
+  if (pos === 0) { return max; }
+
+  return (pos + _utf8len[buf[pos]] > max) ? pos : max;
 };
 
-//Object3D base constructor function
-/** @this {$3Dmol.Object3D} */
-$3Dmol.Object3D = function() {
-    
-    this.id = $3Dmol.Object3DIDCount++;
-    
-    this.name = "";
-    
-    this.parent = undefined;
-    this.children = [];
-    
-    this.position = new $3Dmol.Vector3();
-    this.rotation = new $3Dmol.Vector3();
-    this.matrix = new $3Dmol.Matrix4();
-    this.matrixWorld = new $3Dmol.Matrix4();
-    this.quaternion = new $3Dmol.Quaternion();
-    this.eulerOrder = 'XYZ';
-    
-    this.up = new $3Dmol.Vector3(0, 1, 0);
-    this.scale = new $3Dmol.Vector3(1, 1, 1);
-    
-    this.matrixAutoUpdate = true;
-    this.matrixWorldNeedsUpdate = true;
-    this.rotationAutoUpdate = true;
-    this.useQuaternion = false;
-    
-    this.visible = true;
-    
+},{"./common":1}],3:[function(require,module,exports){
+'use strict';
+
+// Note: adler32 takes 12% for level 0 and 2% for level 6.
+// It doesn't worth to make additional optimizationa as in original.
+// Small size is preferable.
+
+function adler32(adler, buf, len, pos) {
+  var s1 = (adler & 0xffff) |0,
+      s2 = ((adler >>> 16) & 0xffff) |0,
+      n = 0;
+
+  while (len !== 0) {
+    // Set limit ~ twice less than 5552, to keep
+    // s2 in 31-bits, because we force signed ints.
+    // in other case %= will fail.
+    n = len > 2000 ? 2000 : len;
+    len -= n;
+
+    do {
+      s1 = (s1 + buf[pos++]) |0;
+      s2 = (s2 + s1) |0;
+    } while (--n);
+
+    s1 %= 65521;
+    s2 %= 65521;
+  }
+
+  return (s1 | (s2 << 16)) |0;
+}
+
+
+module.exports = adler32;
+
+},{}],4:[function(require,module,exports){
+module.exports = {
+
+  /* Allowed flush values; see deflate() and inflate() below for details */
+  Z_NO_FLUSH:         0,
+  Z_PARTIAL_FLUSH:    1,
+  Z_SYNC_FLUSH:       2,
+  Z_FULL_FLUSH:       3,
+  Z_FINISH:           4,
+  Z_BLOCK:            5,
+  Z_TREES:            6,
+
+  /* Return codes for the compression/decompression functions. Negative values
+  * are errors, positive values are used for special but normal events.
+  */
+  Z_OK:               0,
+  Z_STREAM_END:       1,
+  Z_NEED_DICT:        2,
+  Z_ERRNO:           -1,
+  Z_STREAM_ERROR:    -2,
+  Z_DATA_ERROR:      -3,
+  //Z_MEM_ERROR:     -4,
+  Z_BUF_ERROR:       -5,
+  //Z_VERSION_ERROR: -6,
+
+  /* compression levels */
+  Z_NO_COMPRESSION:         0,
+  Z_BEST_SPEED:             1,
+  Z_BEST_COMPRESSION:       9,
+  Z_DEFAULT_COMPRESSION:   -1,
+
+
+  Z_FILTERED:               1,
+  Z_HUFFMAN_ONLY:           2,
+  Z_RLE:                    3,
+  Z_FIXED:                  4,
+  Z_DEFAULT_STRATEGY:       0,
+
+  /* Possible values of the data_type field (though see inflate()) */
+  Z_BINARY:                 0,
+  Z_TEXT:                   1,
+  //Z_ASCII:                1, // = Z_TEXT (deprecated)
+  Z_UNKNOWN:                2,
+
+  /* The deflate compression method */
+  Z_DEFLATED:               8
+  //Z_NULL:                 null // Use -1 or null inline, depending on var type
 };
 
-$3Dmol.Object3D.prototype = {
-    
-    constructor : $3Dmol.Object3D,
-    
-    lookAt : function(vector) {
-        
-        this.matrix.lookAt(vector, this.position, this.up);
-        
-        if (this.rotationAutoUpdate) {
-            
-            if (this.useQuaternion === true) 
-                this.quaternion.copy(this.matrix.decompose()[1]);
-            else
-                this.rotation.setEulerFromRotationMatrix(this.matrix, this.eulerOrder);
+},{}],5:[function(require,module,exports){
+'use strict';
+
+// Note: we can't get significant speed boost here.
+// So write code to minimize size - no pregenerated tables
+// and array tools dependencies.
+
+
+// Use ordinary array, since untyped makes no boost here
+function makeTable() {
+  var c, table = [];
+
+  for (var n =0; n < 256; n++) {
+    c = n;
+    for (var k =0; k < 8; k++) {
+      c = ((c&1) ? (0xEDB88320 ^ (c >>> 1)) : (c >>> 1));
+    }
+    table[n] = c;
+  }
+
+  return table;
+}
+
+// Create table on load. Just 255 signed longs. Not a problem.
+var crcTable = makeTable();
+
+
+function crc32(crc, buf, len, pos) {
+  var t = crcTable,
+      end = pos + len;
+
+  crc = crc ^ (-1);
+
+  for (var i = pos; i < end; i++) {
+    crc = (crc >>> 8) ^ t[(crc ^ buf[i]) & 0xFF];
+  }
+
+  return (crc ^ (-1)); // >>> 0;
+}
+
+
+module.exports = crc32;
+
+},{}],6:[function(require,module,exports){
+'use strict';
+
+
+function GZheader() {
+  /* true if compressed data believed to be text */
+  this.text       = 0;
+  /* modification time */
+  this.time       = 0;
+  /* extra flags (not used when writing a gzip file) */
+  this.xflags     = 0;
+  /* operating system */
+  this.os         = 0;
+  /* pointer to extra field or Z_NULL if none */
+  this.extra      = null;
+  /* extra field length (valid if extra != Z_NULL) */
+  this.extra_len  = 0; // Actually, we don't need it in JS,
+                       // but leave for few code modifications
+
+  //
+  // Setup limits is not necessary because in js we should not preallocate memory
+  // for inflate use constant limit in 65536 bytes
+  //
+
+  /* space at extra (only when reading header) */
+  // this.extra_max  = 0;
+  /* pointer to zero-terminated file name or Z_NULL */
+  this.name       = '';
+  /* space at name (only when reading header) */
+  // this.name_max   = 0;
+  /* pointer to zero-terminated comment or Z_NULL */
+  this.comment    = '';
+  /* space at comment (only when reading header) */
+  // this.comm_max   = 0;
+  /* true if there was or will be a header crc */
+  this.hcrc       = 0;
+  /* true when done reading gzip header (not used when writing a gzip file) */
+  this.done       = false;
+}
+
+module.exports = GZheader;
+
+},{}],7:[function(require,module,exports){
+'use strict';
+
+// See state defs from inflate.js
+var BAD = 30;       /* got a data error -- remain here until reset */
+var TYPE = 12;      /* i: waiting for type bits, including last-flag bit */
+
+/*
+   Decode literal, length, and distance codes and write out the resulting
+   literal and match bytes until either not enough input or output is
+   available, an end-of-block is encountered, or a data error is encountered.
+   When large enough input and output buffers are supplied to inflate(), for
+   example, a 16K input buffer and a 64K output buffer, more than 95% of the
+   inflate execution time is spent in this routine.
+
+   Entry assumptions:
+
+        state.mode === LEN
+        strm.avail_in >= 6
+        strm.avail_out >= 258
+        start >= strm.avail_out
+        state.bits < 8
+
+   On return, state.mode is one of:
+
+        LEN -- ran out of enough output space or enough available input
+        TYPE -- reached end of block code, inflate() to interpret next block
+        BAD -- error in block data
+
+   Notes:
+
+    - The maximum input bits used by a length/distance pair is 15 bits for the
+      length code, 5 bits for the length extra, 15 bits for the distance code,
+      and 13 bits for the distance extra.  This totals 48 bits, or six bytes.
+      Therefore if strm.avail_in >= 6, then there is enough input to avoid
+      checking for available input while decoding.
+
+    - The maximum bytes that a single length/distance pair can output is 258
+      bytes, which is the maximum length that can be coded.  inflate_fast()
+      requires strm.avail_out >= 258 for each loop to avoid checking for
+      output space.
+ */
+module.exports = function inflate_fast(strm, start) {
+  var state;
+  var _in;                    /* local strm.input */
+  var last;                   /* have enough input while in < last */
+  var _out;                   /* local strm.output */
+  var beg;                    /* inflate()'s initial strm.output */
+  var end;                    /* while out < end, enough space available */
+//#ifdef INFLATE_STRICT
+  var dmax;                   /* maximum distance from zlib header */
+//#endif
+  var wsize;                  /* window size or zero if not using window */
+  var whave;                  /* valid bytes in the window */
+  var wnext;                  /* window write index */
+  var window;                 /* allocated sliding window, if wsize != 0 */
+  var hold;                   /* local strm.hold */
+  var bits;                   /* local strm.bits */
+  var lcode;                  /* local strm.lencode */
+  var dcode;                  /* local strm.distcode */
+  var lmask;                  /* mask for first level of length codes */
+  var dmask;                  /* mask for first level of distance codes */
+  var here;                   /* retrieved table entry */
+  var op;                     /* code bits, operation, extra bits, or */
+                              /*  window position, window bytes to copy */
+  var len;                    /* match length, unused bytes */
+  var dist;                   /* match distance */
+  var from;                   /* where to copy match from */
+  var from_source;
+
+
+  var input, output; // JS specific, because we have no pointers
+
+  /* copy state to local variables */
+  state = strm.state;
+  //here = state.here;
+  _in = strm.next_in;
+  input = strm.input;
+  last = _in + (strm.avail_in - 5);
+  _out = strm.next_out;
+  output = strm.output;
+  beg = _out - (start - strm.avail_out);
+  end = _out + (strm.avail_out - 257);
+//#ifdef INFLATE_STRICT
+  dmax = state.dmax;
+//#endif
+  wsize = state.wsize;
+  whave = state.whave;
+  wnext = state.wnext;
+  window = state.window;
+  hold = state.hold;
+  bits = state.bits;
+  lcode = state.lencode;
+  dcode = state.distcode;
+  lmask = (1 << state.lenbits) - 1;
+  dmask = (1 << state.distbits) - 1;
+
+
+  /* decode literals and length/distances until end-of-block or not enough
+     input data or output space */
+
+  top:
+  do {
+    if (bits < 15) {
+      hold += input[_in++] << bits;
+      bits += 8;
+      hold += input[_in++] << bits;
+      bits += 8;
+    }
+
+    here = lcode[hold & lmask];
+
+    dolen:
+    for (;;) { // Goto emulation
+      op = here >>> 24/*here.bits*/;
+      hold >>>= op;
+      bits -= op;
+      op = (here >>> 16) & 0xff/*here.op*/;
+      if (op === 0) {                          /* literal */
+        //Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+        //        "inflate:         literal '%c'\n" :
+        //        "inflate:         literal 0x%02x\n", here.val));
+        output[_out++] = here & 0xffff/*here.val*/;
+      }
+      else if (op & 16) {                     /* length base */
+        len = here & 0xffff/*here.val*/;
+        op &= 15;                           /* number of extra bits */
+        if (op) {
+          if (bits < op) {
+            hold += input[_in++] << bits;
+            bits += 8;
+          }
+          len += hold & ((1 << op) - 1);
+          hold >>>= op;
+          bits -= op;
         }
-    },
-    
-    //add child object
-    add : function(object) {
-        if (object === this){
-            console.error("Can't add $3Dmol.Object3D to itself");
-            return;
+        //Tracevv((stderr, "inflate:         length %u\n", len));
+        if (bits < 15) {
+          hold += input[_in++] << bits;
+          bits += 8;
+          hold += input[_in++] << bits;
+          bits += 8;
         }
-        
-        object.parent = this;
-        this.children.push(object);
-        
-        //add to the scene (i.e. follow up this instance's parents until reach the top)
-        
-        var scene = this;
-        
-        while (scene.parent !== undefined)
-            scene = scene.parent;
-            
-        if (scene !== undefined && scene instanceof $3Dmol.Scene) 
-            scene.__addObject(object);
-        
-    },
-    
-    remove : function(object) {
-        
-        var index = this.children.indexOf(object);
-        
-        if (index !== -1) {
-            
-            object.parent = undefined;
-            this.children.splice(index, 1);
-            
-            //Remove from scene
-            
-            var scene = this;
-            
-            while (scene.parent !== undefined)
-                scene = scene.parent;
-                
-            if (scene !== undefined && scene instanceof $3Dmol.Scene)
-                scene.__removeObject(object);
-                
+        here = dcode[hold & dmask];
+
+        dodist:
+        for (;;) { // goto emulation
+          op = here >>> 24/*here.bits*/;
+          hold >>>= op;
+          bits -= op;
+          op = (here >>> 16) & 0xff/*here.op*/;
+
+          if (op & 16) {                      /* distance base */
+            dist = here & 0xffff/*here.val*/;
+            op &= 15;                       /* number of extra bits */
+            if (bits < op) {
+              hold += input[_in++] << bits;
+              bits += 8;
+              if (bits < op) {
+                hold += input[_in++] << bits;
+                bits += 8;
+              }
+            }
+            dist += hold & ((1 << op) - 1);
+//#ifdef INFLATE_STRICT
+            if (dist > dmax) {
+              strm.msg = 'invalid distance too far back';
+              state.mode = BAD;
+              break top;
+            }
+//#endif
+            hold >>>= op;
+            bits -= op;
+            //Tracevv((stderr, "inflate:         distance %u\n", dist));
+            op = _out - beg;                /* max distance in output */
+            if (dist > op) {                /* see if copy from window */
+              op = dist - op;               /* distance back in window */
+              if (op > whave) {
+                if (state.sane) {
+                  strm.msg = 'invalid distance too far back';
+                  state.mode = BAD;
+                  break top;
+                }
+
+// (!) This block is disabled in zlib defailts,
+// don't enable it for binary compatibility
+//#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+//                if (len <= op - whave) {
+//                  do {
+//                    output[_out++] = 0;
+//                  } while (--len);
+//                  continue top;
+//                }
+//                len -= op - whave;
+//                do {
+//                  output[_out++] = 0;
+//                } while (--op > whave);
+//                if (op === 0) {
+//                  from = _out - dist;
+//                  do {
+//                    output[_out++] = output[from++];
+//                  } while (--len);
+//                  continue top;
+//                }
+//#endif
+              }
+              from = 0; // window index
+              from_source = window;
+              if (wnext === 0) {           /* very common case */
+                from += wsize - op;
+                if (op < len) {         /* some from window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = _out - dist;  /* rest from output */
+                  from_source = output;
+                }
+              }
+              else if (wnext < op) {      /* wrap around window */
+                from += wsize + wnext - op;
+                op -= wnext;
+                if (op < len) {         /* some from end of window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = 0;
+                  if (wnext < len) {  /* some from start of window */
+                    op = wnext;
+                    len -= op;
+                    do {
+                      output[_out++] = window[from++];
+                    } while (--op);
+                    from = _out - dist;      /* rest from output */
+                    from_source = output;
+                  }
+                }
+              }
+              else {                      /* contiguous in window */
+                from += wnext - op;
+                if (op < len) {         /* some from window */
+                  len -= op;
+                  do {
+                    output[_out++] = window[from++];
+                  } while (--op);
+                  from = _out - dist;  /* rest from output */
+                  from_source = output;
+                }
+              }
+              while (len > 2) {
+                output[_out++] = from_source[from++];
+                output[_out++] = from_source[from++];
+                output[_out++] = from_source[from++];
+                len -= 3;
+              }
+              if (len) {
+                output[_out++] = from_source[from++];
+                if (len > 1) {
+                  output[_out++] = from_source[from++];
+                }
+              }
+            }
+            else {
+              from = _out - dist;          /* copy direct from output */
+              do {                        /* minimum length is three */
+                output[_out++] = output[from++];
+                output[_out++] = output[from++];
+                output[_out++] = output[from++];
+                len -= 3;
+              } while (len > 2);
+              if (len) {
+                output[_out++] = output[from++];
+                if (len > 1) {
+                  output[_out++] = output[from++];
+                }
+              }
+            }
+          }
+          else if ((op & 64) === 0) {          /* 2nd level distance code */
+            here = dcode[(here & 0xffff)/*here.val*/ + (hold & ((1 << op) - 1))];
+            continue dodist;
+          }
+          else {
+            strm.msg = 'invalid distance code';
+            state.mode = BAD;
+            break top;
+          }
+
+          break; // need to emulate goto via "continue"
         }
-    },
-    
-    updateMatrix : function() {
-        
-        this.matrix.setPosition(this.position);
-        
-        if (this.useQuaternion === false) 
-            this.matrix.setRotationFromEuler(this.rotation, this.eulerOrder);
-        else
-            this.matrix.setRotationFromQuaternion(this.quaternion);
-        
-        //TODO: Do I need this??
-        if (this.scale.x !== 1 || this.scale.y !== 1 || this.scale.z !== 1)
-            this.matrix.scale(this.scale);
-            
-        this.matrixWorldNeedsUpdate = true;
-        
-    },
-    
-    updateMatrixWorld : function(force) {
-        
-        if (this.matrixAutoUpdate === true) 
-            this.updateMatrix();
-        
-        if (this.matrixWorldNeedsUpdate === true || force === true) {
-            
-            if (this.parent === undefined)
-                this.matrixWorld.copy(this.matrix);
-            else
-                this.matrixWorld.multiplyMatrices(this.parent.matrixWorld, this.matrix);
-                
+      }
+      else if ((op & 64) === 0) {              /* 2nd level length code */
+        here = lcode[(here & 0xffff)/*here.val*/ + (hold & ((1 << op) - 1))];
+        continue dolen;
+      }
+      else if (op & 32) {                     /* end-of-block */
+        //Tracevv((stderr, "inflate:         end of block\n"));
+        state.mode = TYPE;
+        break top;
+      }
+      else {
+        strm.msg = 'invalid literal/length code';
+        state.mode = BAD;
+        break top;
+      }
+
+      break; // need to emulate goto via "continue"
+    }
+  } while (_in < last && _out < end);
+
+  /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
+  len = bits >> 3;
+  _in -= len;
+  bits -= len << 3;
+  hold &= (1 << bits) - 1;
+
+  /* update state and return */
+  strm.next_in = _in;
+  strm.next_out = _out;
+  strm.avail_in = (_in < last ? 5 + (last - _in) : 5 - (_in - last));
+  strm.avail_out = (_out < end ? 257 + (end - _out) : 257 - (_out - end));
+  state.hold = hold;
+  state.bits = bits;
+  return;
+};
+
+},{}],8:[function(require,module,exports){
+'use strict';
+
+
+var utils = require('../utils/common');
+var adler32 = require('./adler32');
+var crc32   = require('./crc32');
+var inflate_fast = require('./inffast');
+var inflate_table = require('./inftrees');
+
+var CODES = 0;
+var LENS = 1;
+var DISTS = 2;
+
+/* Public constants ==========================================================*/
+/* ===========================================================================*/
+
+
+/* Allowed flush values; see deflate() and inflate() below for details */
+//var Z_NO_FLUSH      = 0;
+//var Z_PARTIAL_FLUSH = 1;
+//var Z_SYNC_FLUSH    = 2;
+//var Z_FULL_FLUSH    = 3;
+var Z_FINISH        = 4;
+var Z_BLOCK         = 5;
+var Z_TREES         = 6;
+
+
+/* Return codes for the compression/decompression functions. Negative values
+ * are errors, positive values are used for special but normal events.
+ */
+var Z_OK            = 0;
+var Z_STREAM_END    = 1;
+var Z_NEED_DICT     = 2;
+//var Z_ERRNO         = -1;
+var Z_STREAM_ERROR  = -2;
+var Z_DATA_ERROR    = -3;
+var Z_MEM_ERROR     = -4;
+var Z_BUF_ERROR     = -5;
+//var Z_VERSION_ERROR = -6;
+
+/* The deflate compression method */
+var Z_DEFLATED  = 8;
+
+
+/* STATES ====================================================================*/
+/* ===========================================================================*/
+
+
+var    HEAD = 1;       /* i: waiting for magic header */
+var    FLAGS = 2;      /* i: waiting for method and flags (gzip) */
+var    TIME = 3;       /* i: waiting for modification time (gzip) */
+var    OS = 4;         /* i: waiting for extra flags and operating system (gzip) */
+var    EXLEN = 5;      /* i: waiting for extra length (gzip) */
+var    EXTRA = 6;      /* i: waiting for extra bytes (gzip) */
+var    NAME = 7;       /* i: waiting for end of file name (gzip) */
+var    COMMENT = 8;    /* i: waiting for end of comment (gzip) */
+var    HCRC = 9;       /* i: waiting for header crc (gzip) */
+var    DICTID = 10;    /* i: waiting for dictionary check value */
+var    DICT = 11;      /* waiting for inflateSetDictionary() call */
+var        TYPE = 12;      /* i: waiting for type bits, including last-flag bit */
+var        TYPEDO = 13;    /* i: same, but skip check to exit inflate on new block */
+var        STORED = 14;    /* i: waiting for stored size (length and complement) */
+var        COPY_ = 15;     /* i/o: same as COPY below, but only first time in */
+var        COPY = 16;      /* i/o: waiting for input or output to copy stored block */
+var        TABLE = 17;     /* i: waiting for dynamic block table lengths */
+var        LENLENS = 18;   /* i: waiting for code length code lengths */
+var        CODELENS = 19;  /* i: waiting for length/lit and distance code lengths */
+var            LEN_ = 20;      /* i: same as LEN below, but only first time in */
+var            LEN = 21;       /* i: waiting for length/lit/eob code */
+var            LENEXT = 22;    /* i: waiting for length extra bits */
+var            DIST = 23;      /* i: waiting for distance code */
+var            DISTEXT = 24;   /* i: waiting for distance extra bits */
+var            MATCH = 25;     /* o: waiting for output space to copy string */
+var            LIT = 26;       /* o: waiting for output space to write literal */
+var    CHECK = 27;     /* i: waiting for 32-bit check value */
+var    LENGTH = 28;    /* i: waiting for 32-bit length (gzip) */
+var    DONE = 29;      /* finished check, done -- remain here until reset */
+var    BAD = 30;       /* got a data error -- remain here until reset */
+var    MEM = 31;       /* got an inflate() memory error -- remain here until reset */
+var    SYNC = 32;      /* looking for synchronization bytes to restart inflate() */
+
+/* ===========================================================================*/
+
+
+
+var ENOUGH_LENS = 852;
+var ENOUGH_DISTS = 592;
+//var ENOUGH =  (ENOUGH_LENS+ENOUGH_DISTS);
+
+var MAX_WBITS = 15;
+/* 32K LZ77 window */
+var DEF_WBITS = MAX_WBITS;
+
+
+function ZSWAP32(q) {
+  return  (((q >>> 24) & 0xff) +
+          ((q >>> 8) & 0xff00) +
+          ((q & 0xff00) << 8) +
+          ((q & 0xff) << 24));
+}
+
+
+function InflateState() {
+  this.mode = 0;             /* current inflate mode */
+  this.last = false;          /* true if processing last block */
+  this.wrap = 0;              /* bit 0 true for zlib, bit 1 true for gzip */
+  this.havedict = false;      /* true if dictionary provided */
+  this.flags = 0;             /* gzip header method and flags (0 if zlib) */
+  this.dmax = 0;              /* zlib header max distance (INFLATE_STRICT) */
+  this.check = 0;             /* protected copy of check value */
+  this.total = 0;             /* protected copy of output count */
+  // TODO: may be {}
+  this.head = null;           /* where to save gzip header information */
+
+  /* sliding window */
+  this.wbits = 0;             /* log base 2 of requested window size */
+  this.wsize = 0;             /* window size or zero if not using window */
+  this.whave = 0;             /* valid bytes in the window */
+  this.wnext = 0;             /* window write index */
+  this.window = null;         /* allocated sliding window, if needed */
+
+  /* bit accumulator */
+  this.hold = 0;              /* input bit accumulator */
+  this.bits = 0;              /* number of bits in "in" */
+
+  /* for string and stored block copying */
+  this.length = 0;            /* literal or length of data to copy */
+  this.offset = 0;            /* distance back to copy string from */
+
+  /* for table and code decoding */
+  this.extra = 0;             /* extra bits needed */
+
+  /* fixed and dynamic code tables */
+  this.lencode = null;          /* starting table for length/literal codes */
+  this.distcode = null;         /* starting table for distance codes */
+  this.lenbits = 0;           /* index bits for lencode */
+  this.distbits = 0;          /* index bits for distcode */
+
+  /* dynamic table building */
+  this.ncode = 0;             /* number of code length code lengths */
+  this.nlen = 0;              /* number of length code lengths */
+  this.ndist = 0;             /* number of distance code lengths */
+  this.have = 0;              /* number of code lengths in lens[] */
+  this.next = null;              /* next available space in codes[] */
+
+  this.lens = new utils.Buf16(320); /* temporary storage for code lengths */
+  this.work = new utils.Buf16(288); /* work area for code table building */
+
+  /*
+   because we don't have pointers in js, we use lencode and distcode directly
+   as buffers so we don't need codes
+  */
+  //this.codes = new utils.Buf32(ENOUGH);       /* space for code tables */
+  this.lendyn = null;              /* dynamic table for length/literal codes (JS specific) */
+  this.distdyn = null;             /* dynamic table for distance codes (JS specific) */
+  this.sane = 0;                   /* if false, allow invalid distance too far */
+  this.back = 0;                   /* bits back of last unprocessed length/lit */
+  this.was = 0;                    /* initial length of match */
+}
+
+function inflateResetKeep(strm) {
+  var state;
+
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  strm.total_in = strm.total_out = state.total = 0;
+  strm.msg = ''; /*Z_NULL*/
+  if (state.wrap) {       /* to support ill-conceived Java test suite */
+    strm.adler = state.wrap & 1;
+  }
+  state.mode = HEAD;
+  state.last = 0;
+  state.havedict = 0;
+  state.dmax = 32768;
+  state.head = null/*Z_NULL*/;
+  state.hold = 0;
+  state.bits = 0;
+  //state.lencode = state.distcode = state.next = state.codes;
+  state.lencode = state.lendyn = new utils.Buf32(ENOUGH_LENS);
+  state.distcode = state.distdyn = new utils.Buf32(ENOUGH_DISTS);
+
+  state.sane = 1;
+  state.back = -1;
+  //Tracev((stderr, "inflate: reset\n"));
+  return Z_OK;
+}
+
+function inflateReset(strm) {
+  var state;
+
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  state.wsize = 0;
+  state.whave = 0;
+  state.wnext = 0;
+  return inflateResetKeep(strm);
+
+}
+
+function inflateReset2(strm, windowBits) {
+  var wrap;
+  var state;
+
+  /* get the state */
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+
+  /* extract wrap request from windowBits parameter */
+  if (windowBits < 0) {
+    wrap = 0;
+    windowBits = -windowBits;
+  }
+  else {
+    wrap = (windowBits >> 4) + 1;
+    if (windowBits < 48) {
+      windowBits &= 15;
+    }
+  }
+
+  /* set number of window bits, free window if different */
+  if (windowBits && (windowBits < 8 || windowBits > 15)) {
+    return Z_STREAM_ERROR;
+  }
+  if (state.window !== null && state.wbits !== windowBits) {
+    state.window = null;
+  }
+
+  /* update state and reset the rest of it */
+  state.wrap = wrap;
+  state.wbits = windowBits;
+  return inflateReset(strm);
+}
+
+function inflateInit2(strm, windowBits) {
+  var ret;
+  var state;
+
+  if (!strm) { return Z_STREAM_ERROR; }
+  //strm.msg = Z_NULL;                 /* in case we return an error */
+
+  state = new InflateState();
+
+  //if (state === Z_NULL) return Z_MEM_ERROR;
+  //Tracev((stderr, "inflate: allocated\n"));
+  strm.state = state;
+  state.window = null/*Z_NULL*/;
+  ret = inflateReset2(strm, windowBits);
+  if (ret !== Z_OK) {
+    strm.state = null/*Z_NULL*/;
+  }
+  return ret;
+}
+
+function inflateInit(strm) {
+  return inflateInit2(strm, DEF_WBITS);
+}
+
+
+/*
+ Return state with length and distance decoding tables and index sizes set to
+ fixed code decoding.  Normally this returns fixed tables from inffixed.h.
+ If BUILDFIXED is defined, then instead this routine builds the tables the
+ first time it's called, and returns those tables the first time and
+ thereafter.  This reduces the size of the code by about 2K bytes, in
+ exchange for a little execution time.  However, BUILDFIXED should not be
+ used for threaded applications, since the rewriting of the tables and virgin
+ may not be thread-safe.
+ */
+var virgin = true;
+
+var lenfix, distfix; // We have no pointers in JS, so keep tables separate
+
+function fixedtables(state) {
+  /* build fixed huffman tables if first call (may not be thread safe) */
+  if (virgin) {
+    var sym;
+
+    lenfix = new utils.Buf32(512);
+    distfix = new utils.Buf32(32);
+
+    /* literal/length table */
+    sym = 0;
+    while (sym < 144) { state.lens[sym++] = 8; }
+    while (sym < 256) { state.lens[sym++] = 9; }
+    while (sym < 280) { state.lens[sym++] = 7; }
+    while (sym < 288) { state.lens[sym++] = 8; }
+
+    inflate_table(LENS,  state.lens, 0, 288, lenfix,   0, state.work, {bits: 9});
+
+    /* distance table */
+    sym = 0;
+    while (sym < 32) { state.lens[sym++] = 5; }
+
+    inflate_table(DISTS, state.lens, 0, 32,   distfix, 0, state.work, {bits: 5});
+
+    /* do this just once */
+    virgin = false;
+  }
+
+  state.lencode = lenfix;
+  state.lenbits = 9;
+  state.distcode = distfix;
+  state.distbits = 5;
+}
+
+
+/*
+ Update the window with the last wsize (normally 32K) bytes written before
+ returning.  If window does not exist yet, create it.  This is only called
+ when a window is already in use, or when output has been written during this
+ inflate call, but the end of the deflate stream has not been reached yet.
+ It is also called to create a window for dictionary data when a dictionary
+ is loaded.
+
+ Providing output buffers larger than 32K to inflate() should provide a speed
+ advantage, since only the last 32K of output is copied to the sliding window
+ upon return from inflate(), and since all distances after the first 32K of
+ output will fall in the output data, making match copies simpler and faster.
+ The advantage may be dependent on the size of the processor's data caches.
+ */
+function updatewindow(strm, src, end, copy) {
+  var dist;
+  var state = strm.state;
+
+  /* if it hasn't been done already, allocate space for the window */
+  if (state.window === null) {
+    state.wsize = 1 << state.wbits;
+    state.wnext = 0;
+    state.whave = 0;
+
+    state.window = new utils.Buf8(state.wsize);
+  }
+
+  /* copy state->wsize or less output bytes into the circular window */
+  if (copy >= state.wsize) {
+    utils.arraySet(state.window,src, end - state.wsize, state.wsize, 0);
+    state.wnext = 0;
+    state.whave = state.wsize;
+  }
+  else {
+    dist = state.wsize - state.wnext;
+    if (dist > copy) {
+      dist = copy;
+    }
+    //zmemcpy(state->window + state->wnext, end - copy, dist);
+    utils.arraySet(state.window,src, end - copy, dist, state.wnext);
+    copy -= dist;
+    if (copy) {
+      //zmemcpy(state->window, end - copy, copy);
+      utils.arraySet(state.window,src, end - copy, copy, 0);
+      state.wnext = copy;
+      state.whave = state.wsize;
+    }
+    else {
+      state.wnext += dist;
+      if (state.wnext === state.wsize) { state.wnext = 0; }
+      if (state.whave < state.wsize) { state.whave += dist; }
+    }
+  }
+  return 0;
+}
+
+function inflate(strm, flush) {
+  var state;
+  var input, output;          // input/output buffers
+  var next;                   /* next input INDEX */
+  var put;                    /* next output INDEX */
+  var have, left;             /* available input and output */
+  var hold;                   /* bit buffer */
+  var bits;                   /* bits in bit buffer */
+  var _in, _out;              /* save starting available input and output */
+  var copy;                   /* number of stored or match bytes to copy */
+  var from;                   /* where to copy match bytes from */
+  var from_source;
+  var here = 0;               /* current decoding table entry */
+  var here_bits, here_op, here_val; // paked "here" denormalized (JS specific)
+  //var last;                   /* parent table entry */
+  var last_bits, last_op, last_val; // paked "last" denormalized (JS specific)
+  var len;                    /* length to copy for repeats, bits to drop */
+  var ret;                    /* return code */
+  var hbuf = new utils.Buf8(4);    /* buffer for gzip header crc calculation */
+  var opts;
+
+  var n; // temporary var for NEED_BITS
+
+  var order = /* permutation of code lengths */
+    [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15];
+
+
+  if (!strm || !strm.state || !strm.output ||
+      (!strm.input && strm.avail_in !== 0)) {
+    return Z_STREAM_ERROR;
+  }
+
+  state = strm.state;
+  if (state.mode === TYPE) { state.mode = TYPEDO; }    /* skip check */
+
+
+  //--- LOAD() ---
+  put = strm.next_out;
+  output = strm.output;
+  left = strm.avail_out;
+  next = strm.next_in;
+  input = strm.input;
+  have = strm.avail_in;
+  hold = state.hold;
+  bits = state.bits;
+  //---
+
+  _in = have;
+  _out = left;
+  ret = Z_OK;
+
+  inf_leave: // goto emulation
+  for (;;) {
+    switch (state.mode) {
+    case HEAD:
+      if (state.wrap === 0) {
+        state.mode = TYPEDO;
+        break;
+      }
+      //=== NEEDBITS(16);
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if ((state.wrap & 2) && hold === 0x8b1f) {  /* gzip header */
+        state.check = 0/*crc32(0L, Z_NULL, 0)*/;
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        state.mode = FLAGS;
+        break;
+      }
+      state.flags = 0;           /* expect zlib header */
+      if (state.head) {
+        state.head.done = false;
+      }
+      if (!(state.wrap & 1) ||   /* check if zlib header allowed */
+        (((hold & 0xff)/*BITS(8)*/ << 8) + (hold >> 8)) % 31) {
+        strm.msg = 'incorrect header check';
+        state.mode = BAD;
+        break;
+      }
+      if ((hold & 0x0f)/*BITS(4)*/ !== Z_DEFLATED) {
+        strm.msg = 'unknown compression method';
+        state.mode = BAD;
+        break;
+      }
+      //--- DROPBITS(4) ---//
+      hold >>>= 4;
+      bits -= 4;
+      //---//
+      len = (hold & 0x0f)/*BITS(4)*/ + 8;
+      if (state.wbits === 0) {
+        state.wbits = len;
+      }
+      else if (len > state.wbits) {
+        strm.msg = 'invalid window size';
+        state.mode = BAD;
+        break;
+      }
+      state.dmax = 1 << len;
+      //Tracev((stderr, "inflate:   zlib header ok\n"));
+      strm.adler = state.check = 1/*adler32(0L, Z_NULL, 0)*/;
+      state.mode = hold & 0x200 ? DICTID : TYPE;
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      break;
+    case FLAGS:
+      //=== NEEDBITS(16); */
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.flags = hold;
+      if ((state.flags & 0xff) !== Z_DEFLATED) {
+        strm.msg = 'unknown compression method';
+        state.mode = BAD;
+        break;
+      }
+      if (state.flags & 0xe000) {
+        strm.msg = 'unknown header flags set';
+        state.mode = BAD;
+        break;
+      }
+      if (state.head) {
+        state.head.text = ((hold >> 8) & 1);
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = TIME;
+      /* falls through */
+    case TIME:
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if (state.head) {
+        state.head.time = hold;
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC4(state.check, hold)
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        hbuf[2] = (hold >>> 16) & 0xff;
+        hbuf[3] = (hold >>> 24) & 0xff;
+        state.check = crc32(state.check, hbuf, 4, 0);
+        //===
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = OS;
+      /* falls through */
+    case OS:
+      //=== NEEDBITS(16); */
+      while (bits < 16) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if (state.head) {
+        state.head.xflags = (hold & 0xff);
+        state.head.os = (hold >> 8);
+      }
+      if (state.flags & 0x0200) {
+        //=== CRC2(state.check, hold);
+        hbuf[0] = hold & 0xff;
+        hbuf[1] = (hold >>> 8) & 0xff;
+        state.check = crc32(state.check, hbuf, 2, 0);
+        //===//
+      }
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = EXLEN;
+      /* falls through */
+    case EXLEN:
+      if (state.flags & 0x0400) {
+        //=== NEEDBITS(16); */
+        while (bits < 16) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
         }
-        
-        this.matrixWorldNeedsUpdate = false;
-        
-        //Update matrices of all children
-        for (var i = 0; i < this.children.length; i++) {
-            this.children[i].updateMatrixWorld(true);
+        //===//
+        state.length = hold;
+        if (state.head) {
+          state.head.extra_len = hold;
         }
-    },
-    
-    clone : function(object) {
-        
-        if (object === undefined)
-            object = new $3Dmol.Object3D();
-            
-        object.name = this.name;
-        
-        object.up.copy(this.up);
-        object.position.copy(this.position);
-        object.rotation.copy(this.rotation);
-        object.eulerOrder = this.eulerOrder;
-        object.scale.copy(this.scale);
+        if (state.flags & 0x0200) {
+          //=== CRC2(state.check, hold);
+          hbuf[0] = hold & 0xff;
+          hbuf[1] = (hold >>> 8) & 0xff;
+          state.check = crc32(state.check, hbuf, 2, 0);
+          //===//
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+      }
+      else if (state.head) {
+        state.head.extra = null/*Z_NULL*/;
+      }
+      state.mode = EXTRA;
+      /* falls through */
+    case EXTRA:
+      if (state.flags & 0x0400) {
+        copy = state.length;
+        if (copy > have) { copy = have; }
+        if (copy) {
+          if (state.head) {
+            len = state.head.extra_len - state.length;
+            if (!state.head.extra) {
+              // Use untyped array for more conveniend processing later
+              state.head.extra = new Array(state.head.extra_len);
+            }
+            utils.arraySet(
+              state.head.extra,
+              input,
+              next,
+              // extra field is limited to 65536 bytes
+              // - no need for additional size check
+              copy,
+              /*len + copy > state.head.extra_max - len ? state.head.extra_max : copy,*/
+              len
+            );
+            //zmemcpy(state.head.extra + len, next,
+            //        len + copy > state.head.extra_max ?
+            //        state.head.extra_max - len : copy);
+          }
+          if (state.flags & 0x0200) {
+            state.check = crc32(state.check, input, copy, next);
+          }
+          have -= copy;
+          next += copy;
+          state.length -= copy;
+        }
+        if (state.length) { break inf_leave; }
+      }
+      state.length = 0;
+      state.mode = NAME;
+      /* falls through */
+    case NAME:
+      if (state.flags & 0x0800) {
+        if (have === 0) { break inf_leave; }
+        copy = 0;
+        do {
+          // TODO: 2 or 1 bytes?
+          len = input[next + copy++];
+          /* use constant limit because in js we should not preallocate memory */
+          if (state.head && len &&
+              (state.length < 65536 /*state.head.name_max*/)) {
+            state.head.name += String.fromCharCode(len);
+          }
+        } while (len && copy < have);
+
+        if (state.flags & 0x0200) {
+          state.check = crc32(state.check, input, copy, next);
+        }
+        have -= copy;
+        next += copy;
+        if (len) { break inf_leave; }
+      }
+      else if (state.head) {
+        state.head.name = null;
+      }
+      state.length = 0;
+      state.mode = COMMENT;
+      /* falls through */
+    case COMMENT:
+      if (state.flags & 0x1000) {
+        if (have === 0) { break inf_leave; }
+        copy = 0;
+        do {
+          len = input[next + copy++];
+          /* use constant limit because in js we should not preallocate memory */
+          if (state.head && len &&
+              (state.length < 65536 /*state.head.comm_max*/)) {
+            state.head.comment += String.fromCharCode(len);
+          }
+        } while (len && copy < have);
+        if (state.flags & 0x0200) {
+          state.check = crc32(state.check, input, copy, next);
+        }
+        have -= copy;
+        next += copy;
+        if (len) { break inf_leave; }
+      }
+      else if (state.head) {
+        state.head.comment = null;
+      }
+      state.mode = HCRC;
+      /* falls through */
+    case HCRC:
+      if (state.flags & 0x0200) {
+        //=== NEEDBITS(16); */
+        while (bits < 16) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        if (hold !== (state.check & 0xffff)) {
+          strm.msg = 'header crc mismatch';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+      }
+      if (state.head) {
+        state.head.hcrc = ((state.flags >> 9) & 1);
+        state.head.done = true;
+      }
+      strm.adler = state.check = 0 /*crc32(0L, Z_NULL, 0)*/;
+      state.mode = TYPE;
+      break;
+    case DICTID:
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      strm.adler = state.check = ZSWAP32(hold);
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = DICT;
+      /* falls through */
+    case DICT:
+      if (state.havedict === 0) {
+        //--- RESTORE() ---
+        strm.next_out = put;
+        strm.avail_out = left;
+        strm.next_in = next;
+        strm.avail_in = have;
+        state.hold = hold;
+        state.bits = bits;
+        //---
+        return Z_NEED_DICT;
+      }
+      strm.adler = state.check = 1/*adler32(0L, Z_NULL, 0)*/;
+      state.mode = TYPE;
+      /* falls through */
+    case TYPE:
+      if (flush === Z_BLOCK || flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case TYPEDO:
+      if (state.last) {
+        //--- BYTEBITS() ---//
+        hold >>>= bits & 7;
+        bits -= bits & 7;
+        //---//
+        state.mode = CHECK;
+        break;
+      }
+      //=== NEEDBITS(3); */
+      while (bits < 3) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.last = (hold & 0x01)/*BITS(1)*/;
+      //--- DROPBITS(1) ---//
+      hold >>>= 1;
+      bits -= 1;
+      //---//
+
+      switch ((hold & 0x03)/*BITS(2)*/) {
+      case 0:                             /* stored block */
+        //Tracev((stderr, "inflate:     stored block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = STORED;
+        break;
+      case 1:                             /* fixed block */
+        fixedtables(state);
+        //Tracev((stderr, "inflate:     fixed codes block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = LEN_;             /* decode codes */
+        if (flush === Z_TREES) {
+          //--- DROPBITS(2) ---//
+          hold >>>= 2;
+          bits -= 2;
+          //---//
+          break inf_leave;
+        }
+        break;
+      case 2:                             /* dynamic block */
+        //Tracev((stderr, "inflate:     dynamic codes block%s\n",
+        //        state.last ? " (last)" : ""));
+        state.mode = TABLE;
+        break;
+      case 3:
+        strm.msg = 'invalid block type';
+        state.mode = BAD;
+      }
+      //--- DROPBITS(2) ---//
+      hold >>>= 2;
+      bits -= 2;
+      //---//
+      break;
+    case STORED:
+      //--- BYTEBITS() ---// /* go to byte boundary */
+      hold >>>= bits & 7;
+      bits -= bits & 7;
+      //---//
+      //=== NEEDBITS(32); */
+      while (bits < 32) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      if ((hold & 0xffff) !== ((hold >>> 16) ^ 0xffff)) {
+        strm.msg = 'invalid stored block lengths';
+        state.mode = BAD;
+        break;
+      }
+      state.length = hold & 0xffff;
+      //Tracev((stderr, "inflate:       stored length %u\n",
+      //        state.length));
+      //=== INITBITS();
+      hold = 0;
+      bits = 0;
+      //===//
+      state.mode = COPY_;
+      if (flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case COPY_:
+      state.mode = COPY;
+      /* falls through */
+    case COPY:
+      copy = state.length;
+      if (copy) {
+        if (copy > have) { copy = have; }
+        if (copy > left) { copy = left; }
+        if (copy === 0) { break inf_leave; }
+        //--- zmemcpy(put, next, copy); ---
+        utils.arraySet(output, input, next, copy, put);
+        //---//
+        have -= copy;
+        next += copy;
+        left -= copy;
+        put += copy;
+        state.length -= copy;
+        break;
+      }
+      //Tracev((stderr, "inflate:       stored end\n"));
+      state.mode = TYPE;
+      break;
+    case TABLE:
+      //=== NEEDBITS(14); */
+      while (bits < 14) {
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+      }
+      //===//
+      state.nlen = (hold & 0x1f)/*BITS(5)*/ + 257;
+      //--- DROPBITS(5) ---//
+      hold >>>= 5;
+      bits -= 5;
+      //---//
+      state.ndist = (hold & 0x1f)/*BITS(5)*/ + 1;
+      //--- DROPBITS(5) ---//
+      hold >>>= 5;
+      bits -= 5;
+      //---//
+      state.ncode = (hold & 0x0f)/*BITS(4)*/ + 4;
+      //--- DROPBITS(4) ---//
+      hold >>>= 4;
+      bits -= 4;
+      //---//
+//#ifndef PKZIP_BUG_WORKAROUND
+      if (state.nlen > 286 || state.ndist > 30) {
+        strm.msg = 'too many length or distance symbols';
+        state.mode = BAD;
+        break;
+      }
+//#endif
+      //Tracev((stderr, "inflate:       table sizes ok\n"));
+      state.have = 0;
+      state.mode = LENLENS;
+      /* falls through */
+    case LENLENS:
+      while (state.have < state.ncode) {
+        //=== NEEDBITS(3);
+        while (bits < 3) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.lens[order[state.have++]] = (hold & 0x07);//BITS(3);
+        //--- DROPBITS(3) ---//
+        hold >>>= 3;
+        bits -= 3;
+        //---//
+      }
+      while (state.have < 19) {
+        state.lens[order[state.have++]] = 0;
+      }
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      //state.next = state.codes;
+      //state.lencode = state.next;
+      // Switch to use dynamic table
+      state.lencode = state.lendyn;
+      state.lenbits = 7;
+
+      opts = {bits: state.lenbits};
+      ret = inflate_table(CODES, state.lens, 0, 19, state.lencode, 0, state.work, opts);
+      state.lenbits = opts.bits;
+
+      if (ret) {
+        strm.msg = 'invalid code lengths set';
+        state.mode = BAD;
+        break;
+      }
+      //Tracev((stderr, "inflate:       code lengths ok\n"));
+      state.have = 0;
+      state.mode = CODELENS;
+      /* falls through */
+    case CODELENS:
+      while (state.have < state.nlen + state.ndist) {
+        for (;;) {
+          here = state.lencode[hold & ((1 << state.lenbits) - 1)];/*BITS(state.lenbits)*/
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        if (here_val < 16) {
+          //--- DROPBITS(here.bits) ---//
+          hold >>>= here_bits;
+          bits -= here_bits;
+          //---//
+          state.lens[state.have++] = here_val;
+        }
+        else {
+          if (here_val === 16) {
+            //=== NEEDBITS(here.bits + 2);
+            n = here_bits + 2;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
+            }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            if (state.have === 0) {
+              strm.msg = 'invalid bit length repeat';
+              state.mode = BAD;
+              break;
+            }
+            len = state.lens[state.have - 1];
+            copy = 3 + (hold & 0x03);//BITS(2);
+            //--- DROPBITS(2) ---//
+            hold >>>= 2;
+            bits -= 2;
+            //---//
+          }
+          else if (here_val === 17) {
+            //=== NEEDBITS(here.bits + 3);
+            n = here_bits + 3;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
+            }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            len = 0;
+            copy = 3 + (hold & 0x07);//BITS(3);
+            //--- DROPBITS(3) ---//
+            hold >>>= 3;
+            bits -= 3;
+            //---//
+          }
+          else {
+            //=== NEEDBITS(here.bits + 7);
+            n = here_bits + 7;
+            while (bits < n) {
+              if (have === 0) { break inf_leave; }
+              have--;
+              hold += input[next++] << bits;
+              bits += 8;
+            }
+            //===//
+            //--- DROPBITS(here.bits) ---//
+            hold >>>= here_bits;
+            bits -= here_bits;
+            //---//
+            len = 0;
+            copy = 11 + (hold & 0x7f);//BITS(7);
+            //--- DROPBITS(7) ---//
+            hold >>>= 7;
+            bits -= 7;
+            //---//
+          }
+          if (state.have + copy > state.nlen + state.ndist) {
+            strm.msg = 'invalid bit length repeat';
+            state.mode = BAD;
+            break;
+          }
+          while (copy--) {
+            state.lens[state.have++] = len;
+          }
+        }
+      }
+
+      /* handle error breaks in while */
+      if (state.mode === BAD) { break; }
+
+      /* check for end-of-block code (better have one) */
+      if (state.lens[256] === 0) {
+        strm.msg = 'invalid code -- missing end-of-block';
+        state.mode = BAD;
+        break;
+      }
+
+      /* build code tables -- note: do not change the lenbits or distbits
+         values here (9 and 6) without reading the comments in inftrees.h
+         concerning the ENOUGH constants, which depend on those values */
+      state.lenbits = 9;
+
+      opts = {bits: state.lenbits};
+      ret = inflate_table(LENS, state.lens, 0, state.nlen, state.lencode, 0, state.work, opts);
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      // state.next_index = opts.table_index;
+      state.lenbits = opts.bits;
+      // state.lencode = state.next;
+
+      if (ret) {
+        strm.msg = 'invalid literal/lengths set';
+        state.mode = BAD;
+        break;
+      }
+
+      state.distbits = 6;
+      //state.distcode.copy(state.codes);
+      // Switch to use dynamic table
+      state.distcode = state.distdyn;
+      opts = {bits: state.distbits};
+      ret = inflate_table(DISTS, state.lens, state.nlen, state.ndist, state.distcode, 0, state.work, opts);
+      // We have separate tables & no pointers. 2 commented lines below not needed.
+      // state.next_index = opts.table_index;
+      state.distbits = opts.bits;
+      // state.distcode = state.next;
+
+      if (ret) {
+        strm.msg = 'invalid distances set';
+        state.mode = BAD;
+        break;
+      }
+      //Tracev((stderr, 'inflate:       codes ok\n'));
+      state.mode = LEN_;
+      if (flush === Z_TREES) { break inf_leave; }
+      /* falls through */
+    case LEN_:
+      state.mode = LEN;
+      /* falls through */
+    case LEN:
+      if (have >= 6 && left >= 258) {
+        //--- RESTORE() ---
+        strm.next_out = put;
+        strm.avail_out = left;
+        strm.next_in = next;
+        strm.avail_in = have;
+        state.hold = hold;
+        state.bits = bits;
+        //---
+        inflate_fast(strm, _out);
+        //--- LOAD() ---
+        put = strm.next_out;
+        output = strm.output;
+        left = strm.avail_out;
+        next = strm.next_in;
+        input = strm.input;
+        have = strm.avail_in;
+        hold = state.hold;
+        bits = state.bits;
+        //---
+
+        if (state.mode === TYPE) {
+          state.back = -1;
+        }
+        break;
+      }
+      state.back = 0;
+      for (;;) {
+        here = state.lencode[hold & ((1 << state.lenbits) -1)];  /*BITS(state.lenbits)*/
+        here_bits = here >>> 24;
+        here_op = (here >>> 16) & 0xff;
+        here_val = here & 0xffff;
+
+        if (here_bits <= bits) { break; }
+        //--- PULLBYTE() ---//
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+        //---//
+      }
+      if (here_op && (here_op & 0xf0) === 0) {
+        last_bits = here_bits;
+        last_op = here_op;
+        last_val = here_val;
+        for (;;) {
+          here = state.lencode[last_val +
+                  ((hold & ((1 << (last_bits + last_op)) -1))/*BITS(last.bits + last.op)*/ >> last_bits)];
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((last_bits + here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        //--- DROPBITS(last.bits) ---//
+        hold >>>= last_bits;
+        bits -= last_bits;
+        //---//
+        state.back += last_bits;
+      }
+      //--- DROPBITS(here.bits) ---//
+      hold >>>= here_bits;
+      bits -= here_bits;
+      //---//
+      state.back += here_bits;
+      state.length = here_val;
+      if (here_op === 0) {
+        //Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+        //        "inflate:         literal '%c'\n" :
+        //        "inflate:         literal 0x%02x\n", here.val));
+        state.mode = LIT;
+        break;
+      }
+      if (here_op & 32) {
+        //Tracevv((stderr, "inflate:         end of block\n"));
+        state.back = -1;
+        state.mode = TYPE;
+        break;
+      }
+      if (here_op & 64) {
+        strm.msg = 'invalid literal/length code';
+        state.mode = BAD;
+        break;
+      }
+      state.extra = here_op & 15;
+      state.mode = LENEXT;
+      /* falls through */
+    case LENEXT:
+      if (state.extra) {
+        //=== NEEDBITS(state.extra);
+        n = state.extra;
+        while (bits < n) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.length += hold & ((1 << state.extra) -1)/*BITS(state.extra)*/;
+        //--- DROPBITS(state.extra) ---//
+        hold >>>= state.extra;
+        bits -= state.extra;
+        //---//
+        state.back += state.extra;
+      }
+      //Tracevv((stderr, "inflate:         length %u\n", state.length));
+      state.was = state.length;
+      state.mode = DIST;
+      /* falls through */
+    case DIST:
+      for (;;) {
+        here = state.distcode[hold & ((1 << state.distbits) -1)];/*BITS(state.distbits)*/
+        here_bits = here >>> 24;
+        here_op = (here >>> 16) & 0xff;
+        here_val = here & 0xffff;
+
+        if ((here_bits) <= bits) { break; }
+        //--- PULLBYTE() ---//
+        if (have === 0) { break inf_leave; }
+        have--;
+        hold += input[next++] << bits;
+        bits += 8;
+        //---//
+      }
+      if ((here_op & 0xf0) === 0) {
+        last_bits = here_bits;
+        last_op = here_op;
+        last_val = here_val;
+        for (;;) {
+          here = state.distcode[last_val +
+                  ((hold & ((1 << (last_bits + last_op)) -1))/*BITS(last.bits + last.op)*/ >> last_bits)];
+          here_bits = here >>> 24;
+          here_op = (here >>> 16) & 0xff;
+          here_val = here & 0xffff;
+
+          if ((last_bits + here_bits) <= bits) { break; }
+          //--- PULLBYTE() ---//
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+          //---//
+        }
+        //--- DROPBITS(last.bits) ---//
+        hold >>>= last_bits;
+        bits -= last_bits;
+        //---//
+        state.back += last_bits;
+      }
+      //--- DROPBITS(here.bits) ---//
+      hold >>>= here_bits;
+      bits -= here_bits;
+      //---//
+      state.back += here_bits;
+      if (here_op & 64) {
+        strm.msg = 'invalid distance code';
+        state.mode = BAD;
+        break;
+      }
+      state.offset = here_val;
+      state.extra = (here_op) & 15;
+      state.mode = DISTEXT;
+      /* falls through */
+    case DISTEXT:
+      if (state.extra) {
+        //=== NEEDBITS(state.extra);
+        n = state.extra;
+        while (bits < n) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        state.offset += hold & ((1 << state.extra) -1)/*BITS(state.extra)*/;
+        //--- DROPBITS(state.extra) ---//
+        hold >>>= state.extra;
+        bits -= state.extra;
+        //---//
+        state.back += state.extra;
+      }
+//#ifdef INFLATE_STRICT
+      if (state.offset > state.dmax) {
+        strm.msg = 'invalid distance too far back';
+        state.mode = BAD;
+        break;
+      }
+//#endif
+      //Tracevv((stderr, "inflate:         distance %u\n", state.offset));
+      state.mode = MATCH;
+      /* falls through */
+    case MATCH:
+      if (left === 0) { break inf_leave; }
+      copy = _out - left;
+      if (state.offset > copy) {         /* copy from window */
+        copy = state.offset - copy;
+        if (copy > state.whave) {
+          if (state.sane) {
+            strm.msg = 'invalid distance too far back';
+            state.mode = BAD;
+            break;
+          }
+// (!) This block is disabled in zlib defailts,
+// don't enable it for binary compatibility
+//#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+//          Trace((stderr, "inflate.c too far\n"));
+//          copy -= state.whave;
+//          if (copy > state.length) { copy = state.length; }
+//          if (copy > left) { copy = left; }
+//          left -= copy;
+//          state.length -= copy;
+//          do {
+//            output[put++] = 0;
+//          } while (--copy);
+//          if (state.length === 0) { state.mode = LEN; }
+//          break;
+//#endif
+        }
+        if (copy > state.wnext) {
+          copy -= state.wnext;
+          from = state.wsize - copy;
+        }
+        else {
+          from = state.wnext - copy;
+        }
+        if (copy > state.length) { copy = state.length; }
+        from_source = state.window;
+      }
+      else {                              /* copy from output */
+        from_source = output;
+        from = put - state.offset;
+        copy = state.length;
+      }
+      if (copy > left) { copy = left; }
+      left -= copy;
+      state.length -= copy;
+      do {
+        output[put++] = from_source[from++];
+      } while (--copy);
+      if (state.length === 0) { state.mode = LEN; }
+      break;
+    case LIT:
+      if (left === 0) { break inf_leave; }
+      output[put++] = state.length;
+      left--;
+      state.mode = LEN;
+      break;
+    case CHECK:
+      if (state.wrap) {
+        //=== NEEDBITS(32);
+        while (bits < 32) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          // Use '|' insdead of '+' to make sure that result is signed
+          hold |= input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        _out -= left;
+        strm.total_out += _out;
+        state.total += _out;
+        if (_out) {
+          strm.adler = state.check =
+              /*UPDATE(state.check, put - _out, _out);*/
+              (state.flags ? crc32(state.check, output, _out, put - _out) : adler32(state.check, output, _out, put - _out));
 
-        object.rotationAutoUpdate = this.rotationAutoUpdate;
-        object.matrix.copy(this.matrix);
-        object.matrixWorld.copy(this.matrixWorld);
-        object.quaternion.copy(this.quaternion);
-        object.matrixAutoUpdate = this.matrixAutoUpdate;
-        object.matrixWorldNeedsUpdate = this.matrixWorldNeedsUpdate;
-        
-        object.useQuaternion = this.useQuaternion;
-        
-        object.visible = this.visible;
-        
-        for (var i = 0; i < this.children.length; i++) {
-            var child = this.children[i];
-            object.add(child.clone());
         }
-        
-        return object;
-        
+        _out = left;
+        // NB: crc32 stored as signed 32-bit int, ZSWAP32 returns signed too
+        if ((state.flags ? hold : ZSWAP32(hold)) !== state.check) {
+          strm.msg = 'incorrect data check';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        //Tracev((stderr, "inflate:   check matches trailer\n"));
+      }
+      state.mode = LENGTH;
+      /* falls through */
+    case LENGTH:
+      if (state.wrap && state.flags) {
+        //=== NEEDBITS(32);
+        while (bits < 32) {
+          if (have === 0) { break inf_leave; }
+          have--;
+          hold += input[next++] << bits;
+          bits += 8;
+        }
+        //===//
+        if (hold !== (state.total & 0xffffffff)) {
+          strm.msg = 'incorrect length check';
+          state.mode = BAD;
+          break;
+        }
+        //=== INITBITS();
+        hold = 0;
+        bits = 0;
+        //===//
+        //Tracev((stderr, "inflate:   length matches trailer\n"));
+      }
+      state.mode = DONE;
+      /* falls through */
+    case DONE:
+      ret = Z_STREAM_END;
+      break inf_leave;
+    case BAD:
+      ret = Z_DATA_ERROR;
+      break inf_leave;
+    case MEM:
+      return Z_MEM_ERROR;
+    case SYNC:
+      /* falls through */
+    default:
+      return Z_STREAM_ERROR;
     }
-    
+  }
+
+  // inf_leave <- here is real place for "goto inf_leave", emulated via "break inf_leave"
+
+  /*
+     Return from inflate(), updating the total counts and the check value.
+     If there was no progress during the inflate() call, return a buffer
+     error.  Call updatewindow() to create and/or update the window state.
+     Note: a memory error from inflate() is non-recoverable.
+   */
+
+  //--- RESTORE() ---
+  strm.next_out = put;
+  strm.avail_out = left;
+  strm.next_in = next;
+  strm.avail_in = have;
+  state.hold = hold;
+  state.bits = bits;
+  //---
+
+  if (state.wsize || (_out !== strm.avail_out && state.mode < BAD &&
+                      (state.mode < CHECK || flush !== Z_FINISH))) {
+    if (updatewindow(strm, strm.output, strm.next_out, _out - strm.avail_out)) {
+      state.mode = MEM;
+      return Z_MEM_ERROR;
+    }
+  }
+  _in -= strm.avail_in;
+  _out -= strm.avail_out;
+  strm.total_in += _in;
+  strm.total_out += _out;
+  state.total += _out;
+  if (state.wrap && _out) {
+    strm.adler = state.check = /*UPDATE(state.check, strm.next_out - _out, _out);*/
+      (state.flags ? crc32(state.check, output, _out, strm.next_out - _out) : adler32(state.check, output, _out, strm.next_out - _out));
+  }
+  strm.data_type = state.bits + (state.last ? 64 : 0) +
+                    (state.mode === TYPE ? 128 : 0) +
+                    (state.mode === LEN_ || state.mode === COPY_ ? 256 : 0);
+  if (((_in === 0 && _out === 0) || flush === Z_FINISH) && ret === Z_OK) {
+    ret = Z_BUF_ERROR;
+  }
+  return ret;
+}
+
+function inflateEnd(strm) {
+
+  if (!strm || !strm.state /*|| strm->zfree == (free_func)0*/) {
+    return Z_STREAM_ERROR;
+  }
+
+  var state = strm.state;
+  if (state.window) {
+    state.window = null;
+  }
+  strm.state = null;
+  return Z_OK;
+}
+
+function inflateGetHeader(strm, head) {
+  var state;
+
+  /* check state */
+  if (!strm || !strm.state) { return Z_STREAM_ERROR; }
+  state = strm.state;
+  if ((state.wrap & 2) === 0) { return Z_STREAM_ERROR; }
+
+  /* save header structure */
+  state.head = head;
+  head.done = false;
+  return Z_OK;
+}
+
+
+exports.inflateReset = inflateReset;
+exports.inflateReset2 = inflateReset2;
+exports.inflateResetKeep = inflateResetKeep;
+exports.inflateInit = inflateInit;
+exports.inflateInit2 = inflateInit2;
+exports.inflate = inflate;
+exports.inflateEnd = inflateEnd;
+exports.inflateGetHeader = inflateGetHeader;
+exports.inflateInfo = 'pako inflate (from Nodeca project)';
+
+/* Not implemented
+exports.inflateCopy = inflateCopy;
+exports.inflateGetDictionary = inflateGetDictionary;
+exports.inflateMark = inflateMark;
+exports.inflatePrime = inflatePrime;
+exports.inflateSetDictionary = inflateSetDictionary;
+exports.inflateSync = inflateSync;
+exports.inflateSyncPoint = inflateSyncPoint;
+exports.inflateUndermine = inflateUndermine;
+*/
+
+},{"../utils/common":1,"./adler32":3,"./crc32":5,"./inffast":7,"./inftrees":9}],9:[function(require,module,exports){
+'use strict';
+
+
+var utils = require('../utils/common');
+
+var MAXBITS = 15;
+var ENOUGH_LENS = 852;
+var ENOUGH_DISTS = 592;
+//var ENOUGH = (ENOUGH_LENS+ENOUGH_DISTS);
+
+var CODES = 0;
+var LENS = 1;
+var DISTS = 2;
+
+var lbase = [ /* Length codes 257..285 base */
+  3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
+  35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0
+];
+
+var lext = [ /* Length codes 257..285 extra */
+  16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
+  19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78
+];
+
+var dbase = [ /* Distance codes 0..29 base */
+  1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
+  257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
+  8193, 12289, 16385, 24577, 0, 0
+];
+
+var dext = [ /* Distance codes 0..29 extra */
+  16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
+  23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
+  28, 28, 29, 29, 64, 64
+];
+
+module.exports = function inflate_table(type, lens, lens_index, codes, table, table_index, work, opts)
+{
+  var bits = opts.bits;
+      //here = opts.here; /* table entry for duplication */
+
+  var len = 0;               /* a code's length in bits */
+  var sym = 0;               /* index of code symbols */
+  var min = 0, max = 0;          /* minimum and maximum code lengths */
+  var root = 0;              /* number of index bits for root table */
+  var curr = 0;              /* number of index bits for current table */
+  var drop = 0;              /* code bits to drop for sub-table */
+  var left = 0;                   /* number of prefix codes available */
+  var used = 0;              /* code entries in table used */
+  var huff = 0;              /* Huffman code */
+  var incr;              /* for incrementing code, index */
+  var fill;              /* index for replicating entries */
+  var low;               /* low bits for current root entry */
+  var mask;              /* mask for low root bits */
+  var next;             /* next available space in table */
+  var base = null;     /* base value table to use */
+  var base_index = 0;
+//  var shoextra;    /* extra bits table to use */
+  var end;                    /* use base and extra for symbol > end */
+  var count = new utils.Buf16(MAXBITS+1); //[MAXBITS+1];    /* number of codes of each length */
+  var offs = new utils.Buf16(MAXBITS+1); //[MAXBITS+1];     /* offsets in table for each length */
+  var extra = null;
+  var extra_index = 0;
+
+  var here_bits, here_op, here_val;
+
+  /*
+   Process a set of code lengths to create a canonical Huffman code.  The
+   code lengths are lens[0..codes-1].  Each length corresponds to the
+   symbols 0..codes-1.  The Huffman code is generated by first sorting the
+   symbols by length from short to long, and retaining the symbol order
+   for codes with equal lengths.  Then the code starts with all zero bits
+   for the first code of the shortest length, and the codes are integer
+   increments for the same length, and zeros are appended as the length
+   increases.  For the deflate format, these bits are stored backwards
+   from their more natural integer increment ordering, and so when the
+   decoding tables are built in the large loop below, the integer codes
+   are incremented backwards.
+
+   This routine assumes, but does not check, that all of the entries in
+   lens[] are in the range 0..MAXBITS.  The caller must assure this.
+   1..MAXBITS is interpreted as that code length.  zero means that that
+   symbol does not occur in this code.
+
+   The codes are sorted by computing a count of codes for each length,
+   creating from that a table of starting indices for each length in the
+   sorted table, and then entering the symbols in order in the sorted
+   table.  The sorted table is work[], with that space being provided by
+   the caller.
+
+   The length counts are used for other purposes as well, i.e. finding
+   the minimum and maximum length codes, determining if there are any
+   codes at all, checking for a valid set of lengths, and looking ahead
+   at length counts to determine sub-table sizes when building the
+   decoding tables.
+   */
+
+  /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
+  for (len = 0; len <= MAXBITS; len++) {
+    count[len] = 0;
+  }
+  for (sym = 0; sym < codes; sym++) {
+    count[lens[lens_index + sym]]++;
+  }
+
+  /* bound code lengths, force root to be within code lengths */
+  root = bits;
+  for (max = MAXBITS; max >= 1; max--) {
+    if (count[max] !== 0) { break; }
+  }
+  if (root > max) {
+    root = max;
+  }
+  if (max === 0) {                     /* no symbols to code at all */
+    //table.op[opts.table_index] = 64;  //here.op = (var char)64;    /* invalid code marker */
+    //table.bits[opts.table_index] = 1;   //here.bits = (var char)1;
+    //table.val[opts.table_index++] = 0;   //here.val = (var short)0;
+    table[table_index++] = (1 << 24) | (64 << 16) | 0;
+
+
+    //table.op[opts.table_index] = 64;
+    //table.bits[opts.table_index] = 1;
+    //table.val[opts.table_index++] = 0;
+    table[table_index++] = (1 << 24) | (64 << 16) | 0;
+
+    opts.bits = 1;
+    return 0;     /* no symbols, but wait for decoding to report error */
+  }
+  for (min = 1; min < max; min++) {
+    if (count[min] !== 0) { break; }
+  }
+  if (root < min) {
+    root = min;
+  }
+
+  /* check for an over-subscribed or incomplete set of lengths */
+  left = 1;
+  for (len = 1; len <= MAXBITS; len++) {
+    left <<= 1;
+    left -= count[len];
+    if (left < 0) {
+      return -1;
+    }        /* over-subscribed */
+  }
+  if (left > 0 && (type === CODES || max !== 1)) {
+    return -1;                      /* incomplete set */
+  }
+
+  /* generate offsets into symbol table for each length for sorting */
+  offs[1] = 0;
+  for (len = 1; len < MAXBITS; len++) {
+    offs[len + 1] = offs[len] + count[len];
+  }
+
+  /* sort symbols by length, by symbol order within each length */
+  for (sym = 0; sym < codes; sym++) {
+    if (lens[lens_index + sym] !== 0) {
+      work[offs[lens[lens_index + sym]]++] = sym;
+    }
+  }
+
+  /*
+   Create and fill in decoding tables.  In this loop, the table being
+   filled is at next and has curr index bits.  The code being used is huff
+   with length len.  That code is converted to an index by dropping drop
+   bits off of the bottom.  For codes where len is less than drop + curr,
+   those top drop + curr - len bits are incremented through all values to
+   fill the table with replicated entries.
+
+   root is the number of index bits for the root table.  When len exceeds
+   root, sub-tables are created pointed to by the root entry with an index
+   of the low root bits of huff.  This is saved in low to check for when a
+   new sub-table should be started.  drop is zero when the root table is
+   being filled, and drop is root when sub-tables are being filled.
+
+   When a new sub-table is needed, it is necessary to look ahead in the
+   code lengths to determine what size sub-table is needed.  The length
+   counts are used for this, and so count[] is decremented as codes are
+   entered in the tables.
+
+   used keeps track of how many table entries have been allocated from the
+   provided *table space.  It is checked for LENS and DIST tables against
+   the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
+   the initial root table size constants.  See the comments in inftrees.h
+   for more information.
+
+   sym increments through all symbols, and the loop terminates when
+   all codes of length max, i.e. all codes, have been processed.  This
+   routine permits incomplete codes, so another loop after this one fills
+   in the rest of the decoding tables with invalid code markers.
+   */
+
+  /* set up for code type */
+  // poor man optimization - use if-else instead of switch,
+  // to avoid deopts in old v8
+  if (type === CODES) {
+    base = extra = work;    /* dummy value--not used */
+    end = 19;
+
+  } else if (type === LENS) {
+    base = lbase;
+    base_index -= 257;
+    extra = lext;
+    extra_index -= 257;
+    end = 256;
+
+  } else {                    /* DISTS */
+    base = dbase;
+    extra = dext;
+    end = -1;
+  }
+
+  /* initialize opts for loop */
+  huff = 0;                   /* starting code */
+  sym = 0;                    /* starting code symbol */
+  len = min;                  /* starting code length */
+  next = table_index;              /* current table to fill in */
+  curr = root;                /* current table index bits */
+  drop = 0;                   /* current bits to drop from code for index */
+  low = -1;                   /* trigger new sub-table when len > root */
+  used = 1 << root;          /* use root table entries */
+  mask = used - 1;            /* mask for comparing low */
+
+  /* check available table space */
+  if ((type === LENS && used > ENOUGH_LENS) ||
+    (type === DISTS && used > ENOUGH_DISTS)) {
+    return 1;
+  }
+
+  var i=0;
+  /* process all codes and make table entries */
+  for (;;) {
+    i++;
+    /* create table entry */
+    here_bits = len - drop;
+    if (work[sym] < end) {
+      here_op = 0;
+      here_val = work[sym];
+    }
+    else if (work[sym] > end) {
+      here_op = extra[extra_index + work[sym]];
+      here_val = base[base_index + work[sym]];
+    }
+    else {
+      here_op = 32 + 64;         /* end of block */
+      here_val = 0;
+    }
+
+    /* replicate for those indices with low len bits equal to huff */
+    incr = 1 << (len - drop);
+    fill = 1 << curr;
+    min = fill;                 /* save offset to next table */
+    do {
+      fill -= incr;
+      table[next + (huff >> drop) + fill] = (here_bits << 24) | (here_op << 16) | here_val |0;
+    } while (fill !== 0);
+
+    /* backwards increment the len-bit code huff */
+    incr = 1 << (len - 1);
+    while (huff & incr) {
+      incr >>= 1;
+    }
+    if (incr !== 0) {
+      huff &= incr - 1;
+      huff += incr;
+    } else {
+      huff = 0;
+    }
+
+    /* go to next symbol, update count, len */
+    sym++;
+    if (--count[len] === 0) {
+      if (len === max) { break; }
+      len = lens[lens_index + work[sym]];
+    }
+
+    /* create new sub-table if needed */
+    if (len > root && (huff & mask) !== low) {
+      /* if first time, transition to sub-tables */
+      if (drop === 0) {
+        drop = root;
+      }
+
+      /* increment past last table */
+      next += min;            /* here min is 1 << curr */
+
+      /* determine length of next table */
+      curr = len - drop;
+      left = 1 << curr;
+      while (curr + drop < max) {
+        left -= count[curr + drop];
+        if (left <= 0) { break; }
+        curr++;
+        left <<= 1;
+      }
+
+      /* check for enough space */
+      used += 1 << curr;
+      if ((type === LENS && used > ENOUGH_LENS) ||
+        (type === DISTS && used > ENOUGH_DISTS)) {
+        return 1;
+      }
+
+      /* point entry in root table to sub-table */
+      low = huff & mask;
+      /*table.op[low] = curr;
+      table.bits[low] = root;
+      table.val[low] = next - opts.table_index;*/
+      table[low] = (root << 24) | (curr << 16) | (next - table_index) |0;
+    }
+  }
+
+  /* fill in remaining table entry if code is incomplete (guaranteed to have
+   at most one remaining entry, since if the code is incomplete, the
+   maximum code length that was allowed to get this far is one bit) */
+  if (huff !== 0) {
+    //table.op[next + huff] = 64;            /* invalid code marker */
+    //table.bits[next + huff] = len - drop;
+    //table.val[next + huff] = 0;
+    table[next + huff] = ((len - drop) << 24) | (64 << 16) |0;
+  }
+
+  /* set return parameters */
+  //opts.table_index += used;
+  opts.bits = root;
+  return 0;
 };
 
-$3Dmol.Object3DIDCount = 0;
+},{"../utils/common":1}],10:[function(require,module,exports){
+'use strict';
+
+module.exports = {
+  '2':    'need dictionary',     /* Z_NEED_DICT       2  */
+  '1':    'stream end',          /* Z_STREAM_END      1  */
+  '0':    '',                    /* Z_OK              0  */
+  '-1':   'file error',          /* Z_ERRNO         (-1) */
+  '-2':   'stream error',        /* Z_STREAM_ERROR  (-2) */
+  '-3':   'data error',          /* Z_DATA_ERROR    (-3) */
+  '-4':   'insufficient memory', /* Z_MEM_ERROR     (-4) */
+  '-5':   'buffer error',        /* Z_BUF_ERROR     (-5) */
+  '-6':   'incompatible version' /* Z_VERSION_ERROR (-6) */
+};
 
-//Geometry class
-//TODO: What can I remove - how can I optimize ?
-$3Dmol.Geometry = (function() {
-   
-    var BUFFERSIZE = 65535; //limited to 16bit indices
-    
-    
-    /** @constructor */
-    var geometryGroup = function(id) {
-        this.id = id || 0;
-        //for performance reasons, callers must directly modify these
-        this.vertexArray = null;
-        this.colorArray = null;
-        this.normalArray = null;
-        this.faceArray = null;
-        this.lineArray = null;
-        this.vertices = 0;
-        this.faceidx = 0;
-        this.lineidx = 0;
-        
-    };
+},{}],11:[function(require,module,exports){
+'use strict';
+
+
+function ZStream() {
+  /* next input byte */
+  this.input = null; // JS specific, because we have no pointers
+  this.next_in = 0;
+  /* number of bytes available at input */
+  this.avail_in = 0;
+  /* total number of input bytes read so far */
+  this.total_in = 0;
+  /* next output byte should be put there */
+  this.output = null; // JS specific, because we have no pointers
+  this.next_out = 0;
+  /* remaining free space at output */
+  this.avail_out = 0;
+  /* total number of bytes output so far */
+  this.total_out = 0;
+  /* last error message, NULL if no error */
+  this.msg = ''/*Z_NULL*/;
+  /* not visible by applications */
+  this.state = null;
+  /* best guess about the data type: binary or text */
+  this.data_type = 2/*Z_UNKNOWN*/;
+  /* adler32 value of the uncompressed data */
+  this.adler = 0;
+}
+
+module.exports = ZStream;
+
+},{}],"/lib/inflate.js":[function(require,module,exports){
+'use strict';
+
+
+var zlib_inflate = require('./zlib/inflate.js');
+var utils = require('./utils/common');
+var strings = require('./utils/strings');
+var c = require('./zlib/constants');
+var msg = require('./zlib/messages');
+var zstream = require('./zlib/zstream');
+var gzheader = require('./zlib/gzheader');
+
+var toString = Object.prototype.toString;
+
+/**
+ * class Inflate
+ *
+ * Generic JS-style wrapper for zlib calls. If you don't need
+ * streaming behaviour - use more simple functions: [[inflate]]
+ * and [[inflateRaw]].
+ **/
+
+/* internal
+ * inflate.chunks -> Array
+ *
+ * Chunks of output data, if [[Inflate#onData]] not overriden.
+ **/
+
+/**
+ * Inflate.result -> Uint8Array|Array|String
+ *
+ * Uncompressed result, generated by default [[Inflate#onData]]
+ * and [[Inflate#onEnd]] handlers. Filled after you push last chunk
+ * (call [[Inflate#push]] with `Z_FINISH` / `true` param) or if you
+ * push a chunk with explicit flush (call [[Inflate#push]] with
+ * `Z_SYNC_FLUSH` param).
+ **/
+
+/**
+ * Inflate.err -> Number
+ *
+ * Error code after inflate finished. 0 (Z_OK) on success.
+ * Should be checked if broken data possible.
+ **/
+
+/**
+ * Inflate.msg -> String
+ *
+ * Error message, if [[Inflate.err]] != 0
+ **/
+
+
+/**
+ * new Inflate(options)
+ * - options (Object): zlib inflate options.
+ *
+ * Creates new inflator instance with specified params. Throws exception
+ * on bad params. Supported options:
+ *
+ * - `windowBits`
+ *
+ * [http://zlib.net/manual.html#Advanced](http://zlib.net/manual.html#Advanced)
+ * for more information on these.
+ *
+ * Additional options, for internal needs:
+ *
+ * - `chunkSize` - size of generated data chunks (16K by default)
+ * - `raw` (Boolean) - do raw inflate
+ * - `to` (String) - if equal to 'string', then result will be converted
+ *   from utf8 to utf16 (javascript) string. When string output requested,
+ *   chunk length can differ from `chunkSize`, depending on content.
+ *
+ * By default, when no options set, autodetect deflate/gzip data format via
+ * wrapper header.
+ *
+ * ##### Example:
+ *
+ * ```javascript
+ * var pako = require('pako')
+ *   , chunk1 = Uint8Array([1,2,3,4,5,6,7,8,9])
+ *   , chunk2 = Uint8Array([10,11,12,13,14,15,16,17,18,19]);
+ *
+ * var inflate = new pako.Inflate({ level: 3});
+ *
+ * inflate.push(chunk1, false);
+ * inflate.push(chunk2, true);  // true -> last chunk
+ *
+ * if (inflate.err) { throw new Error(inflate.err); }
+ *
+ * console.log(inflate.result);
+ * ```
+ **/
+var Inflate = function(options) {
+
+  this.options = utils.assign({
+    chunkSize: 16384,
+    windowBits: 0,
+    to: ''
+  }, options || {});
+
+  var opt = this.options;
+
+  // Force window size for `raw` data, if not set directly,
+  // because we have no header for autodetect.
+  if (opt.raw && (opt.windowBits >= 0) && (opt.windowBits < 16)) {
+    opt.windowBits = -opt.windowBits;
+    if (opt.windowBits === 0) { opt.windowBits = -15; }
+  }
+
+  // If `windowBits` not defined (and mode not raw) - set autodetect flag for gzip/deflate
+  if ((opt.windowBits >= 0) && (opt.windowBits < 16) &&
+      !(options && options.windowBits)) {
+    opt.windowBits += 32;
+  }
+
+  // Gzip header has no info about windows size, we can do autodetect only
+  // for deflate. So, if window size not set, force it to max when gzip possible
+  if ((opt.windowBits > 15) && (opt.windowBits < 48)) {
+    // bit 3 (16) -> gzipped data
+    // bit 4 (32) -> autodetect gzip/deflate
+    if ((opt.windowBits & 15) === 0) {
+      opt.windowBits |= 15;
+    }
+  }
+
+  this.err    = 0;      // error code, if happens (0 = Z_OK)
+  this.msg    = '';     // error message
+  this.ended  = false;  // used to avoid multiple onEnd() calls
+  this.chunks = [];     // chunks of compressed data
+
+  this.strm   = new zstream();
+  this.strm.avail_out = 0;
+
+  var status  = zlib_inflate.inflateInit2(
+    this.strm,
+    opt.windowBits
+  );
+
+  if (status !== c.Z_OK) {
+    throw new Error(msg[status]);
+  }
+
+  this.header = new gzheader();
+
+  zlib_inflate.inflateGetHeader(this.strm, this.header);
+};
+
+/**
+ * Inflate#push(data[, mode]) -> Boolean
+ * - data (Uint8Array|Array|ArrayBuffer|String): input data
+ * - mode (Number|Boolean): 0..6 for corresponding Z_NO_FLUSH..Z_TREE modes.
+ *   See constants. Skipped or `false` means Z_NO_FLUSH, `true` meansh Z_FINISH.
+ *
+ * Sends input data to inflate pipe, generating [[Inflate#onData]] calls with
+ * new output chunks. Returns `true` on success. The last data block must have
+ * mode Z_FINISH (or `true`). That will flush internal pending buffers and call
+ * [[Inflate#onEnd]]. For interim explicit flushes (without ending the stream) you
+ * can use mode Z_SYNC_FLUSH, keeping the decompression context.
+ *
+ * On fail call [[Inflate#onEnd]] with error code and return false.
+ *
+ * We strongly recommend to use `Uint8Array` on input for best speed (output
+ * format is detected automatically). Also, don't skip last param and always
+ * use the same type in your code (boolean or number). That will improve JS speed.
+ *
+ * For regular `Array`-s make sure all elements are [0..255].
+ *
+ * ##### Example
+ *
+ * ```javascript
+ * push(chunk, false); // push one of data chunks
+ * ...
+ * push(chunk, true);  // push last chunk
+ * ```
+ **/
+Inflate.prototype.push = function(data, mode) {
+  var strm = this.strm;
+  var chunkSize = this.options.chunkSize;
+  var status, _mode;
+  var next_out_utf8, tail, utf8str;
+
+  if (this.ended) { return false; }
+  _mode = (mode === ~~mode) ? mode : ((mode === true) ? c.Z_FINISH : c.Z_NO_FLUSH);
+
+  // Convert data if needed
+  if (typeof data === 'string') {
+    // Only binary strings can be decompressed on practice
+    strm.input = strings.binstring2buf(data);
+  } else if (toString.call(data) === '[object ArrayBuffer]') {
+    strm.input = new Uint8Array(data);
+  } else {
+    strm.input = data;
+  }
+
+  strm.next_in = 0;
+  strm.avail_in = strm.input.length;
+
+  do {
+    if (strm.avail_out === 0) {
+      strm.output = new utils.Buf8(chunkSize);
+      strm.next_out = 0;
+      strm.avail_out = chunkSize;
+    }
+
+    status = zlib_inflate.inflate(strm, c.Z_NO_FLUSH);    /* no bad return value */
+
+    if (status !== c.Z_STREAM_END && status !== c.Z_OK) {
+      this.onEnd(status);
+      this.ended = true;
+      return false;
+    }
+
+    if (strm.next_out) {
+      if (strm.avail_out === 0 || status === c.Z_STREAM_END || (strm.avail_in === 0 && (_mode === c.Z_FINISH || _mode === c.Z_SYNC_FLUSH))) {
+
+        if (this.options.to === 'string') {
+
+          next_out_utf8 = strings.utf8border(strm.output, strm.next_out);
+
+          tail = strm.next_out - next_out_utf8;
+          utf8str = strings.buf2string(strm.output, next_out_utf8);
+
+          // move tail
+          strm.next_out = tail;
+          strm.avail_out = chunkSize - tail;
+          if (tail) { utils.arraySet(strm.output, strm.output, next_out_utf8, tail, 0); }
+
+          this.onData(utf8str);
+
+        } else {
+          this.onData(utils.shrinkBuf(strm.output, strm.next_out));
+        }
+      }
+    }
+  } while ((strm.avail_in > 0) && status !== c.Z_STREAM_END);
+
+  if (status === c.Z_STREAM_END) {
+    _mode = c.Z_FINISH;
+  }
+
+  // Finalize on the last chunk.
+  if (_mode === c.Z_FINISH) {
+    status = zlib_inflate.inflateEnd(this.strm);
+    this.onEnd(status);
+    this.ended = true;
+    return status === c.Z_OK;
+  }
+
+  // callback interim results if Z_SYNC_FLUSH.
+  if (_mode === c.Z_SYNC_FLUSH) {
+    this.onEnd(c.Z_OK);
+    strm.avail_out = 0;
+    return true;
+  }
+
+  return true;
+};
+
+
+/**
+ * Inflate#onData(chunk) -> Void
+ * - chunk (Uint8Array|Array|String): ouput data. Type of array depends
+ *   on js engine support. When string output requested, each chunk
+ *   will be string.
+ *
+ * By default, stores data blocks in `chunks[]` property and glue
+ * those in `onEnd`. Override this handler, if you need another behaviour.
+ **/
+Inflate.prototype.onData = function(chunk) {
+  this.chunks.push(chunk);
+};
+
+
+/**
+ * Inflate#onEnd(status) -> Void
+ * - status (Number): inflate status. 0 (Z_OK) on success,
+ *   other if not.
+ *
+ * Called either after you tell inflate that the input stream is
+ * complete (Z_FINISH) or should be flushed (Z_SYNC_FLUSH)
+ * or if an error happened. By default - join collected chunks,
+ * free memory and fill `results` / `err` properties.
+ **/
+Inflate.prototype.onEnd = function(status) {
+  // On success - join
+  if (status === c.Z_OK) {
+    if (this.options.to === 'string') {
+      // Glue & convert here, until we teach pako to send
+      // utf8 alligned strings to onData
+      this.result = this.chunks.join('');
+    } else {
+      this.result = utils.flattenChunks(this.chunks);
+    }
+  }
+  this.chunks = [];
+  this.err = status;
+  this.msg = this.strm.msg;
+};
+
+
+/**
+ * inflate(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * Decompress `data` with inflate/ungzip and `options`. Autodetect
+ * format via wrapper header by default. That's why we don't provide
+ * separate `ungzip` method.
+ *
+ * Supported options are:
+ *
+ * - windowBits
+ *
+ * [http://zlib.net/manual.html#Advanced](http://zlib.net/manual.html#Advanced)
+ * for more information.
+ *
+ * Sugar (options):
+ *
+ * - `raw` (Boolean) - say that we work with raw stream, if you don't wish to specify
+ *   negative windowBits implicitly.
+ * - `to` (String) - if equal to 'string', then result will be converted
+ *   from utf8 to utf16 (javascript) string. When string output requested,
+ *   chunk length can differ from `chunkSize`, depending on content.
+ *
+ *
+ * ##### Example:
+ *
+ * ```javascript
+ * var pako = require('pako')
+ *   , input = pako.deflate([1,2,3,4,5,6,7,8,9])
+ *   , output;
+ *
+ * try {
+ *   output = pako.inflate(input);
+ * } catch (err)
+ *   console.log(err);
+ * }
+ * ```
+ **/
+function inflate(input, options) {
+  var inflator = new Inflate(options);
+
+  inflator.push(input, true);
+
+  // That will never happens, if you don't cheat with options :)
+  if (inflator.err) { throw inflator.msg; }
+
+  return inflator.result;
+}
+
+
+/**
+ * inflateRaw(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * The same as [[inflate]], but creates raw data, without wrapper
+ * (header and adler32 crc).
+ **/
+function inflateRaw(input, options) {
+  options = options || {};
+  options.raw = true;
+  return inflate(input, options);
+}
+
+
+/**
+ * ungzip(data[, options]) -> Uint8Array|Array|String
+ * - data (Uint8Array|Array|String): input data to decompress.
+ * - options (Object): zlib inflate options.
+ *
+ * Just shortcut to [[inflate]], because it autodetects format
+ * by header.content. Done for convenience.
+ **/
+
+
+exports.Inflate = Inflate;
+exports.inflate = inflate;
+exports.inflateRaw = inflateRaw;
+exports.ungzip  = inflate;
+
+},{"./utils/common":1,"./utils/strings":2,"./zlib/constants":4,"./zlib/gzheader":6,"./zlib/inflate.js":8,"./zlib/messages":10,"./zlib/zstream":11}]},{},[])("/lib/inflate.js")
+});
+//This defines the $3Dmol object which is used to create viewers
+//and configure system-wide settings
+
+/** 
+ * All of the functionality of $3Dmol.js is contained within the
+ * $3Dmol global namespace
+ * @namespace */
+$3Dmol = (function(window) {
     
-    geometryGroup.prototype.getNumVertices = function() {
-        return this.vertices;
-    };
+    var my = window['$3Dmol'] || {};
+    //var $ = window['jQuery'];
     
-    geometryGroup.prototype.getVertices = function() {
-        return this.vertexArray;
+    return my;
+
+})(window);
+
+/* The following code "phones home" to register that an ip 
+   address has loaded 3Dmol.js.  Being able track this usage
+   is very helpful when reporting to funding agencies.  Please
+   leave this code in if you would like to increase the 
+   likelihood of 3Dmol.js remaining supported.
+*/
+if('https:' != document.location.protocol) { //not willing to pay for ssl cert
+    $.get("http://3dmol.csb.pitt.edu/track/report.cgi");
+}
+
+/* shims for IE */
+/*
+IE Doesn't have a .startsWith 
+*/
+if (!String.prototype.startsWith) {
+    String.prototype.startsWith = function (str){
+        return this.lastIndexOf(str, 0) === 0;
     };
-    
-    
-    geometryGroup.prototype.getCentroid = function() {
-        
-        var centroid = new $3Dmol.Vector3();
-        var offset, x, y, z;
-        
-        for (var i = 0; i < this.vertices; ++i) {
-            offset = i*3;
-            
-            x = this.vertexArray[offset]; y = this.vertexArray[offset+1]; z = this.vertexArray[offset+2];
-            
-            centroid.x += x; centroid.y += y; centroid.z += z;
-        }
-        
-        //divideScalar checks for 0 denom
-        centroid.divideScalar(this.vertices);
-        
-        return centroid;
+}
+
+// or endsWith
+if (!String.prototype.endsWith) {
+    String.prototype.endsWith = function(suffix) {
+        return this.indexOf(suffix, this.length - suffix.length) !== -1;
     };
+}
     
-    //setup normals - vertex and face array must exist
-    geometryGroup.prototype.setNormals = function() {        
-        
-        var faces = this.faceArray;
-        var verts = this.vertexArray;
-        var norms = this.normalArray;
-        
-        if (! this.vertices || ! this.faceidx) 
-            return;
-        
-        //vertex indices
-        var a, b, c, d,
-        //and actual vertices
-        vA, vB, vC, norm;
-            
-        for (var i = 0; i < faces.length / 3; ++i) {
-            
-            a = faces[i * 3] * 3;
-            b = faces[i * 3 + 1] * 3;
-            c = faces[i * 3 + 2] * 3;
-            
-            vA = new $3Dmol.Vector3(verts[a], verts[a+1], verts[a+2]);
-            vB = new $3Dmol.Vector3(verts[b], verts[b+1], verts[b+2]);
-            vC = new $3Dmol.Vector3(verts[c], verts[c+1], verts[c+2]);
-            
-            vA.subVectors(vA, vB);
-            vC.subVectors(vC, vB);
-            vC.cross(vA);
-            
-            //face normal
-            norm = vC;
-            norm.normalize();
-            
-            norms[a] += norm.x; norms[b] += norm.x; norms[c] += norm.x;
-            norms[a + 1] += norm.y; norms[b + 1] += norm.y; norms[c + 1] += norm.y;
-            norms[a + 2] += norm.z; norms[b + 2] += norm.z; norms[c + 2] += norm.z;
-            
-        }             
-                
-    };
+/**
+ * Create and initialize an appropriate viewer at supplied HTML element using specification in config
+ * @param {Object | string} element - Either HTML element or string identifier
+ * @param {ViewerSpec} config Viewer specification
+ * @return {$3Dmol.GLViewer} GLViewer, null if unable to instantiate WebGL
+ * 
+ * @example
+ * // Assume there exists an HTML div with id "gldiv"
+ * var element = $("#gldiv");
+ * 
+ * // Viewer config - properties 'defaultcolors' and 'callback'
+ * var config = {defaultcolors: $3Dmol.rasmolElementColors };
+ * 
+ * // Create GLViewer within 'gldiv' 
+ * var myviewer = $3Dmol.createViewer(element, config);
+ * //'data' is a string containing molecule data in pdb format  
+ * myviewer.addModel(data, "pdb");
+ * myviewer.zoomTo();
+ * myviewer.render();                        
+ *                        
+ */
+$3Dmol.createViewer = function(element, config)
+{
+    if($.type(element) === "string")
+        element = $("#"+element);
+    if(!element) return;
+
+    config = config || {}; 
+
+    //try to create the  viewer
+    try {
+        return new $3Dmol.GLViewer(element, config);
+    }
+    catch(e) {
+        throw "error creating viewer: "+e;
+    }
     
-    //sets line index array from face arr
-    //Note - assumes all faces are triangles (i.e. there will
-    //be an extra diagonal for four-sided faces - user should 
-    //specify linearr for custom shape generation to show wireframe squares
-    //as rectangles rather than two triangles)
-    geometryGroup.prototype.setLineIndices = function() {
-        
-        if (! this.faceidx)
-            return;
-                    
-        var faceArr = this.faceArray, lineArr = this.lineArray = new Uint16Array(this.faceidx*2);      
-        this.lineidx = this.faceidx*2;         
-        var faceoffset;
-            
-        for (var i = 0; i < this.faceidx / 3; ++i) {
-            
-            faceoffset = i*3; lineoffset = faceoffset*2;          
-            var a = faceArr[faceoffset], b = faceArr[faceoffset+1], c = faceArr[faceoffset+2];
-            
-            lineArr[lineoffset] = a; lineArr[lineoffset+1] = b;
-            lineArr[lineoffset+2] = a; lineArr[lineoffset+3] = c;
-            lineArr[lineoffset+4] = b; lineArr[lineoffset+5] = c;
-            
-        }
-    };
-    
-    geometryGroup.prototype.truncateArrayBuffers = function(mesh, reallocatemem) {
-        
-        mesh = (mesh === true) ? true : false;
-        
-        var vertexArr = this.vertexArray,
-            colorArr = this.colorArray,
-            normalArr = this.normalArray,
-            faceArr = this.faceArray,
-            lineArr = this.lineArray;
+    return null;
+};
+   
+/**
+ * Contains a dictionary of embedded viewers created from HTML elements
+ * with a the viewer_3Dmoljs css class indexed by their id (or numerically
+ * if they do not have an id).
+*/
+$3Dmol.viewers = {};
 
-        //subarray to avoid copying and reallocating memory
-        this.vertexArray = vertexArr.subarray(0,this.vertices*3);
-        this.colorArray = colorArr.subarray(0,this.vertices*3);
-        
-        if (mesh) {
-            this.normalArray = normalArr.subarray(0,this.vertices*3);
-            this.faceArray = faceArr.subarray(0,this.faceidx); 
+/**
+ * Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model
+ * 
+ * @function $3Dmol.download
+ * @param {string} query - String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively
+ * @param {$3Dmol.GLViewer} viewer - Add new model to existing viewer
+ * @param {Object} options - Specify additional options
+ *                           format: file format to download, if multiple are available, default format is pdb
+ *                           pdbUri: URI to retrieve PDB files, default URI is http://www.rcsb.org/pdb/files/
+ * @param {Function} callback - Function to call with model as argument after data is loaded.
 
-            if(this.lineidx > 0) //not always set so reclaim memory
-                this.lineArray = lineArr.subarray(0,this.lineidx); 
-            else
-                this.lineArray = new Uint16Array();
-        }
-        else {
-            this.normalArray = new Float32Array(); 
-            this.faceArray = new Uint16Array(); 
-            this.lineArray = new Uint16Array(); 
-        }
-        
-        if(reallocatemem) { 
-            //actually copy smaller arrays to save memory
-            if(this.normalArray) this.normalArray = new Float32Array(this.normalArray);
-            if(this.faceArray) this.faceArray = new Uint16Array(this.faceArray);
-            if(this.lineArray) this.lineArray = new Uint16Array(this.lineArray);
-            if(this.vertexArray) this.vertexArray = new Float32Array(this.vertexArray);
-            if(this.colorArray) this.colorArray = new Float32Array(this.colorArray);
-            
+ * @example
+ * var myviewer = $3Dmol.createViewer(gldiv);
+ * 
+ * // GLModel 'm' created and loaded into glviewer for PDB id 2POR
+ * // Note that m will not contain the atomic data until after the network request is completed
+ * var m = $3Dmol.download('pdb: 2POR', myviewer, {format:'cif'});
+ * 
+ * @return {$3Dmol.GLModel} GLModel
+ */ 
+$3Dmol.download = function(query, viewer, options, callback) {
+    var baseURL = '';
+    var type = "";
+    var pdbUri = "";
+    var m = viewer.addModel();
+    if (query.substr(0, 4) === 'pdb:') {
+        pdbUri = options && options.pdbUri ? options.pdbUri : "http://www.rcsb.org/pdb/files/";
+        type = options && options.format ? options.format : "pdb";
+        query = query.substr(4).toUpperCase();
+        if (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) {
+           alert("Wrong PDB ID"); return;
         }
-        this.__inittedArrays = true;        
-        
-    };
-    
-    var addGroup = function(geo) {
-        var ret = new geometryGroup(geo.geometryGroups.length);
-        geo.geometryGroups.push(ret);
-        geo.groups = geo.geometryGroups.length;
-        
-        ret.vertexArray = new Float32Array(BUFFERSIZE*3);
-        ret.colorArray = new Float32Array(BUFFERSIZE*3);
-        
-        //TODO: instantiating uint arrays according to max number of vertices
-        // is dangerous, since there exists the possibility that there will be 
-        // more face or line indices than vertex points - but so far that doesn't
-        // seem to be the case for any of the renders 
-        if (geo.mesh) {
-            ret.normalArray = new Float32Array(BUFFERSIZE*3);
-            ret.faceArray = new Uint16Array(BUFFERSIZE*6);
-            ret.lineArray = new Uint16Array(BUFFERSIZE*6);
+        if (options && options.format)
+            uri = pdbUri + query + "." + options.format;
+        else
+            uri = pdbUri + query + ".pdb";
+
+    } else if (query.substr(0, 4) == 'cid:') {
+        type = "sdf";
+        query = query.substr(4);
+        if (!query.match(/^[0-9]+$/)) {
+           alert("Wrong Compound ID"); return;
         }
-        
-        
-        return ret;
-    };
-    /** @constructor */
-    var Geometry = function(mesh) {
-        
-        $3Dmol.EventDispatcher.call(this);
-        
-        this.id = $3Dmol.GeometryIDCount++;
-    
-        this.name = '';
-    
-        this.hasTangents = false;
+        uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query + 
+          "/SDF?record_type=3d";
+    }
+
+   $.get(uri, function(ret) {
+      m.addMolData(ret, type, options);
+      viewer.zoomTo();
+      viewer.render();
+      if(callback) callback(m);
+
+   });
+   
+   return m;
+};
+       
+
+/**
+ * $3Dmol surface types
+ * @enum {number}
+ */
+$3Dmol.SurfaceType = {
+    VDW : 1,
+    MS : 2,
+    SAS : 3,
+    SES  : 4
+};
+
+
+//Miscellaneous functions and classes - to be incorporated into $3Dmol proper
+/**
+ * 
+ * @param {$3Dmol.Geometry} geometry
+ * @param {$3Dmol.Mesh} mesh
+ * @returns {undefined}
+ */
+$3Dmol.mergeGeos = function(geometry, mesh) {
     
-        this.dynamic = true; // the intermediate typed arrays will be deleted when set to false
-        this.mesh = (mesh === true) ? true : false; // Does this geometry represent a mesh (i.e. do we need Face/Line index buffers?)
-        // update flags
+    var meshGeo = mesh.geometry;
     
-        this.verticesNeedUpdate = false;
-        this.elementsNeedUpdate = false;
-        this.normalsNeedUpdate = false;
-        this.colorsNeedUpdate = false;
+    if (meshGeo === undefined) 
+        return;
     
-        this.buffersNeedUpdate = false;
-        
-        this.geometryGroups = [];
-        this.groups = 0;
-        
-    };
+    geometry.geometryGroups.push( meshGeo.geometryGroups[0] );
     
-    Geometry.prototype = {
-        
-        constructor : Geometry,
+};
 
-        //Get geometry group to accomodate addVertices new vertices - create 
-        // new group if necessary       
-        updateGeoGroup : function(addVertices) {
-        
-            addVertices = addVertices || 0;
-            
-            var retGroup = this.groups > 0 ? this.geometryGroups[ this.groups - 1 ] : null;
-            
-            if (!retGroup || retGroup.vertices + addVertices > BUFFERSIZE) 
-                retGroup = addGroup(this);
-                
-            return retGroup;
-            
-        },
-        
-        addGeoGroup : function() {
-            return addGroup(this);  
-        },
-        
-        setUpNormals : function(three) {
-            
-            three = three || false;
-            
-            for (var g = 0; g < this.groups; g++) {
-            
-                var geoGroup = this.geometryGroups[g];            
-                
-                geoGroup.setNormals(three);
-                
-            }  
-                      
-        },
-        
-        setUpWireframe : function() {
-            for (var g = 0; g < this.groups; g++) {
-                var geoGroup = this.geometryGroups[g];
-                
-                geoGroup.setLineIndices();
-            }
-        },
-        
-        //After vertices, colors, etc are collected in regular or typed arrays,
-        //  create typed arrays from regular arrays if they don't already exist,
-        initTypedArrays : function() {
-                
-            for (var g = 0; g < this.groups; g++) {
-                
-                var group = this.geometryGroups[g];
-                
-                if (group.__inittedArrays === true)
-                    continue;
-                
-                //do not actually reallocate smaller memory here because
-                //of the performance hit - if you know your geometry is small,
-                //truncate manually with the second parameter true
-                group.truncateArrayBuffers(this.mesh, false);
-            }
+$3Dmol.multiLineString = function(f) {
+    return f.toString()
+            .replace(/^[^\/]+\/\*!?/, '')
+            .replace(/\*\/[^\/]+$/, '');
             
-        
-        },
-        
-        dispose : function() {
-            this.dispatchEvent( {type : 'dispose'} );
-        }
-    };
+};
 
-    
-    return Geometry;
-    
-})();
+/** 
+ * Render surface synchronously if true
+ * @param {boolean} [$3Dmol.SyncSurface=false]
+ * @type {boolean} */
+$3Dmol.syncSurface = false;
 
-Object.defineProperty($3Dmol.Geometry.prototype, "vertices", {
-    
-    /** @this {$3Dmol.Geometry} */
-    get : function() {
-        var vertices = 0;
-        for (var g = 0; g < this.groups; g++)
-            vertices += this.geometryGroups[g].vertices;
-            
-        return vertices;
-    } 
-        
-});
+// Internet Explorer refuses to allow webworkers in data blobs.  I can find
+// no way of checking for this feature directly, so must do a brower check
+if(window.navigator.userAgent.indexOf('MSIE ') >= 0 ||
+        window.navigator.userAgent.indexOf('Trident/') >= 0) {
+    $3Dmol.syncSurface = true; // can't use webworkers
+}
 
-$3Dmol.GeometryIDCount = 0;
+/**
+ * Parse a string that represents a style or atom selection and convert it
+ * into an object.  The goal is to make it easier to write out these specifications
+ * without resorting to json. Objects cannot be defined recursively.
+ * ; - delineates fields of the object 
+ * : - if the field has a value other than an empty object, it comes after a colon
+ * , - delineates key/value pairs of a value object
+ *     If the value object consists of ONLY keys (no = present) the keys are 
+ *     converted to a list.  Otherwise a object of key/value pairs is created with
+ *     any missing values set to null
+ * = OR ~ - separates key/value pairs of a value object, if not provided value is null
+ *     twiddle is supported since = has special meaning in URLs
+ * @param (String) str
+ * @returns {Object}
+ */
+$3Dmol.specStringToObject = function(str) {
+    if(typeof(str) === "object") {
+        return str; //not string, assume was converted already
+    }
+    else if(typeof(str) === "undefined" || str == null) {
+        return str; 
+    }
+    
+    str = str.replace(/%7E/,'~'); //copy/pasting urls sometimes does this
+    //convert things that look like numbers into numbers
+    var massage = function(val) {
+        if($.isNumeric(val)) {
+           //hexadecimal does not parse as float
+           if(Math.floor(parseFloat(val)) == parseInt(val)) {
+              return parseFloat(val);
+           }
+           else if(val.indexOf('.') >= 0) {
+               return parseFloat(val); // ".7" for example, does not parseInt
+           }
+           else {
+               return parseInt(val);
+           }
+        }
+        //boolean conversions
+        else if(val === 'true') {
+            return true;
+        }
+        else if(val === 'false') {
+            return false;
+        }
+        return val;
+    }
+    
+    var ret = {};
+    var fields = str.split(';');
+    for(var i = 0; i < fields.length; i++) {
+        var fv = fields[i].split(':');
+        var f = fv[0];
+        var val = {};
+        var vstr = fv[1];
+        if(vstr) {
+            vstr = vstr.replace(/~/g,"=");
+            if(vstr.indexOf('=') !== -1) {
+                //has key=value pairs, must be object
+                var kvs = vstr.split(',');
+                for(var j = 0; j < kvs.length; j++) {
+                    var kv = kvs[j].split('=',2);
+                    val[kv[0]] = massage(kv[1]);
+                }
+            }
+            else if(vstr.indexOf(',') !== -1) {
+                //has multiple values, must list
+                val = vstr.split(',');
+            }
+            else {
+                val = massage(vstr); //value itself
+            }
+        }
+        ret[f] = val;
+    }
+
+return ret;
+}
 
 
-//Raycaster
-/** @constructor */
-$3Dmol.Raycaster = (function() {
+/**
+ * computes the bounding box around the provided atoms
+ * @param {AtomSpec[]} atomlist
+ * @return {Array}
+ */
+$3Dmol.getExtent = function(atomlist, ignoreSymmetries) {
+    var xmin, ymin, zmin, xmax, ymax, zmax, xsum, ysum, zsum, cnt;
+    var includeSym = !ignoreSymmetries;
+
+    xmin = ymin = zmin = 9999;
+    xmax = ymax = zmax = -9999;
+    xsum = ysum = zsum = cnt = 0;
     
-    var Raycaster = function(origin, direction, far, near) {
+    if (atomlist.length === 0)
+        return [ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ];
+    for (var i = 0; i < atomlist.length; i++) {
+        var atom = atomlist[i];
+        if (typeof atom === 'undefined' || !isFinite(atom.x) ||
+                !isFinite(atom.y) || !isFinite(atom.z))
+            continue;
+        cnt++;
+        xsum += atom.x;
+        ysum += atom.y;
+        zsum += atom.z;
         
-        this.ray = new $3Dmol.Ray(origin, direction);
+        xmin = (xmin < atom.x) ? xmin : atom.x;
+        ymin = (ymin < atom.y) ? ymin : atom.y;
+        zmin = (zmin < atom.z) ? zmin : atom.z;
+        xmax = (xmax > atom.x) ? xmax : atom.x;
+        ymax = (ymax > atom.y) ? ymax : atom.y;
+        zmax = (zmax > atom.z) ? zmax : atom.z;
         
-        if (this.ray.direction.lengthSq() > 0) 
-            this.ray.direction.normalize();
+        if (atom.symmetries && includeSym) {
+            for (var n = 0; n < atom.symmetries.length; n++) {
+                cnt++;
+                xsum += atom.symmetries[n].x;
+                ysum += atom.symmetries[n].y;
+                zsum += atom.symmetries[n].z;
+                xmin = (xmin < atom.symmetries[n].x) ? xmin : atom.symmetries[n].x;
+                ymin = (ymin < atom.symmetries[n].y) ? ymin : atom.symmetries[n].y;
+                zmin = (zmin < atom.symmetries[n].z) ? zmin : atom.symmetries[n].z;
+                xmax = (xmax > atom.symmetries[n].x) ? xmax : atom.symmetries[n].x;
+                ymax = (ymax > atom.symmetries[n].y) ? ymax : atom.symmetries[n].y;
+                zmax = (zmax > atom.symmetries[n].z) ? zmax : atom.symmetries[n].z; 
+            }
+        }  
+    }
+
+    return [ [ xmin, ymin, zmin ], [ xmax, ymax, zmax ],
+            [ xsum / cnt, ysum / cnt, zsum / cnt ] ];
+};
+
+
+//return the value of an atom property prop, or null if non existent
+//looks first in properties, then in the atom itself
+$3Dmol.getAtomProperty = function(atom, prop) {
+    var val = null;
+    if (atom.properties
+            && typeof (atom.properties[prop]) != "undefined") {
+        val = atom.properties[prop];
+    } else if(typeof(atom[prop]) != 'undefined') {
+        val = atom[prop];
+    }
+    return val;
+};
+
+/* get the min and max values of the specified property in the provided
+* @function $3Dmol.getPropertyRange
+* @param {AtomSpec[]} atomlist - list of atoms to evaluate
+* @param {string} prop - name of property 
+* @return {Array} - [min, max] values
+*/
+$3Dmol.getPropertyRange = function (atomlist, prop) {
+    var min = Number.POSITIVE_INFINITY;
+    var max = Number.NEGATIVE_INFINITY;
+
+    for (var i = 0, n = atomlist.length; i < n; i++) {
+        var atom = atomlist[i];
+        var val = $3Dmol.getAtomProperty(atom, prop);
         
-        this.near = near || 0;
-        this.far = far || Infinity;
-    
-    };
+        if(val != null) {
+            if (val < min)
+                min = val;
+            if (val > max)
+                max = val;                
+        }
+    }
+
+    if (!isFinite(min) && !isFinite(max))
+        min = max = 0;
+    else if (!isFinite(min))
+        min = max;
+    else if (!isFinite(max))
+        max = min;
+
+    return [ min, max ];
+}
+
+/*
+* math-like functionality
+* quaternion, vector, matrix
+*/
+
+var $3Dmol = $3Dmol || {};
+$3Dmol.Math = {
+
+    clamp : function(x, min, max) {
+        return Math.min( Math.max( x, min ), max );
+    },
+
+    degToRad : function() {
+       var degreeToRadiansFactor = Math.PI / 180;
+       
+       return function(deg) {
+           return deg * degreeToRadiansFactor;
+       };
     
-    var sphere = new $3Dmol.Sphere();
-    var cylinder = new $3Dmol.Cylinder();
-    var triangle = new $3Dmol.Triangle();
-    var w_0 = new $3Dmol.Vector3(); // for cylinders, cylinder.c1 - ray.origin
-    var v1 = new $3Dmol.Vector3(); // all purpose local vector
-    var v2 = new $3Dmol.Vector3();
-    var v3 = new $3Dmol.Vector3();
-    //var facePlane = new $3Dmol.Plane();
-    var localRay = new $3Dmol.Ray();
-    var intersectPoint = new $3Dmol.Vector3();
-    var matrixPosition = new $3Dmol.Vector3();
+    }()
     
-    var inverseMatrix = new $3Dmol.Matrix4();
+};
+
+
+// Quaternion
+/** @constructor */
+$3Dmol.Quaternion = function(x, y, z, w) {
+
+    this.x = x || 0;
+    this.y = y || 0;
+    this.z = z || 0;
+    this.w = (w !== undefined) ? w : 1;
+
+};
+
+$3Dmol.Quaternion.prototype = {
+
+    constructor : $3Dmol.Quaternion,
+
+    set : function(x, y, z, w) {
         
-    var descSort = function(a, b) {
-        return a.distance - b.distance;
-    };
+        this.x = x;
+        this.y = y;
+        this.z = z;
+        this.w = w;
 
-    // [-1, 1]
-    var clamp = function(x) {
-        return Math.min(Math.max(x, -1), 1);
-    };
-    
-    //object is a Sphere or (Bounding) Box
-    var intersectObject = function(group, clickable, raycaster, intersects) {
+        return this;
+    },
+
+    copy : function(q) {
         
-        matrixPosition.getPositionFromMatrix(group.matrixWorld);
+        this.x = q.x;
+        this.y = q.y;
+        this.z = q.z;
+        this.w = q.w;
+
+        return this;
+    },
+
+    conjugate : function() {
         
-        if ((clickable.clickable !== true) || (clickable.intersectionShape === undefined))
-            return intersects;
+        this.x *= -1;
+        this.y *= -1;
+        this.z *= -1;
+
+        return this;
+    },
+
+    inverse : function() {
         
-        var intersectionShape = clickable.intersectionShape;
-        var precision = raycaster.linePrecision;
-        precision *= group.matrixWorld.getMaxScaleOnAxis();
-        var precisionSq = precision*precision;
+        return this.conjugate().normalize();
+    },
 
-        //Check for intersection with clickable's bounding sphere, if it exists
-        if (clickable.boundingSphere !== undefined && clickable.boundingSphere instanceof $3Dmol.Sphere) {
-            sphere.copy(clickable.boundingSphere);
-            sphere.applyMatrix4(group.matrixWorld);
-            
-            if (!raycaster.ray.isIntersectionSphere(sphere)) {
-                return intersects;
-            }
-        }
+    length : function() {
         
-        //Iterate through intersection objects
-        var i, il,
-            norm, normProj, cylProj, rayProj,
-            distance, closestDistSq, denom, discriminant,
-            s, t, s_c, t_c;
-        //triangle faces
-        for (i = 0, il = intersectionShape.triangle.length; i < il; i++) {
-            
-            if (intersectionShape.triangle[i] instanceof $3Dmol.Triangle) {
-                
-                triangle.copy(intersectionShape.triangle[i]);
-                triangle.applyMatrix4(group.matrixWorld);
-                
-                norm = triangle.getNormal();
-                
-                normProj = raycaster.ray.direction.dot(norm);
-                
-                //face culling
-                if (normProj >= 0)
-                    continue;
-                
-                w_0.subVectors(triangle.a, raycaster.ray.origin);
-                
-                distance = (norm.dot(w_0)) / normProj;
-                
-                if (distance < 0)
-                    continue;
-                    
-                //intersects with plane, check if P inside triangle
-                v1.copy(raycaster.ray.direction).multiplyScalar(distance).add(raycaster.ray.origin);
-                v1.sub(triangle.a); // from pt a to intersection point P
-                
-                v2.copy(triangle.b).sub(triangle.a); // from pt a to b
-                v3.copy(triangle.c).sub(triangle.a); // from pt a to c
-                var b_dot_c = v2.dot(v3);
-                var b_sq = v2.lengthSq();
-                var c_sq = v3.lengthSq();
-                
-                // P = A + s(v2) + t(v3), inside trianle if 0 <= s, t <=1  and (s + t) <=0
-                
-                t = ( b_sq*v1.dot(v3) - b_dot_c*v1.dot(v2) ) / ( b_sq*c_sq - b_dot_c*b_dot_c );
-                
-                if (t < 0 || t > 1)
-                    continue;
-                
-                s = ( v1.dot(v2) - t*b_dot_c ) / b_sq;
-                
-                if ( (s < 0 || s > 1) || s + t > 1)
-                    continue;
-                    
-                else
-                    intersects.push({clickable : clickable,
-                                     distance : distance});  
-            }
-        }
-        
-        //cylinders
-        for (i = 0, il = intersectionShape.cylinder.length; i < il; i++) {
-            
-            if (intersectionShape.cylinder[i] instanceof $3Dmol.Cylinder){
-                
-                cylinder.copy(intersectionShape.cylinder[i]);
-                cylinder.applyMatrix4(group.matrixWorld);
-                
-                w_0.subVectors(cylinder.c1, raycaster.ray.origin); 
-                
-                cylProj = w_0.dot(cylinder.direction); // Dela
-                rayProj = w_0.dot(raycaster.ray.direction); // Epsilon
-                
-                normProj = clamp(raycaster.ray.direction.dot(cylinder.direction)); // Beta
-                
-                denom = 1 - normProj*normProj;
-                
-                if (denom === 0.0)
-                    continue;
-                
-                s_c = (normProj*rayProj - cylProj) / denom;
-                t_c = (rayProj - normProj*cylProj) / denom;
-                
-                v1.copy(cylinder.direction).multiplyScalar(s_c).add(cylinder.c1);  // Q_c
-                v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
-                
-                closestDistSq = v3.subVectors(v1, v2).lengthSq();
-                var radiusSq = cylinder.radius*cylinder.radius;
-                
-                //Smoothing?
-                //if (closestDistSq > radiusSq) radiusSq += precisionSq;
-                
-                // closest distance between ray and cylinder axis not greater than cylinder radius;
-                // might intersect this cylinder between atom and bond midpoint
-                if (closestDistSq <= radiusSq){
-
-                    //Find points where ray intersects sides of cylinder
-                    discriminant = (normProj*cylProj - rayProj)*(normProj*cylProj - rayProj) - 
-                            denom*(w_0.lengthSq() - cylProj*cylProj - radiusSq);
-                    
-                    // ray tangent to cylinder?
-                    if (discriminant <= 0)
-                        t = distance = Math.sqrt(closestDistSq);
-                    else
-                        t = distance = ( (rayProj - normProj*cylProj) - Math.sqrt(discriminant) ) / denom; 
-                    
-                    //find closest intersection point; make sure it's between atom's position and cylinder midpoint
-                    
-                    s = normProj*t - cylProj;
-                    
-                    //does not intersect cylinder between atom and midpoint,
-                    // or intersects cylinder behind camera
-                    if (s < 0 || s*s > cylinder.lengthSq() || t < 0)
-                        continue;
-                    
-                    else
-                        intersects.push({clickable : clickable,
-                                         distance : distance});
-                    
-                }
-                    
-                
-            }
-            
-        }
-         
-        //lines
-        for (i = 0, il = intersectionShape.line.length; i < il; i += 2) {
-            
-            v1.copy(intersectionShape.line[i]);
-            v1.applyMatrix4(group.matrixWorld);
-            v2.copy(intersectionShape.line[i+1]);
-            v2.applyMatrix4(group.matrixWorld);
-            
-            v3.subVectors(v2, v1);
-            var bondLengthSq = v3.lengthSq();
-            v3.normalize();
-            
-            w_0.subVectors(v1, raycaster.ray.origin);
-            
-            lineProj = w_0.dot(v3);
-            rayProj = w_0.dot(raycaster.ray.direction);
-            
-            normProj = clamp(raycaster.ray.direction.dot(v3));
-            
-            denom = 1 - normProj*normProj;
-            
-            if (denom === 0.0)
-                continue;
-            
-            s_c = (normProj*rayProj - lineProj) / denom;
-            t_c = (rayProj - normProj*lineProj) / denom;
-            
-            v1.add(v3.multiplyScalar(s_c)); // Q_c
-            v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
-            
-            closestDistSq = v3.subVectors(v2, v1).lengthSq();
-            
-            if (closestDistSq < precisionSq && s_c*s_c < bondLengthSq)
-                intersects.push({clickable : clickable,
-                                 distance : t_c
-                                });
-            
-        }
+        return Math.sqrt(this.x * this.x + this.y * this.y + this.z * this.z + this.w * this.w);
+    },
 
-        for (i = 0, il = intersectionShape.sphere.length; i < il; i++) {
-            //sphere
-            if (intersectionShape.sphere[i] instanceof $3Dmol.Sphere) {
-                
-                sphere.copy(intersectionShape.sphere[i]);
-                sphere.applyMatrix4(group.matrixWorld);
-                
-                if (raycaster.ray.isIntersectionSphere(sphere)) {
-                    
-                    v1.subVectors(sphere.center, raycaster.ray.origin);
-                    
-                    //distance from ray origin to point on the ray normal to sphere's center
-                    //must be less than sphere's radius (since ray intersects sphere)
-                    var distanceToCenter = v1.dot(raycaster.ray.direction);
-                    
-                    discriminant = distanceToCenter*distanceToCenter - (v1.lengthSq() - sphere.radius*sphere.radius);
-                    
-                    //Don't select if sphere center behind camera
-                    if (distanceToCenter < 0) 
-                        return intersects;
-                    
-                    //ray tangent to sphere?
-                    if (discriminant <= 0)
-                        distance = distanceToCenter;
-                    
-                    //This is reversed if sphere is closer than ray origin.  Do we have 
-                    //to worry about handling that case?
-                    else 
-                        distance = distanceToCenter - Math.sqrt(discriminant);
-    
-                    intersects.push({clickable : clickable, 
-                                     distance : distance});
-                    return intersects;
-                }
-            }        
-       }
-        
-    };   
-       
-    Raycaster.prototype.precision = 0.0001;
-    Raycaster.prototype.linePrecision = 0.2;
-    
-    Raycaster.prototype.set = function(origin, direction) {
-        
-        this.ray.set(origin, direction);
-          
-    };
-    
-    Raycaster.prototype.intersectObjects = function(group, objects) {
-        
-        var intersects = [];
-        
-        for (var i = 0, l = objects.length; i < l; i++)            
-            intersectObject(group, objects[i], this, intersects);
-            
-        intersects.sort(descSort);
-        
-        return intersects;
+    normalize : function() {
         
-    };
-    
-    return Raycaster;
-    
-})();
+        var l = this.length();
 
+        if (l === 0) {
+            this.x = 0;
+            this.y = 0;
+            this.z = 0;
+            this.w = 1;
+        } else {
+            l = 1 / l;
 
-//$3Dmol Projecion 
-//TODO: can probably strip this down a lot (only used for selection handling)
-/** @constructor */
-$3Dmol.Projector = function () {
+            this.x *= l;
+            this.y *= l;
+            this.z *= l;
+            this.w *= l;
+        }
 
-    var _viewMatrix = new $3Dmol.Matrix4(),
-    _viewProjectionMatrix = new $3Dmol.Matrix4();
+        return this;
 
-    this.projectVector = function ( vector, camera ) {
+    },
 
-        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
+    multiply : function(q) {
+        
+        return this.multiplyQuaternions(this, q);
+    },
 
-        _viewProjectionMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
+    multiplyQuaternions : function(a, b) {
 
-        return vector.applyProjection( _viewProjectionMatrix );
+        var qax = a.x, qay = a.y, qaz = a.z, qaw = a.w;
+        var qbx = b.x, qby = b.y, qbz = b.z, qbw = b.w;
 
-    };
+        this.x = qax * qbw + qaw * qbx + qay * qbz - qaz * qby;
+        this.y = qay * qbw + qaw * qby + qaz * qbx - qax * qbz;
+        this.z = qaz * qbw + qaw * qbz + qax * qby - qay * qbx;
+        this.w = qaw * qbw - qax * qbx - qay * qby - qaz * qbz;
 
-    this.unprojectVector = function ( vector, camera ) {
+    }
+};
 
-        camera.projectionMatrixInverse.getInverse(camera.projectionMatrix);
+//A 2 Vector
+/** @constructor */
+$3Dmol.Vector2 = function(x, y) {
+    
+    this.x = x || 0.0;
+    this.y = y || 0.0;
+};
 
-        _viewProjectionMatrix.multiplyMatrices(camera.matrixWorld, camera.projectionMatrixInverse);
-
-        return vector.applyProjection( _viewProjectionMatrix );
+$3Dmol.Vector2.prototype = {
+    
+    constructor : $3Dmol.Vector2,
+   
+    set : function(x, y) {
+       
+        this.x = x;
+        this.y = y;
+       
+        return this;
+    },
+    
+    subVectors : function(a, b) {
+        
+      this.x = a.x - b.x;
+      this.y = a.y - b.y;
+      
+      return this;
+    },
+   
+    copy : function(v) {
+       
+        this.x = v.x;
+        this.y = v.y;
+       
+        return this;
+    },
+   
+    clone : function() {
+        
+        return new $3Dmol.Vector2(this.x, this.y);
+    }    
+   
+};
 
-    };
+//A 3 Vector
 
+$3Dmol.Vector3 = function(x, y, z) {
+    this.x = x || 0.0;
+    this.y = y || 0.0;
+    this.z = z || 0.0;
 };
-/*
- * Simplified Perspective Camera
- */
-
-/** @constructor */
-$3Dmol.Camera = function(fov, aspect, near, far) {
+/** @this {$3Dmol.Vector3} */
+$3Dmol.Vector3.prototype =  {
     
-    $3Dmol.Object3D.call(this);
+    constructor : $3Dmol.Vector3,
     
-    this.fov = fov !== undefined ? fov : 50;
-    this.aspect = aspect !== undefined ? aspect : 1;
-    this.near = near !== undefined ? near : 0.1;
-    this.far = far !== undefined ? far : 2000;
-
-    this.projectionMatrix = new $3Dmol.Matrix4();
-    this.projectionMatrixInverse = new $3Dmol.Matrix4();
-    this.matrixWorldInverse = new $3Dmol.Matrix4();
+    set : function(x, y, z) {
+        
+        this.x = x;
+        this.y = y;
+        this.z = z;
+        
+        return this;
+    },
     
-    this.updateProjectionMatrix();
+    copy : function(v) {
         
-};
-
-//Inherit Object3D's prototyped methods
-$3Dmol.Camera.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Camera.prototype.lookAt = function(vector){
+        this.x = v.x;
+        this.y = v.y;
+        this.z = v.z;
+        
+        return this;  
+    },
     
-    //Why is the parameter order switched (compared to Object3D)?
-    this.matrix.lookAt(this.position, vector, this.up);
+    add : function(v) {
+        
+        this.x += v.x;
+        this.y += v.y;
+        this.z += v.z;  
+        
+        return this;
+    },
     
-    if (this.rotationAutoUpdate) {    
+    addVectors : function(a, b) {
         
-        if (this.useQuaternion === false) 
-            this.rotation.setEulerFromRotationMatrix( this.matrix, this.eulerOrder );
-        else
-            this.quaternion.copy( this.matrix.decompose()[ 1 ] );    
-            
-    }
+        this.x = a.x + b.x;
+        this.y = a.y + b.y;
+        this.z = a.z + b.z;
+        
+        return this;
+    },
     
-};
-
-$3Dmol.Camera.prototype.updateProjectionMatrix = function () {
-
-    this.projectionMatrix.makePerspective( this.fov, this.aspect, this.near, this.far );
-
-};
-
-
-//Render plugins go here
-
-/**
- * Sprite render plugin
- * @this {$3Dmol.SpritePlugin}
- */
-
-$3Dmol.SpritePlugin = function () {
-
-    var _gl, _renderer, _precision, _sprite = {};
-
-    this.init = function ( renderer ) {
-
-        _gl = renderer.context;
-        _renderer = renderer;
-
-        _precision = renderer.getPrecision();
-
-        _sprite.vertices = new Float32Array( 8 + 8 );
-        _sprite.faces    = new Uint16Array( 6 );
-
-        var i = 0;
-
-        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = -1; // vertex 0
-        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 0;  // uv 0
-
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = -1; // vertex 1
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 0;  // uv 1
-
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // vertex 2
-        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // uv 2
-
-        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = 1;  // vertex 3
-        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 1;  // uv 3
-
-        i = 0;
-
-        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 1; _sprite.faces[ i++ ] = 2;
-        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 2; _sprite.faces[ i++ ] = 3;
-
-        _sprite.vertexBuffer  = _gl.createBuffer();
-        _sprite.elementBuffer = _gl.createBuffer();
-
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, _sprite.vertices, _gl.STATIC_DRAW );
-
-        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
-        _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, _sprite.faces, _gl.STATIC_DRAW );
-
-        _sprite.program = createProgram( $3Dmol.ShaderLib.sprite, _precision );
-
-        _sprite.attributes = {};
-        _sprite.uniforms = {};
-
-        _sprite.attributes.position           = _gl.getAttribLocation ( _sprite.program, "position" );
-        _sprite.attributes.uv                 = _gl.getAttribLocation ( _sprite.program, "uv" );
-
-        _sprite.uniforms.uvOffset             = _gl.getUniformLocation( _sprite.program, "uvOffset" );
-        _sprite.uniforms.uvScale              = _gl.getUniformLocation( _sprite.program, "uvScale" );
-
-        _sprite.uniforms.rotation             = _gl.getUniformLocation( _sprite.program, "rotation" );
-        _sprite.uniforms.scale                = _gl.getUniformLocation( _sprite.program, "scale" );
-        _sprite.uniforms.alignment            = _gl.getUniformLocation( _sprite.program, "alignment" );
-
-        _sprite.uniforms.color                = _gl.getUniformLocation( _sprite.program, "color" );
-        _sprite.uniforms.map                  = _gl.getUniformLocation( _sprite.program, "map" );
-        _sprite.uniforms.opacity              = _gl.getUniformLocation( _sprite.program, "opacity" );
-
-        _sprite.uniforms.useScreenCoordinates = _gl.getUniformLocation( _sprite.program, "useScreenCoordinates" );
-        _sprite.uniforms.screenPosition       = _gl.getUniformLocation( _sprite.program, "screenPosition" );
-        _sprite.uniforms.modelViewMatrix      = _gl.getUniformLocation( _sprite.program, "modelViewMatrix" );
-        _sprite.uniforms.projectionMatrix     = _gl.getUniformLocation( _sprite.program, "projectionMatrix" );
-
-        _sprite.uniforms.fogType              = _gl.getUniformLocation( _sprite.program, "fogType" );
-        _sprite.uniforms.fogDensity           = _gl.getUniformLocation( _sprite.program, "fogDensity" );
-        _sprite.uniforms.fogNear              = _gl.getUniformLocation( _sprite.program, "fogNear" );
-        _sprite.uniforms.fogFar               = _gl.getUniformLocation( _sprite.program, "fogFar" );
-        _sprite.uniforms.fogColor             = _gl.getUniformLocation( _sprite.program, "fogColor" );
-
-        _sprite.uniforms.alphaTest            = _gl.getUniformLocation( _sprite.program, "alphaTest" );
+    sub : function(v) {
+        
+        this.x -= v.x;
+        this.y -= v.y;
+        this.z -= v.z;
+        
+        return this;
+    },
+    
+    subVectors : function(a, b) {
+        
+        this.x = a.x - b.x;
+        this.y = a.y - b.y;
+        this.z = a.z - b.z;
+        
+        return this;
+    },
+    
+    multiplyScalar : function(s) {
+        
+        this.x *= s;
+        this.y *= s;
+        this.z *= s;
+        
+        return this;
+    },
+    
+    divideScalar : function(s) {
+        
+        if (s !== 0) {
+            this.x /= s;
+            this.y /= s;
+            this.z /= s;
+        }
+        
+        else {
+            this.x = 0;
+            this.y = 0;
+            this.z = 0;
+        }
+        
+        return this;
+    },
+    
+    //accumulate maximum
+    max : function(s) {
+        
+        this.x = Math.max(this.x,s.x);
+        this.y = Math.max(this.y,s.y);
+        this.z = Math.max(this.z,s.z);
+        
+        return this;
+    },
+    
+    //accumulate min
+    min : function(s) {
+        
+        this.x = Math.min(this.x,s.x);
+        this.y = Math.min(this.y,s.y);
+        this.z = Math.min(this.z,s.z);
+        
+        return this;
+    },
+    distanceTo: function(v) {
+        return Math.sqrt(this.distanceToSquared(v));
+    },
 
-    };
+    distanceToSquared: function(v) {
+        var dx = this.x - v.x;
+        var dy = this.y - v.y;
+        var dz = this.z - v.z;
 
-    this.render = function ( scene, camera, viewportWidth, viewportHeight ) {
-
-        var sprites = scene.__webglSprites,
-            nSprites = sprites.length;
+        return dx * dx + dy * dy + dz * dz;
+    },
+    
+    applyMatrix4 : function(m) {
+    
+        var x = this.x, y = this.y, z = this.z;
+        
+        var e = m.elements;
+        
+        this.x = e[0]*x + e[4]*y + e[8]*z + e[12];
+        this.y = e[1]*x + e[5]*y + e[9]*z + e[13];
+        this.z = e[2]*x + e[6]*y + e[10]*z + e[14];
+        
+        return this;
+    },
+    
+    applyProjection : function(m) {
+        
+        //input: $3Dmol.Matrix4 projection matrix
+        
+        var x = this.x, y = this.y, z = this.z;
+        
+        var e = m.elements;
+        var d = ( e[3]*x + e[7]*y + e[11]*z + e[15]);
+        
+        this.x = (e[0]*x + e[4]*y + e[8]*z + e[12]) / d;
+        this.y = (e[1]*x + e[5]*y + e[9]*z + e[13]) / d;
+        this.z = (e[2]*x + e[6]*y + e[10]*z + e[14]) / d;
+        
+        return this;
+    },
+    
+    applyQuaternion : function(q) { 
+        
+        //save values
+        var x = this.x;
+        var y = this.y;
+        var z = this.z;
+        
+        var qx = q.x;
+        var qy = q.y;
+        var qz = q.z;
+        var qw = q.w;
+        
+        //compute this as
+        //t = 2 * cross(q.xyz, v)
+        //newv = v + q.w * t + cross(q.xyz, t)
+        //this from molecularmusings
+        //http://molecularmusings.wordpress.com/2013/05/24/a-faster-quaternion-vector-multiplication/
+        var t = {};
+        t.x = 2*(y * qz - z * qy);
+        t.y = 2*(z * qx - x * qz);
+        t.z = 2*(x * qy - y * qx);
+        
+        //cross t with q
+        var t2 = {};
+        t2.x = t.y * qz - t.z * qy;
+        t2.y = t.z * qx - t.x * qz;
+        t2.z = t.x * qy - t.y * qx;
+        
+        this.x = x + q.w*t.x + t2.x;
+        this.y = y + q.w*t.y + t2.y;
+        this.z = z + q.w*t.z + t2.z;
+        
+        return this;
+    },
+    
+    negate : function() {
+        
+        return this.multiplyScalar(-1);
+    },
+    
+    dot : function(v) {
+        
+        return this.x * v.x + this.y * v.y + this.z * v.z;
+    },
+    
+    length : function() {
+        
+        return Math.sqrt(this.x*this.x + this.y*this.y + this.z*this.z);
+    },
+    
+    lengthSq : function() {
+    
+        return (this.x*this.x + this.y*this.y + this.z*this.z);
+    },
+    
+    normalize : function() {
+        
+        return this.divideScalar( this.length() );
+    },
+    
+    cross : function (v) {
+        
+        var x = this.x, y = this.y, z = this.z;
+        
+        this.x = y * v.z - z * v.y;
+        this.y = z * v.x - x * v.z;
+        this.z = x * v.y - y * v.x;
+        
+        return this;
+    },
+    
+    crossVectors : function(a, b) {
+        
+        this.x = a.y * b.z - a.z * b.y;
+        this.y = a.z * b.x - a.x * b.z;
+        this.z = a.x * b.y - a.y * b.x;
+        
+        return this;
+    },
+    
+    getPositionFromMatrix : function(m) {
+        
+        this.x = m.elements[12];
+        this.y = m.elements[13];
+        this.z = m.elements[14];
+        
+        return this;
+    },
 
-        if ( ! nSprites ) return;
+    setEulerFromRotationMatrix : function (m, order) {
 
-        var attributes = _sprite.attributes,
-            uniforms = _sprite.uniforms;
+        // assumes the upper 3x3 of m is a pure rotation matrix (i.e, unscaled)
 
-        var invAspect = viewportHeight / viewportWidth;
+        var te = m.elements;
+        var m11 = te[0], m12 = te[4], m13 = te[8];
+        var m21 = te[1], m22 = te[5], m23 = te[9];
+        var m31 = te[2], m32 = te[6], m33 = te[10];
 
-        var halfViewportWidth = viewportWidth * 0.5,
-            halfViewportHeight = viewportHeight * 0.5;
+        if ( order === undefined || order === 'XYZ' ) {
 
-        // setup gl
+            this.y = Math.asin( $3Dmol.Math.clamp( m13, -1, 1 ) );
 
-        _gl.useProgram( _sprite.program );
+            if ( Math.abs( m13 ) < 0.99999 ) {
 
-        _gl.enableVertexAttribArray( attributes.position );
-        _gl.enableVertexAttribArray( attributes.uv );
+                this.x = Math.atan2( - m23, m33 );
+                this.z = Math.atan2( - m12, m11 );
 
-        _gl.disable( _gl.CULL_FACE );
-        _gl.enable( _gl.BLEND );
+            } else {
 
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
-        _gl.vertexAttribPointer( attributes.position, 2, _gl.FLOAT, false, 2 * 8, 0 );
-        _gl.vertexAttribPointer( attributes.uv, 2, _gl.FLOAT, false, 2 * 8, 8 );
+                this.x = Math.atan2( m32, m22 );
+                this.z = 0;
 
-        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
+            }
+        }
+        
+        else {
+            console.error("Error with vector's setEulerFromRotationMatrix: Unknown order: " + order);
+        }
+        
+        return this;
 
-        _gl.uniformMatrix4fv( uniforms.projectionMatrix, false, camera.projectionMatrix.elements );
+    },
 
-        _gl.activeTexture( _gl.TEXTURE0 );
-        _gl.uniform1i( uniforms.map, 0 );
+    rotateAboutVector : function(axis, ang) {
 
-        var oldFogType = 0;
-        var sceneFogType = 0;
-        var fog = scene.fog;
+        axis.normalize();
+        var cosang = Math.cos(ang);
+        var sinang = Math.sin(ang); 
+        // Rodrigues' rotation formula, from wikipedia
 
-        if ( fog ) {
+        var term1 = this.clone().multiplyScalar(cosang);
+        var term2 = (axis.clone().cross(this)).multiplyScalar(sinang)
+        var term3 = axis.clone().multiplyScalar(axis.clone().dot(this)).multiplyScalar(1-cosang);
 
-            _gl.uniform3f( uniforms.fogColor, fog.color.r, fog.color.g, fog.color.b );
+        var rot = term1.add(term2).add(term3);
+    
+        this.x = rot.x;
+        this.y = rot.y;
+        this.z = rot.z;
 
-            _gl.uniform1f( uniforms.fogNear, fog.near );
-            _gl.uniform1f( uniforms.fogFar, fog.far );
+        return this;
+    },
+    
+    clone : function() {
+        return new $3Dmol.Vector3(this.x, this.y, this.z);
+    }
+    
+};
 
-            _gl.uniform1i( uniforms.fogType, 1 );
-            oldFogType = 1;
-            sceneFogType = 1;
+//Matrices
 
+//Matrix3
+/** @constructor */
+$3Dmol.Matrix3 = function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
+    
+    this.elements = new Float32Array(9);
+    
+    this.set(
+        (n11 !== undefined) ? n11 : 1, n12 || 0, n13 || 0,
+        n21 || 0, (n22 !== undefined) ? n22 : 1, n23 || 0,
+        n31 || 0, n32 || 0, (n33 !== undefined) ? n33 : 1
+    );
+    
+};
 
-        } 
+$3Dmol.Matrix3.prototype = {
+    
+    constructor : $3Dmol.Matrix3,    
+   
+    set : function(n11, n12, n13, n21, n22, n23, n31, n32, n33) {
+        var te = this.elements;
         
-        else {
-
-            _gl.uniform1i( uniforms.fogType, 0 );
-            oldFogType = 0;
-            sceneFogType = 0;
-
-        }
+        te[0] = n11; te[3] = n12; te[6] = n13;
+        te[1] = n21; te[4] = n22; te[7] = n23;
+        te[2] = n31; te[5] = n32; te[8] = n33;
+        
+        return this;
+    },
+    
+    identity : function() {   
+        this.set(
+            1,0,0,
+            0,1,0,
+            0,0,1
+        );
+        
+        return this;
+    },
+   
+    copy : function(m) {
+        var me = m.elements;
+       
+        this.set(
+            me[0], me[3], me[6],
+            me[1], me[4], me[7],
+            me[2], me[5], me[8]
+        );
+    },
+    
+    multiplyScalar: function ( s ) {
+        var te = this.elements;
 
+        te[0] *= s; te[3] *= s; te[6] *= s;
+        te[1] *= s; te[4] *= s; te[7] *= s;
+        te[2] *= s; te[5] *= s; te[8] *= s;
 
-        // update positions and sort
+        return this;
+    },
 
-        var i, sprite, material, screenPosition, size, fogType, scale = [];
+    getInverse: function ( matrix, throwOnInvertible ) {
+        // input: Matrix4
 
-        for( i = 0; i < nSprites; i ++ ) {
+        var me = matrix.elements;
+        var te = this.elements;
 
-            sprite = sprites[ i ];
-            material = sprite.material;
+        te[ 0 ] =   me[10] * me[5] - me[6] * me[9];
+        te[ 1 ] = - me[10] * me[1] + me[2] * me[9];
+        te[ 2 ] =   me[6] * me[1] - me[2] * me[5];
+        te[ 3 ] = - me[10] * me[4] + me[6] * me[8];
+        te[ 4 ] =   me[10] * me[0] - me[2] * me[8];
+        te[ 5 ] = - me[6] * me[0] + me[2] * me[4];
+        te[ 6 ] =   me[9] * me[4] - me[5] * me[8];
+        te[ 7 ] = - me[9] * me[0] + me[1] * me[8];
+        te[ 8 ] =   me[5] * me[0] - me[1] * me[4];
 
-            if ( ! sprite.visible || material.opacity === 0 ) continue;
+        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 3 ] + me[ 2 ] * te[ 6 ];
 
-            if ( ! material.useScreenCoordinates ) {
+        // no inverse
 
-                sprite._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, sprite.matrixWorld );
-                sprite.z = - sprite._modelViewMatrix.elements[ 14 ];
+        if ( det === 0 ) {
+
+            var msg = "Matrix3.getInverse(): can't invert matrix, determinant is 0";
+
+            if ( throwOnInvertible || false ) {
+
+                throw new Error( msg ); 
 
             } else {
 
-                sprite.z = - sprite.position.z;
+                console.warn( msg );
 
             }
 
-        }
+            this.identity();
 
-        sprites.sort( painterSortStable );
+            return this;
 
-        // render all sprites
+        }
 
-        for( i = 0; i < nSprites; i ++ ) {
+        this.multiplyScalar( 1.0 / det );
 
-            sprite = sprites[ i ];
-            material = sprite.material;
+        return this;
+    },
 
-            if ( ! sprite.visible || material.opacity === 0 ) continue;
+    //https://en.wikipedia.org/wiki/Determinant
+    getDeterminant: function() {
+        var m = this.elements;
+
+        /*|a b c|
+          |d e f|
+          |g h i|*/
+
+        var determinant
+            = m[0] * m[4] * m[8] //+aei
+            + m[1] * m[5] * m[6] //+bfg
+            + m[2] * m[3] * m[7] //+cdh
+            - m[2] * m[4] * m[6] //-ceg
+            - m[1] * m[3] * m[8] //-bdi
+            - m[0] * m[5] * m[7];//-afh
+        return determinant;
+    },
+    
+    transpose: function () {
+        var tmp, m = this.elements;
 
-            if ( material.map && material.map.image && material.map.image.width ) {
+        tmp = m[1]; m[1] = m[3]; m[3] = tmp;
+        tmp = m[2]; m[2] = m[6]; m[6] = tmp;
+        tmp = m[5]; m[5] = m[7]; m[7] = tmp;
 
-                _gl.uniform1f( uniforms.alphaTest, material.alphaTest );
-                var w = material.map.image.width;
-                var h = material.map.image.height;
-                
-                scale[ 0 ] = w*_renderer.devicePixelRatio/viewportWidth;
-                scale[ 1 ] = h*_renderer.devicePixelRatio/viewportHeight;
-                
-                if ( material.useScreenCoordinates === true ) {
+        return this;
+    },
+    
+    clone: function () {
+        var te = this.elements;
 
-                    _gl.uniform1i( uniforms.useScreenCoordinates, 1 );
-                    _gl.uniform3f(
-                        uniforms.screenPosition,
-                        ( ( sprite.position.x * _renderer.devicePixelRatio ) - halfViewportWidth  ) / halfViewportWidth,
-                        ( halfViewportHeight - ( sprite.position.y * _renderer.devicePixelRatio ) ) / halfViewportHeight,
-                        Math.max( 0, Math.min( 1, sprite.position.z ) )
-                    );
+        return new $3Dmol.Matrix3(
 
-                } else {
+            te[0], te[3], te[6],
+            te[1], te[4], te[7],
+            te[2], te[5], te[8]
 
-                    _gl.uniform1i( uniforms.useScreenCoordinates, 0 );
-                    _gl.uniformMatrix4fv( uniforms.modelViewMatrix, false, sprite._modelViewMatrix.elements );
-                }
+        );
+    }
+   
+};
 
-                if ( scene.fog && material.fog ) {
+//Matrix 4
+/** @constructor */
+$3Dmol.Matrix4 = function(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44) {
 
-                    fogType = sceneFogType;
+    var te = this.elements = new Float32Array( 16 );
+    
+    te[0] = ( n11 !== undefined ) ? n11 : 1; te[4] = n12 || 0; te[8] = n13 || 0; te[12] = n14 || 0;
+    te[1] = n21 || 0; te[5] = ( n22 !== undefined ) ? n22 : 1; te[9] = n23 || 0; te[13] = n24 || 0;
+    te[2] = n31 || 0; te[6] = n32 || 0; te[10] = ( n33 !== undefined ) ? n33 : 1; te[14] = n34 || 0;
+    te[3] = n41 || 0; te[7] = n42 || 0; te[11] = n43 || 0; te[15] = ( n44 !== undefined ) ? n44 : 1;
 
-                } else {
+};
 
-                    fogType = 0;
+$3Dmol.Matrix4.prototype = {
 
-                }
+    constructor : $3Dmol.Matrix4,
 
-                if ( oldFogType !== fogType ) {
+    set: function ( n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44 ) {
+        var te = this.elements;
 
-                    _gl.uniform1i( uniforms.fogType, fogType );
-                    oldFogType = fogType;
+        te[0] = n11; te[4] = n12; te[8] = n13; te[12] = n14;
+        te[1] = n21; te[5] = n22; te[9] = n23; te[13] = n24;
+        te[2] = n31; te[6] = n32; te[10] = n33; te[14] = n34;
+        te[3] = n41; te[7] = n42; te[11] = n43; te[15] = n44;
 
-                }
+        return this;
+    },
 
-                size = 1 / ( material.scaleByViewport ? viewportHeight : 1 );
+    identity: function () {
+        this.set(
 
-                scale[ 0 ] *= size * sprite.scale.x;
-                scale[ 1 ] *= size * sprite.scale.y;
+            1, 0, 0, 0,
+            0, 1, 0, 0,
+            0, 0, 1, 0,
+            0, 0, 0, 1
 
-                _gl.uniform2f( uniforms.uvScale, material.uvScale.x, material.uvScale.y );
-                _gl.uniform2f( uniforms.uvOffset, material.uvOffset.x, material.uvOffset.y );
-                _gl.uniform2f( uniforms.alignment, material.alignment.x, material.alignment.y );
+        );
 
-                _gl.uniform1f( uniforms.opacity, material.opacity );
-                _gl.uniform3f( uniforms.color, material.color.r, material.color.g, material.color.b );
+        return this;
+    },
 
-                _gl.uniform1f( uniforms.rotation, sprite.rotation );
-                _gl.uniform2fv( uniforms.scale, scale );
+    copy: function ( m ) {
+        var me = m.elements;
 
-                //_renderer.setBlending( material.blending, material.blendEquation, material.blendSrc, material.blendDst );
-                _renderer.setDepthTest( material.depthTest );
-                _renderer.setDepthWrite( material.depthWrite );
-                _renderer.setTexture( material.map, 0 );
+        this.set(
 
-                _gl.drawElements( _gl.TRIANGLES, 6, _gl.UNSIGNED_SHORT, 0 );
+            me[0], me[4], me[8], me[12],
+            me[1], me[5], me[9], me[13],
+            me[2], me[6], me[10], me[14],
+            me[3], me[7], me[11], me[15]
 
-            }
+        );
 
-        }
+        return this;
+    },
 
-        // restore gl
+    matrix3FromTopLeft: function () {
+        var te = this.elements;
+        return new $3Dmol.Matrix3(te[0],te[4],te[8],te[1],te[5],te[9],te[2],te[6],te[10]);
+    },
 
-        _gl.enable( _gl.CULL_FACE );
+    setRotationFromEuler: function ( v, order ) {
 
-    };
+        var te = this.elements;
 
-    function createProgram ( shader, precision ) {
+        var x = v.x, y = v.y, z = v.z;
+        var a = Math.cos( x ), b = Math.sin( x );
+        var c = Math.cos( y ), d = Math.sin( y );
+        var e = Math.cos( z ), f = Math.sin( z );
 
-        var program = _gl.createProgram();
+        if ( order === undefined || order === 'XYZ' ) {
 
-        var fragmentShader = _gl.createShader( _gl.FRAGMENT_SHADER );
-        var vertexShader = _gl.createShader( _gl.VERTEX_SHADER );
+            var ae = a * e, af = a * f, be = b * e, bf = b * f;
 
-        var prefix = "precision " + precision + " float;\n";
+            te[0] = c * e;
+            te[4] = - c * f;
+            te[8] = d;
 
-        _gl.shaderSource( fragmentShader, prefix + shader.fragmentShader );
-        _gl.shaderSource( vertexShader, prefix + shader.vertexShader );
+            te[1] = af + be * d;
+            te[5] = ae - bf * d;
+            te[9] = - b * c;
 
-        _gl.compileShader( fragmentShader );
-        _gl.compileShader( vertexShader );
+            te[2] = bf - ae * d;
+            te[6] = be + af * d;
+            te[10] = a * c;
+
+        } 
         
-        if ( ! _gl.getShaderParameter(fragmentShader, _gl.COMPILE_STATUS) || ! _gl.getShaderParameter(vertexShader,_gl.COMPILE_STATUS) ) {
+        else
+            console.error("Error with matrix4 setRotationFromEuler. Order: " + order);
 
-                console.error(_gl.getShaderInfoLog(fragmentShader));
-                console.error("could not initialize shader");
-                return null;
-        }
+        return this;
 
-        _gl.attachShader( program, fragmentShader );
-        _gl.attachShader( program, vertexShader );
+    },
 
-        _gl.linkProgram( program );
+    setRotationFromQuaternion: function ( q ) {
+        var te = this.elements;
 
-        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
-                console.error("Could not initialize shader");
+        var x = q.x, y = q.y, z = q.z, w = q.w;
+        var x2 = x + x, y2 = y + y, z2 = z + z;
+        var xx = x * x2, xy = x * y2, xz = x * z2;
+        var yy = y * y2, yz = y * z2, zz = z * z2;
+        var wx = w * x2, wy = w * y2, wz = w * z2;
 
-        return program;
+        te[0] = 1 - ( yy + zz );
+        te[4] = xy - wz;
+        te[8] = xz + wy;
 
-    }
+        te[1] = xy + wz;
+        te[5] = 1 - ( xx + zz );
+        te[9] = yz - wx;
 
-    function painterSortStable ( a, b ) {
+        te[2] = xz - wy;
+        te[6] = yz + wx;
+        te[10] = 1 - ( xx + yy );
 
-        if ( a.z !== b.z ) {
+        return this;
+    },
 
-            return b.z - a.z;
+    lookAt: function() {
+        var x = new $3Dmol.Vector3();
+        var y = new $3Dmol.Vector3();
+        var z = new $3Dmol.Vector3();
 
-        } else {
+        return function ( eye, target, up ) {
 
-            return b.id - a.id;
+            var te = this.elements;
 
-        }
+            z.subVectors( eye, target ).normalize();
 
-    }
+            if ( z.length() === 0 ) {
 
-};
+                z.z = 1;
 
-$3Dmol.Light = function(hex, intensity) {
-    
-    $3Dmol.Object3D.call(this);
-    
-    this.color = new $3Dmol.Color(hex);
-    this.position = new $3Dmol.Vector3( 0, 1, 0 );
-    this.target = new $3Dmol.Object3D();
+            }
 
-    this.intensity = ( intensity !== undefined ) ? intensity : 1;
+            x.crossVectors( up, z ).normalize();
 
-    this.castShadow = false;
-    this.onlyShadow = false;
-    
-};
+            if ( x.length() === 0 ) {
 
-$3Dmol.Light.prototype = Object.create($3Dmol.Object3D.prototype);
-/**
- * Line and Mesh material types
- * @constructor
- */
-$3Dmol.Material = function () {
+                z.x += 0.0001;
+                x.crossVectors( up, z ).normalize();
 
-    $3Dmol.EventDispatcher.call( this );
+            }
 
-    this.id = $3Dmol.MaterialIdCount ++;
+            y.crossVectors( z, x );
 
-    this.name = '';
-    
-    //TODO: Which of these instance variables can I remove??
-    this.side = $3Dmol.FrontSide;
 
-    this.opacity = 1;
-    this.transparent = false;
+            te[0] = x.x; te[4] = y.x; te[8] = z.x;
+            te[1] = x.y; te[5] = y.y; te[9] = z.y;
+            te[2] = x.z; te[6] = y.z; te[10] = z.z;
 
-    this.depthTest = true;
-    this.depthWrite = true;
+            return this;
+        };
 
-    this.polygonOffset = false;
-    this.polygonOffsetFactor = 0;
-    this.polygonOffsetUnits = 0;
+    }(),
 
-    this.alphaTest = 0;
+    multiplyMatrices: function ( a, b ) {
+        var ae = a.elements;
+        var be = b.elements;
+        var te = this.elements;
 
-    this.visible = true;
+        var a11 = ae[0], a12 = ae[4], a13 = ae[8], a14 = ae[12];
+        var a21 = ae[1], a22 = ae[5], a23 = ae[9], a24 = ae[13];
+        var a31 = ae[2], a32 = ae[6], a33 = ae[10], a34 = ae[14];
+        var a41 = ae[3], a42 = ae[7], a43 = ae[11], a44 = ae[15];
 
-    this.needsUpdate = true;
+        var b11 = be[0], b12 = be[4], b13 = be[8], b14 = be[12];
+        var b21 = be[1], b22 = be[5], b23 = be[9], b24 = be[13];
+        var b31 = be[2], b32 = be[6], b33 = be[10], b34 = be[14];
+        var b41 = be[3], b42 = be[7], b43 = be[11], b44 = be[15];
 
-};
+        te[0] = a11 * b11 + a12 * b21 + a13 * b31 + a14 * b41;
+        te[4] = a11 * b12 + a12 * b22 + a13 * b32 + a14 * b42;
+        te[8] = a11 * b13 + a12 * b23 + a13 * b33 + a14 * b43;
+        te[12] = a11 * b14 + a12 * b24 + a13 * b34 + a14 * b44;
 
+        te[1] = a21 * b11 + a22 * b21 + a23 * b31 + a24 * b41;
+        te[5] = a21 * b12 + a22 * b22 + a23 * b32 + a24 * b42;
+        te[9] = a21 * b13 + a22 * b23 + a23 * b33 + a24 * b43;
+        te[13] = a21 * b14 + a22 * b24 + a23 * b34 + a24 * b44;
 
-$3Dmol.Material.prototype.setValues = function ( values ) {
+        te[2] = a31 * b11 + a32 * b21 + a33 * b31 + a34 * b41;
+        te[6] = a31 * b12 + a32 * b22 + a33 * b32 + a34 * b42;
+        te[10] = a31 * b13 + a32 * b23 + a33 * b33 + a34 * b43;
+        te[14] = a31 * b14 + a32 * b24 + a33 * b34 + a34 * b44;
 
-    if ( values === undefined ) return;
+        te[3] = a41 * b11 + a42 * b21 + a43 * b31 + a44 * b41;
+        te[7] = a41 * b12 + a42 * b22 + a43 * b32 + a44 * b42;
+        te[11] = a41 * b13 + a42 * b23 + a43 * b33 + a44 * b43;
+        te[15] = a41 * b14 + a42 * b24 + a43 * b34 + a44 * b44;
 
-    for ( var key in values ) {
+        return this;
+    },
+    
+    multiplyScalar: function ( s ) {
+        var te = this.elements;
+    
+        te[0] *= s; te[4] *= s; te[8] *= s; te[12] *= s;
+        te[1] *= s; te[5] *= s; te[9] *= s; te[13] *= s;
+        te[2] *= s; te[6] *= s; te[10] *= s; te[14] *= s;
+        te[3] *= s; te[7] *= s; te[11] *= s; te[15] *= s;
+    
+        return this;
+    },
+    
+    transpose: function () {
+        var te = this.elements;
+        var tmp;
 
-        var newValue = values[ key ];
+        tmp = te[1]; te[1] = te[4]; te[4] = tmp;
+        tmp = te[2]; te[2] = te[8]; te[8] = tmp;
+        tmp = te[6]; te[6] = te[9]; te[9] = tmp;
 
-        if ( newValue === undefined ) {
+        tmp = te[3]; te[3] = te[12]; te[12] = tmp;
+        tmp = te[7]; te[7] = te[13]; te[13] = tmp;
+        tmp = te[11]; te[11] = te[14]; te[14] = tmp;
 
-            console.warn( '$3Dmol.Material: \'' + key + '\' parameter is undefined.' );
-            continue;
+        return this;
+    },
 
-        }
+    getPosition: function() {
+        var v1 = new $3Dmol.Vector3();
 
-        if ( key in this ) {
+        return function () {
 
-            var currentValue = this[ key ];
+            console.warn( 'DEPRECATED: Matrix4\'s .getPosition() has been removed. Use Vector3.getPositionFromMatrix( matrix ) instead.' );
 
-            if ( currentValue instanceof $3Dmol.Color && newValue instanceof $3Dmol.Color ) {
+            var te = this.elements;
+            return v1.set( te[12], te[13], te[14] );
+        };
 
-                currentValue.copy( newValue );
+    }(),
 
-            } else if ( currentValue instanceof $3Dmol.Color ) {
+    setPosition: function ( v ) {
+        var te = this.elements;
 
-                currentValue.set( newValue );
+        te[12] = v.x;
+        te[13] = v.y;
+        te[14] = v.z;
 
-            } else if ( currentValue instanceof $3Dmol.Vector3 && newValue instanceof $3Dmol.Vector3 ) {
+        return this;
+    },
 
-                currentValue.copy( newValue );
+    getInverse: function ( m, throwOnInvertible ) {
+        // based on http://www.euclideanspace.com/maths/algebra/matrix/functions/inverse/fourD/index.htm
+        var te = this.elements;
+        var me = m.elements;
+
+        var n11 = me[0], n12 = me[4], n13 = me[8], n14 = me[12];
+        var n21 = me[1], n22 = me[5], n23 = me[9], n24 = me[13];
+        var n31 = me[2], n32 = me[6], n33 = me[10], n34 = me[14];
+        var n41 = me[3], n42 = me[7], n43 = me[11], n44 = me[15];
+
+        te[0] = n23*n34*n42 - n24*n33*n42 + n24*n32*n43 - n22*n34*n43 - n23*n32*n44 + n22*n33*n44;
+        te[4] = n14*n33*n42 - n13*n34*n42 - n14*n32*n43 + n12*n34*n43 + n13*n32*n44 - n12*n33*n44;
+        te[8] = n13*n24*n42 - n14*n23*n42 + n14*n22*n43 - n12*n24*n43 - n13*n22*n44 + n12*n23*n44;
+        te[12] = n14*n23*n32 - n13*n24*n32 - n14*n22*n33 + n12*n24*n33 + n13*n22*n34 - n12*n23*n34;
+        te[1] = n24*n33*n41 - n23*n34*n41 - n24*n31*n43 + n21*n34*n43 + n23*n31*n44 - n21*n33*n44;
+        te[5] = n13*n34*n41 - n14*n33*n41 + n14*n31*n43 - n11*n34*n43 - n13*n31*n44 + n11*n33*n44;
+        te[9] = n14*n23*n41 - n13*n24*n41 - n14*n21*n43 + n11*n24*n43 + n13*n21*n44 - n11*n23*n44;
+        te[13] = n13*n24*n31 - n14*n23*n31 + n14*n21*n33 - n11*n24*n33 - n13*n21*n34 + n11*n23*n34;
+        te[2] = n22*n34*n41 - n24*n32*n41 + n24*n31*n42 - n21*n34*n42 - n22*n31*n44 + n21*n32*n44;
+        te[6] = n14*n32*n41 - n12*n34*n41 - n14*n31*n42 + n11*n34*n42 + n12*n31*n44 - n11*n32*n44;
+        te[10] = n12*n24*n41 - n14*n22*n41 + n14*n21*n42 - n11*n24*n42 - n12*n21*n44 + n11*n22*n44;
+        te[14] = n14*n22*n31 - n12*n24*n31 - n14*n21*n32 + n11*n24*n32 + n12*n21*n34 - n11*n22*n34;
+        te[3] = n23*n32*n41 - n22*n33*n41 - n23*n31*n42 + n21*n33*n42 + n22*n31*n43 - n21*n32*n43;
+        te[7] = n12*n33*n41 - n13*n32*n41 + n13*n31*n42 - n11*n33*n42 - n12*n31*n43 + n11*n32*n43;
+        te[11] = n13*n22*n41 - n12*n23*n41 - n13*n21*n42 + n11*n23*n42 + n12*n21*n43 - n11*n22*n43;
+        te[15] = n12*n23*n31 - n13*n22*n31 + n13*n21*n32 - n11*n23*n32 - n12*n21*n33 + n11*n22*n33;
+
+        var det = me[ 0 ] * te[ 0 ] + me[ 1 ] * te[ 4 ] + me[ 2 ] * te[ 8 ] + me[ 3 ] * te[ 12 ];
+
+        if ( det === 0 ) {
+
+            var msg = "Matrix4.getInverse(): can't invert matrix, determinant is 0";
+
+            if ( throwOnInvertible || false ) {
+
+                throw new Error( msg ); 
 
             } else {
 
-                this[ key ] = newValue;
+                console.warn( msg );
 
             }
 
+            this.identity();
+
+            return this;
         }
 
-    }
+        this.multiplyScalar( 1 / det );
 
-};
-//TODO: might want to look into blending equations
-$3Dmol.Material.prototype.clone = function ( material ) {
+        return this;
+    },
 
-    if ( material === undefined ) material = new $3Dmol.Material();
+    isReflected: function() {
+        return this.matrix3FromTopLeft().getDeterminant() < 0;
+    },
 
-    material.name = this.name;
+    compose: function() {
+        var mRotation = new $3Dmol.Matrix4(),
+            mScale = new $3Dmol.Matrix4();
+        
+        return function ( translation, rotation, scale ) {
 
-    material.side = this.side;
+            var te = this.elements;
 
-    material.opacity = this.opacity;
-    material.transparent = this.transparent;
+            mRotation.identity();
+            mRotation.setRotationFromQuaternion( rotation );
 
-    material.depthTest = this.depthTest;
-    material.depthWrite = this.depthWrite;
+            mScale.makeScale( scale.x, scale.y, scale.z );
 
-    material.polygonOffset = this.polygonOffset;
-    material.polygonOffsetFactor = this.polygonOffsetFactor;
-    material.polygonOffsetUnits = this.polygonOffsetUnits;
+            this.multiplyMatrices( mRotation, mScale );
 
-    material.alphaTest = this.alphaTest;
+            te[12] = translation.x;
+            te[13] = translation.y;
+            te[14] = translation.z;
 
-    material.overdraw = this.overdraw;
+            return this;
 
-    material.visible = this.visible;
+        };
+    }(),
 
-    return material;
+    decompose: function() {
+        var x = new $3Dmol.Vector3(),
+            y = new $3Dmol.Vector3(),
+            z = new $3Dmol.Vector3(),
+            matrix = new $3Dmol.Matrix4();
 
-};
+        return function ( translation, rotation, scale ) {
 
-$3Dmol.Material.prototype.dispose = function () {
+            var te = this.elements;
 
-    this.dispatchEvent( { type: 'dispose' } );
+            // grab the axis vectors
+            x.set( te[0], te[1], te[2] );
+            y.set( te[4], te[5], te[6] );
+            z.set( te[8], te[9], te[10] );
 
-};
+            translation = ( translation instanceof $3Dmol.Vector3 ) ? translation : new $3Dmol.Vector3();
+            rotation = ( rotation instanceof $3Dmol.Quaternion ) ? rotation : new $3Dmol.Quaternion();
+            scale = ( scale instanceof $3Dmol.Vector3 ) ? scale : new $3Dmol.Vector3();
 
-$3Dmol.MaterialIdCount = 0;
+            scale.x = x.length();
+            scale.y = y.length();
+            scale.z = z.length();
 
-//Line basic material
-/** @constructor */
-$3Dmol.LineBasicMaterial = function(parameters) {
-    
-    $3Dmol.Material.call(this);
-    
-    this.color = new $3Dmol.Color(0xffffff);
-    
-    this.linewidth = 1;
-    this.linecap = 'round';
-    this.linejoin = 'round';
-    
-    this.vertexColors = false;
-    
-    this.fog = true;
-    this.shaderID = "basic";
-    this.setValues(parameters);
-    
-};
+            translation.x = te[12];
+            translation.y = te[13];
+            translation.z = te[14];
 
-$3Dmol.LineBasicMaterial.prototype = Object.create($3Dmol.Material.prototype);
+            // scale the rotation part
 
-$3Dmol.LineBasicMaterial.prototype.clone = function() {
-  
-    var material = new $3Dmol.LineBasicMaterial();
-    
-    $3Dmol.Material.prototype.clone.call(this, material);
-    
-    material.color.copy();
-    return material;
-};
+            matrix.copy( this );
 
-//Mesh Lambert material
-/** @constructor */
-$3Dmol.MeshLambertMaterial = function(parameters) {
-    
-    $3Dmol.Material.call(this);
-    
-    this.color = new $3Dmol.Color(0xffffff);
-    this.ambient = new $3Dmol.Color(0xfffff);
-    this.emissive = new $3Dmol.Color(0x000000);
-    
-    //TODO: Which of these instance variables do I really need?
-    this.wrapAround = false;
-    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
-    
-    this.map = null;
-    
-    this.lightMap = null;
-    
-    this.specularMap = null;
-    
-    this.envMap = null;
-    this.reflectivity = 1;
-    this.refractionRatio = 0.98;
-    
-    this.fog = true;
+            matrix.elements[0] /= scale.x;
+            matrix.elements[1] /= scale.x;
+            matrix.elements[2] /= scale.x;
+
+            matrix.elements[4] /= scale.y;
+            matrix.elements[5] /= scale.y;
+            matrix.elements[6] /= scale.y;
+
+            matrix.elements[8] /= scale.z;
+            matrix.elements[9] /= scale.z;
+            matrix.elements[10] /= scale.z;
+
+            rotation.setFromRotationMatrix( matrix );
+
+            return [ translation, rotation, scale ];
+
+        };
+    }(),
+
+    scale: function ( v ) {
+        var te = this.elements;
+        var x = v.x, y = v.y, z = v.z;
+
+        te[0] *= x; te[4] *= y; te[8] *= z;
+        te[1] *= x; te[5] *= y; te[9] *= z;
+        te[2] *= x; te[6] *= y; te[10] *= z;
+        te[3] *= x; te[7] *= y; te[11] *= z;
+
+        return this;
+    },
     
-    this.wireframe = false;
-    this.wireframeLinewidth = 1;
-    this.wireframeLinecap = 'round';
-    this.wireframeLinejoin = 'round';
+    getMaxScaleOnAxis : function() {
+        
+        var te = this.elements;
+        
+        var scaleXSq = te[0] * te[0] + te[1] * te[1] + te[2] * te[2];
+        var scaleYSq = te[4] * te[4] + te[5] * te[5] + te[6] * te[6];
+        var scaleZSq = te[8] * te[8] + te[9] * te[9] + te[10] * te[10];
+        
+        return Math.sqrt(Math.max(scaleXSq, Math.max(scaleYSq, scaleZSq)));
+        
+    },
+
+    makeFrustum: function ( left, right, bottom, top, near, far ) {
+        var te = this.elements;
+              
+        var x = 2 * near / ( right - left );
+        var y = 2 * near / ( top - bottom );
+
+        var a = ( right + left ) / ( right - left );
+        var b = ( top + bottom ) / ( top - bottom );
+        var c = - ( far + near ) / ( far - near );
+        var d = - 2 * far * near / ( far - near );
+
+        te[0] = x;  te[4] = 0;  te[8] = a;  te[12] = 0;
+        te[1] = 0;  te[5] = y;  te[9] = b;  te[13] = 0;
+        te[2] = 0;  te[6] = 0;  te[10] = c; te[14] = d;
+        te[3] = 0;  te[7] = 0;  te[11] = - 1;   te[15] = 0;
+
+        return this;
+    },
+
+    makePerspective: function ( fov, aspect, near, far ) {
+        var ymax = near * Math.tan( $3Dmol.Math.degToRad( fov * 0.5 ) );
+        var ymin = - ymax;
+        var xmin = ymin * aspect;
+        var xmax = ymax * aspect;
+
+        return this.makeFrustum( xmin, xmax, ymin, ymax, near, far );
+    },
     
-    this.shading = $3Dmol.SmoothShading;
-    this.shaderID = "lambert";
-    this.vertexColors = $3Dmol.NoColors;
+    isEqual : function (m) {
+        var me = m.elements;
+        var te = this.elements;
+        
+        if (te[0] == me[0] && te[4] == me[4] && te[8] == me[8] && te[12] == me[12] &&
+            te[1] == me[1] && te[5] == me[5] && te[9] == me[9] && te[13] == me[13] &&
+            te[2] == me[2] && te[6] == me[6] && te[10] == me[10] && te[14] == me[14] &&
+            te[3] == me[3] && te[7] == me[7] && te[11] == me[11] && te[15] == me[15]) {
+            return true;
+        }
+        else {
+            return false;
+        }
+    },
+
+    clone: function () {
+        var te = this.elements;
+
+        return new $3Dmol.Matrix4(
+
+            te[0], te[4], te[8], te[12],
+            te[1], te[5], te[9], te[13],
+            te[2], te[6], te[10], te[14],
+            te[3], te[7], te[11], te[15]
+
+        );
+    },
     
-    this.skinning = false;
+    isIdentity: function () {
+        var te = this.elements;
+        
+        if (te[0] == 1 && te[4] == 0 && te[8] == 0 && te[12] == 0 &&
+            te[1] == 0 && te[5] == 1 && te[9] == 0 && te[13] == 0 &&
+            te[2] == 0 && te[6] == 0 && te[10] == 1 && te[14] == 0 &&
+            te[3] == 0 && te[7] == 0 && te[11] == 0 && te[15] == 1) {
+            return true;
+        }
+        else {
+            return false;
+        }
+    }
     
-    this.setValues(parameters);
+};
+/** @constructor */
+$3Dmol.Ray = function(origin, direction) {
     
+    this.origin = (origin !== undefined) ? 
+        origin : new $3Dmol.Vector3();
+        
+    this.direction = (direction !== undefined) ?
+        direction : new $3Dmol.Vector3();
+      
 };
 
-$3Dmol.MeshLambertMaterial.prototype = Object.create($3Dmol.Material.prototype);
-
-$3Dmol.MeshLambertMaterial.prototype.clone = function(material) {
-  
-    if ( typeof material === "undefined" ) material = new $3Dmol.MeshLambertMaterial();
+//TODO: Remove methods we don't need (intersectPlane ??)
+$3Dmol.Ray.prototype = {
     
-    $3Dmol.Material.prototype.clone.call(this, material);
+    constructor : $3Dmol.Ray,
+     
+    set : function(origin, direction){
+        
+        this.origin.copy(origin);
+        this.direction.copy(direction);
+        
+        return this;
     
-    material.color.copy(this.color);
-    material.ambient.copy(this.ambient);
-    material.emissive.copy(this.emissive);
+    },
     
-    material.wrapAround = this.wrapAround;
-    material.wrapRGB.copy(this.wrapRGB);
+    copy : function(ray) {
+        
+        this.origin.copy(ray.origin);
+        this.direction.copy(ray.direction);
+        
+        return this;
+        
+    },
     
-    material.map = this.map;
+    at : function(t, optionalTarget) {
+        
+        var result = optionalTarget || new $3Dmol.Vector3();
+        
+        return result.copy(this.direction).multiplyScalar(t).add(this.origin);
+        
+    },
     
-    material.lightMap = this.lightMap;
+    recast : function() {
+        
+        var v1 = new $3Dmol.Vector3();
+        
+        return function(t) {
+            this.origin.copy(this.at(t, v1));
+            
+            return this;
+        };
+        
+    }(),
     
-    material.specularMap = this.specularMap;
+    closestPointToPoint : function(point, optionalTarget) {
+        
+        var result = optionalTarget || new $3Dmol.Vector3();
+        result.subVectors(point, this.origin);
+        var directionDistance = result.dot(this.direction);
+        
+        //returns a point on this ray
+        return result.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
+        
+    },
     
-    material.envMap = this.envMap;
-    material.combine = this.combine;
-    material.reflectivity = this.reflectivity;
-    material.refractionRatio = this.refractionRatio;
+    distanceToPoint : function(point) {
+        
+        var v1 = new $3Dmol.Vector3();
+        
+        return function(point) {
+            var directionDistance = v1.subVectors(point, this.origin).dot(this.direction);
+            v1.copy(this.direction).multiplyScalar(directionDistance).add(this.origin);
+            return v1.distanceTo(point);
+        };
+        
+    }(),
     
-    material.fog = this.fog;
+    isIntersectionCylinder : function() {
+        
+    },
     
-    material.shading = this.shading;
-    material.shaderID = this.shaderID;
-    material.vertexColors = this.vertexColors;
+    isIntersectionSphere : function(sphere) {
+       return (this.distanceToPoint(sphere.center) <= sphere.radius);
+          
+    },
     
-    material.skinning = this.skinning;
-    material.morphTargets = this.morphTargets;
-    material.morphNormals = this.morphNormals;
+    isIntersectionPlane : function(plane) {
+        
+        var denominator = plane.normal.dot(this.direction);
+        
+        //plane and ray are not perpendicular
+        if (denominator !== 0) 
+            return true;
+        
+        if (plane.distanceToPoint(this.origin) === 0) 
+            return true;
+        
+        return false;
+        
+    },
     
-    return material;
+    distanceToPlane : function(plane) {
+       
+       var denominator = plane.normal.dot(this.direction);
+       if (denominator === 0) {
+           
+           //line is coplanar
+       if (plane.distanceToPoint(this.origin) === 0)
+           return 0;
+       
+       //ray is parallel
+           return undefined;
+       }
+       
+       var t = - (this.origin.dot(plane.normal) + plane.constant) / denominator;
+       
+       return t;
+       
+    },
     
-};
-
-//Double sided Mesh Lambert material
-/** @constructor */
-$3Dmol.MeshDoubleLambertMaterial = function(parameters) {
+    intersectPlane : function(plane, optionalTarget) {
+       
+       var t = this.distanceToPlane(plane);
+       
+       if (t === undefined)
+           return undefined;
+       
+       return this.at(t, optionalTarget);
+       
+    },
     
-    $3Dmol.MeshLambertMaterial.call(this, parameters);
-
-    this.shaderID = "lambertdouble";
-    this.side = $3Dmol.DoubleSide;    
+    applyMatrix4 : function(matrix4) {
+       
+       this.direction.add(this.origin).applyMatrix4(matrix4);
+       this.origin.applyMatrix4(matrix4);
+       this.direction.sub(this.origin);
+       
+       return this;
+       
+    },
     
-};
-
-$3Dmol.MeshDoubleLambertMaterial.prototype = Object.create($3Dmol.MeshLambertMaterial.prototype);
-
-$3Dmol.MeshDoubleLambertMaterial.prototype.clone = function() {
-  
-    var material = new $3Dmol.MeshDoubleLambertMaterial();
+    equals : function(ray) {
+       
+       return ray.origin.equals(this.origin) && ray.direction.equals(this.direction);
+       
+    },
     
-    $3Dmol.MeshLambertMaterial.prototype.clone.call(this, material);
-        
-    return material;
+    clone : function() {
+    
+       return new $3Dmol.Ray().copy(this);
     
+    }
+ 
+     
 };
 
+//Intersection sphere and box shapes.  
 
-//Imposter material
-/** @constructor */
-$3Dmol.ImposterMaterial = function(parameters) {
-  
-  $3Dmol.Material.call(this);
-  
-  this.color = new $3Dmol.Color(0xffffff);
-  this.ambient = new $3Dmol.Color(0xfffff);
-  this.emissive = new $3Dmol.Color(0x000000);
-  
-  //TODO: Which of these instance variables do I really need?
-  this.wrapAround = false;
-  this.wrapRGB = new $3Dmol.Vector3(1,1,1);
-  
-  this.map = null;
-  
-  this.lightMap = null;
-  
-  this.specularMap = null;
-  
-  this.envMap = null;
-  this.reflectivity = 1;
-  this.refractionRatio = 0.98;
-  
-  this.fog = true;
-  
-  this.wireframe = false;
-  this.wireframeLinewidth = 1;
-  this.wireframeLinecap = 'round';
-  this.wireframeLinejoin = 'round';
-  
-  this.shading = $3Dmol.SmoothShading;
-  this.shaderID = "sphereimposter";
-  this.vertexColors = $3Dmol.NoColors;
-  
-  this.skinning = false;
-  
-  this.setValues(parameters);
-  
-};
-
-$3Dmol.ImposterMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-$3Dmol.ImposterMaterial.prototype.clone = function() {
+//Intersection sphere for sphere, stick render
+/** @constructor */
+$3Dmol.Sphere = function(center, radius) {
 
-  var material = new $3Dmol.ImposterMaterial();
-  
-  $3Dmol.Material.prototype.clone.call(this, material);
-  
-  material.color.copy(this.color);
-  material.ambient.copy(this.ambient);
-  material.emissive.copy(this.emissive);
-  
-  material.wrapAround = this.wrapAround;
-  material.wrapRGB.copy(this.wrapRGB);
-  
-  material.map = this.map;
-  
-  material.lightMap = this.lightMap;
-  
-  material.specularMap = this.specularMap;
-  
-  material.envMap = this.envMap;
-  material.combine = this.combine;
-  material.reflectivity = this.reflectivity;
-  material.refractionRatio = this.refractionRatio;
-  
-  material.fog = this.fog;
-  
-  material.shading = this.shading;
-  material.shaderID = this.shaderID;
-  material.vertexColors = this.vertexColors;
-  
-  material.skinning = this.skinning;
-  material.morphTargets = this.morphTargets;
-  material.morphNormals = this.morphNormals;
-  
-  return material;
-  
+    this.center = (center !== undefined) ? 
+        center : new $3Dmol.Vector3();
+        
+    this.radius = (radius !== undefined) ?
+        radius : 0;
+        
 };
 
-
-//Sprite material
-/** @constructor */
-$3Dmol.SpriteMaterial = function(parameters) {
-    
-    $3Dmol.Material.call(this);
-    
-    this.color = new $3Dmol.Color(0xffffff);
-    this.map = new $3Dmol.Texture();
-    
-    this.useScreenCoordinates = true;
-    this.depthTest = !this.useScreenCoordinates;
-    this.sizeAttenuation = !this.useScreenCoordinates;
-    this.scaleByViewPort = !this.sizeAttenuation;
-    this.alignment = $3Dmol.SpriteAlignment.center.clone();
+$3Dmol.Sphere.prototype = {
     
-    this.fog = false; // use scene fog
+    constructor : $3Dmol.Sphere,
     
-    this.uvOffset = new $3Dmol.Vector2(0, 0);
-    this.uvScale = new $3Dmol.Vector2(1, 1);
+    set : function(center, radius) {
+        
+        this.center.copy(center);
+        this.radius = radius;
+        
+        return this;
+        
+    },
     
-    this.setValues(parameters);
+    copy : function(sphere) {
+        
+        this.center.copy(sphere.center);
+        this.radius = sphere.radius;
+        
+        return this;
+        
+    },
     
-    parameters = parameters || {};
+    applyMatrix4 : function(matrix) {
+        
+        this.center.applyMatrix4(matrix);
+        this.radius = this.radius * matrix.getMaxScaleOnAxis();
+        
+        return this;
+        
+    },
     
-    if (parameters.depthTest === undefined)
-        this.depthTest = !this.useScreenCoordinates;
-    if (parameters.sizeAttenuation === undefined)
-        this.sizeAttenuation = !this.useScreenCoordinates;
-    if (parameters.scaleByViewPort === undefined)
-        this.scaleByViewPort = !this.sizeAttenuation;
+    translate : function(offset) {
+        
+        this.center.add(offset);
+        
+        return this;
+        
+    },
     
+    equals : function(sphere) {
+        
+        return sphere.center.equals(this.center) && (sphere.radius === this.radius);
+        
+    },
+       
+    clone : function() {
+        
+        return new $3Dmol.Sphere().copy(this);
+        
+    }
+
 };
 
-$3Dmol.SpriteMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-$3Dmol.SpriteMaterial.prototype.clone = function() {
-    
-    var material = new $3Dmol.SpriteMaterial();
-    
-    $3Dmol.Material.prototype.clone.call(this, material);
-    
-    material.color.copy(this.color);
-    material.map = this.map;
-    
-    material.useScreenCoordinates = useScreenCoordinates;
-    material.sizeAttenuation = this.sizeAttenuation;
-    material.scaleByViewport = this.scaleByViewPort;
-    material.alignment.copy(this.alignment);
-    
-    material.uvOffset.copy(this.uvOffset);
-    
-    return material;
+//Bounding cylinder for stick render  
+/** @constructor */
+$3Dmol.Cylinder = function(c1, c2, radius) {
+
+    this.c1 = (c1 !== undefined) ?
+        c1 : new $3Dmol.Vector3();
+
+    this.c2 = (c2 !== undefined) ?
+        c2 : new $3Dmol.Vector3();
+        
+    this.direction = new $3Dmol.Vector3().subVectors(this.c2, this.c1).normalize();
+
+    this.radius = (radius !== undefined) ?
+        radius : 0;
     
 };
 
-//Alignment for Sprites
-
-$3Dmol.SpriteAlignment = {};
-$3Dmol.SpriteAlignment.topLeft = new $3Dmol.Vector2(1, -1);
-$3Dmol.SpriteAlignment.topCenter = new $3Dmol.Vector2(0, -1);
-$3Dmol.SpriteAlignment.topRight = new $3Dmol.Vector2(-1, -1);
-$3Dmol.SpriteAlignment.centerLeft = new $3Dmol.Vector2(1, 0);
-$3Dmol.SpriteAlignment.center = new $3Dmol.Vector2(0, 0);
-$3Dmol.SpriteAlignment.centerRight = new $3Dmol.Vector2(-1, 0);
-$3Dmol.SpriteAlignment.bottomLeft = new $3Dmol.Vector2(1, 1);
-$3Dmol.SpriteAlignment.bottomCenter = new $3Dmol.Vector2(0, 1);
-$3Dmol.SpriteAlignment.bottomRight = new $3Dmol.Vector2(-1, 1);
+$3Dmol.Cylinder.prototype = {
 
+    constructor : $3Dmol.Cylinder,
 
-//Texture
-//We really only create textures from 2d rendering contexts (to display text labels)
-/** @constructor */
-$3Dmol.Texture = function(image) {
+    copy : function(cylinder) {
 
-    $3Dmol.EventDispatcher.call(this);
-    
-    this.id = $3Dmol.TextureIdCount++;
-    
-    this.name = "";
-    
-    this.image = image;
-    this.mipmaps = [];
-    
-    this.mapping = new $3Dmol.UVMapping();
-    
-    this.wrapS = $3Dmol.ClampToEdgeWrapping;
-    this.wrapT = $3Dmol.ClampToEdgeWrapping;
-    
-    this.magFilter = $3Dmol.LinearFilter;
-    this.minFilter = $3Dmol.LinearMipMapLinearFilter;
-    
-    this.anisotropy = 1;
-    
-    this.format = $3Dmol.RGBAFormat;
-    this.type = $3Dmol.UnsignedByteType;
-    
-    this.offset = new $3Dmol.Vector2(0, 0);
-    this.repeat = new $3Dmol.Vector2(1, 1);
+        this.c1.copy(cylinder.c1);
+        this.c2.copy(cylinder.c2);
+        this.direction.copy(cylinder.direction);
+        this.radius = cylinder.radius;
+
+        return this;
+
+    },
     
-    this.generateMipmaps = true;
-    this.premultiplyAlpha = false;
-    this.flipY = true;
-    this.unpackAlignment = 4;
+    lengthSq : function() {
     
-    this.needsUpdate = false;
-    this.onUpdate = null;
+        var vector = new $3Dmol.Vector3();
+        
+        return function(){
+            return vector.subVectors(this.c2, this.c1).lengthSq();
+        };
+        
+    }(),
+
+    applyMatrix4 : function(matrix) {
+        
+        this.direction.add(this.c1).applyMatrix4(matrix);
+        this.c1.applyMatrix4(matrix);
+        this.c2.applyMatrix4(matrix);
+        this.direction.sub(this.c1).normalize();
+        this.radius = this.radius * matrix.getMaxScaleOnAxis();
+
+        return this;
+
+    }
+
+};
+
+
+//plane specified by three points
+/** @constructor */
+$3Dmol.Triangle = function(a, b, c){
+   
+    this.a = (a !== undefined) ?
+        a : new $3Dmol.Vector3();
+
+    this.b = (b !== undefined) ?
+        b : new $3Dmol.Vector3();
     
+    this.c = (c !== undefined) ?
+        c : new $3Dmol.Vector3();   
+  
 };
 
-$3Dmol.Texture.prototype = {
+$3Dmol.Triangle.prototype = {
 
-    constructor : $3Dmol.Texture,
+    constructor : $3Dmol.Triangle,
     
-    clone : function(texture) {
+    copy : function(triangle) {
         
-        if (texture === undefined)
-            texture = new $3Dmol.Texture();
+        this.a.copy(triangle.a);
+        this.b.copy(triangle.b);
+        this.c.copy(triangle.c);
         
-        texture.image = this.image;
-        texture.mipmaps = this.mipmaps.slice(0);
+        return this;
         
-        texture.mapping = this.mapping;
+    },
+    
+    applyMatrix4 : function(matrix) {
         
-        texture.wrapS = this.wrapS;
-        texture.wrapT = this.wrapT;
+        this.a.applyMatrix4(matrix);
+        this.b.applyMatrix4(matrix);
+        this.c.applyMatrix4(matrix);
         
-        texture.magFilter = this.magFilter;
-        texture.minFilter = this.minFilter;
+        return this;
         
-        texture.anisotropy = this.anisotropy;
+    },
+    
+    getNormal : function() {
         
-        texture.format = this.format;
-        texture.type = this.type;
+        var v1 = new $3Dmol.Vector3();
         
-        texture.offset.copy(this.offset);
-        texture.repeat.copy(this.repeat);
+        return function() {
+            
+            var norm = this.a.clone();
+            norm.sub(this.b);
+            v1.subVectors(this.c, this.b);
+            
+            norm.cross(v1);
+            norm.normalize();
+            
+            return norm;
+            
+        };
         
-        texture.generateMipmaps = this.generateMipmaps;
-        texture.premultiplyAlpha = this.premultiplyAlpha;
-        texture.flipY = this.flipY;
-        texture.unpackAlignment = this.unpackAlignment;
+    }()
+
+};
+
+
+/* core Object3D
+ * Base class for Scene, Camera, Geometry
+ * Geometry class
+ */
+
+//Event Handling
+/** @this {$3Dmol.EventDispatcher} */
+$3Dmol.EventDispatcher = function() {
+  
+    var listeners = {};
+    
+    this.addEventListener = function(type, listener) {
+        if (listeners[type] === undefined)
+            listeners[type] = [];
         
-        return texture;
+        if (listeners[type].indexOf(listener) === -1)
+            listeners[type].push(listener);
+    };  
+    
+    this.removeEventListener = function(type, listener) {
         
-    },
+        var index = listeners[type].indexOf(listener);
+        
+        if (index !== -1)
+            listeners[type].splice(index, 1);
+              
+    };
     
-    dispose : function() {
+    this.dispatchEvent = function(event) {
         
-        this.dispatchEvent( {type: 'dispose'});
+        var listenerArray = listeners[event.type];
         
-    }    
+        if (listenerArray !== undefined) {
+            event.target = this;
+            
+            for (var i = 0, l = listenerArray.length; i < l; i++)
+                listenerArray[i].call(this, event);
+                
+        }
+            
+    };
     
 };
 
-$3Dmol.TextureIdCount = 0;
-
-
-// sides
-$3Dmol.FrontSide = 0;
-$3Dmol.BackSide = 1;
-$3Dmol.DoubleSide = 2;
-
-// shading
-$3Dmol.NoShading = 0;
-$3Dmol.FlatShading = 1;
-$3Dmol.SmoothShading = 2;
-
-// colors
-$3Dmol.NoColors = 0;
-$3Dmol.FaceColors = 1;
-$3Dmol.VertexColors = 2;
-
-//Texture constants
-//TODO: Which of these do I need (since I only use textures to display label sprites) ?
-$3Dmol.MultiplyOperation = 0;
-$3Dmol.MixOperation = 1;
-$3Dmol.AddOperation = 2;
-
-// mapping modes
-
-$3Dmol.UVMapping = function() {};
-
-// wrapping modes
-$3Dmol.ClampToEdgeWrapping = 1001;
-
-//Filters
-$3Dmol.LinearFilter = 1006;
-$3Dmol.LinearMipMapLinearFilter = 1008;
-
-//Data types
-$3Dmol.UnsignedByteType = 1009;
-
-//Pixel formats
-$3Dmol.RGBAFormat = 1021;/* 
- * $3Dmol Mesh and Line objects
- */
-
-
-//Line Object
-/** @constructor */
-$3Dmol.Line = function (geometry, material, type) {
-
-    $3Dmol.Object3D.call(this);
-
-    this.geometry = geometry;
-        //TODO: update material and type to webgl
-    this.material = (material !== undefined) ? material : new $3Dmol.LineBasicMaterial( { color: Math.random() * 0xffffff } );
-    this.type = (type !== undefined) ? type : $3Dmol.LineStrip;
+$3Dmol.Color = function( color ){
+    
+    if ( arguments.length > 1) {
+            this.r = arguments[0] || 0.0;
+            this.g = arguments[1] || 0.0;
+            this.b = arguments[2] || 0.0;
 
+            return this;
+    }
+    
+    return this.set(color);
+                
 };
 
-$3Dmol.LineStrip = 0;
-$3Dmol.LinePieces = 1;
+$3Dmol.Color.prototype = {
+    
+    constructor: $3Dmol.Color,
+    
+    r: 0.0, g: 0.0, b: 0.0,
+    
+    set : function(val) {
+        
+            if (val instanceof $3Dmol.Color) 
+                return val.clone();
 
-$3Dmol.Line.prototype = Object.create($3Dmol.Object3D.prototype);
+            else if (typeof val === 'number')
+                this.setHex(val);
+            
+            else if (typeof val === 'object' && "r" in val && "g" in val && "b" in val) {
+                this.r = val.r;
+                this.g = val.g;
+                this.b = val.b;
+            }
+    },
+    
+    setHex: function(hex) {
+        
+            hex = Math.floor(hex);
 
-$3Dmol.Line.prototype.clone = function (object) {
-
-    if (object === undefined) object = new $3Dmol.Line(this.geometry, this.material, this.type);
-
-    $3Dmol.Object3D.prototype.clone.call(this, object);
-
-    return object;
-
-};
-
-
-//Mesh Object
-/** @constructor */
-$3Dmol.Mesh = function(geometry, material) {
-
-    $3Dmol.Object3D.call(this);
-
-    this.geometry = geometry;
-    this.material = (material !== undefined) ? material : new $3Dmol.MeshBasicMaterial( { color: Math.random() * 0xffffff, wireframe: true } );
-
-};
-
-$3Dmol.Mesh.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Mesh.prototype.clone = function (object) {
-
-    if (object === undefined) object = new $3Dmol.Mesh(this.geometry, this.material);
-
-    $3Dmol.Object3D.prototype.clone.call(this, object);
-
-    return object;
-
-};
-
-
-//Sprite object
-/** @constructor */
-$3Dmol.Sprite = function(material) {
+            this.r = (hex >> 16 & 255) / 255;
+            this.g = (hex >> 8 & 255) / 255;
+            this.b = (hex & 255) / 255;                                                                                     
+        
+            return this;
+    },
     
-    $3Dmol.Object3D.call(this);
+    getHex: function() {
+        var R = Math.round(this.r*255);
+        var G = Math.round(this.g*255);
+        var B = Math.round(this.b*255);
+        return R<<16 | G << 8 | B;
+    },
     
-    this.material = (material !== undefined) ? material : new $3Dmol.SpriteMaterial();
-
-    this.rotation3d = this.rotation;
-    this.rotation = 0;
+    clone : function() {
+            return new $3Dmol.Color(this.r, this.g, this.b);
+    },
+        
+    copy : function(color) {
+        this.r = color.r;
+        this.g = color.g;
+        this.b = color.b;
+        
+        return this;
+    },
+    
+    //return object that represents color components from 0 to 255
+    scaled : function() {
+        var ret = {};
+        ret.r = Math.round(this.r*255);
+        ret.g = Math.round(this.g*255);
+        ret.b = Math.round(this.b*255);
+        ret.a = 1.0;
+        return ret;
+    }
     
 };
 
-$3Dmol.Sprite.prototype = Object.create($3Dmol.Object3D.prototype);
-
-$3Dmol.Sprite.prototype.updateMatrix = function() {
-    
-    this.matrix.setPosition(this.position);
+//Object3D base constructor function
+/** @this {$3Dmol.Object3D} */
+$3Dmol.Object3D = function() {
     
-    this.rotation3d.set(0, 0, this.rotation);
-    this.matrix.setRotationFromEuler(this.rotation3d);
+    this.id = $3Dmol.Object3DIDCount++;
     
-    if (this.scale.x !== 1 || this.scale.y !== 1)
-        this.matrix.scale(this.scale);
+    this.name = "";
     
-    this.matrixWorldNeedsUpdate = true;
+    this.parent = undefined;
+    this.children = [];
     
-};
-
-$3Dmol.Sprite.prototype.clone = function(object) {
+    this.position = new $3Dmol.Vector3();
+    this.rotation = new $3Dmol.Vector3();
+    this.matrix = new $3Dmol.Matrix4();
+    this.matrixWorld = new $3Dmol.Matrix4();
+    this.quaternion = new $3Dmol.Quaternion();
+    this.eulerOrder = 'XYZ';
     
-    if (object === undefined)
-        object = new $3Dmol.Sprite(this.material);
+    this.up = new $3Dmol.Vector3(0, 1, 0);
+    this.scale = new $3Dmol.Vector3(1, 1, 1);
     
-    $3Dmol.Object3D.prototype.clone.call(this, object);
+    this.matrixAutoUpdate = true;
+    this.matrixWorldNeedsUpdate = true;
+    this.rotationAutoUpdate = true;
+    this.useQuaternion = false;
     
-    return object;
+    this.visible = true;
     
 };
-/**
-Simplified webGL renderer 
- */
-
-$3Dmol.Renderer = function ( parameters ) {
-    
-    parameters = parameters || {};
-    
-    var _canvas = parameters.canvas !== undefined ? parameters.canvas : document.createElement( 'canvas' ),
-
-    _precision = parameters.precision !== undefined ? parameters.precision : 'highp',
-
-    _alpha = parameters.alpha !== undefined ? parameters.alpha : true,
-    _premultipliedAlpha = parameters.premultipliedAlpha !== undefined ? parameters.premultipliedAlpha : true,
-    _antialias = parameters.antialias !== undefined ? parameters.antialias : false,
-    _stencil = parameters.stencil !== undefined ? parameters.stencil : true,
-    _preserveDrawingBuffer = parameters.preserveDrawingBuffer !== undefined ? parameters.preserveDrawingBuffer : false,
-
-    _clearColor = parameters.clearColor !== undefined ? new $3Dmol.Color( parameters.clearColor ) : new $3Dmol.Color( 0x000000 ),
-    _clearAlpha = parameters.clearAlpha !== undefined ? parameters.clearAlpha : 0;
-    
-    this.domElement = _canvas;
-    this.context = null;
-    this.devicePixelRatio = parameters.devicePixelRatio !== undefined ? 
-    parameters.devicePixelRatio : (self.devicePixelRatio !== undefined) ? 
-                                   self.devicePixelRatio : 1;
-
-    // clearing
-
-    this.autoClear = true;
-    this.autoClearColor = true;
-    this.autoClearDepth = true;
-    this.autoClearStencil = true;
-
-    // scene graph
-
-    this.sortObjects = true;
 
-    this.autoUpdateObjects = true;
-    this.autoUpdateScene = true;
-    
-    this.renderPluginsPost = [];
+$3Dmol.Object3D.prototype = {
     
-    // info
-
-    this.info = {
-
-        memory: {
+    constructor : $3Dmol.Object3D,
     
-        programs: 0,
-        geometries: 0,
-        textures: 0
+    lookAt : function(vector) {
+        
+        this.matrix.lookAt(vector, this.position, this.up);
+        
+        if (this.rotationAutoUpdate) {
+            
+            if (this.useQuaternion === true) 
+                this.quaternion.copy(this.matrix.decompose()[1]);
+            else
+                this.rotation.setEulerFromRotationMatrix(this.matrix, this.eulerOrder);
+        }
+    },
     
-        },
+    //add child object
+    add : function(object) {
+        if (object === this){
+            console.error("Can't add $3Dmol.Object3D to itself");
+            return;
+        }
+        
+        object.parent = this;
+        this.children.push(object);
+        
+        //add to the scene (i.e. follow up this instance's parents until reach the top)
+        
+        var scene = this;
+        
+        while (scene.parent !== undefined)
+            scene = scene.parent;
+            
+        if (scene !== undefined && scene instanceof $3Dmol.Scene) 
+            scene.__addObject(object);
+        
+    },
     
-        render: {
+    remove : function(object) {
+        
+        var index = this.children.indexOf(object);
+        
+        if (index !== -1) {
+            
+            object.parent = undefined;
+            this.children.splice(index, 1);
+            
+            //Remove from scene
+            
+            var scene = this;
+            
+            while (scene.parent !== undefined)
+                scene = scene.parent;
+                
+            if (scene !== undefined && scene instanceof $3Dmol.Scene)
+                scene.__removeObject(object);
+                
+        }
+    },
     
-        calls: 0,
-        vertices: 0,
-        faces: 0,
-        points: 0
+    updateMatrix : function() {
+        
+        this.matrix.setPosition(this.position);
+        
+        if (this.useQuaternion === false) 
+            this.matrix.setRotationFromEuler(this.rotation, this.eulerOrder);
+        else
+            this.matrix.setRotationFromQuaternion(this.quaternion);
+        
+        //TODO: Do I need this??
+        if (this.scale.x !== 1 || this.scale.y !== 1 || this.scale.z !== 1)
+            this.matrix.scale(this.scale);
+            
+        this.matrixWorldNeedsUpdate = true;
+        
+    },
     
+    updateMatrixWorld : function(force) {
+        
+        if (this.matrixAutoUpdate === true) 
+            this.updateMatrix();
+        
+        if (this.matrixWorldNeedsUpdate === true || force === true) {
+            
+            if (this.parent === undefined)
+                this.matrixWorld.copy(this.matrix);
+            else
+                this.matrixWorld.multiplyMatrices(this.parent.matrixWorld, this.matrix);
+                
         }
+        
+        this.matrixWorldNeedsUpdate = false;
+        
+        //Update matrices of all children
+        for (var i = 0; i < this.children.length; i++) {
+            this.children[i].updateMatrixWorld(true);
+        }
+    },
+    
+    clone : function(object) {
+        
+        if (object === undefined)
+            object = new $3Dmol.Object3D();
+            
+        object.name = this.name;
+        
+        object.up.copy(this.up);
+        object.position.copy(this.position);
+        object.rotation.copy(this.rotation);
+        object.eulerOrder = this.eulerOrder;
+        object.scale.copy(this.scale);
 
-    };
-
-    // internal properties
-
-    var _this = this,
-
-    _programs = [],
-    _programs_counter = 0,
-
-    // internal state cache
-
-    _currentProgram = null,
-    _currentFramebuffer = null,
-    _currentMaterialId = -1,
-    _currentGeometryGroupHash = null,
-    _currentCamera = null,
-    _geometryGroupCounter = 0,
-
-    _usedTextureUnits = 0,
-
-    // GL state cache
-
-    _oldDoubleSided = -1,
-    _oldFlipSided = -1,
-
-    _oldBlending = -1,
-
-    _oldBlendEquation = -1,
-    _oldBlendSrc = -1,
-    _oldBlendDst = -1,
-
-    _oldDepthTest = -1,
-    _oldDepthWrite = -1,
-
-    _oldPolygonOffset = null,
-    _oldPolygonOffsetFactor = null,
-    _oldPolygonOffsetUnits = null,
-
-    _oldLineWidth = null,
-
-    _viewportX = 0,
-    _viewportY = 0,
-    _viewportWidth = 0,
-    _viewportHeight = 0,
-    _currentWidth = 0,
-    _currentHeight = 0,
-
-    _enabledAttributes = {},
-
-     // camera matrices cache
-
-    _projScreenMatrix = new $3Dmol.Matrix4(),
-
-    _vector3 = new $3Dmol.Vector3(),
-
-    // light arrays cache
-
-    _direction = new $3Dmol.Vector3(),
-
-    _lightsNeedUpdate = true,
-
-    _lights = {
-
-            ambient: [0,0,0],
-            directional: { length: 0, colors: [], positions: [] },
-            point: { length: 0, colors: [], positions: [], distances: [] },
-            spot: { length: 0, colors: [], positions: [], distances: [], directions: [], anglesCos: [], exponents: [] },
-            hemi: { length: 0, skyColors: [], groundColors: [], positions: [] }
-
-    };
-
-    // initialize
-
-    var _gl;
-
-    initGL();
-
-    setDefaultGLState();
-
-    this.context = _gl;    
-
-    // API
-
-    this.getContext = function () {
-
-            return _gl;
-
-    };
-
-    this.getPrecision = function () {
-
-            return _precision;
-
-    };
-    
-    this.setClearColorHex = function ( hex, alpha ) {
-
-            _clearColor.setHex( hex );
-            _clearAlpha = alpha;
-
-            _gl.clearColor( _clearColor.r, _clearColor.g, _clearColor.b, _clearAlpha );
-
-    };
-
-    this.setSize = function ( width, height ) {
-
-            _canvas.width = width * this.devicePixelRatio;
-            _canvas.height = height * this.devicePixelRatio;
-
-            _canvas.style.width = width + 'px';
-            _canvas.style.height = height + 'px';
-
-            this.setViewport( 0, 0, _canvas.width, _canvas.height );
-
-    };
-
-    this.setViewport = function ( x, y, width, height ) {
-
-            _viewportX = x !== undefined ? x : 0;
-            _viewportY = y !== undefined ? y : 0;
-
-            _viewportWidth = width !== undefined ? width : _canvas.width;
-            _viewportHeight = height !== undefined ? height : _canvas.height;
-
-            _gl.viewport( _viewportX, _viewportY, _viewportWidth, _viewportHeight );
-
-    };
-
-    this.clear = function ( color, depth, stencil ) {
-
-            var bits = 0;
-
-            if ( color === undefined || color ) bits |= _gl.COLOR_BUFFER_BIT;
-            if ( depth === undefined || depth ) bits |= _gl.DEPTH_BUFFER_BIT;
-            if ( stencil === undefined || stencil ) bits |= _gl.STENCIL_BUFFER_BIT;
-            _gl.clear( bits );
-
-    };
-
-    this.clearTarget = function ( color, depth, stencil ) {
-            
-            this.clear( color, depth, stencil );
-
-    };
-
-    this.setMaterialFaces = function ( material ) {
-
-            var doubleSided = material.side === $3Dmol.DoubleSide;
-            var flipSided = material.side === $3Dmol.BackSide;
-
-            if ( _oldDoubleSided !== doubleSided ) {
-
-                if ( doubleSided ) {
-
-                    _gl.disable( _gl.CULL_FACE );
-
-                } else {
-
-                    _gl.enable( _gl.CULL_FACE );
-
-                }
-
-                _oldDoubleSided = doubleSided;
-
-            }
-
-            if ( _oldFlipSided !== flipSided ) {
-
-                if ( flipSided ) {
-
-                    _gl.frontFace( _gl.CW );
-
-                } else {
-
-                    _gl.frontFace( _gl.CCW );
-
-                }
-
-                _oldFlipSided = flipSided;
-
-            }    
-
-    };
-    
-    this.setDepthTest = function ( depthTest ) {
-
-            if ( _oldDepthTest !== depthTest ) {
-
-                if ( depthTest ) {
-
-                    _gl.enable( _gl.DEPTH_TEST );
-
-                } else {
-
-                    _gl.disable( _gl.DEPTH_TEST );
-
-                }
-
-                _oldDepthTest = depthTest;
-
-            }
-
-    };
-
-    this.setDepthWrite = function ( depthWrite ) {
-
-            if ( _oldDepthWrite !== depthWrite ) {
-
-                    _gl.depthMask( depthWrite );
-                    _oldDepthWrite = depthWrite;
-
-            }
-
-    };
-
-    this.setBlending = function( blending ) {
-
-        if (!blending) {
-                _gl.disable( _gl.BLEND );
-
-        } 
-        else {
-            _gl.enable( _gl.BLEND );
-            _gl.blendEquationSeparate( _gl.FUNC_ADD, _gl.FUNC_ADD );
-            _gl.blendFuncSeparate( _gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA, _gl.ONE, _gl.ONE_MINUS_SRC_ALPHA );
-
+        object.rotationAutoUpdate = this.rotationAutoUpdate;
+        object.matrix.copy(this.matrix);
+        object.matrixWorld.copy(this.matrixWorld);
+        object.quaternion.copy(this.quaternion);
+        object.matrixAutoUpdate = this.matrixAutoUpdate;
+        object.matrixWorldNeedsUpdate = this.matrixWorldNeedsUpdate;
+        
+        object.useQuaternion = this.useQuaternion;
+        
+        object.visible = this.visible;
+        
+        for (var i = 0; i < this.children.length; i++) {
+            var child = this.children[i];
+            object.add(child.clone());
         }
-
-        _oldBlending = blending;
-    };
-    
-    // Plugins
+        
+        return object;
+        
+    },
     
-    this.addPostPlugin = function(plugin) {
-
-        plugin.init(this);
-        this.renderPluginsPost.push(plugin);
-
-    };
-
-    // Sorting
-
-    function numericalSort ( a, b ) {
-
-            return b[ 0 ] - a[ 0 ];
-
-    }
-
-    function enableAttribute( attribute ) {
-
-        if ( ! _enabledAttributes[ attribute ] ) {
-
-            _gl.enableVertexAttribArray( attribute );
-            _enabledAttributes[ attribute ] = true;
-
-        }
-
-    }
-
-    function disableAttributes() {
-
-        for ( var attribute in _enabledAttributes ) {
-
-            if ( _enabledAttributes[ attribute ] ) {
-
-                _gl.disableVertexAttribArray( attribute );
-                _enabledAttributes[ attribute ] = false;
-
-            }
-
-        }
-
-    } 
-
-    function setPolygonOffset ( polygonOffset, factor, units) {
-
-        if ( _oldPolygonOffset !== polygonOffset ) {
-
-            if (polygonOffset)
-                _gl.enable( _gl.POLYGON_OFFSET_FILL );
-            else
-                _gl.disable( _gl.POLYGON_OFFSET_FILL );
+    setVisible: function(val) { //recursively set visibility
+        this.visible = val;
+        for (var i = 0; i < this.children.length; i++) {
+            var child = this.children[i];
+            child.setVisible(val);
         }
     }
+};
 
-    function setLineWidth ( width ) {
-
-        if ( width !== _oldLineWidth ) {
-            _gl.lineWidth(width);
-            _oldLineWidth = width;
-        }
+$3Dmol.Object3DIDCount = 0;
 
-    }
+//Geometry class
+//TODO: What can I remove - how can I optimize ?
+$3Dmol.Geometry = (function() {
+   
+    var BUFFERSIZE = 65535; //limited to 16bit indices
     
-    var onGeometryDispose = function(event) {
-        
-        var geometry = event.target;
-        geometry.removeEventListener('dispose', onGeometryDispose);
-        
-        deallocateGeometry(geometry);
-        
-        _this.info.memory.geometries--;
+    
+    /** @constructor */
+    var geometryGroup = function(id) {
+        this.id = id || 0;
+        //for performance reasons, callers must directly modify these
+        this.vertexArray = null;
+        this.colorArray = null;
+        this.normalArray = null;
+        this.faceArray = null;
+        this.radiusArray = null;
+        //this.adjFaceArray=null;
+        this.lineArray = null;
+        this.vertices = 0;
+        this.faceidx = 0;
+        this.lineidx = 0;
         
     };
     
-    var onTextureDispose = function(event) {
-
-        var texture = event.target;
-
-        texture.removeEventListener('dispose', onTextureDispose);
-
-        deallocateTexture(texture);
-
-        _this.info.memory.textures--;
-
-
+    geometryGroup.prototype.getNumVertices = function() {
+        return this.vertices;
     };
     
-    var onMaterialDispose = function(event) {
-        
-        var material = event.target;
-        material.removeEventListener('dispose', onMaterialDispose);
-        
-        deallocateMaterial(material);
-        
+    geometryGroup.prototype.getVertices = function() {
+        return this.vertexArray;
     };
     
-    var deallocateGeometry = function(geometry) {
-        
-        geometry.__webglInit = undefined;
+    
+    geometryGroup.prototype.getCentroid = function() {
         
-        if (geometry.__webglVertexBuffer !== undefined)
-            _gl.deleteBuffer(geometry.__webglVertexBuffer);
+        var centroid = new $3Dmol.Vector3();
+        var offset, x, y, z;
         
-        if (geometry.__webglColorBuffer !== undefined)
-            _gl.deleteBuffer(geometry.__webglColorBuffer);
+        for (var i = 0; i < this.vertices; ++i) {
+            offset = i*3;
+            
+            x = this.vertexArray[offset]; y = this.vertexArray[offset+1]; z = this.vertexArray[offset+2];
+            
+            centroid.x += x; centroid.y += y; centroid.z += z;
+        }
         
-        if (geometry.geometryGroups !== undefined) {
+        //divideScalar checks for 0 denom
+        centroid.divideScalar(this.vertices);
+        
+        return centroid;
+    };
+    
+    //setup normals - vertex and face array must exist
+    geometryGroup.prototype.setNormals = function() {        
+        
+        var faces = this.faceArray;
+        var verts = this.vertexArray;
+        var norms = this.normalArray;
+        
+        if (! this.vertices || ! this.faceidx) 
+            return;
+        
+        //vertex indices
+        var a, b, c, d,
+        //and actual vertices
+        vA, vB, vC, norm;
             
-            for (var g = 0, gl = geometry.groups; g < gl; g++) {  
-                
-                var geometryGroup = geometry.geometryGroups[g];
-
-                if (geometryGroup.__webglVertexBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglVertexBuffer);
-
-                if (geometryGroup.__webglColorBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglColorBuffer);
-                
-                if (geometryGroup.__webglNormalBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglNormalBuffer);  
+        for (var i = 0; i < faces.length / 3; ++i) {
+            
+            a = faces[i * 3] * 3;
+            b = faces[i * 3 + 1] * 3;
+            c = faces[i * 3 + 2] * 3;
+            
+            vA = new $3Dmol.Vector3(verts[a], verts[a+1], verts[a+2]);
+            vB = new $3Dmol.Vector3(verts[b], verts[b+1], verts[b+2]);
+            vC = new $3Dmol.Vector3(verts[c], verts[c+1], verts[c+2]);
+            
+            vA.subVectors(vA, vB);
+            vC.subVectors(vC, vB);
+            vC.cross(vA);
+            
+            //face normal
+            norm = vC;
+            norm.normalize();
+            
+            norms[a] += norm.x; norms[b] += norm.x; norms[c] += norm.x;
+            norms[a + 1] += norm.y; norms[b + 1] += norm.y; norms[c + 1] += norm.y;
+            norms[a + 2] += norm.z; norms[b + 2] += norm.z; norms[c + 2] += norm.z;
+            
+        }             
                 
-                if (geometryGroup.__webglFaceBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglFaceBuffer);
-                    
-                if (geometryGroup.__webglLineBuffer !== undefined)
-                    _gl.deleteBuffer(geometryGroup.__webglLineBuffer);
-                    
-            }
-        }
     };
     
-    var deallocateMaterial = function (material) {
-
-        var program = material.program;
-
-        if ( program === undefined ) return;
-
-        material.program = undefined;
-
-        // only deallocate GL program if this was the last use of shared program
-        // assumed there is only single copy of any program in the _programs list
-        // (that's how it's constructed)
-
-        var i, il, programInfo;
-        var deleteProgram = false;
-
-        for ( i = 0, il = _programs.length; i < il; i ++ ) {
-
-            programInfo = _programs[ i ];
-
-            if ( programInfo.program === program ) {
-
-                programInfo.usedTimes --;
-
-                if ( programInfo.usedTimes === 0 ) {
-
-                    deleteProgram = true;
-
-                }
-
-                break;
-
-            }
-
-        }
-
-        if ( deleteProgram === true ) {
-
-            // avoid using array.splice, this is costlier than creating new array from scratch
-
-            var newPrograms = [];
-
-            for ( i = 0, il = _programs.length; i < il; i ++ ) {
-
-                programInfo = _programs[ i ];
-
-                if ( programInfo.program !== program ) {
-
-                    newPrograms.push( programInfo );
-
-                }
-
-            }
-
-            _programs = newPrograms;
-
-            _gl.deleteProgram( program );
-
-            _this.info.memory.programs --;
-
+    //sets line index array from face arr
+    //Note - assumes all faces are triangles (i.e. there will
+    //be an extra diagonal for four-sided faces - user should 
+    //specify linearr for custom shape generation to show wireframe squares
+    //as rectangles rather than two triangles)
+    geometryGroup.prototype.setLineIndices = function() {
+        
+        if (! this.faceidx)
+            return;
+                    
+        var faceArr = this.faceArray, lineArr = this.lineArray = new Uint16Array(this.faceidx*2);      
+        this.lineidx = this.faceidx*2;         
+        var faceoffset;
+            
+        for (var i = 0; i < this.faceidx / 3; ++i) {
+            
+            faceoffset = i*3; lineoffset = faceoffset*2;          
+            var a = faceArr[faceoffset], b = faceArr[faceoffset+1], c = faceArr[faceoffset+2];
+            
+            lineArr[lineoffset] = a; lineArr[lineoffset+1] = b;
+            lineArr[lineoffset+2] = a; lineArr[lineoffset+3] = c;
+            lineArr[lineoffset+4] = b; lineArr[lineoffset+5] = c;
+            
         }
-
     };
     
-    var deallocateTexture = function(texture) {
-
-        if (texture.image && texture.image.__webglTextureCube) {
-
-            // cube texture
-
-            _gl.deleteTexture(texture.image.__webglTextureCube);
+    geometryGroup.prototype.truncateArrayBuffers = function(mesh, reallocatemem) {
+        
+        mesh = (mesh === true) ? true : false;
+        
+        var vertexArr = this.vertexArray,
+            colorArr = this.colorArray,
+            normalArr = this.normalArray,
+            faceArr = this.faceArray,
+            lineArr = this.lineArray,
+            radiusArr = this.radiusArray;
 
-        } 
+        //subarray to avoid copying and reallocating memory
+        this.vertexArray = vertexArr.subarray(0,this.vertices*3);
+        this.colorArray = colorArr.subarray(0,this.vertices*3);
         
+        if (mesh) {
+            this.normalArray = normalArr.subarray(0,this.vertices*3);
+            this.faceArray = faceArr.subarray(0,this.faceidx); 
+            
+            if(this.lineidx > 0) //not always set so reclaim memory
+                this.lineArray = lineArr.subarray(0,this.lineidx); 
+            else
+                this.lineArray = new Uint16Array();
+                        
+        }        
         else {
-
-            // 2D texture
-
-            if ( ! texture.__webglInit ) return;
-
-            texture.__webglInit = false;
-            _gl.deleteTexture( texture.__webglTexture );
-
+            this.normalArray = new Float32Array(); 
+            this.faceArray = new Uint16Array(); 
+            this.lineArray = new Uint16Array(); 
         }
-
-    };
-
-    //Compile and return shader
-    function getShader (type, str) {
-
-        var shader;
-
-        if (type === "fragment")
-            shader = _gl.createShader( _gl.FRAGMENT_SHADER );
-        else if (type === "vertex")
-            shader = _gl.createShader( _gl.VERTEX_SHADER );
-
-        _gl.shaderSource(shader, str);
-        _gl.compileShader(shader);
-
-        if ( ! _gl.getShaderParameter(shader, _gl.COMPILE_STATUS) ) {
-
-            console.error(_gl.getShaderInfoLog(shader));
-            console.error("could not initialize shader");
-            return null;
-
+        if (radiusArr) {
+            this.radiusArray = radiusArr.subarray(0, this.vertices);
         }
-
-        return shader;
-
-    } 
-
-
-    //Compile appropriate shaders (if necessary) from source code and attach to gl program.
-    function buildProgram(fragmentShader, vertexShader, uniforms, parameters) {
-
-        var p, pl, d, program, code;
-        var chunks = [];
-
-        chunks.push(fragmentShader);
-        chunks.push(vertexShader);
         
-        for (p in parameters) {
-            chunks.push(p);
-            chunks.push(parameters[p]);
+        if(reallocatemem) { 
+            //actually copy smaller arrays to save memory
+            if(this.normalArray) this.normalArray = new Float32Array(this.normalArray);
+            if(this.faceArray) this.faceArray = new Uint16Array(this.faceArray);
+            if(this.lineArray) this.lineArray = new Uint16Array(this.lineArray);
+            if(this.vertexArray) this.vertexArray = new Float32Array(this.vertexArray);
+            if(this.colorArray) this.colorArray = new Float32Array(this.colorArray);
+            if(this.radiusArray) this.radiusArray = new Float32Array(this.radiusArray);
         }
+        this.__inittedArrays = true;        
         
-        code = chunks.join();
-
-        //check if program has already been compiled
-
-        for (p = 0, pl = _programs.length; p < pl; p++) {
-
-            var programInfo = _programs[p];
-
-            if (programInfo.code === code) {
-
-                programInfo.usedTimes++;
-
-                return programInfo.program;
-            }
-        }
-
-        //Set up new program and compile shaders
-
-        program = _gl.createProgram();
+    };
+    
+    var addGroup = function(geo) {
+        var ret = new geometryGroup(geo.geometryGroups.length);
+        geo.geometryGroups.push(ret);
+        geo.groups = geo.geometryGroups.length;
         
-        //set up precision
-        var precision = _precision;
-        var prefix = "precision " + precision + " float;";
+        ret.vertexArray = new Float32Array(BUFFERSIZE*3);
+        ret.colorArray = new Float32Array(BUFFERSIZE*3);
         
-        var prefix_vertex = [
-                             prefix
-                            ].join("\n");
-                            
-        var prefix_fragment = [                               
-                               parameters.wireframe ? "#define WIREFRAME 1" : "",
-                               prefix
-                              ].join("\n");
+        //TODO: instantiating uint arrays according to max number of vertices
+        // is dangerous, since there exists the possibility that there will be 
+        // more face or line indices than vertex points - but so far that doesn't
+        // seem to be the case for any of the renders 
+        if (geo.mesh) {
+            ret.normalArray = new Float32Array(BUFFERSIZE*3);
+            ret.faceArray = new Uint16Array(BUFFERSIZE*6);
+            ret.lineArray = new Uint16Array(BUFFERSIZE*6);
+        }
+        if (geo.radii) {
+            ret.radiusArray = new Float32Array(BUFFERSIZE);
+        }
+        ret.useOffset = geo.offset;
         
-        var glFragmentShader = getShader("fragment", prefix_fragment + fragmentShader);
-        var glVertexShader = getShader("vertex", prefix_vertex + vertexShader);
-
-        _gl.attachShader(program, glVertexShader);
-        _gl.attachShader(program, glFragmentShader);
-
-        _gl.linkProgram(program);
-
-        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
-            console.error("Could not initialize shader");
-
-        //gather and cache uniform variables and attributes
-
-        program.uniforms = {};
-        program.attributes = {};
-
-        var identifiers, u, a, i;
-
-        //uniform vars
-        identifiers = 
-            [ 'viewMatrix', 'modelViewMatrix', 'projectionMatrix', 'normalMatrix', 'modelMatrix', 'cameraPosition' ];
-
-        //custom uniform vars
-        for (u in uniforms) 
-            identifiers.push(u);
-
-        for (i = 0; i < identifiers.length; i++) {
-
-            var uniformVar = identifiers[i];
-            program.uniforms[uniformVar] = _gl.getUniformLocation(program, uniformVar);
-
-        }
-
-        //attributes
-        identifiers = 
-            [ 'position', 'normal', 'color', 'lineDistance' ];
-
-        /*
-        for (a in attributes)
-                identifiers.push(a);
-        */
-
-        for (i = 0; i < identifiers.length; i++) {
-
-            var attributeVar = identifiers[i];
-            program.attributes[attributeVar] = _gl.getAttribLocation(program, attributeVar);
-        }
-
-        program.id = _programs_counter++;
-        _programs.push( {program: program, code: code, usedTimes: 1} );
-        _this.info.memory.programs = _programs.length;
-
-        return program;
-    }
-
-    //TODO: need to set up shader attributes and uniforms as attributes on material object after attaching prgm
-    //We need to attach appropriate uniform variables to material after shaders have been chosen
-    this.initMaterial = function ( material, lights, fog, object ) {
-
-        material.addEventListener('dispose', onMaterialDispose);
-
-        var u, a, identifiers, i, parameters, maxLightCount, maxBones, maxShadows, shaderID;
-
-        shaderID = material.shaderID;
-
-        if (shaderID) {
-
-            var shader = $3Dmol.ShaderLib[shaderID];
-            material.vertexShader = shader.vertexShader;
-            material.fragmentShader = shader.fragmentShader;
-            material.uniforms = $3Dmol.ShaderUtils.clone(shader.uniforms);
-            //TODO: set material uniforms to shader uniform variables
-
-        }
         
-        parameters = {
-            wireframe: material.wireframe
-        };
-
-        material.program = buildProgram(material.fragmentShader, material.vertexShader, material.uniforms, parameters);
-
+        return ret;
     };
-
-    function setProgram( camera, lights, fog, material, object ) {
-
-        if ( material.needsUpdate ) {
-
-            if (material.program)
-                deallocateMaterial(material);
-
-                _this.initMaterial( material, lights, fog, object );
-                material.needsUpdate = false;
-        }
-
-        var refreshMaterial = false;
-
-        //p_uniforms: uniformVarName => uniformLocation
-        //m_uniforms: uniformVarName => uniformJsVal
-        var program = material.program,
-            p_uniforms = program.uniforms,
-            m_uniforms = material.uniforms;
-
-        if (program != _currentProgram) {   
-            _gl.useProgram(program);
-            _currentProgram = program;
-
-            refreshMaterial = true;
-        }
-
-        if (material.id != _currentMaterialId) {
-            _currentMaterialId = material.id;
-            refreshMaterial = true;
-        }
-
-        if (camera != _currentCamera) {    
-            _currentCamera = camera;
-            refreshMaterial = true;
-        }
+    /** @constructor */
+    var Geometry = function(mesh, radii,offset) {
         
-        _gl.uniformMatrix4fv(p_uniforms.projectionMatrix, false, camera.projectionMatrix.elements);
-        _gl.uniformMatrix4fv(p_uniforms.modelViewMatrix, false, object._modelViewMatrix.elements);
-        _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false, object._normalMatrix.elements);
+        $3Dmol.EventDispatcher.call(this);
         
-        //Send projection matrix to uniform variable in shader
-        if (refreshMaterial) {
-
-            //Load projection, model-view matrices for perspective
-
-
-            //Set up correct fog uniform vals
-            m_uniforms.fogColor.value = fog.color;
-            m_uniforms.fogNear.value = fog.near;
-            m_uniforms.fogFar.value = fog.far;
-
-            //Set up lights for lambert shader
-            if (material.shaderID.lastIndexOf("lambert",0) === 0) {
-
-                //load view and normal matrices for directional and object lighting
-                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false, camera.matrixWorldInverse.elements);
-                //_gl.uniformMatrix4fv(p_uniforms.modelMatrix, false, object.matrixWorld.elements);
-
-                if (_lightsNeedUpdate) {
-                    setupLights(program, lights);
-                    _lightsNeedUpdate = false;
-                }
-
-                //Set up correct light uniform var vals
-                m_uniforms.ambientLightColor.value = _lights.ambient;
-                m_uniforms.directionalLightColor.value = _lights.directional.colors;
-                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
-                m_uniforms.ambient.value = material.ambient;
-                m_uniforms.emissive.value = material.emissive;
+        this.id = $3Dmol.GeometryIDCount++;
+    
+        this.name = '';
+    
+        this.hasTangents = false;
+    
+        this.dynamic = true; // the intermediate typed arrays will be deleted when set to false
+        this.mesh = (mesh === true) ? true : false; // Does this geometry represent a mesh (i.e. do we need Face/Line index buffers?)
+        this.radii = radii || false;
+        this.offset = offset || false; //offset buffer used for instancing
+        // update flags
+    
+        this.verticesNeedUpdate = false;
+        this.elementsNeedUpdate = false;
+        this.normalsNeedUpdate = false;
+        this.colorsNeedUpdate = false;
+    
+        this.buffersNeedUpdate = false;
+        
+        this.geometryGroups = [];
+        this.groups = 0;
+        
+    };
+    
+    Geometry.prototype = {
+        
+        constructor : Geometry,
 
+        //Get geometry group to accomodate addVertices new vertices - create 
+        // new group if necessary       
+        updateGeoGroup : function(addVertices) {
+        
+            addVertices = addVertices || 0;
+            
+            var retGroup = this.groups > 0 ? this.geometryGroups[ this.groups - 1 ] : null;
+            
+            if (!retGroup || retGroup.vertices + addVertices > retGroup.vertexArray.length/3) 
+                retGroup = addGroup(this);
+                
+            return retGroup;
+            
+        },
+        
+        addGeoGroup : function() {
+            return addGroup(this);  
+        },
+        
+        setUpNormals : function(three) {
+            
+            three = three || false;
+            
+            for (var g = 0; g < this.groups; g++) {
+            
+                var geoGroup = this.geometryGroups[g];            
+                
+                geoGroup.setNormals(three);
+                
+            }  
+                      
+        },
+        
+        setUpWireframe : function() {
+            for (var g = 0; g < this.groups; g++) {
+                var geoGroup = this.geometryGroups[g];
+                
+                geoGroup.setLineIndices();
             }
-            else if( material.shaderID === "sphereimposter") {
-                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false, camera.matrixWorldInverse.elements);
-                _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false, object._normalMatrix.elements);
-            }
+        },
+        
+        //After vertices, colors, etc are collected in regular or typed arrays,
+        //  create typed arrays from regular arrays if they don't already exist,
+        initTypedArrays : function() {
                 
-
-            //opacity, diffuse, emissive, etc
-            m_uniforms.opacity.value = material.opacity;
-            m_uniforms.diffuse.value = material.color;
-
-            //Load any other material specific uniform variables to gl shaders
-            loadMaterialUniforms(p_uniforms, m_uniforms);
-
+            for (var g = 0; g < this.groups; g++) {
+                
+                var group = this.geometryGroups[g];
+                
+                if (group.__inittedArrays === true)
+                    continue;
+                
+                //do not actually reallocate smaller memory here because
+                //of the performance hit - if you know your geometry is small,
+                //truncate manually with the second parameter true
+                group.truncateArrayBuffers(this.mesh, false);
+            }
+            
+        
+        },
+        
+        dispose : function() {
+            this.dispatchEvent( {type : 'dispose'} );
         }
+    };
 
-        return program;
+    
+    return Geometry;
+    
+})();
 
-    }
+Object.defineProperty($3Dmol.Geometry.prototype, "vertices", {
+    
+    /** @this {$3Dmol.Geometry} */
+    get : function() {
+        var vertices = 0;
+        for (var g = 0; g < this.groups; g++)
+            vertices += this.geometryGroups[g].vertices;
+            
+        return vertices;
+    } 
+        
+});
 
-    function loadMaterialUniforms(p_uniforms, m_uniforms) {
-        var uniformVar, type, uniformVal, uniformLoc;
+$3Dmol.GeometryIDCount = 0;
 
-        for (uniformVar in m_uniforms) {
-            if (! p_uniforms[uniformVar])
-                continue;
 
-            type = m_uniforms[uniformVar].type;
-            uniformVal = m_uniforms[uniformVar].value;
-            uniformLoc = p_uniforms[uniformVar];
+//Raycaster
+/** @constructor */
+$3Dmol.Raycaster = (function() {
+    
+    var Raycaster = function(origin, direction, far, near) {
+        
+        this.ray = new $3Dmol.Ray(origin, direction);
+        
+        if (this.ray.direction.lengthSq() > 0) 
+            this.ray.direction.normalize();
+        
+        this.near = near || 0;
+        this.far = far || Infinity;
+    
+    };
+    
+    var sphere = new $3Dmol.Sphere();
+    var cylinder = new $3Dmol.Cylinder();
+    var triangle = new $3Dmol.Triangle();
+    var w_0 = new $3Dmol.Vector3(); // for cylinders, cylinder.c1 - ray.origin
+    var v1 = new $3Dmol.Vector3(); // all purpose local vector
+    var v2 = new $3Dmol.Vector3();
+    var v3 = new $3Dmol.Vector3();
+    //var facePlane = new $3Dmol.Plane();
+    var localRay = new $3Dmol.Ray();
+    var intersectPoint = new $3Dmol.Vector3();
+    var matrixPosition = new $3Dmol.Vector3();
+    
+    var inverseMatrix = new $3Dmol.Matrix4();
+        
+    var descSort = function(a, b) {
+        return a.distance - b.distance;
+    };
 
-            //single float
-            if (type === 'f')
-                _gl.uniform1f(uniformLoc, uniformVal);
-            //array of floats
-            else if (type === 'fv')
-                _gl.uniform3fv(uniformLoc, uniformVal);
-            //color - r,g,b floats
-            else if (type === 'c')
-                _gl.uniform3f(uniformLoc, uniformVal.r, uniformVal.g, uniformVal.b);
-
-        }
-
-    }
-
-    this.renderBuffer = function ( camera, lights, fog, material, geometryGroup, object ) {
-
-        if ( ! material.visible )
-            return;
-
-        var program, attributes, linewidth, primitives, a, attribute, i, il;
-
-        //Sets up proper vertex and fragment shaders and attaches them to webGL program
-        //Also sets appropriate uniform variables 
-        program = setProgram(camera, lights, fog, material, object);
-
-        attributes = program.attributes;
-
-        var updateBuffers = false,
-            wireframeBit = material.wireframe ? 1 : 0,
-            geometryGroupHash = (geometryGroup.id * 0xffffff) + (program.id * 2) + wireframeBit;
-
-        if (geometryGroupHash !== _currentGeometryGroupHash) {
-            _currentGeometryGroupHash = geometryGroupHash;
-            updateBuffers = true;
-        }
-
-        //rebind shader attributes to appropriate (and already initialized) gl buffers
-        if (updateBuffers) {
-
-            disableAttributes();
-
-            // Vertices
-            if (attributes.position >= 0) {            
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer );
-                enableAttribute( attributes.position );
-                _gl.vertexAttribPointer( attributes.position, 3, _gl.FLOAT, false, 0, 0 );    
-            }
-
-            // Colors
-            if (attributes.color >= 0) {
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer);
-                enableAttribute( attributes.color );
-                _gl.vertexAttribPointer( attributes.color, 3, _gl.FLOAT, false, 0, 0 );
-            }
+    // [-1, 1]
+    var clamp = function(x) {
+        return Math.min(Math.max(x, -1), 1);
+    };
+    
+    //object is a Sphere or (Bounding) Box
+    var intersectObject = function(group, clickable, raycaster, intersects) {
+        
+        matrixPosition.getPositionFromMatrix(group.matrixWorld);
+        
+        if ((clickable.clickable !== true) || (clickable.intersectionShape === undefined))
+            return intersects;       
+        var intersectionShape = clickable.intersectionShape;
+        var precision = raycaster.linePrecision;
+        precision *= group.matrixWorld.getMaxScaleOnAxis();
+        var precisionSq = precision*precision;
 
-            // Normals (lambert shader only)
-            if (attributes.normal >=0) {
-                _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer );
-                enableAttribute( attributes.normal );
-                _gl.vertexAttribPointer( attributes.normal, 3, _gl.FLOAT, false, 0, 0 );
+        //Check for intersection with clickable's bounding sphere, if it exists
+        if (clickable.boundingSphere !== undefined && clickable.boundingSphere instanceof $3Dmol.Sphere) {
+            sphere.copy(clickable.boundingSphere);
+            sphere.applyMatrix4(group.matrixWorld);          
+            if (!raycaster.ray.isIntersectionSphere(sphere)) {             
+				return intersects;
             }
-
-        }
-
-        //Render
-        var faceCount, lineCount;
-        //lambert shaders - draw triangles
-        //TODO: make sure geometryGroup's face count is setup correctly
-        if (object instanceof $3Dmol.Mesh) {
+        }      
+        //Iterate through intersection objects
+        var i, il,
+            norm, normProj, cylProj, rayProj,
+            distance, closestDistSq, denom, discriminant,
+            s, t, s_c, t_c;
+        //triangle faces
+        for (i = 0, il = intersectionShape.triangle.length; i < il; i++) {
             
-            if (material.wireframe) {
-                lineCount = geometryGroup.lineidx;
-                setLineWidth(material.wireframeLinewidth);
+            if (intersectionShape.triangle[i] instanceof $3Dmol.Triangle) {
                 
-                if (updateBuffers)
-                    _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglLineBuffer );
+                triangle.copy(intersectionShape.triangle[i]);
+                triangle.applyMatrix4(group.matrixWorld);
+                
+                norm = triangle.getNormal();
+                
+                normProj = raycaster.ray.direction.dot(norm);
+                
+                //face culling
+                if (normProj >= 0)
+                    continue;
+                
+                w_0.subVectors(triangle.a, raycaster.ray.origin);
+                
+                distance = (norm.dot(w_0)) / normProj;
+                
+                if (distance < 0)
+                    continue;
+                    
+                //intersects with plane, check if P inside triangle
+                v1.copy(raycaster.ray.direction).multiplyScalar(distance).add(raycaster.ray.origin);
+                v1.sub(triangle.a); // from pt a to intersection point P
+                
+                v2.copy(triangle.b).sub(triangle.a); // from pt a to b
+                v3.copy(triangle.c).sub(triangle.a); // from pt a to c
+                var b_dot_c = v2.dot(v3);
+                var b_sq = v2.lengthSq();
+                var c_sq = v3.lengthSq();
+                
+                // P = A + s(v2) + t(v3), inside trianle if 0 <= s, t <=1  and (s + t) <=0
                 
-                _gl.drawElements( _gl.LINES, lineCount, _gl.UNSIGNED_SHORT, 0 );
+                t = ( b_sq*v1.dot(v3) - b_dot_c*v1.dot(v2) ) / ( b_sq*c_sq - b_dot_c*b_dot_c );
+                
+                if (t < 0 || t > 1)
+                    continue;
+                
+                s = ( v1.dot(v2) - t*b_dot_c ) / b_sq;
+                
+                if ( (s < 0 || s > 1) || s + t > 1)
+                    continue;
+                    
+                else{
+                    intersects.push({clickable : clickable,
+                                     distance : distance});
+				}  
             }
+        }    
+        //cylinders
+        for (i = 0, il = intersectionShape.cylinder.length; i < il; i++) {
             
-            else {
-                faceCount = geometryGroup.faceidx;
-
-                if (updateBuffers)
-                    _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglFaceBuffer );
+            if (intersectionShape.cylinder[i] instanceof $3Dmol.Cylinder){
                 
-                _gl.drawElements( _gl.TRIANGLES, faceCount, _gl.UNSIGNED_SHORT, 0 );
+                cylinder.copy(intersectionShape.cylinder[i]);
+                cylinder.applyMatrix4(group.matrixWorld);
                 
-            }
-
-
-            _this.info.render.calls++;
-            _this.info.render.vertices += faceCount;
-            _this.info.render.faces += faceCount / 3;
-        }
-
-        //basic shaders - draw lines
-        else if (object instanceof $3Dmol.Line) {
-            lineCount = geometryGroup.vertices;
-
-            setLineWidth(material.linewidth);
-            _gl.drawArrays( _gl.LINES, 0, lineCount );
-
-            _this.info.render.calls++;
-        }
-
-    };
-
-    //rendering
-    function renderObjects ( renderList, reverse, materialType, camera, lights, fog, useBlending, overrideMaterial)  {
-
-        var webglObject, object, buffer, material, start, end, delta;
-
-        //Forward or backward render
-
-        if (reverse) {
-            start = renderList.length - 1;
-            end = -1;
-            delta = -1;
-        }
-
-        else {
-            start = 0;
-            end = renderList.length;
-            delta = 1;
-        }
-
-        for (var i = start; i !== end; i += delta) {
-
-            webglObject = renderList[i];
-
-            if (webglObject.render) {
-
-                object = webglObject.object;
-                buffer = webglObject.buffer;
-                material = webglObject[materialType];
-
-                if ( ! material )
+                w_0.subVectors(cylinder.c1, raycaster.ray.origin); 
+                
+                cylProj = w_0.dot(cylinder.direction); // Dela
+                rayProj = w_0.dot(raycaster.ray.direction); // Epsilon
+                
+                normProj = clamp(raycaster.ray.direction.dot(cylinder.direction)); // Beta
+                
+                denom = 1 - normProj*normProj;
+                
+                if (denom === 0.0)
                     continue;
+                
+                s_c = (normProj*rayProj - cylProj) / denom;
+                t_c = (rayProj - normProj*cylProj) / denom;
+                
+                v1.copy(cylinder.direction).multiplyScalar(s_c).add(cylinder.c1);  // Q_c
+                v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
+                
+                closestDistSq = v3.subVectors(v1, v2).lengthSq();
+                var radiusSq = cylinder.radius*cylinder.radius;
+                
+                //Smoothing?
+                //if (closestDistSq > radiusSq) radiusSq += precisionSq;
+                
+                // closest distance between ray and cylinder axis not greater than cylinder radius;
+                // might intersect this cylinder between atom and bond midpoint
+                if (closestDistSq <= radiusSq){
 
-                if (useBlending)
-                    _this.setBlending(true);
-
-                _this.setDepthTest(material.depthTest);
-                _this.setDepthWrite(material.depthWrite);
-                setPolygonOffset(material.polygonOffset, material.polygonOffsetFactor, material.polygonOffsetUnits);
-
-                _this.setMaterialFaces(material);
-
-                _this.renderBuffer(camera, lights, fog, material, buffer, object);
+                    //Find points where ray intersects sides of cylinder
+                    discriminant = (normProj*cylProj - rayProj)*(normProj*cylProj - rayProj) - 
+                            denom*(w_0.lengthSq() - cylProj*cylProj - radiusSq);
+                    
+                    // ray tangent to cylinder?
+                    if (discriminant <= 0)
+                        t = distance = Math.sqrt(closestDistSq);
+                    else
+                        t = distance = ( (rayProj - normProj*cylProj) - Math.sqrt(discriminant) ) / denom; 
+                    
+                    //find closest intersection point; make sure it's between atom's position and cylinder midpoint
+                    
+                    s = normProj*t - cylProj;
+                    
+                    //does not intersect cylinder between atom and midpoint,
+                    // or intersects cylinder behind camera
+                    if (s < 0 || s*s > cylinder.lengthSq() || t < 0)
+                        continue;
+                    
+                    else
+                        intersects.push({clickable : clickable,
+                                         distance : distance});
+                    
+                }
+                    
+                
             }
+            
+        }       
+        //lines
+        for (i = 0, il = intersectionShape.line.length; i < il; i += 2) {
+            
+            v1.copy(intersectionShape.line[i]);
+            v1.applyMatrix4(group.matrixWorld);
+            v2.copy(intersectionShape.line[i+1]);
+            v2.applyMatrix4(group.matrixWorld);
+            
+            v3.subVectors(v2, v1);
+            var bondLengthSq = v3.lengthSq();
+            v3.normalize();
+            
+            w_0.subVectors(v1, raycaster.ray.origin);
+            
+            lineProj = w_0.dot(v3);
+            rayProj = w_0.dot(raycaster.ray.direction);
+            
+            normProj = clamp(raycaster.ray.direction.dot(v3));
+            
+            denom = 1 - normProj*normProj;
+            
+            if (denom === 0.0)
+                continue;
+            
+            s_c = (normProj*rayProj - lineProj) / denom;
+            t_c = (rayProj - normProj*lineProj) / denom;
+            
+            v1.add(v3.multiplyScalar(s_c)); // Q_c
+            v2.copy(raycaster.ray.direction).multiplyScalar(t_c).add(raycaster.ray.origin); // P_c
+            
+            closestDistSq = v3.subVectors(v2, v1).lengthSq();
+            
+            if (closestDistSq < precisionSq && s_c*s_c < bondLengthSq)
+                intersects.push({clickable : clickable,
+                                 distance : t_c
+                                });
+            
         }
+        for (i = 0, il = intersectionShape.sphere.length; i < il; i++) {
+            //sphere
+            if (intersectionShape.sphere[i] instanceof $3Dmol.Sphere) {
+                
+                sphere.copy(intersectionShape.sphere[i]);
+                sphere.applyMatrix4(group.matrixWorld);
+                
+                if (raycaster.ray.isIntersectionSphere(sphere)) {
+                    
+                    v1.subVectors(sphere.center, raycaster.ray.origin);
+                    
+                    //distance from ray origin to point on the ray normal to sphere's center
+                    //must be less than sphere's radius (since ray intersects sphere)
+                    var distanceToCenter = v1.dot(raycaster.ray.direction);
+                    
+                    discriminant = distanceToCenter*distanceToCenter - (v1.lengthSq() - sphere.radius*sphere.radius);
+                    
+                    //Don't select if sphere center behind camera
+                    if (distanceToCenter < 0) 
+                        return intersects;
+                    
+                    //ray tangent to sphere?
+                    if (discriminant <= 0)
+                        distance = distanceToCenter;
+                    
+                    //This is reversed if sphere is closer than ray origin.  Do we have 
+                    //to worry about handling that case?
+                    else 
+                        distance = distanceToCenter - Math.sqrt(discriminant);
+    
+                    intersects.push({clickable : clickable, 
+                                     distance : distance});
+                    return intersects;
+                }
+            }        
+       }
+        
+    };   
+       
+    Raycaster.prototype.precision = 0.0001;
+    Raycaster.prototype.linePrecision = 0.2;
+    
+    Raycaster.prototype.set = function(origin, direction) {
+        
+        this.ray.set(origin, direction);
+          
+    };
+    
+    Raycaster.prototype.intersectObjects = function(group, objects) {     
+        var intersects = [];
+        
+        for (var i = 0, l = objects.length; i < l; i++)            
+            intersectObject(group, objects[i], this, intersects);
+            
+        intersects.sort(descSort);
+        
+        return intersects;
+        
+    };
+    
+    return Raycaster;
+    
+})();
 
-    }
-    
-    this.render = function ( scene, camera, forceClear ) {
-
-        if ( camera instanceof $3Dmol.Camera === false )  {
-
-            console.error( '$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.' );
-            return;
-
-        }
-
-        var i, il,
-
-        webglObject, object,
-        renderList,
-
-        lights = scene.__lights,
-        fog = scene.fog;
-
-        // reset caching for this frame
-
-        _currentMaterialId = -1;
-        _lightsNeedUpdate = true;
-
-        // update scene graph
-
-        if ( this.autoUpdateScene ) scene.updateMatrixWorld();
-
-        // update camera matrices
-        //Pretty sure camera's parent is always going to be undefined for our purposes...
-        if ( camera.parent === undefined ) camera.updateMatrixWorld();
-
-        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
-
-        _projScreenMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
-
-        // update WebGL objects
-
-        if ( this.autoUpdateObjects ) this.initWebGLObjects( scene );
-
-
-        _this.info.render.calls = 0;
-        _this.info.render.vertices = 0;
-        _this.info.render.faces = 0;
-        _this.info.render.points = 0;
-
-        _currentWidth = _viewportWidth;
-        _currentHeight = _viewportHeight;
-
-        if ( this.autoClear || forceClear ) {
-            this.clear( this.autoClearColor, this.autoClearDepth, this.autoClearStencil );
-
-        }
-
-        // set matrices for regular objects (frustum culled)
 
-        renderList = scene.__webglObjects;
+//$3Dmol Projecion 
+//TODO: can probably strip this down a lot (only used for selection handling)
+/** @constructor */
+$3Dmol.Projector = function () {
 
-        for ( i = 0, il = renderList.length; i < il; i ++ ) {
+    var _viewMatrix = new $3Dmol.Matrix4(),
+    _viewProjectionMatrix = new $3Dmol.Matrix4();
 
-            webglObject = renderList[ i ];
-            object = webglObject.object;
+    this.projectVector = function ( vector, camera ) {
 
-            webglObject.render = false;
+        camera.matrixWorldInverse.getInverse( camera.matrixWorld );
 
-            if ( object.visible ) {        
-                setupMatrices( object, camera );
-                unrollBufferMaterial( webglObject );
-                webglObject.render = true;
-            }
-        }
+        _viewProjectionMatrix.multiplyMatrices( camera.projectionMatrix, camera.matrixWorldInverse );
 
-        // set matrices for immediate objects
+        return vector.applyProjection( _viewProjectionMatrix );
 
-        var material = null;
+    };
 
-        // opaque pass (front-to-back order)
+    this.unprojectVector = function ( vector, camera ) {
 
-        this.setBlending( false );
+        camera.projectionMatrixInverse.getInverse(camera.projectionMatrix);
 
-        renderObjects( scene.__webglObjects, true, "opaque", camera, lights, fog, false, material );
-        
-        //prime depth buffer
-        renderObjects( scene.__webglObjects, true, "blank", camera, lights, fog, true, material );
+        _viewProjectionMatrix.multiplyMatrices(camera.matrixWorld, camera.projectionMatrixInverse);
 
-        // transparent pass (back-to-front order)
+        return vector.applyProjection( _viewProjectionMatrix );
 
-        renderObjects( scene.__webglObjects, false, "transparent", camera, lights, fog, true, material );
+    };
 
-        // Render plugins (e.g. sprites), and reset state
-        
-        renderPlugins(this.renderPluginsPost, scene, camera);
+};
+/*
+ * Simplified Perspective Camera
+ */
 
-        // Ensure depth buffer writing is enabled so it can be cleared on next render
+/** @constructor */
+$3Dmol.Camera = function(fov, aspect, near, far) {
+    
+    $3Dmol.Object3D.call(this);
+    
+    this.fov = fov !== undefined ? fov : 50;
+    this.aspect = aspect !== undefined ? aspect : 1;
+    this.near = near !== undefined ? near : 0.1;
+    this.far = far !== undefined ? far : 2000;
 
-        this.setDepthTest( true );
-        this.setDepthWrite( true );
+    this.projectionMatrix = new $3Dmol.Matrix4();
+    this.projectionMatrixInverse = new $3Dmol.Matrix4();
+    this.matrixWorldInverse = new $3Dmol.Matrix4();
+    
+    this.updateProjectionMatrix();
+        
+};
 
-        //_gl.finish();
+//Inherit Object3D's prototyped methods
+$3Dmol.Camera.prototype = Object.create($3Dmol.Object3D.prototype);
 
-    };
+$3Dmol.Camera.prototype.lookAt = function(vector){
     
-    function renderPlugins(plugins, scene, camera) {
-        
-        //Reset state once regardless
-        //This should also fix cartoon render bug (after transparent surface render)
-        
-        _currentGeometryGroupHash = -1;
-        _currentProgram = null;
-        _currentCamera = null;
-        _oldBlending = -1;
-        _oldDepthWrite = -1;
-        _oldDepthTest = -1;
-        _oldDoubleSided = -1;
-        _currentMaterialId = -1;
-        _oldFlipSided = -1;
-        
-        
-        if (!plugins.length)
-            return;
+    //Why is the parameter order switched (compared to Object3D)?
+    this.matrix.lookAt(this.position, vector, this.up);
+    
+    if (this.rotationAutoUpdate) {    
         
-        for (var i = 0, il = plugins.length; i < il; i++) {
-            
-            _lightsNeedUpdate = true;
-            
-            plugins[i].render(scene, camera, _currentWidth, _currentHeight);
+        if (this.useQuaternion === false) 
+            this.rotation.setEulerFromRotationMatrix( this.matrix, this.eulerOrder );
+        else
+            this.quaternion.copy( this.matrix.decompose()[ 1 ] );    
             
-            //Reset state after plugin render
-            _currentGeometryGroupHash = -1;
-            _currentProgram = null;
-            _currentCamera = null;
-            _oldBlending = -1;
-            _oldDepthWrite = -1;
-            _oldDepthTest = -1;
-            _oldDoubleSided = -1;
-            _currentMaterialId = -1;
-            _oldFlipSided = -1;       
-                
-        }  
-        
     }
+    
+};
 
-    this.initWebGLObjects = function ( scene ) {
+$3Dmol.Camera.prototype.updateProjectionMatrix = function () {
 
-        if ( !scene.__webglObjects ) {
+    this.projectionMatrix.makePerspective( this.fov, this.aspect, this.near, this.far );
+    this.projectionMatrixInverse.getInverse(this.projectionMatrix);
+};
 
-            scene.__webglObjects = [];
-            scene.__webglObjectsImmediate = [];
-            scene.__webglSprites = [];
-            scene.__webglFlares = [];
 
-        }
+//Render plugins go here
 
-        //Add objects; this sets up buffers for each geometryGroup
-        if (scene.__objectsAdded.length) {
-            
-            while(scene.__objectsAdded.length){
-                addObject(scene.__objectsAdded[0], scene);
-                scene.__objectsAdded.splice(0, 1);
-            }
-            
-            //Force buffer update during render
-            //Hackish fix for initial cartoon-render-then-transparent-surface bug
-            _currentGeometryGroupHash = -1;
-            
-        }
+/**
+ * Sprite render plugin
+ * @this {$3Dmol.SpritePlugin}
+ */
 
-        while (scene.__objectsRemoved.length) {
+$3Dmol.SpritePlugin = function () {
 
-            removeObject(scene.__objectsRemoved[ 0 ], scene);
-            scene.__objectsRemoved.splice(0, 1);
+    var _gl, _renderer, _precision, _sprite = {};
 
-        }
+    this.init = function ( renderer ) {
 
-        // update must be called after objects adding / removal
-        //This sends typed arrays to GL buffers for each geometryGroup
-        for ( var o = 0, ol = scene.__webglObjects.length; o < ol; o ++ ) {
+        _gl = renderer.context;
+        _renderer = renderer;
 
-            updateObject(scene.__webglObjects[ o ].object);
+        _precision = renderer.getPrecision();
 
-        }
+        _sprite.vertices = new Float32Array( 8 + 8 );
+        _sprite.faces    = new Uint16Array( 6 );
 
-    };
-    
-    // Objects adding
+        var i = 0;
 
-    function addObject (object, scene) {
+        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = -1; // vertex 0
+        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 0;  // uv 0
 
-        var g, gl, geometry, material, geometryGroup;
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = -1; // vertex 1
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 0;  // uv 1
 
-        if ( !object.__webglInit ) {
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // vertex 2
+        _sprite.vertices[ i++ ] = 1;  _sprite.vertices[ i++ ] = 1;  // uv 2
 
-            object.__webglInit = true;
+        _sprite.vertices[ i++ ] = -1; _sprite.vertices[ i++ ] = 1;  // vertex 3
+        _sprite.vertices[ i++ ] = 0;  _sprite.vertices[ i++ ] = 1;  // uv 3
 
-            object._modelViewMatrix = new $3Dmol.Matrix4();
-            object._normalMatrix = new $3Dmol.Matrix3();
+        i = 0;
 
-            if (object.geometry !== undefined && object.geometry.__webglInit === undefined) {
+        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 1; _sprite.faces[ i++ ] = 2;
+        _sprite.faces[ i++ ] = 0; _sprite.faces[ i++ ] = 2; _sprite.faces[ i++ ] = 3;
 
-                object.geometry.__webglInit = true;
-                object.geometry.addEventListener('dispose', onGeometryDispose);
+        _sprite.vertexBuffer  = _gl.createBuffer();
+        _sprite.elementBuffer = _gl.createBuffer();
 
-            }
-            
-            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
-                geometry = object.geometry;
-                material = object.material;           
-    
-                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
-    
-                    geometryGroup = geometry.geometryGroups[ g ];
-                    
-                    geometryGroup.id = _geometryGroupCounter++;
+        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
+        _gl.bufferData( _gl.ARRAY_BUFFER, _sprite.vertices, _gl.STATIC_DRAW );
 
-                    // initialise VBO on the first access
+        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
+        _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, _sprite.faces, _gl.STATIC_DRAW );
 
-                    if ( !geometryGroup.__webglVertexBuffer ) {
-                            
-                        if (object instanceof $3Dmol.Mesh) {
-                            createMeshBuffers(geometryGroup);
-                            geometry.elementsNeedUpdate = true;
-                            geometry.normalsNeedUpdate = true;
-                        }
-                            
-                        else if (object instanceof $3Dmol.Line)
-                            createLineBuffers(geometryGroup);
+        _sprite.program = createProgram( $3Dmol.ShaderLib.sprite, _precision );
 
-                        geometry.verticesNeedUpdate = true;
-                        geometry.colorsNeedUpdate = true;
+        _sprite.attributes = {};
+        _sprite.uniforms = {};
 
-                    }
-                        
-                }
-                
-            }
-        
-        }
-        
-        if ( ! object.__webglActive ) {
-            
-            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
-                
-                geometry = object.geometry;
+        _sprite.attributes.position           = _gl.getAttribLocation ( _sprite.program, "position" );
+        _sprite.attributes.uv                 = _gl.getAttribLocation ( _sprite.program, "uv" );
 
-                for ( g = 0, gl = geometry.geometryGroups.length; g < gl; g++ ) {
-                    geometryGroup = geometry.geometryGroups[g];
+        _sprite.uniforms.uvOffset             = _gl.getUniformLocation( _sprite.program, "uvOffset" );
+        _sprite.uniforms.uvScale              = _gl.getUniformLocation( _sprite.program, "uvScale" );
 
-                    addBuffer(scene.__webglObjects, geometryGroup, object);
-                }
-                
-            }
-            
-            //Sprite
-            else if (object instanceof $3Dmol.Sprite) 
-                scene.__webglSprites.push(object);
-         
-                     
-            object.__webglActive = true;
-            
-        }
+        _sprite.uniforms.rotation             = _gl.getUniformLocation( _sprite.program, "rotation" );
+        _sprite.uniforms.scale                = _gl.getUniformLocation( _sprite.program, "scale" );
+        _sprite.uniforms.alignment            = _gl.getUniformLocation( _sprite.program, "alignment" );
 
-    }
+        _sprite.uniforms.color                = _gl.getUniformLocation( _sprite.program, "color" );
+        _sprite.uniforms.map                  = _gl.getUniformLocation( _sprite.program, "map" );
+        _sprite.uniforms.opacity              = _gl.getUniformLocation( _sprite.program, "opacity" );
 
-    function updateObject ( object ) {
+        _sprite.uniforms.useScreenCoordinates = _gl.getUniformLocation( _sprite.program, "useScreenCoordinates" );
+        _sprite.uniforms.screenPosition       = _gl.getUniformLocation( _sprite.program, "screenPosition" );
+        _sprite.uniforms.modelViewMatrix      = _gl.getUniformLocation( _sprite.program, "modelViewMatrix" );
+        _sprite.uniforms.projectionMatrix     = _gl.getUniformLocation( _sprite.program, "projectionMatrix" );
 
-        var geometry = object.geometry, material = object.material,
-                geometryGroup, customAttributesDirty;
-        
-        if ( object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line ) {
-            
-            for (var g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
-                
-                geometryGroup = geometry.geometryGroups[ g ];
+        _sprite.uniforms.fogType              = _gl.getUniformLocation( _sprite.program, "fogType" );
+        _sprite.uniforms.fogDensity           = _gl.getUniformLocation( _sprite.program, "fogDensity" );
+        _sprite.uniforms.fogNear              = _gl.getUniformLocation( _sprite.program, "fogNear" );
+        _sprite.uniforms.fogFar               = _gl.getUniformLocation( _sprite.program, "fogFar" );
+        _sprite.uniforms.fogColor             = _gl.getUniformLocation( _sprite.program, "fogColor" );
 
-                if ( geometry.verticesNeedUpdate || geometry.elementsNeedUpdate || geometry.colorsNeedUpdate || geometry.normalsNeedUpdate) {
-                    setBuffers( geometryGroup, _gl.STATIC_DRAW );
-                }
-            }
-            
-            geometry.verticesNeedUpdate = false;
-            geometry.elementsNeedUpdate = false;
-            geometry.normalsNeedUpdate = false;
-            geometry.colorsNeedUpdate = false;
+        _sprite.uniforms.alphaTest            = _gl.getUniformLocation( _sprite.program, "alphaTest" );
 
-            geometry.buffersNeedUpdate = false;
+    };
 
-        }
+    this.render = function ( scene, camera, viewportWidth, viewportHeight ) {
 
-    }
-    
-    function removeObject( object, scene ) {
+        var sprites = scene.__webglSprites,
+            nSprites = sprites.length;
 
-        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line )
-            removeInstances(scene.__webglObjects, object);
+        if ( ! nSprites ) return;
 
-        else if (object instanceof $3Dmol.Sprite)
-            removeInstancesDirect(scene.__webglSprites, object);
-            
-        object.__webglActive = false;
+        var attributes = _sprite.attributes,
+            uniforms = _sprite.uniforms;
 
-    }
+        var invAspect = viewportHeight / viewportWidth;
 
-    function removeInstances( objList, object ) {
+        var halfViewportWidth = viewportWidth * 0.5,
+            halfViewportHeight = viewportHeight * 0.5;
 
-        for (var o = objList.length - 1; o >= 0; --o) {
+        // setup gl
 
-            if (objList[o].object === object) 
-                objList.splice(o, 1);
+        _gl.useProgram( _sprite.program );
 
-        }
-    }
+        _gl.enableVertexAttribArray( attributes.position );
+        _gl.enableVertexAttribArray( attributes.uv );
 
-    function removeInstancesDirect( objList, object ) {
+        _gl.disable( _gl.CULL_FACE );
+        _gl.enable( _gl.BLEND );
 
-        for (var o = objList.length - 1; o >= 0; --o) {
+        _gl.bindBuffer( _gl.ARRAY_BUFFER, _sprite.vertexBuffer );
+        _gl.vertexAttribPointer( attributes.position, 2, _gl.FLOAT, false, 2 * 8, 0 );
+        _gl.vertexAttribPointer( attributes.uv, 2, _gl.FLOAT, false, 2 * 8, 8 );
 
-            if (objList[o] === object) 
-                objList.splice(o, 1);
+        _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, _sprite.elementBuffer );
 
-        }
-    }
+        _gl.uniformMatrix4fv( uniforms.projectionMatrix, false, camera.projectionMatrix.elements );
 
-    function unrollBufferMaterial( globject ) {
+        _gl.activeTexture( _gl.TEXTURE0 );
+        _gl.uniform1i( uniforms.map, 0 );
 
-        var object = globject.object;
-        var material = object.material;
+        var oldFogType = 0;
+        var sceneFogType = 0;
+        var fog = scene.fog;
 
-        if ( material.transparent) {                    
-            globject.opaque = null;
-            globject.transparent = material;
-            var blankMaterial = material.clone();
-            blankMaterial.opacity = 0;
-            globject.blank = blankMaterial;
-        }
+        if ( fog ) {
 
-        else {
-            globject.opaque = material;
-            globject.transparent = null;
-        }
+            _gl.uniform3f( uniforms.fogColor, fog.color.r, fog.color.g, fog.color.b );
 
-    }
+            _gl.uniform1f( uniforms.fogNear, fog.near );
+            _gl.uniform1f( uniforms.fogFar, fog.far );
 
-    function setBuffers( geometryGroup, hint, line ) {
+            _gl.uniform1i( uniforms.fogType, 1 );
+            oldFogType = 1;
+            sceneFogType = 1;
 
-        var vertexArray = geometryGroup.vertexArray;
-        var colorArray = geometryGroup.colorArray;
-         
-        //vertex buffers
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, vertexArray, hint );        
 
-        //color buffers
-        _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer );
-        _gl.bufferData( _gl.ARRAY_BUFFER, colorArray, hint );    
-              
-        
-        //normal buffers
-        if (geometryGroup.normalArray !== undefined && geometryGroup.__webglNormalBuffer !== undefined) {
-            var normalArray = geometryGroup.normalArray;
-            _gl.bindBuffer( _gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer );
-            _gl.bufferData( _gl.ARRAY_BUFFER, normalArray, hint );       
-             
-        }
-        
-        //face (index) buffers
-        if (geometryGroup.faceArray !== undefined && geometryGroup.__webglFaceBuffer !== undefined) {
-            var faceArray = geometryGroup.faceArray;
-            _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglFaceBuffer );
-            _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, faceArray, hint );  
-                      
-        }
+        } 
         
-        //line (index) buffers (for wireframe)
-        if (geometryGroup.lineArray !== undefined && geometryGroup.__webglLineBuffer !== undefined) {
-            var lineArray = geometryGroup.lineArray;            
-            _gl.bindBuffer( _gl.ELEMENT_ARRAY_BUFFER, geometryGroup.__webglLineBuffer );
-            _gl.bufferData( _gl.ELEMENT_ARRAY_BUFFER, lineArray, hint );
-        }
-
-    }
-    
-    //Creates appropriate gl buffers for geometry chunk
-    //TODO: do we need line buffer for mesh objects?
-    //Also, can we integrate this with createLineBuffers?
-    function createMeshBuffers ( geometryGroup ) {
+        else {
 
-        geometryGroup.__webglVertexBuffer = _gl.createBuffer();
-        geometryGroup.__webglNormalBuffer = _gl.createBuffer();
-        geometryGroup.__webglColorBuffer = _gl.createBuffer();
+            _gl.uniform1i( uniforms.fogType, 0 );
+            oldFogType = 0;
+            sceneFogType = 0;
 
-        geometryGroup.__webglFaceBuffer = _gl.createBuffer();
-        geometryGroup.__webglLineBuffer = _gl.createBuffer();
+        }
 
-        _this.info.memory.geometries++;
-    }
-    
-    function createLineBuffers ( geometry ) {
-        
-        geometry.__webglVertexBuffer = _gl.createBuffer();
-        geometry.__webglColorBuffer = _gl.createBuffer();
-        
-        _this.info.memory.geometries++;
-    }
 
-    function addBuffer (objlist, buffer, object) {
+        // update positions and sort
 
-        objlist.push(
-            {
-                buffer: buffer,
-                object: object,
-                opaque: null,
-                transparent: null
-            }
-        );
+        var i, sprite, material, screenPosition, size, fogType, scale = [];
 
-    }
+        for( i = 0; i < nSprites; i ++ ) {
 
-    function setupMatrices (object, camera) {
+            sprite = sprites[ i ];
+            material = sprite.material;
 
-        object._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, object.matrixWorld );
+            if ( ! sprite.visible || material.opacity === 0 ) continue;
 
-        object._normalMatrix.getInverse( object._modelViewMatrix );
-        object._normalMatrix.transpose();
+            if ( ! material.useScreenCoordinates ) {
 
-    }
+                sprite._modelViewMatrix.multiplyMatrices( camera.matrixWorldInverse, sprite.matrixWorld );
+                sprite.z = - sprite._modelViewMatrix.elements[ 14 ];
 
-    function isPowerOfTwo ( value ) {
+            } else {
 
-        return ( value & ( value - 1 ) ) === 0;
+                sprite.z = - sprite.position.z;
 
-    }
-    
-    // Fallback filters for non-power-of-2 textures
+            }
 
-    function filterFallback ( f ) {
+        }
 
-        return _gl.LINEAR;
+        sprites.sort( painterSortStable );
 
-    }
+        // render all sprites
 
-    function setTextureParameters ( textureType, texture, isImagePowerOfTwo ) {
+        for( i = 0; i < nSprites; i ++ ) {
 
-        if ( isImagePowerOfTwo ) {
+            sprite = sprites[ i ];
+            material = sprite.material;
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_S, paramToGL( texture.wrapS ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_T, paramToGL( texture.wrapT ) );
+            if ( ! sprite.visible || material.opacity === 0 ) continue;
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_MAG_FILTER, paramToGL( texture.magFilter ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_MIN_FILTER, paramToGL( texture.minFilter ) );
+            if ( material.map && material.map.image && material.map.image.width ) {
 
-        } else {
+                _gl.uniform1f( uniforms.alphaTest, material.alphaTest );
+                var w = material.map.image.width;
+                var h = material.map.image.height;
+                
+                scale[ 0 ] = w*_renderer.devicePixelRatio/viewportWidth;
+                scale[ 1 ] = h*_renderer.devicePixelRatio/viewportHeight;
+                
+                if ( material.useScreenCoordinates === true ) {
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_S, _gl.CLAMP_TO_EDGE );
-            _gl.texParameteri( textureType, _gl.TEXTURE_WRAP_T, _gl.CLAMP_TO_EDGE );
+                    _gl.uniform1i( uniforms.useScreenCoordinates, 1 );
+                    _gl.uniform3f(
+                        uniforms.screenPosition,
+                        ( ( sprite.position.x * _renderer.devicePixelRatio ) - halfViewportWidth  ) / halfViewportWidth,
+                        ( halfViewportHeight - ( sprite.position.y * _renderer.devicePixelRatio ) ) / halfViewportHeight,
+                        Math.max( 0, Math.min( 1, sprite.position.z ) )
+                    );
 
-            _gl.texParameteri( textureType, _gl.TEXTURE_MAG_FILTER, filterFallback( texture.magFilter ) );
-            _gl.texParameteri( textureType, _gl.TEXTURE_MIN_FILTER, filterFallback( texture.minFilter ) );
+                } else {
 
-        }
+                    _gl.uniform1i( uniforms.useScreenCoordinates, 0 );
+                    _gl.uniformMatrix4fv( uniforms.modelViewMatrix, false, sprite._modelViewMatrix.elements );
+                }
 
-    }
-    
-    this.setTexture = function (texture, slot) {
+                if ( scene.fog && material.fog ) {
 
-        if (texture.needsUpdate) {
+                    fogType = sceneFogType;
 
-            if ( !texture.__webglInit ) {
+                } else {
 
-                texture.__webglInit = true;
+                    fogType = 0;
 
-                texture.addEventListener('dispose', onTextureDispose);
+                }
 
-                texture.__webglTexture = _gl.createTexture();
+                if ( oldFogType !== fogType ) {
 
-                _this.info.memory.textures++;
+                    _gl.uniform1i( uniforms.fogType, fogType );
+                    oldFogType = fogType;
 
-            }
+                }
 
-            _gl.activeTexture(_gl.TEXTURE0 + slot);
-            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
+                size = 1 / ( material.scaleByViewport ? viewportHeight : 1 );
 
-            _gl.pixelStorei(_gl.UNPACK_FLIP_Y_WEBGL, texture.flipY);
-            _gl.pixelStorei(_gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL, texture.premultiplyAlpha);
-            _gl.pixelStorei(_gl.UNPACK_ALIGNMENT, texture.unpackAlignment);
-
-            var image = texture.image,
-            isImagePowerOfTwo = isPowerOfTwo(image.width) && isPowerOfTwo(image.height),
-            glFormat = paramToGL(texture.format),
-            glType = paramToGL(texture.type);
-
-            setTextureParameters(_gl.TEXTURE_2D, texture, isImagePowerOfTwo);
+                scale[ 0 ] *= size * sprite.scale.x;
+                scale[ 1 ] *= size * sprite.scale.y;
 
-            var mipmap, mipmaps = texture.mipmaps;
+                _gl.uniform2f( uniforms.uvScale, material.uvScale.x, material.uvScale.y );
+                _gl.uniform2f( uniforms.uvOffset, material.uvOffset.x, material.uvOffset.y );
+                _gl.uniform2f( uniforms.alignment, material.alignment.x, material.alignment.y );
 
-            // regular Texture (image, video, canvas)
+                _gl.uniform1f( uniforms.opacity, material.opacity );
+                _gl.uniform3f( uniforms.color, material.color.r, material.color.g, material.color.b );
 
-            // use manually created mipmaps if available
-            // if there are no manual mipmaps
-            // set 0 level mipmap and then use GL to generate other mipmap levels
+                _gl.uniform1f( uniforms.rotation, sprite.rotation );
+                _gl.uniform2fv( uniforms.scale, scale );
 
-            if ( mipmaps.length > 0 && isImagePowerOfTwo ) {
+                //_renderer.setBlending( material.blending, material.blendEquation, material.blendSrc, material.blendDst );
+                _renderer.setDepthTest( material.depthTest );
+                _renderer.setDepthWrite( material.depthWrite );
+                _renderer.setTexture( material.map, 0 );
 
-                for ( var i = 0, il = mipmaps.length; i < il; i ++ ) {
-                    mipmap = mipmaps[ i ];
-                    _gl.texImage2D( _gl.TEXTURE_2D, i, glFormat, glFormat, glType, mipmap );
-                }
-                
-                texture.generateMipmaps = false;
-            } 
-            
-            else 
-                _gl.texImage2D( _gl.TEXTURE_2D, 0, glFormat, glFormat, glType, texture.image );
+                _gl.drawElements( _gl.TRIANGLES, 6, _gl.UNSIGNED_SHORT, 0 );
 
-            
-            if ( texture.generateMipmaps && isImagePowerOfTwo ) _gl.generateMipmap( _gl.TEXTURE_2D );
+            }
 
-            texture.needsUpdate = false;
+        }
 
-            if ( texture.onUpdate ) texture.onUpdate();
+        // restore gl
 
-        } else {
+        _gl.enable( _gl.CULL_FACE );
 
-            _gl.activeTexture( _gl.TEXTURE0 + slot );
-            _gl.bindTexture( _gl.TEXTURE_2D, texture.__webglTexture );
+    };
 
-        }
+    function createProgram ( shader, precision ) {
 
-    };
-    
-    // Map constants to WebGL constants
+        var program = _gl.createProgram();
 
-    function paramToGL ( p ) {
+        var fragmentShader = _gl.createShader( _gl.FRAGMENT_SHADER );
+        var vertexShader = _gl.createShader( _gl.VERTEX_SHADER );
 
-        if ( p === $3Dmol.UnsignedByteType ) return _gl.UNSIGNED_BYTE;
-        if ( p === $3Dmol.RGBAFormat ) return _gl.RGBA;
+        var prefix = "precision " + precision + " float;\n";
 
-        return 0;
+        _gl.shaderSource( fragmentShader, prefix + shader.fragmentShader );
+        _gl.shaderSource( vertexShader, prefix + shader.vertexShader );
 
-    }
-    
-    function setupLights ( program, lights ) {
-        var l, ll, light, n,
-        r = 0, g = 0, b = 0,
-        color,
-        position,
-        intensity,
-        distance,
-        
-        zlights = _lights,
-        
-        dirColors = zlights.directional.colors,
-        dirPositions = zlights.directional.positions,
-        
-        dirCount = 0,
-        dirLength = 0,
-        dirOffset = 0;
+        _gl.compileShader( fragmentShader );
+        _gl.compileShader( vertexShader );
         
-        for ( l = 0, ll = lights.length; l < ll; l++) {
-            
-            light = lights[l];
-            
-            color = light.color;
-            intensity = light.intensity;
-            distance = light.distance;
-            
-            if (light instanceof $3Dmol.Light) {
-                
-                dirCount++;
-                
-                _direction.getPositionFromMatrix(light.matrixWorld);
-                _vector3.getPositionFromMatrix(light.target.matrixWorld);
-                _direction.sub(_vector3);
-                _direction.normalize();
-                
-                if (_direction.x === 0 && _direction.y === 0 && _direction.z === 0)
-                    continue;
-                
-                dirPositions[dirOffset] = _direction.x;
-                dirPositions[dirOffset + 1] = _direction.y;
-                dirPositions[dirOffset + 2] = _direction.z;
+        if ( ! _gl.getShaderParameter(fragmentShader, _gl.COMPILE_STATUS) || ! _gl.getShaderParameter(vertexShader,_gl.COMPILE_STATUS) ) {
 
-                dirColors[dirOffset] = color.r * intensity;
-                dirColors[dirOffset + 1] = color.g * intensity;
-                dirColors[dirOffset + 2] = color.b * intensity;
-                
-                dirOffset += 3;
-                
-                dirLength++;    
-            }
-        
+                console.error(_gl.getShaderInfoLog(fragmentShader));
+                console.error("could not initialize shader");
+                return null;
         }
 
-        zlights.ambient[0] = r;
-        zlights.ambient[1] = g;
-        zlights.ambient[2] = b;
-        zlights.directional.length = dirLength;
-    }
-
-    function initGL () {
+        _gl.attachShader( program, fragmentShader );
+        _gl.attachShader( program, vertexShader );
 
-        try {
+        _gl.linkProgram( program );
 
-            if ( ! ( _gl = _canvas.getContext( 'experimental-webgl', { alpha: _alpha, premultipliedAlpha: _premultipliedAlpha, antialias: _antialias, stencil: _stencil, preserveDrawingBuffer: _preserveDrawingBuffer } ) ) ) {
-                if ( ! ( _gl = _canvas.getContext( 'webgl', { alpha: _alpha, premultipliedAlpha: _premultipliedAlpha, antialias: _antialias, stencil: _stencil, preserveDrawingBuffer: _preserveDrawingBuffer } ) ) ) {
-                throw 'Error creating WebGL context.';
-                }
-            }
+        if (! _gl.getProgramParameter(program, _gl.LINK_STATUS) )
+                console.error("Could not initialize shader");
 
-        } catch ( error ) {
+        return program;
 
-            console.error( error );
-        }
-        var ext = _gl.getExtension('EXT_frag_depth');
     }
 
-    function setDefaultGLState () {
-
-        _gl.clearColor( 0, 0, 0, 1 );
-        _gl.clearDepth( 1 );
-        _gl.clearStencil( 0 );
+    function painterSortStable ( a, b ) {
 
-        _gl.enable( _gl.DEPTH_TEST );
-        _gl.depthFunc( _gl.LEQUAL );
+        if ( a.z !== b.z ) {
 
-        _gl.frontFace( _gl.CCW );
-        _gl.cullFace( _gl.BACK );
-        _gl.enable( _gl.CULL_FACE );
+            return b.z - a.z;
 
-        _gl.enable( _gl.BLEND );
-        _gl.blendEquation( _gl.FUNC_ADD );
-        _gl.blendFunc( _gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA );
+        } else {
 
-        _gl.clearColor( _clearColor.r, _clearColor.g, _clearColor.b, _clearAlpha );
-        var ext = _gl.getExtension('EXT_frag_depth');
+            return b.id - a.id;
 
+        }
 
     }
-    
-    this.addPostPlugin(new $3Dmol.SpritePlugin());
-        
+
 };
 
-/*
- * Scene class
- */
-/** @constructor */
-$3Dmol.Scene = function() {
+$3Dmol.Light = function(hex, intensity) {
     
     $3Dmol.Object3D.call(this);
     
-    this.fog = null;
-    
-    //May not need...
-    this.overrideMaterial = null;
-    
-    this.matrixAutoUpdate = false;
-    
-    this.__objects = [];
-    this.__lights = [];
-    
-    this.__objectsAdded = [];
-    this.__objectsRemoved = [];
-    
-};
+    this.color = new $3Dmol.Color(hex);
+    this.position = new $3Dmol.Vector3( 0, 1, 0 );
+    this.target = new $3Dmol.Object3D();
 
-$3Dmol.Scene.prototype = Object.create($3Dmol.Object3D.prototype);
+    this.intensity = ( intensity !== undefined ) ? intensity : 1;
 
-$3Dmol.Scene.prototype.__addObject = function(object) {
-    
-    //Directional Lighting
-    if (object instanceof $3Dmol.Light) {
-        
-        if (this.__lights.indexOf(object) === -1)
-            this.__lights.push(object);
-        
-        //TODO: Do I need this??
-        if (object.target && object.target.parent === undefined)
-            this.add(object.target);
-            
-    }
-    
-    //Rotation group
-    else {
-        
-        if (this.__objects.indexOf(object) === -1) {
-            
-            this.__objects.push(object);
-            this.__objectsAdded.push(object);
-            
-            //Check if previously removed
-            
-            var idx = this.__objectsRemoved.indexOf(object);
-            
-            if (idx !== -1)
-                this.__objectsRemoved.splice(i, 1);
-                
-        }
-    }
-    
-    //Add object's children
-    
-    for (var i = 0; i < object.children.length; i++) 
-        this.__addObject(object.children[i]);
+    this.castShadow = false;
+    this.onlyShadow = false;
     
 };
 
-$3Dmol.Scene.prototype.__removeObject = function(object) {
-    
-    var idx;
-    if (object instanceof $3Dmol.Light) {
-        
-        idx = this.__lights.indexOf(object);
-        
-        if (idx !== -1)
-            this.__lights.splice(idx, 1);
-            
-    }
-    
-    //Object3D
-    else {
-        
-        idx = this.__objects.indexOf(object);
-        
-        if (idx !== -1) {
-            
-            this.__objects.splice(idx, 1);
-            this.__objectsRemoved.push(object);
-            
-            //Check if previously added
-            
-            var ai = this.__objectsAdded.indexOf(object);
-            
-            if (ai !== -1) 
-                this.__objectsAdded.splice(idx, 1);
-                
-        }
-    
-    }
-    
-    //Remove object's children
-    for (var i = 0; i < object.children.length; i++)
-        this.__removeObject(object.children[i]);
+$3Dmol.Light.prototype = Object.create($3Dmol.Object3D.prototype);
+/**
+ * Line and Mesh material types
+ * @constructor
+ */
+$3Dmol.Material = function () {
+
+    $3Dmol.EventDispatcher.call( this );
+
+    this.id = $3Dmol.MaterialIdCount ++;
+
+    this.name = '';
     
-};
+    //TODO: Which of these instance variables can I remove??
+    this.side = $3Dmol.FrontSide;
 
+    this.opacity = 1;
+    this.transparent = false;
 
-/*
- * Fog Class
- */
+    this.depthTest = true;
+    this.depthWrite = true;
+    
+    this.stencilTest = true;
 
-/** @constructor */
-$3Dmol.Fog = function ( hex, near, far ) {
+    this.polygonOffset = false;
+    this.polygonOffsetFactor = 0;
+    this.polygonOffsetUnits = 0;
 
-    this.name = '';
+    this.alphaTest = 0;
 
-    this.color = new $3Dmol.Color( hex );
+    this.visible = true;
 
-    this.near = ( near !== undefined ) ? near : 1;
-    this.far = ( far !== undefined ) ? far : 1000;
+    this.needsUpdate = true;
 
 };
 
-$3Dmol.Fog.prototype.clone = function () {
 
-    return new $3Dmol.Fog( this.color.getHex(), this.near, this.far );
+$3Dmol.Material.prototype.setValues = function ( values ) {
 
-};/* 
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
+    if ( values === undefined ) return;
+
+    for ( var key in values ) {
+
+        var newValue = values[ key ];
+
+        if ( newValue === undefined ) {
+
+            console.warn( '$3Dmol.Material: \'' + key + '\' parameter is undefined.' );
+            continue;
 
-$3Dmol.ShaderUtils = {
-    
-    clone: function ( uniforms_src ) {
-        
-        var u, p, parameter, parameter_src, uniforms_clone = {};
-        
-        for (u in uniforms_src) {
-            uniforms_clone[u] = {};
-            uniforms_clone[u].type = uniforms_src[u].type;
-            
-            var srcValue = uniforms_src[u].value;
-            
-            if (srcValue instanceof $3Dmol.Color)
-                uniforms_clone[u].value = srcValue.clone();
-            else if (typeof srcValue === "number")
-                uniforms_clone[u].value = srcValue;
-            else if (srcValue instanceof Array) 
-                uniforms_clone[u].value = [];
-            else
-                console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform");
-            
         }
-        
-        return uniforms_clone;
-    }
-};
 
-$3Dmol.ShaderLib = { 
-    'basic' : {
-        fragmentShader : [
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 diffuse;",
-"uniform float opacity;",
+        if ( key in this ) {
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+            var currentValue = this[ key ];
 
-"varying vec3 vColor;",
+            if ( currentValue instanceof $3Dmol.Color && newValue instanceof $3Dmol.Color ) {
 
-"void main() {",
-    
-"    gl_FragColor = vec4( diffuse, opacity );",
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-    
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",    
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
-    
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+                currentValue.copy( newValue );
 
-"}"
-                                                     
-].join("\n"),
-        
-        vertexShader : [
+            } else if ( currentValue instanceof $3Dmol.Color ) {
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
+                currentValue.set( newValue );
 
-"attribute vec3 position;",
-"attribute vec3 color;",
+            } else if ( currentValue instanceof $3Dmol.Vector3 && newValue instanceof $3Dmol.Vector3 ) {
 
-"varying vec3 vColor;",
+                currentValue.copy( newValue );
 
-"void main() {",
+            } else {
 
-"    vColor = color;",
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-"    gl_Position = projectionMatrix * mvPosition;",
+                this[ key ] = newValue;
+
+            }
 
-"}"
-        
-].join("\n"),
-    
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000}
         }
 
-    },
-    
- 'sphereimposter' : {
-        fragmentShader : [
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 diffuse;",
-"uniform float opacity;",
+    }
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+};
+//TODO: might want to look into blending equations
+$3Dmol.Material.prototype.clone = function ( material ) {
 
-"varying vec3 vColor;",
-"varying vec2 mapping;",
+    if ( material === undefined ) material = new $3Dmol.Material();
 
-"void main() {",
-"    float lensqr = dot(mapping,mapping);",
-"    if(lensqr > 2.0)",
-"       discard;",
-"    float w = sqrt(2.0 - lensqr);",
-"    float z = sqrt(sqrt(2.0)-lensqr);",
-"    gl_FragDepthEXT = -.1*z;",
-"    gl_FragColor = vec4( w*vColor, 1 );",
-    
+    material.name = this.name;
 
+    material.side = this.side;
 
-"}"
-                                                     
-].join("\n"),
-        
-        vertexShader : [
+    material.opacity = this.opacity;
+    material.transparent = this.transparent;
 
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
+    material.depthTest = this.depthTest;
+    material.depthWrite = this.depthWrite;
+    material.stencilTest = this.stencilTest;
 
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+    material.polygonOffset = this.polygonOffset;
+    material.polygonOffsetFactor = this.polygonOffsetFactor;
+    material.polygonOffsetUnits = this.polygonOffsetUnits;
 
-"varying vec2 mapping;",
-"varying vec3 vColor;",
+    material.alphaTest = this.alphaTest;
 
-"void main() {",
+    material.overdraw = this.overdraw;
 
-"    vColor = color;",
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
-"    vec4 projPosition = projectionMatrix * mvPosition;",
-"    vec4 adjust = projectionMatrix*vec4(normal, 1.0);  adjust.y *= -1.0; adjust.z = 0.0; adjust.w = 0.0;",
-"    mapping = normal.xy;",
-"    gl_Position = projPosition+adjust;",
+    material.visible = this.visible;
 
-"}"
-        
-].join("\n"),
-    
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000}
-        }
+    return material;
 
-    },
-    
-    
-    'lambert' : { 
-        fragmentShader : [
+};
 
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform float opacity;",
+$3Dmol.Material.prototype.dispose = function () {
 
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
+    this.dispatchEvent( { type: 'dispose' } );
 
-"varying vec3 vLightFront;",
-"varying vec3 vColor;",
+};
 
-"void main() {",
+$3Dmol.MaterialIdCount = 0;
+
+//Line basic material
+/** @constructor */
+$3Dmol.LineBasicMaterial = function(parameters) {
     
-"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    $3Dmol.Material.call(this);
     
-"    #ifndef WIREFRAME",
-"    gl_FragColor.xyz *= vLightFront;",
-"    #endif",
+    this.color = new $3Dmol.Color(0xffffff);
     
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    this.linewidth = 1;
+    this.linecap = 'round';
+    this.linejoin = 'round';
     
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    this.vertexColors = false;
     
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
-
-"}"
-
-
-].join("\n"),
-       
-       vertexShader : [
-
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 ambient;",
-"uniform vec3 diffuse;",
-"uniform vec3 emissive;",
-"uniform vec3 ambientLightColor;",
-"uniform vec3 directionalLightColor[ 1 ];",
-"uniform vec3 directionalLightDirection[ 1 ];",
+    this.fog = true;
+    this.shaderID = "basic";
+    this.setValues(parameters);
+    
+};
 
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+$3Dmol.LineBasicMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-"varying vec3 vColor;",
-"varying vec3 vLightFront;",
+$3Dmol.LineBasicMaterial.prototype.clone = function() {
+  
+    var material = new $3Dmol.LineBasicMaterial();
+    
+    $3Dmol.Material.prototype.clone.call(this, material);
+    
+    material.color.copy(this.color);
+    return material;
+};
 
-"void main() {",
+//Mesh Lambert material
+/** @constructor */
+$3Dmol.MeshLambertMaterial = function(parameters) {
     
-"    vColor = color;",
+    $3Dmol.Material.call(this);
     
-"    vec3 objectNormal = normal;",  
-"    vec3 transformedNormal = normalMatrix * objectNormal;",    
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    this.color = new $3Dmol.Color(0xffffff);
+    this.ambient = new $3Dmol.Color(0xfffff);
+    this.emissive = new $3Dmol.Color(0x000000);
     
-"    vLightFront = vec3( 0.0 );",
+    //TODO: Which of these instance variables do I really need?
+    this.wrapAround = false;
+    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
     
-"    transformedNormal = normalize( transformedNormal );",
+    this.map = null;
     
-"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
-"    vec3 dirVector = normalize( lDirection.xyz );",
-"    float dotProduct = dot( transformedNormal, dirVector );",
-"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
+    this.lightMap = null;
     
-"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
-"    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;",
+    this.specularMap = null;
     
-"    gl_Position = projectionMatrix * mvPosition;",
-"}"
-           
-].join("\n"),
-
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000},           
-            ambient: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            emissive: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            ambientLightColor: { type: 'fv', value: [] },
-            directionalLightColor: { type: 'fv', value: [] },
-            directionalLightDirection: { type: 'fv', value: [] }
-        }
-
-    },
+    this.envMap = null;
+    this.reflectivity = 1;
+    this.refractionRatio = 0.98;
     
-    //for double sided lighting
-    'lambertdouble' : { 
-        fragmentShader : [
-
-"uniform mat4 viewMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform float opacity;",
-
-"uniform vec3 fogColor;",
-"uniform float fogNear;",
-"uniform float fogFar;",
-
-"varying vec3 vLightFront;",
-"varying vec3 vLightBack;",
-
-"varying vec3 vColor;",
-
-"void main() {",
+    this.fog = true;
     
-"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    this.wireframe = false;
+    this.wireframeLinewidth = 1;
+    this.wireframeLinecap = 'round';
+    this.wireframeLinejoin = 'round';
     
-"    #ifndef WIREFRAME",
-"    if ( gl_FrontFacing )",
-"       gl_FragColor.xyz *= vLightFront;",
-"    else",
-"       gl_FragColor.xyz *= vLightBack;",
-"    #endif",
+    this.shading = $3Dmol.SmoothShading;
+    this.shaderID = "lambert";
+    this.vertexColors = $3Dmol.NoColors;
     
-"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
-"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    this.skinning = false;
     
-"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    this.setValues(parameters);
     
-"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
-
-"}"
-
-
-].join("\n"),
-       
-       vertexShader : [
-
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform mat4 viewMatrix;",
-"uniform mat3 normalMatrix;",
-"uniform vec3 cameraPosition;",
-"uniform vec3 ambient;",
-"uniform vec3 diffuse;",
-"uniform vec3 emissive;",
-"uniform vec3 ambientLightColor;",
-"uniform vec3 directionalLightColor[ 1 ];",
-"uniform vec3 directionalLightDirection[ 1 ];",
-
-"attribute vec3 position;",
-"attribute vec3 normal;",
-"attribute vec3 color;",
+};
 
-"varying vec3 vColor;",
-"varying vec3 vLightFront;",
-"varying vec3 vLightBack;",
+$3Dmol.MeshLambertMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-"void main() {",
+$3Dmol.MeshLambertMaterial.prototype.clone = function(material) {
+  
+    if ( typeof material === "undefined" ) material = new $3Dmol.MeshLambertMaterial();
     
-"    vColor = color;",
+    $3Dmol.Material.prototype.clone.call(this, material);
     
-"    vec3 objectNormal = normal;",  
-"    vec3 transformedNormal = normalMatrix * objectNormal;",    
-"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    material.color.copy(this.color);
+    material.ambient.copy(this.ambient);
+    material.emissive.copy(this.emissive);
     
-"    vLightFront = vec3( 0.0 );",
-"    vLightBack = vec3( 0.0 );",
+    material.wrapAround = this.wrapAround;
+    material.wrapRGB.copy(this.wrapRGB);
     
-"    transformedNormal = normalize( transformedNormal );",
+    material.map = this.map;
     
-"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
-"    vec3 dirVector = normalize( lDirection.xyz );",
-"    float dotProduct = dot( transformedNormal, dirVector );",
-"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
-"    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );",
-
-"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
-"    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;",
-
-"    vLightFront = vLightFront * diffuse + ambient * ambientLightColor + emissive;",
-"    vLightBack = vLightBack * diffuse + ambient * ambientLightColor + emissive;",
-
-"    gl_Position = projectionMatrix * mvPosition;",
-"}"
-           
-].join("\n"),
-
-        uniforms : {
-            opacity: { type: 'f', value: 1.0 },
-            diffuse: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            fogNear: { type: 'f', value: 1.0 },
-            fogFar: { type: 'f', value: 2000},           
-            ambient: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            emissive: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
-            ambientLightColor: { type: 'fv', value: [] },
-            directionalLightColor: { type: 'fv', value: [] },
-            directionalLightDirection: { type: 'fv', value: [] }
-        }
-
-    },
+    material.lightMap = this.lightMap;
     
+    material.specularMap = this.specularMap;
     
-    'sprite': {
-        
-        fragmentShader: [
-                                                         
-"uniform vec3 color;",
-"uniform sampler2D map;",
-"uniform float opacity;",
-
-"uniform int fogType;",
-"uniform vec3 fogColor;",
-"uniform float fogDensity;",
-"uniform float fogNear;",
-"uniform float fogFar;",
-"uniform float alphaTest;",
-
-"varying vec2 vUV;",
-
-"void main() {",
+    material.envMap = this.envMap;
+    material.combine = this.combine;
+    material.reflectivity = this.reflectivity;
+    material.refractionRatio = this.refractionRatio;
     
-"    vec4 texture = texture2D(map, vUV);",
+    material.fog = this.fog;
     
-"    if (texture.a < alphaTest) discard;",
+    material.shading = this.shading;
+    material.shaderID = this.shaderID;
+    material.vertexColors = this.vertexColors;
     
-"    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);",
+    material.skinning = this.skinning;
+    material.morphTargets = this.morphTargets;
+    material.morphNormals = this.morphNormals;
     
-"    if (fogType > 0) {",
-        
-"        float depth = gl_FragCoord.z / gl_FragCoord.w;",
-"        float fogFactor = 0.0;",
-        
-"        if (fogType == 1) {",
-"            fogFactor = smoothstep(fogNear, fogFar, depth);",
-"        }",
-        
-"        else {",
-"            const float LOG2 = 1.442695;",
-"            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);",
-"            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);",
-"        }",
-        
-"        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);",
-        
-"    }",
-"}"                                              
-            
-].join("\n"),
-        
-        vertexShader: [
+    return material;
+    
+};
 
-"uniform int useScreenCoordinates;",
-"uniform vec3 screenPosition;",
-"uniform mat4 modelViewMatrix;",
-"uniform mat4 projectionMatrix;",
-"uniform float rotation;",
-"uniform vec2 scale;",
-"uniform vec2 alignment;",
-"uniform vec2 uvOffset;",
-"uniform vec2 uvScale;",
+//Double sided Mesh Lambert material
+/** @constructor */
+$3Dmol.MeshDoubleLambertMaterial = function(parameters) {
+    
+    $3Dmol.MeshLambertMaterial.call(this, parameters);
 
-"attribute vec2 position;",
-"attribute vec2 uv;",
+    this.shaderID = "lambertdouble";
+    this.side = $3Dmol.DoubleSide;    
+    
+};
 
-"varying vec2 vUV;",
+$3Dmol.MeshDoubleLambertMaterial.prototype = Object.create($3Dmol.MeshLambertMaterial.prototype);
 
-"void main() {",
-    
-"    vUV = uvOffset + uv * uvScale;",
-    
-"    vec2 alignedPosition = position + alignment;",
-    
-"    vec2 rotatedPosition;",
-"    rotatedPosition.x = ( cos(rotation) * alignedPosition.x - sin(rotation) * alignedPosition.y ) * scale.x;",
-"    rotatedPosition.y = ( sin(rotation) * alignedPosition.x + cos(rotation) * alignedPosition.y ) * scale.y;",
-    
-"    vec4 finalPosition;",
-    
-"    if(useScreenCoordinates != 0) {",
-"        finalPosition = vec4(screenPosition.xy + rotatedPosition, screenPosition.z, 1.0);",
-"    }",
-    
-"    else {",
-"        finalPosition = projectionMatrix * modelViewMatrix * vec4(0.0, 0.0, 0.0, 1.0); finalPosition /= finalPosition.w;",
-"        finalPosition.xy += rotatedPosition; ",
-"    }",
+$3Dmol.MeshDoubleLambertMaterial.prototype.clone = function() {
+  
+    var material = new $3Dmol.MeshDoubleLambertMaterial();
     
-"    gl_Position = finalPosition;",
+    $3Dmol.MeshLambertMaterial.prototype.clone.call(this, material);
+        
+    return material;
     
-"}"
-       
-].join("\n"),
+};
 
-        uniforms : {
-            
-        }
-        
-    }
+//Outlined Mesh Lamert material
+/** @constructor */
+$3Dmol.MeshOutlineMaterial = function(parameters) {
+    $3Dmol.Material.call(this);
+    parameters = parameters || {};
+    this.fog = true;
+    this.shaderID = "outline";
+    this.wireframe=false;
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
     
-};var $3Dmol = $3Dmol || {};
+};
 
-//properties for mapping
+$3Dmol.MeshOutlineMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-/* partial charges for proteins */
-$3Dmol.partialCharges = {
-"ALA:N": -0.15,
-"ALA:CA": 0.10,
-"ALA:CB": 0.00,
-"ALA:C": 0.60,
-"ALA:O": -0.55,
-"ARG:N": -0.15,
-"ARG:CA": 0.10,
-"ARG:CB": 0.00,
-"ARG:CG": 0.00,
-"ARG:CD": 0.10,
-"ARG:NE": -0.10,
-"ARG:CZ": 0.50,
-"ARG:NH1": 0.25,
-"ARG:NH2": 0.25,
-"ARG:C": 0.60,
-"ARG:O": -0.55,
-"ASN:N": -0.15,
-"ASN:CA": 0.10,
-"ASN:CB": 0.00,
-"ASN:CG": 0.55,
-"ASN:OD1": -0.55,
-"ASN:ND2": 0.00,
-"ASN:C": 0.60,
-"ASN:O": -0.55,
-"ASP:N": -0.15,
-"ASP:CA": 0.10,
-"ASP:CB": 0.00,
-"ASP:CG": 0.14,
-"ASP:OD1": -0.57,
-"ASP:OD2": -0.57,
-"ASP:C": 0.60,
-"ASP:O": -0.55,
-"CYS:N": -0.15,
-"CYS:CA": 0.10,
-"CYS:CB": 0.19,
-"CYS:SG": -0.19,
-"CYS:C": 0.60,
-"CYS:O": -0.55,
-"GLN:N": -0.15,
-"GLN:CA": 0.10,
-"GLN:CB": 0.00,
-"GLN:CG": 0.00,
-"GLN:CD": 0.55,
-"GLN:OE1": -0.55,
-"GLN:NE2": 0.00,
-"GLN:C": 0.60,
-"GLN:O": -0.55,
-"GLU:N": -0.15,
-"GLU:CA": 0.10,
-"GLU:CB": 0.00,
-"GLU:CG": 0.00,
-"GLU:CD": 0.14,
-"GLU:OE1": -0.57,
-"GLU:OE2": -0.57,
-"GLU:C": 0.60,
-"GLU:O": -0.55,
-"GLY:N": -0.15,
-"GLY:CA": 0.10,
-"GLY:C": 0.60,
-"GLY:O": -0.55,
-"HIS:N": -0.15,
-"HIS:CA": 0.10,
-"HIS:CB": 0.00,
-"HIS:CG": 0.10,
-"HIS:ND1": -0.10,
-"HIS:CD2": 0.10,
-"HIS:NE2": -0.40,
-"HIS:CE1": 0.30,
-"HIS:C": 0.60,
-"HIS:O": -0.55,
-"ILE:N": -0.15,
-"ILE:CA": 0.10,
-"ILE:CB": 0.00,
-"ILE:CG2": 0.00,
-"ILE:CG1": 0.00,
-"ILE:CD": 0.00,
-"ILE:C": 0.60,
-"ILE:O": -0.55,
-"LEU:N": -0.15,
-"LEU:CA": 0.10,
-"LEU:CB": 0.00,
-"LEU:CG": 0.00,
-"LEU:CD1": 0.00,
-"LEU:CD2": 0.00,
-"LEU:C": 0.60,
-"LEU:O": -0.55,
-"LYS:N": -0.15,
-"LYS:CA": 0.10,
-"LYS:CB": 0.00,
-"LYS:CG": 0.00,
-"LYS:CD": 0.00,
-"LYS:CE": 0.25,
-"LYS:NZ": 0.75,
-"LYS:C": 0.60,
-"LYS:O": -0.55,
-"MET:N": -0.15,
-"MET:CA": 0.10,
-"MET:CB": 0.00,
-"MET:CG": 0.06,
-"MET:SD": -0.12,
-"MET:CE": 0.06,
-"MET:C": 0.60,
-"MET:O": -0.55,
-"PHE:N": -0.15,
-"PHE:CA": 0.10,
-"PHE:CB": 0.00,
-"PHE:CG": 0.00,
-"PHE:CD1": 0.00,
-"PHE:CD2": 0.00,
-"PHE:CE1": 0.00,
-"PHE:CE2": 0.00,
-"PHE:CZ": 0.00,
-"PHE:C": 0.60,
-"PHE:O": -0.55,
-"PRO:N": -0.25,
-"PRO:CD": 0.10,
-"PRO:CA": 0.10,
-"PRO:CB": 0.00,
-"PRO:CG": 0.00,
-"PRO:C": 0.60,
-"PRO:O": -0.55,
-"SER:N": -0.15,
-"SER:CA": 0.10,
-"SER:CB": 0.25,
-"SER:OG": -0.25,
-"SER:C": 0.60,
-"SER:O": -0.55,
-"THR:N": -0.15,
-"THR:CA": 0.10,
-"THR:CB": 0.25,
-"THR:OG1": -0.25,
-"THR:CG2": 0.00,
-"THR:C": 0.60,
-"THR:O": -0.55,
-"TRP:N": -0.15,
-"TRP:CA": 0.10,
-"TRP:CB": 0.00,
-"TRP:CG": -0.03,
-"TRP:CD2": 0.10,
-"TRP:CE2": -0.04,
-"TRP:CE3": -0.03,
-"TRP:CD1": 0.06,
-"TRP:NE1": -0.06,
-"TRP:CZ2": 0.00,
-"TRP:CZ3": 0.00,
-"TRP:CH2": 0.00,
-"TRP:C": 0.60,
-"TRP:O": -0.55,
-"TYR:N": -0.15,
-"TYR:CA": 0.10,
-"TYR:CB": 0.00,
-"TYR:CG": 0.00,
-"TYR:CD1": 0.00,
-"TYR:CE1": 0.00,
-"TYR:CD2": 0.00,
-"TYR:CE2": 0.00,
-"TYR:CZ": 0.25,
-"TYR:OH": -0.25,
-"TYR:C": 0.60,
-"TYR:O": -0.55,
-"VAL:N": -0.15,
-"VAL:CA": 0.10,
-"VAL:CB": 0.00,
-"VAL:CG1": 0.00,
-"VAL:CG2": 0.00,
-"VAL:C": 0.60,
-"VAL:O": -0.55
+$3Dmol.MeshOutlineMaterial.prototype.clone = function(material) {
+    if ( typeof material === "undefined" ) material = new $3Dmol.MeshOutlineMaterial();
+    $3Dmol.Material.prototype.clone.call(this, material);
+    material.fog = this.fog;
+    material.shaderID = this.shaderID;
+    material.wireframe = this.wireframe;
+    return material;
 };
-    
-//this can be supplied to mapAtomProperties
-$3Dmol.applyPartialCharges = function(atom, keepexisting) {
-    if(!keepexisting || typeof(atom.partialCharge) === "undefined") {
-        if(atom.resn && atom.atom) {
-            var key = atom.resn+":"+atom.atom;
-            atom.properties['partialCharge'] = $3Dmol.partialCharges[key];
-        }
-    }
+
+
+//Imposter material
+/** @constructor */
+$3Dmol.ImposterMaterial = function(parameters) {
+  
+  $3Dmol.Material.call(this);
+  
+  this.color = new $3Dmol.Color(0xffffff);
+  this.ambient = new $3Dmol.Color(0xfffff);
+  this.emissive = new $3Dmol.Color(0x000000);
+  this.imposter = true;
+  
+  //TODO: Which of these instance variables do I really need?
+  this.wrapAround = false;
+  this.wrapRGB = new $3Dmol.Vector3(1,1,1);
+  
+  this.map = null;
+  
+  this.lightMap = null;
+  
+  this.specularMap = null;
+  
+  this.envMap = null;
+  this.reflectivity = 1;
+  this.refractionRatio = 0.98;
+  
+  this.fog = true;
+  
+  this.wireframe = false;
+  this.wireframeLinewidth = 1;
+  this.wireframeLinecap = 'round';
+  this.wireframeLinejoin = 'round';
+  
+  this.shading = $3Dmol.SmoothShading;
+  this.shaderID = null;
+  this.vertexColors = $3Dmol.NoColors;
+  
+  this.skinning = false;
+  
+  this.setValues(parameters);
+  
 };
-$3Dmol = $3Dmol || {};
-//Encapsulate marching cube algorithm for isosurface generation
-// (currently used by protein surface rendering and generic volumetric data reading)
-$3Dmol.MarchingCube = (function() {
-    
-    //Marching cube algorithm - assume data has been pre-treated so isovalue is 0 
-    // (i.e. select points greater than 0)
-    //origin -  vector of origin of volumetric data (default is (0,0,0))
-    // nX, nY, nZ - specifies number of voxels in each dimension
-    // scale - cube diagonal unit vector scale (3Dmol vector) (specifying distance between data points); diagonal of cube
-    // - default is 1 - assumes unit cube (1,1,1) diag)
-    // fulltable - if true, use full marching cubes and tritables - else use trimmed table (e.g. surf render)
-    // voxel - if true, draws with a blocky voxel style (default false)
-    // verts, faces - vertex and face arrays to fill up
-    
-    //to match with protein surface...
-    var ISDONE = 2;
-    var my = {};
-    
-    my.march = function(data, verts, faces, spec) {
 
-        var fulltable = !!(spec.fulltable);
-        var origin = (spec.hasOwnProperty('origin') && spec.origin.hasOwnProperty('x')) ? spec.origin : {x:0, y:0, z:0};
-        var voxel = !!(spec.voxel);
-        
-        var nX = spec.nX || 0;
-        var nY = spec.nY || 0;
-        var nZ = spec.nZ || 0;
-        
-        var scale = spec.scale || 1.0;
-        
-        var unitCube = new $3Dmol.Vector3(1,1,1).multiplyScalar(scale);
-        
-        //keep track of calculated vertices to avoid repeats
-        var vertnums = new Int32Array(nX*nY*nZ);
-        
-        var i, il;
-        
-        for (i = 0, il = vertnums.length; i < il; ++i)
-            vertnums[i] = -1;
+$3Dmol.ImposterMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        // create (or retrieve) a vertex at the appropriate point for
-        // the edge (p1,p2)
-        
-        var getVertex = function(i, j, k, code, p1, p2) {
-            var pt = new $3Dmol.Vector3();
-            pt.copy(origin);
-            var val1 = !!(code & (1 << p1));
-            var val2 = !!(code & (1 << p2));
-             
-            // p1 if they are the same or if !val1
-            var p = p1;
-            if (!val1 && val2)
-                p = p2;
-            
-            // adjust i,j,k by p
-            if (p & 1)
-                k++;
-            if (p & 2)
-                j++;
-            if (p & 4)
-                i++;
+$3Dmol.ImposterMaterial.prototype.clone = function() {
+
+  var material = new $3Dmol.ImposterMaterial();
+  
+  $3Dmol.Material.prototype.clone.call(this, material);
+  
+  material.color.copy(this.color);
+  material.ambient.copy(this.ambient);
+  material.emissive.copy(this.emissive);
+  
+  material.wrapAround = this.wrapAround;
+  material.wrapRGB.copy(this.wrapRGB);
+  
+  material.map = this.map;
+  
+  material.lightMap = this.lightMap;
+  
+  material.specularMap = this.specularMap;
+  
+  material.envMap = this.envMap;
+  material.combine = this.combine;
+  material.reflectivity = this.reflectivity;
+  material.refractionRatio = this.refractionRatio;
+  
+  material.fog = this.fog;
+  
+  material.shading = this.shading;
+  material.shaderID = this.shaderID;
+  material.vertexColors = this.vertexColors;
+  
+  material.skinning = this.skinning;
+  material.morphTargets = this.morphTargets;
+  material.morphNormals = this.morphNormals;
+  
+  return material;
+  
+};
+
+
+$3Dmol.SphereImposterMaterial = function(parameters) {
     
-            pt.x += unitCube.x*i;
-            pt.y += unitCube.y*j;
-            pt.z += unitCube.z*k;
+    $3Dmol.ImposterMaterial.call(this);
+
+    this.shaderID = "sphereimposter";    
+    this.setValues(parameters);
     
-            var index = ((nY * i) + j) * nZ + k;
-            
-            //Have to add option to do voxels
-            if (!voxel) {
-            
-                if (vertnums[index] < 0) // not created yet
-                {
-                    vertnums[index] = verts.length;
-                    verts.push( pt );
-                }
-                return vertnums[index];
-            
-            }
-            
-            else {
-                verts.push(pt);
-                return verts.length - 1;
-            }
-            
-        };
-            
-        var intersects = new Int32Array(12);
-        
-        var etable = (fulltable) ? edgeTable2 : edgeTable;
-        var tritable = (fulltable) ? triTable2 : triTable;
-                
-        //Run marching cubes algorithm
-        for (i = 0; i < nX-1; ++i) {
-            
-            for (var j = 0; j < nY-1; ++j){
-                
-                for (var k = 0; k < nZ-1; ++k){
-                    
-                    var code = 0;
-                    
-                    for (var p = 0; p < 8; ++p) {
-                        var index = ((nY * (i + ((p & 4) >> 2))) + j + ((p & 2) >> 1)) *
-                                        nZ + k + (p & 1);
+};
 
-                        //TODO: Need to fix vpBits in protein surface for this to work
-                        var val = !!(data[index] & ISDONE);
-                        //var val = !!(data[index] > 0);   
-                        
-                        code |= val << p;                        
-                    }
-                    
-                    if (code === 0 || code === 255)
-                        continue;
-                    
-                    var ecode = etable[code];
-                    
-                    if (ecode === 0)
-                        continue;
-                        
-                    var ttable = tritable[code];                        
-                    
-                    if (ecode & 1)
-                        intersects[0] = getVertex(i, j, k, code, 0, 1);
-                    if (ecode & 2)
-                        intersects[1] = getVertex(i, j, k, code, 1, 3);
-                    if (ecode & 4)
-                        intersects[2] = getVertex(i, j, k, code, 3, 2);
-                    if (ecode & 8)
-                        intersects[3] = getVertex(i, j, k, code, 2, 0);
-                    if (ecode & 16)
-                        intersects[4] = getVertex(i, j, k, code, 4, 5);
-                    if (ecode & 32)
-                        intersects[5] = getVertex(i, j, k, code, 5, 7);
-                    if (ecode & 64)
-                        intersects[6] = getVertex(i, j, k, code, 7, 6);
-                    if (ecode & 128)
-                        intersects[7] = getVertex(i, j, k, code, 6, 4);
-                    if (ecode & 256)
-                        intersects[8] = getVertex(i, j, k, code, 0, 4);
-                    if (ecode & 512)
-                        intersects[9] = getVertex(i, j, k, code, 1, 5);
-                    if (ecode & 1024)
-                        intersects[10] = getVertex(i, j, k, code, 3, 7);
-                    if (ecode & 2048)
-                        intersects[11] = getVertex(i, j, k, code, 2, 6);       
-                        
-                    for (var t = 0; t < ttable.length; t += 3) {
-                        
-                        var a = intersects[ttable[t]],
-                            b = intersects[ttable[t+1]],
-                            c = intersects[ttable[t+2]];         
-                                           
-                        if (voxel && t >= 3) {
-                            verts.push(verts[a]); a = verts.length - 1;
-                            verts.push(verts[b]); b = verts.length - 1;
-                            verts.push(verts[c]); c = verts.length - 1;
-                        }
+$3Dmol.SphereImposterMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-                        
-                        faces.push(a); faces.push(b); faces.push(c);                               
-                    }              
-                    
-                }
-                
-            }
-            
-        }
-             
-        
-    };
+$3Dmol.SphereImposterMaterial.prototype.clone = function() {
 
-    my.laplacianSmooth = function(numiter, verts, faces) {
-            var tps = new Array(verts.length);
-            var i, il, j, jl, k, kl;
-            for (i = 0, il = verts.length; i < il; i++)
-                    tps[i] = {
-                        x : 0,
-                        y : 0,
-                        z : 0
-                    };
-            var vertdeg = new Array(20);
-            var flagvert;
-            for (i = 0; i < 20; i++)
-                    vertdeg[i] = new Array(verts.length);
-            for (i = 0, il = verts.length; i < il; i++)
-                    vertdeg[0][i] = 0;
-            for (i = 0, il = faces.length / 3; i < il; i++) {
-                var aoffset = i*3, boffset = i*3 + 1, coffset = i*3 + 2;
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
-                    if (faces[boffset] == vertdeg[j + 1][faces[aoffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[aoffset]]++;
-                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[boffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
-                    if (faces[coffset] == vertdeg[j + 1][faces[aoffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[aoffset]]++;
-                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[coffset];
-                }
-                // b
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
-                    if (faces[aoffset] == vertdeg[j + 1][faces[boffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[boffset]]++;
-                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[aoffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
-                    if (faces[coffset] == vertdeg[j + 1][faces[boffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[boffset]]++;
-                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[coffset];
-                }
-                // c
-                flagvert = true;
-                for (j = 0; j < vertdeg[0][faces[coffset]]; j++) {
-                    if (faces[aoffset] == vertdeg[j + 1][faces[coffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[coffset]]++;
-                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[aoffset];
-                }
-                flagvert = true;
-                for (j = 0, jl = vertdeg[0][faces[coffset]]; j < jl; j++) {
-                    if (faces[boffset] == vertdeg[j + 1][faces[coffset]]) {
-                        flagvert = false;
-                        break;
-                    }
-                }
-                if (flagvert) {
-                    vertdeg[0][faces[coffset]]++;
-                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[boffset];
-                }
-            }
+    var material = new $3Dmol.SphereImposterMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    return material;
+};
 
-            var wt = 1.00;
-            var wt2 = 0.50;
-            var ssign;
-            var scaleFactor = 1;
-            var outwt = 0.75 / (scaleFactor + 3.5); // area-preserving
-            for (k = 0; k < numiter; k++) {
-                    for (i = 0, il = verts.length; i < il; i++) {
-                            if (vertdeg[0][i] < 3) {
-                                    tps[i].x = verts[i].x;
-                                    tps[i].y = verts[i].y;
-                                    tps[i].z = verts[i].z;
-                            } else if (vertdeg[0][i] == 3 || vertdeg[0][i] == 4) {
-                                    tps[i].x = 0;
-                                    tps[i].y = 0;
-                                    tps[i].z = 0;
-                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
-                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
-                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
-                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
-                                    }
-                                    tps[i].x += wt2 * verts[i].x;
-                                    tps[i].y += wt2 * verts[i].y;
-                                    tps[i].z += wt2 * verts[i].z;
-                                    tps[i].x /= wt2 + vertdeg[0][i];
-                                    tps[i].y /= wt2 + vertdeg[0][i];
-                                    tps[i].z /= wt2 + vertdeg[0][i];
-                            } else {
-                                    tps[i].x = 0;
-                                    tps[i].y = 0;
-                                    tps[i].z = 0;
-                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
-                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
-                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
-                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
-                                    }
-                                    tps[i].x += wt * verts[i].x;
-                                    tps[i].y += wt * verts[i].y;
-                                    tps[i].z += wt * verts[i].z;
-                                    tps[i].x /= wt + vertdeg[0][i];
-                                    tps[i].y /= wt + vertdeg[0][i];
-                                    tps[i].z /= wt + vertdeg[0][i];
-                            }
-                    }
-                    for (i = 0, il = verts.length; i < il; i++) {
-                            verts[i].x = tps[i].x;
-                            verts[i].y = tps[i].y;
-                            verts[i].z = tps[i].z;
-                    }
-                    /*
-                     * computenorm(); for (var i = 0; i < vertnumber; i++) { if
-                     * (verts[i].inout) ssign = 1; else ssign = -1; verts[i].x += ssign *
-                     * outwt * verts[i].pn.x; verts[i].y += ssign * outwt *
-                     * verts[i].pn.y; verts[i].z += ssign * outwt * verts[i].pn.z; }
-                     */
-            }
-    };
 
+$3Dmol.SphereImposterOutlineMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-    /*
-     * These tables are based off those by Paul Bourke and Geoffrey Heller:
-     * http://paulbourke.net/geometry/polygonise/
-     * http://paulbourke.net/geometry/polygonise/table2.txt
-     * 
-     * However, they have been substantially modified to reflect a more 
-     * sensible corner numbering scheme and the discrete nature of our voxel data
-     * (resulting in fewer faces).
-     */
-    my.edgeTable = [ 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
-            0xb00, 0x0, 0x0, 0x0, 0x700, 0x0, 0xd00, 0xe00, 0xf00, 0x0, 0x0, 0x0,
-            0x8a, 0x0, 0x15, 0x0, 0x86, 0x0, 0x0, 0x0, 0x28c, 0x0, 0x813, 0xf19,
-            0xe10, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x0, 0x0, 0x126, 0x0, 0x0, 0x15, 0x1c,
-            0x0, 0xf23, 0x419, 0xd20, 0x0, 0xa8, 0xa2, 0xaa, 0x0, 0x285, 0x9ab,
-            0x8a2, 0x0, 0x2af, 0x125, 0xac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x0, 0x0,
-            0x0, 0x0, 0x0, 0x45, 0x0, 0x384, 0x0, 0x0, 0x0, 0x700, 0x8a, 0x83,
-            0x648, 0x780, 0x0, 0x51, 0x0, 0x81a, 0x54, 0x55, 0x54, 0x56, 0x0, 0x51,
-            0x0, 0xe5c, 0x14a, 0x451, 0x759, 0x650, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x45,
-            0x0, 0x1f6, 0x0, 0x0, 0x15, 0xdfc, 0x8a, 0x7f3, 0x4f9, 0x5f0, 0xb00,
-            0x68, 0x921, 0x6a, 0x348, 0x245, 0x16f, 0x66, 0xb00, 0xe6f, 0xd65,
-            0xc6c, 0x76a, 0x663, 0x569, 0x460, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
-            0xf46, 0x0, 0x0, 0x45, 0x24c, 0x2a, 0x823, 0x29, 0xb40, 0x0, 0x0, 0x0,
-            0x6ba, 0x0, 0x8f5, 0xfff, 0xef6, 0x0, 0xff, 0x2f5, 0x2fc, 0x9ea, 0x8f3,
-            0xbf9, 0xaf0, 0x0, 0x0, 0x51, 0x152, 0x0, 0xf55, 0x45f, 0xd56, 0x54,
-            0x357, 0x55, 0x154, 0x852, 0xb53, 0x59, 0x950, 0x700, 0x2c8, 0xc2,
-            0x48a, 0xfc4, 0xec5, 0xdcf, 0xcc6, 0x2c4, 0x2cf, 0xc5, 0xcc, 0xbca,
-            0xac3, 0x9c9, 0x8c0, 0x0, 0x0, 0x0, 0x0, 0xa8, 0x1a4, 0xa8, 0x7a6,
-            0xa2, 0xa2, 0x2a4, 0xbac, 0xaa, 0xa3, 0x2a8, 0x3a0, 0xd00, 0xc18,
-            0xd00, 0xe3a, 0x34, 0x35, 0x73f, 0x636, 0x924, 0x83f, 0xb35, 0xa3c,
-            0x12a, 0x33, 0x339, 0x230, 0xe00, 0xe00, 0xc12, 0xd9a, 0x684, 0x795,
-            0x49f, 0x596, 0x92, 0xb9f, 0x815, 0x99c, 0x9a, 0x393, 0x99, 0x190,
-            0xf00, 0xe08, 0xd01, 0xc0a, 0x704, 0x605, 0x50f, 0x406, 0xb02, 0xa0f,
-            0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
+    this.shaderID = "sphereimposteroutline";
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
     
-    var edgeTable = new Uint32Array(my.edgeTable);
+    this.setValues(parameters);
     
-    var triTable = my.triTable = [ [], [], [], [], [], [], [], [ 11, 9, 8 ], [], [], [],
-            [ 8, 10, 9 ], [], [ 10, 8, 11 ], [ 9, 11, 10 ],
-            [ 8, 10, 9, 8, 11, 10 ], [], [], [], [ 1, 7, 3 ], [], [ 4, 2, 0 ], [],
-            [ 2, 1, 7 ], [], [], [], [ 2, 7, 3, 2, 9, 7 ], [],
-            [ 1, 4, 11, 1, 0, 4 ], [ 3, 8, 0, 11, 9, 4, 11, 10, 9 ],
-            [ 4, 11, 9, 11, 10, 9 ], [], [], [], [ 5, 3, 1 ], [], [], [],
-            [ 2, 5, 8, 2, 1, 5 ], [], [], [ 2, 4, 0 ], [ 3, 2, 4 ], [],
-            [ 0, 9, 1, 8, 10, 5, 8, 11, 10 ], [ 3, 4, 0, 3, 10, 4 ],
-            [ 5, 8, 10, 8, 11, 10 ], [], [ 3, 5, 7 ], [ 7, 1, 5 ],
-            [ 1, 7, 3, 1, 5, 7 ], [], [ 9, 2, 0, 9, 7, 2 ],
-            [ 0, 3, 8, 1, 7, 11, 1, 5, 7 ], [ 11, 1, 7, 1, 5, 7 ], [],
-            [ 9, 1, 0, 5, 3, 2, 5, 7, 3 ], [ 8, 2, 5, 8, 0, 2 ],
-            [ 2, 5, 3, 5, 7, 3 ], [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
-            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
-            [ 11, 5, 7, 11, 10, 5 ], [], [], [], [], [], [ 0, 6, 2 ], [],
-            [ 7, 2, 9, 7, 9, 8 ], [], [], [], [ 8, 10, 9 ], [ 7, 1, 3 ],
-            [ 7, 1, 0 ], [ 6, 9, 3, 6, 10, 9 ], [ 7, 10, 8, 10, 9, 8 ], [],
-            [ 6, 0, 4 ], [], [ 11, 1, 4, 11, 3, 1 ], [ 2, 4, 6 ],
-            [ 2, 0, 4, 2, 4, 6 ], [ 2, 4, 6 ], [ 1, 4, 2, 4, 6, 2 ], [],
-            [ 6, 0, 4 ], [], [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ], [ 8, 6, 1, 8, 1, 3 ],
-            [ 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
-            [ 10, 4, 6, 10, 9, 4 ], [], [], [], [ 5, 3, 1 ], [], [ 0, 6, 2 ], [],
-            [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ], [], [], [ 2, 4, 0 ],
-            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ], [ 7, 1, 3 ],
-            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
-            [ 10, 5, 6, 4, 8, 7 ], [ 9, 11, 8 ], [ 3, 5, 6 ],
-            [ 0, 5, 11, 0, 11, 8 ], [ 6, 3, 5, 3, 1, 5 ], [ 3, 9, 6, 3, 8, 9 ],
-            [ 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
-            [ 1, 6, 2, 1, 5, 6 ], [ 9, 11, 8 ], [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ],
-            [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ], [ 3, 2, 11, 10, 5, 6 ],
-            [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ], [ 0, 9, 1, 5, 6, 10 ],
-            [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ], [], [], [], [], [], [], [],
-            [ 1, 10, 2, 9, 11, 6, 9, 8, 11 ], [], [], [ 6, 0, 2 ],
-            [ 3, 6, 9, 3, 2, 6 ], [ 3, 5, 1 ], [ 0, 5, 1, 0, 11, 5 ], [ 0, 3, 5 ],
-            [ 6, 9, 11, 9, 8, 11 ], [], [], [], [ 4, 5, 9, 7, 1, 10, 7, 3, 1 ], [],
-            [ 11, 6, 7, 2, 4, 5, 2, 0, 4 ],
-            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
-            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [],
-            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ], [ 9, 4, 5, 0, 6, 7, 0, 2, 6 ],
-            [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ], [ 6, 7, 11, 5, 3, 8, 5, 1, 3 ],
-            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
-            [ 9, 4, 5, 7, 11, 6 ], [], [], [ 0, 6, 4 ], [ 8, 6, 4, 8, 1, 6 ], [],
-            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
-            [ 10, 2, 1, 6, 0, 3, 6, 4, 0 ], [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ],
-            [ 4, 2, 6 ], [ 1, 0, 9, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
-            [ 8, 2, 4, 2, 6, 4 ], [ 11, 4, 1, 11, 6, 4 ],
-            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 3, 6, 0, 6, 4, 0 ],
-            [ 8, 6, 4, 8, 11, 6 ], [ 10, 8, 9 ], [ 6, 3, 9, 6, 7, 3 ], [ 6, 7, 1 ],
-            [ 10, 7, 1, 7, 3, 1 ], [ 7, 11, 6, 8, 10, 2, 8, 9, 10 ],
-            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
-            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2 ],
-            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 7, 0, 6, 0, 2, 6 ],
-            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
-            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ], [], [], [],
-            [], [ 5, 3, 7 ], [ 8, 5, 2, 8, 7, 5 ], [ 5, 3, 7 ],
-            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 1, 7, 5 ], [ 1, 7, 5 ],
-            [ 9, 2, 7, 9, 7, 5 ], [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ],
-            [ 1, 3, 7, 1, 7, 5 ], [ 0, 7, 1, 7, 5, 1 ], [ 9, 3, 5, 3, 7, 5 ],
-            [ 9, 7, 5, 9, 8, 7 ], [ 8, 10, 11 ], [ 3, 4, 10, 3, 10, 11 ],
-            [ 8, 10, 11 ], [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ], [ 2, 4, 5 ],
-            [ 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
-            [ 2, 1, 10, 9, 4, 5 ], [ 2, 8, 5, 2, 11, 8 ],
-            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
-            [ 11, 3, 2, 9, 4, 5 ], [ 8, 5, 3, 5, 1, 3 ], [ 5, 0, 4, 5, 1, 0 ],
-            [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ], [ 11, 9, 10 ], [ 11, 9, 10 ],
-            [ 1, 11, 4, 1, 10, 11 ], [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
-            [ 2, 7, 9, 2, 9, 10 ], [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ],
-            [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ], [ 10, 2, 1, 8, 7, 4 ], [ 1, 7, 4 ],
-            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 11, 4, 2, 4, 0, 2 ],
-            [ 2, 11, 3, 7, 4, 8 ], [ 4, 1, 7, 1, 3, 7 ], [ 1, 0, 9, 8, 7, 4 ],
-            [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ], [ 8, 9, 10, 8, 10, 11 ],
-            [ 3, 9, 11, 9, 10, 11 ], [ 0, 10, 8, 10, 11, 8 ],
-            [ 10, 3, 1, 10, 11, 3 ], [ 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
-            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 1, 11, 9, 11, 8, 9 ],
-            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
-            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
-     
-    var edgeTable2 = [ 0x0, 0x109, 0x203, 0x30a, 0x80c, 0x905, 0xa0f,
-            0xb06, 0x406, 0x50f, 0x605, 0x70c, 0xc0a, 0xd03, 0xe09, 0xf00, 0x190,
-            0x99, 0x393, 0x29a, 0x99c, 0x895, 0xb9f, 0xa96, 0x596, 0x49f, 0x795,
-            0x69c, 0xd9a, 0xc93, 0xf99, 0xe90, 0x230, 0x339, 0x33, 0x13a, 0xa3c,
-            0xb35, 0x83f, 0x936, 0x636, 0x73f, 0x435, 0x53c, 0xe3a, 0xf33, 0xc39,
-            0xd30, 0x3a0, 0x2a9, 0x1a3, 0xaa, 0xbac, 0xaa5, 0x9af, 0x8a6, 0x7a6,
-            0x6af, 0x5a5, 0x4ac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x8c0, 0x9c9, 0xac3,
-            0xbca, 0xcc, 0x1c5, 0x2cf, 0x3c6, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x4ca,
-            0x5c3, 0x6c9, 0x7c0, 0x950, 0x859, 0xb53, 0xa5a, 0x15c, 0x55, 0x35f,
-            0x256, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x55a, 0x453, 0x759, 0x650, 0xaf0,
-            0xbf9, 0x8f3, 0x9fa, 0x2fc, 0x3f5, 0xff, 0x1f6, 0xef6, 0xfff, 0xcf5,
-            0xdfc, 0x6fa, 0x7f3, 0x4f9, 0x5f0, 0xb60, 0xa69, 0x963, 0x86a, 0x36c,
-            0x265, 0x16f, 0x66, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x76a, 0x663, 0x569,
-            0x460, 0x460, 0x569, 0x663, 0x76a, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x66,
-            0x16f, 0x265, 0x36c, 0x86a, 0x963, 0xa69, 0xb60, 0x5f0, 0x4f9, 0x7f3,
-            0x6fa, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x1f6, 0xff, 0x3f5, 0x2fc, 0x9fa,
-            0x8f3, 0xbf9, 0xaf0, 0x650, 0x759, 0x453, 0x55a, 0xe5c, 0xf55, 0xc5f,
-            0xd56, 0x256, 0x35f, 0x55, 0x15c, 0xa5a, 0xb53, 0x859, 0x950, 0x7c0,
-            0x6c9, 0x5c3, 0x4ca, 0xfcc, 0xec5, 0xdcf, 0xcc6, 0x3c6, 0x2cf, 0x1c5,
-            0xcc, 0xbca, 0xac3, 0x9c9, 0x8c0, 0xca0, 0xda9, 0xea3, 0xfaa, 0x4ac,
-            0x5a5, 0x6af, 0x7a6, 0x8a6, 0x9af, 0xaa5, 0xbac, 0xaa, 0x1a3, 0x2a9,
-            0x3a0, 0xd30, 0xc39, 0xf33, 0xe3a, 0x53c, 0x435, 0x73f, 0x636, 0x936,
-            0x83f, 0xb35, 0xa3c, 0x13a, 0x33, 0x339, 0x230, 0xe90, 0xf99, 0xc93,
-            0xd9a, 0x69c, 0x795, 0x49f, 0x596, 0xa96, 0xb9f, 0x895, 0x99c, 0x29a,
-            0x393, 0x99, 0x190, 0xf00, 0xe09, 0xd03, 0xc0a, 0x70c, 0x605, 0x50f,
-            0x406, 0xb06, 0xa0f, 0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
-     
-    var triTable2 = [ [], [ 8, 3, 0 ], [ 9, 0, 1 ], [ 8, 3, 1, 8, 1, 9 ],
-            [ 11, 2, 3 ], [ 11, 2, 0, 11, 0, 8 ], [ 11, 2, 3, 0, 1, 9 ],
-            [ 2, 1, 11, 1, 9, 11, 11, 9, 8 ], [ 10, 1, 2 ], [ 8, 3, 0, 1, 2, 10 ],
-            [ 9, 0, 2, 9, 2, 10 ], [ 3, 2, 8, 2, 10, 8, 8, 10, 9 ],
-            [ 10, 1, 3, 10, 3, 11 ], [ 1, 0, 10, 0, 8, 10, 10, 8, 11 ],
-            [ 0, 3, 9, 3, 11, 9, 9, 11, 10 ], [ 8, 10, 9, 8, 11, 10 ], [ 8, 4, 7 ],
-            [ 3, 0, 4, 3, 4, 7 ], [ 1, 9, 0, 8, 4, 7 ],
-            [ 9, 4, 1, 4, 7, 1, 1, 7, 3 ], [ 2, 3, 11, 7, 8, 4 ],
-            [ 7, 11, 4, 11, 2, 4, 4, 2, 0 ], [ 3, 11, 2, 4, 7, 8, 9, 0, 1 ],
-            [ 2, 7, 11, 2, 1, 7, 1, 4, 7, 1, 9, 4 ], [ 10, 1, 2, 8, 4, 7 ],
-            [ 2, 10, 1, 0, 4, 7, 0, 7, 3 ], [ 4, 7, 8, 0, 2, 10, 0, 10, 9 ],
-            [ 2, 7, 3, 2, 9, 7, 7, 9, 4, 2, 10, 9 ],
-            [ 8, 4, 7, 11, 10, 1, 11, 1, 3 ],
-            [ 11, 4, 7, 1, 4, 11, 1, 11, 10, 1, 0, 4 ],
-            [ 3, 8, 0, 7, 11, 4, 11, 9, 4, 11, 10, 9 ],
-            [ 7, 11, 4, 4, 11, 9, 11, 10, 9 ], [ 9, 5, 4 ], [ 3, 0, 8, 4, 9, 5 ],
-            [ 5, 4, 0, 5, 0, 1 ], [ 4, 8, 5, 8, 3, 5, 5, 3, 1 ],
-            [ 11, 2, 3, 9, 5, 4 ], [ 9, 5, 4, 8, 11, 2, 8, 2, 0 ],
-            [ 3, 11, 2, 1, 5, 4, 1, 4, 0 ],
-            [ 8, 5, 4, 2, 5, 8, 2, 8, 11, 2, 1, 5 ], [ 2, 10, 1, 9, 5, 4 ],
-            [ 0, 8, 3, 5, 4, 9, 10, 1, 2 ], [ 10, 5, 2, 5, 4, 2, 2, 4, 0 ],
-            [ 3, 4, 8, 3, 2, 4, 2, 5, 4, 2, 10, 5 ],
-            [ 5, 4, 9, 1, 3, 11, 1, 11, 10 ],
-            [ 0, 9, 1, 4, 8, 5, 8, 10, 5, 8, 11, 10 ],
-            [ 3, 4, 0, 3, 10, 4, 4, 10, 5, 3, 11, 10 ],
-            [ 4, 8, 5, 5, 8, 10, 8, 11, 10 ], [ 9, 5, 7, 9, 7, 8 ],
-            [ 0, 9, 3, 9, 5, 3, 3, 5, 7 ], [ 8, 0, 7, 0, 1, 7, 7, 1, 5 ],
-            [ 1, 7, 3, 1, 5, 7 ], [ 11, 2, 3, 8, 9, 5, 8, 5, 7 ],
-            [ 9, 2, 0, 9, 7, 2, 2, 7, 11, 9, 5, 7 ],
-            [ 0, 3, 8, 2, 1, 11, 1, 7, 11, 1, 5, 7 ],
-            [ 2, 1, 11, 11, 1, 7, 1, 5, 7 ], [ 1, 2, 10, 5, 7, 8, 5, 8, 9 ],
-            [ 9, 1, 0, 10, 5, 2, 5, 3, 2, 5, 7, 3 ],
-            [ 5, 2, 10, 8, 2, 5, 8, 5, 7, 8, 0, 2 ],
-            [ 10, 5, 2, 2, 5, 3, 5, 7, 3 ],
-            [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
-            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
-            [ 11, 5, 7, 11, 10, 5 ], [ 11, 7, 6 ], [ 0, 8, 3, 11, 7, 6 ],
-            [ 9, 0, 1, 11, 7, 6 ], [ 7, 6, 11, 3, 1, 9, 3, 9, 8 ],
-            [ 2, 3, 7, 2, 7, 6 ], [ 8, 7, 0, 7, 6, 0, 0, 6, 2 ],
-            [ 1, 9, 0, 3, 7, 6, 3, 6, 2 ], [ 7, 6, 2, 7, 2, 9, 2, 1, 9, 7, 9, 8 ],
-            [ 1, 2, 10, 6, 11, 7 ], [ 2, 10, 1, 7, 6, 11, 8, 3, 0 ],
-            [ 11, 7, 6, 10, 9, 0, 10, 0, 2 ],
-            [ 7, 6, 11, 3, 2, 8, 8, 2, 10, 8, 10, 9 ],
-            [ 6, 10, 7, 10, 1, 7, 7, 1, 3 ],
-            [ 6, 10, 1, 6, 1, 7, 7, 1, 0, 7, 0, 8 ],
-            [ 9, 0, 3, 6, 9, 3, 6, 10, 9, 6, 3, 7 ],
-            [ 6, 10, 7, 7, 10, 8, 10, 9, 8 ], [ 8, 4, 6, 8, 6, 11 ],
-            [ 11, 3, 6, 3, 0, 6, 6, 0, 4 ], [ 0, 1, 9, 4, 6, 11, 4, 11, 8 ],
-            [ 1, 9, 4, 11, 1, 4, 11, 3, 1, 11, 4, 6 ],
-            [ 3, 8, 2, 8, 4, 2, 2, 4, 6 ], [ 2, 0, 4, 2, 4, 6 ],
-            [ 1, 9, 0, 3, 8, 2, 2, 8, 4, 2, 4, 6 ], [ 9, 4, 1, 1, 4, 2, 4, 6, 2 ],
-            [ 10, 1, 2, 11, 8, 4, 11, 4, 6 ],
-            [ 10, 1, 2, 11, 3, 6, 6, 3, 0, 6, 0, 4 ],
-            [ 0, 2, 10, 0, 10, 9, 4, 11, 8, 4, 6, 11 ],
-            [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ],
-            [ 8, 4, 6, 8, 6, 1, 6, 10, 1, 8, 1, 3 ],
-            [ 1, 0, 10, 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
-            [ 10, 4, 6, 10, 9, 4 ], [ 9, 5, 4, 7, 6, 11 ],
-            [ 4, 9, 5, 3, 0, 8, 11, 7, 6 ], [ 6, 11, 7, 4, 0, 1, 4, 1, 5 ],
-            [ 6, 11, 7, 4, 8, 5, 5, 8, 3, 5, 3, 1 ], [ 4, 9, 5, 6, 2, 3, 6, 3, 7 ],
-            [ 9, 5, 4, 8, 7, 0, 0, 7, 6, 0, 6, 2 ],
-            [ 4, 0, 1, 4, 1, 5, 6, 3, 7, 6, 2, 3 ], [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ],
-            [ 6, 11, 7, 1, 2, 10, 9, 5, 4 ],
-            [ 11, 7, 6, 8, 3, 0, 1, 2, 10, 9, 5, 4 ],
-            [ 11, 7, 6, 10, 5, 2, 2, 5, 4, 2, 4, 0 ],
-            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ],
-            [ 4, 9, 5, 6, 10, 7, 7, 10, 1, 7, 1, 3 ],
-            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
-            [ 10, 5, 6, 4, 8, 7 ], [ 5, 6, 9, 6, 11, 9, 9, 11, 8 ],
-            [ 0, 9, 5, 0, 5, 3, 3, 5, 6, 3, 6, 11 ],
-            [ 0, 1, 5, 0, 5, 11, 5, 6, 11, 0, 11, 8 ],
-            [ 11, 3, 6, 6, 3, 5, 3, 1, 5 ], [ 9, 5, 6, 3, 9, 6, 3, 8, 9, 3, 6, 2 ],
-            [ 5, 6, 9, 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
-            [ 1, 6, 2, 1, 5, 6 ], [ 1, 2, 10, 5, 6, 9, 9, 6, 11, 9, 11, 8 ],
-            [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ], [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ],
-            [ 3, 2, 11, 10, 5, 6 ], [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ],
-            [ 0, 9, 1, 5, 6, 10 ], [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ],
-            [ 10, 6, 5 ], [ 8, 3, 0, 10, 6, 5 ], [ 0, 1, 9, 5, 10, 6 ],
-            [ 10, 6, 5, 9, 8, 3, 9, 3, 1 ], [ 3, 11, 2, 10, 6, 5 ],
-            [ 6, 5, 10, 2, 0, 8, 2, 8, 11 ], [ 1, 9, 0, 6, 5, 10, 11, 2, 3 ],
-            [ 1, 10, 2, 5, 9, 6, 9, 11, 6, 9, 8, 11 ], [ 1, 2, 6, 1, 6, 5 ],
-            [ 0, 8, 3, 2, 6, 5, 2, 5, 1 ], [ 5, 9, 6, 9, 0, 6, 6, 0, 2 ],
-            [ 9, 6, 5, 3, 6, 9, 3, 9, 8, 3, 2, 6 ], [ 11, 6, 3, 6, 5, 3, 3, 5, 1 ],
-            [ 0, 5, 1, 0, 11, 5, 5, 11, 6, 0, 8, 11 ],
-            [ 0, 5, 9, 0, 3, 5, 3, 6, 5, 3, 11, 6 ],
-            [ 5, 9, 6, 6, 9, 11, 9, 8, 11 ], [ 10, 6, 5, 4, 7, 8 ],
-            [ 5, 10, 6, 7, 3, 0, 7, 0, 4 ], [ 5, 10, 6, 0, 1, 9, 8, 4, 7 ],
-            [ 4, 5, 9, 6, 7, 10, 7, 1, 10, 7, 3, 1 ],
-            [ 7, 8, 4, 2, 3, 11, 10, 6, 5 ],
-            [ 11, 6, 7, 10, 2, 5, 2, 4, 5, 2, 0, 4 ],
-            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
-            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [ 7, 8, 4, 5, 1, 2, 5, 2, 6 ],
-            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ],
-            [ 9, 4, 5, 8, 0, 7, 0, 6, 7, 0, 2, 6 ], [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ],
-            [ 6, 7, 11, 4, 5, 8, 5, 3, 8, 5, 1, 3 ],
-            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
-            [ 9, 4, 5, 7, 11, 6 ], [ 10, 6, 4, 10, 4, 9 ],
-            [ 8, 3, 0, 9, 10, 6, 9, 6, 4 ], [ 1, 10, 0, 10, 6, 0, 0, 6, 4 ],
-            [ 8, 6, 4, 8, 1, 6, 6, 1, 10, 8, 3, 1 ],
-            [ 2, 3, 11, 6, 4, 9, 6, 9, 10 ],
-            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
-            [ 10, 2, 1, 11, 6, 3, 6, 0, 3, 6, 4, 0 ],
-            [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ], [ 9, 1, 4, 1, 2, 4, 4, 2, 6 ],
-            [ 1, 0, 9, 3, 2, 8, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
-            [ 3, 2, 8, 8, 2, 4, 2, 6, 4 ],
-            [ 1, 4, 9, 11, 4, 1, 11, 1, 3, 11, 6, 4 ],
-            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 11, 6, 3, 3, 6, 0, 6, 4, 0 ],
-            [ 8, 6, 4, 8, 11, 6 ], [ 6, 7, 10, 7, 8, 10, 10, 8, 9 ],
-            [ 9, 3, 0, 6, 3, 9, 6, 9, 10, 6, 7, 3 ],
-            [ 6, 1, 10, 6, 7, 1, 7, 0, 1, 7, 8, 0 ],
-            [ 6, 7, 10, 10, 7, 1, 7, 3, 1 ],
-            [ 7, 11, 6, 3, 8, 2, 8, 10, 2, 8, 9, 10 ],
-            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
-            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2, 2, 9, 1, 7, 8, 9 ],
-            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 8, 0, 7, 7, 0, 6, 0, 2, 6 ],
-            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
-            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ],
-            [ 11, 7, 5, 11, 5, 10 ], [ 3, 0, 8, 7, 5, 10, 7, 10, 11 ],
-            [ 9, 0, 1, 10, 11, 7, 10, 7, 5 ],
-            [ 3, 1, 9, 3, 9, 8, 7, 10, 11, 7, 5, 10 ],
-            [ 10, 2, 5, 2, 3, 5, 5, 3, 7 ],
-            [ 5, 10, 2, 8, 5, 2, 8, 7, 5, 8, 2, 0 ],
-            [ 9, 0, 1, 10, 2, 5, 5, 2, 3, 5, 3, 7 ],
-            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 2, 11, 1, 11, 7, 1, 1, 7, 5 ],
-            [ 0, 8, 3, 2, 11, 1, 1, 11, 7, 1, 7, 5 ],
-            [ 9, 0, 2, 9, 2, 7, 2, 11, 7, 9, 7, 5 ],
-            [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ], [ 1, 3, 7, 1, 7, 5 ],
-            [ 8, 7, 0, 0, 7, 1, 7, 5, 1 ], [ 0, 3, 9, 9, 3, 5, 3, 7, 5 ],
-            [ 9, 7, 5, 9, 8, 7 ], [ 4, 5, 8, 5, 10, 8, 8, 10, 11 ],
-            [ 3, 0, 4, 3, 4, 10, 4, 5, 10, 3, 10, 11 ],
-            [ 0, 1, 9, 4, 5, 8, 8, 5, 10, 8, 10, 11 ],
-            [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ],
-            [ 3, 8, 4, 3, 4, 2, 2, 4, 5, 2, 5, 10 ],
-            [ 10, 2, 5, 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
-            [ 2, 1, 10, 9, 4, 5 ], [ 8, 4, 5, 2, 8, 5, 2, 11, 8, 2, 5, 1 ],
-            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
-            [ 11, 3, 2, 9, 4, 5 ], [ 4, 5, 8, 8, 5, 3, 5, 1, 3 ],
-            [ 5, 0, 4, 5, 1, 0 ], [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ],
-            [ 7, 4, 11, 4, 9, 11, 11, 9, 10 ],
-            [ 3, 0, 8, 7, 4, 11, 11, 4, 9, 11, 9, 10 ],
-            [ 11, 7, 4, 1, 11, 4, 1, 10, 11, 1, 4, 0 ],
-            [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
-            [ 2, 3, 7, 2, 7, 9, 7, 4, 9, 2, 9, 10 ],
-            [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ], [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ],
-            [ 10, 2, 1, 8, 7, 4 ], [ 2, 11, 7, 2, 7, 1, 1, 7, 4, 1, 4, 9 ],
-            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 7, 4, 11, 11, 4, 2, 4, 0, 2 ],
-            [ 2, 11, 3, 7, 4, 8 ], [ 9, 1, 4, 4, 1, 7, 1, 3, 7 ],
-            [ 1, 0, 9, 8, 7, 4 ], [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ],
-            [ 8, 9, 10, 8, 10, 11 ], [ 0, 9, 3, 3, 9, 11, 9, 10, 11 ],
-            [ 1, 10, 0, 0, 10, 8, 10, 11, 8 ], [ 10, 3, 1, 10, 11, 3 ],
-            [ 3, 8, 2, 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
-            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 2, 11, 1, 1, 11, 9, 11, 8, 9 ],
-            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
-            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
-            
-            return my;
-})();
-
-
+};
 
-/*  ProteinSurface.js by biochem_fan
+$3Dmol.SphereImposterOutlineMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-Ported and modified for Javascript based on EDTSurf,
-  whose license is as follows.
+$3Dmol.SphereImposterOutlineMaterial.prototype.clone = function() {
 
-Permission to use, copy, modify, and distribute this program for any
-purpose, with or without fee, is hereby granted, provided that this
-copyright notice and the reference information appear in all copies or
-substantial portions of the Software. It is provided "as is" without
-express or implied warranty. 
+    var material = new $3Dmol.SphereImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    material.outlineColor = this.outlineColor;
+    material.outlineWidth = this.outlineWidth;
+    material.outlinePushback = this.outlinePushback;
+    return material;
+};
 
-Reference:
-http://zhanglab.ccmb.med.umich.edu/EDTSurf/
-D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces
-by Euclidean Distance Transform. PLoS ONE 4(12): e8140.
 
-=======
+$3Dmol.StickImposterMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-TODO: Improved performance on Firefox
-      Reduce memory consumption
-      Refactor!
- */
+    this.shaderID = "stickimposter";    
+    this.setValues(parameters);
+    
+};
 
+$3Dmol.StickImposterMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-// dkoes
-// Surface calculations.  This must be safe to use within a web worker.
-if (typeof console === 'undefined') {
-    // this should only be true inside of a webworker
-    console = {
-        log : function() {
-        }
-    };
-}
+$3Dmol.StickImposterMaterial.prototype.clone = function() {
 
-$3Dmol.ProteinSurface = function() {
+    var material = new $3Dmol.StickImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    return material;
+};
 
-    // constants for vpbits bitmasks
-    /** @const */
-    var INOUT = 1;
-    /** @const */
-    var ISDONE = 2;
-    /** @const */
-    var ISBOUND = 4;
 
-    var ptranx = 0, ptrany = 0, ptranz = 0;
-    var probeRadius = 1.4;
-    var defaultScaleFactor = 2;
-    var scaleFactor = defaultScaleFactor; // 2 is .5A grid; if this is made user configurable,
-                            // also have to adjust offset used to find non-shown
-                            // atoms
-    var pHeight = 0, pWidth = 0, pLength = 0;
-    var cutRadius = 0;
-    var vpBits = null; // uint8 array of bitmasks
-    var vpDistance = null; // floatarray of _squared_ distances
-    var vpAtomID = null; // intarray
-    var vertnumber = 0, facenumber = 0;
-    var pminx = 0, pminy = 0, pminz = 0, pmaxx = 0, pmaxy = 0, pmaxz = 0;
+$3Dmol.StickImposterOutlineMaterial = function(parameters) {
+    
+    $3Dmol.ImposterMaterial.call(this);
 
-    var vdwRadii = {
-            "H" : 1.2,
-            "Li" : 1.82,
-            "Na" : 2.27,
-            "K" : 2.75,
-            "C" : 1.7,
-            "N" : 1.55,
-            "O" : 1.52,
-            "F" : 1.47,
-            "P" : 1.80,
-            "S" : 1.80,
-            "CL" : 1.75,
-            "BR" : 1.85,
-            "SE" : 1.90,
-            "ZN" : 1.39,
-            "CU" : 1.4,
-            "NI" : 1.63,
-            "X" : 2
-        };
+    this.shaderID = "stickimposteroutline";
+    this.outlineColor= parameters.color || new $3Dmol.Color(0.0,0.0,0.0);
+    this.outlineWidth= parameters.width || 0.1;
+    this.outlinePushback= parameters.pushback || 1.0;
     
-    /** @param {AtomSpec} atom */
-    var getVDWIndex = function(atom) {
-        if(!atom.elem || typeof(vdwRadii[atom.elem]) == "undefined") {
-            return "X";
-        }
-        return atom.elem;
-    };
+    this.setValues(parameters);
     
-    var depty = {}, widxz = {};
-    var faces, verts;
-    var nb = [ new Int32Array([ 1, 0, 0 ]), new Int32Array([ -1, 0, 0 ]), 
-               new Int32Array([ 0, 1, 0 ]), new Int32Array([ 0, -1, 0 ]),
-               new Int32Array([ 0, 0, 1 ]), 
-               new Int32Array([ 0, 0, -1 ]), 
-               new Int32Array([ 1, 1, 0 ]), 
-               new Int32Array([ 1, -1, 0 ]), 
-               new Int32Array([ -1, 1, 0 ]),
-               new Int32Array([ -1, -1, 0 ]), 
-               new Int32Array([ 1, 0, 1 ]), 
-               new Int32Array([ 1, 0, -1 ]), 
-               new Int32Array([ -1, 0, 1 ]),
-               new Int32Array([ -1, 0, -1 ]), 
-               new Int32Array([ 0, 1, 1 ]), 
-               new Int32Array([ 0, 1, -1 ]), 
-               new Int32Array([ 0, -1, 1 ]),
-               new Int32Array([ 0, -1, -1 ]), 
-               new Int32Array([ 1, 1, 1 ]), 
-               new Int32Array([ 1, 1, -1 ]), 
-               new Int32Array([ 1, -1, 1 ]),
-               new Int32Array([ -1, 1, 1 ]), 
-               new Int32Array([ 1, -1, -1 ]), 
-               new Int32Array([ -1, -1, 1 ]), 
-               new Int32Array([ -1, 1, -1 ]),
-               new Int32Array([ -1, -1, -1 ]) ];
-
-    var origextent;
+};
 
-    var inOrigExtent = function(x, y, z) {
-        if (x < origextent[0][0] || x > origextent[1][0])
-            return false;
-        if (y < origextent[0][1] || y > origextent[1][1])
-            return false;
-        if (z < origextent[0][2] || z > origextent[1][2])
-            return false;
-        return true;
-    };
+$3Dmol.StickImposterOutlineMaterial.prototype = Object.create($3Dmol.ImposterMaterial.prototype);
 
-    this.getFacesAndVertices = function(atomlist) {
-        var atomsToShow = {};
-        var i, il;
-        for (i = 0, il = atomlist.length; i < il; i++)
-            atomsToShow[atomlist[i]] = true;
-        var vertices = verts;
-        for (i = 0, il = vertices.length; i < il; i++) {
-            vertices[i].x = vertices[i].x / scaleFactor - ptranx;
-            vertices[i].y = vertices[i].y / scaleFactor - ptrany;
-            vertices[i].z = vertices[i].z / scaleFactor - ptranz;
-        }
+$3Dmol.StickImposterOutlineMaterial.prototype.clone = function() {
 
-        var finalfaces = [];
-        for (i = 0, il = faces.length; i < il; i += 3) {
-            //var f = faces[i];
-            var fa = faces[i], fb = faces[i+1], fc = faces[i+2];
-            var a = vertices[fa]['atomid'], b = vertices[fb]['atomid'], c = vertices[fc]['atomid'];
+    var material = new $3Dmol.StickImposterOutlineMaterial();
+    $3Dmol.ImposterMaterial.prototype.clone.call(this, material);
+    material.outlineColor = this.outlineColor;
+    material.outlineWidth = this.outlineWidth;
+    material.outlinePushback = this.outlinePushback;
+    return material;
+};
 
-            // must be a unique face for each atom
-            var which = a;
-            if (b < which)
-                which = b;
-            if (c < which)
-                which = c;
-            if (!atomsToShow[which]) {
-                continue;
-            }
-            var av = vertices[faces[i]];
-            var bv = vertices[faces[i+1]];
-            var cv = vertices[faces[i+2]];
 
-            if (fa !== fb && fb !== fc && fa !== fc){
-                finalfaces.push(fa); 
-                finalfaces.push(fb); 
-                finalfaces.push(fc); 
-            }
-               
-        }
+$3Dmol.InstancedMaterial = function(parameters) {
 
-        //try to help the garbage collector
-        vpBits = null; // uint8 array of bitmasks
-        vpDistance = null; // floatarray
-        vpAtomID = null; // intarray
-        
-        return {
-            'vertices' : vertices,
-            'faces' : finalfaces
-        };
-    };
+    $3Dmol.Material.call(this);
 
+    this.color = new $3Dmol.Color(0xffffff);
+    this.ambient = new $3Dmol.Color(0xfffff);
+    this.emissive = new $3Dmol.Color(0x000000);
 
-    this.initparm = function(extent, btype, volume) {
-        if(volume > 1000000) //heuristical decrease resolution to avoid large memory consumption
-            scaleFactor = defaultScaleFactor/2;
-        
-        var margin = (1 / scaleFactor) * 5.5; // need margin to avoid
-                                                // boundary/round off effects
-        origextent = extent;
-        pminx = extent[0][0]; pmaxx = extent[1][0];
-        pminy = extent[0][1]; pmaxy = extent[1][1];
-        pminz = extent[0][2]; pmaxz = extent[1][2];
+    //TODO: Which of these instance variables do I really need?
+    this.wrapAround = false;
+    this.wrapRGB = new $3Dmol.Vector3(1,1,1);
 
-        if (!btype) {
-            pminx -= margin;
-            pminy -= margin;
-            pminz -= margin;
-            pmaxx += margin;
-            pmaxy += margin;
-            pmaxz += margin;
-        } else {
-            pminx -= probeRadius + margin;
-            pminy -= probeRadius + margin;
-            pminz -= probeRadius + margin;
-            pmaxx += probeRadius + margin;
-            pmaxy += probeRadius + margin;
-            pmaxz += probeRadius + margin;
-        }
+    this.map = null;
 
-        pminx = Math.floor(pminx * scaleFactor) / scaleFactor;
-        pminy = Math.floor(pminy * scaleFactor) / scaleFactor;
-        pminz = Math.floor(pminz * scaleFactor) / scaleFactor;
-        pmaxx = Math.ceil(pmaxx * scaleFactor) / scaleFactor;
-        pmaxy = Math.ceil(pmaxy * scaleFactor) / scaleFactor;
-        pmaxz = Math.ceil(pmaxz * scaleFactor) / scaleFactor;
+    this.lightMap = null;
 
-        ptranx = -pminx;
-        ptrany = -pminy;
-        ptranz = -pminz;
+    this.specularMap = null;
 
-        pLength = Math.ceil(scaleFactor * (pmaxx - pminx)) + 1;
-        pWidth = Math.ceil(scaleFactor * (pmaxy - pminy)) + 1;
-        pHeight = Math.ceil(scaleFactor * (pmaxz - pminz)) + 1;
+    this.envMap = null;
+    this.reflectivity = 1;
+    this.refractionRatio = 0.98;
 
-        this.boundingatom(btype);
-        cutRadius = probeRadius * scaleFactor;
+    this.fog = true;
 
-        vpBits = new Uint8Array(pLength * pWidth * pHeight);
-        vpDistance = new Float64Array(pLength * pWidth * pHeight); // float 32
-        // doesn't
-        // play
-        // nicely
-        // with
-        // native
-        // floats
-        vpAtomID = new Int32Array(pLength * pWidth * pHeight);
-        console.log("Box size: ", pLength, pWidth, pHeight, vpBits.length);
-    };
+    this.wireframe = false;
+    this.wireframeLinewidth = 1;
+    this.wireframeLinecap = 'round';
+    this.wireframeLinejoin = 'round';
 
-    this.boundingatom = function(btype) {
-        var tradius = [];
-        var txz, tdept, sradius, idx;
-        flagradius = btype;
+    this.shading = $3Dmol.SmoothShading;
+    this.shaderID = "instanced";
+    this.vertexColors = $3Dmol.NoColors;
 
-        for ( var i in vdwRadii) {
-            if(!vdwRadii.hasOwnProperty(i))
-                continue;
-            var r = vdwRadii[i];
-            if (!btype)
-                tradius[i] = r * scaleFactor + 0.5;
-            else
-                tradius[i] = (r + probeRadius) * scaleFactor + 0.5;
+    this.skinning = false;
 
-            sradius = tradius[i] * tradius[i];
-            widxz[i] = Math.floor(tradius[i]) + 1;
-            depty[i] = new Int32Array(widxz[i] * widxz[i]);
-            indx = 0;
-            for (j = 0; j < widxz[i]; j++) {
-                for (k = 0; k < widxz[i]; k++) {
-                    txz = j * j + k * k;
-                    if (txz > sradius)
-                        depty[i][indx] = -1; // outside
-                    else {
-                        tdept = Math.sqrt(sradius - txz);
-                        depty[i][indx] = Math.floor(tdept);
-                    }
-                    indx++;
-                }
-            }
-        }
-    };
+    this.sphere = null;
 
-    this.fillvoxels = function(atoms, atomlist) { // (int seqinit,int
-        // seqterm,bool
-        // atomtype,atom*
-        // proseq,bool bcolor)
-        var i, il;
-        for (i = 0, il = vpBits.length; i < il; i++) {
-            vpBits[i] = 0;
-            vpDistance[i] = -1.0;
-            vpAtomID[i] = -1;
-        }
+    this.setValues(parameters);
 
-        for (i in atomlist) {
-            var atom = atoms[atomlist[i]];
-            if (atom === undefined)
-                continue;
-            this.fillAtom(atom, atoms);
-        }
+};
 
-        for (i = 0, il = vpBits.length; i < il; i++)
-            if (vpBits[i] & INOUT)
-                vpBits[i] |= ISDONE;
+$3Dmol.InstancedMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-    };
+$3Dmol.InstancedMaterial.prototype.clone = function() {
 
+    var material = new $3Dmol.InstancedMaterial();
 
-    this.fillAtom = function(atom, atoms) {
-        var cx, cy, cz, ox, oy, oz, mi, mj, mk, i, j, k, si, sj, sk;
-        var ii, jj, kk, n;
-        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
-        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
-        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
+    $3Dmol.Material.prototype.clone.call(this, material);
 
-        var at = getVDWIndex(atom);
-        var nind = 0;
-        var cnt = 0;
-        var pWH = pWidth*pHeight;
-        
-        for (i = 0, n = widxz[at]; i < n; i++) {
-            for (j = 0; j < n; j++) {
-                if (depty[at][nind] != -1) {
-                    for (ii = -1; ii < 2; ii++) {
-                        for (jj = -1; jj < 2; jj++) {
-                            for (kk = -1; kk < 2; kk++) {
-                                if (ii !== 0 && jj !== 0 && kk !== 0) {
-                                    mi = ii * i;
-                                    mk = kk * j;
-                                    for (k = 0; k <= depty[at][nind]; k++) {
-                                        mj = k * jj;
-                                        si = cx + mi;
-                                        sj = cy + mj;
-                                        sk = cz + mk;
-                                        if (si < 0 || sj < 0 || 
-                                                sk < 0 ||
-                                                si >= pLength || 
-                                                sj >= pWidth || 
-                                                sk >= pHeight)
-                                            continue;
-                                        var index = si * pWH + sj * pHeight + sk;
+    material.color.copy(this.color);
+    material.ambient.copy(this.ambient);
+    material.emissive.copy(this.emissive);
 
-                                        if (!(vpBits[index] & INOUT)) {
-                                            vpBits[index] |= INOUT;
-                                            vpAtomID[index] = atom.serial;
-                                        } else {
-                                            var atom2 = atoms[vpAtomID[index]];
-                                            if(atom2.serial != atom.serial) {
-                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.x + ptranx));
-                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.y + ptrany));
-                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.z + ptranz));
-                                                if (mi * mi + mj * mj + mk * mk < ox *
-                                                        ox + oy * oy + oz * oz)
-                                                    vpAtomID[index] = atom.serial;
-                                            }
-                                        }
+    material.wrapAround = this.wrapAround;
+    material.wrapRGB.copy(this.wrapRGB);
 
-                                    }// k
-                                }// if
-                            }// kk
-                        }// jj
-                    }// ii
-                }// if
-                nind++;
-            }// j
-        }// i
-    };
+    material.map = this.map;
 
-    this.fillvoxelswaals = function(atoms, atomlist) {
-        var i, il;
-        for (i = 0, il = vpBits.length; i < il; i++)
-            vpBits[i] &= ~ISDONE; // not isdone
+    material.lightMap = this.lightMap;
 
-        for (i in atomlist) {
-            var atom = atoms[atomlist[i]];
-            if (atom === undefined)
-                continue;
+    material.specularMap = this.specularMap;
 
-            this.fillAtomWaals(atom, atoms);
-        }
-    };
+    material.envMap = this.envMap;
+    material.combine = this.combine;
+    material.reflectivity = this.reflectivity;
+    material.refractionRatio = this.refractionRatio;
 
-    this.fillAtomWaals = function(atom, atoms) {
-        var cx, cy, cz, ox, oy, oz, nind = 0;
-        var mi, mj, mk, si, sj, sk, i, j, k, ii, jj, kk, n;
-        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
-        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
-        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
+    material.fog = this.fog;
 
-        var at = getVDWIndex(atom);
-        var pWH = pWidth*pHeight;
-        for (i = 0, n = widxz[at]; i < n; i++) {
-            for (j = 0; j < n; j++) {
-                if (depty[at][nind] != -1) {
-                    for (ii = -1; ii < 2; ii++) {
-                        for (jj = -1; jj < 2; jj++) {
-                            for (kk = -1; kk < 2; kk++) {
-                                if (ii !== 0 && jj !== 0 && kk !== 0) {
-                                    mi = ii * i;
-                                    mk = kk * j;
-                                    for (k = 0; k <= depty[at][nind]; k++) {
-                                        mj = k * jj;
-                                        si = cx + mi;
-                                        sj = cy + mj;
-                                        sk = cz + mk;
-                                        if (si < 0 || sj < 0 || 
-                                                sk < 0 || 
-                                                si >= pLength || 
-                                                sj >= pWidth || 
-                                                sk >= pHeight)
-                                            continue;
-                                        var index = si * pWH + sj * pHeight + sk;
-                                        if (!(vpBits[index] & ISDONE)) {
-                                            vpBits[index] |= ISDONE;
-                                            vpAtomID[index] = atom.serial;
-                                        }  else {
-                                            var atom2 = atoms[vpAtomID[index]];
-                                            if(atom2.serial != atom.serial) {
-                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.x + ptranx));
-                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.y + ptrany));
-                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
-                                                        (atom2.z + ptranz));
-                                                if (mi * mi + mj * mj + mk * mk < ox *
-                                                        ox + oy * oy + oz * oz)
-                                                    vpAtomID[index] = atom.serial;
-                                            }
-                                        }
-                                    }// k
-                                }// if
-                            }// kk
-                        }// jj
-                    }// ii
-                }// if
-                nind++;
-            }// j
-        }// i
-    };
+    material.shading = this.shading;
+    material.shaderID = this.shaderID;
+    material.vertexColors = this.vertexColors;
 
-    this.buildboundary = function() {
-        var pWH = pWidth*pHeight;
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pHeight; j++) {
-                for (k = 0; k < pWidth; k++) {
-                    var index = i * pWH + k * pHeight + j;
-                    if (vpBits[index] & INOUT) {
-                        var flagbound = false;
-                        var ii = 0;
-                        while (ii < 26) {
-                            var ti = i + nb[ii][0], tj = j + nb[ii][2], tk = k +
-                                    nb[ii][1];
-                            if (ti > -1 && 
-                                ti < pLength && 
-                                tk > -1 && 
-                                tk < pWidth && 
-                                tj > -1 && 
-                                tj < pHeight && 
-                                !(vpBits[ti * pWH + tk * pHeight + tj] & INOUT)) {
-                                vpBits[index] |= ISBOUND;
-                                break;
-                            } else
-                                ii++;
-                        }
-                    }
-                }
-            }
-        }
-    };
+    material.skinning = this.skinning;
+    material.morphTargets = this.morphTargets;
+    material.morphNormals = this.morphNormals;
 
-    // a little class for 3d array, should really generalize this and
-    // use throughout...
-    var PointGrid = function(length, width, height) {
-        // the standard says this is zero initialized
-        var data = new Int32Array(length * width * height * 3);
+    material.sphere = this.sphere;
 
-        // set position x,y,z to pt, which has ix,iy,and iz
-        this.set = function(x, y, z, pt) {
-            var index = ((((x * width) + y) * height) + z) * 3;
-            data[index] = pt.ix;
-            data[index + 1] = pt.iy;
-            data[index + 2] = pt.iz;
-        };
+  return material;
 
-        // return point at x,y,z
-        this.get = function(x, y, z) {
-            var index = ((((x * width) + y) * height) + z) * 3;
-            return {
-                ix : data[index],
-                iy : data[index + 1],
-                iz : data[index + 2]
-            };
-        };
-    };
+};
 
-    this.fastdistancemap = function() {
-        var eliminate = 0;
-        var certificate;
-        var i, j, k, n;
 
-        var boundPoint = new PointGrid(pLength, pWidth, pHeight);
-        var pWH = pWidth*pHeight;
-        var cutRSq = cutRadius*cutRadius;
-        
-        var inarray = [];
-        var outarray = [];
-        
-        var index;
-        
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pWidth; j++) {
-                for (k = 0; k < pHeight; k++) {
-                    index = i * pWH + j * pHeight + k;
-                    vpBits[index] &= ~ISDONE; // isdone = false
-                    if (vpBits[index] & INOUT) {
-                        if (vpBits[index] & ISBOUND) {
-                            var triple = {
-                                ix : i,
-                                iy : j,
-                                iz : k
-                            };
-                            boundPoint.set(i, j, k, triple);
-                            inarray.push(triple);
-                            vpDistance[index] = 0;
-                            vpBits[index] |= ISDONE;
-                            vpBits[index] &= ~ISBOUND;
-                        } 
-                    }
-                }
-            }
-        }
+//Sprite material
+/** @constructor */
+$3Dmol.SpriteMaterial = function(parameters) {
+    
+    $3Dmol.Material.call(this);
+    
+    this.color = new $3Dmol.Color(0xffffff);
+    this.map = new $3Dmol.Texture();
+    
+    this.useScreenCoordinates = true;
+    this.depthTest = !this.useScreenCoordinates;
+    this.sizeAttenuation = !this.useScreenCoordinates;
+    this.scaleByViewPort = !this.sizeAttenuation;
+    this.alignment = $3Dmol.SpriteAlignment.center.clone();
+    
+    this.fog = false; // use scene fog
+    
+    this.uvOffset = new $3Dmol.Vector2(0, 0);
+    this.uvScale = new $3Dmol.Vector2(1, 1);
+    
+    this.setValues(parameters);
+    
+    parameters = parameters || {};
+    
+    if (parameters.depthTest === undefined)
+        this.depthTest = !this.useScreenCoordinates;
+    if (parameters.sizeAttenuation === undefined)
+        this.sizeAttenuation = !this.useScreenCoordinates;
+    if (parameters.scaleByViewPort === undefined)
+        this.scaleByViewPort = !this.sizeAttenuation;
+    
+};
 
-        do {
-            outarray = this.fastoneshell(inarray, boundPoint);
-            inarray = [];
-            for (i = 0, n = outarray.length; i < n; i++) {
-                index = pWH * outarray[i].ix + pHeight *
-                    outarray[i].iy + outarray[i].iz;
-                vpBits[index] &= ~ISBOUND;
-                if (vpDistance[index] <= 1.0404 * cutRSq) {
-                    inarray.push({
-                        ix : outarray[i].ix,
-                        iy : outarray[i].iy,
-                        iz : outarray[i].iz
-                    });
-                }
-            }
-        } while (inarray.length !== 0);
+$3Dmol.SpriteMaterial.prototype = Object.create($3Dmol.Material.prototype);
 
-        inarray = [];
-        outarray = [];
-        boundPoint = null;
-        
-        var cutsf = scaleFactor - 0.5;
-        if (cutsf < 0)
-            cutsf = 0;
-        var cutoff = cutRSq - 0.50 / (0.1 + cutsf);
-        for (i = 0; i < pLength; i++) {
-            for (j = 0; j < pWidth; j++) {
-                for (k = 0; k < pHeight; k++) {
-                    index = i * pWH + j * pHeight + k;
-                    vpBits[index] &= ~ISBOUND;
-                    // ses solid
-                    if (vpBits[index] & INOUT) {
-                        if (!(vpBits[index] & ISDONE) ||
-                                ((vpBits[index] & ISDONE) && vpDistance[index] >= cutoff)) {
-                            vpBits[index] |= ISBOUND;
-                        }
-                    }
-                }
-            }
-        }
+$3Dmol.SpriteMaterial.prototype.clone = function() {
+    
+    var material = new $3Dmol.SpriteMaterial();
+    
+    $3Dmol.Material.prototype.clone.call(this, material);
+    
+    material.color.copy(this.color);
+    material.map = this.map;
+    
+    material.useScreenCoordinates = useScreenCoordinates;
+    material.sizeAttenuation = this.sizeAttenuation;
+    material.scaleByViewport = this.scaleByViewPort;
+    material.alignment.copy(this.alignment);
+    
+    material.uvOffset.copy(this.uvOffset);
+    
+    return material;
+    
+};
 
-    };
+//Alignment for Sprites
 
-    this.fastoneshell = function(inarray, boundPoint) { // (int* innum,int
-        // *allocout,voxel2
-        // ***boundPoint, int*
-        // outnum, int *elimi)
-        var tx, ty, tz;
-        var dx, dy, dz;
-        var i, j, n;
-        var square;
-        var bp, index;
-        var outarray = [];
-        if (inarray.length === 0)
-            return outarray;
+$3Dmol.SpriteAlignment = {};
+$3Dmol.SpriteAlignment.topLeft = new $3Dmol.Vector2(1, -1);
+$3Dmol.SpriteAlignment.topCenter = new $3Dmol.Vector2(0, -1);
+$3Dmol.SpriteAlignment.topRight = new $3Dmol.Vector2(-1, -1);
+$3Dmol.SpriteAlignment.centerLeft = new $3Dmol.Vector2(1, 0);
+$3Dmol.SpriteAlignment.center = new $3Dmol.Vector2(0, 0);
+$3Dmol.SpriteAlignment.centerRight = new $3Dmol.Vector2(-1, 0);
+$3Dmol.SpriteAlignment.bottomLeft = new $3Dmol.Vector2(1, 1);
+$3Dmol.SpriteAlignment.bottomCenter = new $3Dmol.Vector2(0, 1);
+$3Dmol.SpriteAlignment.bottomRight = new $3Dmol.Vector2(-1, 1);
 
-        tnv = {
-            ix : -1,
-            iy : -1,
-            iz : -1
-        };
-        var pWH = pWidth*pHeight;
-        for ( i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
 
-            for (j = 0; j < 6; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
-                
-                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
-                    
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+//Texture
+//We really only create textures from 2d rendering contexts (to display text labels)
+/** @constructor */
+$3Dmol.Texture = function(image) {
+
+    $3Dmol.EventDispatcher.call(this);
     
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
+    this.id = $3Dmol.TextureIdCount++;
     
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
+    this.name = "";
     
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+    this.image = image;
+    this.mipmaps = [];
     
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
-        }
-
-        // console.log("part1", positout);
-
-        for (i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
+    this.mapping = new $3Dmol.UVMapping();
+    
+    this.wrapS = $3Dmol.ClampToEdgeWrapping;
+    this.wrapT = $3Dmol.ClampToEdgeWrapping;
+    
+    this.magFilter = $3Dmol.LinearFilter;
+    this.minFilter = $3Dmol.LinearMipMapLinearFilter;
+    
+    this.anisotropy = 1;
+    
+    this.format = $3Dmol.RGBAFormat;
+    this.type = $3Dmol.UnsignedByteType;
+    
+    this.offset = new $3Dmol.Vector2(0, 0);
+    this.repeat = new $3Dmol.Vector2(1, 1);
+    
+    this.generateMipmaps = true;
+    this.premultiplyAlpha = false;
+    this.flipY = true;
+    this.unpackAlignment = 4;
+    
+    this.needsUpdate = false;
+    this.onUpdate = null;
+    
+};
 
-            for (j = 6; j < 18; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
+$3Dmol.Texture.prototype = {
 
-                if(tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
-                    
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+    constructor : $3Dmol.Texture,
     
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
+    clone : function(texture) {
+        
+        if (texture === undefined)
+            texture = new $3Dmol.Texture();
+        
+        texture.image = this.image;
+        texture.mipmaps = this.mipmaps.slice(0);
+        
+        texture.mapping = this.mapping;
+        
+        texture.wrapS = this.wrapS;
+        texture.wrapT = this.wrapT;
+        
+        texture.magFilter = this.magFilter;
+        texture.minFilter = this.minFilter;
+        
+        texture.anisotropy = this.anisotropy;
+        
+        texture.format = this.format;
+        texture.type = this.type;
+        
+        texture.offset.copy(this.offset);
+        texture.repeat.copy(this.repeat);
+        
+        texture.generateMipmaps = this.generateMipmaps;
+        texture.premultiplyAlpha = this.premultiplyAlpha;
+        texture.flipY = this.flipY;
+        texture.unpackAlignment = this.unpackAlignment;
+        
+        return texture;
+        
+    },
     
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
-        }
+    dispose : function() {
+        
+        this.dispatchEvent( {type: 'dispose'});
+        
+    }    
+    
+};
 
-        // console.log("part2", positout);
+$3Dmol.TextureIdCount = 0;
 
-        for (i = 0, n = inarray.length; i < n; i++) {
-            tx = inarray[i].ix;
-            ty = inarray[i].iy;
-            tz = inarray[i].iz;
-            bp = boundPoint.get(tx, ty, tz);
 
-            for (j = 18; j < 26; j++) {
-                tnv.ix = tx + nb[j][0];
-                tnv.iy = ty + nb[j][1];
-                tnv.iz = tz + nb[j][2];
+// sides
+$3Dmol.FrontSide = 0;
+$3Dmol.BackSide = 1;
+$3Dmol.DoubleSide = 2;
 
-                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
-                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
-                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+// shading
+$3Dmol.NoShading = 0;
+$3Dmol.FlatShading = 1;
+$3Dmol.SmoothShading = 2;
 
-                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
-                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+// colors
+$3Dmol.NoColors = 0;
+$3Dmol.FaceColors = 1;
+$3Dmol.VertexColors = 2;
 
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        vpDistance[index] = square;
-                        vpBits[index] |= ISDONE;
-                        vpBits[index] |= ISBOUND;
+//Texture constants
+//TODO: Which of these do I need (since I only use textures to display label sprites) ?
+$3Dmol.MultiplyOperation = 0;
+$3Dmol.MixOperation = 1;
+$3Dmol.AddOperation = 2;
 
-                        outarray.push({
-                            ix : tnv.ix,
-                            iy : tnv.iy,
-                            iz : tnv.iz
-                        });
-                    } else if ((vpBits[index] & INOUT)  && (vpBits[index] & ISDONE)) {
-                        dx = tnv.ix - bp.ix;
-                        dy = tnv.iy - bp.iy;
-                        dz = tnv.iz - bp.iz;
-                        square = dx * dx + dy * dy + dz * dz;
-                        if (square < vpDistance[index]) {
-                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+// mapping modes
 
-                            vpDistance[index] = square;
-                            if (!(vpBits[index] & ISBOUND)) {
-                                vpBits[index] |= ISBOUND;
-                                outarray.push({
-                                    ix : tnv.ix,
-                                    iy : tnv.iy,
-                                    iz : tnv.iz
-                                });
-                            }
-                        }
-                    }
-                }
-            }
-        }
+$3Dmol.UVMapping = function() {};
 
-        // console.log("part3", positout);
-        return outarray;
-    };
+// wrapping modes
+$3Dmol.ClampToEdgeWrapping = 1001;
 
-    this.marchingcubeinit = function(stype) {
-        for ( var i = 0, lim = vpBits.length; i < lim; i++) {
-            if (stype == 1) {// vdw
-                vpBits[i] &= ~ISBOUND;
-            } else if (stype == 4) { // ses
-                vpBits[i] &= ~ISDONE;
-                if (vpBits[i] & ISBOUND)
-                    vpBits[i] |= ISDONE;
-                vpBits[i] &= ~ISBOUND;
-            } else if (stype == 2) {// after vdw
-                if ((vpBits[i] & ISBOUND) && (vpBits[i] & ISDONE))
-                    vpBits[i] &= ~ISBOUND;
-                else if ((vpBits[i] & ISBOUND) && !(vpBits[i] & ISDONE))
-                    vpBits[i] |= ISDONE;
-            } else if (stype == 3) { // sas
-                vpBits[i] &= ~ISBOUND;
-            }
-        }
-    };
+//Filters
+$3Dmol.LinearFilter = 1006;
+$3Dmol.LinearMipMapLinearFilter = 1008;
 
-    // this code allows me to empirically prune the marching cubes code tables
-    // to more efficiently handle discrete data
-    var counter = function() {
-        var data = Array(256);
-        for ( var i = 0; i < 256; i++)
-            data[i] = [];
+//Data types
+$3Dmol.UnsignedByteType = 1009;
 
-        this.incrementUsed = function(i, j) {
-            if (typeof data[i][j] === 'undefined')
-                data[i][j] = {
-                    used : 0,
-                    unused : 0
-                };
-            data[i][j].used++;
-        };
+//Pixel formats
+$3Dmol.RGBAFormat = 1021;
+/* 
+ * $3Dmol Mesh and Line objects
+ */
 
-        this.incrementUnused = function(i, j) {
-            if (typeof data[i][j] === 'undefined')
-                data[i][j] = {
-                    used : 0,
-                    unused : 0
-                };
-            data[i][j].unused++;
 
-        };
+//Line Object
+/** @constructor */
+$3Dmol.Line = function (geometry, material, type) {
 
-        var redoTable = function(triTable) {
-            var str = "[";
-            for ( var i = 0; i < triTable.length; i++) {
-                var code = 0;
-                var table = triTable[i];
-                for ( var j = 0; j < table.length; j++) {
-                    code |= (1 << (table[j]));
-                }
-                str += "0x" + code.toString(16) + ", ";
-            }
-            str += "]";
-            console.log(str);
-        };
+    $3Dmol.Object3D.call(this);
 
-        this.print = function() {
+    this.geometry = geometry;
+        //TODO: update material and type to webgl
+    this.material = (material !== undefined) ? material : new $3Dmol.LineBasicMaterial( { color: Math.random() * 0xffffff } );
+    this.type = (type !== undefined) ? type : $3Dmol.LineStrip;
 
-            var table = MarchingCube.triTable;
-            var str;
-            var newtable = [];
-            for ( var i = 0; i < table.length; i++) {
-                var newarr = [];
-                for ( var j = 0; j < table[i].length; j += 3) {
-                    var k = j / 3;
-                    if (typeof data[i][k] === 'undefined' || !data[i][k].unused) {
-                        newarr.push(table[i][j]);
-                        newarr.push(table[i][j + 1]);
-                        newarr.push(table[i][j + 2]);
-                    }
-                    if (typeof data[i][k] === 'undefined')
-                        console.log("undef " + i + "," + k);
-                }
-                newtable.push(newarr);
-            }
-            console.log(JSON.stringify(newtable));
-            redoTable(newtable);
-        };
-    };
-    
-    this.marchingcube = function(stype) {
-        this.marchingcubeinit(stype);
-        verts = []; faces = [];   
-        $3Dmol.MarchingCube.march(vpBits, verts, faces, {
-            smooth : 1,
-            nX : pLength,
-            nY : pWidth,
-            nZ : pHeight        
-        });      
+};
 
-        var pWH = pWidth*pHeight;
-        for (var i = 0, vlen = verts.length; i < vlen; i++) {
-            verts[i]['atomid'] = vpAtomID[verts[i].x * pWH + pHeight *
-                    verts[i].y + verts[i].z];
-        }  
+$3Dmol.LineStrip = 0;
+$3Dmol.LinePieces = 1;
 
-        $3Dmol.MarchingCube.laplacianSmooth(1, verts, faces);
+$3Dmol.Line.prototype = Object.create($3Dmol.Object3D.prototype);
 
-    };
+$3Dmol.Line.prototype.clone = function (object) {
 
+    if (object === undefined) object = new $3Dmol.Line(this.geometry, this.material, this.type);
 
-};
+    $3Dmol.Object3D.prototype.clone.call(this, object);
 
-//This defines the $3Dmol object which is used to create viewers
-//and configure system-wide settings
+    return object;
 
-/** 
- * All of the functionality of $3Dmol.js is contained within the
- * $3Dmol global namespace
- * @namespace */
-$3Dmol = (function(window) {
-    
-    var my = window['$3Dmol'] || {};
-    //var $ = window['jQuery'];
-    
-    return my;
+};
 
-})(window);
 
-/* The following code "phones home" to register that an ip 
-   address has loaded 3Dmol.js.  Being able track this usage
-   is very helpful when reporting to funding agencies.  Please
-   leave this code in if you would like to increase the 
-   likelihood of 3Dmol.js remaining supported.
-*/
-$.get("http://3dmol.csb.pitt.edu/track/report.cgi");
-    
-/**
- * Create and initialize an appropriate viewer at supplied HTML element using specification in config
- * @param {Object | string} element - Either HTML element or string identifier
- * @param {ViewerSpec} config Viewer specification
- * @return {$3Dmol.GLViewer} GLViewer, null if unable to instantiate WebGL
- * 
- * @example
- * // Assume there exists an HTML div with id "gldiv"
- * var element = $("#gldiv");
- * 
- * // Viewer config - properties 'defaultcolors' and 'callback'
- * var config = {defaultcolors: $3Dmol.rasmolElementColors };
- * 
- * // Create GLViewer within 'gldiv' 
- * var myviewer = $3Dmol.createViewer(element, config);
- * //'data' is a string containing molecule data in pdb format  
- * myviewer.addModel(data, "pdb");
- * myviewer.zoomTo();
- * myviewer.render();                        
- *                        
- */
-$3Dmol.createViewer = function(element, config)
-{
-    if($.type(element) === "string")
-        element = $("#"+element);
-    if(!element) return;
+//Mesh Object
+/** @constructor */
+$3Dmol.Mesh = function(geometry, material) {
 
-    config = config || {}; 
+    $3Dmol.Object3D.call(this);
+
+    this.geometry = geometry;
+    this.material = (material !== undefined) ? material : new $3Dmol.MeshBasicMaterial( { color: Math.random() * 0xffffff, wireframe: true } );
 
-    //try to create the  viewer
-    try {
-        return new $3Dmol.GLViewer(element, config);
-    }
-    catch(e) {
-        throw "error creating viewer: "+e;
-    }
-    
-    return null;
 };
-   
-/**
- * Contains a dictionary of embedded viewers created from HTML elements
- * with a the viewer_3Dmoljs css class indexed by their id (or numerically
- * if they do not have an id).
-*/
-$3Dmol.viewers = {};
 
-/**
- * Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model
- * 
- * @function $3Dmol.download
- * @param {string} query String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively
- * @param {$3Dmol.GLViewer} viewer - Add new model to existing viewer
- * @example
- * var myviewer = $3Dmol.createViewer(gldiv);
- * 
- * // GLModel 'm' created and loaded into glviewer for PDB id 2POR
- * // Note that m will not contain the atomic data until after the network request is completed
- * var m = $3Dmol.download('pdb: 2POR', myviewer);
- * 
- * @return {$3Dmol.GLModel} GLModel
- */ 
-$3Dmol.download = function(query, viewer, options, callback) {
-    var baseURL = '';
-    var type = "";
-    var m = viewer.addModel();
-    if (query.substr(0, 4) === 'pdb:') {
-        type = "pdb";
-        query = query.substr(4).toUpperCase();
-        if (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) {
-           alert("Wrong PDB ID"); return;
-        }
-        uri = "http://www.rcsb.org/pdb/files/" + query + ".pdb";
-    } else if (query.substr(0, 4) == 'cid:') {
-        type = "sdf";
-        query = query.substr(4);
-        if (!query.match(/^[1-9]+$/)) {
-           alert("Wrong Compound ID"); return;
-        }
-        uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query + 
-          "/SDF?record_type=3d";
-    }
+$3Dmol.Mesh.prototype = Object.create($3Dmol.Object3D.prototype);
 
-   $.get(uri, function(ret) {
-      m.addMolData(ret, type, options);
-      viewer.zoomTo();
-      viewer.render();
-      if(callback) callback(m);
+$3Dmol.Mesh.prototype.clone = function (object) {
+
+    if (object === undefined) object = new $3Dmol.Mesh(this.geometry, this.material);
+
+    $3Dmol.Object3D.prototype.clone.call(this, object);
+
+    return object;
 
-   });
-   
-   return m;
 };
-       
 
-/**
- * $3Dmol surface types
- * @enum {number}
- */
-$3Dmol.SurfaceType = {
-    VDW : 1,
-    MS : 2,
-    SAS : 3,
-    SES  : 4
+
+//Sprite object
+/** @constructor */
+$3Dmol.Sprite = function(material) {
+    
+    $3Dmol.Object3D.call(this);
+    
+    this.material = (material !== undefined) ? material : new $3Dmol.SpriteMaterial();
+
+    this.rotation3d = this.rotation;
+    this.rotation = 0;
+    
 };
 
+$3Dmol.Sprite.prototype = Object.create($3Dmol.Object3D.prototype);
 
-//Miscellaneous functions and classes - to be incorporated into $3Dmol proper
-/**
- * 
- * @param {$3Dmol.Geometry} geometry
- * @param {$3Dmol.Mesh} mesh
- * @returns {undefined}
- */
-$3Dmol.mergeGeos = function(geometry, mesh) {
+$3Dmol.Sprite.prototype.updateMatrix = function() {
     
-    var meshGeo = mesh.geometry;
+    this.matrix.setPosition(this.position);
     
-    if (meshGeo === undefined) 
-        return;
+    this.rotation3d.set(0, 0, this.rotation);
+    this.matrix.setRotationFromEuler(this.rotation3d);
     
-    geometry.geometryGroups.push( meshGeo.geometryGroups[0] );
+    if (this.scale.x !== 1 || this.scale.y !== 1)
+        this.matrix.scale(this.scale);
+    
+    this.matrixWorldNeedsUpdate = true;
     
 };
 
-$3Dmol.multiLineString = function(f) {
-    return f.toString()
-            .replace(/^[^\/]+\/\*!?/, '')
-            .replace(/\*\/[^\/]+$/, '');
-            
+$3Dmol.Sprite.prototype.clone = function(object) {
+    
+    if (object === undefined)
+        object = new $3Dmol.Sprite(this.material);
+    
+    $3Dmol.Object3D.prototype.clone.call(this, object);
+    
+    return object;
+    
 };
+/**
+ * Simplified webGL renderer
+ */
 
-/** 
- * Render surface synchronously if true
- * @param {boolean} [$3Dmol.SyncSurface=false]
- * @type {boolean} */
-$3Dmol.syncSurface = false;
+$3Dmol.Renderer = function(parameters) {
 
-// Internet Explorer refuses to allow webworkers in data blobs.  I can find
-// no way of checking for this feature directly, so must do a brower check
-if(window.navigator.userAgent.indexOf('MSIE ') >= 0 ||
-        window.navigator.userAgent.indexOf('Trident/') >= 0) {
-    $3Dmol.syncSurface = true; // can't use webworkers
-}
+    parameters = parameters || {};
 
-/**
- * Parse a string that represents a style or atom selection and convert it
- * into an object.  The goal is to make it easier to write out these specifications
- * without resorting to json. Objects cannot be defined recursively.
- * ; - delineates fields of the object 
- * : - if the field has a value other than an empty object, it comes after a colon
- * , - delineates key/value pairs of a value object
- *     If the value object consists of ONLY keys (no = present) the keys are 
- *     converted to a list.  Otherwise a object of key/value pairs is created with
- *     any missing values set to null
- * = OR ~ - separates key/value pairs of a value object, if not provided value is null
- *     twiddle is supported since = has special meaning in URLs
- * @param (String) str
- * @returns {Object}
- */
-$3Dmol.specStringToObject = function(str) {
-    if(typeof(str) === "object") {
-        return str; //not string, assume was converted already
-    }
-    else if(typeof(str) === "undefined" || str == null) {
-        return str; 
-    }
-    var ret = {};
-    var fields = str.split(';');
-    for(var i = 0; i < fields.length; i++) {
-        var fv = fields[i].split(':');
-        var f = fv[0];
-        var val = {};
-        var vstr = fv[1];
-        if(vstr) {
-            vstr = vstr.replace(/~/g,"=");
-            if(vstr.indexOf('=') !== -1) {
-                //has key=value pairs, must be object
-                var kvs = vstr.split(',');
-                for(var j = 0; j < kvs.length; j++) {
-                    var kv = kvs[j].split('=',2);
-                    val[kv[0]] = kv[1];
-                }
-            }
-            else if(vstr.indexOf(',') !== -1) {
-                //has multiple values, must list
-                val = vstr.split(',');
-            }
-            else {
-                val = vstr; //value itself
-            }
-        }
-        ret[f] = val;
-    }
+    var _canvas = parameters.canvas !== undefined ? parameters.canvas
+            : document.createElement('canvas'),
+
+    _precision = parameters.precision !== undefined ? parameters.precision
+            : 'highp', _alpha = parameters.alpha !== undefined ? parameters.alpha
+            : true, _premultipliedAlpha = parameters.premultipliedAlpha !== undefined ? parameters.premultipliedAlpha
+            : true, _antialias = parameters.antialias !== undefined ? parameters.antialias
+            : false, _stencil = parameters.stencil !== undefined ? parameters.stencil
+            : true, _preserveDrawingBuffer = parameters.preserveDrawingBuffer !== undefined ? parameters.preserveDrawingBuffer
+            : false, _clearColor = parameters.clearColor !== undefined ? new $3Dmol.Color(
+            parameters.clearColor)
+            : new $3Dmol.Color(0x000000), _clearAlpha = parameters.clearAlpha !== undefined ? parameters.clearAlpha
+            : 0, _outlineMaterial = parameters.outline !== undefined ? new $3Dmol.MeshOutlineMaterial(
+            parameters.outline)
+            : null;
 
-return ret;
-}
+    this.domElement = _canvas;
+    this.context = null;
+    this.devicePixelRatio = parameters.devicePixelRatio !== undefined ? parameters.devicePixelRatio
+            : (self.devicePixelRatio !== undefined) ? self.devicePixelRatio : 1;
 
-// computes the bounding box around the provided atoms
-/**
- * @param {AtomSpec[]} atomlist
- * @return {Array}
- */
-$3Dmol.getExtent = function(atomlist, ignoreSymmetries) {
-    var xmin, ymin, zmin, xmax, ymax, zmax, xsum, ysum, zsum, cnt;
-    var includeSym = !ignoreSymmetries;
+    // clearing
 
-    xmin = ymin = zmin = 9999;
-    xmax = ymax = zmax = -9999;
-    xsum = ysum = zsum = cnt = 0;
+    this.autoClear = true;
+    this.autoClearColor = true;
+    this.autoClearDepth = true;
+    this.autoClearStencil = true;
+
+    // scene graph
+
+    this.sortObjects = true;
+
+    this.autoUpdateObjects = true;
+    this.autoUpdateScene = true;
+
+    this.renderPluginsPost = [];
+
+    // info
+
+    this.info = {
+        memory : {
+
+            programs : 0,
+            geometries : 0,
+            textures : 0
+
+        },
+        render : {
+
+            calls : 0,
+            vertices : 0,
+            faces : 0,
+            points : 0
+
+        }
+    };
+
+    // internal properties
+    var _this = this,
+    _programs = [], _programs_counter = 0,
     
-    if (atomlist.length === 0)
-        return [ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ];
-    for (var i = 0; i < atomlist.length; i++) {
-        var atom = atomlist[i];
-        if (atom === undefined)
-            continue;
-        cnt++;
-        xsum += atom.x;
-        ysum += atom.y;
-        zsum += atom.z;
-        
-        xmin = (xmin < atom.x) ? xmin : atom.x;
-        ymin = (ymin < atom.y) ? ymin : atom.y;
-        zmin = (zmin < atom.z) ? zmin : atom.z;
-        xmax = (xmax > atom.x) ? xmax : atom.x;
-        ymax = (ymax > atom.y) ? ymax : atom.y;
-        zmax = (zmax > atom.z) ? zmax : atom.z;
-        
-        if (atom.symmetries && includeSym) {
-            for (var n = 0; n < atom.symmetries.length; n++) {
-                cnt++;
-                xsum += atom.symmetries[n].x;
-                ysum += atom.symmetries[n].y;
-                zsum += atom.symmetries[n].z;
-                xmin = (xmin < atom.symmetries[n].x) ? xmin : atom.symmetries[n].x;
-                ymin = (ymin < atom.symmetries[n].y) ? ymin : atom.symmetries[n].y;
-                zmin = (zmin < atom.symmetries[n].z) ? zmin : atom.symmetries[n].z;
-                xmax = (xmax > atom.symmetries[n].x) ? xmax : atom.symmetries[n].x;
-                ymax = (ymax > atom.symmetries[n].y) ? ymax : atom.symmetries[n].y;
-                zmax = (zmax > atom.symmetries[n].z) ? zmax : atom.symmetries[n].z; 
-            }
-        }  
-    }
+    // internal state cache
+    _currentProgram = null, _currentFramebuffer = null, _currentMaterialId = -1, _currentGeometryGroupHash = null, _currentCamera = null, _geometryGroupCounter = 0,
+    _usedTextureUnits = 0,
 
-    return [ [ xmin, ymin, zmin ], [ xmax, ymax, zmax ],
-            [ xsum / cnt, ysum / cnt, zsum / cnt ] ];
-};
+    // GL state cache
+    _oldDoubleSided = -1, _oldFlipSided = -1,
+    _oldBlending = -1,
+    _oldBlendEquation = -1, _oldBlendSrc = -1, _oldBlendDst = -1,
+    _oldDepthTest = -1, _oldDepthWrite = -1,
+    _oldPolygonOffset = null, _oldPolygonOffsetFactor = null, _oldPolygonOffsetUnits = null,
+    _oldLineWidth = null,
 
+    _viewportX = 0, _viewportY = 0, _viewportWidth = 0, _viewportHeight = 0, _currentWidth = 0, _currentHeight = 0,
+    _enabledAttributes = {},
 
-/*
-//Hackish way to create webworker (independent of $3Dmol namespace) within minified file
-//Had to hard-code uglify-js minified version of worker string in order to work with closure compiler...
-$3Dmol.workerString = function(){
+    // camera matrices cache
+    _projScreenMatrix = new $3Dmol.Matrix4(),
+    _vector3 = new $3Dmol.Vector3(),
 
-    self.onmessage = function(oEvent) {
-        var obj = oEvent.data;
-        var type = obj.type;
-        if (type < 0) // sending atom data, initialize
-        {
-            self.atomData = obj.atoms;
-            self.volume = obj.volume;
-            self.ps = new ProteinSurface();
-        } else {
-            var ps = self.ps;
-            ps.initparm(obj.expandedExtent, (type == 1) ? false : true, self.volume);
-            ps.fillvoxels(self.atomData, obj.extendedAtoms);
-            ps.buildboundary();
-            if (type === 4 || type === 2) {
-                ps.fastdistancemap();
-                ps.boundingatom(false);
-                ps.fillvoxelswaals(self.atomData, obj.extendedAtoms);    
-            }        
-            ps.marchingcube(type);
-            var VandF = ps.getFacesAndVertices(obj.atomsToShow);
-            self.postMessage(VandF);
+    // light arrays cache
+    _direction = new $3Dmol.Vector3(),
+    _lightsNeedUpdate = true,
+
+    _lights = {
+        ambient : [ 0, 0, 0 ],
+        directional : {
+            length : 0,
+            colors : [],
+            positions : []
+        },
+        point : {
+            length : 0,
+            colors : [],
+            positions : [],
+            distances : []
+        },
+        spot : {
+            length : 0,
+            colors : [],
+            positions : [],
+            distances : [],
+            directions : [],
+            anglesCos : [],
+            exponents : []
+        },
+        hemi : {
+            length : 0,
+            skyColors : [],
+            groundColors : [],
+            positions : []
         }
+
+    };
+
+    // initialize
+    var _gl;
+
+    initGL();
+    setDefaultGLState();
+
+    this.context = _gl;
+    var _extInstanced = _gl.getExtension("ANGLE_instanced_arrays");
+    var _extFragDepth = _gl.getExtension("EXT_frag_depth");
+
+    // API
+    
+    this.supportedExtensions = function() {
+        return {supportsAIA: Boolean(_extInstanced),
+            supportsImposters:  Boolean(_extFragDepth)
+            };
     };
     
-}.toString().replace(/(^.*?\{|\}$)/g, "");
-$3Dmol.workerString += ";var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}}"
-$3Dmol.workerString += ";var ISDONE=2";
-$3Dmol.workerString += ",ProteinSurface=" + $3Dmol.ProteinSurface.toString().replace(/$3Dmol.MarchingCube./g, "");
-$3Dmol.workerString += ",march=" + $3Dmol.MarchingCube.march.toString().replace(/$3Dmol./g, "");
-$3Dmol.workerString += ",laplacianSmooth=" + $3Dmol.MarchingCube.laplacianSmooth.toString();
+    this.getContext = function() {
+        return _gl;
+    };
 
-$3Dmol.workerString += ",edgeTable=new Uint32Array([" + $3Dmol.MarchingCube.edgeTable.toString() + "])";
+    this.getPrecision = function() {
+        return _precision;
+    };
 
-$3Dmol.workerString += ",triTable=[";
+    this.setClearColorHex = function(hex, alpha) {
+        _clearColor.setHex(hex);
+        _clearAlpha = alpha;
 
-for (var i = 0, il = $3Dmol.MarchingCube.triTable.length; i < il - 1; i++)
-    $3Dmol.workerString += "[" + $3Dmol.MarchingCube.triTable[i].toString() + "],";
+        _gl.clearColor(_clearColor.r, _clearColor.g, _clearColor.b,
+                        _clearAlpha);
+    };
 
-$3Dmol.workerString += "[]]";
-*/
+    this.enableOutline = function(parameters) {
+        _outlineMaterial = new $3Dmol.MeshOutlineMaterial(parameters);
+        _outlineSphereImposterMaterial = new $3Dmol.SphereImposterOutlineMaterial(parameters);
+        _outlineStickImposterMaterial = new $3Dmol.StickImposterOutlineMaterial(parameters);
+    };
 
-//TODO: Make this dynamic
-//Otherwise, must uncomment and run the above with 3Dmol-min.js, and cut and paste below everytime ProteinSurface or MarchingCube modified
-$3Dmol.workerString = 'self.onmessage=function(oEvent){var obj=oEvent.data,type=obj.type;if(0>type)self.atomData=obj.atoms,self.volume=obj.volume,self.ps=new ProteinSurface;else{var ps=self.ps;ps.initparm(obj.expandedExtent,1==type?!1:!0,self.volume),ps.fillvoxels(self.atomData,obj.extendedAtoms),ps.buildboundary(),(4===type||2===type)&&(ps.fastdistancemap(),ps.boundingatom(!1),ps.fillvoxelswaals(self.atomData,obj.extendedAtoms)),ps.marchingcube(type);var VandF=ps.getFacesAndVertices(obj.atomsToShow);self.postMessage(VandF)}};var Vector3=function(x,y,z){this.x=x||0,this.y=y||0,this.z=z||0};Vector3.prototype={constructor:Vector3,copy:function(v){return this.x=v.x,this.y=v.y,this.z=v.z,this},multiplyScalar:function(s){return this.x*=s,this.y*=s,this.z*=s,this}};var ISDONE=2,ProteinSurface=function (){var faces,verts,origextent,INOUT=1,ISDONE=2,ISBOUND=4,ptranx=0,ptrany=0,ptranz=0,probeRadius=1.4,defaultScaleFactor=2,scaleFactor=defaultScaleFactor,pHeight=0,pWidth=0,pLength=0,cutRadius=0,vpBits=null,vpDistance=null,vpAtomID=null,pminx=0,pminy=0,pminz=0,pmaxx=0,pmaxy=0,pmaxz=0,vdwRadii={H:1.2,Li:1.82,Na:2.27,K:2.75,C:1.7,N:1.55,O:1.52,F:1.47,P:1.8,S:1.8,CL:1.75,BR:1.85,SE:1.9,ZN:1.39,CU:1.4,NI:1.63,X:2},getVDWIndex=function(atom){return atom.elem&&"undefined"!=typeof vdwRadii[atom.elem]?atom.elem:"X"},depty={},widxz={},nb=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,-1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];this.getFacesAndVertices=function(atomlist){var i,il,atomsToShow={};for(i=0,il=atomlist.length;il>i;i++)atomsToShow[atomlist[i]]=!0;var vertices=verts;for(i=0,il=vertices.length;il>i;i++)vertices[i].x=vertices[i].x/scaleFactor-ptranx,vertices[i].y=vertices[i].y/scaleFactor-ptrany,vertices[i].z=vertices[i].z/scaleFactor-ptranz;var finalfaces=[];for(i=0,il=faces.length;il>i;i+=3){var fa=faces[i],fb=faces[i+1],fc=faces[i+2],a=vertices[fa].atomid,b=vertices[fb].atomid,c=vertices[fc].atomid,which=a;if(which>b&&(which=b),which>c&&(which=c),atomsToShow[which]){{vertices[faces[i]],vertices[faces[i+1]],vertices[faces[i+2]]}fa!==fb&&fb!==fc&&fa!==fc&&(finalfaces.push(fa),finalfaces.push(fb),finalfaces.push(fc))}}return vpBits=null,vpDistance=null,vpAtomID=null,{vertices:vertices,faces:finalfaces}},this.initparm=function(extent,btype,volume){volume>1e6&&(scaleFactor=defaultScaleFactor/2);var margin=1/scaleFactor*5.5;origextent=extent,pminx=extent[0][0],pmaxx=extent[1][0],pminy=extent[0][1],pmaxy=extent[1][1],pminz=extent[0][2],pmaxz=extent[1][2],btype?(pminx-=probeRadius+margin,pminy-=probeRadius+margin,pminz-=probeRadius+margin,pmaxx+=probeRadius+margin,pmaxy+=probeRadius+margin,pmaxz+=probeRadius+margin):(pminx-=margin,pminy-=margin,pminz-=margin,pmaxx+=margin,pmaxy+=margin,pmaxz+=margin),pminx=Math.floor(pminx*scaleFactor)/scaleFactor,pminy=Math.floor(pminy*scaleFactor)/scaleFactor,pminz=Math.floor(pminz*scaleFactor)/scaleFactor,pmaxx=Math.ceil(pmaxx*scaleFactor)/scaleFactor,pmaxy=Math.ceil(pmaxy*scaleFactor)/scaleFactor,pmaxz=Math.ceil(pmaxz*scaleFactor)/scaleFactor,ptranx=-pminx,ptrany=-pminy,ptranz=-pminz,pLength=Math.ceil(scaleFactor*(pmaxx-pminx))+1,pWidth=Math.ceil(scaleFactor*(pmaxy-pminy))+1,pHeight=Math.ceil(scaleFactor*(pmaxz-pminz))+1,this.boundingatom(btype),cutRadius=probeRadius*scaleFactor,vpBits=new Uint8Array(pLength*pWidth*pHeight),vpDistance=new Float64Array(pLength*pWidth*pHeight),vpAtomID=new Int32Array(pLength*pWidth*pHeight)},this.boundingatom=function(btype){var txz,tdept,sradius,tradius=[];flagradius=btype;for(var i in vdwRadii)if(vdwRadii.hasOwnProperty(i)){var r=vdwRadii[i];for(tradius[i]=btype?(r+probeRadius)*scaleFactor+.5:r*scaleFactor+.5,sradius=tradius[i]*tradius[i],widxz[i]=Math.floor(tradius[i])+1,depty[i]=new Int32Array(widxz[i]*widxz[i]),indx=0,j=0;j<widxz[i];j++)for(k=0;k<widxz[i];k++)txz=j*j+k*k,txz>sradius?depty[i][indx]=-1:(tdept=Math.sqrt(sradius-txz),depty[i][indx]=Math.floor(tdept)),indx++}},this.fillvoxels=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]=0,vpDistance[i]=-1,vpAtomID[i]=-1;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtom(atom,atoms)}for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&INOUT&&(vpBits[i]|=ISDONE)},this.fillAtom=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,i,j,k,si,sj,sk,ii,jj,kk,n;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),nind=0,pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&INOUT){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=INOUT,vpAtomID[index]=atom.serial}nind++}},this.fillvoxelswaals=function(atoms,atomlist){var i,il;for(i=0,il=vpBits.length;il>i;i++)vpBits[i]&=~ISDONE;for(i in atomlist){var atom=atoms[atomlist[i]];void 0!==atom&&this.fillAtomWaals(atom,atoms)}},this.fillAtomWaals=function(atom,atoms){var cx,cy,cz,ox,oy,oz,mi,mj,mk,si,sj,sk,i,j,k,ii,jj,kk,n,nind=0;cx=Math.floor(.5+scaleFactor*(atom.x+ptranx)),cy=Math.floor(.5+scaleFactor*(atom.y+ptrany)),cz=Math.floor(.5+scaleFactor*(atom.z+ptranz));var at=getVDWIndex(atom),pWH=pWidth*pHeight;for(i=0,n=widxz[at];n>i;i++)for(j=0;n>j;j++){if(-1!=depty[at][nind])for(ii=-1;2>ii;ii++)for(jj=-1;2>jj;jj++)for(kk=-1;2>kk;kk++)if(0!==ii&&0!==jj&&0!==kk)for(mi=ii*i,mk=kk*j,k=0;k<=depty[at][nind];k++)if(mj=k*jj,si=cx+mi,sj=cy+mj,sk=cz+mk,!(0>si||0>sj||0>sk||si>=pLength||sj>=pWidth||sk>=pHeight)){var index=si*pWH+sj*pHeight+sk;if(vpBits[index]&ISDONE){var atom2=atoms[vpAtomID[index]];ox=Math.floor(.5+scaleFactor*(atom2.x+ptranx)),oy=Math.floor(.5+scaleFactor*(atom2.y+ptrany)),oz=Math.floor(.5+scaleFactor*(atom2.z+ptranz)),ox*ox+oy*oy+oz*oz>mi*mi+mj*mj+mk*mk&&(vpAtomID[index]=atom.serial)}else vpBits[index]|=ISDONE,vpAtomID[index]=atom.serial}nind++}},this.buildboundary=function(){var pWH=pWidth*pHeight;for(i=0;pLength>i;i++)for(j=0;pHeight>j;j++)for(k=0;pWidth>k;k++){var index=i*pWH+k*pHeight+j;if(vpBits[index]&INOUT)for(var ii=0;26>ii;){var ti=i+nb[ii][0],tj=j+nb[ii][2],tk=k+nb[ii][1];if(ti>-1&&pLength>ti&&tk>-1&&pWidth>tk&&tj>-1&&pHeight>tj&&!(vpBits[ti*pWH+tk*pHeight+tj]&INOUT)){vpBits[index]|=ISBOUND;break}ii++}}};var PointGrid=function(length,width,height){var data=new Int32Array(length*width*height*3);this.set=function(x,y,z,pt){var index=3*((x*width+y)*height+z);data[index]=pt.ix,data[index+1]=pt.iy,data[index+2]=pt.iz},this.get=function(x,y,z){var index=3*((x*width+y)*height+z);return{ix:data[index],iy:data[index+1],iz:data[index+2]}}};this.fastdistancemap=function(){var i,j,k,n,index,boundPoint=new PointGrid(pLength,pWidth,pHeight),pWH=pWidth*pHeight,cutRSq=cutRadius*cutRadius,inarray=[],outarray=[];for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)if(index=i*pWH+j*pHeight+k,vpBits[index]&=~ISDONE,vpBits[index]&INOUT&&vpBits[index]&ISBOUND){var triple={ix:i,iy:j,iz:k};boundPoint.set(i,j,k,triple),inarray.push(triple),vpDistance[index]=0,vpBits[index]|=ISDONE,vpBits[index]&=~ISBOUND}do for(outarray=this.fastoneshell(inarray,boundPoint),inarray=[],i=0,n=outarray.length;n>i;i++)index=pWH*outarray[i].ix+pHeight*outarray[i].iy+outarray[i].iz,vpBits[index]&=~ISBOUND,vpDistance[index]<=1.0404*cutRSq&&inarray.push({ix:outarray[i].ix,iy:outarray[i].iy,iz:outarray[i].iz});while(0!==inarray.length);inarray=[],outarray=[],boundPoint=null;var cutsf=scaleFactor-.5;0>cutsf&&(cutsf=0);var cutoff=cutRSq-.5/(.1+cutsf);for(i=0;pLength>i;i++)for(j=0;pWidth>j;j++)for(k=0;pHeight>k;k++)index=i*pWH+j*pHeight+k,vpBits[index]&=~ISBOUND,vpBits[index]&INOUT&&(!(vpBits[index]&ISDONE)||vpBits[index]&ISDONE&&vpDistance[index]>=cutoff)&&(vpBits[index]|=ISBOUND)},this.fastoneshell=function(inarray,boundPoint){var tx,ty,tz,dx,dy,dz,i,j,n,square,bp,index,outarray=[];if(0===inarray.length)return outarray;tnv={ix:-1,iy:-1,iz:-1};var pWH=pWidth*pHeight;for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=0;6>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=6;18>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));for(i=0,n=inarray.length;n>i;i++)for(tx=inarray[i].ix,ty=inarray[i].iy,tz=inarray[i].iz,bp=boundPoint.get(tx,ty,tz),j=18;26>j;j++)tnv.ix=tx+nb[j][0],tnv.iy=ty+nb[j][1],tnv.iz=tz+nb[j][2],tnv.ix<pLength&&tnv.ix>-1&&tnv.iy<pWidth&&tnv.iy>-1&&tnv.iz<pHeight&&tnv.iz>-1&&(index=tnv.ix*pWH+pHeight*tnv.iy+tnv.iz,vpBits[index]&INOUT&&!(vpBits[index]&ISDONE)?(boundPoint.set(tnv.ix,tnv.iy,tz+nb[j][2],bp),dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,vpDistance[index]=square,vpBits[index]|=ISDONE,vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})):vpBits[index]&INOUT&&vpBits[index]&ISDONE&&(dx=tnv.ix-bp.ix,dy=tnv.iy-bp.iy,dz=tnv.iz-bp.iz,square=dx*dx+dy*dy+dz*dz,square<vpDistance[index]&&(boundPoint.set(tnv.ix,tnv.iy,tnv.iz,bp),vpDistance[index]=square,vpBits[index]&ISBOUND||(vpBits[index]|=ISBOUND,outarray.push({ix:tnv.ix,iy:tnv.iy,iz:tnv.iz})))));return outarray},this.marchingcubeinit=function(stype){for(var i=0,lim=vpBits.length;lim>i;i++)1==stype?vpBits[i]&=~ISBOUND:4==stype?(vpBits[i]&=~ISDONE,vpBits[i]&ISBOUND&&(vpBits[i]|=ISDONE),vpBits[i]&=~ISBOUND):2==stype?vpBits[i]&ISBOUND&&vpBits[i]&ISDONE?vpBits[i]&=~ISBOUND:vpBits[i]&ISBOUND&&!(vpBits[i]&ISDONE)&&(vpBits[i]|=ISDONE):3==stype&&(vpBits[i]&=~ISBOUND)};this.marchingcube=function(stype){this.marchingcubeinit(stype),verts=[],faces=[],march(vpBits,verts,faces,{smooth:1,nX:pLength,nY:pWidth,nZ:pHeight});for(var pWH=pWidth*pHeight,i=0,vlen=verts.length;vlen>i;i++)verts[i].atomid=vpAtomID[verts[i].x*pWH+pHeight*verts[i].y+verts[i].z];laplacianSmooth(1,verts,faces)}},march=function (data,verts,faces,spec){var i,il,fulltable=!!spec.fulltable,origin=spec.hasOwnProperty("origin")&&spec.origin.hasOwnProperty("x")?spec.origin:{x:0,y:0,z:0},voxel=!!spec.voxel,nX=spec.nX||0,nY=spec.nY||0,nZ=spec.nZ||0,scale=spec.scale||1,unitCube=new Vector3(1,1,1).multiplyScalar(scale),vertnums=new Int32Array(nX*nY*nZ);for(i=0,il=vertnums.length;il>i;++i)vertnums[i]=-1;var getVertex=function(i,j,k,code,p1,p2){var pt=new Vector3;pt.copy(origin);var val1=!!(code&1<<p1),val2=!!(code&1<<p2),p=p1;!val1&&val2&&(p=p2),1&p&&k++,2&p&&j++,4&p&&i++,pt.x+=unitCube.x*i,pt.y+=unitCube.y*j,pt.z+=unitCube.z*k;var index=(nY*i+j)*nZ+k;return voxel?(verts.push(pt),verts.length-1):(vertnums[index]<0&&(vertnums[index]=verts.length,verts.push(pt)),vertnums[index])},intersects=new Int32Array(12),etable=fulltable?edgeTable2:edgeTable,tritable=fulltable?triTable2:triTable;for(i=0;nX-1>i;++i)for(var j=0;nY-1>j;++j)for(var k=0;nZ-1>k;++k){for(var code=0,p=0;8>p;++p){var index=(nY*(i+((4&p)>>2))+j+((2&p)>>1))*nZ+k+(1&p),val=!!(data[index]&ISDONE);code|=val<<p}if(0!==code&&255!==code){var ecode=etable[code];if(0!==ecode){var ttable=tritable[code];1&ecode&&(intersects[0]=getVertex(i,j,k,code,0,1)),2&ecode&&(intersects[1]=getVertex(i,j,k,code,1,3)),4&ecode&&(intersects[2]=getVertex(i,j,k,code,3,2)),8&ecode&&(intersects[3]=getVertex(i,j,k,code,2,0)),16&ecode&&(intersects[4]=getVertex(i,j,k,code,4,5)),32&ecode&&(intersects[5]=getVertex(i,j,k,code,5,7)),64&ecode&&(intersects[6]=getVertex(i,j,k,code,7,6)),128&ecode&&(intersects[7]=getVertex(i,j,k,code,6,4)),256&ecode&&(intersects[8]=getVertex(i,j,k,code,0,4)),512&ecode&&(intersects[9]=getVertex(i,j,k,code,1,5)),1024&ecode&&(intersects[10]=getVertex(i,j,k,code,3,7)),2048&ecode&&(intersects[11]=getVertex(i,j,k,code,2,6));for(var t=0;t<ttable.length;t+=3){var a=intersects[ttable[t]],b=intersects[ttable[t+1]],c=intersects[ttable[t+2]];voxel&&t>=3&&(verts.push(verts[a]),a=verts.length-1,verts.push(verts[b]),b=verts.length-1,verts.push(verts[c]),c=verts.length-1),faces.push(a),faces.push(b),faces.push(c)}}}}},laplacianSmooth=function (numiter,verts,faces){var i,il,j,jl,k,tps=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)tps[i]={x:0,y:0,z:0};var flagvert,vertdeg=new Array(20);for(i=0;20>i;i++)vertdeg[i]=new Array(verts.length);for(i=0,il=verts.length;il>i;i++)vertdeg[0][i]=0;for(i=0,il=faces.length/3;il>i;i++){var aoffset=3*i,boffset=3*i+1,coffset=3*i+2;for(flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[boffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[aoffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[aoffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[aoffset]]++,vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]]=faces[coffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[aoffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[boffset]];jl>j;j++)if(faces[coffset]==vertdeg[j+1][faces[boffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[boffset]]++,vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]]=faces[coffset]),flagvert=!0,j=0;j<vertdeg[0][faces[coffset]];j++)if(faces[aoffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}for(flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[aoffset]),flagvert=!0,j=0,jl=vertdeg[0][faces[coffset]];jl>j;j++)if(faces[boffset]==vertdeg[j+1][faces[coffset]]){flagvert=!1;break}flagvert&&(vertdeg[0][faces[coffset]]++,vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]]=faces[boffset])}var wt=1,wt2=.5;for(k=0;numiter>k;k++){for(i=0,il=verts.length;il>i;i++)if(vertdeg[0][i]<3)tps[i].x=verts[i].x,tps[i].y=verts[i].y,tps[i].z=verts[i].z;else if(3==vertdeg[0][i]||4==vertdeg[0][i]){for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt2*verts[i].x,tps[i].y+=wt2*verts[i].y,tps[i].z+=wt2*verts[i].z,tps[i].x/=wt2+vertdeg[0][i],tps[i].y/=wt2+vertdeg[0][i],tps[i].z/=wt2+vertdeg[0][i]}else{for(tps[i].x=0,tps[i].y=0,tps[i].z=0,j=0,jl=vertdeg[0][i];jl>j;j++)tps[i].x+=verts[vertdeg[j+1][i]].x,tps[i].y+=verts[vertdeg[j+1][i]].y,tps[i].z+=verts[vertdeg[j+1][i]].z;tps[i].x+=wt*verts[i].x,tps[i].y+=wt*verts[i].y,tps[i].z+=wt*verts[i].z,tps[i].x/=wt+vertdeg[0][i],tps[i].y/=wt+vertdeg[0][i],tps[i].z/=wt+vertdeg[0][i]}for(i=0,il=verts.length;il>i;i++)verts[i].x=tps[i].x,verts[i].y=tps[i].y,verts[i].z=tps[i].z}},edgeTable=new Uint32Array([0,0,0,0,0,0,0,2816,0,0,0,1792,0,3328,3584,3840,0,0,0,138,0,21,0,134,0,0,0,652,0,2067,3865,3600,0,0,0,42,0,0,0,294,0,0,21,28,0,3875,1049,3360,0,168,162,170,0,645,2475,2210,0,687,293,172,4010,3747,3497,3232,0,0,0,0,0,69,0,900,0,0,0,1792,138,131,1608,1920,0,81,0,2074,84,85,84,86,0,81,0,3676,330,1105,1881,1616,0,0,0,42,0,69,0,502,0,0,21,3580,138,2035,1273,1520,2816,104,2337,106,840,581,367,102,2816,3695,3429,3180,1898,1635,1385,1120,0,0,0,0,0,0,0,3910,0,0,69,588,42,2083,41,2880,0,0,0,1722,0,2293,4095,3830,0,255,757,764,2538,2291,3065,2800,0,0,81,338,0,3925,1119,3414,84,855,85,340,2130,2899,89,2384,1792,712,194,1162,4036,3781,3535,3270,708,719,197,204,3018,2755,2505,2240,0,0,0,0,168,420,168,1958,162,162,676,2988,170,163,680,928,3328,3096,3328,3642,52,53,1855,1590,2340,2111,2869,2620,298,51,825,560,3584,3584,3090,3482,1668,1941,1183,1430,146,2975,2069,2460,154,915,153,400,3840,3592,3329,3082,1796,1541,1295,1030,2818,2575,2309,2060,778,515,265,0]),triTable=[[],[],[],[],[],[],[],[11,9,8],[],[],[],[8,10,9],[],[10,8,11],[9,11,10],[8,10,9,8,11,10],[],[],[],[1,7,3],[],[4,2,0],[],[2,1,7],[],[],[],[2,7,3,2,9,7],[],[1,4,11,1,0,4],[3,8,0,11,9,4,11,10,9],[4,11,9,11,10,9],[],[],[],[5,3,1],[],[],[],[2,5,8,2,1,5],[],[],[2,4,0],[3,2,4],[],[0,9,1,8,10,5,8,11,10],[3,4,0,3,10,4],[5,8,10,8,11,10],[],[3,5,7],[7,1,5],[1,7,3,1,5,7],[],[9,2,0,9,7,2],[0,3,8,1,7,11,1,5,7],[11,1,7,1,5,7],[],[9,1,0,5,3,2,5,7,3],[8,2,5,8,0,2],[2,5,3,5,7,3],[3,9,1,3,8,9,7,11,10,7,10,5],[9,1,0,10,7,11,10,5,7],[3,8,0,7,10,5,7,11,10],[11,5,7,11,10,5],[],[],[],[],[],[0,6,2],[],[7,2,9,7,9,8],[],[],[],[8,10,9],[7,1,3],[7,1,0],[6,9,3,6,10,9],[7,10,8,10,9,8],[],[6,0,4],[],[11,1,4,11,3,1],[2,4,6],[2,0,4,2,4,6],[2,4,6],[1,4,2,4,6,2],[],[6,0,4],[],[2,11,3,6,9,4,6,10,9],[8,6,1,8,1,3],[10,0,6,0,4,6],[8,0,3,9,6,10,9,4,6],[10,4,6,10,9,4],[],[],[],[5,3,1],[],[0,6,2],[],[7,4,8,5,2,1,5,6,2],[],[],[2,4,0],[7,4,8,2,11,3,10,5,6],[7,1,3],[5,6,10,0,9,1,8,7,4],[5,6,10,7,0,3,7,4,0],[10,5,6,4,8,7],[9,11,8],[3,5,6],[0,5,11,0,11,8],[6,3,5,3,1,5],[3,9,6,3,8,9],[9,6,0,6,2,0],[0,3,8,2,5,6,2,1,5],[1,6,2,1,5,6],[9,11,8],[1,0,9,6,10,5,11,3,2],[6,10,5,2,8,0,2,11,8],[3,2,11,10,5,6],[10,5,6,9,3,8,9,1,3],[0,9,1,5,6,10],[8,0,3,10,5,6],[10,5,6],[],[],[],[],[],[],[],[1,10,2,9,11,6,9,8,11],[],[],[6,0,2],[3,6,9,3,2,6],[3,5,1],[0,5,1,0,11,5],[0,3,5],[6,9,11,9,8,11],[],[],[],[4,5,9,7,1,10,7,3,1],[],[11,6,7,2,4,5,2,0,4],[11,6,7,8,0,3,1,10,2,9,4,5],[6,7,11,1,10,2,9,4,5],[],[4,1,0,4,5,1,6,7,3,6,3,2],[9,4,5,0,6,7,0,2,6],[4,5,9,6,3,2,6,7,3],[6,7,11,5,3,8,5,1,3],[6,7,11,4,1,0,4,5,1],[4,5,9,3,8,0,11,6,7],[9,4,5,7,11,6],[],[],[0,6,4],[8,6,4,8,1,6],[],[0,10,2,0,9,10,4,8,11,4,11,6],[10,2,1,6,0,3,6,4,0],[10,2,1,11,4,8,11,6,4],[4,2,6],[1,0,9,2,4,8,2,6,4],[2,4,0,2,6,4],[8,2,4,2,6,4],[11,4,1,11,6,4],[0,9,1,4,11,6,4,8,11],[3,6,0,6,4,0],[8,6,4,8,11,6],[10,8,9],[6,3,9,6,7,3],[6,7,1],[10,7,1,7,3,1],[7,11,6,8,10,2,8,9,10],[11,6,7,10,0,9,10,2,0],[2,1,10,7,11,6,8,0,3],[1,10,2,6,7,11],[7,2,6,7,9,2],[1,0,9,3,6,7,3,2,6],[7,0,6,0,2,6],[2,7,3,2,6,7],[7,11,6,3,9,1,3,8,9],[9,1,0,11,6,7],[0,3,8,11,6,7],[11,6,7],[],[],[],[],[5,3,7],[8,5,2,8,7,5],[5,3,7],[1,10,2,5,8,7,5,9,8],[1,7,5],[1,7,5],[9,2,7,9,7,5],[11,3,2,8,5,9,8,7,5],[1,3,7,1,7,5],[0,7,1,7,5,1],[9,3,5,3,7,5],[9,7,5,9,8,7],[8,10,11],[3,4,10,3,10,11],[8,10,11],[5,9,4,1,11,3,1,10,11],[2,4,5],[5,2,4,2,0,4],[0,3,8,5,9,4,10,2,1],[2,1,10,9,4,5],[2,8,5,2,11,8],[3,2,11,1,4,5,1,0,4],[9,4,5,8,2,11,8,0,2],[11,3,2,9,4,5],[8,5,3,5,1,3],[5,0,4,5,1,0],[3,8,0,4,5,9],[9,4,5],[11,9,10],[11,9,10],[1,11,4,1,10,11],[8,7,4,11,1,10,11,3,1],[2,7,9,2,9,10],[4,8,7,0,10,2,0,9,10],[2,1,10,0,7,4,0,3,7],[10,2,1,8,7,4],[1,7,4],[3,2,11,4,8,7,9,1,0],[11,4,2,4,0,2],[2,11,3,7,4,8],[4,1,7,1,3,7],[1,0,9,8,7,4],[3,4,0,3,7,4],[8,7,4],[8,9,10,8,10,11],[3,9,11,9,10,11],[0,10,8,10,11,8],[10,3,1,10,11,3],[2,8,10,8,9,10],[9,2,0,9,10,2],[8,0,3,1,10,2],[10,2,1],[1,11,9,11,8,9],[11,3,2,0,9,1],[11,0,2,11,8,0],[11,3,2],[8,1,3,8,9,1],[9,1,0],[8,0,3],[]]';
+    this.disableOutline = function() {
+        _outlineMaterial = null;
+        _outlineSphereImposterMaterial = null;
+        _outlineStickImposterMaterial = null;
+    };
 
-$3Dmol.SurfaceWorker = window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type: 'text/javascript'}));
+    this.setSize = function(width, height) {
 
-$3Dmol['workerString'] = $3Dmol.workerString;
-$3Dmol['SurfaceWorker'] = $3Dmol.SurfaceWorker;
-//auto-initialization
-//Create embedded viewer from HTML attributes if true
+        _canvas.width = width * this.devicePixelRatio;
+        _canvas.height = height * this.devicePixelRatio;
 
-$(document).ready(function() {
+        _canvas.style.width = width + 'px';
+        _canvas.style.height = height + 'px';
+
+        this.setViewport(0, 0, _canvas.width, _canvas.height);
+
+    };
+
+    this.setViewport = function(x, y, width, height) {
+
+        _viewportX = x !== undefined ? x : 0;
+        _viewportY = y !== undefined ? y : 0;
+
+        _viewportWidth = width !== undefined ? width : _canvas.width;
+        _viewportHeight = height !== undefined ? height : _canvas.height;
+
+        _gl.viewport(_viewportX, _viewportY, _viewportWidth, _viewportHeight);
+
+    };
+
+    this.clear = function(color, depth, stencil) {
+
+        var bits = 0;
+
+        if (color === undefined || color)
+            bits |= _gl.COLOR_BUFFER_BIT;
+        if (depth === undefined || depth)
+            bits |= _gl.DEPTH_BUFFER_BIT;
+        if (stencil === undefined || stencil)
+            bits |= _gl.STENCIL_BUFFER_BIT;
+        _gl.clear(bits);
+
+    };
+
+    this.clearTarget = function(color, depth, stencil) {
+
+        this.clear(color, depth, stencil);
+
+    };
+
+    this.setMaterialFaces = function(material, reflected) {
+
+        var doubleSided = material.side === $3Dmol.DoubleSide;
+        var flipSided = material.side === $3Dmol.BackSide;
+        flipSided = reflected ? !flipSided : flipSided;
+
+        if (_oldDoubleSided !== doubleSided) {
+
+            if (doubleSided) {
+
+                _gl.disable(_gl.CULL_FACE);
+
+            } else {
+
+                _gl.enable(_gl.CULL_FACE);
 
-    if ($(".viewer_3Dmoljs")[0] !== undefined)
-        $3Dmol.autoinit = true;
-        
-    if ($3Dmol.autoinit) { 
-        $3Dmol.viewers = {};
-        var nviewers = 0;
-        $(".viewer_3Dmoljs").each( function() {
-            var viewerdiv = $(this);
-            var datauri = null;
-            
-        
-            var callback = (typeof(window[viewerdiv.data("callback")]) === 'function') ? 
-                    window[viewerdiv.data("callback")] : null;
-            
-            var type = null;
-            if (viewerdiv.data("pdb")) {
-                datauri = "http://www.pdb.org/pdb/files/" + viewerdiv.data("pdb") + ".pdb";
-                type = "pdb";
-            } else if(viewerdiv.data("cid")) {
-                //this doesn't actually work since pubchem does have CORS enabled
-                type = "sdf";
-                datauri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.data("cid") + 
-                "/SDF?record_type=3d";
             }
-            else if (viewerdiv.data("href"))
-                datauri = viewerdiv.data("href");
-                
-            var bgcolor = Number(viewerdiv.data("backgroundcolor")) || 0x000000;
-            var style = {line:{}};
-            if(viewerdiv.data("style")) style = $3Dmol.specStringToObject(viewerdiv.data("style"));
-            var select = {};
-            if(viewerdiv.data("select")) select = $3Dmol.specStringToObject(viewerdiv.data("select"));
-            var selectstylelist = [];
-            var surfaces = [];
-            var labels = [];
-            var d = viewerdiv.data();
-            
-            //let users specify individual but matching select/style tags, eg.
-            //data-select1 data-style1
-            var stylere = /style(.+)/;
-            var surfre = /surface(.*)/;
-            var reslabre = /labelres(.*)/;
-            var keys = [];
-            for(var dataname in d) {
-                if(d.hasOwnProperty(dataname)) {
-                    keys.push(dataname);
-                }
-            }
-            keys.sort();
-            for(var i = 0; i < keys.length; i++) {
-                var dataname = keys[i];
-                var m = stylere.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    selectstylelist.push([newsel,styleobj]);
-                }         
-                m = surfre.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    surfaces.push([newsel,styleobj]);
-                }
-                m = reslabre.exec(dataname);
-                if(m) {
-                    var selname = "select"+m[1];
-                    var newsel = $3Dmol.specStringToObject(d[selname]);
-                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
-                    labels.push([newsel,styleobj]);
-                }
-            }
-            
-            try {
-                var glviewer = $3Dmol.viewers[this.id || nviewers++] = $3Dmol.createViewer(viewerdiv, {defaultcolors: $3Dmol.rasmolElementColors, callback: function(viewer) {            
-                    viewer.setBackgroundColor(bgcolor);            
-                }});
-            } catch ( error ) {
-                //for autoload, provide a useful error message
-                window.location = "http://get.webgl.org";                    
-            }
-            
-            
-            if (datauri) {  
-                
-                type = viewerdiv.data("type") || viewerdiv.data("datatype") || type;
-                if(!type) {
-                    type = datauri.substr(datauri.lastIndexOf('.')+1);
-                }
-                                
-                $.get(datauri, function(ret) {
-                    glviewer.addModel(ret, type);
-                    glviewer.setStyle(select,style);
-                    for(var i = 0; i < selectstylelist.length; i++) {
-                        var sel = selectstylelist[i][0] || {};
-                        var sty = selectstylelist[i][1] || {"line":{}}
-                        glviewer.setStyle(sel, sty);
-                    }
-                    for(var i = 0; i < surfaces.length; i++) {
-                        var sel = surfaces[i][0] || {};
-                        var sty = surfaces[i][1] || {}
-                        glviewer.addSurface($3Dmol.SurfaceType.VDW, sty, sel, sel);
-                    }
-                    for(var i = 0; i < labels.length; i++) {
-                        var sel = labels[i][0] || {};
-                        var sty = labels[i][1] || {}
-                        glviewer.addResLabels(sel, sty);
-                    }
-                    // Allowing us to fire callback after viewer has added model
-                    if (callback) 
-                        callback(glviewer);                    
-                    
-                    glviewer.zoomTo();
-                    glviewer.render();          
-                    
-                }, 'text');
-           
+
+            _oldDoubleSided = doubleSided;
+
+        }
+
+        if (_oldFlipSided !== flipSided) {
+
+            if (flipSided) {
+
+                _gl.frontFace(_gl.CW);
+
+            } else {
+
+                _gl.frontFace(_gl.CCW);
+
             }
-            
-            else {
-                
-                if (viewerdiv.data("element")) {
-                    var moldata = $("#" + viewerdiv.data("element")).val() || "";
-                    var type = viewerdiv.data("type") || viewerdiv.data("datatype");
 
-                    if (!type){
+            _oldFlipSided = flipSided;
 
-                        console.log("Warning: No type specified for embedded viewer with moldata from " + viewerdiv.data("element") +
-                                    "\n assuming type 'pdb'")
+        }
 
-                        type = 'pdb';
-                    }
+    };
 
-                    glviewer.addModel(moldata, type);
-                    glviewer.setStyle(select, style);
-                    for(var i = 0; i < selectstylelist.length; i++) {
-                        var sel = selectstylelist[i][0] || {};
-                        var sty = selectstylelist[i][1] || {"line":{}}
-                        glviewer.setStyle(sel, sty);
-                    }                
-                }
+    this.setDepthTest = function(depthTest) {
 
+        if (_oldDepthTest !== depthTest) {
+
+            if (depthTest) {
+
+                _gl.enable(_gl.DEPTH_TEST);
+
+            } else {
+
+                _gl.disable(_gl.DEPTH_TEST);
 
-                if (callback) 
-                    callback(glviewer);
-                
-                glviewer.zoomTo();
-                glviewer.render();
             }
-            
-        });              
-    }
-});
-    
 
+            _oldDepthTest = depthTest;
 
-// in an attempt to reduce memory overhead, cache all $3Dmol.Colors
-// this makes things a little faster
-$3Dmol.CC = {
-    cache : {},
-    color : function(hex) {
+        }
+
+    };
+
+    this.setDepthWrite = function(depthWrite) {
+
+        if (_oldDepthWrite !== depthWrite) {
+
+            _gl.depthMask(depthWrite);
+            _oldDepthWrite = depthWrite;
 
-        if(typeof(this.cache[hex]) !== "undefined") {
-            return this.cache[hex];
         }
-        else {
-            hex = this.getHex(hex);
-            var c = new $3Dmol.Color(hex);
-            this.cache[hex] = c;
-            return c;
+
+    };
+
+    this.setBlending = function(blending) {
+
+        if (!blending) {
+            _gl.disable(_gl.BLEND);
+
+        } else {
+            _gl.enable(_gl.BLEND);
+            _gl.blendEquationSeparate(_gl.FUNC_ADD, _gl.FUNC_ADD);
+            _gl.blendFuncSeparate(_gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA,
+                    _gl.ONE, _gl.ONE_MINUS_SRC_ALPHA);
+
         }
-    },
-    colorTab : {
-        'white' : 0xFFFFFF,
-        'silver' : 0xC0C0C0,
-        'gray' : 0x808080,
-        'grey' : 0x808080,
-        'black' : 0x000000,
-        'red' : 0xFF0000,
-        'maroon' : 0x800000,
-        'yellow' : 0xFFFF00,
-        'orange' : 0xFF6600,
-        'olive' : 0x808000,
-        'lime' : 0x00FF00,
-        'green' : 0x008000,
-        'aqua' : 0x00FFFF,
-        'cyan' : 0x00FFFF,
-        'teal' : 0x008080,
-        'blue' : 0x0000FF,
-        'navy' : 0x000080,
-        'fuchsia' : 0xFF00FF,
-        'magenta' : 0xFF00FF,
-        'purple' : 0x800080
-    },    
-    getHex : function(hex) {
-        if (parseInt(hex))
-            return parseInt(hex);
-        
-        else if (typeof(hex) === 'string') {
-            
-            return this.colorTab[hex.trim().toLowerCase()] || 0x000000;
+
+        _oldBlending = blending;
+    };
+
+    // Plugins
+
+    this.addPostPlugin = function(plugin) {
+
+        plugin.init(this);
+        this.renderPluginsPost.push(plugin);
+
+    };
+
+    // Sorting
+
+    function numericalSort(a, b) {
+
+        return b[0] - a[0];
+
+    }
+
+    function enableAttribute(attribute) {
+
+        if (!_enabledAttributes[attribute]) {
+
+            _gl.enableVertexAttribArray(attribute);
+            _enabledAttributes[attribute] = true;
+
         }
-        
+
     }
-    
-};
 
+    function disableAttributes() {
 
-$3Dmol['CC'] = $3Dmol.CC;
-$3Dmol['CC']['color'] = $3Dmol.CC.color;
+        for ( var attribute in _enabledAttributes) {
 
+            if (_enabledAttributes[attribute]) {
 
+                _gl.disableVertexAttribArray(attribute);
+                _enabledAttributes[attribute] = false;
 
-/** Return proper color for atom given style
- * @param {AtomSpec} atom
- * @param {AtomStyle} style
- * @return {$3Dmol.Color}
- */
-$3Dmol.getColorFromStyle = function(atom, style) {
-    var color = atom.color;
-    if (typeof (style.color) != "undefined" && style.color != "spectrum")
-        color = style.color;
-    if(typeof(style.colorscheme) != "undefined") {
-        if(typeof($3Dmol.elementColors[style.colorscheme]) != "undefined") {
-            //name of builtin colorscheme
-            var scheme = $3Dmol.elementColors[style.colorscheme];
-            if(typeof(scheme[atom.elem]) != "undefined") {
-                color = scheme[atom.elem];
             }
-        } else if(typeof(style.colorscheme[atom.elem]) != 'undefined') {
-            //actual color scheme provided
-            color = style.colorscheme[atom.elem];
+
         }
+
     }
-    var C = $3Dmol.CC.color(color);
-    return C;
-}
 
-/** Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
- * @struct
- */
-$3Dmol.elementColors = $3Dmol.elementColors || {};
+    function setPolygonOffset(polygonOffset, factor, units) {
 
-$3Dmol.elementColors.defaultColor = 0xff1493;
+        if (_oldPolygonOffset !== polygonOffset) {
 
-/** @property Jmol-like element colors*/
-$3Dmol.elementColors.Jmol = {
-        'H': 0xFFFFFF,
-        'He': 0xD9FFFF,
-        'HE': 0xD9FFFF,
-        'Li': 0xCC80FF,
-        'LI': 0xCC80FF,
-        'B': 0xFFB5B5,
-        'C': 0x909090,
-        'N': 0x3050F8,
-        'O': 0xFF0D0D,
-        'F': 0x90E050,
-        'Na': 0xAB5CF2,
-        'NA': 0xAB5CF2,
-        'Mg': 0x8AFF00,
-        'MG': 0x8AFF00,
-        'Al': 0xBFA6A6,
-        'AL': 0xBFA6A6,
-        'Si': 0xF0C8A0,
-        'SI': 0xF0C8A0,
-        'P': 0xFF8000,
-        'S': 0xFFFF30,
-        'Cl': 0x1FF01F,
-        'CL': 0x1FF01F,
-        'Ca': 0x3DFF00,
-        'CA': 0x3DFF00,
-        'Ti': 0xBFC2C7,
-        'TI': 0xBFC2C7,
-        'Cr': 0x8A99C7,
-        'CR': 0x8A99C7,
-        'Mn': 0x9C7AC7,
-        'MN': 0x9C7AC7,
-        'Fe': 0xE06633,
-        'FE': 0xE06633,
-        'Ni': 0x50D050,
-        'NI': 0x50D050,
-        'Cu': 0xC88033,
-        'CU': 0xC88033,
-        'Zn': 0x7D80B0,
-        'ZN': 0x7D80B0,
-        'Br': 0xA62929,
-        'BR': 0xA62929,
-        'Ag': 0xC0C0C0,
-        'AG': 0xC0C0C0,
-        'I': 0x940094,
-        'Ba': 0x00C900,
-        'BA': 0x00C900,
-        'Au': 0xFFD123,
-        'AU': 0xFFD123
-};
+            if (polygonOffset)
+                _gl.enable(_gl.POLYGON_OFFSET_FILL);
+            else
+                _gl.disable(_gl.POLYGON_OFFSET_FILL);
+        }
+    }
 
-/** @property rasmol-like element colors */
-$3Dmol.elementColors.rasmol = {
-        'H': 0xFFFFFF,
-        'He': 0xFFC0CB,
-        'HE': 0xFFC0CB,
-        'Li': 0xB22222,
-        'LI': 0xB22222,
-        'B': 0x00FF00,
-        'C': 0xC8C8C8,
-        'N': 0x8F8FFF,
-        'O': 0xF00000,
-        'F': 0xDAA520,
-        'Na': 0x0000FF,
-        'NA': 0x0000FF,
-        'Mg': 0x228B22,
-        'MG': 0x228B22,
-        'Al': 0x808090,
-        'AL': 0x808090,
-        'Si': 0xDAA520,
-        'SI': 0xDAA520,
-        'P': 0xFFA500,
-        'S': 0xFFC832,
-        'Cl': 0x00FF00,
-        'CL': 0x00FF00,
-        'Ca': 0x808090,
-        'CA': 0x808090,
-        'Ti': 0x808090,
-        'TI': 0x808090,
-        'Cr': 0x808090,
-        'CR': 0x808090,
-        'Mn': 0x808090,
-        'MN': 0x808090,
-        'Fe': 0xFFA500,
-        'FE': 0xFFA500,
-        'Ni': 0xA52A2A,
-        'NI': 0xA52A2A,
-        'Cu': 0xA52A2A,
-        'CU': 0xA52A2A,
-        'Zn': 0xA52A2A,
-        'ZN': 0xA52A2A,
-        'Br': 0xA52A2A,
-        'BR': 0xA52A2A,
-        'Ag': 0x808090,
-        'AG': 0x808090,
-        'I': 0xA020F0,
-        'Ba': 0xFFA500,
-        'BA': 0xFFA500,
-        'Au': 0xDAA520,
-        'AU': 0xDAA520    
-};
+    function setLineWidth(width) {
 
-$3Dmol.elementColors.defaultColors = $3Dmol.elementColors.rasmol;
+        if (width !== _oldLineWidth) {
+            _gl.lineWidth(width);
+            _oldLineWidth = width;
+        }
 
-$3Dmol.elementColors.greenCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
+    }
 
-$3Dmol.elementColors.cyanCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
+    var onGeometryDispose = function(event) {
 
-$3Dmol.elementColors.magentaCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
+        var geometry = event.target;
+        geometry.removeEventListener('dispose', onGeometryDispose);
 
-$3Dmol.elementColors.yellowCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
+        deallocateGeometry(geometry);
 
-$3Dmol.elementColors.whiteCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
+        _this.info.memory.geometries--;
 
-$3Dmol.elementColors.orangeCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
+    };
 
-$3Dmol.elementColors.purpleCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
+    var onTextureDispose = function(event) {
 
-$3Dmol.elementColors.blueCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
-$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
-//glcartoon.js
-//This contains all the routines for rendering a cartoon given a set
-//of atoms with assigned secondary structure
+        var texture = event.target;
 
-//TODO: generate normals directly in drawStrip and drawThinStrip
+        texture.removeEventListener('dispose', onTextureDispose);
 
-var $3Dmol = $3Dmol || {};
+        deallocateTexture(texture);
 
+        _this.info.memory.textures--;
 
-/**@typedef CartoonStyleSpec
- * @prop {string} color - solid color, may specify as 'spectrum'
- * @prop {string} style - style of cartoon rendering (currently just default and trace)
- * @prop {number} thickness - cartoon strand thickness, default is 0.4
- * In nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which
- * is 'N1' for purines (resn: '  A', '  G', ' DA', ' DG') and 'N3' for pyrimidines (resn: '  C', '  U', ' DC', ' DT').
- * The different nucleobases can therefore be distinguished as follows:
- * @example
- * viewer.setStyle({resn:' DA', atom:'N1'}, {cartoon:{color:'red'}});
- * viewer.setStyle({resn:' DG', atom:'N1'}, {cartoon:{color:'green'}});
- * viewer.setStyle({resn:' DC', atom:'N3'}, {cartoon:{color:'blue'}});
- * viewer.setStyle({resn:' DT', atom:'N3'}, {cartoon:{color:'yellow'}});
- */
+    };
 
-/**
- * @ignore
- * @param {$3Dmol.Object3D} group
- * @param {AtomSpec} atomlist
- * @param {$3Dmol.Gradient} gradientscheme
- */
-$3Dmol.drawCartoon = (function() {
+    var onMaterialDispose = function(event) {
 
-    var axisDIV = 5; // 3 still gives acceptable quality
-    var strandDIV = 6;
-    var nucleicAcidStrandDIV = 4;
-    var tubeDIV = 8;
-    var coilWidth = 0.3;
-    var helixSheetWidth = 1.3;
-    var nucleicAcidWidth = 0.8;
-    var defaultThickness = 0.4; 
+        var material = event.target;
+        material.removeEventListener('dispose', onMaterialDispose);
 
-    // helper functions
+        deallocateMaterial(material);
 
-    // Catmull-Rom subdivision
-    var subdivide = function(_points, DIV) { // points as Vector3
-        var ret = [];
-        var points = _points;
-        points = []; // Smoothing test
-        points.push(_points[0]);
-        
-        var i, lim, size;
-        var p0, p1, p2, p3, v0, v1;
-        
-        for (i = 1, lim = _points.length - 1; i < lim; i++) {
-            p1 = _points[i]; p2 = _points[i + 1];
-            if (p1.smoothen)
-                points.push(new $3Dmol.Vector3((p1.x + p2.x) / 2, (p1.y + p2.y) / 2,
-                        (p1.z + p2.z) / 2));
-            else
-                points.push(p1);
-        }
-        points.push(_points[_points.length - 1]);
+    };
 
-        
-        for (i = -1, size = points.length; i <= size - 3; i++) {
-            p0 = points[(i === -1) ? 0 : i];
-            p1 = points[i + 1]; p2 = points[i + 2];
-            p3 = points[(i === size - 3) ? size - 1 : i + 3];
-            v0 = new $3Dmol.Vector3().subVectors(p2, p0).multiplyScalar(0.5);
-            v1 = new $3Dmol.Vector3().subVectors(p3, p1).multiplyScalar(0.5);
+    var deallocateGeometry = function(geometry) {
 
-            for ( var j = 0; j < DIV; j++) {
-                var t = 1.0 / DIV * j;
-                var x = p1.x + t * v0.x + t * t * 
-                        (-3 * p1.x + 3 * p2.x - 2 * v0.x - v1.x) + t * t * t *
-                        (2 * p1.x - 2 * p2.x + v0.x + v1.x);
-                var y = p1.y + t * v0.y + t * t * 
-                        (-3 * p1.y + 3 * p2.y - 2 * v0.y - v1.y) + t * t * t *
-                        (2 * p1.y - 2 * p2.y + v0.y + v1.y);
-                var z = p1.z + t * v0.z + t * t * 
-                        (-3 * p1.z + 3 * p2.z - 2 * v0.z - v1.z) + t * t * t * 
-                        (2 * p1.z - 2 * p2.z + v0.z + v1.z);
-                        
-                var pt = new $3Dmol.Vector3(x, y, z);
-                
-                var atomIndex = Math.floor( (ret.length+2) / DIV);
-                
-                if (_points[atomIndex] !== undefined && _points[atomIndex].atom !== undefined)
-                    pt.atom = _points[atomIndex].atom;
-                    
-                ret.push(pt);
-            }
-        }
-        ret.push(points[points.length - 1]);
-        return ret;
-    };
+        geometry.__webglInit = undefined;
 
-    var drawThinStrip = function(group, p1, p2, colors, div) {
-    
-        var geo = new $3Dmol.Geometry(true);       
-        var offset, vertoffset;
-        var color;
+        if (geometry.__webglVertexBuffer !== undefined)
+            _gl.deleteBuffer(geometry.__webglVertexBuffer);
 
-        
-        for ( var i = 0, lim = p1.length; i < lim; i++) {
-            
-            color = $3Dmol.CC.color(colors[Math.round((i - 1) / div)]);
-           
-            geoGroup = geo.updateGeoGroup(2);
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var faceArray = geoGroup.faceArray;
-            offset = geoGroup.vertices; vertoffset = offset*3;
-            
-            vertexArray[vertoffset] = p1[i].x;
-            vertexArray[vertoffset+1] = p1[i].y;
-            vertexArray[vertoffset+2] = p1[i].z;
-            
-            vertexArray[vertoffset+3] = p2[i].x;
-            vertexArray[vertoffset+4] = p2[i].y;
-            vertexArray[vertoffset+5] = p2[i].z;
-            
-            for (var j = 0; j < 6; ++j) {                
-                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
-            }            
-           
-            if (i > 0) {
-                var faces = [offset, offset + 1, offset - 1, offset - 2];
-                var faceoffset = geoGroup.faceidx;
-                
-                faceArray[faceoffset] = faces[0]; faceArray[faceoffset+1] = faces[1]; faceArray[faceoffset+2] = faces[3];
-                faceArray[faceoffset+3] = faces[1]; faceArray[faceoffset+4] = faces[2]; faceArray[faceoffset+5] = faces[3];
+        if (geometry.__webglColorBuffer !== undefined)
+            _gl.deleteBuffer(geometry.__webglColorBuffer);
+
+        if (geometry.geometryGroups !== undefined) {
+
+            for (var g = 0, gl = geometry.groups; g < gl; g++) {
+
+                var geometryGroup = geometry.geometryGroups[g];
+
+                if (geometryGroup.__webglVertexBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglVertexBuffer);
+
+                if (geometryGroup.__webglColorBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglColorBuffer);
+
+                if (geometryGroup.__webglNormalBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglNormalBuffer);
+
+                if (geometryGroup.__webglFaceBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglFaceBuffer);
+
+                if (geometryGroup.__webglLineBuffer !== undefined)
+                    _gl.deleteBuffer(geometryGroup.__webglLineBuffer);
 
-                geoGroup.faceidx += 6;
             }
-            
-            geoGroup.vertices += 2;
         }
-        
-        geo.initTypedArrays();
-        geo.setUpNormals();
-        
-        var material = new $3Dmol.MeshLambertMaterial();
-        material.vertexColors = $3Dmol.FaceColors;
-                material.side = $3Dmol.DoubleSide;
-        var mesh = new $3Dmol.Mesh(geo, material);
-        group.add(mesh);
     };
 
-    var drawStrip = function(group, p1, p2, colors, div, thickness) {
-        if ((p1.length) < 2)
+    var deallocateMaterial = function(material) {
+
+        var program = material.program;
+
+        if (program === undefined)
             return;
-        div = div || axisDIV;
-        p1 = subdivide(p1, div);
-        p2 = subdivide(p2, div);
-        if (!thickness)
-            return drawThinStrip(group, p1, p2, colors, div);
 
-        var geo = new $3Dmol.Geometry(true);
-        
-        //var vs = geo.vertices, fs = geo.faces;
-                var vs = [], fs = [];
-        var axis, p1v, p2v, a1v, a2v;
-        
-        var faces = [ [ 0, 2, -6, -8 ], [ -4, -2, 6, 4 ], [ 7, -1, -5, 3 ],
-                [ -3, 5, 1, -7 ] ];
-                
-        var offset, vertoffset, faceoffset;
-        var color;
-        var currentAtom, lastAtom;
-        var i, lim, j;
-        var face1, face2, face3;
-        var geoGroup;
-        
-        for (i = 0, lim = p1.length; i < lim; i++) {
-        
-            color = $3Dmol.CC.color(colors[Math.round((i - 1) / div)]);
-            
-            vs.push(p1v = p1[i]); // 0
-            vs.push(p1v); // 1
-            vs.push(p2v = p2[i]); // 2
-            vs.push(p2v); // 3
-            if (i < lim - 1) {
-                var toNext = p1[i + 1].clone().sub(p1[i]);
-                var toSide = p2[i].clone().sub(p1[i]);
-                axis = toSide.cross(toNext).normalize().multiplyScalar(
-                        thickness);
-            }
-            vs.push(a1v = p1[i].clone().add(axis)); // 4
-            vs.push(a1v); // 5
-            vs.push(a2v = p2[i].clone().add(axis)); // 6
-            vs.push(a2v); // 7
-            
-            if (p1v.atom !== undefined)
-                currentAtom = p1v.atom;
-            
-            geoGroup = geo.updateGeoGroup(8);
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var faceArray = geoGroup.faceArray;
-            offset = geoGroup.vertices; vertoffset = offset*3;
-            
-            vertexArray[vertoffset] = p1v.x; vertexArray[vertoffset+1] = p1v.y; vertexArray[vertoffset+2] = p1v.z;
-            vertexArray[vertoffset+3] = p1v.x; vertexArray[vertoffset+4] = p1v.y; vertexArray[vertoffset+5] = p1v.z;
-            vertexArray[vertoffset+6] = p2v.x; vertexArray[vertoffset+7] = p2v.y; vertexArray[vertoffset+8] = p2v.z;
-            vertexArray[vertoffset+9] = p2v.x; vertexArray[vertoffset+10] = p2v.y; vertexArray[vertoffset+11] = p2v.z;
-            vertexArray[vertoffset+12] = a1v.x; vertexArray[vertoffset+13] = a1v.y; vertexArray[vertoffset+14] = a1v.z;
-            vertexArray[vertoffset+15] = a1v.x; vertexArray[vertoffset+16] = a1v.y; vertexArray[vertoffset+17] = a1v.z;
-            vertexArray[vertoffset+18] = a2v.x; vertexArray[vertoffset+19] = a2v.y; vertexArray[vertoffset+20] = a2v.z;
-            vertexArray[vertoffset+21] = a2v.x; vertexArray[vertoffset+22] = a2v.y; vertexArray[vertoffset+23] = a2v.z;
-            
-            for (j = 0; j < 8; ++j) {                
-                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
-            }
-            
-            if (i > 0) {
-             
-                //both points have distinct atoms
-                var diffAtoms = ((lastAtom !== undefined && currentAtom !== undefined) && lastAtom.serial !== currentAtom.serial);
-                
-                for (j = 0; j < 4; j++ ) {
-                
-                    var face = [offset + faces[j][0], offset + faces[j][1], offset + faces[j][2], offset + faces[j][3]];
-                    
-                    faceoffset = geoGroup.faceidx;    
-                    
-                    faceArray[faceoffset] = face[0]; faceArray[faceoffset+1] = face[1]; faceArray[faceoffset+2] = face[3];
-                    faceArray[faceoffset+3] = face[1]; faceArray[faceoffset+4] = face[2]; faceArray[faceoffset+5] = face[3];
-                    
-                    geoGroup.faceidx += 6;
-                    
-                    if (currentAtom.clickable || lastAtom.clickable) {
-                        
-                        var p1a = vs[face[3]].clone(), p1b = vs[face[0]].clone(),
-                            p2a = vs[face[2]].clone(), p2b = vs[face[1]].clone();
-                        
-                        p1a.atom = vs[face[3]].atom || null; //should be same
-                        p2a.atom = vs[face[2]].atom || null; 
-                        
-                        
-                        p1b.atom = vs[face[0]].atom || null; //should be same                      
-                        p2b.atom = vs[face[1]].atom || null; 
-                        
-                        if (diffAtoms) {
-                            var m1 = p1a.clone().add(p1b).multiplyScalar(0.5);
-                            var m2 = p2a.clone().add(p2b).multiplyScalar(0.5);
-                            var m = p1a.clone().add(p2b).multiplyScalar(0.5);
-                            
-                            if (j % 2 === 0)
-                            {
-                                if (lastAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
-                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
-                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
-                                    lastAtom.intersectionShape.triangle.push(face1);
-                                    lastAtom.intersectionShape.triangle.push(face2);
-                                    lastAtom.intersectionShape.triangle.push(face3);
-                                }
-                                
-                                if (currentAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
-                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
-                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
-                                    currentAtom.intersectionShape.triangle.push(face1);
-                                    currentAtom.intersectionShape.triangle.push(face2);
-                                    currentAtom.intersectionShape.triangle.push(face3);
-                                }
-                            }
-                            else {
-                                if (currentAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
-                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
-                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
-                                    currentAtom.intersectionShape.triangle.push(face1);
-                                    currentAtom.intersectionShape.triangle.push(face2);
-                                    currentAtom.intersectionShape.triangle.push(face3);
-                                }
-                                
-                                if (lastAtom.clickable) {
-                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
-                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
-                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
-                                    lastAtom.intersectionShape.triangle.push(face1);
-                                    lastAtom.intersectionShape.triangle.push(face2);
-                                    lastAtom.intersectionShape.triangle.push(face3);
-                                }                          
-                            }
-                            
-                        }
-                        
-                        //face for single atom
-                        else if (currentAtom.clickable) {
-                            face1 = new $3Dmol.Triangle(p1b, p2b, p1a);
-                            face2 = new $3Dmol.Triangle(p2b, p2a, p1a);
-                            currentAtom.intersectionShape.triangle.push(face1);
-                            currentAtom.intersectionShape.triangle.push(face2);
-                        }
-                        
-                    }
-                    
-                }
-            }
-            
-            geoGroup.vertices += 8;
-            lastAtom = currentAtom;
-        }
-        
+        material.program = undefined;
 
-        var vsize = vs.length - 8; // Cap
-        
-        geoGroup = geo.updateGeoGroup(8);
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        offset = geoGroup.vertices; vertoffset = offset*3; faceoffset = geoGroup.faceidx;
-        
-        for (i = 0; i < 4; i++) {
-            vs.push(vs[i * 2]);
-            vs.push(vs[vsize + i * 2]);
-            
-            var v1 = vs[i * 2], v2 = vs[vsize + i * 2];
-            
-            vertexArray[vertoffset+6*i] = v1.x; vertexArray[vertoffset+1+6*i] = v1.y; vertexArray[vertoffset+2+6*i] = v1.z;
-            vertexArray[vertoffset+3+6*i] = v2.x; vertexArray[vertoffset+4+6*i] = v2.y; vertexArray[vertoffset+5+6*i] = v2.z;
-            
-            colorArray[vertoffset+6*i] = color.r; colorArray[vertoffset+1+6*i] = color.g; colorArray[vertoffset+2+6*i] = color.b;
-            colorArray[vertoffset+3+6*i] = color.r; colorArray[vertoffset+4+6*i] = color.g; colorArray[vertoffset+5+6*i] = color.b;
+        // only deallocate GL program if this was the last use of shared program
+        // assumed there is only single copy of any program in the _programs
+        // list
+        // (that's how it's constructed)
 
-        }
-        
-        vsize += 8;
-                
-        face1 = [offset, offset + 2, offset + 6, offset + 4];
-        face2 = [offset + 1, offset + 5, offset + 7, offset + 3];
-        
-        faceArray[faceoffset] = face1[0]; faceArray[faceoffset+1] = face1[1]; faceArray[faceoffset+2] = face1[3];
-        faceArray[faceoffset+3] = face1[1]; faceArray[faceoffset+4] = face1[2]; faceArray[faceoffset+5] = face1[3];
-        faceArray[faceoffset+6] = face2[0]; faceArray[faceoffset+7] = face2[1]; faceArray[faceoffset+8] = face2[3];
-        faceArray[faceoffset+9] = face2[1]; faceArray[faceoffset+10] = face2[2]; faceArray[faceoffset+11] = face2[3];
-        
-        geoGroup.faceidx += 12;
-        geoGroup.vertices += 8;
-        
-        //TODO: Add intersection planes for caps
-        
-        geo.initTypedArrays();
-        geo.setUpNormals();
-        
-        var material = new $3Dmol.MeshLambertMaterial();
-        material.vertexColors = $3Dmol.FaceColors;
-        material.side = $3Dmol.DoubleSide;
-        var mesh = new $3Dmol.Mesh(geo, material);
-        group.add(mesh);
-        
-    };
+        var i, il, programInfo;
+        var deleteProgram = false;
 
-    //TODO: Need to update this (will we ever use this?)
-    var drawSmoothCurve = function(group, _points, width, colors, div) {
-        if (_points.length === 0)
-            return;
+        for (i = 0, il = _programs.length; i < il; i++) {
 
-        div = (div === undefined) ? 5 : div;
+            programInfo = _programs[i];
 
-        var geo = new $3Dmol.Geometry();
-        var points = subdivide(_points, div);
-                /*
-        for ( var i = 0; i < points.length; i++) {
-            geo.vertices.push(points[i]);
-            geo.colors.push($3Dmol.color(colors[(i == 0) ? 0 : Math.round((i - 1)
-                    / div)]));
-        }
-                */
-        var lineMaterial = new $3Dmol.LineBasicMaterial({
-            linewidth : width
-        });
-        lineMaterial.vertexColors = true;
-        var line = new $3Dmol.Line(geo, lineMaterial);
-        line.type = $3Dmol.LineStrip;
-        group.add(line);
-    };
+            if (programInfo.program === program) {
 
-    var drawStrand = function(group, atomList, num, div, fill, coilWidth, helixSheetWidth, doNotSmoothen, gradientScheme, geo)
-    {
-        num = num || strandDIV;
-        div = div || axisDIV;
-        doNotSmoothen = !!(doNotSmoothen);
+                programInfo.usedTimes--;
 
-                        //  proteins    na backbone  na terminus                  nucleobases
-        var cartoonAtoms = ["CA", "O",  "P", "OP2",  "O5'", "O3'", "C5'", "C2'",  "N1", "N3"];
-        var purResns = [" DA", " DG", "  A", "  G"];
-        var pyrResns = [" DT", " DC", "  U", "  C"];
+                if (programInfo.usedTimes === 0) {
 
-        var cartoon, curr, next, currColor, nextColor, thickness, i;
-        var backbonePt, orientPt, prevOrientPt, terminalPt, termOrientPt, baseStartPt, baseEndPt;
-        var traceGeo = null;
-        var colors = [];
-        var points = [];
-        for (var i = 0; i < num; i++)
-            points[i] = [];
+                    deleteProgram = true;
 
-        for (i in atomList)
-        {
-            next = atomList[i];
-            
-            if (next === undefined || $.inArray(next.atom, cartoonAtoms) === -1 || next.hetflag)
-                continue; // skip array holes, heteroatoms, and atoms not involved in cartoon drawing
+                }
 
-            // determine cartoon style
-            cartoon = next.style.cartoon;
-            if (cartoon.style === "trace") // draw cylinders connecting consecutive 'backbone' atoms
-            {
-                /* "trace" style just draws cylinders between consecutive 'backbone' atoms,
-                    such as alpha carbon for polypeptides and phosphorus for DNA. */
+                break;
 
-                if (!traceGeo) traceGeo = new $3Dmol.Geometry(true);
+            }
 
-                if (next.atom === "CA" || next.atom === "P")
-                {
-                    // determine cylinder color
-                    if (gradientScheme)
-                        nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
-                    else
-                        nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                    colors.push(nextColor);
+        }
 
-                    // determine cylinder thickness
-                    if ($.isNumeric(cartoon.thickness))
-                        thickness = cartoon.thickness;
-                    else
-                        thickness = defaultThickness;
+        if (deleteProgram === true) {
 
-                    /* do not draw connections between different chains, but ignore
-                       differences in reschain to properly support CA-only files */
-                    if (curr && curr.chain === next.chain && curr.resi + 1 === next.resi)
-                    {
-                        // if both atoms are same color, draw single cylinder
-                        if (nextColor == currColor)
-                        {
-                            var color = $3Dmol.CC.color(nextColor);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, next, thickness, color, true, true);
-                        }
+            // avoid using array.splice, this is costlier than creating new
+            // array from scratch
 
-                        else // otherwise draw cylinders for each color (split down the middle)
-                        {
-                            var midpoint = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
-                            var color1 = $3Dmol.CC.color(currColor);
-                            var color2 = $3Dmol.CC.color(nextColor);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, midpoint, thickness, color1, true, false);
-                            $3Dmol.GLDraw.drawCylinder(traceGeo, midpoint, next, thickness, color2, false, true);
-                        } // note that an atom object can be duck-typed as a 3-vector in this case
-                    }
+            var newPrograms = [];
+
+            for (i = 0, il = _programs.length; i < il; i++) {
+
+                programInfo = _programs[i];
+
+                if (programInfo.program !== program) {
+
+                    newPrograms.push(programInfo);
 
-                    curr = next;
-                    currColor = nextColor;
                 }
+
             }
 
-            else // draw default-style cartoons based on secondary structure
-            {
-                // draw backbone through these atoms
-                if (next.atom === "CA" || next.atom === "P" || next.atom === "O5'")
-                {
-                    // end of a chain of connected residues
-                    if (curr != undefined && (curr.chain != next.chain || !(curr.resi === next.resi || curr.resi + 1 === next.resi)
-                        || curr.reschain != next.reschain))
-                    { 
+            _programs = newPrograms;
 
-                        if (baseEndPt) // draw the last base if it's a NA chain
-                        {
-                            if (terminalPt)
-                                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
-                            else
-                                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+            _gl.deleteProgram(program);
 
-                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-                            addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr);
-                            colors.push(nextColor);
-                            
-                            baseStartPt = null;
-                            baseEndPt = null;
-                        }
+            _this.info.memory.programs--;
 
-                        // draw accumulated strand points
-                        for (i = 0; !thickness && i < num; i++)
-                            drawSmoothCurve(group, points[i], 1, colors, div);
-                        if (fill)
-                            drawStrip(group, points[0], points[num - 1], colors, div, thickness);
+        }
 
-                        // clear arrays for points and colors
-                        points = [];
-                        for (i = 0; i < num; i++)
-                            points[i] = [];
-                        colors = [];
-                    }
+    };
 
-                    // backbone atom of next residue
-                    if (curr === undefined || curr.resi != next.resi)
-                    {
-                        if (baseEndPt) // draw last NA residue's base
-                        {
-                            // start the cylinder at the midpoint between consecutive backbone atoms
-                            baseStartPt = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
-                            //var startFix = baseStartPt.clone().sub(baseEndPt).multiplyScalar(0.04);
-                            //baseStartPt.add(startFix);
-                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-                            baseStartPt = null;
-                            baseEndPt = null;   
-                        }
+    var deallocateTexture = function(texture) {
 
-                        // determine color and thickness of the next strand segment
-                        if (gradientScheme)
-                            nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
-                        else
-                            nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                        colors.push(nextColor);
-                        if ($.isNumeric(cartoon.thickness))
-                            thickness = cartoon.thickness;
-                        else
-                            thickness = defaultThickness;
+        if (texture.image && texture.image.__webglTextureCube) {
 
-                        curr = next; // advance pointer
-                        backbonePt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
-                        backbonePt.resi = curr.resi;
-                        currColor = nextColor; // used for NA bases
-                    }
+            // cube texture
 
-                    // click handling
-                    if (next.clickable === true &&
-                        (next.intersectionShape === undefined || next.intersectionShape.triangle === undefined)) 
-                        next.intersectionShape = {sphere : null, cylinder : [], line : [], triangle : []};
+            _gl.deleteTexture(texture.image.__webglTextureCube);
 
-                }
+        }
 
-                // atoms used to orient the backbone strand
-                else if (next.atom === "O"  && curr.atom === "CA"
-                      || next.atom === "OP2" && curr.atom === "P"
-                      || next.atom === "C5'" && curr.atom === "O5'")
-                {
-                    orientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                    orientPt.resi = next.resi;
-                    if (next.atom === "OP2") // for NA 3' terminus
-                        termOrientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                }
+        else {
 
-                // NA 3' terminus is an edge case, need a vector for most recent O3'
-                else if (next.atom === "O3'")
-                {
-                    terminalPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                }
+            // 2D texture
 
-                // atoms used for drawing the NA base cylinders (diff for purines and pyramidines)
-                else if ((next.atom === "N1" && $.inArray(next.resn, purResns) != -1) ||
-                         (next.atom === "N3" && $.inArray(next.resn, pyrResns) != -1))
-                {
-                    baseEndPt = new $3Dmol.Vector3(next.x, next.y, next.z);
-                    baseEndPt.color = $3Dmol.getColorFromStyle(next, cartoon).getHex();
-                }
+            if (!texture.__webglInit)
+                return;
+
+            texture.__webglInit = false;
+            _gl.deleteTexture(texture.__webglTexture);
 
-                // when we have a backbone point and orientation point in the same residue, accumulate strand points
-                if (orientPt && backbonePt && orientPt.resi === backbonePt.resi)
-                {
-                    addBackbonePoints(points, num, !doNotSmoothen, backbonePt, orientPt, prevOrientPt, curr);
-                    prevOrientPt = orientPt;
-                    backbonePt = null;
-                    orientPt = null;
-                }
-            }  
         }
 
-        if (baseEndPt) // draw last NA base if needed
-        {
-            if (terminalPt)
-                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
-            else
-                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+    };
 
-            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), false, true);
-            addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr);
-            colors.push(nextColor);
-        }
+    // Compile and return shader
+    function getShader(type, str) {
 
-        // for default style, draw the last strand
-        for (i = 0; !thickness && i < num; i++)
-            drawSmoothCurve(group, points[i], 1, colors, div);
-        if (fill)
-            drawStrip(group, points[0], points[num - 1], colors, div, thickness);
+        var shader;
 
-        if (traceGeo) // generate mesh for trace geometry
-        {
-            var traceMaterial = new $3Dmol.MeshLambertMaterial();
-            traceMaterial.vertexColors = $3Dmol.FaceColors;
-            traceMaterial.side = $3Dmol.DoubleSide;
-            var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
-            group.add(traceMesh);
-        }
-    };
+        if (type === "fragment")
+            shader = _gl.createShader(_gl.FRAGMENT_SHADER);
+        else if (type === "vertex")
+            shader = _gl.createShader(_gl.VERTEX_SHADER);
 
-    //TODO document me
-    var addBackbonePoints = function(pointsArray, num, smoothen, backbonePt, orientPt, prevOrientPt, backboneAtom)
-    {
-        var widthScalar, i, delta, v;
-        orientPt.sub(backbonePt);
-        orientPt.normalize();
-        if (backboneAtom.ss === "c")
-        {
-            if (backboneAtom.atom === "P")
-                widthScalar = nucleicAcidWidth;
-            else
-                widthScalar = coilWidth;
-        } else
-            widthScalar = helixSheetWidth;
-        orientPt.multiplyScalar(widthScalar);
+        _gl.shaderSource(shader, str);
+        _gl.compileShader(shader);
 
-        if (prevOrientPt != null && orientPt.dot(prevOrientPt) < 0)
-        {
-            orientPt.negate();
-        }
+        if (!_gl.getShaderParameter(shader, _gl.COMPILE_STATUS)) {
+
+            console.error(_gl.getShaderInfoLog(shader));
+            console.error("could not initialize shader");
+            return null;
 
-        for (i = 0; i < num; i++)
-        {
-            delta = -1 + i * 2 /(num - 1); // produces num increments from -1 to 1
-            v = new $3Dmol.Vector3(backbonePt.x + delta * orientPt.x,
-                                   backbonePt.y + delta * orientPt.y,
-                                   backbonePt.z + delta * orientPt.z);
-            v.atom = backboneAtom;
-            if (smoothen && backboneAtom.ss === "s") 
-                v.smoothen = true;
-            pointsArray[i].push(v);
         }
-    }
 
-    // actual function call
-    var drawCartoon = function(group, atomlist, geo, gradientscheme) {
-        
-        drawStrand(group, atomlist, 2, undefined, true, coilWidth, helixSheetWidth,
-                false, gradientscheme, geo);
-    };
+        return shader;
 
-    return drawCartoon;
-})();
-//
+    }
 
-var $3Dmol = $3Dmol || {};
+    // Compile appropriate shaders (if necessary) from source code and attach to
+    // gl program.
+    function buildProgram(fragmentShader, vertexShader, uniforms, parameters) {
 
-/**
- * Lower level utilities for creating WebGL shape geometries.
- * These are not intended for general consumption.
- * @namespace $3Dmol.GLDraw
-  */
-$3Dmol.GLDraw = (function() {
+        var p, pl, d, program, code;
+        var chunks = [];
 
-    var draw = {}; // object for exporting functions
+        chunks.push(fragmentShader);
+        chunks.push(vertexShader);
 
-    // Rotation matrix around z and x axis -
-    // according to y basis vector
-    // TODO: Try to optimize this (square roots?)
-    var getRotationMatrix = function() {
+        for (p in parameters) {
+            chunks.push(p);
+            chunks.push(parameters[p]);
+        }
 
-        var d = new $3Dmol.Vector3();
-        // var rot = new Float32Array(9);
+        code = chunks.join();
 
-        return function(dir) {
+        // check if program has already been compiled
 
-            d.set(dir[0], dir[1], dir[2]);
+        for (p = 0, pl = _programs.length; p < pl; p++) {
 
-            var dx = d.x, dy = d.y, dz = d.z;
+            var programInfo = _programs[p];
 
-            var dxy = Math.sqrt(dx * dx + dy * dy);
-            var dxz, dyz;
+            if (programInfo.code === code) {
 
-            var sinA, cosA, sinB, cosB, sinC, cosC;
+                programInfo.usedTimes++;
 
-            // about z axis - Phi
-            if (dxy < 0.0001) {
-                sinA = 0;
-                cosA = 1;
+                return programInfo.program;
             }
+        }
 
-            else {
-                sinA = -dx / dxy;
-                cosA = dy / dxy;
-            }
+        // Set up new program and compile shaders
 
-            // recast dy in terms of new axes - z is the same
+        program = _gl.createProgram();
 
-            dy = -sinA * dx + cosA * dy;
-            dyz = Math.sqrt(dy * dy + dz * dz);
+        // set up precision
+        var precision = _precision;
+        var prefix = "precision " + precision + " float;";
 
-            // about new x axis - Theta
+        var prefix_vertex = [ prefix ].join("\n");
 
-            if (dyz < 0.0001) {
-                sinB = 0;
-                cosB = 1;
-            }
+        var prefix_fragment = [
+                parameters.fragdepth ? "#extension GL_EXT_frag_depth: enable"
+                        : "",
+                parameters.wireframe ? "#define WIREFRAME 1" : "", prefix ]
+                .join("\n");
 
-            else {
-                sinB = dz / dyz;
-                cosB = dy / dyz;
-            }
+        var glFragmentShader = getShader("fragment", prefix_fragment
+                + fragmentShader);
+        var glVertexShader = getShader("vertex", prefix_vertex + vertexShader);
 
-            var rot = new Float32Array(9);
-            rot[0] = cosA;
-            rot[1] = sinA;
-            rot[2] = 0;
-            rot[3] = -sinA * cosB;
-            rot[4] = cosA * cosB;
-            rot[5] = sinB;
-            rot[6] = sinA * sinB;
-            rot[7] = -cosA * sinB;
-            rot[8] = cosB;
+        _gl.attachShader(program, glVertexShader);
+        _gl.attachShader(program, glFragmentShader);
 
-            return rot;
+        _gl.linkProgram(program);
 
-        };
+        if (!_gl.getProgramParameter(program, _gl.LINK_STATUS))
+            console.error("Could not initialize shader");
 
-    }();
-    
-    // Ortho normal vectors for cylinder radius/ sphere cap equator and cones
-    // Direction is j basis (0,1,0)
-    var basisVectors = function() {
+        // gather and cache uniform variables and attributes
 
-        var ret = {
-            vertices : [],
-            norms : []
-        };
+        program.uniforms = {};
+        program.attributes = {};
 
-        var nvecs = [];
+        var identifiers, u, a, i;
 
-        var subdivisions = 4; // including the initial 2, eg. 4 => 16 subintervals
-        var N = Math.pow(2, subdivisions);  // eg. 2**4 = 16 subintervals in total
-        var i = 2;  // start with 2 subdivisions already done
-        var M = Math.pow(2, i); // 4
-        var spacing = N/M;  // 16/4 = 4; if there were 5 subdivs, then 32/4 = 8.
-        var j;
+        // uniform vars
+        identifiers = [ 'viewMatrix', 'modelViewMatrix', 'projectionMatrix', 
+                'normalMatrix'];
 
-        nvecs[0] = new $3Dmol.Vector3(-1, 0, 0);
-        nvecs[spacing] = new $3Dmol.Vector3(0, 0, 1);
-        nvecs[spacing*2] = new $3Dmol.Vector3(1, 0, 0);
-        nvecs[spacing*3] = new $3Dmol.Vector3(0, 0, -1);
+        // custom uniform vars
+        for (u in uniforms)
+            identifiers.push(u);
+
+        for (i = 0; i < identifiers.length; i++) {
+
+            var uniformVar = identifiers[i];
+            program.uniforms[uniformVar] = _gl.getUniformLocation(program,
+                    uniformVar);
 
-        for ( i = 3; i <= subdivisions; i ++ ) {
-            // eg. i=3, we need to add 2**(3-1) = 4 new vecs. Call it M.
-            // their spacing is N/M, eg. N=16, M=4, N/M=4; M=8, N/M=2.
-            // they start off at half this spacing
-            // and are equal to the average of the two vectors on either side
-            M = Math.pow(2, (i-1));
-            spacing = N/M;
-            for ( j = 0; j < (M-1); j ++ ) {
-                nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[(j+1)*spacing]).normalize();
-            }
-            // treat the last one specially so it wraps around to zero
-            j = M - 1;
-            nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[0]).normalize();
         }
 
+        // attributes
+        identifiers = [ 'position', 'normal', 'color', 'lineDistance',
+                'offset', 'radius' ];
+
         /*
-         * nvecs[0] = new $3Dmol.Vector3(-1,0,0); nvecs[1] = new
-         * $3Dmol.Vector3(0,0,1); nvecs[2] = new $3Dmol.Vector3(1,0,0);
-         * nvecs[3] = new $3Dmol.Vector3(0,0,-1);
+         * for (a in attributes) identifiers.push(a);
          */
-        return nvecs;
 
-    }();
+        for (i = 0; i < identifiers.length; i++) {
 
-    // memoize capped cylinder for given radius
-    var cylVertexCache = {
+            var attributeVar = identifiers[i];
+            program.attributes[attributeVar] = _gl.getAttribLocation(program,
+                    attributeVar);
+        }
 
-        cache : {},
+        program.id = _programs_counter++;
+        _programs.push({
+            program : program,
+            code : code,
+            usedTimes : 1
+        });
+        _this.info.memory.programs = _programs.length;
 
-        getVerticesForRadius : function(radius) {
+        return program;
+    }
 
-            if (this.cache[radius] !== undefined)
-                return this.cache[radius];
+    // TODO: need to set up shader attributes and uniforms as attributes on
+    // material object after attaching prgm
+    // We need to attach appropriate uniform variables to material after shaders
+    // have been chosen
+    this.initMaterial = function(material, lights, fog, object) {
 
-            var dir = new $3Dmol.Vector3(0, 1, 0);
-            var w = basisVectors.length;
-            var nvecs = [], norms = [];
-            var n;
+        material.addEventListener('dispose', onMaterialDispose);
 
-            for (var i = 0; i < w; i++) {
-                // bottom
-                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
-                // top
-                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
+        var u, a, identifiers, i, parameters, maxLightCount, maxBones, maxShadows, shaderID;
 
-                // NOTE: this normal is used for constructing sphere caps -
-                // cylinder normals taken care of in drawCylinder
-                n = basisVectors[i].clone().normalize();
-                norms.push(n);
-                norms.push(n);
-            }
+        shaderID = material.shaderID;
 
-            // norms[0]
+        if (shaderID) {
 
-            var verticesRows = [];
+            var shader = $3Dmol.ShaderLib[shaderID];
+            material.vertexShader = shader.vertexShader;
+            material.fragmentShader = shader.fragmentShader;
+            material.uniforms = $3Dmol.ShaderUtils.clone(shader.uniforms);
+            // TODO: set material uniforms to shader uniform variables
 
-            // Require that heightSegments is even and >= 2
-            // Equator points at h/2 (theta = pi/2)
-            // (repeated) polar points at 0 and h (theta = 0 and pi)
-            var heightSegments = 10, widthSegments = w; // 16 or however many
-                                                        // basis vectors for
-                                                        // cylinder
+        }
 
-            if (heightSegments % 2 !== 0 || !heightSegments) {
-                console.error("heightSegments must be even");
+        parameters = {
+            wireframe : material.wireframe,
+            fragdepth : material.imposter
+        };
 
-                return null;
-            }
+        material.program = buildProgram(material.fragmentShader,
+                material.vertexShader, material.uniforms, parameters);
 
-            var phiStart = 0;
-            var phiLength = Math.PI * 2;
+    };
 
-            var thetaStart = 0;
-            var thetaLength = Math.PI;
+    function setProgram(camera, lights, fog, material, object) {
 
-            var x, y;
-            var polar = false, equator = false;
+        if (material.needsUpdate) {
 
-            for (y = 0; y <= heightSegments; y++) {
+            if (material.program)
+                deallocateMaterial(material);
 
-                polar = (y === 0 || y === heightSegments) ? true : false;
-                equator = (y === heightSegments / 2) ? true : false;
+            _this.initMaterial(material, lights, fog, object);
+            material.needsUpdate = false;
+        }
 
-                var verticesRow = [], toRow = [];
+        var refreshMaterial = false;
 
-                for (x = 0; x <= widthSegments; x++) {
+        // p_uniforms: uniformVarName => uniformLocation
+        // m_uniforms: uniformVarName => uniformJsVal
+        var program = material.program, p_uniforms = program.uniforms, m_uniforms = material.uniforms;
 
-                    // Two vertices rows for equator pointing to previously
-                    // constructed cyl points
-                    if (equator) {
-                        var xi = (x < widthSegments) ? 2 * x : 0;
-                        toRow.push(xi + 1);
-                        verticesRow.push(xi);
+        if (program != _currentProgram) {
+            _gl.useProgram(program);
+            _currentProgram = program;
 
-                        continue;
-                    }
+            refreshMaterial = true;
+        }
 
-                    var u = x / widthSegments;
-                    var v = y / heightSegments;
+        if (material.id != _currentMaterialId) {
+            _currentMaterialId = material.id;
+            refreshMaterial = true;
+        }
 
-                    // Only push first polar point
+        if (camera != _currentCamera) {
+            _currentCamera = camera;
+            refreshMaterial = true;
+        }
 
-                    if (!polar || x === 0) {
+        _gl.uniformMatrix4fv(p_uniforms.projectionMatrix, false,
+                camera.projectionMatrix.elements);
+        _gl.uniformMatrix4fv(p_uniforms.modelViewMatrix, false,
+                object._modelViewMatrix.elements);
+        _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false,
+                object._normalMatrix.elements);
 
-                        if (x < widthSegments) {
-                            var vertex = new $3Dmol.Vector3();
-                            vertex.x = -radius
-                                    * Math.cos(phiStart + u * phiLength)
-                                    * Math.sin(thetaStart + v * thetaLength);
-                            vertex.y = radius
-                                    * Math.cos(thetaStart + v * thetaLength);
-                            vertex.z = radius
-                                    * Math.sin(phiStart + u * phiLength)
-                                    * Math.sin(thetaStart + v * thetaLength);
+        // Send projection matrix to uniform variable in shader
+        if (refreshMaterial) {
 
-                            if (Math.abs(vertex.x) < 1e-5)
-                                vertex.x = 0;
-                            if (Math.abs(vertex.y) < 1e-5)
-                                vertex.y = 0;
-                            if (Math.abs(vertex.z) < 1e-5)
-                                vertex.z = 0;
+            // Load projection, model-view matrices for perspective
 
-                            n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
-                            n.normalize();
+            // Set up correct fog uniform vals
+            m_uniforms.fogColor.value = fog.color;
+            m_uniforms.fogNear.value = fog.near;
+            m_uniforms.fogFar.value = fog.far;
 
-                            nvecs.push(vertex);
-                            norms.push(n);
+            // Set up lights for lambert shader
+            if (material.shaderID.startsWith("lambert")
+                    || material.shaderID === "instanced"
+                    || material.shaderID.endsWith("imposter")) {
 
-                            verticesRow.push(nvecs.length - 1);
-                        }
+                // load view and normal matrices for directional and object
+                // lighting
+                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false,
+                        camera.matrixWorldInverse.elements);
 
-                        // last point is just the first point for this row
-                        else {
-                            verticesRow.push(nvecs.length - widthSegments);
-                        }
+                if (_lightsNeedUpdate) {
+                    setupLights(program, lights);
+                    _lightsNeedUpdate = false;
+                }
 
-                    }
+                // Set up correct light uniform var vals
+                m_uniforms.directionalLightColor.value = _lights.directional.colors;
+                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
 
-                    // x > 0; index to already added point
-                    else if (polar)
-                        verticesRow.push(nvecs.length - 1);
+            } else if (material.shaderID.endsWith("outline")) {
+                m_uniforms.outlineColor.value = material.outlineColor;
+                m_uniforms.outlineWidth.value = material.outlineWidth;
+                m_uniforms.outlinePushback.value = material.outlinePushback;
+            } else if (material.shaderID === "sphereimposter") {
+                _gl.uniformMatrix4fv(p_uniforms.viewMatrix, false,
+                        camera.matrixWorldInverse.elements);
+                _gl.uniformMatrix3fv(p_uniforms.normalMatrix, false,
+                        object._normalMatrix.elements);
+                m_uniforms.directionalLightColor.value = _lights.directional.colors;
+                m_uniforms.directionalLightDirection.value = _lights.directional.positions;
+            }
 
-                }
+            // opacity, diffuse, emissive, etc
+            m_uniforms.opacity.value = material.opacity;
 
-                // extra equator row
-                if (equator)
-                    verticesRows.push(toRow);
+            // Load any other material specific uniform variables to gl shaders
+            loadMaterialUniforms(p_uniforms, m_uniforms);
 
-                verticesRows.push(verticesRow);
+        }
 
-            }
+        return program;
 
-            var obj = {
-                vertices : nvecs,
-                normals : norms,
-                verticesRows : verticesRows,
-                w : widthSegments,
-                h : heightSegments
-            };
+    }
 
-            this.cache[radius] = obj;
+    function loadMaterialUniforms(p_uniforms, m_uniforms) {
+        var uniformVar, type, uniformVal, uniformLoc;
 
-            return obj;
+        for (uniformVar in m_uniforms) {
+            if (!p_uniforms[uniformVar])
+                continue;
+
+            type = m_uniforms[uniformVar].type;
+            uniformVal = m_uniforms[uniformVar].value;
+            uniformLoc = p_uniforms[uniformVar];
+
+            // single float
+            if (type === 'f')
+                _gl.uniform1f(uniformLoc, uniformVal);
+            // array of floats
+            else if (type === 'fv')
+                _gl.uniform3fv(uniformLoc, uniformVal);
+            // color - r,g,b floats
+            else if (type === 'c')
+                _gl.uniform3f(uniformLoc, uniformVal.r, uniformVal.g,
+                        uniformVal.b);
+            else if (type === 'f4')
+                _gl.uniform4f(uniformLoc, uniformVal[0], uniformVal[1],
+                        uniformVal[2],uniformVal[3]);
 
         }
-    };
 
-    // creates a cylinder
-    var drawnC = 0;
-    
-    /** Create a cylinder 
-     * @function $3Dmol.GLDraw.drawCylinder
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            from
-     * @param {Point}
-     *            to
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     * @param {boolean} fromCap
-     * @param {boolean} toCap
-     *            
-     * */
-    draw.drawCylinder = function(geo, from, to, radius, color, fromCap, toCap) {
-        if (!from || !to)
+    }
+
+    this.renderBuffer = function(camera, lights, fog, material, geometryGroup,
+            object) {
+
+        if (!material.visible)
             return;
-        drawnC++;
-        // vertices
-        var drawcaps = fromCap || toCap;
-        color = color || {r:0, g:0, b:0};
 
-        /** @type {Array.<number>} */
-        var dir = [ to.x, to.y, to.z ];
-        dir[0] -= from.x;
-        dir[1] -= from.y;
-        dir[2] -= from.z;
+        var program, attributes, linewidth, primitives, a, attribute, i, il;
 
-        var e = getRotationMatrix(dir);
-        // get orthonormal vectors from cache
-        // TODO: Will have orient with model view matrix according to direction
-        var vobj = cylVertexCache.getVerticesForRadius(radius);
+        // Sets up proper vertex and fragment shaders and attaches them to webGL
+        // program
+        // Also sets appropriate uniform variables
+        program = setProgram(camera, lights, fog, material, object);
 
-        // w (n) corresponds to the number of orthonormal vectors for cylinder
-        // (default 16)
-        var n = vobj.w, h = vobj.h;
-        var w = n;
-        // get orthonormal vector
-        var n_verts = (drawcaps) ? h * n + 2 : 2 * n;
+        attributes = program.attributes;
 
-        var geoGroup = geo.updateGeoGroup(n_verts);
+        var updateBuffers = false, wireframeBit = material.wireframe ? 1 : 0, geometryGroupHash = (geometryGroup.id * 0xffffff)
+                + (program.id * 2) + wireframeBit;
 
-        var vertices = vobj.vertices, normals = vobj.normals, verticesRows = vobj.verticesRows;
-        var toRow = verticesRows[h / 2], fromRow = verticesRows[h / 2 + 1];
+        if (geometryGroupHash !== _currentGeometryGroupHash) {
+            _currentGeometryGroupHash = geometryGroupHash;
+            updateBuffers = true;
+        }
 
-        var start = geoGroup.vertices;
-        var offset, faceoffset;
-        var i, x, y, z;
+        // rebind shader attributes to appropriate (and already initialized) gl
+        // buffers
+        if (updateBuffers) {
 
-        var vertexArray = geoGroup.vertexArray;
-        var normalArray = geoGroup.normalArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        // add vertices, opposing vertices paired together
-        for (i = 0; i < n; ++i) {
+            disableAttributes();
 
-            var vi = 2 * i;
+            // Vertices
+            if (attributes.position >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglVertexBuffer);
+                enableAttribute(attributes.position);
+                _gl.vertexAttribPointer(attributes.position, 3, _gl.FLOAT,
+                        false, 0, 0);
+            }
 
-            x = e[0] * vertices[vi].x + e[3] * vertices[vi].y + e[6]
-                    * vertices[vi].z;
-            y = e[1] * vertices[vi].x + e[4] * vertices[vi].y + e[7]
-                    * vertices[vi].z;
-            z = e[5] * vertices[vi].y + e[8] * vertices[vi].z;
+            // Colors
+            if (attributes.color >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglColorBuffer);
+                enableAttribute(attributes.color);
+                _gl.vertexAttribPointer(attributes.color, 3, _gl.FLOAT, false,
+                        0, 0);
+            }
 
-            // var xn = x/radius, yn = y/radius, zn = z/radius;
+            // Normals
+            if (attributes.normal >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglNormalBuffer);
+                enableAttribute(attributes.normal);
+                _gl.vertexAttribPointer(attributes.normal, 3, _gl.FLOAT, false,
+                        0, 0);
+            }
 
-            offset = 3 * (start + vi);
-            faceoffset = geoGroup.faceidx;
+            // Offsets (Instanced only)
+            if (attributes.offset >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglOffsetBuffer);
+                enableAttribute(attributes.offset);
+                _gl.vertexAttribPointer(attributes.offset, 3, _gl.FLOAT, false,
+                        0, 0);
+            }
 
-            // from
-            vertexArray[offset] = x + from.x;
-            vertexArray[offset + 1] = y + from.y;
-            vertexArray[offset + 2] = z + from.z;
-            // to
-            vertexArray[offset + 3] = x + to.x;
-            vertexArray[offset + 4] = y + to.y;
-            vertexArray[offset + 5] = z + to.z;
+            // Radii (Instanced only)
+            if (attributes.radius >= 0) {
+                _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                        geometryGroup.__webglRadiusBuffer);
+                enableAttribute(attributes.radius);
+                _gl.vertexAttribPointer(attributes.radius, 1, _gl.FLOAT, false,
+                        0, 0);
+            }
 
-            // normals
-            normalArray[offset] = x;
-            normalArray[offset + 3] = x;
-            normalArray[offset + 1] = y;
-            normalArray[offset + 4] = y;
-            normalArray[offset + 2] = z;
-            normalArray[offset + 5] = z;
+        }
 
-            // colors
-            colorArray[offset] = color.r;
-            colorArray[offset + 3] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 4] = color.g;
-            colorArray[offset + 2] = color.b;
-            colorArray[offset + 5] = color.b;
+        // Render
+        var faceCount, lineCount;
+        // lambert shaders - draw triangles
+        // TODO: make sure geometryGroup's face count is setup correctly
+        if (object instanceof $3Dmol.Mesh) {
 
-            // faces
-            // 0 - 2 - 1
-            faceArray[faceoffset] = fromRow[i] + start;
-            faceArray[faceoffset + 1] = fromRow[i + 1] + start;
-            faceArray[faceoffset + 2] = toRow[i] + start;
-            // 1 - 2 - 3
-            faceArray[faceoffset + 3] = toRow[i] + start;
-            faceArray[faceoffset + 4] = fromRow[i + 1] + start;
-            faceArray[faceoffset + 5] = toRow[i + 1] + start;
-
-            geoGroup.faceidx += 6;
+            if (material.shaderID === "instanced") {
+                var sphereGeometryGroup = material.sphere.geometryGroups[0];
+                if (updateBuffers) {
+                    _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                            geometryGroup.__webglVertexBuffer);
+                    _gl.bufferData(_gl.ARRAY_BUFFER,
+                            sphereGeometryGroup.vertexArray, _gl.STATIC_DRAW);
+                    _gl.bindBuffer(_gl.ARRAY_BUFFER,
+                            geometryGroup.__webglNormalBuffer);
+                    _gl.bufferData(_gl.ARRAY_BUFFER,
+                            sphereGeometryGroup.normalArray, _gl.STATIC_DRAW);
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglFaceBuffer);
+                    _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER,
+                            sphereGeometryGroup.faceArray, _gl.STATIC_DRAW);
+                }
 
-        }
+                faceCount = sphereGeometryGroup.faceidx;
 
-        // SPHERE CAPS
+                _extInstanced.vertexAttribDivisorANGLE(attributes.offset, 1);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.radius, 1);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.color, 1);
 
-        if (drawcaps) {
+                _extInstanced.drawElementsInstancedANGLE(_gl.TRIANGLES,
+                        faceCount, _gl.UNSIGNED_SHORT, 0,
+                        geometryGroup.radiusArray.length);
 
-            // h - sphere rows, verticesRows.length - 2
-            var ystart = (toCap) ? 0 : h / 2;
-            var yend = (fromCap) ? h + 1 : h / 2 + 1;
+                _extInstanced.vertexAttribDivisorANGLE(attributes.offset, 0);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.radius, 0);
+                _extInstanced.vertexAttribDivisorANGLE(attributes.color, 0);
 
-            var v1, v2, v3, v4, x1, x2, x3, x4, y1, y2, y3, y4, z1, z2, z3, z4, nx1, nx2, nx3, nx4, ny1, ny2, ny3, ny4, nz1, nz2, nz3, nz4, v1offset, v2offset, v3offset, v4offset;
+            }
 
-            for (y = ystart; y < yend; y++) {
-                if (y === h / 2)
-                    continue;
-                // n number of points for each level (verticesRows[i].length -
-                // 1)
-                var cap = (y <= h / 2) ? to : from;
+            else if (material.wireframe) {
+                lineCount = geometryGroup.lineidx;
+                setLineWidth(material.wireframeLinewidth);
 
-                for (x = 0; x < n; x++) {
+                if (updateBuffers)
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglLineBuffer);
 
-                    faceoffset = geoGroup.faceidx;
+                _gl.drawElements(_gl.LINES, lineCount, _gl.UNSIGNED_SHORT, 0);
+            }
 
-                    v1 = verticesRows[y][x + 1];
-                    v1offset = (v1 + start) * 3;
-                    v2 = verticesRows[y][x];
-                    v2offset = (v2 + start) * 3;
-                    v3 = verticesRows[y + 1][x];
-                    v3offset = (v3 + start) * 3;
-                    v4 = verticesRows[y + 1][x + 1];
-                    v4offset = (v4 + start) * 3;
+            else {
+                faceCount = geometryGroup.faceidx;
 
-                    // rotate sphere vectors
-                    x1 = e[0] * vertices[v1].x + e[3] * vertices[v1].y + e[6]
-                            * vertices[v1].z;
-                    x2 = e[0] * vertices[v2].x + e[3] * vertices[v2].y + e[6]
-                            * vertices[v2].z;
-                    x3 = e[0] * vertices[v3].x + e[3] * vertices[v3].y + e[6]
-                            * vertices[v3].z;
-                    x4 = e[0] * vertices[v4].x + e[3] * vertices[v4].y + e[6]
-                            * vertices[v4].z;
+                if (updateBuffers)
+                    _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                            geometryGroup.__webglFaceBuffer);
+                _gl.drawElements(_gl.TRIANGLES, faceCount, _gl.UNSIGNED_SHORT,
+                        0);
 
-                    y1 = e[1] * vertices[v1].x + e[4] * vertices[v1].y + e[7]
-                            * vertices[v1].z;
-                    y2 = e[1] * vertices[v2].x + e[4] * vertices[v2].y + e[7]
-                            * vertices[v2].z;
-                    y3 = e[1] * vertices[v3].x + e[4] * vertices[v3].y + e[7]
-                            * vertices[v3].z;
-                    y4 = e[1] * vertices[v4].x + e[4] * vertices[v4].y + e[7]
-                            * vertices[v4].z;
+            }
 
-                    z1 = e[5] * vertices[v1].y + e[8] * vertices[v1].z;
-                    z2 = e[5] * vertices[v2].y + e[8] * vertices[v2].z;
-                    z3 = e[5] * vertices[v3].y + e[8] * vertices[v3].z;
-                    z4 = e[5] * vertices[v4].y + e[8] * vertices[v4].z;
+            _this.info.render.calls++;
+            _this.info.render.vertices += faceCount;
+            _this.info.render.faces += faceCount / 3;
+        }
 
-                    vertexArray[v1offset] = x1 + cap.x;
-                    vertexArray[v2offset] = x2 + cap.x;
-                    vertexArray[v3offset] = x3 + cap.x;
-                    vertexArray[v4offset] = x4 + cap.x;
+        // basic shaders - draw lines
+        else if (object instanceof $3Dmol.Line) {
+            lineCount = geometryGroup.vertices;
 
-                    vertexArray[v1offset + 1] = y1 + cap.y;
-                    vertexArray[v2offset + 1] = y2 + cap.y;
-                    vertexArray[v3offset + 1] = y3 + cap.y;
-                    vertexArray[v4offset + 1] = y4 + cap.y;
+            setLineWidth(material.linewidth);
+            _gl.drawArrays(_gl.LINES, 0, lineCount);
 
-                    vertexArray[v1offset + 2] = z1 + cap.z;
-                    vertexArray[v2offset + 2] = z2 + cap.z;
-                    vertexArray[v3offset + 2] = z3 + cap.z;
-                    vertexArray[v4offset + 2] = z4 + cap.z;
+            _this.info.render.calls++;
+        }
 
-                    colorArray[v1offset] = color.r;
-                    colorArray[v2offset] = color.r;
-                    colorArray[v3offset] = color.r;
-                    colorArray[v4offset] = color.r;
+    };
 
-                    colorArray[v1offset + 1] = color.g;
-                    colorArray[v2offset + 1] = color.g;
-                    colorArray[v3offset + 1] = color.g;
-                    colorArray[v4offset + 1] = color.g;
+    // rendering
+    function renderObjects(renderList, reverse, materialType, camera, lights,
+            fog, useBlending, overrideMaterial) {
 
-                    colorArray[v1offset + 2] = color.b;
-                    colorArray[v2offset + 2] = color.b;
-                    colorArray[v3offset + 2] = color.b;
-                    colorArray[v4offset + 2] = color.b;
+        var webglObject, object, buffer, material, start, end, delta;
 
-                    nx1 = e[0] * normals[v1].x + e[3] * normals[v1].y + e[6]
-                            * normals[v1].z;
-                    nx2 = e[0] * normals[v2].x + e[3] * normals[v2].y + e[6]
-                            * normals[v2].z;
-                    nx3 = e[0] * normals[v3].x + e[3] * normals[v3].y + e[6]
-                            * normals[v3].z;
-                    nx4 = e[0] * normals[v4].x + e[3] * normals[v4].y + e[6]
-                            * normals[v4].z;
+        // Forward or backward render
 
-                    ny1 = e[1] * normals[v1].x + e[4] * normals[v1].y + e[7]
-                            * normals[v1].z;
-                    ny2 = e[1] * normals[v2].x + e[4] * normals[v2].y + e[7]
-                            * normals[v2].z;
-                    ny3 = e[1] * normals[v3].x + e[4] * normals[v3].y + e[7]
-                            * normals[v3].z;
-                    ny4 = e[1] * normals[v4].x + e[4] * normals[v4].y + e[7]
-                            * normals[v4].z;
+        if (reverse) {
+            start = renderList.length - 1;
+            end = -1;
+            delta = -1;
+        }
 
-                    nz1 = e[5] * normals[v1].y + e[8] * normals[v1].z;
-                    nz2 = e[5] * normals[v2].y + e[8] * normals[v2].z;
-                    nz3 = e[5] * normals[v3].y + e[8] * normals[v3].z;
-                    nz4 = e[5] * normals[v4].y + e[8] * normals[v4].z;
+        else {
+            start = 0;
+            end = renderList.length;
+            delta = 1;
+        }
 
-                    // if (Math.abs(vobj.sphereVertices[v1].y) === radius) {
-                    if (y === 0) {
-                        // face = [v1, v3, v4];
-                        // norm = [n1, n3, n4];
+        for (var i = start; i !== end; i += delta) {
 
-                        normalArray[v1offset] = nx1;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v3offset + 2] = nz3;
-                        normalArray[v4offset + 2] = nz4;
+            webglObject = renderList[i];
 
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v3 + start;
-                        faceArray[faceoffset + 2] = v4 + start;
+            if (webglObject.render) {
 
-                        geoGroup.faceidx += 3;
+                object = webglObject.object;
+                buffer = webglObject.buffer;
+                material = webglObject[materialType];
 
-                    }
+                if (!material)
+                    continue;
 
-                    // else if (Math.abs(vobj.sphereVertices[v3].y) === radius)
-                    // {
-                    else if (y === yend - 1) {
-                        // face = [v1, v2, v3];
-                        // norm = [n1, n2, n3];
+                if (useBlending)
+                    _this.setBlending(true);
 
-                        normalArray[v1offset] = nx1;
-                        normalArray[v2offset] = nx2;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v3offset + 2] = nz3;
+                _this.setDepthTest(material.depthTest);
+                _this.setDepthWrite(material.depthWrite);
+                setPolygonOffset(material.polygonOffset,
+                        material.polygonOffsetFactor,
+                        material.polygonOffsetUnits);
 
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v2 + start;
-                        faceArray[faceoffset + 2] = v3 + start;
+                var reflected = object._modelViewMatrix.isReflected();
 
-                        geoGroup.faceidx += 3;
+                _this.setMaterialFaces(material, reflected);
 
+                _this.renderBuffer(camera, lights, fog, material, buffer,
+                        object);
+                if (_outlineMaterial) {                  
+                    if(material.shaderID == 'sphereimposter') {
+                        _this.renderBuffer(camera, lights, fog, _outlineSphereImposterMaterial,
+                                buffer, object);                        
+                    }
+                    else if(material.shaderID == 'stickimposter') {
+                        _this.renderBuffer(camera, lights, fog, _outlineStickImposterMaterial,
+                                buffer, object);                        
+                    }
+                    else if(!material.wireframe                
+                        && material.shaderID !== 'basic'
+                        && material.opacity !== 0.0) {
+                        _this.renderBuffer(camera, lights, fog, _outlineMaterial,
+                            buffer, object);
                     }
+                }
+            }
+        }
 
-                    else {
-                        // face = [v1, v2, v3, v4];
-                        // norm = [n1, n2, n3, n4];
+    }
 
-                        normalArray[v1offset] = nx1;
-                        normalArray[v2offset] = nx2;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v1offset + 1] = ny1;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v1offset + 2] = nz1;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v4offset + 2] = nz4;
+    this.render = function(scene, camera, forceClear) {
 
-                        normalArray[v2offset] = nx2;
-                        normalArray[v3offset] = nx3;
-                        normalArray[v4offset] = nx4;
-                        normalArray[v2offset + 1] = ny2;
-                        normalArray[v3offset + 1] = ny3;
-                        normalArray[v4offset + 1] = ny4;
-                        normalArray[v2offset + 2] = nz2;
-                        normalArray[v3offset + 2] = nz3;
-                        normalArray[v4offset + 2] = nz4;
+        if (camera instanceof $3Dmol.Camera === false) {
 
-                        faceArray[faceoffset] = v1 + start;
-                        faceArray[faceoffset + 1] = v2 + start;
-                        faceArray[faceoffset + 2] = v4 + start;
+            console
+                    .error('$3Dmol.Renderer.render: camera is not an instance of $3Dmol.Camera.');
+            return;
 
-                        faceArray[faceoffset + 3] = v2 + start;
-                        faceArray[faceoffset + 4] = v3 + start;
-                        faceArray[faceoffset + 5] = v4 + start;
+        }
 
-                        geoGroup.faceidx += 6;
-                    }
+        var i, il,
 
-                }
-            }
+        webglObject, object, renderList,
 
-        }
+        lights = scene.__lights, fog = scene.fog;
 
-        geoGroup.vertices += n_verts;
-    };
+        // reset caching for this frame
 
-    /** Create a cone 
-     * @function $3Dmol.GLDraw.drawCone
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            from
-     * @param {Point}
-     *            to
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     *            */
-    draw.drawCone = function(geo, from, to, radius, color) {
-        if (!from || !to)
-            return;
+        _currentMaterialId = -1;
+        _lightsNeedUpdate = true;
 
-        color = color || {r:0, g:0, b:0};
+        // update scene graph
 
-        var dir =[to.x, to.y, to.z ];        
-        dir.x -= from.x;
-        dir.y -= from.y;
-        dir.z -= from.z;
+        if (this.autoUpdateScene)
+            scene.updateMatrixWorld();
 
-        var e = getRotationMatrix(dir);
+        // update camera matrices
+        // Pretty sure camera's parent is always going to be undefined for our
+        // purposes...
+        if (camera.parent === undefined)
+            camera.updateMatrixWorld();
 
+        camera.matrixWorldInverse.getInverse(camera.matrixWorld);
 
-        // n vertices around bottom plust the two points
-        var n = basisVectors.length;
-        var basis = basisVectors;
-        var n_verts =  n + 2;
+        _projScreenMatrix.multiplyMatrices(camera.projectionMatrix,
+                camera.matrixWorldInverse);
 
-        
-        //setup geo structures
-        var geoGroup = geo.updateGeoGroup(n_verts);
-        var start = geoGroup.vertices;    
-        var offset, faceoffset;
-        var i, x, y, z;
-        var vertexArray = geoGroup.vertexArray;
-        var normalArray = geoGroup.normalArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        
-        var offset = start*3;
-        var ndir = new $3Dmol.Vector3(dir[0],dir[1],dir[2]).normalize();
-        //base point first vertex
-        vertexArray[offset] = from.x;
-        vertexArray[offset+1] = from.y;
-        vertexArray[offset+2] = from.z;
-        normalArray[offset] = -ndir.x;
-        normalArray[offset + 1] = -ndir.y;
-        normalArray[offset + 2] = -ndir.z;
-        colorArray[offset] = color.r;
-        colorArray[offset + 1] = color.g;
-        colorArray[offset + 2] = color.b;
-        
-        //second vertex top
-        vertexArray[offset+3] = to.x;
-        vertexArray[offset+4] = to.y;
-        vertexArray[offset+5] = to.z;
-        
-        normalArray[offset+3] = ndir.x;
-        normalArray[offset+4] = ndir.y;
-        normalArray[offset+5] = ndir.z;
-        colorArray[offset+3] = color.r;
-        colorArray[offset + 4] = color.g;
-        colorArray[offset + 5] = color.b;
-        
-        offset += 6;
-        
-        // add circle vertices
-        for (i = 0; i < n; ++i) {
-            var vec = basis[i].clone();
-            vec.multiplyScalar(radius);
-            x = e[0] * vec.x + e[3] * vec.y + e[6]
-                    * vec.z;
-            y = e[1] * vec.x + e[4] * vec.y + e[7]
-                    * vec.z;
-            z = e[5] * vec.y + e[8] * vec.z;
+        // update WebGL objects
 
-            // from
-            vertexArray[offset] = x + from.x;
-            vertexArray[offset + 1] = y + from.y;
-            vertexArray[offset + 2] = z + from.z;
+        if (this.autoUpdateObjects)
+            this.initWebGLObjects(scene);
 
-            // normals
-            normalArray[offset] = x;
-            normalArray[offset + 1] = y;
-            normalArray[offset + 2] = z;
+        _this.info.render.calls = 0;
+        _this.info.render.vertices = 0;
+        _this.info.render.faces = 0;
+        _this.info.render.points = 0;
 
-            // colors
-            colorArray[offset] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 2] = color.b;
-            
-            offset += 3;
+        _currentWidth = _viewportWidth;
+        _currentHeight = _viewportHeight;
+
+        if (this.autoClear || forceClear) {
+            this.clear(this.autoClearColor, this.autoClearDepth,
+                    this.autoClearStencil);
 
         }
-        geoGroup.vertices += (n+2);
-        //faces
-        var faceoffset = geoGroup.faceidx;
-        for( i = 0; i < n; i++) {
-            //two neighboring circle vertices
-            var v1 = start+2+i;
-            var v2 = start+2+ ((i+1)%n);
-            
-            faceArray[faceoffset] = v1;
-            faceArray[faceoffset+1] = v2;
-            faceArray[faceoffset+2] = start;
-            faceoffset += 3;
-            faceArray[faceoffset] = v1;
-            faceArray[faceoffset+1] = v2;
-            faceArray[faceoffset+2] = start+1;
-            faceoffset += 3;
-        }
-        geoGroup.faceidx += 6*n;
-    };
 
-    
-    // Sphere component
-    var sphereVertexCache = {
-        cache : {},
-        getVerticesForRadius : function(radius) {
+        // set matrices for regular objects (frustum culled)
 
-            if (typeof (this.cache[radius]) !== "undefined")
-                return this.cache[radius];
+        renderList = scene.__webglObjects;
 
-            var obj = {
-                vertices : [],
-                verticesRows : [],
-                normals : []
-            };
-            // scale quality with radius heuristically
-            var sphereQuality = 1;
-            var widthSegments = 16 * sphereQuality;
-            var heightSegments = 10 * sphereQuality;
-            if (radius < 1) {
-                widthSegments = 10 * sphereQuality;
-                heightSegments = 8 * sphereQuality;
-            }
+        for (i = 0, il = renderList.length; i < il; i++) {
 
-            var phiStart = 0;
-            var phiLength = Math.PI * 2;
+            webglObject = renderList[i];
+            object = webglObject.object;
 
-            var thetaStart = 0;
-            var thetaLength = Math.PI;
+            webglObject.render = false;
 
-            var x, y, vertices = [], uvs = [];
+            if (object.visible) {
+                setupMatrices(object, camera);
+                unrollBufferMaterial(webglObject);
+                webglObject.render = true;
+            }
+        }
 
-            for (y = 0; y <= heightSegments; y++) {
+        // set matrices for immediate objects
 
-                var verticesRow = [];
-                for (x = 0; x <= widthSegments; x++) {
+        var material = null;
 
-                    var u = x / widthSegments;
-                    var v = y / heightSegments;
+        // opaque pass (front-to-back order)
 
-                    var vertex = {};
-                    vertex.x = -radius * Math.cos(phiStart + u * phiLength)
-                            * Math.sin(thetaStart + v * thetaLength);
-                    vertex.y = radius * Math.cos(thetaStart + v * thetaLength);
-                    vertex.z = radius * Math.sin(phiStart + u * phiLength)
-                            * Math.sin(thetaStart + v * thetaLength);
+        this.setBlending(false);
 
-                    var n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
-                    n.normalize();
+        renderObjects(scene.__webglObjects, true, "opaque", camera, lights,
+                fog, false, material);
 
-                    obj.vertices.push(vertex);
-                    obj.normals.push(n);
+        // prime depth buffer
+        renderObjects(scene.__webglObjects, true, "blank", camera, lights, fog,
+                true, material);
 
-                    verticesRow.push(obj.vertices.length - 1);
+        // transparent pass (back-to-front order)
 
-                }
+        renderObjects(scene.__webglObjects, false, "transparent", camera,
+                lights, fog, true, material);
 
-                obj.verticesRows.push(verticesRow);
+        // Render plugins (e.g. sprites), and reset state
 
-            }
+        renderPlugins(this.renderPluginsPost, scene, camera);
 
-            this.cache[radius] = obj;
-            return obj;
-        }
+        // Ensure depth buffer writing is enabled so it can be cleared on next
+        // render
 
-    };
+        this.setDepthTest(true);
+        this.setDepthWrite(true);
 
-    /** Create a sphere.
-     * @function $3Dmol.GLDraw.drawSphere
-     * @param {geometry}
-     *            geo
-     * @param {Point}
-     *            pos
-     * @param {float}
-     *            radius
-     * @param {$3Dmol.Color}
-     *            color
-     */
-    draw.drawSphere = function(geo, pos, radius, color) {
+        // _gl.finish();
 
-        var center = new $3Dmol.Vector3(pos.x, pos.y, pos.z);
+    };
 
-        var x, y;
-        var vobj = sphereVertexCache.getVerticesForRadius(radius);
+    function renderPlugins(plugins, scene, camera) {
 
-        var vertices = vobj.vertices;
-        var normals = vobj.normals;
+        // Reset state once regardless
+        // This should also fix cartoon render bug (after transparent surface
+        // render)
 
-        var geoGroup = geo.updateGeoGroup(vertices.length);
+        _currentGeometryGroupHash = -1;
+        _currentProgram = null;
+        _currentCamera = null;
+        _oldBlending = -1;
+        _oldDepthWrite = -1;
+        _oldDepthTest = -1;
+        _oldDoubleSided = -1;
+        _currentMaterialId = -1;
+        _oldFlipSided = -1;
 
-        var start = geoGroup.vertices;
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        var lineArray = geoGroup.lineArray;
-        var normalArray = geoGroup.normalArray;
+        if (!plugins.length)
+            return;
 
-        for (var i = 0, il = vertices.length; i < il; ++i) {
-            var offset = 3 * (start + i);
-            var v = vertices[i];
+        for (var i = 0, il = plugins.length; i < il; i++) {
 
-            vertexArray[offset] = (v.x + pos.x);
-            vertexArray[offset + 1] = (v.y + pos.y);
-            vertexArray[offset + 2] = (v.z + pos.z);
+            _lightsNeedUpdate = true;
 
-            colorArray[offset] = color.r;
-            colorArray[offset + 1] = color.g;
-            colorArray[offset + 2] = color.b;
+            plugins[i].render(scene, camera, _currentWidth, _currentHeight);
+
+            // Reset state after plugin render
+            _currentGeometryGroupHash = -1;
+            _currentProgram = null;
+            _currentCamera = null;
+            _oldBlending = -1;
+            _oldDepthWrite = -1;
+            _oldDepthTest = -1;
+            _oldDoubleSided = -1;
+            _currentMaterialId = -1;
+            _oldFlipSided = -1;
 
         }
 
-        geoGroup.vertices += vertices.length;
+    }
 
-        var verticesRows = vobj.verticesRows;
-        var h = verticesRows.length - 1;
+    this.initWebGLObjects = function(scene) {
 
-        for (y = 0; y < h; y++) {
-            var w = verticesRows[y].length - 1;
-            for (x = 0; x < w; x++) {
+        if (!scene.__webglObjects) {
 
-                var faceoffset = geoGroup.faceidx, lineoffset = geoGroup.lineidx;
+            scene.__webglObjects = [];
+            scene.__webglObjectsImmediate = [];
+            scene.__webglSprites = [];
+            scene.__webglFlares = [];
 
-                var v1 = verticesRows[y][x + 1] + start, v1offset = v1 * 3;
-                var v2 = verticesRows[y][x] + start, v2offset = v2 * 3;
-                var v3 = verticesRows[y + 1][x] + start, v3offset = v3 * 3;
-                var v4 = verticesRows[y + 1][x + 1] + start, v4offset = v4 * 3;
+        }
 
-                var n1 = normals[v1 - start];
-                var n2 = normals[v2 - start];
-                var n3 = normals[v3 - start];
-                var n4 = normals[v4 - start];
-                var face, norm;
-                if (Math.abs(vertices[v1 - start].y) === radius) {
-                    // face = [v1, v3, v4];
-                    // norm = [n1, n3, n4];
+        // Add objects; this sets up buffers for each geometryGroup
+        if (scene.__objectsAdded.length) {
 
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v3offset + 2] = n3.z;
-                    normalArray[v4offset + 2] = n4.z;
+            while (scene.__objectsAdded.length) {
+                addObject(scene.__objectsAdded[0], scene);
+                scene.__objectsAdded.splice(0, 1);
+            }
 
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v3;
-                    faceArray[faceoffset + 2] = v4;
+            // Force buffer update during render
+            // Hackish fix for initial cartoon-render-then-transparent-surface
+            // bug
+            _currentGeometryGroupHash = -1;
 
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v3;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v4;
-                    lineArray[lineoffset + 4] = v3;
-                    lineArray[lineoffset + 5] = v4;
+        }
 
-                    geoGroup.faceidx += 3;
-                    geoGroup.lineidx += 6;
+        while (scene.__objectsRemoved.length) {
 
-                } else if (Math.abs(vertices[v3 - start].y) === radius) {
-                    // face = [v1, v2, v3];
-                    // norm = [n1, n2, n3];
+            removeObject(scene.__objectsRemoved[0], scene);
+            scene.__objectsRemoved.splice(0, 1);
 
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v3offset + 2] = n3.z;
+        }
 
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v2;
-                    faceArray[faceoffset + 2] = v3;
+        // update must be called after objects adding / removal
+        // This sends typed arrays to GL buffers for each geometryGroup
+        for (var o = 0, ol = scene.__webglObjects.length; o < ol; o++) {
 
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v2;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v3;
-                    lineArray[lineoffset + 4] = v2;
-                    lineArray[lineoffset + 5] = v3;
+            updateObject(scene.__webglObjects[o].object);
 
-                    geoGroup.faceidx += 3;
-                    geoGroup.lineidx += 6;
+        }
 
-                } else {
-                    // face = [v1, v2, v3, v4];
-                    // norm = [n1, n2, n3, n4];
+    };
 
-                    normalArray[v1offset] = n1.x;
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v1offset + 1] = n1.y;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v1offset + 2] = n1.z;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v4offset + 2] = n4.z;
+    // Objects adding
 
-                    normalArray[v2offset] = n2.x;
-                    normalArray[v3offset] = n3.x;
-                    normalArray[v4offset] = n4.x;
-                    normalArray[v2offset + 1] = n2.y;
-                    normalArray[v3offset + 1] = n3.y;
-                    normalArray[v4offset + 1] = n4.y;
-                    normalArray[v2offset + 2] = n2.z;
-                    normalArray[v3offset + 2] = n3.z;
-                    normalArray[v4offset + 2] = n4.z;
+    function addObject(object, scene) {
 
-                    faceArray[faceoffset] = v1;
-                    faceArray[faceoffset + 1] = v2;
-                    faceArray[faceoffset + 2] = v4;
+        var g, gl, geometry, material, geometryGroup;
 
-                    faceArray[faceoffset + 3] = v2;
-                    faceArray[faceoffset + 4] = v3;
-                    faceArray[faceoffset + 5] = v4;
+        if (!object.__webglInit) {
 
-                    lineArray[lineoffset] = v1;
-                    lineArray[lineoffset + 1] = v2;
-                    lineArray[lineoffset + 2] = v1;
-                    lineArray[lineoffset + 3] = v4;
+            object.__webglInit = true;
 
-                    lineArray[lineoffset + 4] = v2;
-                    lineArray[lineoffset + 5] = v3;
-                    lineArray[lineoffset + 6] = v3;
-                    lineArray[lineoffset + 7] = v4;
+            object._modelViewMatrix = new $3Dmol.Matrix4();
+            object._normalMatrix = new $3Dmol.Matrix3();
 
-                    geoGroup.faceidx += 6;
-                    geoGroup.lineidx += 8;
+            if (object.geometry !== undefined
+                    && object.geometry.__webglInit === undefined) {
 
-                }
+                object.geometry.__webglInit = true;
+                object.geometry.addEventListener('dispose', onGeometryDispose);
 
             }
-        }
-
-    };
-
-    return draw;
 
-})();// A model is a collection of related atoms.  Bonds are only allowed between
-//atoms in the same model.  An atom is uniquely specified by its model id and
-//its serial number.
-//A glmodel knows how to apply the styles on each atom to create a gl object
+            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
+                geometry = object.geometry;
+                material = object.material;
 
-var $3Dmol = $3Dmol || {};
+                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
 
-/**
- * GLModel represents a group of related atoms
- * @constructor 
- * @param {number=} mid 
- * @param {Object=} defaultcolors Object defining default atom colors as atom => color property value pairs
- * @see $3Dmol.download
- */
-$3Dmol.GLModel = (function() {
+                    geometryGroup = geometry.geometryGroups[g];
 
-    // class variables go here
-    var defaultAtomStyle = {
-        line : {}
-    };
+                    geometryGroup.id = _geometryGroupCounter++;
 
-    var Nucleotides = [ '  G', '  A', '  T', '  C', '  U', ' DG', ' DA', ' DT',
-            ' DC', ' DU' ];
+                    // initialise VBO on the first access
 
-    var defaultlineWidth = 1.0;
+                    if (!geometryGroup.__webglVertexBuffer) {
 
-    // Reference: A. Bondi, J. Phys. Chem., 1964, 68, 441.
-    var vdwRadii = {
-        "H" : 1.2,
-        "Li" : 1.82,
-        "LI" : 1.82,
-        "Na" : 2.27,
-        "NA" : 2.27,
-        "K" : 2.75,
-        "C" : 1.7,
-        "N" : 1.55,
-        "O" : 1.52,
-        "F" : 1.47,
-        "P" : 1.80,
-        "S" : 1.80,
-        "CL" : 1.75,
-        "Cl" : 1.75,
-        "BR" : 1.85,
-        "Br" : 1.85,
-        "SE" : 1.90,
-        "Se" : 1.90,
-        "ZN" : 1.39,
-        "Zn" : 1.39,
-        "CU" : 1.4,
-        "Cu" : 1.4,
-        "NI" : 1.63,
-        "Ni" : 1.63
-    };
+                        if (object instanceof $3Dmol.Mesh) {
+                            createMeshBuffers(geometryGroup);
+                            geometry.elementsNeedUpdate = true;
+                            geometry.normalsNeedUpdate = true;
+                        }
 
-    // class functions
+                        else if (object instanceof $3Dmol.Line)
+                            createLineBuffers(geometryGroup);
 
-    // return true if a and b represent the same style
-    var sameObj = function(a,b) {
-        if(a && b)
-            return JSON.stringify(a) == JSON.stringify(b);
-        else
-            return a == b;
-    };    
+                        geometry.verticesNeedUpdate = true;
+                        geometry.colorsNeedUpdate = true;
 
-   
-    function GLModel(mid, defaultcolors) {
-        // private variables
-        var atoms = [];
-        var id = mid;
-        var molObj = null;
-        var renderedMolObj = null;
-        var lastColors = null;
-        var copyMatrices = []; //transformation + rot matrices
-        var idMatrix = new $3Dmol.Matrix4();
-        idMatrix.identity();
-        var noAssembly;
-        var dontDuplicateAtoms;
-        
-        var defaultColor = $3Dmol.elementColors.defaultColor;
-        
-        var ElementColors = (defaultcolors) ? defaultcolors : $3Dmol.elementColors.defaultColors;
+                    }
 
+                }
 
-        // drawing functions must be associated with model object since
-        // geometries can't span multiple canvases
+            }
 
-        // sphere drawing
-        var defaultSphereRadius = 1.5;
+        }
 
-        // return proper radius for atom given style
-        /** 
-         * 
-         * @param {AtomSpec} atom
-         * @param {atomstyle} style
-         * @return {number} 
-         * 
-         */
-        var getRadiusFromStyle = function(atom, style) {
-            var r = defaultSphereRadius;
-            if (typeof (style.radius) != "undefined")
-                r = style.radius;
-            else if (vdwRadii[atom.elem])
-                r = vdwRadii[atom.elem];
+        if (!object.__webglActive) {
 
-            if (typeof (style.scale) != "undefined")
-                r *= style.scale;
-            return r;
-        };
+            if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
 
-        // cross drawing
-        /** @typedef CrossStyleSpec
-         * @prop {boolean} hidden - do not show 
-         * @prop {number} linewidth 
-         * @prop {number} radius 
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        /**
-         * 
-         * @param {AtomSpec} atom
-         * @param {$3Dmol.Geometry[]} geos
-         */
-        var drawAtomCross = function(atom, geos) {
-            if (!atom.style.cross)
-                return;
-            var style = atom.style.cross;
-            if (style.hidden)
-                return;
-            var linewidth = (style.linewidth || defaultlineWidth);
-            if (!geos[linewidth])
-                geos[linewidth] = new $3Dmol.Geometry();
-                
-            var geoGroup = geos[linewidth].updateGeoGroup(6);
-            
-            var delta = getRadiusFromStyle(atom, style);
+                geometry = object.geometry;
 
-            var points = [ [ delta, 0, 0 ], [ -delta, 0, 0 ], [ 0, delta, 0 ],
-                    [ 0, -delta, 0 ], [ 0, 0, delta ], [ 0, 0, -delta ] ];
+                for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
+                    geometryGroup = geometry.geometryGroups[g];
 
-            var clickable = atom.clickable;
-            if (clickable && atom.intersectionShape === undefined)
-                atom.intersectionShape = {sphere : [], cylinder : [], line : []};
-            
-            var c = $3Dmol.getColorFromStyle(atom, style);
-            
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            
-            for ( var j = 0; j < 6; j++) {
-                
-                var offset = geoGroup.vertices*3;
-                
-                geoGroup.vertices++;
-                vertexArray[offset] = atom.x + points[j][0];
-                vertexArray[offset+1] = atom.y + points[j][1];
-                vertexArray[offset+2] = atom.z + points[j][2];
-                colorArray[offset] = c.r;
-                colorArray[offset+1] = c.g;
-                colorArray[offset+2] = c.b;
-                
-                if (clickable){
-                    var point = new $3Dmol.Vector3(points[j][0], points[j][1], points[j][2]);
-                    
-                    //decrease cross size for selection to prevent misselection from atom overlap
-                    point.multiplyScalar(0.1);
-                    point.set(point.x+atom.x, point.y+atom.y, point.z+atom.z);
-                    atom.intersectionShape.line.push(point);
+                    addBuffer(scene.__webglObjects, geometryGroup, object);
                 }
 
             }
-                        
-        };
 
-        //from atom, return a normalized vector v that is orthogonal and along which
-        //it is appropraite to draw multiple bonds
-        var getSideBondV = function(atom, atom2, i) {
+            // Sprite
+            else if (object instanceof $3Dmol.Sprite)
+                scene.__webglSprites.push(object);
 
-            var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-            var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
+            object.__webglActive = true;
 
-            var dir = p2.clone();
-            var v = null;
-            dir.sub(p1);
+        }
 
-            var p1a, p1b, p2a, p2b;
-            var i2, j2, atom3, p3, dir2;
-            if (atom.bonds.length === 1) {
-                if (atom2.bonds.length === 1) {
-                    v = dir.clone();
-                    if (Math.abs(v.x) > 0.0001)
-                        v.y += 1;
-                    else
-                        v.x += 1;
-                } else {
-                    i2 = (i + 1) % atom2.bonds.length;
-                    j2 = atom2.bonds[i2];
-                    atom3 = atoms[j2];
-                    p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+    }
 
-                    dir2 = p3.clone();
-                    dir2.sub(p1);
+    function updateObject(object) {
 
-                    v = dir2.clone();
-                    v.cross(dir);
-                }
-            } else {
-                // get vector 2 different neighboring atom
-                i2 = (i + 1) % atom.bonds.length;
-                j2 = atom.bonds[i2];
-                atom3 = atoms[j2];
-                p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+        var geometry = object.geometry, material = object.material, geometryGroup, customAttributesDirty;
 
-                dir2 = p3.clone();
-                dir2.sub(p1);
+        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line) {
 
-                v = dir2.clone();
-                v.cross(dir);
-            }
+            for (var g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {
 
-            // especially for C#C (triple bond) dir and dir2
-            // may be opposites resulting in a zero v
-            if (v.lengthSq() < 0.01) {
-                v = dir.clone();
-                if (Math.abs(v.x) > 0.0001)
-                    v.y += 1;
-                else
-                    v.x += 1;
+                geometryGroup = geometry.geometryGroups[g];
+
+                if (geometry.verticesNeedUpdate || geometry.elementsNeedUpdate
+                        || geometry.colorsNeedUpdate
+                        || geometry.normalsNeedUpdate) {
+                    setBuffers(geometryGroup, _gl.STATIC_DRAW);
+                }
             }
 
-            v.cross(dir);
-            v.normalize();
-            
-            return v;
-            
-            v.multiplyScalar(r * 1.5);
+            geometry.verticesNeedUpdate = false;
+            geometry.elementsNeedUpdate = false;
+            geometry.normalsNeedUpdate = false;
+            geometry.colorsNeedUpdate = false;
+
+            geometry.buffersNeedUpdate = false;
 
         }
-        
-        var getTripleBondPoints = function() {
-            
-            v.cross(dir);
-            v.normalize();
-            v.multiplyScalar(r * 3);
 
-            p1a = p1.clone();
-            p1a.add(v);
-            p1b = p1.clone();
-            p1b.sub(v);
+    }
 
-            p2a = p1a.clone();
-            p2a.add(dir);
-            p2b = p1b.clone();
-            p2b.add(dir);
-        }
-        
-        var addLine = function(vertexArray, colorArray, offset, p1, p2, c1) {
-            //make line from p1 to p2, does not incremeant counts
-            vertexArray[offset] = p1.x; vertexArray[offset+1] = p1.y; vertexArray[offset+2] = p1.z;
-            colorArray[offset] = c1.r; colorArray[offset+1] = c1.g; colorArray[offset+2] = c1.b;
-            vertexArray[offset+3] = p2.x; vertexArray[offset+4] = p2.y; vertexArray[offset+5] = p2.z;
-            colorArray[offset+3] = c1.r; colorArray[offset+4] = c1.g; colorArray[offset+5] = c1.b;            
-        }
-        
-        /**@typedef LineStyleSpec
-         * @prop {boolean} hidden - do not show line
-         * @prop {number} linewidth 
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        // bonds - both atoms must match bond style
-        // standardize on only drawing for lowest to highest
-        /**
-         * 
-         * @param {AtomSpec}
-         *            atom
-         * @param {AtomSpec[]} atoms
-         * @param {$3Dmol.Geometry[]} geos
-         */
-        var drawBondLines = function(atom, atoms, geos) {
-            if (!atom.style.line)
-                return;
-            var style = atom.style.line;
-            if (style.hidden)
-                return;
+    function removeObject(object, scene) {
 
-            // have a separate geometry for each linewidth
-            var linewidth = (style.linewidth || defaultlineWidth);
+        if (object instanceof $3Dmol.Mesh || object instanceof $3Dmol.Line)
+            removeInstances(scene.__webglObjects, object);
 
-            if (!geos[linewidth])
-                geos[linewidth] = new $3Dmol.Geometry();
-            /** @type {geometryGroup} */
-            var geoGroup = geos[linewidth].updateGeoGroup(2*atom.bonds.length);
-            
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            
-            for ( var i = 0; i < atom.bonds.length; i++) {
-                var j = atom.bonds[i]; // our neighbor
-                
-                var atom2 = atoms[j];
-                if (!atom2.style.line)
-                    continue; // don't sweat the details
+        else if (object instanceof $3Dmol.Sprite)
+            removeInstancesDirect(scene.__webglSprites, object);
 
-                if (atom.serial >= atom2.serial) // only draw if less, this way we can do multi bonds correctly
-                    continue;
-                var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);                
-                var mp = p1.clone().add(p2).multiplyScalar(0.5);
-                var singleBond = false;               
-                
-                if (atom.clickable){
-                    if (atom.intersectionShape === undefined)
-                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                    atom.intersectionShape.line.push(p1);
-                    atom.intersectionShape.line.push(p2);
-                }
+        object.__webglActive = false;
 
-                if (atom2.clickable){
-                    if (atom2.intersectionShape === undefined)
-                        atom2.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                    atom2.intersectionShape.line.push(p2);
-                    atom2.intersectionShape.line.push(p1);
-                }
+    }
 
-                var c1 = $3Dmol.getColorFromStyle(atom, atom.style.line);
-                var c2 = $3Dmol.getColorFromStyle(atom2, atom2.style.line);
-               
-                if(atom.bondStyles && atom.bondStyles[i]) {
-                    var bstyle = atom.bondStyles[i];
-                    if(!bstyle.iswire) {
-                        continue;
-                    }
-                    if(bstyle.radius) bondR = bstyle.radius;
-                    if(bstyle.singleBond) singleBond = true;
-                    if(typeof(bstyle.color1) != "undefined") {
-                        c1 = $3Dmol.CC.color(bstyle.color1);
-                    }
-                    if(typeof(bstyle.color2) != "undefined") {
-                        c2 = $3Dmol.CC.color(bstyle.color2);
-                    }
-                }
+    function removeInstances(objList, object) {
 
-                var offset = geoGroup.vertices*3;
-                
-                if(atom.bondOrder[i] > 1 && atom.bondOrder[i] < 4 && !singleBond) {
-                    var v = getSideBondV(atom, atom2, i);
-                    var dir = p2.clone();
-                    dir.sub(p1);
-                    
-                    if(atom.bondOrder[i] == 2) { //double
-                        
-                        v.multiplyScalar(.1);
-                           p1a = p1.clone();
-                        p1a.add(v);
-                        p1b = p1.clone();
-                        p1b.sub(v);
+        for (var o = objList.length - 1; o >= 0; --o) {
 
-                        p2a = p1a.clone();
-                        p2a.add(dir);
-                        p2b = p1b.clone();
-                        p2b.add(dir);
-                        
-                        if(c1 == c2) {
-                            geoGroup.vertices += 4;
-                            addLine(vertexArray, colorArray, offset, p1a, p2a, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, p1b, p2b, c1);                            
-                        }
-                        else {
-                            geoGroup.vertices += 8;
-                            dir.multiplyScalar(0.5);
-                            var mpa = p1a.clone();
-                            mpa.add(dir);
-                            var mpb = p1b.clone();
-                            mpb.add(dir);
-                            
-                            addLine(vertexArray, colorArray, offset, p1a, mpa, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, mpa, p2a, c2);                            
-                            addLine(vertexArray, colorArray, offset+12, p1b, mpb, c1); 
-                            addLine(vertexArray, colorArray, offset+18, mpb, p2b, c2); 
-                        }
-                    }
-                    else if(atom.bondOrder[i] == 3) { //triple
-                        
-                        v.multiplyScalar(.1);
-                           p1a = p1.clone();
-                        p1a.add(v);
-                        p1b = p1.clone();
-                        p1b.sub(v);
+            if (objList[o].object === object)
+                objList.splice(o, 1);
 
-                        p2a = p1a.clone();
-                        p2a.add(dir);
-                        p2b = p1b.clone();
-                        p2b.add(dir);
-                        
-                        if(c1 == c2) {
-                            geoGroup.vertices += 6;
-                            addLine(vertexArray, colorArray, offset, p1, p2, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, p1a, p2a, c1);                            
-                            addLine(vertexArray, colorArray, offset+12, p1b, p2b, c1);                            
-                        }
-                        else {
-                            geoGroup.vertices += 12;
-                            dir.multiplyScalar(0.5);
-                            var mpa = p1a.clone();
-                            mpa.add(dir);
-                            var mpb = p1b.clone();
-                            mpb.add(dir);
+        }
+    }
 
-                            addLine(vertexArray, colorArray, offset, p1, mp, c1);                            
-                            addLine(vertexArray, colorArray, offset+6, mp, p2, c2);
-                            addLine(vertexArray, colorArray, offset+12, p1a, mpa, c1);                            
-                            addLine(vertexArray, colorArray, offset+18, mpa, p2a, c2);                            
-                            addLine(vertexArray, colorArray, offset+24, p1b, mpb, c1); 
-                            addLine(vertexArray, colorArray, offset+30, mpb, p2b, c2); 
-                        }
-                    }
-                }
-                else { //single bond                                    
-                    if(c1 == c2) {
-                        geoGroup.vertices += 2;
-                        addLine(vertexArray, colorArray, offset, p1, p2, c1);
-                    } else {
-                        geoGroup.vertices += 4;
-                        addLine(vertexArray, colorArray, offset, p1, mp, c1);
-                        addLine(vertexArray, colorArray, offset+6, mp, p2, c2);                        
-                    }
-                    
-                }
-            }
+    function removeInstancesDirect(objList, object) {
 
-        };
+        for (var o = objList.length - 1; o >= 0; --o) {
 
-        // bonds as cylinders
-        var defaultStickRadius = 0.25;
+            if (objList[o] === object)
+                objList.splice(o, 1);
 
-        /**@typedef SphereStyleSpec
-         * @prop {boolean} hidden - do not show atom
-         * @prop {number} radius - override van der waals radius
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        //sphere drawing
-        //See also: drawCylinder
-        /** 
-         * 
-         * @param {AtomSpec} atom
-         * @param {$3Dmol.Geometry} geo
-         */
-        var drawAtomSphere = function(atom, geo) {
-            
-            if (!atom.style.sphere)
-                return;
-            var style = atom.style.sphere;
-            if (style.hidden)
-                return;
-                                                                 
-            var C = $3Dmol.getColorFromStyle(atom, style);
-            
-            var x, y;
-            var radius = getRadiusFromStyle(atom, style);
-            
-            if ((atom.clickable === true) && (atom.intersectionShape !== undefined)) {
-                var center = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                atom.intersectionShape.sphere.push(new $3Dmol.Sphere(center, radius));
-            }
-            
-            $3Dmol.GLDraw.drawSphere(geo, atom, radius, C);    
-            
-        };
-        
-        //dkoes - test code for sphere imposters
-        var drawAtomImposter = function(atom, geo) {
-            
-            if (!atom.style.spherei)
-                return;
-            var style = atom.style.spherei;
-            if (style.hidden)
-                return;
-            
-            var radius = getRadiusFromStyle(atom, style);
-            var C = $3Dmol.getColorFromStyle(atom, style);
-            
-            //create flat square                       
-            
-            var geoGroup = geo.updateGeoGroup(4);
-            var startv =  geoGroup.vertices;
-            var start = startv*3;
-            var vertexArray = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            
-            //use center point for each vertex
-            for(var i = 0; i < 4; i++) {
-                vertexArray[start+3*i] = atom.x;
-                vertexArray[start+3*i+1] = atom.y ;
-                vertexArray[start+3*i+2] = atom.z;                           
-            }
-            
+        }
+    }
 
-            //same colors for all 4 vertices
-            var normalArray = geoGroup.normalArray;
-            var colorArray = geoGroup.colorArray;
-            for(var i = 0; i < 4; i++) {
-                colorArray[start+3*i] = C.r;
-                colorArray[start+3*i+1] = C.g;
-                colorArray[start+3*i+2] = C.b;
-                
+    function unrollBufferMaterial(globject) {
+
+        var object = globject.object;
+        var material = object.material;
+
+        if (material.transparent) {
+            globject.opaque = null;
+            globject.transparent = material;
+            if (!material.wireframe) {
+                var blankMaterial = material.clone();
+                blankMaterial.opacity = 0.0;
+                globject.blank = blankMaterial;
             }
-            
-            normalArray[start+0] = -radius;
-            normalArray[start+1] = -radius;
-            normalArray[start+2] = 0;
-            
-            normalArray[start+3] = -radius;
-            normalArray[start+4] = radius;
-            normalArray[start+5] = 0;
-            
-            normalArray[start+6] = radius;
-            normalArray[start+7] = radius;
-            normalArray[start+8] = 0;
-            
-            normalArray[start+9] = radius;
-            normalArray[start+10] = -radius;
-            normalArray[start+11] = 0;
-            
-            geoGroup.vertices += 4;
-            
-            //two faces
-            var faceArray = geoGroup.faceArray;
-            var faceoffset = geoGroup.faceidx; //not number faces, but index
-            faceArray[faceoffset+0] = startv;
-            faceArray[faceoffset+1] = startv+1;
-            faceArray[faceoffset+2] = startv+2;
-            faceArray[faceoffset+3] = startv+2;
-            faceArray[faceoffset+4] = startv+3;
-            faceArray[faceoffset+5] = startv;
-            geoGroup.faceidx += 6;
-            
-        };
-                
-           
-        /**@typedef StickStyleSpec
-         * @prop {boolean} hidden - do not show 
-         * @prop {number} radius 
-         * @prop {boolean} singleBonds - draw all bonds as single bonds if set
-         * @prop {string} colorscheme - element based coloring
-         * @prop {string} color - fixed coloring, overrides colorscheme
-         */
-        
-        // draws cylinders and small spheres (at bond radius)
-        var drawBondSticks = function(atom, atoms, geo) {
-            if (!atom.style.stick)
-                return;
-            var style = atom.style.stick;
-            if (style.hidden)
-                return;
+        }
 
-            var atomBondR = style.radius || defaultStickRadius;
-            var bondR = atomBondR;
-            var atomSingleBond = style.singleBonds || false;
-            var fromCap = false, toCap = false;
+        else {
+            globject.opaque = material;
+            globject.transparent = null;
 
-            var C1 = $3Dmol.getColorFromStyle(atom, style);
+        }
 
-            var mp, mp1, mp2;
-            
-            if (!atom.capDrawn && atom.bonds.length < 4)
-                fromCap = true;              
-                
-            for (var i = 0; i < atom.bonds.length; i++) {
-                var j = atom.bonds[i]; // our neighbor
-                var atom2 = atoms[j]; //parsePDB, etc should only add defined bonds
-                
-                if (atom.serial < atom2.serial) {// only draw if less, this
-                    // lets us combine
-                    // cylinders of the same
-                    // color
-                    var style2 = atom2.style;
-                    if (!style2.stick)
-                        continue; // don't sweat the details                     
-                   
-                    var C2 = $3Dmol.getColorFromStyle(atom2, style2.stick);
-                    
-                    //support bond specific styles
-                    bondR = atomBondR;                    
-                    var singleBond = atomSingleBond;
-                    if(atom.bondStyles && atom.bondStyles[i]) {
-                        var bstyle = atom.bondStyles[i];
-                        if(bstyle.iswire) {
-                            continue;
-                        }
-                        if(bstyle.radius) bondR = bstyle.radius;
-                        if(bstyle.singleBond) singleBond = true;
-                        if(typeof(bstyle.color1) != "undefined") {
-                            C1 = $3Dmol.CC.color(bstyle.color1);
-                        }
-                        if(typeof(bstyle.color2) != "undefined") {
-                            C2 = $3Dmol.CC.color(bstyle.color2);
-                        }
-                    }
-                    var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
-                    var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
+    }
 
-                    // draw cylinders
-                    if (atom.bondOrder[i] === 1 || singleBond) {
+    function setBuffers(geometryGroup, hint, line) {
 
-                        if (!atom2.capDrawn && atom2.bonds.length < 4)
-                            toCap = true;       
-                                                
-                        if (C1 != C2) {
-                            mp = new $3Dmol.Vector3().addVectors(p1, p2)
-                                    .multiplyScalar(0.5);
-                            $3Dmol.GLDraw.drawCylinder(geo, p1, mp, bondR, C1, fromCap, false);
-                            $3Dmol.GLDraw.drawCylinder(geo, mp, p2, bondR, C2, false, toCap);
-                        } else {
-                            $3Dmol.GLDraw.drawCylinder(geo, p1, p2, bondR, C1, fromCap, toCap);
-                        }
-                        
-                        if (atom.clickable || atom2.clickable) {
-                            mp = new $3Dmol.Vector3().addVectors(p1, p2).multiplyScalar(0.5);
-                            if (atom.clickable){
-                                var cylinder1 = new $3Dmol.Cylinder(p1 , mp , bondR);
-                                var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                atom.intersectionShape.cylinder.push(cylinder1);   
-                                atom.intersectionShape.sphere.push(sphere1);                             
-                            }
-                            if (atom2.clickable){
-                                var cylinder2 = new $3Dmol.Cylinder(p2 , mp , bondR);
-                                var sphere2 = new $3Dmol.Sphere(p2 , bondR);
-                                atom2.intersectionShape.cylinder.push(cylinder2);
-                                atom2.intersectionShape.sphere.push(sphere2);
-                            }
+        var vertexArray = geometryGroup.vertexArray;
+        var colorArray = geometryGroup.colorArray;
 
-                        }
-                        
-                    } 
-                    
-                    else if (atom.bondOrder[i] > 1) {
-                        var mfromCap = false; mtoCap = false; //multi bond caps
-                        
-                        if(bondR != atomBondR) {
-                            //assume jmol style multiple bonds - the radius doesn't fit within atom sphere
-                            mfromCap = true;
-                            mtoCap = true;
-                        }
-                        
-                        var dir = p2.clone();
-                        var v = null;
-                        dir.sub(p1);
-                        
-                        var r, p1a, p1b, p2a, p2b;
-                        var v = getSideBondV(atom, atom2, i);
-                        
-                        if (atom.bondOrder[i] == 2) {
-                            var r = bondR/2.5;
-                            var v = getSideBondV(atom, atom2, i);
-                            
-                            v.multiplyScalar(r*1.5);
-                            p1a = p1.clone();
-                            p1a.add(v);
-                            p1b = p1.clone();
-                            p1b.sub(v);
+        // offset buffers
+        if (geometryGroup.__webglOffsetBuffer !== undefined ) {
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglOffsetBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, vertexArray, hint);
+        }
+        else {
+            //normal, non-instanced case
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglVertexBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, vertexArray, hint);            
+        }
+        // color buffers
+        _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglColorBuffer);
+        _gl.bufferData(_gl.ARRAY_BUFFER, colorArray, hint);
 
-                            p2a = p1a.clone();
-                            p2a.add(dir);
-                            p2b = p1b.clone();
-                            p2b.add(dir);
+        // normal buffers
+        if (geometryGroup.normalArray
+                && geometryGroup.__webglNormalBuffer !== undefined) {
+            var normalArray = geometryGroup.normalArray;
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglNormalBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, normalArray, hint);
 
-                                                                 
-                            if (C1 != C2) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, mp, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp, p2a, r, C2, false, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, mp2, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp2, p2b, r, C2, false, mtoCap);
-                            } else {
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
-                            }
-                            if (atom.clickable || atom2.clickable){
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                               .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                                .multiplyScalar(0.5);
-                                if (atom.clickable) {
-                                    cylinder1a = new $3Dmol.Cylinder(p1a , mp , r);
-                                    cylinder1b = new $3Dmol.Cylinder(p1b , mp2 , r);
-                                    atom.intersectionShape.cylinder.push(cylinder1a);
-                                    atom.intersectionShape.cylinder.push(cylinder1b);
-                                    
-                                    var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                    atom.intersectionShape.sphere.push(sphere1);                             
-                                }
-                                if (atom2.clickable) {
-                                    cylinder2a = new $3Dmol.Cylinder(p2a , mp , r);
-                                    cylinder2b = new $3Dmol.Cylinder(p2b , mp2 , r);
-                                    atom2.intersectionShape.cylinder.push(cylinder2a);
-                                    atom2.intersectionShape.cylinder.push(cylinder2b);          
-                                    var sphere2 = new $3Dmol.Sphere(p2, bondR);
-                                    atom2.intersectionShape.sphere.push(sphere1);  
-                                }
-                            }
-                        } 
-                        else if (atom.bondOrder[i] == 3) {
-                            r = bondR / 4;
-                            v.cross(dir);
-                            v.normalize();
-                            v.multiplyScalar(r * 3);
+        }
 
-                            p1a = p1.clone();
-                            p1a.add(v);
-                            p1b = p1.clone();
-                            p1b.sub(v);
 
-                            p2a = p1a.clone();
-                            p2a.add(dir);
-                            p2b = p1b.clone();
-                            p2b.add(dir);
 
-                            if (C1 != C2) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
-                                        .multiplyScalar(0.5);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, mp, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp, p2a, r, C2, false, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1, mp3, r, C1, fromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp3, p2, r, C2, false, toCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, mp2, r, C1, mfromCap, false);
-                                $3Dmol.GLDraw.drawCylinder(geo, mp2, p2b, r, C2, false, mtoCap);
-                            } else {
-                                $3Dmol.GLDraw.drawCylinder(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1, p2, r, C1, fromCap, toCap);
-                                $3Dmol.GLDraw.drawCylinder(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
+        // radius buffers
+        if (geometryGroup.radiusArray
+                && geometryGroup.__webglRadiusBuffer !== undefined) {
+            _gl.bindBuffer(_gl.ARRAY_BUFFER, geometryGroup.__webglRadiusBuffer);
+            _gl.bufferData(_gl.ARRAY_BUFFER, geometryGroup.radiusArray, hint);
+        }
 
-                            }
-                            if (atom.clickable || atom2.clickable) {
-                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
-                                        .multiplyScalar(0.5);
-                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
-                                        .multiplyScalar(0.5);
-                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
-                                        .multiplyScalar(0.5);
-                                                                
-                                if (atom.clickable) {
-                                    cylinder1a = new $3Dmol.Cylinder(p1a.clone(), mp.clone(), r);
-                                    cylinder1b = new $3Dmol.Cylinder(p1b.clone(), mp2.clone(), r);
-                                    cylinder1c = new $3Dmol.Cylinder(p1.clone(), mp3.clone(), r);
-                                    atom.intersectionShape.cylinder.push(cylinder1a);
-                                    atom.intersectionShape.cylinder.push(cylinder1b);
-                                    atom.intersectionShape.cylinder.push(cylinder1c);
-                                    var sphere1 = new $3Dmol.Sphere(p1 , bondR);
-                                    atom.intersectionShape.sphere.push(sphere1);  
-                                } 
-                                if (atom2.clickable) {                               
-                                    cylinder2a = new $3Dmol.Cylinder(p2a.clone(), mp.clone(), r);
-                                    cylinder2b = new $3Dmol.Cylinder(p2b.clone(), mp2.clone(), r);
-                                    cylinder2c = new $3Dmol.Cylinder(p2.clone(), mp3.clone(), r);
-                                    atom2.intersectionShape.cylinder.push(cylinder2a);
-                                    atom2.intersectionShape.cylinder.push(cylinder2b);
-                                    atom2.intersectionShape.cylinder.push(cylinder2c);      
-                                    var sphere1 = new $3Dmol.Sphere(p2 , bondR);
-                                    atom2.intersectionShape.sphere.push(sphere1);  
-                                }
-                            }
-                        }
-                    }
-                     
-                }                   
-                                 
-            }            
+        // face (index) buffers
+        if (geometryGroup.faceArray
+                && geometryGroup.__webglFaceBuffer !== undefined) {
+            var faceArray = geometryGroup.faceArray;
+            _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                    geometryGroup.__webglFaceBuffer);
+            _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER, faceArray, hint);
 
-            // draw non bonded heteroatoms as spheres
-            var drawSphere = false;
-            var numsinglebonds = 0;
-            var differentradii = false;
-            //also, if any bonds were drawn as multiples, need sphere
-            for(var i = 0; i < atom.bonds.length; i++) {
-                var singleBond = atomSingleBond;
-                if(atom.bondStyles && atom.bondStyles[i]) {
-                    var bstyle = atom.bondStyles[i];
-                    if(bstyle.singleBond) singleBond = true;
-                    if(bstyle.radius && bstyle.radius != atomBondR) {
-                        differentradii = true;
-                    }
-                }
-                if(singleBond || atom.bondOrder[i] == 1) {
-                    numsinglebonds++;
-                }
-            }
-            
-            if(differentradii) { //jmol style double/triple bonds - no sphere
-                if(numsinglebonds > 0) drawSphere = true; //unless needed as a cap
-            }
-            else if(numsinglebonds == 0 && atom.bonds.length > 0) {
-                drawSphere = true;
-            }
-           
-            if (drawSphere) {
-                var savedstyle = atom.style;
-                bondR = atomBondR;
-                //do not use bond style as this can be variable, particularly
-                //with jmol export of double/triple bonds
-                $3Dmol.GLDraw.drawSphere(geo, atom, bondR, C1);    
-            }
-            
-        };
+        }
 
-        // go through all the atoms and regenerate their geometries
-        // we try to have one geometry for each style since this is much much
-        // faster
-        // at some point we should optimize this to avoid unnecessary
-        // recalculation
-        /** param {AtomSpec[]} atoms */
-        var createMolObj = function(atoms) {
+        // line (index) buffers (for wireframe)
+        if (geometryGroup.lineArray
+                && geometryGroup.__webglLineBuffer !== undefined) {
+            var lineArray = geometryGroup.lineArray;
+            _gl.bindBuffer(_gl.ELEMENT_ARRAY_BUFFER,
+                    geometryGroup.__webglLineBuffer);
+            _gl.bufferData(_gl.ELEMENT_ARRAY_BUFFER, lineArray, hint);
+        }
 
-            //console.log("creating for "+id);
-            var ret = new $3Dmol.Object3D();
-            var cartoonAtoms = [];
-            var lineGeometries = {};
-            var crossGeometries = {};
-            var sphereGeometry = new $3Dmol.Geometry(true);                                                         
-            var imposterGeometry = new $3Dmol.Geometry(true);                                                         
-            var stickGeometry = new $3Dmol.Geometry(true);
-            var cartoonGeometry = new $3Dmol.Geometry(true);
-            var i, n;
-            var range = [Number.POSITIVE_INFINITY, Number.NEGATIVE_INFINITY];
-            for (i = 0, n = atoms.length; i < n; i++) {
-                var atom = atoms[i];
-                // recreate gl info for each atom as necessary
-                // set up appropriate intersection spheres for clickable atoms
-                if (atom && atom.style) {
-                    if (atom.clickable && atom.intersectionShape === undefined)
-                        atom.intersectionShape = {sphere: [], cylinder: [], line: [], triangle : []};                    
-                    drawAtomSphere(atom, sphereGeometry);
-                    drawAtomImposter(atom, imposterGeometry);
-                    drawAtomCross(atom, crossGeometries);
-                    drawBondLines(atom, atoms, lineGeometries);
-                    drawBondSticks(atom, atoms, stickGeometry);
-                    if (typeof (atom.style.cartoon) !== "undefined" && !atom.style.cartoon.hidden) {
-                        //gradient color scheme range
-                        if (atom.style.cartoon.color === 'spectrum' && typeof(atom.resi) === "number") {                            
-                            if (atom.resi < range[0])
-                                range[0] = atom.resi;
-                            if (atom.resi > range[1])
-                                range[1] = atom.resi;
-                        }
-                        
-                        cartoonAtoms.push(atom);
-                    }
-                    
+    }
 
-                }
-            }
-            // create cartoon if needed - this is a whole model analysis
-            if (cartoonAtoms.length > 0) {
-                var gradientscheme = null;
-                //TODO: Should have an option to choose gradient type
-                if (range[0] < range[1])
-                    gradientscheme = new $3Dmol.Gradient.Sinebow(range[0], range[1]);
+    // Creates appropriate gl buffers for geometry chunk
+    // TODO: do we need line buffer for mesh objects?
+    // Also, can we integrate this with createLineBuffers?
+    function createMeshBuffers(geometryGroup) {
 
-                $3Dmol.drawCartoon(ret, cartoonAtoms, cartoonGeometry, gradientscheme);
-                
-                for (i = 0; i < ret.children.length; i++){
-                    var geo = ret.children[i].geometry;
-                }
-            }
+        if (geometryGroup.radiusArray) {
+            geometryGroup.__webglRadiusBuffer = _gl.createBuffer();
+        }
+        if(geometryGroup.useOffset) {
+            geometryGroup.__webglOffsetBuffer = _gl.createBuffer();
+        }
+        geometryGroup.__webglVertexBuffer = _gl.createBuffer();
+        geometryGroup.__webglNormalBuffer = _gl.createBuffer();
+        geometryGroup.__webglColorBuffer = _gl.createBuffer();
 
-            // add sphere geometry
-            if (sphereGeometry.vertices > 0) {
-                var sphereMaterial = new $3Dmol.MeshLambertMaterial({
-                    ambient : 0x000000,
-                    vertexColors : true,
-                    reflectivity : 0,
-                });
-                
-                //Initialize buffers in geometry                
-                sphereGeometry.initTypedArrays();
-                
-                var sphere = new $3Dmol.Mesh(sphereGeometry, sphereMaterial);
-                ret.add(sphere);
-            }
-            
-            // add imposter geometry
-            if (imposterGeometry.vertices > 0) {
-                var imposterMaterial = new $3Dmol.ImposterMaterial({
-                    ambient : 0x000000,
-                    vertexColors : true,
-                    reflectivity : 0
-                });
-                
-                //Initialize buffers in geometry                
-                imposterGeometry.initTypedArrays();
-                
-                var spherei = new $3Dmol.Mesh(imposterGeometry, imposterMaterial);
-                console
-                        .log("spherei geometry " + imposterGeometry.vertices.length);
+        geometryGroup.__webglFaceBuffer = _gl.createBuffer();
+        geometryGroup.__webglLineBuffer = _gl.createBuffer();
 
-                ret.add(spherei);
-            }
-            
-            // add stick geometry
-            if (stickGeometry.vertices > 0) {
-                var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
-                    vertexColors : true,
-                    ambient : 0x000000,
-                    reflectivity : 0
-                });
+        _this.info.memory.geometries++;
+    }
 
-                //Initialize buffers in geometry                
-                stickGeometry.initTypedArrays();
-                
-                if (cylinderMaterial.wireframe)
-                    stickGeometry.setUpWireframe();
-                
-                var sticks = new $3Dmol.Mesh(stickGeometry, cylinderMaterial);
-                ret.add(sticks);
-            }
+    function createLineBuffers(geometry) {
 
-            // This is only for DNA ladder rendering right now
-            if (cartoonGeometry.vertices > 0) {
-                var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
-                    vertexColors : true,
-                    ambient : 0x000000,
-                    reflectivity : 0
-                });
+        geometry.__webglVertexBuffer = _gl.createBuffer();
+        geometry.__webglColorBuffer = _gl.createBuffer();
 
-                cartoonGeometry.initTypedArrays();
+        _this.info.memory.geometries++;
+    }
 
-                if (cylinderMaterial.wireframe)
-                    cartoonGeometry.setUpWireframe();
+    function addBuffer(objlist, buffer, object) {
 
-                var ladder = new $3Dmol.Mesh(cartoonGeometry, cylinderMaterial);
-                ret.add(ladder);
-            }
-            
-            //var linewidth;
-            // add any line geometries, distinguished by line width
-            for (i in lineGeometries) {
-                if (lineGeometries.hasOwnProperty(i)) {
-                    var linewidth = i;
-                    var lineMaterial = new $3Dmol.LineBasicMaterial({
-                        linewidth : linewidth,
-                        vertexColors : true
-                    });
-                    
-                    lineGeometries[i].initTypedArrays();
-                    
-                    var line = new $3Dmol.Line(lineGeometries[i], lineMaterial,
-                            $3Dmol.LinePieces);
+        objlist.push({
+            buffer : buffer,
+            object : object,
+            opaque : null,
+            transparent : null
+        });
 
-                    ret.add(line);
-                }
-            }
+    }
 
-            // add any cross geometries
-            for (i in crossGeometries) {
-                if (crossGeometries.hasOwnProperty(i)) {
-                    var linewidth = i;
-                    var crossMaterial = new $3Dmol.LineBasicMaterial({
-                        linewidth : linewidth,
-                        vertexColors : true
-                    });
+    function setupMatrices(object, camera) {
 
-                    crossGeometries[i].initTypedArrays();
-                    
-                    var cross = new $3Dmol.Line(crossGeometries[i], crossMaterial,
-                            $3Dmol.LinePieces);
+        object._modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse,
+                object.matrixWorld);
 
-                    ret.add(cross);
-                }
-            }
-            
-            //for BIOMT assembly
-            if (dontDuplicateAtoms && !noAssembly) {
-                var symRet = new $3Dmol.Object3D();
-                var t;
-                for (t = 0; t < copyMatrices.length; t++) {
-                    var transformedRet = new $3Dmol.Object3D();
-                    transformedRet = ret.clone();
-                    transformedRet.matrix.copy(copyMatrices[t]);
-                    transformedRet.matrixAutoUpdate = false;
-                    symRet.add(transformedRet);
-                }
-                ret = symRet;
-            }
-            
-            return ret;
-            
-        };
-        
-        /**
-         * Returns list of rotational/translational matrices if there is BIOMT data
-         * Otherwise returns a list of just the ID matrix
-         *
-         * @function $3Dmol.GlModel#getSymmetries
-         * @return {Array<$3Dmol.Matrix4>}
-         *
-         */
-        this.getSymmetries = function() {
-            if (copyMatrices.length > 0) {
-                return copyMatrices;
-            }
-            else {
-                var idList = [idMatrix];
-                return idList;
-            }
-        };
-        
-        /**
-         * Sets symmetries based on specified matrices in list
-         *
-         * @function $3Dmol.GlModel#setSymmetries
-         * @param {Array<$3Dmol.Matrix4>} list
-         *
-         */
-        this.setSymmetries = function(list) {
-            if (typeof(list) == "undefined") { //delete sym data
-                var idList = [idMatrix];
-                copyMatrices = idList;
-            }
-            else {
-                copyMatrices = list;
-            }
-        };
+        object._normalMatrix.getInverse(object._modelViewMatrix);
+        object._normalMatrix.transpose();
 
-        /**
-         * Returns model id number
-         * 
-         * @function $3Dmol.GLMode#getID
-         * @return {number} Model ID
-         */
-        this.getID = function() {
-            return id;
-        };
+    }
 
-        // set default style and colors for atoms
-        var setAtomDefaults = function(atoms, id) {
-            for ( var i = 0; i < atoms.length; i++) {
-                var atom = atoms[i];
-                if (atom) {
-                    atom.style = atom.style || defaultAtomStyle;
-                    atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
-                    atom.model = id;
-                    if (atom.clickable)
-                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
-                }
-            }
-        };
+    function isPowerOfTwo(value) {
 
-        /** add atoms to this model from molecular data string
-         * 
-         * @function $3Dmol.GLModel#addMolData
-         * @param {string} data - atom structure file input data string
-         * @param {string} format - input file string format (e.g 'pdb', 'sdf', etc.)
-         * @param {Object} options - format dependent options (e.g. 'options.keepH' to keep hydrogens)
-         */
-        this.addMolData = function(data, format, options) {
-            options = options || {}; 
-            format = format || "";
-            if (!data)
-                return; //leave an empty model
-            if(typeof($3Dmol.Parsers[format]) == "undefined") {
-            	//let someone provide a file name and get format from extension
-            	format = format.split('.').pop();
-            	if(typeof($3Dmol.Parsers[format] == "undefined")) {            	
-	                console.log("Unknown format: "+format);
-	                //try to guess correct format from data contents
-	                if(data.match(/^@<TRIPOS>MOLECULE/)) {
-	                    format = "mol2";
-	                } else if(data.match(/^HETATM/) || data.match(/^ATOM/)) {
-	                    format = "pdb";
-	                } else if(data.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/)){
-	                    format = "sdf"; //could look at line 3
-	                } else {
-	                    format = "xyz";
-	                }
-	                console.log("Best guess: "+format);
-            	}
-            }
-            var parse = $3Dmol.Parsers[format];
-            parse(atoms, data, options, copyMatrices)
-            noAssembly = !options.doAssembly; //for BIOMT uses
-            dontDuplicateAtoms = !options.duplicateAssemblyAtoms;
-            setAtomDefaults(atoms, id);
-        };
-        
-        /** given a selection specification, return true if atom is selected
-         * 
-         * @function $3Dmol.GLModel#atomIsSelected
-         * @param {AtomSpec} atom
-         * @param {AtomSelectionSpec} sel
-         * @return {boolean}
-         */
-        this.atomIsSelected = function(atom, sel) {
-            if (typeof (sel) === "undefined")
-                return true; // undef gets all
-            var invert = !!sel.invert;
-            var ret = true;
-            for ( var key in sel) {
-                if(key === 'predicate') { //a user supplied function for evaluating atoms
-                    if(!sel['predicate'](atom) ) {
-                        ret = false;
-                        break;
-                    }
-                }
+        return (value & (value - 1)) === 0;
 
-                else if (sel.hasOwnProperty(key) && key != "props" && key != "invert" && key != "model" && key != "byres" && key != "expand" && key != "within") {
+    }
 
-                    // if something is in sel, atom must have it                    
-                    if (typeof (atom[key]) === "undefined") {
-                        ret = false;
-                        break;
-                    }
-                    var isokay = false;
-                    if(key === "bonds") {
-                        //special case counting number of bonds, for selecting nonbonded mostly
-                        var val = sel[key];
-                        if(val != atom.bonds.length) {
-                            ret = false;
-                            break;
-                        }
-                    }
-                    else if ($.isArray(sel[key])) {
-                        // can be any of the listed values
-                        var valarr = sel[key];
-                        for ( var i = 0; i < valarr.length; i++) {
-                            if (atom[key] == valarr[i]) {
-                                isokay = true;
-                                break;
-                            }
-                        }
-                        if (!isokay) {
-                            ret = false;
-                            break;
-                        }
-                    } else { // single match
-                        var val = sel[key];
-                        if (atom[key] != val) {
-                            ret = false;
-                            break;
-                        }
-                    }
-                }
-            }
-            
-            return invert ? !ret : ret;
-        };
+    // Fallback filters for non-power-of-2 textures
 
+    function filterFallback(f) {
 
-        /** return list of atoms selected by sel, this is specific to glmodel
-         * 
-         * @function $3Dmol.GLModel#selectedAtoms
-         * @param {AtomSelectionSpec} sel
-         * @return {Array.<Object>}
-         */
-        this.selectedAtoms = function(sel, from) {
-            var ret = [];
-            if (!from) from = atoms;
-            var aLength = from.length;
-            for ( var i = 0; i < aLength; i++) {
-                var atom = from[i];
-                if (atom) {
-                    if (this.atomIsSelected(atom, sel))
-                        ret.push(atom);
-                }
-            }
+        return _gl.LINEAR;
 
-            // expand selection by some distance
-            if (sel.hasOwnProperty("expand")) {
+    }
 
-                // get atoms in expanded bounding box
-                var expand = expandAtomList(ret, sel.expand)
-                var retlen = ret.length
-                for (var i = 0; i < expand.length; i++) {
-                    for (var j = 0; j < retlen; j++) {
+    function setTextureParameters(textureType, texture, isImagePowerOfTwo) {
 
-                        var dist = squaredDistance(expand[i], ret[j]);
-                        var thresh = Math.pow(sel.expand, 2);
-                        if (dist < thresh && dist > 0) {
-                            ret.push(expand[i]);
-                        }
-                    }
-                }
-            }
+        if (isImagePowerOfTwo) {
 
-            // selection within distance of sub-selection
-            if (sel.hasOwnProperty("within") && sel.within.hasOwnProperty("sel") && sel.within.hasOwnProperty("distance")) {
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_S,
+                    paramToGL(texture.wrapS));
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_T,
+                    paramToGL(texture.wrapT));
 
-                // get atoms in second selection
-                var sel2 = this.selectedAtoms(sel.within.sel, atoms)
-                var within = []
-                for (var i = 0; i < sel2.length; i++) {
-                    for (var j = 0; j < ret.length; j++) {
+            _gl.texParameteri(textureType, _gl.TEXTURE_MAG_FILTER,
+                    paramToGL(texture.magFilter));
+            _gl.texParameteri(textureType, _gl.TEXTURE_MIN_FILTER,
+                    paramToGL(texture.minFilter));
 
-                        var dist = squaredDistance(sel2[i], ret[j]);
-                        var thresh = Math.pow(sel.within.distance, 2);
-                        if (dist < thresh && dist > 0) {
-                            within.push(ret[j]);
-                        }
-                    }
-                }
-                ret = within;
-            }
+        } else {
 
-            // byres selection flag
-            if (sel.hasOwnProperty("byres")) {
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_S,
+                    _gl.CLAMP_TO_EDGE);
+            _gl.texParameteri(textureType, _gl.TEXTURE_WRAP_T,
+                    _gl.CLAMP_TO_EDGE);
 
-                // Keep track of visited residues, visited atoms, and atom stack
-                var vResis = {};
-                var vAtoms = [];
-                var stack = [];
+            _gl.texParameteri(textureType, _gl.TEXTURE_MAG_FILTER,
+                    filterFallback(texture.magFilter));
+            _gl.texParameteri(textureType, _gl.TEXTURE_MIN_FILTER,
+                    filterFallback(texture.minFilter));
 
-                for (var i = 0; i < ret.length; i++) {
-                    
-                    // Check if atom is part of a residue, and that the residue hasn't been traversed yet
-                    var atom = ret[i];
-                    var c = atom.chain;
-                    var r = atom.resi;
-                    if (vResis[c] === undefined) vResis[c] = {};
-                    if (atom.hasOwnProperty("resi") && vResis[c][r] === undefined) {
+        }
 
-                        // Perform a depth-first search of atoms with the same resi
-                        vResis[c][r] = true;
-                        stack.push(atom);
-                        while(stack.length > 0) {
-                            atom = stack.pop();
-                            c = atom.chain;
-                            r = atom.resi;
-                            if (vAtoms[atom.index] === undefined) {
-                                vAtoms[atom.index] = true;
-                                for (var j = 0; j < atom.bonds.length; j++) {
-                                    var atom2 = atoms[atom.bonds[j]];
-                                    if (vAtoms[atom2.index] === undefined && atom2.hasOwnProperty("resi") && atom2.chain == c && atom2.resi == r) {
-                                        stack.push(atom2);
-                                        ret.push(atom2);
-                                    }
-                                }
-                            }
-                        }
-                    }   
-                }
-            }
+    }
 
-            return ret;
-        };
+    this.setTexture = function(texture, slot) {
 
-        var squaredDistance = function(atom1, atom2) {
-            var xd = atom2.x - atom1.x;
-            var yd = atom2.y - atom1.y;
-            var zd = atom2.z - atom1.z;
-            return (Math.pow(xd, 2) + Math.pow(yd, 2) + Math.pow(zd, 2));
-        };
+        if (texture.needsUpdate) {
 
-        /** returns a list of atoms in the expanded bounding box, but not in the current one
-         *
-         *  Bounding box:
-         *
-         *    [ [ xmin, ymin, zmin ],
-         *      [ xmax, ymax, zmax ],
-         *      [ xctr, yctr, zctr ] ]
-         *
-         **/
-        var expandAtomList = function(atomList, amt) {
+            if (!texture.__webglInit) {
 
-            var pb = $3Dmol.getExtent(atomList);
-            var nb = [[],[],[]];
+                texture.__webglInit = true;
 
-            for (var i = 0; i < 3; i++)
-            {
-                nb[0][i] = pb[0][i]-amt;
-                nb[1][i] = pb[1][i]+amt;
-                nb[2][i] = pb[2][i];
-            }
+                texture.addEventListener('dispose', onTextureDispose);
 
-            // look in added box "shell" for new atoms
-            var expand = [];
-            for (var i = 0; i < atoms.length; i++) {
+                texture.__webglTexture = _gl.createTexture();
 
-                var x = atoms[i].x;
-                var y = atoms[i].y;
-                var z = atoms[i].z;
+                _this.info.memory.textures++;
 
-                if (x >= nb[0][0] && x < pb[0][0] || x > pb[1][0] && x <= nb[1][0]) {
-                    if (y >= nb[0][1] && y < pb[0][1] || y > pb[1][1] && y <= nb[1][1]) {
-                        if (z >= nb[0][2] && z < pb[0][2] || z > pb[1][2] && z <= nb[1][2]) {
-                            expand.push(atoms[i]);
-                        }
-                    }
-                }
-            }
-            return expand;
-        };
-        
-        /** Add list of new atoms to model.  Adjusts bonds appropriately.
-         * 
-         * @function $3Dmol.GLModel#addAtoms
-         * @param {type} newatoms
-         */        
-        this.addAtoms = function(newatoms) {
-            molObj = null;
-            var start = atoms.length;
-            var indexmap = [];
-            // mapping from old index to new index
-            var i;
-            for(i = 0; i < newatoms.length; i++) {
-                indexmap[newatoms[i].index] = start+i;
             }
-            
-            // copy and push newatoms onto atoms
-            for(i = 0; i < newatoms.length; i++) {
-                var olda = newatoms[i];
-                var nindex = indexmap[olda.index];
-                var a = $.extend(false, {}, olda);
-                a.index = nindex;
-                a.bonds = [];
-                a.bondOrder = [];
-                // copy over all bonds contained in selection,
-                // updating indices appropriately
-                for(var j = 0; j < olda.bonds.length; j++) {
-                    var neigh = indexmap[olda.bonds[j]];
-                    if(typeof(neigh) != "undefined") {
-                        a.bonds.push(neigh);
-                        a.bondOrder.push(olda.bondOrder[j]);
-                    }                
+
+            _gl.activeTexture(_gl.TEXTURE0 + slot);
+            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
+
+            _gl.pixelStorei(_gl.UNPACK_FLIP_Y_WEBGL, texture.flipY);
+            _gl.pixelStorei(_gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL,
+                    texture.premultiplyAlpha);
+            _gl.pixelStorei(_gl.UNPACK_ALIGNMENT, texture.unpackAlignment);
+
+            var image = texture.image, isImagePowerOfTwo = isPowerOfTwo(image.width)
+                    && isPowerOfTwo(image.height), glFormat = paramToGL(texture.format), glType = paramToGL(texture.type);
+
+            setTextureParameters(_gl.TEXTURE_2D, texture, isImagePowerOfTwo);
+
+            var mipmap, mipmaps = texture.mipmaps;
+
+            // regular Texture (image, video, canvas)
+
+            // use manually created mipmaps if available
+            // if there are no manual mipmaps
+            // set 0 level mipmap and then use GL to generate other mipmap
+            // levels
+
+            if (mipmaps.length > 0 && isImagePowerOfTwo) {
+
+                for (var i = 0, il = mipmaps.length; i < il; i++) {
+                    mipmap = mipmaps[i];
+                    _gl.texImage2D(_gl.TEXTURE_2D, i, glFormat, glFormat,
+                            glType, mipmap);
                 }
-                atoms.push(a);
-            }
-        };
 
-        /** Remove specified atoms from model
-         * 
-         * @function $3Dmol.GLModel#removeAtoms
-         * @param {type} badatoms
-         * @return {removeAtoms}
-         */
-        this.removeAtoms = function(badatoms) {
-            molObj = null;
-            // make map of all baddies
-            var baddies = [];
-            var i;
-            for(i = 0; i < badatoms.length; i++) {
-                baddies[badatoms[i].index] = true;
-            }
-            
-            // create list of good atoms
-            var newatoms = [];
-            for(i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                if(!baddies[a.index])
-                    newatoms.push(a);
+                texture.generateMipmaps = false;
             }
-            
-            // clear it all out
-            atoms = [];
-            // and add back in to get updated bonds
-            this.addAtoms(newatoms);
-        };
-        
-        
-        /** Set atom style of selected atoms
-         * 
-         * @function $3Dmol.GLModel#setStyle
-         * @param {AtomSelectionSpec} sel
-         * @param {AtomStyleSpec} style
-         * @param {boolean} add - if true, add to current style, don't replace
-         */
-        this.setStyle = function(sel, style, add) {           
 
-            // do a copy to enforce style changes through this function
-            var mystyle = $.extend(true, {}, style);
-            var changedAtoms = false;
-            // somethings we only calculate if there is a change in a certain
-            // style, although these checks will only catch cases where both
-            // are either null or undefined
+            else
+                _gl.texImage2D(_gl.TEXTURE_2D, 0, glFormat, glFormat, glType,
+                        texture.image);
 
-            var selected = this.selectedAtoms(sel, atoms);
-            for ( var i = 0; i < atoms.length; i++) {
-                if(atoms[i]) atoms[i].capDrawn = false; //reset for proper stick render
-            }
+            if (texture.generateMipmaps && isImagePowerOfTwo)
+                _gl.generateMipmap(_gl.TEXTURE_2D);
 
-            for ( var i = 0; i < selected.length; i++) {                
-                changedAtoms = true;
-                //even though clickable and callback are atom properties, let them
-                //be set through styles
-                if(typeof(mystyle.clickable) != 'undefined') 
-                    selected[i].clickable = mystyle.clickable;
-                if(typeof(mystyle.callback) != 'undefined') 
-                    selected[i].callback = mystyle.callback;
-                
-                if (selected[i].clickable) 
-                    selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};                    
-                   
-                if(!add) selected[i].style = {};
-                for(var s in mystyle) {
-                    if(mystyle.hasOwnProperty(s)) {
-                        selected[i].style[s] = mystyle[s];
-                    }
-                }
-            }
-            
-            if (changedAtoms)
-                molObj = null; //force rebuild
-            
-        };
-        
-        /** given a mapping from element to color, set atom colors
-         * 
-         * @function $3Dmol.GLModel#setColorByElement
-         * @param {type} sel
-         * @param {type} colors
-         */
-        this.setColorByElement = function(sel, colors) {
-            
-            if(molObj !== null && sameObj(colors,lastColors))
-                return; // don't recompute
-            lastColors = colors;
-            var atoms = this.selectedAtoms(sel, atoms);
-            if(atoms.length > 0)
-                molObj = null; // force rebuild
-            for ( var i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                if(typeof(colors[a.elem]) !== "undefined") {
-                    a.color = colors[a.elem];
-                }
-            }
-        };
-        
-        /**
-         * @function $3Dmol.GLModel.setColorByProperty
-         * @param {type} sel
-         * @param {type} prop
-         * @param {type} scheme
-         */
-        this.setColorByProperty = function(sel, prop, scheme) {
-            var atoms = this.selectedAtoms(sel, atoms);
-            lastColors = null; // don't bother memoizing
-            if(atoms.length > 0)
-                molObj = null; // force rebuild
-            var min =  Number.POSITIVE_INFINITY;
-            var max =  Number.NEGATIVE_INFINITY;
-            var i, a;
-            // compute the range            
-            for (i = 0; i < atoms.length; i++) {
-                a = atoms[i];
-                if(a.properties && typeof(a.properties[prop]) !== undefined) {
-                    var p = parseFloat(a.properties[prop]);
-                    if(p < min) min = p;
-                    if(p > max) max = p;
-                }                    
-            }
-            // now apply colors using scheme
-            for (i = 0; i < atoms.length; i++) {
-                a = atoms[i];
-                if(a.properties && typeof(a.properties[prop]) !== undefined) {
-                    var c = scheme.valueToHex(parseFloat(a.properties[prop]), [min,max]);
-                    a.color = c;
-                }                    
-            }
-        };
+            texture.needsUpdate = false;
 
+            if (texture.onUpdate)
+                texture.onUpdate();
 
-        /** manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
-         * 
-         * @function $3Dmol.GLModel#globj
-         * @param {$3Dmol.Object3D} group
-         */
-        this.globj = function(group) {
-            var time = new Date();
-            if(molObj === null) { // have to regenerate
-                molObj = createMolObj(atoms);
-                var time2 = new Date();
-                //console.log("object creation time: " + (time2 - time));
-                if(renderedMolObj) { // previously rendered, remove
-                    group.remove(renderedMolObj);
-                    renderedMolObj = null;
-                }
-                renderedMolObj = molObj.clone();
-                group.add(renderedMolObj);
-            }
-        };
-        
-        /** Remove any renderable mol object from scene
-         * 
-         * @function $3Dmol.GLModel#removegl
-         * @param {$3Dmol.Object3D} group
-         */
-        this.removegl = function(group) {
-            if(renderedMolObj) {
-                //dispose of geos and materials
-                if (renderedMolObj.geometry !== undefined) renderedMolObj.geometry.dispose();             
-                if (renderedMolObj.material !== undefined) renderedMolObj.material.dispose();
-                group.remove(renderedMolObj);
-                renderedMolObj = null;
-            }
-            molObj = null;
-        };
-        
-        /** Create labels for residues of selected atoms.
-         * Will create a single label at the center of mass of all atoms
-         * with the same chain,resn, and resi.
-         * @function $3Dmol.GLModel#addResLabels
-         * 
-         * @param {AtomSelectionSpec} sel
-         * @param {$3Dmol.GLViewer} viewer
-         */
-        this.addResLabels = function(sel, viewer, style) {
-            var atoms = this.selectedAtoms(sel, atoms);
-            var bylabel = {}
-            //collect by chain:resn:resi
-            for(var i = 0; i < atoms.length; i++) {
-                var a = atoms[i];
-                var c = a.chain;
-                var resn = a.resn;
-                var resi = a.resi;
-                var label =  resn + '' + resi;
-                if(!bylabel[c]) bylabel[c] = {};
-                if(!bylabel[c][label]) bylabel[c][label] = []
-                bylabel[c][label].push(a);
-            }
-            
-            var mystyle = $.extend(true, {}, style);
-            //now compute centers of mass
-            for(var c in bylabel) {
-                if(bylabel.hasOwnProperty(c)) {
-                    var labels = bylabel[c];
-                    for(var label in labels) {
-                        if(labels.hasOwnProperty(label)) {
-                            var atoms = labels[label];
-                            var sum = new $3Dmol.Vector3(0,0,0);
-                            for(var i = 0; i < atoms.length; i++) {
-                                var a = atoms[i];
-                                sum.x += a.x;
-                                sum.y += a.y;
-                                sum.z += a.z;
-                            }
-                            sum.divideScalar(atoms.length);
-                            mystyle.position = sum;
-                            viewer.addLabel(label, mystyle);
-                        }                        
-                    }
-                }
-            }
-        }
+        } else {
 
-    }
+            _gl.activeTexture(_gl.TEXTURE0 + slot);
+            _gl.bindTexture(_gl.TEXTURE_2D, texture.__webglTexture);
 
-    return GLModel;
-    
-})();
-/**
- * A GLShape is a collection of user specified shapes.
- * 
- * @constructor $3Dmol.GLShape
- * @extends {ShapeSpec}
- * @param {number} sid - Unique identifier
- * @param {ShapeSpec} stylespec - shape style specification
- */
-$3Dmol.GLShape = (function() {
+        }
 
-    // Marching cube, to match with protein surface generation
-    var ISDONE = 2;
+    };
 
-    /**
-     * 
-     * @param {$3Dmol.Geometry}
-     *            geo
-     * @param {$3Dmol.Color |
-     *            colorlike} color
-     */
-    var updateColor = function(geo, color) {
+    // Map constants to WebGL constants
 
-        var C = color || $3Dmol.CC.color(color);
-        geo.colorsNeedUpdate = true;
+    function paramToGL(p) {
 
-        for ( var g in geo.geometryGroups) {
+        if (p === $3Dmol.UnsignedByteType)
+            return _gl.UNSIGNED_BYTE;
+        if (p === $3Dmol.RGBAFormat)
+            return _gl.RGBA;
 
-            var geoGroup = geo.geometryGroups[g];
-            var colorArr = geoGroup.colorArray;
+        return 0;
 
-            for (var i = 0, il = geoGroup.vertices; i < il; ++i) {
-                colorArr[i * 3] = C.r;
-                colorArr[i * 3 + 1] = C.g;
-                colorArr[i * 3 + 2] = C.b;
-            }
-        }
+    }
 
-    };
+    function setupLights(program, lights) {
+        var l, ll, light, n, r = 0, g = 0, b = 0, color, position, intensity, distance,
 
+        zlights = _lights,
 
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {ArrowSpec}
-     *            spec
-     */
-    var drawArrow = function(shape, geoGroup, spec) {
+        dirColors = zlights.directional.colors, dirPositions = zlights.directional.positions,
 
-        var from = spec.start, end = spec.end, radius = spec.radius, radiusRatio = spec.radiusRatio, mid = spec.mid;
+        dirCount = 0, dirLength = 0, dirOffset = 0;
 
-        if (!(from && end))
-            return;
+        for (l = 0, ll = lights.length; l < ll; l++) {
 
-        // vertices
+            light = lights[l];
 
-        var dir = end.clone();
-        dir.sub(from).multiplyScalar(mid);
-        var to = from.clone().add(dir);
-        var negDir = dir.clone().negate();
+            color = light.color;
+            intensity = light.intensity;
+            distance = light.distance;
 
-        shape.intersectionShape.cylinder.push(new $3Dmol.Cylinder(from.clone(),
-                to.clone(), radius));
-        shape.intersectionShape.sphere.push(new $3Dmol.Sphere(from.clone(),
-                radius));
+            if (light instanceof $3Dmol.Light) {
 
-        // get orthonormal vector
-        var nvecs = [];
-        nvecs[0] = dir.clone();
-        if (Math.abs(nvecs[0].x) > 0.0001)
-            nvecs[0].y += 1;
-        else
-            nvecs[0].x += 1;
-        nvecs[0].cross(dir);
-        nvecs[0].normalize();
+                dirCount++;
 
-        nvecs[0] = nvecs[0];
-        // another orth vector
-        nvecs[4] = nvecs[0].clone();
-        nvecs[4].crossVectors(nvecs[0], dir);
-        nvecs[4].normalize();
-        nvecs[8] = nvecs[0].clone().negate();
-        nvecs[12] = nvecs[4].clone().negate();
+                _direction.getPositionFromMatrix(light.matrixWorld);
+                _vector3.getPositionFromMatrix(light.target.matrixWorld);
+                _direction.sub(_vector3);
+                _direction.normalize();
 
-        // now quarter positions
-        nvecs[2] = nvecs[0].clone().add(nvecs[4]).normalize();
-        nvecs[6] = nvecs[4].clone().add(nvecs[8]).normalize();
-        nvecs[10] = nvecs[8].clone().add(nvecs[12]).normalize();
-        nvecs[14] = nvecs[12].clone().add(nvecs[0]).normalize();
+                if (_direction.x === 0 && _direction.y === 0
+                        && _direction.z === 0)
+                    continue;
 
-        // eights
-        nvecs[1] = nvecs[0].clone().add(nvecs[2]).normalize();
-        nvecs[3] = nvecs[2].clone().add(nvecs[4]).normalize();
-        nvecs[5] = nvecs[4].clone().add(nvecs[6]).normalize();
-        nvecs[7] = nvecs[6].clone().add(nvecs[8]).normalize();
-        nvecs[9] = nvecs[8].clone().add(nvecs[10]).normalize();
-        nvecs[11] = nvecs[10].clone().add(nvecs[12]).normalize();
-        nvecs[13] = nvecs[12].clone().add(nvecs[14]).normalize();
-        nvecs[15] = nvecs[14].clone().add(nvecs[0]).normalize();
+                dirPositions[dirOffset] = _direction.x;
+                dirPositions[dirOffset + 1] = _direction.y;
+                dirPositions[dirOffset + 2] = _direction.z;
 
-        // var start = geo.vertices.length;
-        var start = geoGroup.vertices;
-        var vertexArray = geoGroup.vertexArray;
-        var colorArray = geoGroup.colorArray;
-        var faceArray = geoGroup.faceArray;
-        var normalArray = geoGroup.normalArray;
-        var lineArray = geoGroup.lineArray;
+                dirColors[dirOffset] = color.r * intensity;
+                dirColors[dirOffset + 1] = color.g * intensity;
+                dirColors[dirOffset + 2] = color.b * intensity;
 
-        var offset, i, n;
-        // add vertices, opposing vertices paired together
-        for (i = 0, n = nvecs.length; i < n; ++i) {
-            offset = 3 * (start + 3 * i);
-            var bottom = nvecs[i].clone().multiplyScalar(radius).add(from);
-            var top = nvecs[i].clone().multiplyScalar(radius).add(to);
-            var conebase = nvecs[i].clone()
-                    .multiplyScalar(radius * radiusRatio).add(to);
+                dirOffset += 3;
 
-            vertexArray[offset] = bottom.x;
-            vertexArray[offset + 1] = bottom.y;
-            vertexArray[offset + 2] = bottom.z;
+                dirLength++;
+            }
 
-            vertexArray[offset + 3] = top.x;
-            vertexArray[offset + 4] = top.y;
-            vertexArray[offset + 5] = top.z;
+        }
 
-            vertexArray[offset + 6] = conebase.x;
-            vertexArray[offset + 7] = conebase.y;
-            vertexArray[offset + 8] = conebase.z;
+        zlights.ambient[0] = r;
+        zlights.ambient[1] = g;
+        zlights.ambient[2] = b;
+        zlights.directional.length = dirLength;
+    }
 
-            if (i > 0) {
-                var prev_x = vertexArray[offset - 3];
-                var prev_y = vertexArray[offset - 2];
-                var prev_z = vertexArray[offset - 1];
+    function initGL() {
 
-                var c = new $3Dmol.Vector3(prev_x, prev_y, prev_z);
-                var b = end.clone(), b2 = to.clone();
-                var a = new $3Dmol.Vector3(conebase.x, conebase.y, conebase.z);
+        try {
 
-                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(a, b,
-                        c));
-                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(c
-                        .clone(), b2, a.clone()));
+            if (!(_gl = _canvas.getContext('experimental-webgl', {
+                alpha : _alpha,
+                premultipliedAlpha : _premultipliedAlpha,
+                antialias : _antialias,
+                stencil : _stencil,
+                preserveDrawingBuffer : _preserveDrawingBuffer
+            }))) {
+                if (!(_gl = _canvas.getContext('webgl', {
+                    alpha : _alpha,
+                    premultipliedAlpha : _premultipliedAlpha,
+                    antialias : _antialias,
+                    stencil : _stencil,
+                    preserveDrawingBuffer : _preserveDrawingBuffer
+                }))) {
+                    throw 'Error creating WebGL context.';
+                }
             }
+
+        } catch (error) {
+
+            console.error(error);
         }
+    }
 
-        geoGroup.vertices += 48;
-        offset = geoGroup.vertices * 3;
+    function setDefaultGLState() {
 
-        // caps
-        vertexArray[offset] = from.x;
-        vertexArray[offset + 1] = from.y;
-        vertexArray[offset + 2] = from.z;
+        _gl.clearColor(0, 0, 0, 1);
+        _gl.clearDepth(1);
+        _gl.clearStencil(0);
 
-        vertexArray[offset + 3] = to.x;
-        vertexArray[offset + 4] = to.y;
-        vertexArray[offset + 5] = to.z;
+        _gl.enable(_gl.DEPTH_TEST);
+        _gl.depthFunc(_gl.LEQUAL);
 
-        vertexArray[offset + 6] = end.x;
-        vertexArray[offset + 7] = end.y;
-        vertexArray[offset + 8] = end.z;
+        _gl.frontFace(_gl.CCW);
+        _gl.cullFace(_gl.BACK);
+        _gl.enable(_gl.CULL_FACE);
 
-        geoGroup.vertices += 3;
+        _gl.enable(_gl.BLEND);
+        _gl.blendEquation(_gl.FUNC_ADD);
+        _gl.blendFunc(_gl.SRC_ALPHA, _gl.ONE_MINUS_SRC_ALPHA);
 
-        // now faces
-        var face, norm, faceoffset, lineoffset;
-        var t1, t2, t2b, t3, t3b, t4, t1offset, t2offset, t2boffset, t3offset, t3boffset, t4offset;
-        var n1, n2, n3, n4;
-        var n_vertices = 0;
-        var fromi = geoGroup.vertices - 3, toi = geoGroup.vertices - 2, endi = geoGroup.vertices - 1;
-        var fromoffset = fromi * 3, tooffset = toi * 3, endoffset = endi * 3;
-        for (i = 0, n = nvecs.length - 1; i < n; ++i) {
+        _gl.clearColor(_clearColor.r, _clearColor.g, _clearColor.b,
+                        _clearAlpha);
+    }
 
-            var ti = start + 3 * i;
-            offset = ti * 3;
-            faceoffset = geoGroup.faceidx;
-            lineoffset = geoGroup.lineidx;
+    this.addPostPlugin(new $3Dmol.SpritePlugin());
 
-            t1 = ti;
-            t1offset = t1 * 3;
-            t2 = ti + 1;
-            t2offset = t2 * 3;
-            t2b = ti + 2;
-            t2boffset = t2b * 3;
-            t3 = ti + 4;
-            t3offset = t3 * 3;
-            t3b = ti + 5;
-            t3boffset = t3b * 3;
-            t4 = ti + 3;
-            t4offset = t4 * 3;
+};
+/*
+ * Scene class
+ */
+/** @constructor */
+$3Dmol.Scene = function() {
+    
+    $3Dmol.Object3D.call(this);
+    
+    this.fog = null;
+    
+    //May not need...
+    this.overrideMaterial = null;
+    
+    this.matrixAutoUpdate = false;
+    
+    this.__objects = [];
+    this.__lights = [];
+    
+    this.__objectsAdded = [];
+    this.__objectsRemoved = [];
+    
+};
 
-            // face = [t1, t2, t4], [t2, t3, t4];
-            // face = [t1, t2, t3, t4];
+$3Dmol.Scene.prototype = Object.create($3Dmol.Object3D.prototype);
 
-            norm = [ nvecs[i], nvecs[i], nvecs[i + 1], nvecs[i + 1] ];
+$3Dmol.Scene.prototype.__addObject = function(object) {
+    
+    //Directional Lighting
+    if (object instanceof $3Dmol.Light) {
+        
+        if (this.__lights.indexOf(object) === -1)
+            this.__lights.push(object);
+        
+        //TODO: Do I need this??
+        if (object.target && object.target.parent === undefined)
+            this.add(object.target);
+            
+    }
+    
+    //Rotation group
+    else {
+        
+        if (this.__objects.indexOf(object) === -1) {
+            
+            this.__objects.push(object);
+            this.__objectsAdded.push(object);
+            
+            //Check if previously removed
+            
+            var idx = this.__objectsRemoved.indexOf(object);
+            
+            if (idx !== -1)
+                this.__objectsRemoved.splice(i, 1);
+                
+        }
+    }
+    
+    //Add object's children
+    
+    for (var i = 0; i < object.children.length; i++) 
+        this.__addObject(object.children[i]);
+    
+};
 
-            n1 = n2 = nvecs[i];
-            n3 = n4 = nvecs[i + 1];
+$3Dmol.Scene.prototype.__removeObject = function(object) {
+    
+    var idx;
+    if (object instanceof $3Dmol.Light) {
+        
+        idx = this.__lights.indexOf(object);
+        
+        if (idx !== -1)
+            this.__lights.splice(idx, 1);
+            
+    }
+    
+    //Object3D
+    else {
+        
+        idx = this.__objects.indexOf(object);
+        
+        if (idx !== -1) {
+            
+            this.__objects.splice(idx, 1);
+            this.__objectsRemoved.push(object);
+            
+            //Check if previously added
+            
+            var ai = this.__objectsAdded.indexOf(object);
+            
+            if (ai !== -1) 
+                this.__objectsAdded.splice(idx, 1);
+                
+        }
+    
+    }
+    
+    //Remove object's children
+    for (var i = 0; i < object.children.length; i++)
+        this.__removeObject(object.children[i]);
+    
+};
 
-            normalArray[t1offset] = n1.x;
-            normalArray[t2offset] = n2.x;
-            normalArray[t4offset] = n4.x;
-            normalArray[t1offset + 1] = n1.y;
-            normalArray[t2offset + 1] = n2.y;
-            normalArray[t4offset + 1] = n4.y;
-            normalArray[t1offset + 2] = n1.z;
-            normalArray[t2offset + 2] = n2.z;
-            normalArray[t4offset + 2] = n4.z;
 
-            normalArray[t2offset] = n2.x;
-            normalArray[t3offset] = n3.x;
-            normalArray[t4offset] = n4.x;
-            normalArray[t2offset + 1] = n2.y;
-            normalArray[t3offset + 1] = n3.y;
-            normalArray[t4offset + 1] = n4.y;
-            normalArray[t2offset + 2] = n2.z;
-            normalArray[t3offset + 2] = n3.z;
-            normalArray[t4offset + 2] = n4.z;
+/*
+ * Fog Class
+ */
 
-            normalArray[t2boffset] = n2.x;
-            normalArray[t3boffset] = n3.x;
-            normalArray[t2boffset + 1] = n2.y;
-            normalArray[t3boffset + 1] = n3.y;
-            normalArray[t2boffset + 2] = n2.z;
-            normalArray[t3boffset + 2] = n3.z;
+/** @constructor */
+$3Dmol.Fog = function ( hex, near, far ) {
 
-            // sides
-            faceArray[faceoffset] = t1;
-            faceArray[faceoffset + 1] = t2;
-            faceArray[faceoffset + 2] = t4;
-            faceArray[faceoffset + 3] = t2;
-            faceArray[faceoffset + 4] = t3;
-            faceArray[faceoffset + 5] = t4;
-            // caps
-            faceArray[faceoffset + 6] = t1;
-            faceArray[faceoffset + 7] = t4;
-            faceArray[faceoffset + 8] = fromi;
-            faceArray[faceoffset + 9] = t2b;
-            faceArray[faceoffset + 10] = toi;
-            faceArray[faceoffset + 11] = t3b;
-            // arrowhead
-            faceArray[faceoffset + 12] = t2b;
-            faceArray[faceoffset + 13] = endi;
-            faceArray[faceoffset + 14] = t3b;
+    this.name = '';
 
-            // sides
-            lineArray[lineoffset] = t1;
-            lineArray[lineoffset + 1] = t2;
-            lineArray[lineoffset + 2] = t1;
-            lineArray[lineoffset + 3] = t4;
-            // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
-            lineArray[lineoffset + 4] = t3;
-            lineArray[lineoffset + 5] = t4;
-            // caps
-            lineArray[lineoffset + 6] = t1;
-            lineArray[lineoffset + 7] = t4;
-            // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
-            // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
-
-            lineArray[lineoffset + 8] = t2b;
-            lineArray[lineoffset + 9] = t2; // toi
-            lineArray[lineoffset + 10] = t2b;
-            lineArray[lineoffset + 11] = t3b;
-            lineArray[lineoffset + 12] = t3;
-            lineArray[lineoffset + 13] = t3b; // toi
-            // arrowhead
-            lineArray[lineoffset + 14] = t2b;
-            lineArray[lineoffset + 15] = endi;
-            lineArray[lineoffset + 16] = t2b;
-            lineArray[lineoffset + 17] = t3b;
-            lineArray[lineoffset + 18] = endi;
-            lineArray[lineoffset + 19] = t3b;
-
-            geoGroup.faceidx += 15;
-            geoGroup.lineidx += 20;
+    this.color = new $3Dmol.Color( hex );
 
-        }
-        // final face
+    this.near = ( near !== undefined ) ? near : 1;
+    this.far = ( far !== undefined ) ? far : 1000;
 
-        face = [ start + 45, start + 46, start + 1, start, start + 47,
-                start + 2 ];
-        norm = [ nvecs[15], nvecs[15], nvecs[0], nvecs[0] ];
+};
 
-        faceoffset = geoGroup.faceidx;
-        lineoffset = geoGroup.lineidx;
+$3Dmol.Fog.prototype.clone = function () {
 
-        t1 = face[0];
-        t1offset = t1 * 3;
-        t2 = face[1];
-        t2offset = t2 * 3;
-        t2b = face[4];
-        t2boffset = t2b * 3;
-        t3 = face[2];
-        t3offset = t3 * 3;
-        t3b = face[5];
-        t3boffset = t3b * 3;
-        t4 = face[3];
-        t4offset = t4 * 3;
+    return new $3Dmol.Fog( this.color.getHex(), this.near, this.far );
 
-        n1 = n2 = nvecs[15];
-        n3 = n4 = nvecs[0];
+};
 
-        normalArray[t1offset] = n1.x;
-        normalArray[t2offset] = n2.x;
-        normalArray[t4offset] = n4.x;
-        normalArray[t1offset + 1] = n1.y;
-        normalArray[t2offset + 1] = n2.y;
-        normalArray[t4offset + 1] = n4.y;
-        normalArray[t1offset + 2] = n1.z;
-        normalArray[t2offset + 2] = n2.z;
-        normalArray[t4offset + 2] = n4.z;
+$3Dmol.ShaderUtils = {
+    
+    clone: function ( uniforms_src ) {
+        
+        var u, p, parameter, parameter_src, uniforms_clone = {};
+        
+        for (u in uniforms_src) {
+            uniforms_clone[u] = {};
+            uniforms_clone[u].type = uniforms_src[u].type;
+            
+            var srcValue = uniforms_src[u].value;
+            
+            if (srcValue instanceof $3Dmol.Color)
+                uniforms_clone[u].value = srcValue.clone();
+            else if (typeof srcValue === "number")
+                uniforms_clone[u].value = srcValue;
+            else if (srcValue instanceof Array) 
+                uniforms_clone[u].value = [];
+            else
+                console.error("Error copying shader uniforms from ShaderLib: unknown type for uniform");
+            
+        }
+        
+        return uniforms_clone;
+    },
+    //fragment shader reused by outline shader
+    stickimposterFragmentShader: [
+     "uniform float opacity;",
+     "uniform mat4 projectionMatrix;",
+
+     "uniform vec3 fogColor;",
+     "uniform float fogNear;",
+     "uniform float fogFar;",
+
+     "varying vec3 vLight;",
+     "varying vec3 vColor;",
+     "varying vec3 cposition;",
+     "varying vec3 p1;",
+     "varying vec3 p2;",
+     "varying float r;",
+
+
+     //cylinder-ray intersection testing taken from http://mrl.nyu.edu/~dzorin/cg05/lecture12.pdf
+     //also useful: http://stackoverflow.com/questions/9595300/cylinder-impostor-in-glsl
+     //with a bit more care (caps) this could be a general cylinder imposter (see also outline)
+     "void main() {",   
+     "    vec3 color = abs(vColor);",
+     "    vec3 pos = cposition;",
+     "    vec3 p = pos;", //ray point
+     "    vec3 v = normalize(pos);", //ray normal
+     "    vec3 pa = p1;", //cyl start
+     "    vec3 va = normalize(p2-p1);", //cyl norm
+     "    vec3 tmp1 = v-(dot(v,va)*va);",
+     "    vec3 deltap = p-pa;",
+     "    float A = dot(tmp1,tmp1);",
+     "    if(A == 0.0) discard;",
+     "    vec3 tmp2 = deltap-(dot(deltap,va)*va);",
+     "    float B = 2.0*dot(tmp1, tmp2);",
+     "    float C = dot(tmp2,tmp2)-r*r;",
+     //quadratic equation!
+     "    float det = (B*B) - (4.0*A*C);",
+     "    if(det < 0.0) discard;",
+     "    float sqrtDet = sqrt(det);",
+     "    float posT = (-B+sqrtDet)/(2.0*A);",
+     "    float negT = (-B-sqrtDet)/(2.0*A);",
+     "    float intersectionT = min(posT,negT);",
+     "    vec3 qi = p+v*intersectionT;", 
+     "    float dotp1 = dot(va,qi-p1);",
+     "    float dotp2 = dot(va,qi-p2);",
+     "    vec3 norm;",
+     "    if( dotp1 < 0.0 || dotp2 > 0.0) {", //(p-c)^2 + 2(p-c)vt +v^2+t^2 - r^2 = 0
+     "       vec3 cp;",
+     "       if( dotp1 < 0.0) {" +
+     //"        if(vColor.x < 0.0 ) discard;", //color sign bit indicates if we should cap or not
+     "        cp = p1;",
+     "       } else {",
+     //"          if(vColor.y < 0.0 ) discard;",
+     "          cp = p2;",
+     "       }",
+     "       vec3 diff = p-cp;",
+     "       A = dot(v,v);",
+     "       B = dot(diff,v)*2.0;",
+     "       C = dot(diff,diff)-r*r;",
+     "       det = (B*B) - (4.0*C);",
+     "       if(det < 0.0) discard;",
+     "       sqrtDet = sqrt(det);",
+     "       posT = (-B+sqrtDet)/(2.0);",
+     "       negT = (-B-sqrtDet)/(2.0);",
+     "       float t = min(posT,negT);",
+     "       qi = p+v*t;",
+     "       norm = normalize(qi-cp);",
+     "    } else {",
+     "       norm = normalize(qi-(dotp1*va + p1));",
+     "    }",
+     "    vec4 clipPos = projectionMatrix * vec4(qi, 1.0);",
+     "    float ndcDepth = clipPos.z / clipPos.w;",
+     "    float depth = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+     "    gl_FragDepthEXT = depth;",
+    ].join("\n")  
+};
 
-        normalArray[t2offset] = n2.x;
-        normalArray[t3offset] = n3.x;
-        normalArray[t4offset] = n4.x;
-        normalArray[t2offset + 1] = n2.y;
-        normalArray[t3offset + 1] = n3.y;
-        normalArray[t4offset + 1] = n4.y;
-        normalArray[t2offset + 2] = n2.z;
-        normalArray[t3offset + 2] = n3.z;
-        normalArray[t4offset + 2] = n4.z;
+$3Dmol.ShaderLib = { 
+    'basic' : {
+        fragmentShader : [                    
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-        normalArray[t2boffset] = n2.x;
-        normalArray[t3boffset] = n3.x;
-        normalArray[t2boffset + 1] = n2.y;
-        normalArray[t3boffset + 1] = n3.y;
-        normalArray[t2boffset + 2] = n2.z;
-        normalArray[t3boffset + 2] = n3.z;
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-        // Cap normals
-        dir.normalize();
-        negDir.normalize();
-        normalArray[fromoffset] = negDir.x;
-        normalArray[tooffset] = normalArray[endoffset] = dir.x;
-        normalArray[fromoffset + 1] = negDir.y;
-        normalArray[tooffset + 1] = normalArray[endoffset + 1] = dir.y;
-        normalArray[fromoffset + 2] = negDir.z;
-        normalArray[tooffset + 2] = normalArray[endoffset + 2] = dir.z;
+"varying vec3 vColor;",
 
-        // Final side
-        faceArray[faceoffset] = t1;
-        faceArray[faceoffset + 1] = t2;
-        faceArray[faceoffset + 2] = t4;
-        faceArray[faceoffset + 3] = t2;
-        faceArray[faceoffset + 4] = t3;
-        faceArray[faceoffset + 5] = t4;
-        // final caps
-        faceArray[faceoffset + 6] = t1;
-        faceArray[faceoffset + 7] = t4;
-        faceArray[faceoffset + 8] = fromi;
-        faceArray[faceoffset + 9] = t2b;
-        faceArray[faceoffset + 10] = toi;
-        faceArray[faceoffset + 11] = t3b;
-        // final arrowhead
-        faceArray[faceoffset + 12] = t2b;
-        faceArray[faceoffset + 13] = endi;
-        faceArray[faceoffset + 14] = t3b;
+"void main() {",
+    
+"    gl_FragColor = vec4( vColor, opacity );",
+    
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-        // sides
-        lineArray[lineoffset] = t1;
-        lineArray[lineoffset + 1] = t2;
-        lineArray[lineoffset + 2] = t1;
-        lineArray[lineoffset + 3] = t4;
-        // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
-        lineArray[lineoffset + 4] = t3;
-        lineArray[lineoffset + 5] = t4;
-        // caps
-        lineArray[lineoffset + 6] = t1;
-        lineArray[lineoffset + 7] = t4;
-        // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
-        // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+"}"
+                                                     
+].join("\n"),
+        
+        vertexShader : [
 
-        lineArray[lineoffset + 8] = t2b;
-        lineArray[lineoffset + 9] = t2; // toi
-        lineArray[lineoffset + 10] = t2b;
-        lineArray[lineoffset + 11] = t3b;
-        lineArray[lineoffset + 12] = t3;
-        lineArray[lineoffset + 13] = t3b; // toi
-        // arrowhead
-        lineArray[lineoffset + 14] = t2b;
-        lineArray[lineoffset + 15] = endi;
-        lineArray[lineoffset + 16] = t2b;
-        lineArray[lineoffset + 17] = t3b;
-        lineArray[lineoffset + 18] = endi;
-        lineArray[lineoffset + 19] = t3b;
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
 
-        geoGroup.faceidx += 15;
-        geoGroup.lineidx += 20;
+"attribute vec3 position;",
+"attribute vec3 color;",
 
-    };
+"varying vec3 vColor;",
 
-    // handles custom shape generation from user supplied arrays
-    // May need to generate normal and/or line indices
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {CustomSpec}
-     *            customSpec
-     */
-    var drawCustom = function(shape, geoGroup, customSpec) {
+"void main() {",
 
-        var vertexArr = customSpec.vertexArr, normalArr = customSpec.normalArr, faceArr = customSpec.faceArr, lineArr = customSpec.lineArr;
+"    vColor = color;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    gl_Position = projectionMatrix * mvPosition;",
 
-        if (vertexArr.length === 0 || faceArr.length === 0) {
-            console
-                    .warn("Error adding custom shape component: No vertices and/or face indices supplied!");
+"}"
+        
+].join("\n"),
+    
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000}
         }
 
-        geoGroup.vertices = vertexArr.length;
-        geoGroup.faceidx = faceArr.length;
-
-        var offset, v, a, b, c, i, il;
+    },
+    
+ 'sphereimposter' : {
+        fragmentShader : [
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
+"uniform mat4 projectionMatrix;",
 
-        for (i = 0, il = geoGroup.vertices; i < il; ++i) {
-            offset = i * 3;
-            v = vertexArr[i];
-            geoGroup.vertexArray[offset] = v.x;
-            geoGroup.vertexArray[offset + 1] = v.y;
-            geoGroup.vertexArray[offset + 2] = v.z;
-        }
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform float uDepth;",
+"uniform vec3 directionalLightColor[ 1 ];",
 
-        for (i = 0, il = geoGroup.faceidx / 3; i < il; ++i) {
-            offset = i * 3;
-            a = faceArr[offset];
-            b = faceArr[offset + 1];
-            c = faceArr[offset + 2];
-            var vA = new $3Dmol.Vector3(), vB = new $3Dmol.Vector3(), vC = new $3Dmol.Vector3();
-            shape.intersectionShape.triangle.push(new $3Dmol.Triangle(vA
-                    .copy(vertexArr[a]), vB.copy(vertexArr[b]), vC
-                    .copy(vertexArr[c])));
-        }
+"varying vec3 vColor;",
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 vLight;",
+"varying vec3 center;",
 
-        geoGroup.faceArray = new Uint16Array(faceArr);
 
-        geoGroup.truncateArrayBuffers(true, true);
+"void main() {",
+"    float lensqr = dot(mapping,mapping);",
+"    float rsqr = rval*rval;",
+"    if(lensqr > rsqr)",
+"       discard;",
+"    float z = sqrt(rsqr-lensqr);",
+"    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z);",
+"    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);",
+"    float ndcDepth = clipPos.z / clipPos.w;",
+"    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+"    vec3 norm = normalize(vec3(mapping.x,mapping.y,z));",
+"    float dotProduct = dot( norm, vLight );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",    
+"    vec3 vLight = directionalLightColor[ 0 ] * directionalLightWeighting;",
+"    gl_FragColor = vec4(vLight*vColor, opacity*opacity );", 
+"    float fogFactor = smoothstep( fogNear, fogFar, gl_FragDepthEXT/gl_FragCoord.w );",
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-        if (normalArr.length < geoGroup.vertices)
-            geoGroup.setNormals();
-        else {
 
-            geoGroup.normalArray = new Float32Array(geoGroup.vertices * 3);
-            var n;
-            for (i = 0, il = geoGroup.vertices; i < il; ++i) {
-                offset = i * 3;
-                n = normalArr[i];
-                geoGroup.normalArray[offset] = n.x;
-                geoGroup.normalArray[offset + 1] = n.y;
-                geoGroup.normalArray[offset + 2] = n.z;
-            }
-        }
+"}"
+                                                     
+].join("\n"),
+        
+        vertexShader : [
 
-        if (!lineArr.length)
-            geoGroup.setLineIndices();
-        else
-            geoGroup.lineArray = new Uint16Array(lineArr);
-
-        geoGroup.lineidx = geoGroup.lineArray.length;
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-    };
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-    // Read a cube file - generate model and possibly shape(s)
-    /**
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {geometryGroup}
-     *            geoGroup
-     * @param {string}
-     *            str
-     * @param {number}
-     *            isoval
-     * @param {boolean}
-     *            voxel
-     */
-    var parseCube = function(shape, geoGroup, str, isoval, voxel) {
+"varying vec2 mapping;",
+"varying vec3 vColor;",
+"varying float rval;",
+"varying vec3 vLight;",
+"varying vec3 center;",
 
-        var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
+"void main() {",
 
-        if (lines.length < 6)
-            return;
+"    vColor = color;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    center = mvPosition.xyz;",
+"    vec4 projPosition = projectionMatrix * mvPosition;",
+"    vec4 adjust = projectionMatrix* vec4(normal,0.0); adjust.z = 0.0; adjust.w = 0.0;",
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vLight = normalize( lDirection.xyz );",
+"    mapping = normal.xy;",
+"    rval = abs(normal.x);",
+"    gl_Position = projPosition+adjust;",
 
-        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
-                " ");
+"}"
+        
+].join("\n"),
+    
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-        var natoms = Math.abs(parseFloat(lineArr[0]));
-        var origin = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]));
+    },
+    
+    
+    'lambert' : { 
+        fragmentShader : [
 
-        lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-        // might have to convert from bohr units to angstroms
-        var convFactor = (parseFloat(lineArr[0]) > 0) ? 0.529177 : 1;
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-        origin.multiplyScalar(convFactor);
+"varying vec3 vLightFront;",
+"varying vec3 vColor;",
 
-        var nX = Math.abs(lineArr[0]);
-        var xVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
+"void main() {",
+    
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    
+"    #ifndef WIREFRAME",
+"    gl_FragColor.xyz *= vLightFront;",
+"    #endif",
+    
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-        lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+"}"
 
-        var nY = Math.abs(lineArr[0]);
-        var yVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
 
-        lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+].join("\n"),
+       
+       vertexShader : [
 
-        var nZ = Math.abs(lineArr[0]);
-        var zVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
-                parseFloat(lineArr[2]), parseFloat(lineArr[3]))
-                .multiplyScalar(convFactor);
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-        // lines.splice(6, natoms).join("\n");
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-        lines = new Float32Array(lines.splice(natoms + 7).join(" ").replace(
-                /^\s+/, "").split(/[\s\r]+/));
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
 
-        var vertnums = new Int16Array(nX * nY * nZ);
+"void main() {",
+    
+"    vColor = color;",
+    
+"    vec3 objectNormal = normal;",  
+"    vec3 transformedNormal = normalMatrix * objectNormal;",    
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    
+"    vLightFront = vec3( 0.0 );",
+    
+"    transformedNormal = normalize( transformedNormal );",
+    
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
+    
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
+    
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
+           
+].join("\n"),
 
-        var i, il;
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-        for (i = 0, il = vertnums.length; i < il; ++i)
-            vertnums[i] = -1;
+    },
 
-        var bitdata = new Uint8Array(nX * nY * nZ);
 
-        for (i = 0, il = lines.length; i < il; ++i) {
-            var val = (isoval >= 0) ? lines[i] - isoval : isoval - lines[i];
+    'instanced' : {
+        fragmentShader : [
 
-            if (val > 0)
-                bitdata[i] |= ISDONE;
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-        }
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-        var verts = [], faces = [];
+"varying vec3 vLightFront;",
+"varying vec3 vColor;",
 
-        $3Dmol.MarchingCube.march(bitdata, verts, faces, {
-            fulltable : true,
-            voxel : voxel,
-            scale : xVec.length(),
-            origin : origin,
-            nX : nX,
-            nY : nY,
-            nZ : nZ
-        });
+"void main() {",
 
-        if (!voxel)
-            $3Dmol.MarchingCube.laplacianSmooth(10, verts, faces);
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
 
-        drawCustom(shape, geoGroup, {
-            vertexArr : verts,
-            faceArr : faces,
-            normalArr : [],
-            lineArr : []
-        });
+"    #ifndef WIREFRAME",
+"    gl_FragColor.xyz *= vLightFront;",
+"    #endif",
 
-    };
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
 
-    // Update a bounding sphere's position and radius
-    // from list of centroids and new points
-    /**
-     * @param {$3Dmol.Sphere}
-     *            sphere
-     * @param {Object}
-     *            components
-     * @param {Array}
-     *            points
-     */
-    var updateBoundingFromPoints = function(sphere, components, points) {
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
 
-        sphere.center.set(0, 0, 0);
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-        var i, il;
+"}"
 
-        if (components.length > 0) {
 
-            for (i = 0, il = components.length; i < il; ++i) {
-                var centroid = components[i].centroid;
-                sphere.center.add(centroid);
-            }
+].join("\n"),
 
-            sphere.center.divideScalar(components.length);
-        }
+       vertexShader : [
 
-        var maxRadiusSq = sphere.radius * sphere.radius;
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-        for (i = 0, il = points.length / 3; i < il; i++) {
-            var x = points[i * 3], y = points[i * 3 + 1], z = points[i * 3 + 2];
-            var radiusSq = sphere.center.distanceToSquared({
-                x : x,
-                y : y,
-                z : z
-            });
-            maxRadiusSq = Math.max(maxRadiusSq, radiusSq);
-        }
+"attribute vec3 offset;",
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-        sphere.radius = Math.sqrt(maxRadiusSq);
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
 
-    };
+"void main() {",
 
-    /**
-     * 
-     * @param {$3Dmol.GLShape}
-     *            shape
-     * @param {ShapeSpec}
-     *            stylespec
-     * @returns {undefined}
-     */
-    var updateFromStyle = function(shape, stylespec) {
-        shape.color = stylespec.color || new $3Dmol.Color();
-        if(! (stylespec.color instanceof $3Dmol.Color))
-            shape.color = $3Dmol.CC.color(stylespec.color);
-        shape.wireframe = stylespec.wireframe ? true : false;
-        shape.alpha = stylespec.alpha ? $3Dmol.Math.clamp(stylespec.alpha, 0.0,
-                1.0) : 1.0;
-        shape.side = (stylespec.side !== undefined) ? stylespec.side
-                : $3Dmol.DoubleSide;
-        shape.linewidth = typeof(stylespec.linewidth) == 'undefined' ? 1 : stylespec.linewidth;
-        // Click handling
-        shape.clickable = stylespec.clickable ? true : false;
-        shape.callback = typeof (stylespec.callback) === "function" ? stylespec.callback
-                : null;
-    };
+"    vColor = color;",
 
-    /**
-     * Custom renderable shape
-     * 
-     * @constructor $3Dmol.GLShape
-     * 
-     * @param {Object}
-     *            stylespec
-     * @returns {$3Dmol.GLShape}
-     */
-    function GLShape(stylespec) {
+"    vec3 objectNormal = normal;",
+"    vec3 transformedNormal = normalMatrix * objectNormal;",
+"    vec4 mvPosition = modelViewMatrix * vec4( position * radius + offset, 1.0 );",
 
-        stylespec = stylespec || {};
-        $3Dmol.ShapeIDCount++;
+"    vLightFront = vec3( 0.0 );",
 
-        this.boundingSphere = new $3Dmol.Sphere();
-        /** @type {IntersectionShapes} */
-        this.intersectionShape = {
-            sphere : [],
-            cylinder : [],
-            line : [],
-            triangle : []
-        };
+"    transformedNormal = normalize( transformedNormal );",
 
-        updateFromStyle(this, stylespec);
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
 
-        // Keep track of shape components and their centroids
-        var components = [];
-        var shapeObj = null;
-        var renderedShapeObj = null;
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
 
-        var geo = new $3Dmol.Geometry(true);
-        var linegeo = new $3Dmol.Geometry(true);
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
 
-        /** Update shape with new style specification
-         * @param {ShapeSpec} newspec
-         * @return {$3Dmol.GLShape}
-         */
-        this.updateStyle = function(newspec) {
+].join("\n"),
 
-            for ( var prop in newspec) {
-                stylespec[prop] = newspec[prop];
-            }
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
+        }
 
-            updateFromStyle(this, stylespec);
-        };
+    },
+ 
+//for outline
+     'outline' : { 
+        fragmentShader : [
 
-        /**
-         * Creates a custom shape from supplied vertex and face arrays
-         * @param {CustomSpec} customSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCustom = function(customSpec) {
+"uniform float opacity;",
+"uniform vec3 outlineColor;",
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-            customSpec.vertexArr = customSpec.vertexArr || [];
-            customSpec.faceArr = customSpec.faceArr || [];
-            customSpec.normalArr = customSpec.normalArr || [];
-            customSpec.lineArr = customSpec.lineArr || [];
+"void main() {",
+    
+"    gl_FragColor = vec4( outlineColor, 1 );",
+"}"
 
-            // Force creation of new geometryGroup for each added component
-            var geoGroup = geo.addGeoGroup();
-            drawCustom(this, geoGroup, customSpec);
-            geoGroup.truncateArrayBuffers(true, true);
 
-            for (var i = 0; i < geoGroup.colorArray.length / 3; ++i) {
-                geoGroup.colorArray[i * 3] = this.color.r;
-                geoGroup.colorArray[i * 3 + 1] = this.color.g;
-                geoGroup.colorArray[i * 3 + 2] = this.color.b;
-            }
+].join("\n"),
+       
+       vertexShader : [
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : geoGroup.getCentroid()
-            });
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
-        };
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-        /**
-         * Creates a sphere shape
-         * @param {SphereSpec} sphereSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addSphere = function(sphereSpec) {
+"void main() {",
 
-            sphereSpec.center = sphereSpec.center || {
-                x : 0,
-                y : 0,
-                z : 0
-            };
-            sphereSpec.radius = sphereSpec.radius ? $3Dmol.Math.clamp(
-                    sphereSpec.radius, 0, Infinity) : 1.5;
-            sphereSpec.color = $3Dmol.CC.color(sphereSpec.color);
-            
-            this.intersectionShape.sphere.push(new $3Dmol.Sphere(
-                    sphereSpec.center, sphereSpec.radius));
+"    vec4 norm = modelViewMatrix*vec4(normalize(normal),0.0);",
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    mvPosition.xy += norm.xy*outlineWidth;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    mvPosition.z -= outlinePushback;", //go backwards in model space
+"    vec4 pushpos = projectionMatrix*mvPosition;", //project to get z in projection space, I'm probably missing some simple math to do the same thing..
+"    gl_Position.z = gl_Position.w*pushpos.z/pushpos.w;",
+"}"
+           
+].join("\n"),
 
-            var geoGroup = geo.addGeoGroup();
-            $3Dmol.GLDraw.drawSphere(geo, sphereSpec.center,
-                    sphereSpec.radius, sphereSpec.color);
-            geoGroup.truncateArrayBuffers(true, true);
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},           
+            outlineWidth: { type: 'f', value: 0.1 },
+            outlinePushback: { type: 'f', value: 1.0 },
+        }
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup, // has to be last group added
-                centroid : new $3Dmol.Vector3(sphereSpec.center.x,
-                        sphereSpec.center.y, sphereSpec.center.z)
-            });
+    },
+//for outlining sphere imposter
+    'sphereimposteroutline' : { 
+       fragmentShader : [
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
-        };
+"uniform float opacity;",
+"uniform vec3 outlineColor;",
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform mat4 projectionMatrix;",
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 center;",
 
-        /**
-         * Creates a cylinder shape
-         * @param {CylinderSpec} cylinderSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCylinder = function(cylinderSpec) {
+"uniform float outlinePushback;",
 
-            cylinderSpec.start = cylinderSpec.start || {};
-            cylinderSpec.end = cylinderSpec.end || {};
 
-            var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
-                    cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
-            var end = new $3Dmol.Vector3(cylinderSpec.end.x,
-                    cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
-        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+"void main() {",
+"    float lensqr = dot(mapping,mapping);",
+"    float rsqr = rval*rval;",
+"    if(lensqr > rsqr)",
+"       discard;",
+"    float z = sqrt(rsqr-lensqr);",
+"    vec3 cameraPos = center+ vec3(mapping.x,mapping.y,z-outlinePushback);",
+"    vec4 clipPos = projectionMatrix * vec4(cameraPos, 1.0);",
+"    float ndcDepth = clipPos.z / clipPos.w;",
+"    gl_FragDepthEXT = ((gl_DepthRange.diff * ndcDepth) + gl_DepthRange.near + gl_DepthRange.far) / 2.0;",
+"    gl_FragColor = vec4(outlineColor, 1 );",
+"}"
 
-            var radius = cylinderSpec.radius || 0.1;
-            var color = $3Dmol.CC.color(cylinderSpec.color);
-            
-            this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(start, end, radius));
 
-            var geoGroup = geo.addGeoGroup();
-            $3Dmol.GLDraw.drawCylinder(geo, start, end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);            
-            geoGroup.truncateArrayBuffers(true, true);
-            
-            var centroid = new $3Dmol.Vector3();
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
-            });
+].join("\n"),
+      
+      vertexShader : [
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-        };
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-        /**
-         * Creates a line shape
-         * @param {LineSpec} lineSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addLine = function(lineSpec) {
-        	lineSpec.start = lineSpec.start || {};
-        	lineSpec.end = lineSpec.end || {};
+"varying vec2 mapping;",
+"varying float rval;",
+"varying vec3 center;",
 
-        	var start = new $3Dmol.Vector3(lineSpec.start.x || 0,
-        			lineSpec.start.y || 0, lineSpec.start.z || 0);
-        	var end = new $3Dmol.Vector3(lineSpec.end.x,
-        			lineSpec.end.y || 0, lineSpec.end.z || 0);            
-        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
-    
-            var geoGroup = geo.addGeoGroup();
+"void main() {",
 
-            //make line from start to end
-            //for consistency with rest of shapes, uses vertices and lines rather
-            //than a separate line geometry
-            var vstart = geoGroup.vertices;
-            var i = vstart*3;
-            var vertexArray = geoGroup.vertexArray;
-            vertexArray[i] = start.x;
-            vertexArray[i+1] = start.y;
-            vertexArray[i+2] = start.z;
-            vertexArray[i+3] = end.x;
-            vertexArray[i+4] = end.y;
-            vertexArray[i+5] = end.z;
-            geoGroup.vertices += 2;
-            
-            var lineArray = geoGroup.lineArray;
-            var li =  geoGroup.lineidx;
-            lineArray[li] = vstart;
-            lineArray[li+1] = vstart+1;
-            geoGroup.lineidx += 2;
-            
-            geoGroup.truncateArrayBuffers(true, true);
-        }
-        /**
-         * Creates an arrow shape
-         * @param {ArrowSpec} arrowSpec
-         * @return {$3Dmol.GLShape}
-         */
-        this.addArrow = function(arrowSpec) {
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+"    center = mvPosition.xyz;",
+"    vec4 projPosition = projectionMatrix * mvPosition;",
+"    vec2 norm = normal.xy + vec2(sign(normal.x)*outlineWidth,sign(normal.y)*outlineWidth);", 
+"    vec4 adjust = projectionMatrix* vec4(norm,normal.z,0.0); adjust.z = 0.0; adjust.w = 0.0;",
+"    mapping = norm.xy;",
+"    rval = abs(norm.x);",
+"    gl_Position = projPosition+adjust;",
+"}"
+          
+].join("\n"),
 
-            arrowSpec.start = arrowSpec.start || {};
-            arrowSpec.end = arrowSpec.end || {};
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},           
+           outlineWidth: { type: 'f', value: 0.1 },
+           outlinePushback: { type: 'f', value: 1.0 },
+       }
 
-            arrowSpec.start = new $3Dmol.Vector3(arrowSpec.start.x || 0,
-                    arrowSpec.start.y || 0, arrowSpec.start.z || 0);
+   },
+   //stick imposters
+   'stickimposter' : { 
+      fragmentShader : [$3Dmol.ShaderUtils.stickimposterFragmentShader,
+    "    float dotProduct = dot( norm, vLight );",
+    "    vec3 light = vec3( max( dotProduct, 0.0 ) );",    
+    "    gl_FragColor = vec4(light*color, opacity*opacity );", 
+    "    float fogFactor = smoothstep( fogNear, fogFar, depth );",   
+    "    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
+    "}"].join("\n"),
+      vertexShader : [
 
-            if (arrowSpec.dir instanceof $3Dmol.Vector3
-                    && arrowSpec.length instanceof number) {
-                var end = arrowSpec.dir.clone().multiplyScalar(arrowSpec.length).add(
-                        start);
-                arrowSpec.end = end;
-            }
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-            else {
-                arrowSpec.end = new $3Dmol.Vector3(arrowSpec.end.x,
-                        arrowSpec.end.y || 0, arrowSpec.end.z || 0);
-            	if(typeof(arrowSpec.end.x) == 'undefined') arrowSpec.end.x = 3; //show something even if undefined
-            }
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-            arrowSpec.radius = arrowSpec.radius || 0.1;
+"varying vec3 vColor;",
+"varying vec3 vLight;",
+"varying vec3 cposition;",
+"varying vec3 p1;",
+"varying vec3 p2;",
+"varying float r;",
 
-            arrowSpec.radiusRatio = arrowSpec.radiusRatio || 1.618034;
-            arrowSpec.mid = (0 < arrowSpec.mid && arrowSpec.mid < 1) ? arrowSpec.mid
-                    : 0.618034;
+"void main() {",
+   
+"    vColor = color; vColor.z = abs(vColor.z);", //z indicates which vertex and so would vary
+"    r = abs(radius);",
+"    vec4 to = modelViewMatrix*vec4(normal, 1.0);", //normal is other point of cylinder
+"    vec4 pt = modelViewMatrix*vec4(position, 1.0);",
+"    vec4 mvPosition = pt;",
+"    p1 = pt.xyz; p2 = to.xyz;",
+"    vec3 norm = to.xyz-pt.xyz;","" +
+"    float mult = 1.1;", //slop to account for perspective of sphere
+"    if(length(p1) > length(p2)) {", //billboard at level of closest point
+"       mvPosition = to;",
+"    }",
+"    vec3 n = normalize(mvPosition.xyz);",
+//intersect with the plane defined by the camera looking at the billboard point
+"    if(color.z >= 0.0) {", //p1
+"       vec3 pnorm = normalize(p1);",
+"       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p1+t*pnorm;",
+"    } else {",
+"       vec3 pnorm = normalize(p2);",
+"       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p2+t*pnorm;",
+"       mult *= -1.0;",
+"    }",
+"    vec3 cr = normalize(cross(mvPosition.xyz,norm))*radius;", 
+"    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*radius;", 
+"    mvPosition.xy +=  mult*(cr + doublecr).xy;",
+"    cposition = mvPosition.xyz;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vLight = normalize( lDirection.xyz )*directionalLightColor[0];", //not really sure this is right, but color is always white so..
+"}"
+          
+].join("\n"),
 
-            var geoGroup = geo.addGeoGroup();
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},         
+           directionalLightColor: { type: 'fv', value: [] },
+           directionalLightDirection: { type: 'fv', value: [] }
+       }
 
-            drawArrow(this, geoGroup, arrowSpec);
-            geoGroup.truncateArrayBuffers(true, true);
+   },
+   //stick imposter outlines
+   'stickimposteroutline' : { 
+      fragmentShader : $3Dmol.ShaderUtils.stickimposterFragmentShader + 'gl_FragColor = vec4(color,1.0);}',   
+      vertexShader : [
 
-            var centroid = new $3Dmol.Vector3();
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : centroid.addVectors(arrowSpec.start, arrowSpec.end)
-                        .multiplyScalar(0.5)
-            });
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
+"uniform vec3 outlineColor;",
+"uniform float outlineWidth;",
+"uniform float outlinePushback;",
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
 
-        };
-        
-        /** 
-         * Creates custom shape from volumetric data 
-         * @param {string} data - Volumetric input data 
-         * @param {string} fmt - Input data format (e.g. 'cube' for cube file format)
-         * @param {VolSpec} volSpec - Volumetric data shape specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addVolumetricData = function(data, fmt, volSpec) {
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
+"attribute float radius;",
 
-            // str, fmt, isoval, vxl
-            var isoval = (volSpec.isoval !== undefined && typeof (volSpec.isoval) === "number") ? volSpec.isoval
-                    : 0.0;
-            var vxl = (volSpec.voxel) ? true : false;
+"varying vec3 vColor;",
+"varying vec3 vLight;",
+"varying vec3 cposition;",
+"varying vec3 p1;",
+"varying vec3 p2;",
+"varying float r;",
 
-            var geoGroup = geo.addGeoGroup();
+"void main() {",
+   
+"    vColor = outlineColor;",
+"    float rad = radius+sign(radius)*outlineWidth;",
+"    r = abs(rad);",
+"    vec4 to = modelViewMatrix*vec4(normal, 1.0);", //normal is other point of cylinder
+"    vec4 pt = modelViewMatrix*vec4(position, 1.0);",
+//pushback
+"    to.xyz += normalize(to.xyz)*outlinePushback;",
+"    pt.xyz += normalize(pt.xyz)*outlinePushback;",
+
+"    vec4 mvPosition = pt;",
+"    p1 = pt.xyz; p2 = to.xyz;",
+"    vec3 norm = to.xyz-pt.xyz;","" +
+"    float mult = 1.1;", //slop to account for perspective of sphere
+"    if(length(p1) > length(p2)) {", //billboard at level of closest point
+"       mvPosition = to;",
+"    }",
+"    vec3 n = normalize(mvPosition.xyz);",
+//intersect with the plane defined by the camera looking at the billboard point
+"    if(color.z >= 0.0) {", //p1
+"       vec3 pnorm = normalize(p1);",
+"       float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p1+t*pnorm;",
+"    } else {",
+"       vec3 pnorm = normalize(p2);",
+"       float t = dot(mvPosition.xyz-p2,n)/dot(pnorm,n);",
+"       mvPosition.xyz = p2+t*pnorm;",
+"       mult *= -1.0;",
+"    }",
+"    vec3 cr = normalize(cross(mvPosition.xyz,norm))*rad;", 
+"    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*rad;", 
+"    mvPosition.xy +=  mult*(cr + doublecr).xy;",
+"    cposition = mvPosition.xyz;",
+"    gl_Position = projectionMatrix * mvPosition;",
+"    vLight = vec3(1.0,1.0,1.0);",
+"}"
+          
+].join("\n"),
 
-            // TODO: Initialize geometry group here (parseCube currently calls
-            // addCustom...)
-            switch (fmt) {
-            case "cube":
-                parseCube(this, geoGroup, data, isoval, vxl);
-                break;
-            }
+       uniforms : {
+           opacity: { type: 'f', value: 1.0 },
+           fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+           fogNear: { type: 'f', value: 1.0 },
+           fogFar: { type: 'f', value: 2000},         
+           outlineColor: { type: 'c', value: new $3Dmol.Color(0.0, 0.0, 0.0) },         
+           outlineWidth: { type: 'f', value: 0.1 },
+           outlinePushback: { type: 'f', value: 1.0 },         
+       }
 
-            components.push({
-                id : geoGroup.id,
-                geoGroup : geoGroup,
-                centroid : geoGroup.getCentroid()
-            });
+   },
+    //for double sided lighting
+    'lambertdouble' : { 
+        fragmentShader : [
 
-            this.updateStyle(volSpec);
+"uniform mat4 viewMatrix;",
+"uniform float opacity;",
 
-            updateBoundingFromPoints(this.boundingSphere, components,
-                    geoGroup.vertexArray);
+"uniform vec3 fogColor;",
+"uniform float fogNear;",
+"uniform float fogFar;",
 
-        };
+"varying vec3 vLightFront;",
+"varying vec3 vLightBack;",
 
-        /**
-         * Initialize webgl objects for rendering
-         * @param {$3Dmol.Object3D} group
-         * 
-         */  
-        this.globj = function(group) {
+"varying vec3 vColor;",
 
-            geo.initTypedArrays();
+"void main() {",
+    
+"    gl_FragColor = vec4( vec3 ( 1.0 ), opacity );",
+    
+"    #ifndef WIREFRAME",
+"    if ( gl_FrontFacing )",
+"       gl_FragColor.xyz *= vLightFront;",
+"    else",
+"       gl_FragColor.xyz *= vLightBack;",
+"    #endif",
+    
+"    gl_FragColor = gl_FragColor * vec4( vColor, opacity );",
+"    float depth = gl_FragCoord.z / gl_FragCoord.w;",
+    
+"    float fogFactor = smoothstep( fogNear, fogFar, depth );",
+    
+"    gl_FragColor = mix( gl_FragColor, vec4( fogColor, gl_FragColor.w ), fogFactor );",
 
-            updateColor(geo, this.color);
+"}"
 
-            shapeObj = new $3Dmol.Object3D();
-            var material = new $3Dmol.MeshLambertMaterial({
-                wireframe : this.wireframe,
-                vertexColors : true,
-                ambient : 0x000000,
-                reflectivity : 0,
-                side : this.side,
-                transparent : (this.alpha < 1) ? true : false,
-                opacity : this.alpha,
-                wireframeLinewidth: this.linewidth
-            });
-            
-            var mesh = new $3Dmol.Mesh(geo, material);
-            shapeObj.add(mesh);
-            
-            var lineMaterial = new $3Dmol.LineBasicMaterial({
-                linewidth : this.linewidth,
-                color: this.color
-            });
-            var line = new $3Dmol.Line(linegeo, lineMaterial,
-                    $3Dmol.LinePieces);
-            shapeObj.add(line);
 
-            if (renderedShapeObj) {
-                group.remove(renderedShapeObj);
-                renderedShapeObj = null;
-            }
-            renderedShapeObj = shapeObj.clone();
-            group.add(renderedShapeObj);
+].join("\n"),
+       
+       vertexShader : [
 
-        };
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform mat4 viewMatrix;",
+"uniform mat3 normalMatrix;",
+"uniform vec3 directionalLightColor[ 1 ];",
+"uniform vec3 directionalLightDirection[ 1 ];",
 
-        this.removegl = function(group) {
-            if (renderedShapeObj) {
-                // dispose of geos and materials
-                if (renderedShapeObj.geometry !== undefined)
-                    renderedShapeObj.geometry.dispose();
-                if (renderedShapeObj.material !== undefined)
-                    renderedShapeObj.material.dispose();
-                group.remove(renderedShapeObj);
-                renderedShapeObj = null;
-            }
-            shapeObj = null;
-        };
+"attribute vec3 position;",
+"attribute vec3 normal;",
+"attribute vec3 color;",
 
-    };
+"varying vec3 vColor;",
+"varying vec3 vLightFront;",
+"varying vec3 vLightBack;",
 
-    Object.defineProperty(GLShape.prototype, "position", {
+"void main() {",
+    
+"    vColor = color;",
+    
+"    vec3 objectNormal = normal;",  
+"    vec3 transformedNormal = normalMatrix * objectNormal;",    
+"    vec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );",
+    
+"    vLightFront = vec3( 0.0 );",
+"    vLightBack = vec3( 0.0 );",
+    
+"    transformedNormal = normalize( transformedNormal );",
+    
+"    vec4 lDirection = viewMatrix * vec4( directionalLightDirection[ 0 ], 0.0 );",
+"    vec3 dirVector = normalize( lDirection.xyz );",
+"    float dotProduct = dot( transformedNormal, dirVector );",
+"    vec3 directionalLightWeighting = vec3( max( dotProduct, 0.0 ) );",
+"    vec3 directionalLightWeightingBack = vec3( max( -dotProduct, 0.0 ) );",
 
-        get : function() {
-            return this.boundingSphere.center;
+"    vLightFront += directionalLightColor[ 0 ] * directionalLightWeighting;",
+"    vLightBack += directionalLightColor[ 0 ] * directionalLightWeightingBack;",
+
+"    gl_Position = projectionMatrix * mvPosition;",
+"}"
+           
+].join("\n"),
+
+        uniforms : {
+            opacity: { type: 'f', value: 1.0 },
+            fogColor: { type: 'c', value: new $3Dmol.Color(1.0, 1.0, 1.0) },
+            fogNear: { type: 'f', value: 1.0 },
+            fogFar: { type: 'f', value: 2000},           
+            directionalLightColor: { type: 'fv', value: [] },
+            directionalLightDirection: { type: 'fv', value: [] }
         }
 
-    });
+    },
+    
+    
+    'sprite': {
+        
+        fragmentShader: [
+                                                         
+"uniform vec3 color;",
+"uniform sampler2D map;",
+"uniform float opacity;",
 
-    Object.defineProperty(GLShape.prototype, "x", {
+"uniform int fogType;",
+"uniform vec3 fogColor;",
+"uniform float fogDensity;",
+"uniform float fogNear;",
+"uniform float fogFar;",
+"uniform float alphaTest;",
 
-        get : function() {
-            return this.boundingSphere.center.x;
-        }
+"varying vec2 vUV;",
 
-    });
+"void main() {",
+    
+"    vec4 texture = texture2D(map, vUV);",
+    
+"    if (texture.a < alphaTest) discard;",
+    
+"    gl_FragColor = vec4(color * texture.xyz, texture.a * opacity);",
+    
+"    if (fogType > 0) {",
+        
+"        float depth = gl_FragCoord.z / gl_FragCoord.w;",
+"        float fogFactor = 0.0;",
+        
+"        if (fogType == 1) {",
+"            fogFactor = smoothstep(fogNear, fogFar, depth);",
+"        }",
+        
+"        else {",
+"            const float LOG2 = 1.442695;",
+"            float fogFactor = exp2(- fogDensity * fogDensity * depth * depth * LOG2);",
+"            fogFactor = 1.0 - clamp(fogFactor, 0.0, 1.0);",
+"        }",
+        
+"        gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w), fogFactor);",
+        
+"    }",
+"}"                                              
+            
+].join("\n"),
+        
+        vertexShader: [
 
-    Object.defineProperty(GLShape.prototype, "y", {
+"uniform int useScreenCoordinates;",
+"uniform vec3 screenPosition;",
+"uniform mat4 modelViewMatrix;",
+"uniform mat4 projectionMatrix;",
+"uniform float rotation;",
+"uniform vec2 scale;",
+"uniform vec2 alignment;",
+"uniform vec2 uvOffset;",
+"uniform vec2 uvScale;",
 
-        get : function() {
-            return this.boundingSphere.center.y;
-        }
+"attribute vec2 position;",
+"attribute vec2 uv;",
 
-    });
+"varying vec2 vUV;",
 
-    Object.defineProperty(GLShape.prototype, "z", {
+"void main() {",
+    
+"    vUV = uvOffset + uv * uvScale;",
+    
+"    vec2 alignedPosition = position + alignment;",
+    
+"    vec2 rotatedPosition;",
+"    rotatedPosition.x = ( cos(rotation) * alignedPosition.x - sin(rotation) * alignedPosition.y ) * scale.x;",
+"    rotatedPosition.y = ( sin(rotation) * alignedPosition.x + cos(rotation) * alignedPosition.y ) * scale.y;",
+    
+"    vec4 finalPosition;",
+    
+"    if(useScreenCoordinates != 0) {",
+"        finalPosition = vec4(screenPosition.xy + rotatedPosition, screenPosition.z, 1.0);",
+"    }",
+    
+"    else {",
+"        finalPosition = projectionMatrix * modelViewMatrix * vec4(0.0, 0.0, 0.0, 1.0); finalPosition /= finalPosition.w;",
+"        finalPosition.xy += rotatedPosition; ",
+"    }",
+    
+"    gl_Position = finalPosition;",
+    
+"}"
+       
+].join("\n"),
 
-        get : function() {
-            return this.boundingSphere.center.z;
+        uniforms : {
+            
         }
+        
+    }
+    
+};
+/*  ProteinSurface.js by biochem_fan
 
-    });
+Ported and modified for Javascript based on EDTSurf,
+  whose license is as follows.
 
-    return GLShape;
+Permission to use, copy, modify, and distribute this program for any
+purpose, with or without fee, is hereby granted, provided that this
+copyright notice and the reference information appear in all copies or
+substantial portions of the Software. It is provided "as is" without
+express or implied warranty. 
 
-}());
+Reference:
+http://zhanglab.ccmb.med.umich.edu/EDTSurf/
+D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces
+by Euclidean Distance Transform. PLoS ONE 4(12): e8140.
 
-$3Dmol.ShapeIDCount = 0;//a molecular viewer based on GLMol
+=======
 
+TODO: Improved performance on Firefox
+      Reduce memory consumption
+      Refactor!
+ */
 
 
-/**
- * WebGL-based 3Dmol.js viewer
- * Note: The preferred method of instantiating a GLViewer is through {@link $3Dmol.createViewer} 
- * 
- * @constructor 
- * @param {Object} element HTML element within which to create viewer
- * @param {function} callback - Callback function to be immediately executed on this viewer
- * @param {Object} defaultcolors - Object defining default atom colors as atom => color property value pairs for all models within this viewer
- */
-$3Dmol.GLViewer = (function() {
-    // private class variables
-    var numWorkers = 4; // number of threads for surface generation
-    var maxVolume = 64000; // how much to break up surface calculations
-
-    // private class helper functions
-
-    function GLViewer(element, config) { 
-        // set variables
-    	config = config || {};
-    	var callback = config.callback;
-    	var defaultcolors = config.defaultcolors;    	
-        if(!defaultcolors)
-            defaultcolors = $3Dmol.elementColors.defaultColors;
-    	var nomouse = config.nomouse;
-    	var bgColor = 0;
-    	
-    	if(typeof(config.backgroundColor) != undefined) {
-            bgColor = $3Dmol.CC.color(config.backgroundColor).getHex();
-    	}
-        var _viewer = this;
-        var container = element;
-        var id = container.id;
-
-        var models = []; // atomistic molecular models
-        var surfaces = [];
-        var shapes = []; // Generic shapes
-        var labels = [];
-        var clickables = []; //things you can click on
-        var WIDTH = container.width();
-        var HEIGHT = container.height();
-
-        // set dimensions
-        // $(container).width(WIDTH);
-        // $(container).height(HEIGHT);
+// dkoes
+// Surface calculations.  This must be safe to use within a web worker.
+if (typeof console === 'undefined') {
+    // this should only be true inside of a webworker
+    console = {
+        log : function() {
+        }
+    };
+}
 
-        var ASPECT = WIDTH / HEIGHT;
-        var NEAR = 1, FAR = 800;
-        var CAMERA_Z = 150;
-        var fov = 20;
+$3Dmol.ProteinSurface = function() {
 
+    // constants for vpbits bitmasks
+    /** @const */
+    var INOUT = 1;
+    /** @const */
+    var ISDONE = 2;
+    /** @const */
+    var ISBOUND = 4;
 
-        var renderer = new $3Dmol.Renderer({
-            antialias : true,
-            premultipliedAlpha : false /* more traditional compositing with background */
-        });
+    var ptranx = 0, ptrany = 0, ptranz = 0;
+    var probeRadius = 1.4;
+    var defaultScaleFactor = 2;
+    var scaleFactor = defaultScaleFactor; // 2 is .5A grid; if this is made user configurable,
+                            // also have to adjust offset used to find non-shown
+                            // atoms
+    var pHeight = 0, pWidth = 0, pLength = 0;
+    var cutRadius = 0;
+    var vpBits = null; // uint8 array of bitmasks
+    var vpDistance = null; // floatarray of _squared_ distances
+    var vpAtomID = null; // intarray
+    var vertnumber = 0, facenumber = 0;
+    var pminx = 0, pminy = 0, pminz = 0, pmaxx = 0, pmaxy = 0, pmaxz = 0;
 
-        renderer.domElement.style.width = "100%";
-        renderer.domElement.style.height = "100%";
-        renderer.domElement.style.padding = "0";
-        renderer.domElement.style.position = "absolute"; //TODO: get rid of this
-        renderer.domElement.style.top = "0px";
-        renderer.domElement.style.zIndex = "0";
-        container.append(renderer.domElement);
-        renderer.setSize(WIDTH, HEIGHT);
-        var camera = new $3Dmol.Camera(fov, ASPECT, NEAR, FAR);
-        camera.position = new $3Dmol.Vector3(0, 0, CAMERA_Z);
-        var lookingAt = new $3Dmol.Vector3();
-        camera.lookAt(lookingAt);
+    var vdwRadii = {
+            "H" : 1.2,
+            "Li" : 1.82,
+            "Na" : 2.27,
+            "K" : 2.75,
+            "C" : 1.7,
+            "N" : 1.55,
+            "O" : 1.52,
+            "F" : 1.47,
+            "P" : 1.80,
+            "S" : 1.80,
+            "CL" : 1.75,
+            "BR" : 1.85,
+            "SE" : 1.90,
+            "ZN" : 1.39,
+            "CU" : 1.4,
+            "NI" : 1.63,
+            "X" : 2
+        };
+    
+    /** @param {AtomSpec} atom */
+    var getVDWIndex = function(atom) {
+        if(!atom.elem || typeof(vdwRadii[atom.elem]) == "undefined") {
+            return "X";
+        }
+        return atom.elem;
+    };
+    
+    var depty = {}, widxz = {};
+    var faces, verts;
+    var nb = [ new Int32Array([ 1, 0, 0 ]), new Int32Array([ -1, 0, 0 ]), 
+               new Int32Array([ 0, 1, 0 ]), new Int32Array([ 0, -1, 0 ]),
+               new Int32Array([ 0, 0, 1 ]), 
+               new Int32Array([ 0, 0, -1 ]), 
+               new Int32Array([ 1, 1, 0 ]), 
+               new Int32Array([ 1, -1, 0 ]), 
+               new Int32Array([ -1, 1, 0 ]),
+               new Int32Array([ -1, -1, 0 ]), 
+               new Int32Array([ 1, 0, 1 ]), 
+               new Int32Array([ 1, 0, -1 ]), 
+               new Int32Array([ -1, 0, 1 ]),
+               new Int32Array([ -1, 0, -1 ]), 
+               new Int32Array([ 0, 1, 1 ]), 
+               new Int32Array([ 0, 1, -1 ]), 
+               new Int32Array([ 0, -1, 1 ]),
+               new Int32Array([ 0, -1, -1 ]), 
+               new Int32Array([ 1, 1, 1 ]), 
+               new Int32Array([ 1, 1, -1 ]), 
+               new Int32Array([ 1, -1, 1 ]),
+               new Int32Array([ -1, 1, 1 ]), 
+               new Int32Array([ 1, -1, -1 ]), 
+               new Int32Array([ -1, -1, 1 ]), 
+               new Int32Array([ -1, 1, -1 ]),
+               new Int32Array([ -1, -1, -1 ]) ];
 
-        var raycaster = new $3Dmol.Raycaster(new $3Dmol.Vector3(0, 0, 0),
-                new $3Dmol.Vector3(0, 0, 0));
-        var projector = new $3Dmol.Projector();
-        var mouseVector = new $3Dmol.Vector3(0, 0, 0);
+    var origextent;
 
-        var scene = null;
-        var rotationGroup = null; // which contains modelGroup
-        var modelGroup = null;
+    var inOrigExtent = function(x, y, z) {
+        if (x < origextent[0][0] || x > origextent[1][0])
+            return false;
+        if (y < origextent[0][1] || y > origextent[1][1])
+            return false;
+        if (z < origextent[0][2] || z > origextent[1][2])
+            return false;
+        return true;
+    };
 
-        var fogStart = 0.4;
-        var slabNear = -50; // relative to the center of rotationGroup
-        var slabFar = 50;
+    this.getFacesAndVertices = function(atomlist) {
+        var atomsToShow = {};
+        var i, il;
+        for (i = 0, il = atomlist.length; i < il; i++)
+            atomsToShow[atomlist[i]] = true;
+        var vertices = verts;
+        for (i = 0, il = vertices.length; i < il; i++) {
+            vertices[i].x = vertices[i].x / scaleFactor - ptranx;
+            vertices[i].y = vertices[i].y / scaleFactor - ptrany;
+            vertices[i].z = vertices[i].z / scaleFactor - ptranz;
+        }
 
-        // UI variables
-        var cq = new $3Dmol.Quaternion(0, 0, 0, 1);
-        var dq = new $3Dmol.Quaternion(0, 0, 0, 1);
-        var isDragging = false;
-        var mouseStartX = 0;
-        var mouseStartY = 0;
-        var touchDistanceStart = 0;
-        var currentModelPos = 0;
-        var cz = 0;
-        var cslabNear = 0;
-        var cslabFar = 0;
+        var finalfaces = [];
+        for (i = 0, il = faces.length; i < il; i += 3) {
+            //var f = faces[i];
+            var fa = faces[i], fb = faces[i+1], fc = faces[i+2];
+            var a = vertices[fa]['atomid'], b = vertices[fb]['atomid'], c = vertices[fc]['atomid'];
 
-        var setSlabAndFog = function() {
-            var center = camera.position.z - rotationGroup.position.z;
-            if (center < 1)
-                center = 1;
-            camera.near = center + slabNear;
-            if (camera.near < 1)
-                camera.near = 1;
-            camera.far = center + slabFar;
-            if (camera.near + 1 > camera.far)
-                camera.far = camera.near + 1;
-            if (camera instanceof $3Dmol.Camera) {
-                camera.fov = fov;
-            } else {
-                camera.right = center * Math.tan(Math.PI / 180 * fov);
-                camera.left = -camera.right;
-                camera.top = camera.right / ASPECT;
-                camera.bottom = -camera.top;
+            // must be a unique face for each atom
+            var which = a;
+            if (b < which)
+                which = b;
+            if (c < which)
+                which = c;
+            if (!atomsToShow[which]) {
+                continue;
             }
-            camera.updateProjectionMatrix();
-            scene.fog.near = camera.near + fogStart
-                    * (camera.far - camera.near);
-            // if (scene.fog.near > center) scene.fog.near = center;
-            scene.fog.far = camera.far;
-        };
+            var av = vertices[faces[i]];
+            var bv = vertices[faces[i+1]];
+            var cv = vertices[faces[i+2]];
 
-        // display scene
-        var show = function() {
-            if (!scene)
-                return;
+            if (fa !== fb && fb !== fc && fa !== fc){
+                finalfaces.push(fa); 
+                finalfaces.push(fb); 
+                finalfaces.push(fc); 
+            }
+               
+        }
 
-            // var time = new Date();
-            setSlabAndFog();
-            renderer.render(scene, camera);
-            // console.log("rendered in " + (+new Date() - time) + "ms");
+        //try to help the garbage collector
+        vpBits = null; // uint8 array of bitmasks
+        vpDistance = null; // floatarray
+        vpAtomID = null; // intarray
+        
+        return {
+            'vertices' : vertices,
+            'faces' : finalfaces
         };
+    };
 
-        var initializeScene = function() {
-
-            scene = new $3Dmol.Scene();
-            scene.fog = new $3Dmol.Fog(bgColor, 100, 200);
-
-            modelGroup = new $3Dmol.Object3D();
-            rotationGroup = new $3Dmol.Object3D();
-            rotationGroup.useQuaternion = true;
-            rotationGroup.quaternion = new $3Dmol.Quaternion(0, 0, 0, 1);
-            rotationGroup.add(modelGroup);
 
-            scene.add(rotationGroup);
+    this.initparm = function(extent, btype, volume) {
+        if(volume > 1000000) //heuristical decrease resolution to avoid large memory consumption
+            scaleFactor = defaultScaleFactor/2;
+        
+        var margin = (1 / scaleFactor) * 5.5; // need margin to avoid
+                                                // boundary/round off effects
+        origextent = extent;
+        pminx = extent[0][0]; pmaxx = extent[1][0];
+        pminy = extent[0][1]; pmaxy = extent[1][1];
+        pminz = extent[0][2]; pmaxz = extent[1][2];
 
-            // setup lights
-            var directionalLight = new $3Dmol.Light(0xFFFFFF);
-            directionalLight.position = new $3Dmol.Vector3(0.2, 0.2, 1)
-                    .normalize();
-            directionalLight.intensity = 1.0;
-            scene.add(directionalLight);
-        };
-
-        initializeScene();
-
-        renderer.setClearColorHex(bgColor, 1.0);
-        scene.fog.color = $3Dmol.CC.color(bgColor);
-
-        var clickedAtom = null;
-        // enable mouse support
-        var glDOM = $(renderer.domElement);
+        if (!btype) {
+            pminx -= margin;
+            pminy -= margin;
+            pminz -= margin;
+            pmaxx += margin;
+            pmaxy += margin;
+            pmaxz += margin;
+        } else {
+            pminx -= probeRadius + margin;
+            pminy -= probeRadius + margin;
+            pminz -= probeRadius + margin;
+            pmaxx += probeRadius + margin;
+            pmaxy += probeRadius + margin;
+            pmaxz += probeRadius + margin;
+        }
 
-        //regenerate the list of clickables
-        var updateClickables = function() {
-            clickables = [];
-            var i, il;
+        pminx = Math.floor(pminx * scaleFactor) / scaleFactor;
+        pminy = Math.floor(pminy * scaleFactor) / scaleFactor;
+        pminz = Math.floor(pminz * scaleFactor) / scaleFactor;
+        pmaxx = Math.ceil(pmaxx * scaleFactor) / scaleFactor;
+        pmaxy = Math.ceil(pmaxy * scaleFactor) / scaleFactor;
+        pmaxz = Math.ceil(pmaxz * scaleFactor) / scaleFactor;
 
-            for (i = 0, il = models.length; i < il; i++) {
-                var model = models[i];
-                if(model) {
-                    var atoms = model.selectedAtoms({
-                        clickable : true
-                    });
-                    clickables = clickables.concat(atoms);
-                }
-            }
+        ptranx = -pminx;
+        ptrany = -pminy;
+        ptranz = -pminz;
 
-            for (i = 0, il = shapes.length; i < il; i++) {
+        pLength = Math.ceil(scaleFactor * (pmaxx - pminx)) + 1;
+        pWidth = Math.ceil(scaleFactor * (pmaxy - pminy)) + 1;
+        pHeight = Math.ceil(scaleFactor * (pmaxz - pminz)) + 1;
 
-                var shape = shapes[i];
-                if (shape && shape.clickable) {
-                    clickables.push(shape);
-                }
-            }
-        };
-        
-        // Checks for selection intersects on mousedown
-        var handleClickSelection = function(mouseX, mouseY, event) {
-            if(clickables.length == 0) return;
-            var mouse = {
-                x : mouseX,
-                y : mouseY,
-                z : -1.0
-            };
-            mouseVector.set(mouse.x, mouse.y, mouse.z);
-            projector.unprojectVector(mouseVector, camera);
-            mouseVector.sub(camera.position).normalize();
+        this.boundingatom(btype);
+        cutRadius = probeRadius * scaleFactor;
 
-            raycaster.set(camera.position, mouseVector);
+        vpBits = new Uint8Array(pLength * pWidth * pHeight);
+        vpDistance = new Float64Array(pLength * pWidth * pHeight); // float 32
+        // doesn't
+        // play
+        // nicely
+        // with
+        // native
+        // floats
+        vpAtomID = new Int32Array(pLength * pWidth * pHeight);
+        //console.log("Box size: ", pLength, pWidth, pHeight, vpBits.length);
+    };
 
-            var intersects = [];
+    this.boundingatom = function(btype) {
+        var tradius = [];
+        var txz, tdept, sradius, idx;
+        flagradius = btype;
 
-            intersects = raycaster.intersectObjects(modelGroup, clickables);
+        for ( var i in vdwRadii) {
+            if(!vdwRadii.hasOwnProperty(i))
+                continue;
+            var r = vdwRadii[i];
+            if (!btype)
+                tradius[i] = r * scaleFactor + 0.5;
+            else
+                tradius[i] = (r + probeRadius) * scaleFactor + 0.5;
 
-            if (intersects.length) {
-                var selected = intersects[0].clickable;
-                if (selected.callback !== undefined
-                        && typeof (selected.callback) === "function") {
-                    selected.callback(selected, _viewer, event, container);
+            sradius = tradius[i] * tradius[i];
+            widxz[i] = Math.floor(tradius[i]) + 1;
+            depty[i] = new Int32Array(widxz[i] * widxz[i]);
+            indx = 0;
+            for (j = 0; j < widxz[i]; j++) {
+                for (k = 0; k < widxz[i]; k++) {
+                    txz = j * j + k * k;
+                    if (txz > sradius)
+                        depty[i][indx] = -1; // outside
+                    else {
+                        tdept = Math.sqrt(sradius - txz);
+                        depty[i][indx] = Math.floor(tdept);
+                    }
+                    indx++;
                 }
             }
-        };
+        }
+    };
 
-        var calcTouchDistance = function(ev) { // distance between first two
-                                                // fingers
-            var xdiff = ev.originalEvent.targetTouches[0].pageX
-                    - ev.originalEvent.targetTouches[1].pageX;
-            var ydiff = ev.originalEvent.targetTouches[0].pageY
-                    - ev.originalEvent.targetTouches[1].pageY;
-            return Math.sqrt(xdiff * xdiff + ydiff * ydiff);
+    this.fillvoxels = function(atoms, atomlist) { // (int seqinit,int
+        // seqterm,bool
+        // atomtype,atom*
+        // proseq,bool bcolor)
+        var i, il;
+        for (i = 0, il = vpBits.length; i < il; i++) {
+            vpBits[i] = 0;
+            vpDistance[i] = -1.0;
+            vpAtomID[i] = -1;
         }
-        
-        //check targetTouches as well
-        var getXY = function(ev) {
-            var x = ev.pageX, y = ev.pageY;
-            if (ev.originalEvent.targetTouches
-                    && ev.originalEvent.targetTouches[0]) {
-                x = ev.originalEvent.targetTouches[0].pageX;
-                y = ev.originalEvent.targetTouches[0].pageY;
-            }
-            else if (ev.originalEvent.changedTouches
-                    && ev.originalEvent.changedTouches[0]) {
-                x = ev.originalEvent.changedTouches[0].pageX;
-                y = ev.originalEvent.changedTouches[0].pageY;
-            }            
-            return [x,y];
-        };
 
-        //for a given screen (x,y) displacement return model displacement 
-        var screenXY2model = function(x,y) {
-            var dx = x/WIDTH;
-            var dy = y/HEIGHT;
-            var zpos = rotationGroup.position.z; 
-            var q = rotationGroup.quaternion;                        
-            var t = new $3Dmol.Vector3(0,0,zpos);
-            projector.projectVector(t, camera);
-            t.x += dx*2;
-            t.y -= dy*2;
-            projector.unprojectVector(t, camera);
-            t.z = 0;                            
-            t.applyQuaternion(q);
-            return t;
+        for (i in atomlist) {
+            var atom = atoms[atomlist[i]];
+            if (atom === undefined)
+                continue;
+            this.fillAtom(atom, atoms);
         }
-        
-        if (!nomouse) {
-            // user can request that the mouse handlers not be installed
-            glDOM.bind('mousedown touchstart', function(ev) {
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                var xy = getXY(ev);
-                var x = xy[0];
-                var y = xy[1];
-                
-                if (x === undefined)
-                    return;
-                isDragging = true;
-                clickedAtom = null;
-                mouseButton = ev.which;
-                mouseStartX = x;
-                mouseStartY = y;
-                touchDistanceStart = 0;
-                if (ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 2) {
-                    touchDistanceStart = calcTouchDistance(ev);
-                }
-                cq = rotationGroup.quaternion;
-                cz = rotationGroup.position.z;
-                currentModelPos = modelGroup.position.clone();
-                cslabNear = slabNear;
-                cslabFar = slabFar;
 
-            });
+        for (i = 0, il = vpBits.length; i < il; i++)
+            if (vpBits[i] & INOUT)
+                vpBits[i] |= ISDONE;
 
-            glDOM.bind('DOMMouseScroll mousewheel', function(ev) { // Zoom
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                var scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
-                if (ev.originalEvent.detail) { // Webkit
-                    rotationGroup.position.z += scaleFactor
-                            * ev.originalEvent.detail / 10;
-                } else if (ev.originalEvent.wheelDelta) { // Firefox
-                    rotationGroup.position.z -= scaleFactor
-                            * ev.originalEvent.wheelDelta / 400;
-                }
-                if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+    };
 
-                show();
-            });
 
-            glDOM.bind("contextmenu", function(ev) {
-                ev.preventDefault();
-            });
-            $('body').bind('mouseup touchend', function(ev) {
-                // handle selection
-                if(isDragging && scene) { //saw mousedown, haven't moved
-                    var xy = getXY(ev);
-                    var x = xy[0];
-                    var y = xy[1];
-                    if(x == mouseStartX && y == mouseStartY) {
-                        var offset = $(container).offset();
-                        var mouseX = ((x - offset.left) / WIDTH) * 2 - 1;
-                        var mouseY = -((y - offset.top) / HEIGHT) * 2 + 1;
-
-                        handleClickSelection(mouseX, mouseY, ev, container);
-                    }
-                }
-                
-                isDragging = false;
+    this.fillAtom = function(atom, atoms) {
+        var cx, cy, cz, ox, oy, oz, mi, mj, mk, i, j, k, si, sj, sk;
+        var ii, jj, kk, n;
+        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
+        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
+        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
 
-            });
+        var at = getVDWIndex(atom);
+        var nind = 0;
+        var cnt = 0;
+        var pWH = pWidth*pHeight;
+        
+        for (i = 0, n = widxz[at]; i < n; i++) {
+            for (j = 0; j < n; j++) {
+                if (depty[at][nind] != -1) {
+                    for (ii = -1; ii < 2; ii++) {
+                        for (jj = -1; jj < 2; jj++) {
+                            for (kk = -1; kk < 2; kk++) {
+                                if (ii !== 0 && jj !== 0 && kk !== 0) {
+                                    mi = ii * i;
+                                    mk = kk * j;
+                                    for (k = 0; k <= depty[at][nind]; k++) {
+                                        mj = k * jj;
+                                        si = cx + mi;
+                                        sj = cy + mj;
+                                        sk = cz + mk;
+                                        if (si < 0 || sj < 0 || 
+                                                sk < 0 ||
+                                                si >= pLength || 
+                                                sj >= pWidth || 
+                                                sk >= pHeight)
+                                            continue;
+                                        var index = si * pWH + sj * pHeight + sk;
 
-            glDOM.bind('mousemove touchmove', function(ev) { // touchmove
-                ev.preventDefault();
-                if (!scene)
-                    return;
-                if (!isDragging)
-                    return;
-                var mode = 0;
+                                        if (!(vpBits[index] & INOUT)) {
+                                            vpBits[index] |= INOUT;
+                                            vpAtomID[index] = atom.serial;
+                                        } else {
+                                            var atom2 = atoms[vpAtomID[index]];
+                                            if(atom2.serial != atom.serial) {
+                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.x + ptranx));
+                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.y + ptrany));
+                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.z + ptranz));
+                                                if (mi * mi + mj * mj + mk * mk < ox *
+                                                        ox + oy * oy + oz * oz)
+                                                    vpAtomID[index] = atom.serial;
+                                            }
+                                        }
 
-                var xy = getXY(ev);
-                var x = xy[0];
-                var y = xy[1];
-                if (x === undefined)
-                    return;
-                var dx = (x - mouseStartX) / WIDTH;
-                var dy = (y - mouseStartY) / HEIGHT;
-                // check for pinch
-                if (touchDistanceStart != 0
-                        && ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 2) {
-                    var newdist = calcTouchDistance(ev);
-                    // change to zoom
-                    mode = 2;
-                    dy = (touchDistanceStart - newdist) * 2
-                            / (WIDTH + HEIGHT);
-                } else if (ev.originalEvent.targetTouches
-                        && ev.originalEvent.targetTouches.length == 3) {
-                    // translate
-                    mode = 1;
-                }
+                                    }// k
+                                }// if
+                            }// kk
+                        }// jj
+                    }// ii
+                }// if
+                nind++;
+            }// j
+        }// i
+    };
 
-                var r = Math.sqrt(dx * dx + dy * dy);
-                var scaleFactor;
-                if (mode == 3
-                        || (mouseButton == 3 && ev.ctrlKey)) { // Slab
-                    slabNear = cslabNear + dx * 100;
-                    slabFar = cslabFar + dy * 100;
-                } else if (mode == 2 || mouseButton == 3
-                        || ev.shiftKey) { // Zoom
-                    scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
-                    if (scaleFactor < 80)
-                        scaleFactor = 80;
-                    rotationGroup.position.z = cz - dy
-                            * scaleFactor;
-                    if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
-                } else if (mode == 1 || mouseButton == 2
-                        || ev.ctrlKey) { // Translate
-                    var t = screenXY2model(x-mouseStartX, y-mouseStartY);
-                    modelGroup.position.addVectors(currentModelPos,t);
-                    
-                } else if ((mode === 0 || mouseButton == 1)
-                        && r !== 0) { // Rotate
-                    var rs = Math.sin(r * Math.PI) / r;
-                    dq.x = Math.cos(r * Math.PI);
-                    dq.y = 0;
-                    dq.z = rs * dx;
-                    dq.w = -rs * dy;
-                    rotationGroup.quaternion = new $3Dmol.Quaternion(
-                            1, 0, 0, 0);
-                    rotationGroup.quaternion.multiply(dq);
-                    rotationGroup.quaternion.multiply(cq);
-                }
-                show();
-            });
-        }
-        // public methods
-        /**
-         * Set the background color (default white)
-         * 
-         * @function $3Dmol.GLViewer#setBackgroundColor
-         * @param {number}
-         *            hex Hexcode specified background color, or standard color spec
-         * @param {number}
-         *            a Alpha level (default 1.0)
-         * 
-         * @example
-         * 
-         * //Set 'myviewer' background color to white
-         * myviewer.setBackgroundColor(0xffffff)
-         * 
-         */
-        this.setBackgroundColor = function(hex, a) {
-            if(typeof(a) == "undefined") {
-                a = 1.0;
-            }
-            else if(a < 0 || a > 1.0) {
-                a = 1.0;
-            }
-            var c = $3Dmol.CC.color(hex);
-            scene.fog.color = c;
-            bgColor = c.getHex();
-            renderer.setClearColorHex(c.getHex(), a);
-            show();
-        };
-
-        /**
-         * Set viewer width
-         * 
-         * @function $3Dmol.GLViewer#setWidth
-         * @param {number}
-         *            w Width in pixels
-         */
-        this.setWidth = function(w) {
-            WIDTH = w || WIDTH;
-            renderer.setSize(WIDTH, HEIGHT);
-        };
+    this.fillvoxelswaals = function(atoms, atomlist) {
+        var i, il;
+        for (i = 0, il = vpBits.length; i < il; i++)
+            vpBits[i] &= ~ISDONE; // not isdone
 
-        /**
-         * Set viewer height
-         * 
-         * @function $3Dmol.GLViewer#setHeight
-         * @param {number}
-         *            h Height in pixels
-         */
-        this.setHeight = function(h) {
-            HEIGHT = h || HEIGHT;
-            renderer.setSize(WIDTH, HEIGHT);
-        };
+        for (i in atomlist) {
+            var atom = atoms[atomlist[i]];
+            if (atom === undefined)
+                continue;
 
-        /**
-         * Resize viewer according to containing HTML element's dimensions
-         * 
-         * @function $3Dmol.GLViewer#resize
-         */
-        this.resize = function() {
-            WIDTH = container.width();
-            HEIGHT = container.height();
-            ASPECT = WIDTH / HEIGHT;
-            renderer.setSize(WIDTH, HEIGHT);
-            camera.aspect = ASPECT;
-            camera.updateProjectionMatrix();
-            show();
-        };
+            this.fillAtomWaals(atom, atoms);
+        }
+    };
 
-        $(window).resize(this.resize);
+    this.fillAtomWaals = function(atom, atoms) {
+        var cx, cy, cz, ox, oy, oz, nind = 0;
+        var mi, mj, mk, si, sj, sk, i, j, k, ii, jj, kk, n;
+        cx = Math.floor(0.5 + scaleFactor * (atom.x + ptranx));
+        cy = Math.floor(0.5 + scaleFactor * (atom.y + ptrany));
+        cz = Math.floor(0.5 + scaleFactor * (atom.z + ptranz));
 
-        /**
-         * Return specified model
-         * 
-         * @function $3Dmol.GLViewer#getModel
-         * @param {number}
-         *            [id=last model id] - Retrieve model with specified id
-         * @default Returns last model added to viewer
-         * @return {GLModel}
-         * 
-         * @example // Retrieve reference to first GLModel added var m =
-         *          glviewer.getModel(0);
-         */
-        this.getModel = function(id) {
-            id = id || models.length - 1;
-            return models[id];
-        };
+        var at = getVDWIndex(atom);
+        var pWH = pWidth*pHeight;
+        for (i = 0, n = widxz[at]; i < n; i++) {
+            for (j = 0; j < n; j++) {
+                if (depty[at][nind] != -1) {
+                    for (ii = -1; ii < 2; ii++) {
+                        for (jj = -1; jj < 2; jj++) {
+                            for (kk = -1; kk < 2; kk++) {
+                                if (ii !== 0 && jj !== 0 && kk !== 0) {
+                                    mi = ii * i;
+                                    mk = kk * j;
+                                    for (k = 0; k <= depty[at][nind]; k++) {
+                                        mj = k * jj;
+                                        si = cx + mi;
+                                        sj = cy + mj;
+                                        sk = cz + mk;
+                                        if (si < 0 || sj < 0 || 
+                                                sk < 0 || 
+                                                si >= pLength || 
+                                                sj >= pWidth || 
+                                                sk >= pHeight)
+                                            continue;
+                                        var index = si * pWH + sj * pHeight + sk;
+                                        if (!(vpBits[index] & ISDONE)) {
+                                            vpBits[index] |= ISDONE;
+                                            vpAtomID[index] = atom.serial;
+                                        }  else {
+                                            var atom2 = atoms[vpAtomID[index]];
+                                            if(atom2.serial != atom.serial) {
+                                                ox = cx + mi - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.x + ptranx));
+                                                oy = cy + mj - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.y + ptrany));
+                                                oz = cz + mk - Math.floor(0.5 + scaleFactor *
+                                                        (atom2.z + ptranz));
+                                                if (mi * mi + mj * mj + mk * mk < ox *
+                                                        ox + oy * oy + oz * oz)
+                                                    vpAtomID[index] = atom.serial;
+                                            }
+                                        }
+                                    }// k
+                                }// if
+                            }// kk
+                        }// jj
+                    }// ii
+                }// if
+                nind++;
+            }// j
+        }// i
+    };
 
-        /**
-         * Rotate scene by angle degrees around axis
-         * 
-         * @function $3Dmol.GLViewer#rotate
-         * @param {number}
-         *            [angle] - Angle, in degrees, to rotate by.
-         * @param {string}
-         *            [angle] - Axis ("x", "y", or "z") to rotate around.
-         *            Default "y"
-         * 
-         */
-        this.rotate = function(angle, axis) {
-            if (typeof (axis) === "undefined") {
-                axis = "y";
+    this.buildboundary = function() {
+        var pWH = pWidth*pHeight;
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pHeight; j++) {
+                for (k = 0; k < pWidth; k++) {
+                    var index = i * pWH + k * pHeight + j;
+                    if (vpBits[index] & INOUT) {
+                        var flagbound = false;
+                        var ii = 0;
+                        while (ii < 26) {
+                            var ti = i + nb[ii][0], tj = j + nb[ii][2], tk = k +
+                                    nb[ii][1];
+                            if (ti > -1 && 
+                                ti < pLength && 
+                                tk > -1 && 
+                                tk < pWidth && 
+                                tj > -1 && 
+                                tj < pHeight && 
+                                !(vpBits[ti * pWH + tk * pHeight + tj] & INOUT)) {
+                                vpBits[index] |= ISBOUND;
+                                break;
+                            } else
+                                ii++;
+                        }
+                    }
+                }
             }
-            var i = 0, j = 0, k = 0;
-            var rangle = Math.PI * angle / 180.0;
-            var s = Math.sin(rangle / 2.0);
-            var c = Math.cos(rangle / 2.0);
-            if (axis == "x")
-                i = s;
-            if (axis == "y")
-                j = s;
-            if (axis == "z")
-                k = s;
+        }
+    };
 
-            var q = new $3Dmol.Quaternion(i, j, k, c).normalize();
-            rotationGroup.quaternion.multiply(q);
-            show();
-        };
+    // a little class for 3d array, should really generalize this and
+    // use throughout...
+    var PointGrid = function(length, width, height) {
+        // the standard says this is zero initialized
+        var data = new Int32Array(length * width * height * 3);
 
-        /** Returns an array representing the current viewpoint.
-         * Translation, zoom, and rotation quaternion. 
-         * @function $3Dmol.GLViewer#getView
-         * @returns {Array.<number>} arg
-         *  */
-        this.getView = function() {
-            if (!modelGroup)
-                return [ 0, 0, 0, 0, 0, 0, 0, 1 ];
-            var pos = modelGroup.position;
-            var q = rotationGroup.quaternion;
-            return [ pos.x, pos.y, pos.z, rotationGroup.position.z, q.x, q.y,
-                    q.z, q.w ];
+        // set position x,y,z to pt, which has ix,iy,and iz
+        this.set = function(x, y, z, pt) {
+            var index = ((((x * width) + y) * height) + z) * 3;
+            data[index] = pt.ix;
+            data[index + 1] = pt.iy;
+            data[index + 2] = pt.iz;
         };
 
-        /** Sets the view to the specified translation, zoom, and rotation.
-         * 
-         * @function $3Dmol.GLViewer#setView
-         * @param {Array.<number>} arg Array formatted identically to the return value of getView */
-        this.setView = function(arg) {
+        // return point at x,y,z
+        this.get = function(x, y, z) {
+            var index = ((((x * width) + y) * height) + z) * 3;
+            return {
+                ix : data[index],
+                iy : data[index + 1],
+                iz : data[index + 2]
+            };
+        };
+    };
 
-            if (arg === undefined
-                    || !(arg instanceof Array || arg.length !== 8))
-                return;
+    this.fastdistancemap = function() {
+        var eliminate = 0;
+        var certificate;
+        var i, j, k, n;
 
-            if (!modelGroup || !rotationGroup)
-                return;
-            modelGroup.position.x = arg[0];
-            modelGroup.position.y = arg[1];
-            modelGroup.position.z = arg[2];
-            rotationGroup.position.z = arg[3];
-            rotationGroup.quaternion.x = arg[4];
-            rotationGroup.quaternion.y = arg[5];
-            rotationGroup.quaternion.z = arg[6];
-            rotationGroup.quaternion.w = arg[7];
-            if(typeof(arg[8]) != "undefined") {
-                rotationGroup.position.x = arg[8];
-                rotationGroup.position.y = arg[9];
+        var boundPoint = new PointGrid(pLength, pWidth, pHeight);
+        var pWH = pWidth*pHeight;
+        var cutRSq = cutRadius*cutRadius;
+        
+        var inarray = [];
+        var outarray = [];
+        
+        var index;
+        
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pWidth; j++) {
+                for (k = 0; k < pHeight; k++) {
+                    index = i * pWH + j * pHeight + k;
+                    vpBits[index] &= ~ISDONE; // isdone = false
+                    if (vpBits[index] & INOUT) {
+                        if (vpBits[index] & ISBOUND) {
+                            var triple = {
+                                ix : i,
+                                iy : j,
+                                iz : k
+                            };
+                            boundPoint.set(i, j, k, triple);
+                            inarray.push(triple);
+                            vpDistance[index] = 0;
+                            vpBits[index] |= ISDONE;
+                            vpBits[index] &= ~ISBOUND;
+                        } 
+                    }
+                }
             }
-            show();
-        };
-
-        // apply styles, models, etc in viewer
-        /**
-         * Render current state of viewer, after 
-         * adding/removing models, applying styles, etc.
-         * 
-         * @function $3Dmol.GLViewer#render
-         */
-        this.render = function() {
+        }
 
-            updateClickables(); //must render for clickable styles to take effect
-            var time1 = new Date();
-            var view = this.getView();
-            
-            var i, n;
-            for (i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    models[i].globj(modelGroup);
+        do {
+            outarray = this.fastoneshell(inarray, boundPoint);
+            inarray = [];
+            for (i = 0, n = outarray.length; i < n; i++) {
+                index = pWH * outarray[i].ix + pHeight *
+                    outarray[i].iy + outarray[i].iz;
+                vpBits[index] &= ~ISBOUND;
+                if (vpDistance[index] <= 1.0404 * cutRSq) {
+                    inarray.push({
+                        ix : outarray[i].ix,
+                        iy : outarray[i].iy,
+                        iz : outarray[i].iz
+                    });
                 }
             }
+        } while (inarray.length !== 0);
 
-            for (i = 0; i < shapes.length; i++) {
-                if (shapes[i]) {
-                    shapes[i].globj(modelGroup);
+        inarray = [];
+        outarray = [];
+        boundPoint = null;
+        
+        var cutsf = scaleFactor - 0.5;
+        if (cutsf < 0)
+            cutsf = 0;
+        var cutoff = cutRSq - 0.50 / (0.1 + cutsf);
+        for (i = 0; i < pLength; i++) {
+            for (j = 0; j < pWidth; j++) {
+                for (k = 0; k < pHeight; k++) {
+                    index = i * pWH + j * pHeight + k;
+                    vpBits[index] &= ~ISBOUND;
+                    // ses solid
+                    if (vpBits[index] & INOUT) {
+                        if (!(vpBits[index] & ISDONE) ||
+                                ((vpBits[index] & ISDONE) && vpDistance[index] >= cutoff)) {
+                            vpBits[index] |= ISBOUND;
+                        }
+                    }
                 }
             }
-            
-            for (i in surfaces) { // this is an array with possible holes
-                var surfArr = surfaces[i];
-                for (n = 0; n < surfArr.length; n++) {
-                    if (surfArr.hasOwnProperty(n)) {
-                        var geo = surfArr[n].geo;
-                        // async surface generation can cause
-                        // the geometry to be webgl initialized before it is fully
-                        // formed; force various recalculations until full surface
-                        // is
-                        // available
-                        if (!surfArr[n].finished) {
-                            geo.verticesNeedUpdate = true;
-                            geo.elementsNeedUpdate = true;
-                            geo.normalsNeedUpdate = true;
-                            geo.colorsNeedUpdate = true;
-                            geo.buffersNeedUpdate = true;
-                            geo.boundingSphere = null;
+        }
 
-                            if (surfArr[n].done)
-                                surfArr[n].finished = true;
+    };
 
-                            // remove partially rendered surface
-                            if (surfArr[n].lastGL)
-                                modelGroup.remove(surfArr[n].lastGL);
+    this.fastoneshell = function(inarray, boundPoint) { // (int* innum,int
+        // *allocout,voxel2
+        // ***boundPoint, int*
+        // outnum, int *elimi)
+        var tx, ty, tz;
+        var dx, dy, dz;
+        var i, j, n;
+        var square;
+        var bp, index;
+        var outarray = [];
+        if (inarray.length === 0)
+            return outarray;
 
-                            // create new surface
-                            var smesh = null;
+        tnv = {
+            ix : -1,
+            iy : -1,
+            iz : -1
+        };
+        var pWH = pWidth*pHeight;
+        for ( i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-                            if(surfArr[n].mat instanceof $3Dmol.LineBasicMaterial) {
-                                //special case line meshes
-                                smesh = new $3Dmol.Line(geo, surfArr[n].mat);
-                            }
-                            else {
-                                smesh = new $3Dmol.Mesh(geo, surfArr[n].mat);
-                            }
-                            if(surfArr[n].mat.transparent && surfArr[n].mat.opacity == 0) {
-                                //don't bother with hidden surfaces
-                                smesh.visible = false;
-                            } else {
-                                smesh.visible = true;
-                            }
-                            if (surfArr[n].symmetries.length > 1 || 
-                            (surfArr[n].symmetries.length == 1 && 
-                            !(surfArr[n].symmetries[n].isIdentity()))) {
-                                var j;
-                                var tmeshes = new $3Dmol.Object3D(); //transformed meshes
-                                for (j = 0; j < surfArr[n].symmetries.length; j++) {
-                                    var tmesh = smesh.clone();
-                                    tmesh.matrix = surfArr[n].symmetries[j];
-                                    tmesh.matrixAutoUpdate = false;
-                                    tmeshes.add(tmesh);
-                                }
-                                surfArr[n].lastGL = tmeshes;
-                                modelGroup.add(tmeshes);
-                            }
-                            else {
-                                surfArr[n].lastGL = smesh;
-                                modelGroup.add(smesh);
+            for (j = 0; j < 6; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
+                
+                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+                    
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+    
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
+    
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
+    
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+    
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
                             }
-                        } // else final surface already there
+                        }
                     }
                 }
             }
-            
-            this.setView(view); // Calls show() => renderer render
-            var time2 = new Date();
-            //console.log("render time: " + (time2 - time1));
-        };
-
-        /**
-         * 
-         * @param {AtomSelectionSpec}
-         *            sel
-         * @return {AtomSpec[]}
-         */
-        function getAtomsFromSel(sel) {
-            var atoms = [];
-            if (typeof (sel) === "undefined")
-                sel = {};
-
-            var ms = [];
-            var i;
+        }
 
-            if (typeof sel.model === "undefined") {
-                for (i = 0; i < models.length; i++) {
-                    if (models[i])
-                        ms.push(models[i]);
-                }
-            } else { // specific to some models
-                ms = sel.model;
-                if (!$.isArray(ms))
-                    ms = [ ms ];
-            }
+        // console.log("part1", positout);
 
-            for (i = 0; i < ms.length; i++) {
-                atoms = atoms.concat(ms[i].selectedAtoms(sel));
-            }
+        for (i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-            return atoms;
-        }
+            for (j = 6; j < 18; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
 
-        /**
-         * 
-         * @param {AtomSpec}
-         *            atom
-         * @param {AtomSpec}
-         *            sel
-         * @return {boolean}
-         */
-        function atomIsSelected(atom, sel) {
-            if (typeof (sel) === "undefined")
-                sel = {};
-
-            var ms = [];
-            var i;
-
-            if (typeof sel.model === "undefined") {
-                for (i = 0; i < models.length; i++) {
-                    if (models[i])
-                        ms.push(models[i]);
+                if(tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
+                    
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
+    
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
+    
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT) && (vpBits[index] & ISDONE)) {
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
+                            }
+                        }
+                    }
                 }
-            } else { // specific to some models
-                ms = sel.model;
-                if (!$.isArray(ms))
-                    ms = [ ms ];
             }
+        }
 
-            for (i = 0; i < ms.length; i++) {
-                if (ms[i].atomIsSelected(atom, sel))
-                    return true;
-            }
+        // console.log("part2", positout);
 
-            return false;
-        }
+        for (i = 0, n = inarray.length; i < n; i++) {
+            tx = inarray[i].ix;
+            ty = inarray[i].iy;
+            tz = inarray[i].iz;
+            bp = boundPoint.get(tx, ty, tz);
 
-        /**
-         * Return pdb output of selected atoms (if atoms from pdb input)
-         * 
-         * @function $3Dmol.GLViewer#pdbData  
-         * @param {Object=} [sel] - Selection specification specifying model and atom properties to select.  Default: all atoms in viewer
-         * @return {string} PDB string of selected atoms
-         */
-        this.pdbData = function(sel) {
-            var atoms = getAtomsFromSel(sel);
-            var ret = "";
-            for (var i = 0, n = atoms.length; i < n; ++i) {
-                ret += atoms[i].pdbline + "\n";
-            }
-            return ret;
-        };
+            for (j = 18; j < 26; j++) {
+                tnv.ix = tx + nb[j][0];
+                tnv.iy = ty + nb[j][1];
+                tnv.iz = tz + nb[j][2];
 
-        /**
-         * Zoom current view by a constant factor
-         * 
-         * @function $3Dmol.GLViewer#zoom
-         * @param {number}
-         *            [factor] - Magnification factor. Values greater than 1
-         *            will zoom in, less than one will zoom out. Default 2.
-         * 
-         */
-        this.zoom = function(factor) {
-            var factor = factor || 2;
-            var scale = (CAMERA_Z - rotationGroup.position.z) / factor;
-            rotationGroup.position.z = CAMERA_Z - scale;
-            show();
-        };
-        
-        /**
-         * Translate current view by x,y screen coordinates
-         * This pans the camera rather than translating the model.
-         * 
-         * @function $3Dmol.GLViewer#translate
-         * @param {number} x
-         * @param {number} y
-         * 
-         */
-        this.translate = function(x, y) {
-            
-            var dx = x/WIDTH;
-            var dy = y/HEIGHT;
-            var v = new $3Dmol.Vector3(0,0,-CAMERA_Z);
+                if (tnv.ix < pLength && tnv.ix > -1 && tnv.iy < pWidth &&
+                        tnv.iy > -1 && tnv.iz < pHeight && tnv.iz > -1) {
+                    index = tnv.ix * pWH + pHeight * tnv.iy + tnv.iz;
 
-            projector.projectVector(v, camera);
-            v.x -= dx;
-            v.y -= dy;
-            projector.unprojectVector(v, camera);
-            v.z = 0;            
-            lookingAt.add(v);
-            camera.lookAt(lookingAt);
-            show();
-        };
-        
+                    if ((vpBits[index] & INOUT) && !(vpBits[index] & ISDONE)) {
+                        boundPoint.set(tnv.ix, tnv.iy, tz + nb[j][2], bp);
 
-        /**
-         * Zoom to center of atom selection
-         * 
-         * @function $3Dmol.GLViewer#zoomTo
-         * @param {Object}
-         *            [sel] - Selection specification specifying model and atom
-         *            properties to select. Default: all atoms in viewer
-         * @example // Assuming we have created a model of a protein with
-         *          multiple chains (e.g. from a PDB file), focus on atoms in
-         *          chain B glviewer.zoomTo({chain: 'B'});
-         *  // Focus on centroid of all atoms of all models in this
-         * viewer glviewer.zoomTo(); // (equivalent to glviewer.zoomTo({}) )
-         */
-        this.zoomTo = function(sel) {
-            var allatoms, alltmp;
-            sel = sel || {};
-            var atoms = getAtomsFromSel(sel);
-            var tmp = $3Dmol.getExtent(atoms);
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        vpDistance[index] = square;
+                        vpBits[index] |= ISDONE;
+                        vpBits[index] |= ISBOUND;
 
-            if($.isEmptyObject(sel)) {
-                //include shapes when zooming to full scene
-                //TODO: figure out a good way to specify shapes as part of a selection
-                $.each(shapes, function(i, shape) {
-                	if(shape.boundingSphere && shape.boundingSphere.center)
-                		atoms.push(shape.boundingSphere.center);
-                });
-                tmp = $3Dmol.getExtent(atoms);
-                allatoms = atoms;
-                alltmp = tmp;
+                        outarray.push({
+                            ix : tnv.ix,
+                            iy : tnv.iy,
+                            iz : tnv.iz
+                        });
+                    } else if ((vpBits[index] & INOUT)  && (vpBits[index] & ISDONE)) {
+                        dx = tnv.ix - bp.ix;
+                        dy = tnv.iy - bp.iy;
+                        dz = tnv.iz - bp.iz;
+                        square = dx * dx + dy * dy + dz * dz;
+                        if (square < vpDistance[index]) {
+                            boundPoint.set(tnv.ix, tnv.iy, tnv.iz, bp);
 
+                            vpDistance[index] = square;
+                            if (!(vpBits[index] & ISBOUND)) {
+                                vpBits[index] |= ISBOUND;
+                                outarray.push({
+                                    ix : tnv.ix,
+                                    iy : tnv.iy,
+                                    iz : tnv.iz
+                                });
+                            }
+                        }
+                    }
+                }
             }
-            else {
-                allatoms = getAtomsFromSel({});
-                alltmp = $3Dmol.getExtent(allatoms);
+        }
+
+        // console.log("part3", positout);
+        return outarray;
+    };
+
+    this.marchingcubeinit = function(stype) {
+        for ( var i = 0, lim = vpBits.length; i < lim; i++) {
+            if (stype == 1) {// vdw
+                vpBits[i] &= ~ISBOUND;
+            } else if (stype == 4) { // ses
+                vpBits[i] &= ~ISDONE;
+                if (vpBits[i] & ISBOUND)
+                    vpBits[i] |= ISDONE;
+                vpBits[i] &= ~ISBOUND;
+            } else if (stype == 2) {// after vdw
+                if ((vpBits[i] & ISBOUND) && (vpBits[i] & ISDONE))
+                    vpBits[i] &= ~ISBOUND;
+                else if ((vpBits[i] & ISBOUND) && !(vpBits[i] & ISDONE))
+                    vpBits[i] |= ISDONE;
+            } else if (stype == 3) { // sas
+                vpBits[i] &= ~ISBOUND;
             }
+        }
+    };
 
-            // use selection for center
-            var center = new $3Dmol.Vector3(tmp[2][0], tmp[2][1], tmp[2][2]);
-            modelGroup.position = center.clone().multiplyScalar(-1);
-            // but all for bounding box
-            var x = alltmp[1][0] - alltmp[0][0], y = alltmp[1][1]
-                    - alltmp[0][1], z = alltmp[1][2] - alltmp[0][2];
+    // this code allows me to empirically prune the marching cubes code tables
+    // to more efficiently handle discrete data
+    var counter = function() {
+        var data = Array(256);
+        for ( var i = 0; i < 256; i++)
+            data[i] = [];
 
-            var maxD = Math.sqrt(x * x + y * y + z * z);
-            if (maxD < 5)
-                maxD = 5;
+        this.incrementUsed = function(i, j) {
+            if (typeof data[i][j] === 'undefined')
+                data[i][j] = {
+                    used : 0,
+                    unused : 0
+                };
+            data[i][j].used++;
+        };
 
-            // use full bounding box for slab/fog
-            slabNear = -maxD / 1.9;
-            slabFar = maxD / 2;
+        this.incrementUnused = function(i, j) {
+            if (typeof data[i][j] === 'undefined')
+                data[i][j] = {
+                    used : 0,
+                    unused : 0
+                };
+            data[i][j].unused++;
 
-            // for zoom, use selection box
-            x = tmp[1][0] - tmp[0][0];
-            y = tmp[1][1] - tmp[0][1];
-            z = tmp[1][2] - tmp[0][2];
-            maxD = Math.sqrt(x * x + y * y + z * z);
-            if (maxD < 5)
-                maxD = 5;
-            
-            //find the farthest atom from center to get max distance needed for view
-            var maxDsq = 25;
-            for (var i = 0; i < atoms.length; i++) {
-                if(atoms[i]) {
-                    var dsq = center.distanceToSquared(atoms[i]);
-                    if(dsq > maxDsq)
-                        maxDsq = dsq;
-                }
-            }
-            
-            var maxD = Math.sqrt(maxDsq)*2;
-
-            rotationGroup.position.z = -(maxD * 0.5
-                    / Math.tan(Math.PI / 180.0 * camera.fov / 2) - CAMERA_Z);
-            show();
-        };
-        /**
-         * Add label to viewer
-         * 
-         * @function $3Dmol.GLViewer#addLabel
-         * @param {string}
-         *            text - Label text
-         * @param {Object}
-         *            data - Label style specification
-         * @return {$3Dmol.Label}
-         * 
-         * @example
-         *  // Assuming glviewer contains a model representing a protein, label
-         * all alpha carbons with their residue name
-         *  // Select all alpha carbons (have property atom : "CA") from last
-         * model added var atoms =
-         * glviewer.getModel().selectedAtoms({atom:"CA"}); var labels = [];
-         * 
-         * for (var a in atoms) { var atom = atoms[a];
-         *  // Create label at alpha carbon's position displaying atom's residue
-         * and residue number var labelText = atom.resname + " " + atom.resi;
-         * 
-         * var l = glviewer.createLabel(labelText, {fontSize: 12, position: {x:
-         * atom.x, y: atom.y, z: atom.z});
-         * 
-         * labels.push(l); }
-         *  // Render labels glviewer.render();
-         */
-        this.addLabel = function(text, data) {
-            var label = new $3Dmol.Label(text, data);
-            label.setContext();
-            modelGroup.add(label.sprite);
-            labels.push(label);
-            show();
-            return label;
         };
-        
-        /** Add residue labels.  This will generate one label per a
-         * residue within the selected atoms.  The label will be at the
-         * centroid of the atoms and styled according to the passed style.
-         * The label text will be [resn][resi]
-         * 
-         * @param {Object} sel
-         * @param {Object} style
-         */
-        this.addResLabels = function(sel, style) {
-            applyToModels("addResLabels", sel, this, style);
-        }
 
-        /**
-         * Remove label from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeLabel
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * 
-         * @example // Remove labels created in [addLabel example]{@link $3Dmol.GLViewer#addLabel}
-         * 
-         * for (var i = 0; i < labels.length; i++) {
-         * glviewer.removeLabel(label); }
-         * 
-         * glviewer.render();
-         */
-        this.removeLabel = function(label) {
-            //todo: don't do the linear search
-            for(var i = 0; i < labels.length; i++) {
-                if(labels[i] == label) {
-                    labels.splice(i,1);
-                    label.dispose();
-                    modelGroup.remove(label.sprite);
-                    break;
+        var redoTable = function(triTable) {
+            var str = "[";
+            for ( var i = 0; i < triTable.length; i++) {
+                var code = 0;
+                var table = triTable[i];
+                for ( var j = 0; j < table.length; j++) {
+                    code |= (1 << (table[j]));
                 }
+                str += "0x" + code.toString(16) + ", ";
             }
-
+            str += "]";
+            console.log(str);
         };
 
-        /**
-         * Remove all labels from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeAllLabels
-         */
-        this.removeAllLabels = function() {
-            for (var i = 0; i < labels.length; i++) {
-                modelGroup.remove(labels[i].sprite);
+        this.print = function() {
+
+            var table = MarchingCube.triTable;
+            var str;
+            var newtable = [];
+            for ( var i = 0; i < table.length; i++) {
+                var newarr = [];
+                for ( var j = 0; j < table[i].length; j += 3) {
+                    var k = j / 3;
+                    if (typeof data[i][k] === 'undefined' || !data[i][k].unused) {
+                        newarr.push(table[i][j]);
+                        newarr.push(table[i][j + 1]);
+                        newarr.push(table[i][j + 2]);
+                    }
+                    if (typeof data[i][k] === 'undefined')
+                        console.log("undef " + i + "," + k);
+                }
+                newtable.push(newarr);
             }
-            labels = [];
+            console.log(JSON.stringify(newtable));
+            redoTable(newtable);
         };
-        
-        // Modify label style
-        /**
-         * Modify existing label's style
-         * 
-         * @function $3Dmol.GLViewer#setLabelStyle
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * @param {Object}
-         *            stylespec - Label style specification
-         * @return {$3Dmol.Label}
-         */
-        this.setLabelStyle = function(label, stylespec) {
-            modelGroup.remove(label.sprite);
-            label.dispose();
-            label.stylespec = stylespec;
-            label.setContext();
-            modelGroup.add(label.sprite);
-            show();
-            return label;
+    };
+    
+    this.marchingcube = function(stype) {
+        this.marchingcubeinit(stype);
+        verts = []; faces = [];   
+        $3Dmol.MarchingCube.march(vpBits, verts, faces, {
+            smooth : 1,
+            nX : pLength,
+            nY : pWidth,
+            nZ : pHeight        
+        });      
 
-        };
+        var pWH = pWidth*pHeight;
+        for (var i = 0, vlen = verts.length; i < vlen; i++) {
+            verts[i]['atomid'] = vpAtomID[verts[i].x * pWH + pHeight *
+                    verts[i].y + verts[i].z];
+        }  
 
-        // Change label text
-        /**
-         * Modify existing label's text
-         * 
-         * @function $3Dmol.GLViewer#setLabelText
-         * @param {$3Dmol.Label}
-         *            label - $3Dmol label
-         * @param {String}
-         *            text - Label text
-         * @return {$3Dmol.Label}
-         */
-        this.setLabelText = function(label, text) {
-            modelGroup.remove(label.sprite);
-            label.dispose();
-            label.text = text;
-            label.setContext();
-            modelGroup.add(label.sprite);
-            show();
-            return label;
+        $3Dmol.MarchingCube.laplacianSmooth(1, verts, faces);
 
-        };
+    };
 
-        /**
-         * Add shape object to viewer 
-         * @see {@link $3Dmol.GLShape}
-         * 
-         * @function $3Dmol.GLViewer#addShape
-         * @param {ShapeSpec} shapeSpec - style specification for label
-         * @return {$3Dmol.GLShape}
-         */
-        this.addShape = function(shapeSpec) {
-            shapeSpec = shapeSpec || {};
-            var shape = new $3Dmol.GLShape(shapeSpec);
-            shape.shapePosition = shapes.length;
-            shapes.push(shape);
 
-            return shape;
+};
+//auto-initialization
+//Create embedded viewer from HTML attributes if true
 
-        };
+$(document).ready(function() {
 
-        /**
-         * Remove shape object from viewer
-         *
-         * @function $3Dmol.GLViewer#removeShape
-         * @param {$3Dmol.GLShape} shape - Reference to shape object to remove
-         */
-        this.removeShape = function(shape) {
-            if (!shape)
-                return;
-            shape.removegl(modelGroup);
-            delete shapes[shape.shapePosition];
-            // clear off back of model array
-            while (shapes.length > 0
-                    && typeof (shapes[shapes.length - 1]) === "undefined")
-                shapes.pop();
-        };
+    if ($(".viewer_3Dmoljs")[0] !== undefined)
+        $3Dmol.autoinit = true;
         
-        /**
-         * Remove all shape objects from viewer
-         * @function $3Dmol.GLViewer#removeAllShapes
-         */
-        this.removeAllShapes = function() {
-            for (var i = 0; i < shapes.length; i++) {
-                var shape = shapes[i];
-                shape.removegl(modelGroup);
+    if ($3Dmol.autoinit) { 
+        $3Dmol.viewers = {};
+        var nviewers = 0;
+        $(".viewer_3Dmoljs").each( function() {
+            var viewerdiv = $(this);
+            var datauri = null;
+            
+        
+            var callback = (typeof(window[viewerdiv.data("callback")]) === 'function') ? 
+                    window[viewerdiv.data("callback")] : null;
+            
+            var type = null;
+            if (viewerdiv.data("pdb")) {
+                datauri = "http://www.rcsb.org/pdb/files/" + viewerdiv.data("pdb") + ".pdb";
+                type = "pdb";
+            } else if(viewerdiv.data("cid")) {
+                //this doesn't actually work since pubchem does have CORS enabled
+                type = "sdf";
+                datauri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.data("cid") + 
+                "/SDF?record_type=3d";
             }
-            shapes = [];
-        }
-
-        /**
-         * Create and add sphere shape. This method provides a shorthand 
-         * way to create a spherical shape object
-         * 
-         * @function $3Dmol.GLViewer#addSphere
-         * @param {SphereSpec} spec - Sphere shape style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addSphere = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addSphere(spec);
-            shapes.push(s);
+            else if (viewerdiv.data("href"))
+                datauri = viewerdiv.data("href");
+                
+            var bgcolor = $3Dmol.CC.color(viewerdiv.data("backgroundcolor"));
+            var style = {line:{}};
+            if(viewerdiv.data("style")) style = $3Dmol.specStringToObject(viewerdiv.data("style"));
+            var select = {};
+            if(viewerdiv.data("select")) select = $3Dmol.specStringToObject(viewerdiv.data("select"));
+            var selectstylelist = [];
+            var surfaces = [];
+            var labels = [];
+            var d = viewerdiv.data();
+            
+            //let users specify individual but matching select/style tags, eg.
+            //data-select1 data-style1
+            var stylere = /style(.+)/;
+            var surfre = /surface(.*)/;
+            var reslabre = /labelres(.*)/;
+            var keys = [];
+            for(var dataname in d) {
+                if(d.hasOwnProperty(dataname)) {
+                    keys.push(dataname);
+                }
+            }
+            keys.sort();
+            for(var i = 0; i < keys.length; i++) {
+                var dataname = keys[i];
+                var m = stylere.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    selectstylelist.push([newsel,styleobj]);
+                }         
+                m = surfre.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    surfaces.push([newsel,styleobj]);
+                }
+                m = reslabre.exec(dataname);
+                if(m) {
+                    var selname = "select"+m[1];
+                    var newsel = $3Dmol.specStringToObject(d[selname]);
+                    var styleobj = $3Dmol.specStringToObject(d[dataname]);
+                    labels.push([newsel,styleobj]);
+                }
+            }
+            
+            //apply all the selections/styles parsed out above to the passed viewer
+            var applyStyles = function(glviewer) {
+                glviewer.setStyle(select,style);
+                for(var i = 0; i < selectstylelist.length; i++) {
+                    var sel = selectstylelist[i][0] || {};
+                    var sty = selectstylelist[i][1] || {"line":{}}
+                    glviewer.setStyle(sel, sty);
+                }
+                for(var i = 0; i < surfaces.length; i++) {
+                    var sel = surfaces[i][0] || {};
+                    var sty = surfaces[i][1] || {}
+                    glviewer.addSurface($3Dmol.SurfaceType.VDW, sty, sel, sel);
+                }
+                for(var i = 0; i < labels.length; i++) {
+                    var sel = labels[i][0] || {};
+                    var sty = labels[i][1] || {}
+                    glviewer.addResLabels(sel, sty);
+                }               
+                
+                glviewer.zoomTo();
+                glviewer.render();             
+            }
+            
+            
+            var glviewer = null;
+            try {
+                glviewer = $3Dmol.viewers[this.id || nviewers++] = $3Dmol.createViewer(viewerdiv, {defaultcolors: $3Dmol.rasmolElementColors});
+                glviewer.setBackgroundColor(bgcolor);                            
+            } catch ( error ) {
+                //for autoload, provide a useful error message
+                window.location = "http://get.webgl.org";                    
+            }           
+            
+            if (datauri) {  
+                
+                type = viewerdiv.data("type") || viewerdiv.data("datatype") || type;
+                if(!type) {
+                    type = datauri.substr(datauri.lastIndexOf('.')+1);
+                }
+                                
+                $.get(datauri, function(ret) {
+                    glviewer.addModel(ret, type);
+                    applyStyles(glviewer);       
+                    if (callback) 
+                        callback(glviewer);
+                }, 'text');         
+            }
+            
+            else {
+                
+                if (viewerdiv.data("element")) {
+                    var moldata = $("#" + viewerdiv.data("element")).val() || "";
+                    var type = viewerdiv.data("type") || viewerdiv.data("datatype");
 
-            return s;
-        };
+                    if (!type){
 
-        /**
-         * Create and add arrow shape
-         * 
-         * @function $3Dmol.GLViewer#addArrow
-         * @param {ArrowSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addArrow = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addArrow(spec);
-            shapes.push(s);
+                        console.log("Warning: No type specified for embedded viewer with moldata from " + viewerdiv.data("element") +
+                                    "\n assuming type 'pdb'")
 
-            return s;
-        };
-        
-        /**
-         * Create and add cylinder shape
-         * 
-         * @function $3Dmol.GLViewer#addCylinder
-         * @param {CylinderSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCylinder = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addCylinder(spec);
-            shapes.push(s);
+                        type = 'pdb';
+                    }
 
-            return s;
-        };
+                    glviewer.addModel(moldata, type);        
+                }
 
-        /**
-         * Create and add line shape
-         * 
-         * @function $3Dmol.GLViewer#addLine
-         * @param {LineSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addLine = function(spec) {
-            spec = spec || {};
-            spec.wireframe = true;
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addLine(spec);
-            shapes.push(s);
+                applyStyles(glviewer);                
+                if (callback) 
+                    callback(glviewer);
+            }
+            
+        });              
+    }
+});
+    
+//this is only used for create the enum documentation in JSDoc
+(function() {
+/**
+ * Color representation. 
+ * @typedef ColorSpec
+ * @prop {string} 0xAF10AB - any hex number
+ * @prop {string} white   - 0xFFFFFF
+ * @prop {string} silver  - 0xC0C0C0
+ * @prop {string} gray    - 0x808080
+ * @prop {string} grey    - 0x808080
+ * @prop {string} black   - 0x000000
+ * @prop {string} red     - 0xFF0000
+ * @prop {string} maroon  - 0x800000
+ * @prop {string} yellow  - 0xFFFF00
+ * @prop {string} orange  - 0xFF6600
+ * @prop {string} olive   - 0x808000
+ * @prop {string} lime    - 0x00FF00
+ * @prop {string} green   - 0x008000
+ * @prop {string} aqua    - 0x00FFFF
+ * @prop {string} cyan    - 0x00FFFF
+ * @prop {string} teal    - 0x008080
+ * @prop {string} blue    - 0x0000FF
+ * @prop {string} navy    - 0x000080
+ * @prop {string} fuchsia - 0xFF00FF
+ * @prop {string} magenta - 0xFF00FF
+ * @prop {string} purple  - 0x800080
+ */
 
-            return s;
-        };
+$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
 
-        /**
-         * Add custom shape component from user supplied function
-         * 
-         * @function $3Dmol.GLViewer#addCustom
-         * @param {CustomSpec} spec - Style specification
-         * @return {$3Dmol.GLShape}
-         */
-        this.addCustom = function(spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addCustom(spec);
-            shapes.push(s);
 
-            return s;
-        };
+$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
 
-        /**
-         * Construct isosurface from volumetric data in gaussian cube format
-         * 
-         * @function $3Dmol.GLViewer#addVolumetricData
-         * @param {String} data - Input file contents 
-         * @param {String} format - Input file format (currently only supports "cube")
-         * @param {VolSpec} spec - Shape style specification
-         * @return {$3Dmol.GLShape}
-         * 
-         * @example
-         * viewer.addVolumetricData(data, "cube", {isoval: 0.01, color: "blue", alpha: 0.95});              
-         * viewer.addVolumetricData(data, "cube", {isoval: -0.01, color: "red", alpha: 0.95}); 
-         */
-        this.addVolumetricData = function(data, format, spec) {
-            spec = spec || {};
-            var s = new $3Dmol.GLShape(spec);
-            s.shapePosition = shapes.length;
-            s.addVolumetricData(data, format, spec);
-            shapes.push(s);
 
-            return s;
-        };
+$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
 
-        /**
-         * Create and add model to viewer, given molecular data and its format 
-         * (pdb, sdf, xyz, or mol2)
-         * 
-         * @function $3Dmol.GLViewer#addModel
-         * @param {string} data - Input data
-         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
-         * @return {$3Dmol.GLModel}
-         */
-        this.addModel = function(data, format, options) {
 
-            var m = new $3Dmol.GLModel(models.length, defaultcolors);
-            m.addMolData(data, format, options);
-            models.push(m);
+$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
 
-            return m;
-        };
 
-        /**
-         * Delete specified model from viewer
-         * 
-         * @function $3Dmol.GLViewer#removeModel
-         * @param {$3Dmol.GLModel} model
-         */
-        this.removeModel = function(model) {
-            if (!model)
-                return;
-            model.removegl(modelGroup);
-            delete models[model.getID()];
-            // clear off back of model array
-            while (models.length > 0
-                    && typeof (models[models.length - 1]) === "undefined")
-                models.pop();
-        };
+$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
 
-        /** 
-         * Delete all existing models
-         * @function $3Dmol.GLViewer#removeAllModels
-         */
-        this.removeAllModels = function() {
-            for (var i = 0; i < models.length; i++) {
-                var model = models[i];
-                model.removegl(modelGroup);
 
-            }
-            models = [];
-        };
+$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
 
-        /**
-         * Create a new model from atoms specified by sel.
-         * If extract, removes selected atoms from existing models 
-         * 
-         * @function $3Dmol.GLViewer#createModelFrom
-         * @param {Object} sel - Atom selection specification
-         * @param {boolean=} extract - If true, remove selected atoms from existing models
-         * @return {$3Dmol.GLModel}
-         */
-        this.createModelFrom = function(sel, extract) {
-            var m = new $3Dmol.GLModel(models.length, defaultcolors);
-            for (var i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    var atoms = models[i].selectedAtoms(sel);
-                    m.addAtoms(atoms);
-                    if (extract)
-                        models[i].removeAtoms(atoms);
-                }
-            }
-            models.push(m);
-            return m;
-        };
 
-        function applyToModels(func, sel, value1, value2) {
-            for (var i = 0; i < models.length; i++) {
-                if (models[i]) {
-                    models[i][func](sel, value1, value2);
-                }
-            }
-        }
-
-        /**
-         * Set style properties to all selected atoms
-         * 
-         * @function $3Dmol.GLViewer#setStyle
-         * @param {AtomSelectionSpec} sel - Atom selection specification
-         * @param {AtomStyleSpec} style - Style spec to apply to specified atoms
-         * 
-         * @example
-         * viewer.setStyle({}, {stick:{}}); //set all atoms to stick
-         * viewer.setStyle({chain: 'B'}, {carton: {color: spectrum}}); //set chain B to rainbow cartoon
-         */
-        this.setStyle = function(sel, style) {
-            applyToModels("setStyle", sel, style, false);
-        };
-
-        /**
-         * Add style properties to all selected atoms
-         * 
-         * @function $3Dmol.GLViewer#addStyle
-         * @param {AtomSelectionSpec} sel - Atom selection specification
-         * @param {AtomStyleSpec} style - style spec to add to specified atoms
-         */
-        this.addStyle = function(sel, style) {
-            applyToModels("setStyle", sel, style, true);
-        };
-
-        /**
-         * @function $3Dmol.GLViewer#setColorByProperty
-         * @param {AtomSelectionSpec} sel
-         * @param {type} prop
-         * @param {type} scheme
-         */
-        this.setColorByProperty = function(sel, prop, scheme) {
-            applyToModels("setColorByProperty", sel, prop, scheme);
-        };
-
-        /**
-         * @function $3Dmol.GLViewer#setColorByElement
-         * @param {AtomSelectionSpec} sel
-         * @param {type} colors
-         */
-        this.setColorByElement = function(sel, colors) {
-            applyToModels("setColorByElement", sel, colors);
-        };
-
-        /**
-         * 
-         * @param {AtomSpec[]} atomlist
-         * @param {Array}
-         *            extent
-         * @return {Array}
-         */
-        var getAtomsWithin = function(atomlist, extent) {
-            var ret = [];
-
-            for (var i = 0; i < atomlist.length; i++) {
-                var atom = atomlist[i];
-                if (typeof (atom) == "undefined")
-                    continue;
-
-                if (atom.x < extent[0][0] || atom.x > extent[1][0])
-                    continue;
-                if (atom.y < extent[0][1] || atom.y > extent[1][1])
-                    continue;
-                if (atom.z < extent[0][2] || atom.z > extent[1][2])
-                    continue;
-                ret.push(i);
-            }
-            return ret;
-        };
-
-        // return volume of extent
-        var volume = function(extent) {
-            var w = extent[1][0] - extent[0][0];
-            var h = extent[1][1] - extent[0][1];
-            var d = extent[1][2] - extent[0][2];
-            return w * h * d;
-        }; // volume
-        /*
-         * Break up bounding box/atoms into smaller pieces so we can parallelize
-         * with webworkers and also limit the size of the working memory Returns
-         * a list of bounding boxes with the corresponding atoms. These extents
-         * are expanded by 4 angstroms on each side.
-         */
-        /**
-         * 
-         * @param {Array}
-         *            extent
-         * @param {AtomSpec[]} atomlist
-         * @param {AtomSpec[]} atomstoshow
-         * @return {Array}
-         */
-        var carveUpExtent = function(extent, atomlist, atomstoshow) {
-            var ret = [];
+$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
 
-            var copyExtent = function(extent) {
-                // copy just the dimensions
-                var ret = [];
-                ret[0] = [ extent[0][0], extent[0][1], extent[0][2] ];
-                ret[1] = [ extent[1][0], extent[1][1], extent[1][2] ];
-                return ret;
-            }; // copyExtent
-            var splitExtentR = function(extent) {
-                // recursively split until volume is below maxVol
-                if (volume(extent) < maxVolume) {
-                    return [ extent ];
-                } else {
-                    // find longest edge
-                    var w = extent[1][0] - extent[0][0];
-                    var h = extent[1][1] - extent[0][1];
-                    var d = extent[1][2] - extent[0][2];
+$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
 
-                    var index;
+ /**
+ * Color scheme representation. 
+ * @typedef ColorschemeSpec
+ * @prop {string} greenCarbon   - 0x00FF00
+ * @prop {string} cyanCarbon    - 0x00FFFF
+ * @prop {string} magentaCarbon - 0xFF00FF
+ * @prop {string} yellowCarbon  - 0xFFFF00
+ * @prop {string} whiteCarbon   - 0xFFFFFF
+ * @prop {string} orangeCarbon  - 0xFF6600
+ * @prop {string} purpleCarbon  - 0x100080
+ * @prop {string} blueCarbon    - 0x0000FF
+ */
+ 
+});
 
-                    if (w > h && w > d) {
-                        index = 0;
-                    } else if (h > w && h > d) {
-                        index = 1;
-                    } else {
-                        index = 2;
-                    }
+// in an attempt to reduce memory overhead, cache all $3Dmol.Colors
+// this makes things a little faster
+$3Dmol.CC = {
+    cache : {0:new $3Dmol.Color(0)},
+    color : function color_(hex) {
+        // Undefined values default to black
+        if(!hex)
+            return this.cache[0];
+        // cache hits
+        if(typeof(this.cache[hex]) !== "undefined") {
+            return this.cache[hex];
+        }
+        // arrays
+        else if(hex && hex.constructor === Array) {
+            // parse elements recursively
+            return hex.map(color_,this);
+        }
+        // numbers and hex strings
+        hex = this.getHex(hex);
+        if(typeof hex === 'number') {
+            var c = new $3Dmol.Color(hex);
+            this.cache[hex] = c;
+            return c;
+        } else {
+            // pass through $3Dmol.Color & other objects
+            return hex;
+        }
+    },
+ 
+    colorTab : {
+        'white' : 0xFFFFFF,
+        'silver' : 0xC0C0C0,
+        'gray' : 0x808080,
+        'grey' : 0x808080,
+        'black' : 0x000000,
+        'red' : 0xFF0000,
+        'maroon' : 0x800000,
+        'yellow' : 0xFFFF00,
+        'orange' : 0xFF6600,
+        'olive' : 0x808000,
+        'lime' : 0x00FF00,
+        'green' : 0x008000,
+        'aqua' : 0x00FFFF,
+        'cyan' : 0x00FFFF,
+        'teal' : 0x008080,
+        'blue' : 0x0000FF,
+        'navy' : 0x000080,
+        'fuchsia' : 0xFF00FF,
+        'magenta' : 0xFF00FF,
+        'purple' : 0x800080
+    },    
+    getHex : function(hex) {
+        if (!isNaN(parseInt(hex)))
+            return parseInt(hex);
+        
+        else if (typeof(hex) === 'string') {
+            
+            return this.colorTab[hex.trim().toLowerCase()] || 0x000000;
+        }
+        return hex;
+    }
+    
+};
 
-                    // create two halves, splitting at index
-                    var a = copyExtent(extent);
-                    var b = copyExtent(extent);
-                    var mid = (extent[1][index] - extent[0][index]) / 2
-                            + extent[0][index];
-                    a[1][index] = mid;
-                    b[0][index] = mid;
 
-                    var alist = splitExtentR(a);
-                    var blist = splitExtentR(b);
-                    return alist.concat(blist);
-                }
-            }; // splitExtentR
+$3Dmol['CC'] = $3Dmol.CC;
+$3Dmol['CC']['color'] = $3Dmol.CC.color;
 
-            // divide up extent
-            var splits = splitExtentR(extent);
-            // now compute atoms within expanded (this could be more efficient)
-            var off = 6; // enough for water and 2*r, also depends on scale
-            // factor
-            for (var i = 0, n = splits.length; i < n; i++) {
-                var e = copyExtent(splits[i]);
-                e[0][0] -= off;
-                e[0][1] -= off;
-                e[0][2] -= off;
-                e[1][0] += off;
-                e[1][1] += off;
-                e[1][2] += off;
 
-                var atoms = getAtomsWithin(atomlist, e);
-                var toshow = getAtomsWithin(atomstoshow, splits[i]);
 
-                // ultimately, divide up by atom for best meshing
-                ret.push({
-                    extent : splits[i],
-                    atoms : atoms,
-                    toshow : toshow
-                });
+/** Return proper color for atom given style
+ * @param {AtomSpec} atom
+ * @param {AtomStyle} style
+ * @return {$3Dmol.Color}
+ */
+$3Dmol.getColorFromStyle = function(atom, style) {
+    var color = atom.color;
+    if (typeof (style.color) != "undefined" && style.color != "spectrum")
+        color = style.color;
+    if(typeof(style.colorscheme) != "undefined") {
+        if(typeof($3Dmol.elementColors[style.colorscheme]) != "undefined") {
+            //name of builtin colorscheme
+            var scheme = $3Dmol.elementColors[style.colorscheme];
+            if(typeof(scheme[atom.elem]) != "undefined") {
+                color = scheme[atom.elem];
+            }
+        } else if(typeof(style.colorscheme[atom.elem]) != 'undefined') {
+            //actual color scheme provided
+            color = style.colorscheme[atom.elem];
+        } else if(typeof(style.colorscheme.prop) != 'undefined' &&
+                typeof(style.colorscheme.gradient) != 'undefined') {         
+            //apply a property mapping
+            var prop = style.colorscheme.prop;
+            var scheme = style.colorscheme.gradient;
+            var range = scheme.range() || [-1,1]; //sensible default
+            var val = $3Dmol.getAtomProperty(atom, prop);
+            if(val != null) {
+                color = scheme.valueToHex(val, range);
             }
+        }
+    } 
+    else if(typeof(style.colorfunc) != "undefined") {
+    	//this is a user provided function for turning an atom into a color
+    	color = style.colorfunc(atom);
+    }
+    
+    var C = $3Dmol.CC.color(color);
+    return C;
+}
 
-            return ret;
-        };
+/** Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
+ * @struct
+ */
+$3Dmol.elementColors = $3Dmol.elementColors || {};
 
-        // create a mesh defined from the passed vertices and faces and material
-        // Just create a single geometry chunk - broken up whether sync or not
-        /**
-         * 
-         * @param {AtomSpec[]} atoms
-         * @param {{vertices:number,faces:number}}
-         *            VandF
-         * @param {$3Dmol.MeshLambertMaterial}
-         *            mat
-         * @return {$3Dmol.Mesh}
-         */
-        var generateSurfaceMesh = function(atoms, VandF, mat) {
+$3Dmol.elementColors.defaultColor = 0xff1493;
 
-            var geo = new $3Dmol.Geometry(true);
-            // Only one group per call to generate surface mesh (addSurface
-            // should split up mesh render)
-            var geoGroup = geo.updateGeoGroup(0);
+/** @property Jmol-like element colors*/
+$3Dmol.elementColors.Jmol = {
+        'H': 0xFFFFFF,
+        'He': 0xD9FFFF,
+        'HE': 0xD9FFFF,
+        'Li': 0xCC80FF,
+        'LI': 0xCC80FF,
+        'B': 0xFFB5B5,
+        'C': 0x909090,
+        'N': 0x3050F8,
+        'O': 0xFF0D0D,
+        'F': 0x90E050,
+        'Na': 0xAB5CF2,
+        'NA': 0xAB5CF2,
+        'Mg': 0x8AFF00,
+        'MG': 0x8AFF00,
+        'Al': 0xBFA6A6,
+        'AL': 0xBFA6A6,
+        'Si': 0xF0C8A0,
+        'SI': 0xF0C8A0,
+        'P': 0xFF8000,
+        'S': 0xFFFF30,
+        'Cl': 0x1FF01F,
+        'CL': 0x1FF01F,
+        'Ca': 0x3DFF00,
+        'CA': 0x3DFF00,
+        'Ti': 0xBFC2C7,
+        'TI': 0xBFC2C7,
+        'Cr': 0x8A99C7,
+        'CR': 0x8A99C7,
+        'Mn': 0x9C7AC7,
+        'MN': 0x9C7AC7,
+        'Fe': 0xE06633,
+        'FE': 0xE06633,
+        'Ni': 0x50D050,
+        'NI': 0x50D050,
+        'Cu': 0xC88033,
+        'CU': 0xC88033,
+        'Zn': 0x7D80B0,
+        'ZN': 0x7D80B0,
+        'Br': 0xA62929,
+        'BR': 0xA62929,
+        'Ag': 0xC0C0C0,
+        'AG': 0xC0C0C0,
+        'I': 0x940094,
+        'Ba': 0x00C900,
+        'BA': 0x00C900,
+        'Au': 0xFFD123,
+        'AU': 0xFFD123
+};
 
-            var vertexArray = geoGroup.vertexArray;
-            // reconstruct vertices and faces
-            var v = VandF['vertices'];
-            var offset;
-            var i, il;
-            for (i = 0, il = v.length; i < il; i++) {
-                offset = geoGroup.vertices * 3;
-                vertexArray[offset] = v[i].x;
-                vertexArray[offset + 1] = v[i].y;
-                vertexArray[offset + 2] = v[i].z;
-                geoGroup.vertices++;
-            }
+/** @property rasmol-like element colors */
+$3Dmol.elementColors.rasmol = {
+        'H': 0xFFFFFF,
+        'He': 0xFFC0CB,
+        'HE': 0xFFC0CB,
+        'Li': 0xB22222,
+        'LI': 0xB22222,
+        'B': 0x00FF00,
+        'C': 0xC8C8C8,
+        'N': 0x8F8FFF,
+        'O': 0xF00000,
+        'F': 0xDAA520,
+        'Na': 0x0000FF,
+        'NA': 0x0000FF,
+        'Mg': 0x228B22,
+        'MG': 0x228B22,
+        'Al': 0x808090,
+        'AL': 0x808090,
+        'Si': 0xDAA520,
+        'SI': 0xDAA520,
+        'P': 0xFFA500,
+        'S': 0xFFC832,
+        'Cl': 0x00FF00,
+        'CL': 0x00FF00,
+        'Ca': 0x808090,
+        'CA': 0x808090,
+        'Ti': 0x808090,
+        'TI': 0x808090,
+        'Cr': 0x808090,
+        'CR': 0x808090,
+        'Mn': 0x808090,
+        'MN': 0x808090,
+        'Fe': 0xFFA500,
+        'FE': 0xFFA500,
+        'Ni': 0xA52A2A,
+        'NI': 0xA52A2A,
+        'Cu': 0xA52A2A,
+        'CU': 0xA52A2A,
+        'Zn': 0xA52A2A,
+        'ZN': 0xA52A2A,
+        'Br': 0xA52A2A,
+        'BR': 0xA52A2A,
+        'Ag': 0x808090,
+        'AG': 0x808090,
+        'I': 0xA020F0,
+        'Ba': 0xFFA500,
+        'BA': 0xFFA500,
+        'Au': 0xDAA520,
+        'AU': 0xDAA520    
+};
 
-            var faces = VandF['faces'];
-            geoGroup.faceidx = faces.length;// *3;
-            geo.initTypedArrays();
+$3Dmol.elementColors.defaultColors = $3Dmol.elementColors.rasmol;
 
-            // set colors for vertices
-            var colors = [];
-            for (i = 0, il = atoms.length; i < il; i++) {
-                var atom = atoms[i];
-                if (atom) {
-                    if (typeof (atom.surfaceColor) != "undefined") {
-                        colors[i] = atom.surfaceColor;
-                    } else if (atom.color) // map from atom
-                        colors[i] = $3Dmol.CC.color(atom.color);
-                }
-            }
+$3Dmol.elementColors.greenCarbon = $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.greenCarbon['C'] = 0x00ff00;
 
-            var verts = geoGroup.vertexArray;
-            var colorArray = geoGroup.colorArray;
-            var normalArray = geoGroup.normalArray;
-            var vA, vB, vC, norm;
+$3Dmol.elementColors.cyanCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.cyanCarbon['C'] = 0x00ffff;
 
-            // Setup colors, faces, and normals
-            for (i = 0, il = faces.length; i < il; i += 3) {
+$3Dmol.elementColors.magentaCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.magentaCarbon['C'] = 0xff00ff;
 
-                // var a = faces[i].a, b = faces[i].b, c = faces[i].c;
-                var a = faces[i], b = faces[i + 1], c = faces[i + 2];
-                var A = v[a]['atomid'];
-                var B = v[b]['atomid'];
-                var C = v[c]['atomid'];
+$3Dmol.elementColors.yellowCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.yellowCarbon['C'] = 0xffff00;
 
-                var offsetA = a * 3, offsetB = b * 3, offsetC = c * 3;
+$3Dmol.elementColors.whiteCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.whiteCarbon['C'] = 0xffffff;
 
-                colorArray[offsetA] = colors[A].r;
-                colorArray[offsetA + 1] = colors[A].g;
-                colorArray[offsetA + 2] = colors[A].b;
-                colorArray[offsetB] = colors[B].r;
-                colorArray[offsetB + 1] = colors[B].g;
-                colorArray[offsetB + 2] = colors[B].b;
-                colorArray[offsetC] = colors[C].r;
-                colorArray[offsetC + 1] = colors[C].g;
-                colorArray[offsetC + 2] = colors[C].b;
+$3Dmol.elementColors.orangeCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.orangeCarbon['C'] = 0xff6600;
 
-                // setup Normals
+$3Dmol.elementColors.purpleCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.purpleCarbon['C'] = 0x800080;
 
-                vA = new $3Dmol.Vector3(verts[offsetA], verts[offsetA + 1],
-                        verts[offsetA + 2]);
-                vB = new $3Dmol.Vector3(verts[offsetB], verts[offsetB + 1],
-                        verts[offsetB + 2]);
-                vC = new $3Dmol.Vector3(verts[offsetC], verts[offsetC + 1],
-                        verts[offsetC + 2]);
+$3Dmol.elementColors.blueCarbon =  $.extend({},$3Dmol.elementColors.defaultColors);
+$3Dmol.elementColors.blueCarbon['C'] = 0x0000ff;
+//glcartoon.js
+//This contains all the routines for rendering a cartoon given a set
+//of atoms with assigned secondary structure
 
-                vC.subVectors(vC, vB);
-                vA.subVectors(vA, vB);
-                vC.cross(vA);
+//TODO: generate normals directly in drawStrip and drawThinStrip
 
-                // face normal
-                norm = vC;
-                norm.normalize();
+var $3Dmol = $3Dmol || {};
 
-                normalArray[offsetA] += norm.x;
-                normalArray[offsetB] += norm.x;
-                normalArray[offsetC] += norm.x;
-                normalArray[offsetA + 1] += norm.y;
-                normalArray[offsetB + 1] += norm.y;
-                normalArray[offsetC + 1] += norm.y;
-                normalArray[offsetA + 2] += norm.z;
-                normalArray[offsetB + 2] += norm.z;
-                normalArray[offsetC + 2] += norm.z;
 
-            }
-            geoGroup.faceArray = new Uint16Array(faces);
-            var mesh = new $3Dmol.Mesh(geo, mat);
-            mesh.doubleSided = true;
-            
-            return mesh;
-        };
+/**@typedef CartoonStyleSpec
+ * @prop {ColorSpec} color - strand color, may specify as 'spectrum'
+ * @prop {string} style - style of cartoon rendering (trace, oval, rectangle (default), parabola, edged)
+ * @prop {boolean} ribbon - whether to use constant strand width, disregarding secondary structure; use thickness to adjust radius
+ * @prop {boolean} arrows - whether to add arrows showing beta-sheet directionality; does not apply to trace or ribbon
+ * @prop {boolean} tubes - whether to display alpha helices as simple cylinders; does not apply to trace
+ * @prop {number} thickness - cartoon strand thickness, default is 0.4
+ * @prop {number} width - cartoon strand width, default is secondary structure-dependent; does not apply to trace or ribbon
+ * @prop {number} opacity - set opacity from 0-1; transparency is set per-chain with a warning outputted in the event of ambiguity
+ * @prop {}
+ * In nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which
+ * is 'N1' for purines (resn: 'A', 'G', 'DA', 'DG') and 'N3' for pyrimidines (resn: 'C', 'U', 'DC', 'DT').
+ * The different nucleobases can therefore be distinguished as follows:
+ * @example
+ * viewer.setStyle({resn:'DA', atom:'N1'}, {cartoon:{color:'red'}});
+ * viewer.setStyle({resn:'DG', atom:'N1'}, {cartoon:{color:'green'}});
+ * viewer.setStyle({resn:'DC', atom:'N3'}, {cartoon:{color:'blue'}});
+ * viewer.setStyle({resn:'DT', atom:'N3'}, {cartoon:{color:'yellow'}});
+ */
 
-        // do same thing as worker in main thread
-        /**
-         * 
-         * @param {$3Dmol.SurfaceType}
-         *            type
-         * @param {Array}
-         *            expandedExtent
-         * @param {Array}
-         *            extendedAtoms
-         * @param {Array}
-         *            atomsToShow
-         * @param {AtomSpec[]} atoms
-         * @param {number}
-         *            vol
-         * @return {Object}
-         */
-        var generateMeshSyncHelper = function(type, expandedExtent,
-                extendedAtoms, atomsToShow, atoms, vol) {
-            var time = new Date();
-            var ps = new $3Dmol.ProteinSurface();
-            ps.initparm(expandedExtent, (type === 1) ? false : true, vol);
+/**
+ * @ignore
+ * @param {$3Dmol.Object3D} group
+ * @param {AtomSpec} atomlist
+ * @param {$3Dmol.Gradient} gradientscheme
+ */
+$3Dmol.drawCartoon = (function() {
 
-            var time2 = new Date();
-            //console.log("initialize " + (time2 - time) + "ms");
+    var defaultNum = 5; // for cross-sectional shape
+    var defaultDiv = 5; // for length-wise splicing
 
-            ps.fillvoxels(atoms, extendedAtoms);
+    var coilWidth = 0.5;
+    var helixSheetWidth = 1.3;
+    var nucleicAcidWidth = 0.8;
+    var arrowTipWidth = 0.1;
+    var defaultThickness = 0.4; 
 
-            var time3 = new Date();
-            //console.log("fillvoxels " + (time3 - time2) + "  " + (time3 - time) + "ms");
+    // helper functions
 
-            ps.buildboundary();
+    // Catmull-Rom subdivision
+    var subdivide = function(_points, DIV) { // points as Vector3
+        var ret = [];
+        var points = _points;
+        points = []; // Smoothing test
+        points.push(_points[0]);
+        
+        var i, lim, size;
+        var p0, p1, p2, p3, v0, v1;
+        
+        for (i = 1, lim = _points.length - 1; i < lim; i++) {
+            p1 = _points[i]; p2 = _points[i + 1];
+            if (p1.smoothen)
+                points.push(new $3Dmol.Vector3((p1.x + p2.x) / 2, (p1.y + p2.y) / 2,
+                        (p1.z + p2.z) / 2));
+            else
+                points.push(p1);
+        }
+        points.push(_points[_points.length - 1]);
 
-            if (type == $3Dmol.SurfaceType.SES) {
-                ps.fastdistancemap();
-                ps.boundingatom(false);
-                ps.fillvoxelswaals(atoms, extendedAtoms);
+        
+        for (i = -1, size = points.length; i <= size - 3; i++) {
+            p0 = points[(i === -1) ? 0 : i];
+            p1 = points[i + 1]; p2 = points[i + 2];
+            p3 = points[(i === size - 3) ? size - 1 : i + 3];
+            v0 = new $3Dmol.Vector3().subVectors(p2, p0).multiplyScalar(0.5);
+            v1 = new $3Dmol.Vector3().subVectors(p3, p1).multiplyScalar(0.5);
+            if (p2.skip) continue;
+
+            for ( var j = 0; j < DIV; j++) {
+                var t = 1.0 / DIV * j;
+                var x = p1.x + t * v0.x + t * t * 
+                        (-3 * p1.x + 3 * p2.x - 2 * v0.x - v1.x) + t * t * t *
+                        (2 * p1.x - 2 * p2.x + v0.x + v1.x);
+                var y = p1.y + t * v0.y + t * t * 
+                        (-3 * p1.y + 3 * p2.y - 2 * v0.y - v1.y) + t * t * t *
+                        (2 * p1.y - 2 * p2.y + v0.y + v1.y);
+                var z = p1.z + t * v0.z + t * t * 
+                        (-3 * p1.z + 3 * p2.z - 2 * v0.z - v1.z) + t * t * t * 
+                        (2 * p1.z - 2 * p2.z + v0.z + v1.z);
+                        
+                var pt = new $3Dmol.Vector3(x, y, z);
+                
+                var atomIndex = Math.floor( (ret.length+2) / DIV);
+                
+                if (_points[atomIndex] !== undefined && _points[atomIndex].atom !== undefined)
+                    pt.atom = _points[atomIndex].atom;
+                    
+                ret.push(pt);
             }
+        }
+        ret.push(points[points.length - 1]);
+        return ret;
+    };
 
-            var time4 = new Date();
-            console.log("buildboundaryetc " + (time4 - time3) + "  "
-                    + (time4 - time) + "ms");
+    var drawThinStrip = function(group, p1, p2, colors, div, opacity) {
+    
+        var geo = new $3Dmol.Geometry(true);       
+        var offset, vertoffset;
+        var color, colori;
 
-            ps.marchingcube(type);
+        
+        for ( var i = 0, lim = p1.length; i < lim; i++) {
+            
+            colori = Math.round(i*(colors.length-1)/lim);
+            color = $3Dmol.CC.color(colors[colori]);
+           
+            geoGroup = geo.updateGeoGroup(2);
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            offset = geoGroup.vertices; vertoffset = offset*3;
+            
+            vertexArray[vertoffset] = p1[i].x;
+            vertexArray[vertoffset+1] = p1[i].y;
+            vertexArray[vertoffset+2] = p1[i].z;
+            
+            vertexArray[vertoffset+3] = p2[i].x;
+            vertexArray[vertoffset+4] = p2[i].y;
+            vertexArray[vertoffset+5] = p2[i].z;
+            
+            for (var j = 0; j < 6; ++j)
+            {
+                colorArray[vertoffset+3*j] = color.r;
+                colorArray[vertoffset+1+3*j] = color.g;
+                colorArray[vertoffset+2+3*j] = color.b;
+            }
+           
+            if (i > 0) {
+                var faces = [offset, offset + 1, offset - 1, offset - 2];
+                var faceoffset = geoGroup.faceidx;
+                
+                faceArray[faceoffset] = faces[0]; faceArray[faceoffset+1] = faces[1]; faceArray[faceoffset+2] = faces[3];
+                faceArray[faceoffset+3] = faces[1]; faceArray[faceoffset+4] = faces[2]; faceArray[faceoffset+5] = faces[3];
 
-            var time5 = new Date();
-            //console.log("marching cube " + (time5 - time4) + "  "+ (time5 - time) + "ms");
+                geoGroup.faceidx += 6;
+            }
+            
+            geoGroup.vertices += 2;
+        }
+        
+        geo.initTypedArrays();
+        geo.setUpNormals();
+        
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        if(typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        material.vertexColors = $3Dmol.FaceColors;
+        var mesh = new $3Dmol.Mesh(geo, material);
 
-            return ps.getFacesAndVertices(atomsToShow);
-        };
+        group.add(mesh);
+    };
 
-        /**
-         * 
-         * @param {matSpec}
-         *            style
-         * @return {$3Dmol.MeshLambertMaterial}
-         */
-        function getMatWithStyle(style) {
-            var mat = new $3Dmol.MeshLambertMaterial();
-            mat.vertexColors = $3Dmol.VertexColors;
+    var drawShapeStrip = function(group, points, colors, div, thickness, opacity, shape) {
 
-            for ( var prop in style) {
-                if (prop === "color" || prop === "map") {
-                    // ignore
-                } else if (style.hasOwnProperty(prop))
-                    mat[prop] = style[prop];
-            }
-            if (style.opacity !== undefined) {
-                if (style.opacity === 1)
-                    mat.transparent = false;
-                else
-                    mat.transparent = true;
-            }
+        // points is a 2D array, dimensionality given by [num = cross-sectional resolution][len = length of strip]
+        var i, j, num, len;
+        num = points.length;
+        if (num < 2 || points[0].length < 2) return;
 
-            return mat;
+        div = div || axisDIV;
+        for (i = 0; i < num; i++) { // spline to generate greater length-wise resolution
+            points[i] = subdivide(points[i], div)
         }
+        len = points[0].length;
 
-        // get the min and max values of the specified property in the provided
-        // atoms
-        function getPropertyRange(atomlist, prop) {
-            var min = Number.POSITIVE_INFINITY;
-            var max = Number.NEGATIVE_INFINITY;
+        if (!thickness) // if thickness is 0, we can use a smaller geometry than this function generates
+            return drawThinStrip(group, points[0], points[num-1], colors, div, opacity);
 
-            for (var i = 0, n = atomlist.length; i < n; i++) {
-                var atom = atomlist[i];
-                if (atom.properties
-                        && typeof (atom.properties[prop]) != "undefined") {
-                    var val = atom.properties[prop];
-                    if (val < min)
-                        min = val;
-                    if (val > max)
-                        max = val;
-                }
-            }
 
-            if (!isFinite(min) && !isFinite(max))
-                min = max = 0;
-            else if (!isFinite(min))
-                min = max;
-            else if (!isFinite(max))
-                max = min;
+        var geo = new $3Dmol.Geometry(true);
+        var axis, cs_shape, cs_bottom, cs_top, last_cs_bottom, last_cs_top;
+
+        // cache the available cross-sectional shapes
+        var cs_ellipse = [], cs_rectangle = [], cs_parabola = [];
+        for (j=0; j < num; j++) {
+            cs_ellipse.push(0.25 + 1.5*Math.sqrt((num-1)*j - Math.pow(j, 2))/(num-1));
+            cs_rectangle.push(0.5);
+            cs_parabola.push(2*(Math.pow(j/num, 2) - j/num) + 0.6);
+        }
+
+        /* face_refs array is used to generate faces from vertexArray iteratively.
+           As we move through each cross-sectional segment of points, we draw lateral
+           faces backwards to the previous cross-sectional segment.
+
+           To correctly identify the points needed to make each face we use this
+           array as a lookup table for the relative indices of each needed point
+           in the vertices array.
+
+           4 points are used to create 2 faces.
+        */
 
-            return [ min, max ];
+        var face_refs = [];
+        for (j = 0; j < num*2-1; j++) {
+            /* [curr vertex in curr cross-section,
+                next vertex in curr cross-section,
+                next vertex in prev cross-section,
+                curr vertex in prev cross-section] */
+            face_refs[j] = [j, j+1, j+1-2*num, j-2*num];
         }
+        // last face is different. easier to conceptualize this by drawing a diagram
+        face_refs[num*2-1] = [j, j+1-2*num, j+1-4*num, j-2*num];
 
+                
+        var v_offset, va_offset, f_offset;
+        var currentAtom, lastAtom
+        var color, colori;
+        var geoGroup = geo.updateGeoGroup(2*num*len); // ensure vertex capacity
         
-        /**
-         * Adds an explicit mesh as a surface object.
-         * 
-         * @param {$3Dmol.Mesh}
-         *            mesh
-         * @param {Object}
-         *            style
-         * @returns {Number} surfid
-         */
-        this.addMesh = function(mesh) {
-            var surfobj = {
-                geo : mesh.geometry,
-                mat : mesh.material,
-                done : true,
-                finished : false //the rendered finishes surfaces when they are done
-            };
-            var surfid = surfaces.length;
-            surfaces[surfid] = surfobj;
-            return surfid;
-        }
+        for (i = 0; i < len; i++) {
+        
+            colori = Math.round(i*(colors.length-1)/len);
+            color = $3Dmol.CC.color(colors[colori]);
+            
+            last_cs_bottom = cs_bottom;
+            last_cs_top = cs_top;
+            cs_bottom = [];
+            cs_top = [];
+            axis = [];
 
-        //return a shallow copy of list l, e.g., for atoms so we can
-        //ignore superficial changes (ie surfacecolor, position) that happen
-        //while we're surface building
-        var shallowCopy = function(l) {
-            var ret = [];
-            $.each(l, function(k,v) {
-                ret[k] = $.extend({},v);
-            });
-            return ret;
-        }
-        /**
-         * Add surface representation to atoms
-         *  @function $3Dmol.GLViewer#addSurface
-         * @param {$3Dmol.SurfaceType} type - Surface type
-         * @param {SurfaceStyleSpec} style - optional style specification for surface material (e.g. for different coloring scheme, etc)
-         * @param {AtomSelectionSpec} atomsel - Show surface for atoms in this selection
-         * @param {AtomSelectionSpec} allsel - Use atoms in this selection to calculate surface; may be larger group than 'atomsel' 
-         * @param {AtomSelectionSpec} focus - Optionally begin rendering surface specified atoms
-         * 
-         * @return {number} surfid - Identifying number for this surface
-         */
-        this.addSurface = function(type, style, atomsel, allsel, focus) {
-            // type 1: VDW 3: SAS 4: MS 2: SES
-            // if sync is true, does all work in main thread, otherwise uses
-            // workers
-            // with workers, must ensure group is the actual modelgroup since
-            // surface
-            // will get added asynchronously
-            // all atoms in atomlist are used to compute surfaces, but only the
-            // surfaces
-            // of atomsToShow are displayed (e.g., for showing cavities)
-            // if focusSele is specified, will start rending surface around the
-            // atoms specified by this selection
-            var atomlist = null, focusSele = null;
-            //TODO: currently generating a shallow copy to avoid problems when atoms are chagned
-            //during surface generation - come up with a better solution
-            var atomsToShow = shallowCopy(getAtomsFromSel(atomsel));
-            if(!allsel) {
-                atomlist = atomsToShow;
+            if (points[0][i].atom !== undefined) // TODO better edge case handling
+            {
+                currentAtom = points[0][i].atom;
+                if (shape === "oval")
+                    cs_shape = cs_ellipse;
+                else if (shape === "rectangle")
+                    cs_shape = cs_rectangle;
+                else if (shape === "parabola")
+                    cs_shape = cs_parabola;
             }
-            else {
-                atomlist = shallowCopy(getAtomsFromSel(allsel));
+            if (!cs_shape) cs_shape = cs_rectangle;
+
+            
+            // calculate thickness at each width point, from cross-sectional shape
+            var toNext, toSide;
+            for (j = 0; j < num; j++)
+            {
+                if (i < len-1)
+                    toNext = points[j][i+1].clone().sub(points[j][i]);
+                else
+                    toNext = points[j][i-1].clone().sub(points[j][i]).negate();
+
+                if (j < num-1)
+                    toSide = points[j+1][i].clone().sub(points[j][i]);
+                else
+                    toSide = points[j-1][i].clone().sub(points[j][i]).negate();
+
+                axis[j] = toSide.cross(toNext).normalize().multiplyScalar(thickness*cs_shape[j]);
             }
+
+            // generate vertices by applying cross-sectional shape thickness to input points
+            for (j = 0; j < num; j++)
+                cs_bottom[j] = points[j][i].clone().add(axis[j].clone().negate());
+            for (j = 0; j < num; j++)
+                cs_top[j] = points[j][i].clone().add(axis[j]);
             
-            var symmetries = false;
-            var n;
-            for (n = 0; n < models.length; n++) { 
-                var symMatrices = models[n].getSymmetries();
-                if (symMatrices.length > 1 || (symMatrices.length == 1 && !(symMatrices[0].isIdentity()))) {
-                    symmetries = true;
-                    break;
-                }
+
+            /* Until this point the vertices have been dealt with as $3Dmol.Vector3() objects,
+               but we need to serialize them into the geoGroup.vertexArray, where every three
+               indices represents the next vertex. The colorArray is analogous.
+
+               In the following for-loops, j iterates through VERTICES so we need to index
+               them in vertexArray by 3*j + either 0, 1, or 2 for xyz or rgb component.
+            */
+
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            v_offset = geoGroup.vertices; va_offset = v_offset*3; // in case geoGroup already contains vertices
+
+            // bottom edge of cross-section, vertices [0, num)
+            for (j = 0; j < num; j++) {
+                vertexArray[va_offset + 3*j + 0] = cs_bottom[j].x;
+                vertexArray[va_offset + 3*j + 1] = cs_bottom[j].y;
+                vertexArray[va_offset + 3*j + 2] = cs_bottom[j].z;
             }
 
-            var addSurfaceHelper = function addSurfaceHelper(surfobj, atomlist, atomsToShow) {
+            // top edge of cross-section, vertices [num, 2*num)
+            // add these backwards, so that each cross-section's vertices are added sequentially to vertexArray
+            for (j = 0; j < num; j++) {
+                vertexArray[va_offset + 3*j + 0 + 3*num] = cs_top[num-1-j].x;
+                vertexArray[va_offset + 3*j + 1 + 3*num] = cs_top[num-1-j].y;
+                vertexArray[va_offset + 3*j + 2 + 3*num] = cs_top[num-1-j].z;
+            }
             
-                if(!focus) {
-                    focusSele = atomsToShow;
-                } else {
-                    focusSele = shallowCopy(getAtomsFromSel(focus));
+            for (j = 0; j < 2*num; ++j) {
+                colorArray[va_offset + 3*j + 0] = color.r;
+                colorArray[va_offset + 3*j + 1] = color.g;
+                colorArray[va_offset + 3*j + 2] = color.b;
+            }
+            
+            if (i > 0) {
+             
+                for (j = 0; j < num*2; j++) {
+                
+                    // get VERTEX indices of the 4 points of a rectangular face (as opposed to literal vertexArray indices)
+                    var face = [v_offset + face_refs[j][0],
+                                v_offset + face_refs[j][1],
+                                v_offset + face_refs[j][2],
+                                v_offset + face_refs[j][3]];
+                    
+                    f_offset = geoGroup.faceidx;    
+                    
+                    // need 2 triangles to draw a face between 4 points
+                    faceArray[f_offset]   = face[0];
+                    faceArray[f_offset+1] = face[1]; 
+                    faceArray[f_offset+2] = face[3];
+
+                    faceArray[f_offset+3] = face[1];
+                    faceArray[f_offset+4] = face[2];
+                    faceArray[f_offset+5] = face[3];
+                    
+                    geoGroup.faceidx += 6;
+
+                    // TODO implement clickable the right way. midpoints of strand between consecutive atoms
                 }
+                    
+                if (currentAtom.clickable)
+                {
+                    var faces = [];
 
-                var atom;
-                var time = new Date();
-                var extent = $3Dmol.getExtent(atomsToShow, true);
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[0], cs_bottom[0], cs_bottom[num-1]));
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[0], cs_bottom[num-1], last_cs_bottom[num-1]));
 
-                var i, il;
-                if (style['map'] && style['map']['prop']) {
-                    // map color space using already set atom properties
-                    /** @type {AtomSpec} */
-                    var prop = style['map']['prop'];
-                    /** @type {Gradient} */
-                    var scheme = style['map']['scheme'] || new $3Dmol.Gradient.RWB();
-                    var range = scheme.range();
-                    if (!range) {
-                        range = getPropertyRange(atomsToShow, prop);
-                    }
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[num-1], cs_bottom[num-1], cs_top[num-1]));
+                    faces.push(new $3Dmol.Triangle(last_cs_bottom[num-1], cs_top[num-1], last_cs_top[num-1]));
 
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        atom.surfaceColor = $3Dmol.CC.color(scheme.valueToHex(
-                                atom.properties[prop], range));
-                    }
-                }
-                else if(typeof(style['color']) != 'undefined') {
-                    //explicitly set color, otherwise material color just blends
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        atom.surfaceColor = $3Dmol.CC.color(style['color']);
-                    }
-                }
-                else if(typeof(style['colorscheme']) != 'undefined') {
-                    for (i = 0, il = atomlist.length; i < il; i++) {
-                        atom = atomlist[i];
-                        var scheme = $3Dmol.elementColors[style.colorscheme];
-                                if(scheme && typeof(scheme[atom.elem]) != "undefined") {
-                                    atom.surfaceColor = $3Dmol.CC.color(scheme[atom.elem]);
-                                }
+                    faces.push(new $3Dmol.Triangle(cs_top[0], last_cs_top[0], last_cs_top[num-1]));
+                    faces.push(new $3Dmol.Triangle(cs_top[num-1], cs_top[0], last_cs_top[num-1]));
+
+                    faces.push(new $3Dmol.Triangle(cs_bottom[0], last_cs_bottom[0], last_cs_top[0]));
+                    faces.push(new $3Dmol.Triangle(cs_top[0], cs_bottom[0], last_cs_top[0]));
+
+                    for (j in faces)
+                    {
+                        currentAtom.intersectionShape.triangle.push(faces[j]);
+                        
                     }
                 }
 
-                var totalVol = volume(extent); // used to scale resolution
-                var extents = carveUpExtent(extent, atomlist, atomsToShow);
-
-                if (focusSele && focusSele.length && focusSele.length > 0) {
-                    var seleExtent = $3Dmol.getExtent(focusSele, true);
-                    // sort by how close to center of seleExtent
-                    var sortFunc = function(a, b) {
-                        var distSq = function(ex, sele) {
-                            // distance from e (which has no center of mass) and
-                            // sele which does
-                            var e = ex.extent;
-                            var x = e[1][0] - e[0][0];
-                            var y = e[1][1] - e[0][1];
-                            var z = e[1][2] - e[0][2];
-                            var dx = (x - sele[2][0]);
-                            dx *= dx;
-                            var dy = (y - sele[2][1]);
-                            dy *= dy;
-                            var dz = (z - sele[2][2]);
-                            dz *= dz;
-
-                            return dx + dy + dz;
-                        };
-                        var d1 = distSq(a, seleExtent);
-                        var d2 = distSq(b, seleExtent);
-                        return d1 - d2;
-                    };
-                    extents.sort(sortFunc);
-                }
-
-                //console.log("Extents " + extents.length + "  "+ (+new Date() - time) + "ms");
+            }
+            
+            geoGroup.vertices += 2*num;
+            lastAtom = currentAtom;
+        }
 
+        // for terminal faces
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        v_offset = geoGroup.vertices; va_offset = v_offset*3; f_offset = geoGroup.faceidx;
 
-                var reducedAtoms = [];
-                // to reduce amount data transfered, just pass x,y,z,serial and elem
-                for (i = 0, il = atomlist.length; i < il; i++) {
-                    atom = atomlist[i];
-                    reducedAtoms[i] = {
-                        x : atom.x,
-                        y : atom.y,
-                        z : atom.z,
-                        serial : i,
-                        elem : atom.elem
-                    };
-                }
+        for (i = 0; i<num-1; i++) // "rear" face
+        {
+            var face = [i, i+1, 2*num-2-i, 2*num-1-i];
 
-                var sync = !!($3Dmol.syncSurface);
-                if (sync) { // don't use worker, still break up for memory purposes
+            f_offset = geoGroup.faceidx;
 
-                    // to keep the browser from locking up, call through setTimeout
-                    var callSyncHelper = function callSyncHelper(i) {
-                        if (i >= extents.length)
-                            return;
+            faceArray[f_offset]   = face[0];
+            faceArray[f_offset+1] = face[1]; 
+            faceArray[f_offset+2] = face[3];
 
-                        var VandF = generateMeshSyncHelper(type, extents[i].extent,
-                                extents[i].atoms, extents[i].toshow, reducedAtoms,
-                                totalVol);
-                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
-                        $3Dmol.mergeGeos(surfobj.geo, mesh);
-                        _viewer.render();
+            faceArray[f_offset+3] = face[1];
+            faceArray[f_offset+4] = face[2];
+            faceArray[f_offset+5] = face[3];
 
-                        setTimeout(callSyncHelper, 1, i + 1);
-                    }
+            geoGroup.faceidx += 6;
+        }
 
-                    setTimeout(callSyncHelper, 1, 0);
+        for (i = 0; i<num-1; i++) // "front" face
+        {
+            var face = [v_offset-1-i, v_offset-2-i, v_offset-2*num+i+1, v_offset-2*num+i];
 
-                    // TODO: Asynchronously generate geometryGroups (not separate
-                    // meshes) and merge them into a single geometry
-                } else { // use worker
+            f_offset = geoGroup.faceidx;
 
-                    var workers = [];
-                    if (type < 0)
-                        type = 0; // negative reserved for atom data
-                    for (i = 0, il = numWorkers; i < il; i++) {
-                        // var w = new Worker('3Dmol/SurfaceWorker.js');
-                        var w = new Worker($3Dmol.SurfaceWorker);
-                        workers.push(w);
-                        w.postMessage({
-                            'type' : -1,
-                            'atoms' : reducedAtoms,
-                            'volume' : totalVol
-                        });
-                    }
-                    var cnt = 0;
+            faceArray[f_offset]   = face[0];
+            faceArray[f_offset+1] = face[1]; 
+            faceArray[f_offset+2] = face[3];
 
-                    var rfunction = function(event) {
-                        var VandF = event.data;
-                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
-                        $3Dmol.mergeGeos(surfobj.geo, mesh);
-                        _viewer.render();
-                    //    console.log("async mesh generation " + (+new Date() - time) + "ms");
-                        cnt++;
-                        if (cnt == extents.length)
-                            surfobj.done = true;
-                    };
+            faceArray[f_offset+3] = face[1];
+            faceArray[f_offset+4] = face[2];
+            faceArray[f_offset+5] = face[3];
 
-                    var efunction = function(event) {
-                        console.log(event.message + " (" + event.filename + ":" + event.lineno + ")");
-                    };
+            geoGroup.faceidx += 6;
+        }
+        
+        geo.initTypedArrays();
+        geo.setUpNormals();
+        
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        material.vertexColors = $3Dmol.FaceColors;
+        if (typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        var mesh = new $3Dmol.Mesh(geo, material);
+        group.add(mesh);
+    };
 
-                    for (i = 0; i < extents.length; i++) {
-                        var worker = workers[i % workers.length];
-                        worker.onmessage = rfunction;
+    var drawPlainStrip = function(group, points, colors, div, thickness, opacity) {
+        if ((points.length) < 2)
+            return;
 
-                        worker.onerror = efunction;
+        var p1, p2;
+        p1 = points[0];
+        p2 = points[points.length-1];
 
-                        worker.postMessage({
-                            'type' : type,
-                            'expandedExtent' : extents[i].extent,
-                            'extendedAtoms' : extents[i].atoms,
-                            'atomsToShow' : extents[i].toshow
-                        });
-                    }
-                }
+        div = div || axisDIV;
+        p1 = subdivide(p1, div);
+        p2 = subdivide(p2, div);
+        if (!thickness)
+            return drawThinStrip(group, p1, p2, colors, div, opacity);
 
-                // NOTE: This is misleading if 'async' mesh generation - returns
-                // immediately
-                //console.log("full mesh generation " + (+new Date() - time) + "ms");
+        var geo = new $3Dmol.Geometry(true);
+        
+        //var vs = geo.vertices, fs = geo.faces;
+        var vs = [], fs = [];
+        var axis, p1v, p2v, a1v, a2v;
+        
+        var faces = [ [ 0, 2, -6, -8 ],
+                      [ -4, -2, 6, 4 ],
+                      [ 7, -1, -5, 3 ],
+                      [ -3, 5, 1, -7 ] ];
+                
+        var offset, vertoffset, faceoffset;
+        var color, colori;
+        var currentAtom, lastAtom;
+        var i, lim, j;
+        var face1, face2, face3;
+        var geoGroup;
+        
+        for (i = 0, lim = p1.length; i < lim; i++) {
+        
+            colori = Math.round(i*(colors.length-1)/lim);
+            color = $3Dmol.CC.color(colors[colori]);
+            
+            vs.push(p1v = p1[i]); // 0
+            vs.push(p1v);         // 1
+            vs.push(p2v = p2[i]); // 2
+            vs.push(p2v);         // 3
+            if (i < lim - 1) {
+                var toNext = p1[i + 1].clone().sub(p1[i]);
+                var toSide = p2[i].clone().sub(p1[i]);
+                axis = toSide.cross(toNext).normalize().multiplyScalar(
+                        thickness);
             }
+            vs.push(a1v = p1[i].clone().add(axis)); // 4
+            vs.push(a1v); // 5
+            vs.push(a2v = p2[i].clone().add(axis)); // 6
+            vs.push(a2v); // 7
             
-            style = style || {};
-            var mat = getMatWithStyle(style);
-            var surfobj = [];
+            if (p1v.atom !== undefined)
+                currentAtom = p1v.atom;
             
-            if (symmetries) { //do preprocessing
-                var modelsAtomList = {};
-                var modelsAtomsToShow = {};
-                for (n = 0; n < models.length; n++) {
-                    modelsAtomList[n] = [];
-                    modelsAtomsToShow[n] = [];
-                }
-                for (n = 0; n < atomlist.length; n++) {
-                    modelsAtomList[atomlist[n].model].push(atomlist[n]);
-                }
-                for (n = 0; n < atomsToShow.length; n++) {
-                    modelsAtomsToShow[atomsToShow[n].model].push(atomsToShow[n]);
-                }
-                for (n = 0; n < models.length; n++) {
-                    surfobj.push({
-                        geo : new $3Dmol.Geometry(true),
-                        mat : mat,
-                        done : false,
-                        finished : false,
-                        symmetries : models[n].getSymmetries()
-                    // also webgl initialized
-                    });
-                    addSurfaceHelper(surfobj[n], modelsAtomList[n], modelsAtomsToShow[n]);
-                }
-            }
-            else {
-                surfobj.push({
-                    geo : new $3Dmol.Geometry(true),
-                    mat : mat,
-                    done : false,
-                    finished : false,
-                    symmetries : [new $3Dmol.Matrix4()]
-                });
-                addSurfaceHelper(surfobj[surfobj.length-1], atomlist, atomsToShow);
-            } 
-            var surfid = surfaces.length;
-            surfaces[surfid] = surfobj;
+            geoGroup = geo.updateGeoGroup(8);
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var faceArray = geoGroup.faceArray;
+            offset = geoGroup.vertices; vertoffset = offset*3;
             
-            return surfid;
-
-        };
-
-        /**
-         * Set the surface material to something else, must render change
-         * 
-         * @param {number} surf - Surface ID to apply changes to
-         * @param {matSpec} style - new material style specification
-         */ 
-        this.setSurfaceMaterialStyle = function(surf, style) {
-            if (surfaces[surf]) {
-                surfArr = surfaces[surf];
-                for (var i = 0; i < surfArr.length; i++) {
-                    surfArr[i].mat = getMatWithStyle(style);
-                    surfArr[i].mat.side = $3Dmol.FrontSide;
-                    surfArr[i].finished = false; // trigger redraw
-                }
-            }
-        };
-
-        /**
-         * Remove surface with given ID
-         * 
-         * @param {number} surf - surface id
-         */
-        this.removeSurface = function(surf) {
-            var surfArr = surfaces[surf];
-            for (var i = 0; i < surfArr.length; i++) {
-                if (surfArr[i] && surfArr[i].lastGL) {
-                    if (surfArr[i].geo !== undefined)
-                        surfArr[i].geo.dispose();
-                    if (surfArr[i].mat !== undefined)
-                        surfArr[i].mat.dispose();
-                    modelGroup.remove(surfArr[i].lastGL); // remove from scene
-                }
-            }
-            delete surfaces[surf];
-            show();
-        };
-        
-        /** Remove all surfaces.
-         * @function $3Dmol.GLViewer#removeAllSurfaces */
-        this.removeAllSurfaces = function() {
-            for (var n = 0; n < surfaces.length; n++) {
-                surfArr = surfaces[n];
-                for(var i = 0; i < surfArr.length; i++) {
-                    if (surfArr[i] && surfArr[i].lastGL) {
-                        if (surfArr[i].geo !== undefined)
-                            surfArr[i].geo.dispose();
-                        if (surfArr[i].mat !== undefined)
-                            surfArr[i].mat.dispose();
-                        modelGroup.remove(surfArr[i].lastGL); // remove from scene
-                    }
-                }
-                delete surfaces[n];
+            vertexArray[vertoffset]    = p1v.x; vertexArray[vertoffset+1]  = p1v.y; vertexArray[vertoffset+2]  = p1v.z;
+            vertexArray[vertoffset+3]  = p1v.x; vertexArray[vertoffset+4]  = p1v.y; vertexArray[vertoffset+5]  = p1v.z;
+            vertexArray[vertoffset+6]  = p2v.x; vertexArray[vertoffset+7]  = p2v.y; vertexArray[vertoffset+8]  = p2v.z;
+            vertexArray[vertoffset+9]  = p2v.x; vertexArray[vertoffset+10] = p2v.y; vertexArray[vertoffset+11] = p2v.z;
+            vertexArray[vertoffset+12] = a1v.x; vertexArray[vertoffset+13] = a1v.y; vertexArray[vertoffset+14] = a1v.z;
+            vertexArray[vertoffset+15] = a1v.x; vertexArray[vertoffset+16] = a1v.y; vertexArray[vertoffset+17] = a1v.z;
+            vertexArray[vertoffset+18] = a2v.x; vertexArray[vertoffset+19] = a2v.y; vertexArray[vertoffset+20] = a2v.z;
+            vertexArray[vertoffset+21] = a2v.x; vertexArray[vertoffset+22] = a2v.y; vertexArray[vertoffset+23] = a2v.z;
+            
+            for (j = 0; j < 8; ++j) {                
+                colorArray[vertoffset+3*j] = color.r; colorArray[vertoffset+1+3*j] = color.g; colorArray[vertoffset+2+3*j] = color.b;
             }
-            show();
             
-        };
-
-        /** return Jmol moveto command to position this scene */
-        this.jmolMoveTo = function() {
-            var pos = modelGroup.position;
-            // center on same position
-            var ret = "center { " + (-pos.x) + " " + (-pos.y) + " " + (-pos.z)
-                    + " }; ";
-            // apply rotation
-            var q = rotationGroup.quaternion;
-            ret += "moveto .5 quaternion { " + q.x + " " + q.y + " " + q.z
-                    + " " + q.w + " };";
-            // zoom is tricky.. maybe i would be best to let callee zoom on
-            // selection?
-            // can either do a bunch of math, or maybe zoom to the center with a
-            // fixed
-            // but reasonable percentage
+            if (i > 0) {
+             
+                //both points have distinct atoms
+                var diffAtoms = ((lastAtom !== undefined && currentAtom !== undefined) && lastAtom.serial !== currentAtom.serial);
+                
+                for (j = 0; j < 4; j++ ) {
+                
+                    var face = [offset + faces[j][0], offset + faces[j][1], offset + faces[j][2], offset + faces[j][3]];
+                    
+                    faceoffset = geoGroup.faceidx;    
+                    
+                    faceArray[faceoffset] = face[0]; faceArray[faceoffset+1] = face[1]; faceArray[faceoffset+2] = face[3];
+                    faceArray[faceoffset+3] = face[1]; faceArray[faceoffset+4] = face[2]; faceArray[faceoffset+5] = face[3];
+                    
+                    geoGroup.faceidx += 6;
+                    
+                    if (currentAtom.clickable || lastAtom.clickable) {
+                        
+                        var p1a = vs[face[3]].clone(), p1b = vs[face[0]].clone(),
+                            p2a = vs[face[2]].clone(), p2b = vs[face[1]].clone();
+                        
+                        p1a.atom = vs[face[3]].atom || null; //should be same
+                        p2a.atom = vs[face[2]].atom || null; 
+                        
+                        
+                        p1b.atom = vs[face[0]].atom || null; //should be same                      
+                        p2b.atom = vs[face[1]].atom || null; 
+                        
+                        if (diffAtoms) {
+                            var m1 = p1a.clone().add(p1b).multiplyScalar(0.5);
+                            var m2 = p2a.clone().add(p2b).multiplyScalar(0.5);
+                            var m = p1a.clone().add(p2b).multiplyScalar(0.5);
+                            
+                            if (j % 2 === 0)
+                            {
+                                if (lastAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
+                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
+                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
+                                    lastAtom.intersectionShape.triangle.push(face1);
+                                    lastAtom.intersectionShape.triangle.push(face2);
+                                    lastAtom.intersectionShape.triangle.push(face3);
+                                }
+                                
+                                if (currentAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
+                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
+                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
+                                    currentAtom.intersectionShape.triangle.push(face1);
+                                    currentAtom.intersectionShape.triangle.push(face2);
+                                    currentAtom.intersectionShape.triangle.push(face3);
+                                }
+                            }
+                            else {
+                                if (currentAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(m1, m, p1a);
+                                    face2 = new $3Dmol.Triangle(m2, p2a, m);
+                                    face3 = new $3Dmol.Triangle(m, p2a, p1a);
+                                    currentAtom.intersectionShape.triangle.push(face1);
+                                    currentAtom.intersectionShape.triangle.push(face2);
+                                    currentAtom.intersectionShape.triangle.push(face3);
+                                }
+                                
+                                if (lastAtom.clickable) {
+                                    face1 = new $3Dmol.Triangle(p1b, p2b, m);
+                                    face2 = new $3Dmol.Triangle(p2b, m2, m);
+                                    face3 = new $3Dmol.Triangle(p1b, m, m1);
+                                    lastAtom.intersectionShape.triangle.push(face1);
+                                    lastAtom.intersectionShape.triangle.push(face2);
+                                    lastAtom.intersectionShape.triangle.push(face3);
+                                }                          
+                            }
+                            
+                        }
+                        
+                        //face for single atom
+                        else if (currentAtom.clickable) {
+                            face1 = new $3Dmol.Triangle(p1b, p2b, p1a);
+                            face2 = new $3Dmol.Triangle(p2b, p2a, p1a);
+                            currentAtom.intersectionShape.triangle.push(face1);
+                            currentAtom.intersectionShape.triangle.push(face2);
+                        }
+                        
+                    }
+                    
+                }
+            }
+            
+            geoGroup.vertices += 8;
+            lastAtom = currentAtom;
+        }
+        
 
-            return ret;
-        };
+        var vsize = vs.length - 8; // Cap
+        
+        geoGroup = geo.updateGeoGroup(8);
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        offset = geoGroup.vertices; vertoffset = offset*3; faceoffset = geoGroup.faceidx;
+        
+        for (i = 0; i < 4; i++) {
+            vs.push(vs[i * 2]);
+            vs.push(vs[vsize + i * 2]);
+            
+            var v1 = vs[i * 2], v2 = vs[vsize + i * 2];
+            
+            vertexArray[vertoffset+6*i] = v1.x; vertexArray[vertoffset+1+6*i] = v1.y; vertexArray[vertoffset+2+6*i] = v1.z;
+            vertexArray[vertoffset+3+6*i] = v2.x; vertexArray[vertoffset+4+6*i] = v2.y; vertexArray[vertoffset+5+6*i] = v2.z;
+            
+            colorArray[vertoffset+6*i] = color.r; colorArray[vertoffset+1+6*i] = color.g; colorArray[vertoffset+2+6*i] = color.b;
+            colorArray[vertoffset+3+6*i] = color.r; colorArray[vertoffset+4+6*i] = color.g; colorArray[vertoffset+5+6*i] = color.b;
 
-        /** Clear scene of all objects 
-         * @function $3Dmol.GLViewer#clear
-         * */
-        this.clear = function() {
-            this.removeAllSurfaces();
-            this.removeAllModels();
-            this.removeAllLabels();
-            this.removeAllShapes();
-            show();
+        }
+        
+        vsize += 8;
+                
+        face1 = [offset, offset + 2, offset + 6, offset + 4];
+        face2 = [offset + 1, offset + 5, offset + 7, offset + 3];
+        
+        faceArray[faceoffset] = face1[0]; faceArray[faceoffset+1] = face1[1]; faceArray[faceoffset+2] = face1[3];
+        faceArray[faceoffset+3] = face1[1]; faceArray[faceoffset+4] = face1[2]; faceArray[faceoffset+5] = face1[3];
+        faceArray[faceoffset+6] = face2[0]; faceArray[faceoffset+7] = face2[1]; faceArray[faceoffset+8] = face2[3];
+        faceArray[faceoffset+9] = face2[1]; faceArray[faceoffset+10] = face2[2]; faceArray[faceoffset+11] = face2[3];
+        
+        geoGroup.faceidx += 12;
+        geoGroup.vertices += 8;
+        
+        //TODO: Add intersection planes for caps
+        
+        geo.initTypedArrays();
+        geo.setUpNormals();
+        
+                // HalfEdgeRec used to store adjacency info of mesh
+        var HalfEdge=function(vertIdx){
+            this.vert=vertIdx; // Vertex index at the end of this half-edge
+            this.twin=null;    // Oppositely oriented adjacent half-edge
+            this.next=null;    //Next half-edge around the face
         };
-
-        // props is a list of objects that select certain atoms and enumerate
-        // properties for those atoms
-        /**
-         * Add specified properties to all atoms matching input argument
-         * @param {Object} props, either array of atom selectors with associated props, or function that takes atom and sets its properties
-         * @param {AtomSelectionSpec} sel
-         */
-        this.mapAtomProperties = function(props, sel) {
-            sel = sel || {};
-            var atoms = getAtomsFromSel(sel);
+        
+        var computeAdjacency=function(faces,faceCount,vertCount){
+            //all pieces of the half-edge data structure
+            edges=[];
             
-            if(typeof(props) == "function") {
-                for (var a = 0, numa = atoms.length; a < numa; a++) {
-                    var atom = atoms[a];
-                    props(atom);
+            // a hash table to hold the adjaceney info
+            // - Keys are pairs of vertex indices
+            // - Values are pointers to half-edge
+            var edgeTable={};
+            var len=0;
+            
+            //Plow through faces and fill all half-edge info except twin pointers:
+            for(var i=0;i<faceCount;i+=3){
+                var A=faces[i];
+                var B=faces[i+1];
+                var C=faces[i+2];
+               // console.log("A="+A+ " B="+ B+ " C="+C);
+                
+                //create the half-edge that goes from C to A
+                var CA=new HalfEdge(A);
+                edges.push(CA);
+                //create the half-edge that goes from A to B
+                var AB=new HalfEdge(B);
+                edges.push(AB);
+                //create the half-edge that goes from B to C
+                var BC=new HalfEdge(C);
+                edges.push(BC);
+                
+                CA.next=AB;
+                AB.next=BC;
+                BC.next=CA;
+                
+                edgeTable[C|(A<<16)]=CA; 
+                edgeTable[A|(B<<16)]=AB; 
+                edgeTable[B|(C<<16)]=BC;
+            }
+            
+            //verify that the mesh is clean
+            for(var key in edgeTable){
+                if(edgeTable.hasOwnProperty(key)){
+                    len++;
                 }
             }
-            else {
-                for (var a = 0, numa = atoms.length; a < numa; a++) {
-                    var atom = atoms[a];
-                    for (var i = 0, n = props.length; i < n; i++) {
-                        var prop = props[i];
-                        if (prop.props) {
-                            for ( var p in prop.props) {
-                                if (prop.props.hasOwnProperty(p)) {
-                                    // check the atom
-                                    if (atomIsSelected(atom, prop)) {
-                                        if (!atom.properties)
-                                            atom.properties = {};
-                                        atom.properties[p] = prop.props[p];
-                                    }
-                                }
-                            }
-                        }
+            if(len!=faceCount*3){
+                console.warn("Bad mesh: duplicated edges or inconsistent winding.len="+len+" faceCount="+faceCount+" vertCount="+vertCount);
+            }
+            
+            //Populate the twin pointers by iterating over the hash table
+            var boundaryCount=0;
+            for(var key in edgeTable){
+                if(edgeTable.hasOwnProperty(key)){
+                    var twinKey=((key&0xffff)<<16)|(key>>16);
+                    if(edgeTable.hasOwnProperty(twinKey)){
+                        edgeTable[key].twin=edgeTable[twinKey];
+                        edgeTable[twinKey].twin=edgeTable[key];
+                    }else{
+                        boundaryCount+=1;
                     }
                 }
             }
+            
+            var ret=new Uint16Array(faceCount*6);
+            // Now that we have a half-edge structure, it's easy to create adjacency info for WebGL
+            if(boundaryCount>0){
+                console.log("Mesh is not watertight. Contains "+boundaryCount +" edges");
+                
+                for(var i=0;i<faceCount;i+=3){
+                    ret[i*2+0]=edges[i+2].vert;
+                    ret[i*2+1]=edges[i+0].twin==null?ret[i*2+0]:edges[i+0].twin.next.vert;
+                    ret[i*2+2]=edges[i+0].vert;
+                    ret[i*2+3]=edges[i+1].twin==null?ret[i*2+1]:edges[i+1].twin.next.vert;                  
+                    ret[i*2+4]=edges[i+1].vert;
+                    ret[i*2+5]=edges[i+2].twin==null?ret[i*2+2]:edges[i+2].twin.next.vert;
+                }
+            }
+            else{
+                for(var i=0;i<faceCount;i+=3){
+                    ret[i*2+0]=edges[i+2].vert;
+                    ret[i*2+1]=edges[i+0].twin.next.vert;
+                    ret[i*2+2]=edges[i+0].vert;
+                    ret[i*2+3]=edges[i+1].twin.next.vert;                   
+                    ret[i*2+4]=edges[i+1].vert;
+                    ret[i*2+5]=edges[i+2].twin.next.vert;
+                } 
+            }
+            
+            return ret;
         };
+        
+        //geoGroup.adjFaceArray = computeAdjacency(faceArray,faceArray.length,offset);
+        
+        var material = new $3Dmol.MeshDoubleLambertMaterial();
+        material.vertexColors = $3Dmol.FaceColors;
+        if(typeof(opacity) === 'number' && opacity >= 0 && opacity < 1) {
+            material.transparent = true;
+            material.opacity = opacity;
+        }
+        var mesh = new $3Dmol.Mesh(geo, material);
+        group.add(mesh);   
+    };
 
-        var getModelGroup = function() {
-            return modelGroup;
-        };
+    //TODO: Need to update this (will we ever use this?)
+    var drawSmoothCurve = function(group, _points, width, colors, div) {
+        if (_points.length === 0)
+            return;
 
-        try {
-            if (typeof (callback) === "function")
-                callback(this);
-        } catch (e) {
-            // errors in callback shouldn't invalidate the viewer
-            console.log("error with glviewer callback: " + e);
+        div = (div === undefined) ? 5 : div;
+
+        var geo = new $3Dmol.Geometry();
+        var points = subdivide(_points, div);
+                /*
+        for ( var i = 0; i < points.length; i++) {
+            geo.vertices.push(points[i]);
+            geo.colors.push($3Dmol.color(colors[(i == 0) ? 0 : Math.round((i - 1)
+                    / div)]));
         }
+                */
+        var lineMaterial = new $3Dmol.LineBasicMaterial({
+            linewidth : width
+        });
+        lineMaterial.vertexColors = true;
+        var line = new $3Dmol.Line(geo, lineMaterial);
+        line.type = $3Dmol.LineStrip;
+        group.add(line);
+    };
+
+    var drawStrip = function(group, points, colors, div, thickness, opacity, shape)
+    {    
+        if (!shape || shape === "default")
+            shape = "rectangle";
+        if(shape === 'edged')
+            drawPlainStrip(group, points, colors, div, thickness, opacity);
+        else if (shape === "rectangle" || shape === "oval" || shape === "parabola")
+            drawShapeStrip(group, points, colors, div, thickness, opacity, shape);
     }
 
-    return GLViewer;
+    // check if given atom is an alpha carbon
+    var isAlphaCarbon = function(atom)
+    {
+        return atom && atom.elem === "C" && atom.atom === "CA"; // note that calcium is also CA
+    }
 
-})();
+    // check whether two atoms are members of the same residue or subsequent, connected residues (a before b)
+    var inConnectedResidues = function(a, b)
+    {
+        if(a && b && a.chain === b.chain) {
+            if((a.reschain === b.reschain) && (a.resi === b.resi || a.resi === b.resi-1))
+                return true;
+            if(a.resi < b.resi) {
+                //some PDBs have gaps in the numbering but the residues are still connected
+                //assume if within 4A they are connected
+                var av = new $3Dmol.Vector3(a.x, a.y, a.z);
+                var bv = new $3Dmol.Vector3(b.x, b.y, b.z);
+                var dist = av.distanceToSquared(bv);
+                if(dist < 16.0) return true; //calpha dist
+            }
+        }
 
-$3Dmol['glmolViewer'] = $3Dmol.GLViewer;
-//color scheme mappings
-var $3Dmol = $3Dmol || {};
-
-/** Color mapping gradiens
- * @interface
- * @param {number} min
- * @param {number} max
- */
-$3Dmol.Gradient = function(min, max) {};
-
-/**
- * Map value to hex color
- * @param {number} val
- * @param {number} range
- * @returns {number}
- */
-$3Dmol.Gradient.valueToHex = function(val, range) {};
-$3Dmol.Gradient.jmolID = function() {};
-//return range used for color mapping, null if none set
-$3Dmol.Gradient.range = function() {};
+        return false;
 
+    }
 
+    var drawCartoon = function(group, atomList, gradientScheme, fill, doNotSmoothen, num, div)
+    {
+        num = num || defaultNum;
+        div = div || defaultDiv;
 
-/**
- * Color scheme red to white to blue, for charges
- * @constructor
- * @implements {$3Dmol.Gradient}
- */
-$3Dmol.Gradient.RWB = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
-    
-        if(val === undefined)
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var middle = (hi+lo)/2;
-        var scale, color;
-        
-        //scale bottom from red to white
-        if(val <= middle) {
-            scale = Math.floor(255*Math.sqrt((val-lo)/(middle-lo)));
-            color = 0xff0000 + 0x100*scale + scale;
-            return color;
-        }
-        else { //form white to blue
-            scale = Math.floor(255*Math.sqrt((1-(val-middle)/(hi-middle))));
-            color =  0x10000*scale+0x100*scale+0xff;
-            return color;
-        }
-    };
-    
-    this.jmolID = function() {
-        return "rwb";
-    };
+                        //  proteins    na backbone  na terminus                  nucleobases
+        var cartoonAtoms = ["CA", "O",  "P", "OP2", "O2P", "O5'", "O3'", "C5'", "C2'","O5*", "O3*", "C5*", "C2*", "N1", "N3"];
+        var purResns = ["DA", "DG", "A", "G"];
+        var pyrResns = ["DT", "DC", "U", "C", "T"];
+        var naResns  =  purResns.concat(pyrResns);
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
-        }
-        return null;
-    };
+        var geo, cartoon, prev, curr, next, currColor, nextColor, thickness, i, nextResAtom, arrow;
+        var backbonePt, orientPt, prevOrientPt, terminalPt, termOrientPt, baseStartPt, baseEndPt;
+        var tubeStart, tubeEnd, drawingTube;
+        var traceGeo = null;
+        var colors = [];
+        var points = [];
+        for (var i = 0; i < num; i++)
+            points[i] = [];
 
-};
+        // first determine where beta sheet arrows and alpha helix tubes belong
+        var inSheet = false;
+        var inHelix = false;
+        i = 0;
+        for (i in atomList)
+        {
+            next = atomList[i];
+            if (next.elem === 'C' && next.atom === 'CA')
+            {
+                var connected = inConnectedResidues(curr, next);
 
-/**
- * rainbow gradient, but without purple to match jmol
- * @constructor
- * @implements {$3Dmol.Gradient}
- */
-$3Dmol.Gradient.ROYGB = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
-    
-        if(typeof(val) == "undefined")
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var mid = (lo+hi)/2;
-        var q1 = (lo+mid)/2;
-        var q3 = (mid+hi)/2;
-        
-        var scale, color;
-        
-        if(val < q1) { //scale green up, red up, blue down
-            scale = Math.floor(255*Math.sqrt((val-lo)/(q1-lo)));
-            color = 0xff0000 + 0x100*scale + 0;
-            return color;
-        }
-        else if(val < mid) { //scale red down, green up, blue down
-            scale = Math.floor(255*Math.sqrt((1-(val-q1)/(mid-q1))));
-            color =  0x010000*scale+0xff00+0x0;
-            return color;
-        }
-        else if(val < q3) { //scale blue up, red down, green up
-            scale = Math.floor(255*Math.sqrt((val-mid)/(q3-mid)));
-            color = 0x000000 + 0xff00 + 0x1*scale;
-            return color;
-        }
-        else { //scale green down, blue up, red down
-            scale = Math.floor(255*Math.sqrt((1-(val-q3)/(hi-q3))));
-            color =  0x000000+0x0100*scale+0xff;
-            return color;
-        }        
-    };
-    
-    this.jmolID = function() {
-        return "roygb";
-    };
+                // last two residues in a beta sheet become arrowhead
+                if (connected && next.ss === "s")
+                {
+                    inSheet = true;
+                }
+                else if (inSheet)
+                {   
+                    if (curr && prev && curr.style.cartoon.arrows && prev.style.cartoon.arrows)
+                    {
+                        curr.ss = "arrow end";
+                        prev.ss = "arrow start";
+                    }
+                    inSheet = false; 
+                }
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
+                // first and last residues in a helix are used to draw tube
+                if (connected && curr.ss === "h")
+                {
+                    if (!inHelix && next.style.cartoon.tubes) next.ss = "tube start";
+                    inHelix = true;
+                }
+                else if (inHelix && curr.ss !== "tube start")
+                {
+                    if (prev && prev.style.cartoon.tubes) prev.ss = "tube end";
+                    inHelix = false;
+                }
+                prev = curr;
+                curr = next;
+            }
         }
-        return null;
-    };
 
-};
+        // then accumulate points
+        curr = undefined;
+        for (i in atomList)
+        {
+            next = atomList[i];
+            
+            if (next === undefined || $.inArray(next.atom, cartoonAtoms) === -1)
+                continue; // skip array holes, heteroatoms, and atoms not involved in cartoon drawing
 
-/**
- * rainbow gradient with constant saturation, all the way to purple!
- * @constructor
- * @implements {$3Dmol.Gradient}
- */
-$3Dmol.Gradient.Sinebow = function(min, max) {
-    
-    //map value to hex color, range is provided
-    this.valueToHex = function(val, range) {
-        var lo, hi;
-        if(range) {
-            lo = range[0];
-            hi = range[1];
-        }
-        else {
-            lo = min;
-            hi = max;
-        }
-    
-        if(typeof(val) == "undefined")
-            return 0xffffff;
-        
-        if(val < lo) val = lo;
-        if(val > hi) val = hi;
-        
-        var scale = (val-lo)/(hi-lo);
-        var h = (5*scale/6.0+0.5);
-        var r = Math.sin(Math.PI*h);
-        r *= r*255;
-        var g = Math.sin(Math.PI*(h+1/3.0));
-        g *= g*255;
-        var b = Math.sin(Math.PI*(h+2/3.0));
-        b *= b*255;
-        
-        return 0x10000*Math.floor(r)+0x100*Math.floor(b)+0x1*Math.floor(g);
-    };
-    
-    this.jmolID = function() {
-        return "sinebow";
-    };
+            var inNucleicAcid = ($.inArray(next.resn.trim(), naResns) != -1)
 
-    //return range used for color mapping, null if none set
-    this.range = function() {
-        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
-            return [min,max];
-        }
-        return null;
-    };
+            // determine cartoon style
+            cartoon = next.style.cartoon;
+            if (cartoon.style === "trace") // draw cylinders connecting consecutive 'backbone' atoms
+            {
+                /* "trace" style just draws cylinders between consecutive 'backbone' atoms,
+                    such as alpha carbon for polypeptides and phosphorus for DNA. */
 
-};
-//Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
+                if (!traceGeo) traceGeo = new $3Dmol.Geometry(true);
 
-$3Dmol.LabelCount = 0;
+                if (next.elem === 'C' && next.atom === 'CA' || inNucleicAcid && next.atom === "P")
+                {
+                    // determine cylinder color
+                    if (gradientScheme && cartoon.color === 'spectrum')
+                        nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
+                    else
+                        nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                    colors.push(nextColor);
 
-/**
- * Renderable labels
- * @constructor $3Dmol.Label
- * @param {string} tag - Label text
- * @param {LabelSpec} parameters Label style and font specifications
- */
-$3Dmol.Label = function(text, parameters) {
+                    // determine cylinder thickness
+                    if ($.isNumeric(cartoon.thickness))
+                        thickness = cartoon.thickness;
+                    else
+                        thickness = defaultThickness;
 
-    this.id = $3Dmol.LabelCount++;
-    this.stylespec = parameters || {};
+                    if (inConnectedResidues(curr, next))
+                    {
+                        // if both atoms are same color, draw single cylinder
+                        if (nextColor == currColor)
+                        {
+                            var color = $3Dmol.CC.color(nextColor);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, next, thickness, color, 2, 2);
+                        }
 
-    this.canvas = document.createElement('canvas');
-    //todo: implement resizing canvas..
-    this.canvas.width = 134;
-    this.canvas.height = 35;
-    this.context = this.canvas.getContext('2d');
-    this.sprite = new $3Dmol.Sprite();
-    this.text = text;
+                        else // otherwise draw cylinders for each color (split down the middle)
+                        {
+                            var midpoint = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
+                            var color1 = $3Dmol.CC.color(currColor);
+                            var color2 = $3Dmol.CC.color(nextColor);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, curr, midpoint, thickness, color1, 2, 0);
+                            $3Dmol.GLDraw.drawCylinder(traceGeo, midpoint, next, thickness, color2, 0, 2);
+                        } // note that an atom object can be duck-typed as a $3Dmol.Vector3 in this case
+                    }
 
-};
+                    if (curr && traceGeo && (curr.style.cartoon && curr.style.cartoon.style != "trace"
+                        || curr.chain != next.chain))
+                    {
+                        var traceMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+                        traceMaterial.vertexColors = $3Dmol.FaceColors;
+                        if ( typeof(traceGeo.opacity) === "number" && traceGeo.opacity >= 0 && traceGeo.opacity < 1) {
+                            traceMaterial.transparent = true;
+                            traceMaterial.opacity = traceGeo.opacity;
+                            delete traceGeo.opacity;
+                        }
+                        var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
+                        group.add(traceMesh);
+                        traceGeo = null;
+                    } else if (curr) // make sure whole chain is same opacity
+                    {
+                        if (traceGeo.opacity && curr.style.cartoon.opacity)
+                        {
+                            if (traceGeo.opacity != curr.style.cartoon.opacity)
+                            {
+                                console.log("Warning: a trace-style chain's opacity is ambiguous");
+                                traceGeo.opacity = 1;
+                            }
+                        }
+                        else traceGeo.opacity = parseFloat(curr.style.cartoon.opacity) || 1;
+                    }
 
-$3Dmol.Label.prototype = {
+                    curr = next;
+                    currColor = nextColor;
+                }
+            }
 
-    constructor : $3Dmol.Label,
+            else // draw default-style cartoons based on secondary structure
+            {
+                if (!geo) geo = new $3Dmol.Geometry(true);
 
-    getStyle : function () { return this.stylespec; }, 
-    
-    setContext : function() {
-        // function for drawing rounded rectangles - for Label drawing
-        var roundRect = function(ctx, x, y, w, h, r, drawBorder) {
+                // draw backbone through these atoms
+                if (isAlphaCarbon(next) ||
+                    inNucleicAcid && (next.atom === "P" || next.atom.indexOf('O5') == 0))
+                {
+                    if (drawingTube)
+                    {
+                        if (next.ss === "tube end")
+                        {
+                            drawingTube = false;
+                            tubeEnd = new $3Dmol.Vector3(next.x, next.y, next.z);
+                            $3Dmol.GLDraw.drawCylinder(geo, tubeStart, tubeEnd, 2, $3Dmol.CC.color(currColor), 1, 1);
+                            next.ss = "h";
 
-            ctx.beginPath();
-            ctx.moveTo(x + r, y);
-            ctx.lineTo(x + w - r, y);
-            ctx.quadraticCurveTo(x + w, y, x + w, y + r);
-            ctx.lineTo(x + w, y + h - r);
-            ctx.quadraticCurveTo(x + w, y + h, x + w - r, y + h);
-            ctx.lineTo(x + r, y + h);
-            ctx.quadraticCurveTo(x, y + h, x, y + h - r);
-            ctx.lineTo(x, y + r);
-            ctx.quadraticCurveTo(x, y, x + r, y);
-            ctx.closePath();
-            ctx.fill();
-            if(drawBorder)
-                ctx.stroke();
+                        }
+                        else continue; // don't accumulate strand points while in the middle of drawing a tube
+                    }
 
-        };
+                    // end of a chain of connected residues (of same style)
+                    if (curr && (!inConnectedResidues(curr, next) || curr.style.cartoon.style !== next.style.cartoon.style ||
+                        curr.ss === "tube start"))
+                    { 
+                        if (curr.ss === "tube start")
+                        {
+                            drawingTube = true;
+                            tubeStart = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+                            curr.ss = "h";
+                        }
+
+                        if (baseEndPt) // draw the last base if it's a NA chain
+                        {
+                            if (terminalPt)
+                                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
+                            else
+                                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+
+                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+                            arrow = addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr, atomList, i);
+                            colors.push(nextColor);
+                            if (arrow) colors.push(nextColor);
+                            
+                            baseStartPt = null;
+                            baseEndPt = null;
+                        }
+
+                        // draw accumulated strand points
+                        for (i = 0; !thickness && i < num; i++)
+                            drawSmoothCurve(group, points[i], 1, colors, div, points.opacity);
+                        if (fill && points[0].length > 0) 
+                            drawStrip(group, points, colors, div, thickness, points.opacity, points.style);
+                        
+                        if (geo != null && geo.vertices > 0)
+                        {
+                            var cartoonMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+                            cartoonMaterial.vertexColors = $3Dmol.FaceColors;
+                            if (typeof(points.opacity) === "number" && points.opacity >= 0 && points.opacity < 1) {
+                                cartoonMaterial.transparent = true;
+                                cartoonMaterial.opacity = points.opacity;
+                            }
+                            var cartoonMesh = new $3Dmol.Mesh(geo, cartoonMaterial);
+                            group.add(cartoonMesh);
+                            geo = null;
+                        }
+
+                        // clear arrays for points and colors
+                        points = [];
+                        for (i = 0; i < num; i++)
+                            points[i] = [];
+                        colors = [];
+                    }
+
+                    // reached next residue (potentially the first residue)
+                    if (curr === undefined || curr.rescode != next.rescode || curr.resi != next.resi)
+                    {
+                        if (baseEndPt) // draw last NA residue's base
+                        {
+                            // start the cylinder at the midpoint between consecutive backbone atoms
+                            baseStartPt = new $3Dmol.Vector3().addVectors(curr, next).multiplyScalar(0.5);
+                            var startFix = baseStartPt.clone().sub(baseEndPt).multiplyScalar(0.02); //TODO: apply this as function of thickness
+                            baseStartPt.add(startFix);
+
+                            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+                            baseStartPt = null;
+                            baseEndPt = null;   
+                        }
+
+                        // determine color and thickness of the next strand segment
+                        if (gradientScheme && cartoon.color === 'spectrum')
+                            nextColor = gradientScheme.valueToHex(next.resi, gradientScheme.range());
+                        else
+                            nextColor = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                        colors.push(nextColor);
+                        if ($.isNumeric(cartoon.thickness))
+                            thickness = cartoon.thickness;
+                        else
+                            thickness = defaultThickness;
+
+                        
+                        curr = next; // advance backbone
+                        //nextResAtom = atomList[parseInt(i) + resSize[curr.resn]];
+                        backbonePt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+                        backbonePt.resi = curr.resi;
+                        currColor = nextColor;
+                    }
+
+                    // click handling
+                    if (next.clickable === true &&
+                        (next.intersectionShape === undefined || next.intersectionShape.triangle === undefined)) 
+                        next.intersectionShape = {sphere : null, cylinder : [], line : [], triangle : []};
+                }
+
+                // atoms used to orient the backbone strand
+                else if (isAlphaCarbon(curr) && next.atom === "O"
+                      || inNucleicAcid && curr.atom === "P" && (next.atom === "OP2" || next.atom === "O2P")
+                      || inNucleicAcid && curr.atom.indexOf("O5") == 0 && next.atom.indexOf("C5") == 0)
+                {
+                    orientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                    orientPt.resi = next.resi;
+                    if (next.atom === "OP2" || next.atom === "O2P") // for NA 3' terminus
+                        termOrientPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                }
+
+                // NA 3' terminus is an edge case, need a vector for most recent O3'
+                else if (inNucleicAcid && next.atom.indexOf("O3") == 0)
+                {
+                    terminalPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                }
+
+                // atoms used for drawing the NA base cylinders (diff for purines and pyramidines)
+                else if ((next.atom === "N1" && $.inArray(next.resn.trim(), purResns) != -1) ||
+                         (next.atom === "N3" && $.inArray(next.resn.trim(), pyrResns) != -1))
+                {
+                    baseEndPt = new $3Dmol.Vector3(next.x, next.y, next.z);
+                    baseEndPt.color = $3Dmol.getColorFromStyle(next, cartoon).getHex();
+                }
+
+                // when we have a backbone point and orientation point in the same residue, accumulate strand points
+                if (orientPt && backbonePt && orientPt.resi === backbonePt.resi)
+                {
+                    arrow = addBackbonePoints(points, num, !doNotSmoothen, backbonePt, orientPt, prevOrientPt, curr, atomList, i);
+                    prevOrientPt = orientPt;
+                    backbonePt = null;
+                    orientPt = null;
+                    colors.push(nextColor);
+                    if (arrow) colors.push(nextColor);
+                }
+            }
+        }
+
+        if (baseEndPt) // draw last NA base if needed
+        {
+            if (terminalPt)
+                baseStartPt = new $3Dmol.Vector3().addVectors(curr, terminalPt).multiplyScalar(0.5);
+            else
+                baseStartPt = new $3Dmol.Vector3(curr.x, curr.y, curr.z);
+
+            $3Dmol.GLDraw.drawCylinder(geo, baseStartPt, baseEndPt, 0.4, $3Dmol.CC.color(baseEndPt.color), 0, 2);
+            arrow = addBackbonePoints(points, num, !doNotSmoothen, terminalPt, termOrientPt, prevOrientPt, curr, atomList, i);
+            colors.push(nextColor);
+            if (arrow) colors.push(nextColor);
+        }
+
+        // for default style, draw the last strand
+        for (i = 0; !thickness && i < num; i++)
+            drawSmoothCurve(group, points[i], 1, colors, div, points.opacity);
+        if (fill && points[0].length > 0)
+        {
+            drawStrip(group, points, colors, div, thickness, points.opacity, points.style);
+        }
+        if (geo != null && geo.vertices > 0)
+        {
+            var cartoonMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+            cartoonMaterial.vertexColors = $3Dmol.FaceColors;
+            if (typeof(points.opacity) === "number" && points.opacity >= 0 && points.opacity < 1) {
+                cartoonMaterial.transparent = true;
+                cartoonMaterial.opacity = points.opacity;
+            }
+            var cartoonMesh = new $3Dmol.Mesh(geo, cartoonMaterial);
+            group.add(cartoonMesh);
+            geo = null;
+        }
+
+        if (traceGeo != null && traceGeo.vertices > 0) // generate last mesh for trace geometry
+        {
+            var traceMaterial = new $3Dmol.MeshDoubleLambertMaterial();
+            traceMaterial.vertexColors = $3Dmol.FaceColors;
+            if (typeof(traceGeo.opacity) === "number" && traceGeo.opacity >= 0 && traceGeo.opacity < 1) {
+                traceMaterial.transparent = true;
+                traceMaterial.opacity = traceGeo.opacity;
+                delete traceGeo.opacity;
+            }
+            var traceMesh = new $3Dmol.Mesh(traceGeo, traceMaterial);
+            group.add(traceMesh);
+        }
+    };
+
+    var addBackbonePoints = function(points, num, smoothen, backbonePt, orientPt, prevOrientPt, backboneAtom, atomList, atomi)
+    {
+        var widthScalar, i, delta, v, addArrowPoints, testOpacity, testStyle;
         
-        //do all the checks to figure out what color is desired
-        var getColor = function(style, stylealpha, init) {
-            var ret = init;
-            if(typeof(style) != 'undefined') {
-                //convet regular colors
-                 if(style instanceof $3Dmol.Color) 
-                     ret = style.scaled();
-                 else //hex or name
-                    ret = $3Dmol.CC.color(style).scaled();                    
+        // dictionary of standard amino acid sizes, in number of atoms
+        var resSize = {ALA: 5, ARG: 11, ASN:8, ASP:8, CYS:6, GLN:9, GLU: 9, GLY:4, HIS:10,
+            ILE:8, LEU: 8, LYS: 9, MET:8, PHE:11, PRO:7, SER:6, THR:7, TRP:14, TYR:12, VAL:7}
+        
+        if(!backbonePt || !orientPt || !backboneAtom)
+            return;
+        
+        // the side vector points along the axis from backbone atom to orientation atom (eg. CA to O, in peptides)
+        var sideVec = orientPt.sub(backbonePt);
+        sideVec.normalize();
+
+        // the forward vector points along the axis from backbone atom to next backbone atom
+        var forwardVec = atomList[parseInt(atomi) + resSize[backboneAtom.resn]];
+        forwardVec = forwardVec ? new $3Dmol.Vector3(forwardVec.x, forwardVec.y, forwardVec.z) : new $3Dmol.Vector3(0, 0, 0);
+        forwardVec.sub(backbonePt);
+
+        // adjustments for proper beta arrow appearance
+        if (backboneAtom.ss === "arrow start")
+        {
+            var adjustment = forwardVec.clone().multiplyScalar(0.3).cross(orientPt); // adjust perpendicularly to strand face
+            backbonePt.add(adjustment);
+
+            var upVec = forwardVec.clone().cross(sideVec).normalize();
+            sideVec.rotateAboutVector(upVec, 0.43);
+        }
+
+        // determine from cartoon style or secondary structure how wide the strand should be here
+        // ribbon shape should have same width as thickness
+        if (backboneAtom.style.cartoon.ribbon)
+        {
+            widthScalar = backboneAtom.style.cartoon.thickness || defaultThickness;
+
+        } else // depending on secondary structure, multiply the orientation vector by some scalar
+        {
+            if (!backboneAtom.style.cartoon.width)
+            {
+                if (backboneAtom.ss === "c")
+                {
+                    if (backboneAtom.atom === "P")
+                        widthScalar = nucleicAcidWidth;
+                    else
+                        widthScalar = coilWidth;
+                } else if (backboneAtom.ss === "arrow start")
+                {
+                    widthScalar = helixSheetWidth;
+                    addArrowPoints = true;
+
+                } else if (backboneAtom.ss === "arrow end")
+                    widthScalar = coilWidth;
+                
+                else if (backboneAtom.ss === "h" && backboneAtom.style.cartoon.tubes || backboneAtom.ss === "tube start")
+                    widthScalar = coilWidth;
+
+                else
+                    widthScalar = helixSheetWidth;
             }
-            if(typeof(stylealpha) != 'undefined') {
-                ret.a = parseFloat(stylealpha);
+            else widthScalar = backboneAtom.style.cartoon.width;  
+        }
+
+        // make sure the strand orientation doesn't twist more than 90 degrees
+        if (prevOrientPt != null && sideVec.dot(prevOrientPt) < 0)
+            sideVec.negate();
+
+
+        sideVec.multiplyScalar(widthScalar);
+        for (i = 0; i < num; i++)
+        {
+            // produces NUM incremental points from backbone atom minus orientation vector
+            //  to backbone atom plus orientation vector
+            delta = -1 + i * 2/(num - 1); // -1 to 1 incrementing by num
+            v = new $3Dmol.Vector3(backbonePt.x + delta * sideVec.x,
+                                   backbonePt.y + delta * sideVec.y,
+                                   backbonePt.z + delta * sideVec.z);
+            v.atom = backboneAtom;
+            if (smoothen && backboneAtom.ss === "s") 
+                v.smoothen = true;
+            points[i].push(v); // a num-length array of arrays, where each inner array contains length-wise points
+                               // along the backbone offset by some constant pertaining to its cell in the outer array
+        }
+
+        if (addArrowPoints)
+        {
+
+            sideVec.multiplyScalar(2);
+            for (i = 0; i < num; i++)
+            {
+                delta = -1 + i * 2/(num - 1); // -1 to 1 incrementing by num
+                v = new $3Dmol.Vector3(backbonePt.x + delta * sideVec.x,
+                                       backbonePt.y + delta * sideVec.y,
+                                       backbonePt.z + delta * sideVec.z);
+                v.atom = backboneAtom;
+                v.smoothen = false;
+                v.skip = true;
+                points[i].push(v);
             }
-            return ret;
         }
 
-        /**
-         * Label type specification
-         * @typedef LabelSpec
-         * @struct
-         * @prop {string} font - font name, default sans-serif
-         * @prop {number} fontSize - height of text, default 18
-         * @prop {string} fontColor - font color, default white
-         * @prop {number} fontOpacity - font opacity, default 1
-         * @prop {number} borderThickness - line width of border around label, default 0
-         * @prop {string} borderColor - color of border, default backgroundColor
-         * @prop {string} borderOpacity - color of border
-         * @prop {string} backgroundColor - color of background, default black
-         * @prop {string} backgroundOpacity - opacity of background, default 1
-         * @prop {Object} position - x,y,z coordinates for label
-         * @prop {boolean} inFront - always put labels in from of model
-         * @prop {boolean} showBackground - show background rounded rectangle, default true
-         */
-        return function() {
-            
-            var style = this.stylespec;
-            var useScreen =  typeof(style.useScreen) == "undefined" ? false : style.useScreen;
+        // make sure the strand is all the same opacity and style
+        testOpacity = parseFloat(backboneAtom.style.cartoon.opacity) || 1;
+        if (points.opacity)
+        {
+            if (points.opacity != testOpacity)
+            {
+                console.log("Warning: a cartoon-style chain's opacity is ambiguous");
+                points.opacity = 1;
+            }
+
+        } else points.opacity = testOpacity;
+
+        testStyle = backboneAtom.style.cartoon.style || 'default';
+        if (points.style)
+        {
+            if (points.style != testStyle)
+            {
+                console.log("Warning: a cartoon chain's strand-style is ambiguous");
+                points.style = 'default';
+            }
+
+        } else points.style = testStyle;
+
+        // revert ss keywords used for arrow rendering back to original value
+        if (backboneAtom.ss === "arrow start" || backboneAtom.ss === "arrow end")
+            backboneAtom.ss = "s";
+
+        return addArrowPoints;
+    };
+
+    var defaultDrawCartoon = function(group, atomList, gradientScheme, quality)
+    {
+        quality = parseInt(parseFloat(quality)*5) || 5;
+        drawCartoon(group, atomList, gradientScheme, fill=true, doNotSmoothen=false, num=quality, div=quality);
+    }
+
+    return defaultDrawCartoon;
+})();
+//
+
+var $3Dmol = $3Dmol || {};
+
+/**
+ * Lower level utilities for creating WebGL shape geometries.
+ * These are not intended for general consumption.
+ * @namespace $3Dmol.GLDraw
+  */
+$3Dmol.GLDraw = (function() {
+
+    var draw = {}; // object for exporting functions
+
+    // Rotation matrix around z and x axis -
+    // according to y basis vector
+    // TODO: Try to optimize this (square roots?)
+    var getRotationMatrix = function() {
+
+        var d = new $3Dmol.Vector3();
+        // var rot = new Float32Array(9);
+
+        return function(dir) {
+
+            d.set(dir[0], dir[1], dir[2]);
+
+            var dx = d.x, dy = d.y, dz = d.z;
+
+            var dxy = Math.sqrt(dx * dx + dy * dy);
+            var dxz, dyz;
+
+            var sinA, cosA, sinB, cosB, sinC, cosC;
+
+            // about z axis - Phi
+            if (dxy < 0.0001) {
+                sinA = 0;
+                cosA = 1;
+            }
+
+            else {
+                sinA = -dx / dxy;
+                cosA = dy / dxy;
+            }
+
+            // recast dy in terms of new axes - z is the same
+
+            dy = -sinA * dx + cosA * dy;
+            dyz = Math.sqrt(dy * dy + dz * dz);
+
+            // about new x axis - Theta
+
+            if (dyz < 0.0001) {
+                sinB = 0;
+                cosB = 1;
+            }
+
+            else {
+                sinB = dz / dyz;
+                cosB = dy / dyz;
+            }
+
+            var rot = new Float32Array(9);
+            rot[0] = cosA;
+            rot[1] = sinA;
+            rot[2] = 0;
+            rot[3] = -sinA * cosB;
+            rot[4] = cosA * cosB;
+            rot[5] = sinB;
+            rot[6] = sinA * sinB;
+            rot[7] = -cosA * sinB;
+            rot[8] = cosB;
+
+            return rot;
+
+        };
+
+    }();
+    
+    // Ortho normal vectors for cylinder radius/ sphere cap equator and cones
+    // Direction is j basis (0,1,0)
+    var basisVectors = function() {
+
+        var ret = {
+            vertices : [],
+            norms : []
+        };
+
+        var nvecs = [];
+
+        var subdivisions = 4; // including the initial 2, eg. 4 => 16 subintervals
+        var N = Math.pow(2, subdivisions);  // eg. 2**4 = 16 subintervals in total
+        var i = 2;  // start with 2 subdivisions already done
+        var M = Math.pow(2, i); // 4
+        var spacing = N/M;  // 16/4 = 4; if there were 5 subdivs, then 32/4 = 8.
+        var j;
+
+        nvecs[0] = new $3Dmol.Vector3(-1, 0, 0);
+        nvecs[spacing] = new $3Dmol.Vector3(0, 0, 1);
+        nvecs[spacing*2] = new $3Dmol.Vector3(1, 0, 0);
+        nvecs[spacing*3] = new $3Dmol.Vector3(0, 0, -1);
+
+        for ( i = 3; i <= subdivisions; i ++ ) {
+            // eg. i=3, we need to add 2**(3-1) = 4 new vecs. Call it M.
+            // their spacing is N/M, eg. N=16, M=4, N/M=4; M=8, N/M=2.
+            // they start off at half this spacing
+            // and are equal to the average of the two vectors on either side
+            M = Math.pow(2, (i-1));
+            spacing = N/M;
+            for ( j = 0; j < (M-1); j ++ ) {
+                nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[(j+1)*spacing]).normalize();
+            }
+            // treat the last one specially so it wraps around to zero
+            j = M - 1;
+            nvecs[spacing/2 + j*spacing] = nvecs[j*spacing].clone().add(nvecs[0]).normalize();
+        }
+
+        /*
+         * nvecs[0] = new $3Dmol.Vector3(-1,0,0); nvecs[1] = new
+         * $3Dmol.Vector3(0,0,1); nvecs[2] = new $3Dmol.Vector3(1,0,0);
+         * nvecs[3] = new $3Dmol.Vector3(0,0,-1);
+         */
+        return nvecs;
+
+    }();
+
+    // memoize capped cylinder for given radius
+    var cylVertexCache = {
+
+        // memoize both rounded and flat caps (hemisphere and circle)
+        cache : {false:{}, true:{}},
+
+        getVerticesForRadius : function(radius, flat) {
+
+            if (this.cache[flat][radius] !== undefined)
+                return this.cache[flat][radius];
+
+            var dir = new $3Dmol.Vector3(0, 1, 0);
+            var w = basisVectors.length;
+            var nvecs = [], norms = [];
+            var n;
+
+            for (var i = 0; i < w; i++) {
+                // bottom
+                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
+                // top
+                nvecs.push(basisVectors[i].clone().multiplyScalar(radius));
+
+                // NOTE: this normal is used for constructing sphere caps -
+                // cylinder normals taken care of in drawCylinder
+                n = basisVectors[i].clone().normalize();
+                norms.push(n);
+                norms.push(n);
+            }
+
+            // norms[0]
+
+            var verticesRows = [];
+
+            // Require that heightSegments is even and >= 2
+            // Equator points at h/2 (theta = pi/2)
+            // (repeated) polar points at 0 and h (theta = 0 and pi)
+            var heightSegments = 10, widthSegments = w; // 16 or however many
+                                                        // basis vectors for
+                                                        // cylinder
+
+            if (heightSegments % 2 !== 0 || !heightSegments) {
+                console.error("heightSegments must be even");
+
+                return null;
+            }
+
+            var phiStart = 0;
+            var phiLength = Math.PI * 2;
+
+            var thetaStart = 0;
+            var thetaLength = Math.PI;
+
+            var x, y;
+            var polar = false, equator = false;
+
+            for (y = 0; y <= heightSegments; y++) {
+
+                polar = (y === 0 || y === heightSegments) ? true : false;
+                equator = (y === heightSegments / 2) ? true : false;
+
+                var verticesRow = [], toRow = [];
+
+                for (x = 0; x <= widthSegments; x++) {
+
+                    // Two vertices rows for equator pointing to previously
+                    // constructed cyl points
+                    if (equator) {
+                        var xi = (x < widthSegments) ? 2 * x : 0;
+                        toRow.push(xi + 1);
+                        verticesRow.push(xi);
+
+                        continue;
+                    }
+
+                    var u = x / widthSegments;
+                    var v = y / heightSegments;
+
+                    // Only push first polar point
+
+                    if (!polar || x === 0) {
+
+                        if (x < widthSegments) {
+                            var vertex = new $3Dmol.Vector3();
+                            vertex.x = -radius
+                                    * Math.cos(phiStart + u * phiLength)
+                                    * Math.sin(thetaStart + v * thetaLength);
+                            vertex.y = flat ? 0 : radius * Math.cos(thetaStart + v * thetaLength);
+                            vertex.z = radius
+                                    * Math.sin(phiStart + u * phiLength)
+                                    * Math.sin(thetaStart + v * thetaLength);
+
+                            if (Math.abs(vertex.x) < 1e-5)
+                                vertex.x = 0;
+                            if (Math.abs(vertex.y) < 1e-5)
+                                vertex.y = 0;
+                            if (Math.abs(vertex.z) < 1e-5)
+                                vertex.z = 0;
+
+                            if (flat) {
+                                n = new $3Dmol.Vector3(0, Math.cos(thetaStart + v * thetaLength), 0);
+                                n.normalize();
+                            }
+                            else {
+                                n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
+                                n.normalize();
+                            }
+
+                            nvecs.push(vertex);
+                            norms.push(n);
+
+                            verticesRow.push(nvecs.length - 1);
+                        }
+
+                        // last point is just the first point for this row
+                        else {
+                            verticesRow.push(nvecs.length - widthSegments);
+                        }
+
+                    }
+
+                    // x > 0; index to already added point
+                    else if (polar)
+                        verticesRow.push(nvecs.length - 1);
+
+                }
+
+                // extra equator row
+                if (equator)
+                    verticesRows.push(toRow);
+
+                verticesRows.push(verticesRow);
+
+            }
+
+            var obj = {
+                vertices : nvecs,
+                normals : norms,
+                verticesRows : verticesRows,
+                w : widthSegments,
+                h : heightSegments
+            };
+
+            this.cache[flat][radius] = obj;
+
+            return obj;
+
+        }
+    };
+
+    // creates a cylinder
+    var drawnC = 0;
+    
+    /** Create a cylinder 
+     * @function $3Dmol.GLDraw.drawCylinder
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            from
+     * @param {Point}
+     *            to
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     * @param {integer} fromCap - 0 for none, 1 for flat, 2 for round; Note: currently do not support different styles of caps on the same cylinder.
+     * @param {integer} toCap = 0 for none, 1 for flat, 2 for round
+     *            
+     * */
+    draw.drawCylinder = function(geo, from, to, radius, color, fromCap, toCap) {
+        if (!from || !to)
+            return;
+        drawnC++;
+        // vertices
+        var drawcaps = fromCap || toCap;
+
+        var flat = false;
+        if (fromCap == 1 && toCap == 1) // 0 is none, 1 is flat, 2 is round
+          	flat = true;
+
+        color = color || {r:0, g:0, b:0};
+
+        /** @type {Array.<number>} */
+        var dir = [ to.x, to.y, to.z ];
+        dir[0] -= from.x;
+        dir[1] -= from.y;
+        dir[2] -= from.z;
+
+        var e = getRotationMatrix(dir);
+        // get orthonormal vectors from cache
+        // TODO: Will have orient with model view matrix according to direction
+        var vobj = cylVertexCache.getVerticesForRadius(radius, flat);
+
+        // w (n) corresponds to the number of orthonormal vectors for cylinder
+        // (default 16)
+        var n = vobj.w, h = vobj.h;
+        var w = n;
+        // get orthonormal vector
+        var n_verts = (drawcaps) ? h * n + 2 : 2 * n;
+
+        var geoGroup = geo.updateGeoGroup(n_verts);
+
+        var vertices = vobj.vertices, normals = vobj.normals, verticesRows = vobj.verticesRows;
+        var toRow = verticesRows[h / 2], fromRow = verticesRows[h / 2 + 1];
+
+        var start = geoGroup.vertices;
+        var offset, faceoffset;
+        var i, x, y, z;
+
+        var vertexArray = geoGroup.vertexArray;
+        var normalArray = geoGroup.normalArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        // add vertices, opposing vertices paired together
+        for (i = 0; i < n; ++i) {
+
+            var vi = 2 * i;
+
+            x = e[0] * vertices[vi].x + e[3] * vertices[vi].y + e[6]
+                    * vertices[vi].z;
+            y = e[1] * vertices[vi].x + e[4] * vertices[vi].y + e[7]
+                    * vertices[vi].z;
+            z = e[5] * vertices[vi].y + e[8] * vertices[vi].z;
+
+            // var xn = x/radius, yn = y/radius, zn = z/radius;
+
+            offset = 3 * (start + vi);
+            faceoffset = geoGroup.faceidx;
+
+            // from
+            vertexArray[offset] = x + from.x;
+            vertexArray[offset + 1] = y + from.y;
+            vertexArray[offset + 2] = z + from.z;
+            // to
+            vertexArray[offset + 3] = x + to.x;
+            vertexArray[offset + 4] = y + to.y;
+            vertexArray[offset + 5] = z + to.z;
+
+            // normals
+            normalArray[offset] = x;
+            normalArray[offset + 3] = x;
+            normalArray[offset + 1] = y;
+            normalArray[offset + 4] = y;
+            normalArray[offset + 2] = z;
+            normalArray[offset + 5] = z;
+
+            // colors
+            colorArray[offset] = color.r;
+            colorArray[offset + 3] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 4] = color.g;
+            colorArray[offset + 2] = color.b;
+            colorArray[offset + 5] = color.b;
+
+            // faces
+            // 0 - 2 - 1
+            faceArray[faceoffset] = fromRow[i] + start;
+            faceArray[faceoffset + 1] = fromRow[i + 1] + start;
+            faceArray[faceoffset + 2] = toRow[i] + start;
+            // 1 - 2 - 3
+            faceArray[faceoffset + 3] = toRow[i] + start;
+            faceArray[faceoffset + 4] = fromRow[i + 1] + start;
+            faceArray[faceoffset + 5] = toRow[i + 1] + start;
+
+            geoGroup.faceidx += 6;
+
+        }
+
+        // SPHERE CAPS
+
+        if (drawcaps) {
+
+            // h - sphere rows, verticesRows.length - 2
+            var ystart = (toCap) ? 0 : h / 2;
+            var yend = (fromCap) ? h + 1 : h / 2 + 1;
+
+            var v1, v2, v3, v4, x1, x2, x3, x4, y1, y2, y3, y4, z1, z2, z3, z4, nx1, nx2, nx3, nx4, ny1, ny2, ny3, ny4, nz1, nz2, nz3, nz4, v1offset, v2offset, v3offset, v4offset;
+
+            for (y = ystart; y < yend; y++) {
+                if (y === h / 2)
+                    continue;
+                // n number of points for each level (verticesRows[i].length -
+                // 1)
+                var cap = (y <= h / 2) ? to : from;
+
+                for (x = 0; x < n; x++) {
+
+                    faceoffset = geoGroup.faceidx;
+
+                    v1 = verticesRows[y][x + 1];
+                    v1offset = (v1 + start) * 3;
+                    v2 = verticesRows[y][x];
+                    v2offset = (v2 + start) * 3;
+                    v3 = verticesRows[y + 1][x];
+                    v3offset = (v3 + start) * 3;
+                    v4 = verticesRows[y + 1][x + 1];
+                    v4offset = (v4 + start) * 3;
+
+                    // rotate sphere vectors
+                    x1 = e[0] * vertices[v1].x + e[3] * vertices[v1].y + e[6]
+                            * vertices[v1].z;
+                    x2 = e[0] * vertices[v2].x + e[3] * vertices[v2].y + e[6]
+                            * vertices[v2].z;
+                    x3 = e[0] * vertices[v3].x + e[3] * vertices[v3].y + e[6]
+                            * vertices[v3].z;
+                    x4 = e[0] * vertices[v4].x + e[3] * vertices[v4].y + e[6]
+                            * vertices[v4].z;
+
+                    y1 = e[1] * vertices[v1].x + e[4] * vertices[v1].y + e[7]
+                            * vertices[v1].z;
+                    y2 = e[1] * vertices[v2].x + e[4] * vertices[v2].y + e[7]
+                            * vertices[v2].z;
+                    y3 = e[1] * vertices[v3].x + e[4] * vertices[v3].y + e[7]
+                            * vertices[v3].z;
+                    y4 = e[1] * vertices[v4].x + e[4] * vertices[v4].y + e[7]
+                            * vertices[v4].z;
+
+                    z1 = e[5] * vertices[v1].y + e[8] * vertices[v1].z;
+                    z2 = e[5] * vertices[v2].y + e[8] * vertices[v2].z;
+                    z3 = e[5] * vertices[v3].y + e[8] * vertices[v3].z;
+                    z4 = e[5] * vertices[v4].y + e[8] * vertices[v4].z;
+
+                    vertexArray[v1offset] = x1 + cap.x;
+                    vertexArray[v2offset] = x2 + cap.x;
+                    vertexArray[v3offset] = x3 + cap.x;
+                    vertexArray[v4offset] = x4 + cap.x;
+
+                    vertexArray[v1offset + 1] = y1 + cap.y;
+                    vertexArray[v2offset + 1] = y2 + cap.y;
+                    vertexArray[v3offset + 1] = y3 + cap.y;
+                    vertexArray[v4offset + 1] = y4 + cap.y;
+
+                    vertexArray[v1offset + 2] = z1 + cap.z;
+                    vertexArray[v2offset + 2] = z2 + cap.z;
+                    vertexArray[v3offset + 2] = z3 + cap.z;
+                    vertexArray[v4offset + 2] = z4 + cap.z;
+
+                    colorArray[v1offset] = color.r;
+                    colorArray[v2offset] = color.r;
+                    colorArray[v3offset] = color.r;
+                    colorArray[v4offset] = color.r;
+
+                    colorArray[v1offset + 1] = color.g;
+                    colorArray[v2offset + 1] = color.g;
+                    colorArray[v3offset + 1] = color.g;
+                    colorArray[v4offset + 1] = color.g;
+
+                    colorArray[v1offset + 2] = color.b;
+                    colorArray[v2offset + 2] = color.b;
+                    colorArray[v3offset + 2] = color.b;
+                    colorArray[v4offset + 2] = color.b;
+
+                    nx1 = e[0] * normals[v1].x + e[3] * normals[v1].y + e[6]
+                            * normals[v1].z;
+                    nx2 = e[0] * normals[v2].x + e[3] * normals[v2].y + e[6]
+                            * normals[v2].z;
+                    nx3 = e[0] * normals[v3].x + e[3] * normals[v3].y + e[6]
+                            * normals[v3].z;
+                    nx4 = e[0] * normals[v4].x + e[3] * normals[v4].y + e[6]
+                            * normals[v4].z;
+
+                    ny1 = e[1] * normals[v1].x + e[4] * normals[v1].y + e[7]
+                            * normals[v1].z;
+                    ny2 = e[1] * normals[v2].x + e[4] * normals[v2].y + e[7]
+                            * normals[v2].z;
+                    ny3 = e[1] * normals[v3].x + e[4] * normals[v3].y + e[7]
+                            * normals[v3].z;
+                    ny4 = e[1] * normals[v4].x + e[4] * normals[v4].y + e[7]
+                            * normals[v4].z;
+
+                    nz1 = e[5] * normals[v1].y + e[8] * normals[v1].z;
+                    nz2 = e[5] * normals[v2].y + e[8] * normals[v2].z;
+                    nz3 = e[5] * normals[v3].y + e[8] * normals[v3].z;
+                    nz4 = e[5] * normals[v4].y + e[8] * normals[v4].z;
+
+                    // if (Math.abs(vobj.sphereVertices[v1].y) === radius) {
+                    if (y === 0) {
+                        // face = [v1, v3, v4];
+                        // norm = [n1, n3, n4];
+
+                        normalArray[v1offset] = nx1;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v3offset + 2] = nz3;
+                        normalArray[v4offset + 2] = nz4;
+
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v3 + start;
+                        faceArray[faceoffset + 2] = v4 + start;
+
+                        geoGroup.faceidx += 3;
+
+                    }
+
+                    // else if (Math.abs(vobj.sphereVertices[v3].y) === radius)
+                    // {
+                    else if (y === yend - 1) {
+                        // face = [v1, v2, v3];
+                        // norm = [n1, n2, n3];
+
+                        normalArray[v1offset] = nx1;
+                        normalArray[v2offset] = nx2;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v3offset + 2] = nz3;
+
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v2 + start;
+                        faceArray[faceoffset + 2] = v3 + start;
+
+                        geoGroup.faceidx += 3;
+
+                    }
+
+                    else {
+                        // face = [v1, v2, v3, v4];
+                        // norm = [n1, n2, n3, n4];
+
+                        normalArray[v1offset] = nx1;
+                        normalArray[v2offset] = nx2;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v1offset + 1] = ny1;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v1offset + 2] = nz1;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v4offset + 2] = nz4;
+
+                        normalArray[v2offset] = nx2;
+                        normalArray[v3offset] = nx3;
+                        normalArray[v4offset] = nx4;
+                        normalArray[v2offset + 1] = ny2;
+                        normalArray[v3offset + 1] = ny3;
+                        normalArray[v4offset + 1] = ny4;
+                        normalArray[v2offset + 2] = nz2;
+                        normalArray[v3offset + 2] = nz3;
+                        normalArray[v4offset + 2] = nz4;
+
+                        faceArray[faceoffset] = v1 + start;
+                        faceArray[faceoffset + 1] = v2 + start;
+                        faceArray[faceoffset + 2] = v4 + start;
+
+                        faceArray[faceoffset + 3] = v2 + start;
+                        faceArray[faceoffset + 4] = v3 + start;
+                        faceArray[faceoffset + 5] = v4 + start;
+
+                        geoGroup.faceidx += 6;
+                    }
+
+                }
+            }
+
+        }
+
+        geoGroup.vertices += n_verts;
+    };
+
+    /** Create a cone 
+     * @function $3Dmol.GLDraw.drawCone
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            from
+     * @param {Point}
+     *            to
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     *            */
+    draw.drawCone = function(geo, from, to, radius, color) {
+        if (!from || !to)
+            return;
+
+        color = color || {r:0, g:0, b:0};
+
+        var dir =[to.x, to.y, to.z ];        
+        dir.x -= from.x;
+        dir.y -= from.y;
+        dir.z -= from.z;
+
+        var e = getRotationMatrix(dir);
+
+
+        // n vertices around bottom plust the two points
+        var n = basisVectors.length;
+        var basis = basisVectors;
+        var n_verts =  n + 2;
+
+        
+        //setup geo structures
+        var geoGroup = geo.updateGeoGroup(n_verts);
+        var start = geoGroup.vertices;    
+        var offset, faceoffset;
+        var i, x, y, z;
+        var vertexArray = geoGroup.vertexArray;
+        var normalArray = geoGroup.normalArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        
+        var offset = start*3;
+        var ndir = new $3Dmol.Vector3(dir[0],dir[1],dir[2]).normalize();
+        //base point first vertex
+        vertexArray[offset] = from.x;
+        vertexArray[offset+1] = from.y;
+        vertexArray[offset+2] = from.z;
+        normalArray[offset] = -ndir.x;
+        normalArray[offset + 1] = -ndir.y;
+        normalArray[offset + 2] = -ndir.z;
+        colorArray[offset] = color.r;
+        colorArray[offset + 1] = color.g;
+        colorArray[offset + 2] = color.b;
+        
+        //second vertex top
+        vertexArray[offset+3] = to.x;
+        vertexArray[offset+4] = to.y;
+        vertexArray[offset+5] = to.z;
+        
+        normalArray[offset+3] = ndir.x;
+        normalArray[offset+4] = ndir.y;
+        normalArray[offset+5] = ndir.z;
+        colorArray[offset+3] = color.r;
+        colorArray[offset + 4] = color.g;
+        colorArray[offset + 5] = color.b;
+        
+        offset += 6;
+        
+        // add circle vertices
+        for (i = 0; i < n; ++i) {
+            var vec = basis[i].clone();
+            vec.multiplyScalar(radius);
+            x = e[0] * vec.x + e[3] * vec.y + e[6]
+                    * vec.z;
+            y = e[1] * vec.x + e[4] * vec.y + e[7]
+                    * vec.z;
+            z = e[5] * vec.y + e[8] * vec.z;
+
+            // from
+            vertexArray[offset] = x + from.x;
+            vertexArray[offset + 1] = y + from.y;
+            vertexArray[offset + 2] = z + from.z;
+
+            // normals
+            normalArray[offset] = x;
+            normalArray[offset + 1] = y;
+            normalArray[offset + 2] = z;
+
+            // colors
+            colorArray[offset] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 2] = color.b;
+            
+            offset += 3;
+
+        }
+        geoGroup.vertices += (n+2);
+        //faces
+        var faceoffset = geoGroup.faceidx;
+        for( i = 0; i < n; i++) {
+            //two neighboring circle vertices
+            var v1 = start+2+i;
+            var v2 = start+2+ ((i+1)%n);
+            
+            faceArray[faceoffset] = v1;
+            faceArray[faceoffset+1] = v2;
+            faceArray[faceoffset+2] = start;
+            faceoffset += 3;
+            faceArray[faceoffset] = v1;
+            faceArray[faceoffset+1] = v2;
+            faceArray[faceoffset+2] = start+1;
+            faceoffset += 3;
+        }
+        geoGroup.faceidx += 6*n;
+    };
+
+    
+    // Sphere component
+    var sphereVertexCache = {
+        cache : {},
+        getVerticesForRadius : function(radius) {
+
+            if (typeof (this.cache[radius]) !== "undefined")
+                return this.cache[radius];
+
+            var obj = {
+                vertices : [],
+                verticesRows : [],
+                normals : []
+            };
+            // scale quality with radius heuristically
+            var sphereQuality = 1;
+            var widthSegments = 16 * sphereQuality;
+            var heightSegments = 10 * sphereQuality;
+            if (radius < 1) {
+                widthSegments = 10 * sphereQuality;
+                heightSegments = 8 * sphereQuality;
+            }
+
+            var phiStart = 0;
+            var phiLength = Math.PI * 2;
+
+            var thetaStart = 0;
+            var thetaLength = Math.PI;
+
+            var x, y, vertices = [], uvs = [];
+
+            for (y = 0; y <= heightSegments; y++) {
+
+                var verticesRow = [];
+                for (x = 0; x <= widthSegments; x++) {
+
+                    var u = x / widthSegments;
+                    var v = y / heightSegments;
+
+                    var vertex = {};
+                    vertex.x = -radius * Math.cos(phiStart + u * phiLength)
+                            * Math.sin(thetaStart + v * thetaLength);
+                    vertex.y = radius * Math.cos(thetaStart + v * thetaLength);
+                    vertex.z = radius * Math.sin(phiStart + u * phiLength)
+                            * Math.sin(thetaStart + v * thetaLength);
+
+                    var n = new $3Dmol.Vector3(vertex.x, vertex.y, vertex.z);
+                    n.normalize();
+
+                    obj.vertices.push(vertex);
+                    obj.normals.push(n);
+
+                    verticesRow.push(obj.vertices.length - 1);
+
+                }
+
+                obj.verticesRows.push(verticesRow);
+
+            }
+
+            this.cache[radius] = obj;
+            return obj;
+        }
+
+    };
+
+    /** Create a sphere.
+     * @function $3Dmol.GLDraw.drawSphere
+     * @param {geometry}
+     *            geo
+     * @param {Point}
+     *            pos
+     * @param {float}
+     *            radius
+     * @param {$3Dmol.Color}
+     *            color
+     */
+    draw.drawSphere = function(geo, pos, radius, color) {
+
+        var center = new $3Dmol.Vector3(pos.x, pos.y, pos.z);
+
+        var x, y;
+        var vobj = sphereVertexCache.getVerticesForRadius(radius);
+
+        var vertices = vobj.vertices;
+        var normals = vobj.normals;
+
+        var geoGroup = geo.updateGeoGroup(vertices.length);
+
+        var start = geoGroup.vertices;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        var lineArray = geoGroup.lineArray;
+        var normalArray = geoGroup.normalArray;
+
+        for (var i = 0, il = vertices.length; i < il; ++i) {
+            var offset = 3 * (start + i);
+            var v = vertices[i];
+
+            vertexArray[offset] = (v.x + pos.x);
+            vertexArray[offset + 1] = (v.y + pos.y);
+            vertexArray[offset + 2] = (v.z + pos.z);
+
+            colorArray[offset] = color.r;
+            colorArray[offset + 1] = color.g;
+            colorArray[offset + 2] = color.b;
+
+        }
+
+        geoGroup.vertices += vertices.length;
+
+        var verticesRows = vobj.verticesRows;
+        var h = verticesRows.length - 1;
+
+        for (y = 0; y < h; y++) {
+            var w = verticesRows[y].length - 1;
+            for (x = 0; x < w; x++) {
+
+                var faceoffset = geoGroup.faceidx, lineoffset = geoGroup.lineidx;
+
+                var v1 = verticesRows[y][x + 1] + start, v1offset = v1 * 3;
+                var v2 = verticesRows[y][x] + start, v2offset = v2 * 3;
+                var v3 = verticesRows[y + 1][x] + start, v3offset = v3 * 3;
+                var v4 = verticesRows[y + 1][x + 1] + start, v4offset = v4 * 3;
+
+                var n1 = normals[v1 - start];
+                var n2 = normals[v2 - start];
+                var n3 = normals[v3 - start];
+                var n4 = normals[v4 - start];
+                var face, norm;
+                if (Math.abs(vertices[v1 - start].y) === radius) {
+                    // face = [v1, v3, v4];
+                    // norm = [n1, n3, n4];
+
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v3offset + 2] = n3.z;
+                    normalArray[v4offset + 2] = n4.z;
+
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v3;
+                    faceArray[faceoffset + 2] = v4;
+
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v3;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v4;
+                    lineArray[lineoffset + 4] = v3;
+                    lineArray[lineoffset + 5] = v4;
+
+                    geoGroup.faceidx += 3;
+                    geoGroup.lineidx += 6;
+
+                } else if (Math.abs(vertices[v3 - start].y) === radius) {
+                    // face = [v1, v2, v3];
+                    // norm = [n1, n2, n3];
+
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v3offset + 2] = n3.z;
+
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v2;
+                    faceArray[faceoffset + 2] = v3;
+
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v2;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v3;
+                    lineArray[lineoffset + 4] = v2;
+                    lineArray[lineoffset + 5] = v3;
+
+                    geoGroup.faceidx += 3;
+                    geoGroup.lineidx += 6;
+
+                } else {
+                    // face = [v1, v2, v3, v4];
+                    // norm = [n1, n2, n3, n4];
+
+                    normalArray[v1offset] = n1.x;
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v1offset + 1] = n1.y;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v1offset + 2] = n1.z;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v4offset + 2] = n4.z;
+
+                    normalArray[v2offset] = n2.x;
+                    normalArray[v3offset] = n3.x;
+                    normalArray[v4offset] = n4.x;
+                    normalArray[v2offset + 1] = n2.y;
+                    normalArray[v3offset + 1] = n3.y;
+                    normalArray[v4offset + 1] = n4.y;
+                    normalArray[v2offset + 2] = n2.z;
+                    normalArray[v3offset + 2] = n3.z;
+                    normalArray[v4offset + 2] = n4.z;
+
+                    faceArray[faceoffset] = v1;
+                    faceArray[faceoffset + 1] = v2;
+                    faceArray[faceoffset + 2] = v4;
+
+                    faceArray[faceoffset + 3] = v2;
+                    faceArray[faceoffset + 4] = v3;
+                    faceArray[faceoffset + 5] = v4;
+
+                    lineArray[lineoffset] = v1;
+                    lineArray[lineoffset + 1] = v2;
+                    lineArray[lineoffset + 2] = v1;
+                    lineArray[lineoffset + 3] = v4;
+
+                    lineArray[lineoffset + 4] = v2;
+                    lineArray[lineoffset + 5] = v3;
+                    lineArray[lineoffset + 6] = v3;
+                    lineArray[lineoffset + 7] = v4;
+
+                    geoGroup.faceidx += 6;
+                    geoGroup.lineidx += 8;
+
+                }
+
+            }
+        }
+
+    };
+
+    return draw;
+
+})();// A model is a collection of related atoms.  Bonds are only allowed between
+//atoms in the same model.  An atom is uniquely specified by its model id and
+//its serial number.
+//A glmodel knows how to apply the styles on each atom to create a gl object
+
+var $3Dmol = $3Dmol || {};
+
+/**
+ * GLModel represents a group of related atoms
+ * @constructor 
+ * @param {number=} mid 
+ * @param {Object=} defaultcolors Object defining default atom colors as atom => color property value pairs
+ * @see $3Dmol.download
+ */
+$3Dmol.GLModel = (function() {
+
+    // class variables go here
+    var defaultAtomStyle = {
+        line : {}
+    };
+
+    var Nucleotides = [ '  G', '  A', '  T', '  C', '  U', ' DG', ' DA', ' DT',
+            ' DC', ' DU' ];
+
+    var defaultlineWidth = 1.0;
+
+    // Reference: A. Bondi, J. Phys. Chem., 1964, 68, 441.
+    var vdwRadii = {
+        "H" : 1.2,
+        "Li" : 1.82,
+        "LI" : 1.82,
+        "Na" : 2.27,
+        "NA" : 2.27,
+        "K" : 2.75,
+        "C" : 1.7,
+        "N" : 1.55,
+        "O" : 1.52,
+        "F" : 1.47,
+        "P" : 1.80,
+        "S" : 1.80,
+        "CL" : 1.75,
+        "Cl" : 1.75,
+        "BR" : 1.85,
+        "Br" : 1.85,
+        "SE" : 1.90,
+        "Se" : 1.90,
+        "ZN" : 1.39,
+        "Zn" : 1.39,
+        "CU" : 1.4,
+        "Cu" : 1.4,
+        "NI" : 1.63,
+        "Ni" : 1.63
+    };
+
+    var validAtomSpecs = [
+        "resn", // Parent residue name
+        "x", // Atom's x coordinate
+        "y", // Atom's y coordinate
+        "z", // Atom's z coordinate
+        "color", // Atom's color, as hex code
+        "surfaceColor", // Hex code for color to be used for surface patch over this atom
+        "elem", // Element abbreviation (e.g. 'H', 'Ca', etc)
+        "hetflag", // Set to true if atom is a heteroatom
+        "chain", // Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)
+        "resi", // Residue number 
+        "icode",
+        "rescode",
+        "serial", // Atom's serial id numbermodels
+        "atom", // Atom name; may be more specific than 'elem' (e.g 'CA' for alpha carbon)
+        "bonds", // Array of atom ids this atom is bonded to
+        "ss", // Secondary structure identifier (for cartoon render; e.g. 'h' for helix)
+        "singleBonds", // true if this atom forms only single bonds or no bonds at all
+        "bondOrder", // Array of this atom's bond orders, corresponding to bonds identfied by 'bonds'
+        "properties", // Optional mapping of additional properties
+        "b", // Atom b factor data
+        "pdbline", // If applicable, this atom's record entry from the input PDB file (used to output new PDB from models)
+        "clickable", // Set this flag to true to enable click selection handling for this atom
+        "callback", // Callback click handler function to be executed on this atom and its parent viewer
+        "invert" // for selection, inverts the meaning of the selection
+    ];
+
+    var validAtomSelectionSpecs = validAtomSpecs.concat([  // valid atom specs are ok too
+        "model", // a single model or list of models from which atoms should be selected
+        "bonds", // overloaded to select number of bonds, e.g. {bonds: 0} will select all nonbonded atoms
+        "predicate", // user supplied function that gets passed an {AtomSpec} and should return true if the atom should be selected
+        "invert", // if set, inverts the meaning of the selection
+        "byres", // if set, expands the selection to include all atoms of any residue that has any atom selected
+        "expand", // expands the selection to include all atoms within a given distance from the selection
+        "within" // intersects the selection with the set of atoms within a given distance from another selection
+    ]);
+
+    var validAtomStyleSpecs = [
+        "line", // draw bonds as lines
+        "cross", // draw atoms as crossed lines (aka stars)
+        "stick", // draw bonds as capped cylinders
+        "sphere", // draw atoms as spheres
+        "cartoon" // draw cartoon representation of secondary structure
+    ];
+
+    // class functions
+
+    // return true if a and b represent the same style
+    var sameObj = function(a,b) {
+        if(a && b)
+            return JSON.stringify(a) == JSON.stringify(b);
+        else
+            return a == b;
+    };    
+
+   
+    function GLModel(mid, defaultcolors) {
+        // private variables
+        var atoms = [];
+        var frames = [];
+        var id = mid;
+        var hidden = false;
+        var molObj = null;
+        var renderedMolObj = null;
+        var lastColors = null;
+        var modelData = {};
+        var idMatrix = new $3Dmol.Matrix4();
+        var dontDuplicateAtoms;
+        var defaultColor = $3Dmol.elementColors.defaultColor;
+        
+        var ElementColors = (defaultcolors) ? defaultcolors : $3Dmol.elementColors.defaultColors;
+
+
+        // drawing functions must be associated with model object since
+        // geometries can't span multiple canvases
+
+        // sphere drawing
+        var defaultSphereRadius = 1.5;
+
+        // return proper radius for atom given style
+        /** 
+         * 
+         * @param {AtomSpec} atom
+         * @param {atomstyle} style
+         * @return {number} 
+         * 
+         */
+        var getRadiusFromStyle = function(atom, style) {
+            var r = defaultSphereRadius;
+            if (typeof (style.radius) != "undefined")
+                r = style.radius;
+            else if (vdwRadii[atom.elem])
+                r = vdwRadii[atom.elem];
+
+            if (typeof (style.scale) != "undefined")
+                r *= style.scale;
+            return r;
+        };
+
+        // cross drawing
+        /** @typedef CrossStyleSpec
+         * @prop {boolean} hidden - do not show 
+         * @prop {number} linewidth 
+         * @prop {number} radius 
+         * @prop {number} scale - scale radius by specified amount
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+         */
+        
+        /**
+         * 
+         * @param {AtomSpec} atom
+         * @param {$3Dmol.Geometry[]} geos
+         */
+        var drawAtomCross = function(atom, geos) {
+            if (!atom.style.cross)
+                return;
+            var style = atom.style.cross;
+            if (style.hidden)
+                return;
+            var linewidth = (style.linewidth || defaultlineWidth);
+            if (!geos[linewidth])
+                geos[linewidth] = new $3Dmol.Geometry();
+                
+            var geoGroup = geos[linewidth].updateGeoGroup(6);
+            
+            var delta = getRadiusFromStyle(atom, style);
+
+            var points = [ [ delta, 0, 0 ], [ -delta, 0, 0 ], [ 0, delta, 0 ],
+                    [ 0, -delta, 0 ], [ 0, 0, delta ], [ 0, 0, -delta ] ];
+
+            var clickable = atom.clickable;
+            if (clickable && atom.intersectionShape === undefined)
+                atom.intersectionShape = {sphere : [], cylinder : [], line : []};
+            
+            var c = $3Dmol.getColorFromStyle(atom, style);
+            
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            
+            for ( var j = 0; j < 6; j++) {
+                
+                var offset = geoGroup.vertices*3;
+                
+                geoGroup.vertices++;
+                vertexArray[offset] = atom.x + points[j][0];
+                vertexArray[offset+1] = atom.y + points[j][1];
+                vertexArray[offset+2] = atom.z + points[j][2];
+                colorArray[offset] = c.r;
+                colorArray[offset+1] = c.g;
+                colorArray[offset+2] = c.b;
+                
+                if (clickable){
+                    var point = new $3Dmol.Vector3(points[j][0], points[j][1], points[j][2]);
+                    
+                    //decrease cross size for selection to prevent misselection from atom overlap
+                    point.multiplyScalar(0.1);
+                    point.set(point.x+atom.x, point.y+atom.y, point.z+atom.z);
+                    atom.intersectionShape.line.push(point);
+                }
+
+            }
+                        
+        };
+
+        //from atom, return a normalized vector v that is orthogonal and along which
+        //it is appropraite to draw multiple bonds
+        var getSideBondV = function(atom, atom2, i) {
+
+            var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+            var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
+
+            var dir = p2.clone();
+            var v = null;
+            dir.sub(p1);
+
+            var p1a, p1b, p2a, p2b;
+            var i2, j2, atom3, p3, dir2;
+            if (atom.bonds.length === 1) {
+                if (atom2.bonds.length === 1) {
+                    v = dir.clone();
+                    if (Math.abs(v.x) > 0.0001)
+                        v.y += 1;
+                    else
+                        v.x += 1;
+                } else {
+                    i2 = (i + 1) % atom2.bonds.length;
+                    j2 = atom2.bonds[i2];
+                    atom3 = atoms[j2];
+                    p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+
+                    dir2 = p3.clone();
+                    dir2.sub(p1);
+
+                    v = dir2.clone();
+                    v.cross(dir);
+                }
+            } else {
+                // get vector 2 different neighboring atom
+                i2 = (i + 1) % atom.bonds.length;
+                j2 = atom.bonds[i2];
+                atom3 = atoms[j2];
+                p3 = new $3Dmol.Vector3(atom3.x, atom3.y, atom3.z);
+
+                dir2 = p3.clone();
+                dir2.sub(p1);
+
+                v = dir2.clone();
+                v.cross(dir);
+            }
+
+            // especially for C#C (triple bond) dir and dir2
+            // may be opposites resulting in a zero v
+            if (v.lengthSq() < 0.01) {
+                v = dir.clone();
+                if (Math.abs(v.x) > 0.0001)
+                    v.y += 1;
+                else
+                    v.x += 1;
+            }
+
+            v.cross(dir);
+            v.normalize();
+            
+            return v;
+            
+            //v.multiplyScalar(r * 1.5);
+
+        }
+        
+        var getTripleBondPoints = function() {
+            
+            v.cross(dir);
+            v.normalize();
+            v.multiplyScalar(r * 3);
+
+            p1a = p1.clone();
+            p1a.add(v);
+            p1b = p1.clone();
+            p1b.sub(v);
+
+            p2a = p1a.clone();
+            p2a.add(dir);
+            p2b = p1b.clone();
+            p2b.add(dir);
+        }
+        
+        var addLine = function(vertexArray, colorArray, offset, p1, p2, c1) {
+            //make line from p1 to p2, does not incremeant counts
+            vertexArray[offset] = p1.x; vertexArray[offset+1] = p1.y; vertexArray[offset+2] = p1.z;
+            colorArray[offset] = c1.r; colorArray[offset+1] = c1.g; colorArray[offset+2] = c1.b;
+            vertexArray[offset+3] = p2.x; vertexArray[offset+4] = p2.y; vertexArray[offset+5] = p2.z;
+            colorArray[offset+3] = c1.r; colorArray[offset+4] = c1.g; colorArray[offset+5] = c1.b;            
+        }
+        
+        /**@typedef LineStyleSpec
+         * @prop {boolean} hidden - do not show line
+         * @prop {number} linewidth 
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+         */
+        
+        // bonds - both atoms must match bond style
+        // standardize on only drawing for lowest to highest
+        /**
+         * 
+         * @param {AtomSpec}
+         *            atom
+         * @param {AtomSpec[]} atoms
+         * @param {$3Dmol.Geometry[]} geos
+         */
+        var drawBondLines = function(atom, atoms, geos) {
+            if (!atom.style.line)
+                return;
+            var style = atom.style.line;
+            if (style.hidden)
+                return;
+
+            // have a separate geometry for each linewidth
+            var linewidth = (style.linewidth || defaultlineWidth);
+
+            if (!geos[linewidth])
+                geos[linewidth] = new $3Dmol.Geometry();
+            /** @type {geometryGroup} */
+            var geoGroup = geos[linewidth].updateGeoGroup(6*atom.bonds.length); //reserve enough space even for triple bonds
+            
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            
+            for ( var i = 0; i < atom.bonds.length; i++) {
+                var j = atom.bonds[i]; // our neighbor
+                
+                var atom2 = atoms[j];
+                if (!atom2.style.line)
+                    continue; // don't sweat the details
+
+                if (atom.serial >= atom2.serial) // only draw if less, this way we can do multi bonds correctly
+                    continue;
+                var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);                
+                var mp = p1.clone().add(p2).multiplyScalar(0.5);
+                var singleBond = false;               
+                
+                if (atom.clickable){
+                    if (atom.intersectionShape === undefined)
+                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                    atom.intersectionShape.line.push(p1);
+                    atom.intersectionShape.line.push(p2);
+                }
+
+                var c1 = $3Dmol.getColorFromStyle(atom, atom.style.line);
+                var c2 = $3Dmol.getColorFromStyle(atom2, atom2.style.line);
+               
+                if(atom.bondStyles && atom.bondStyles[i]) {
+                    var bstyle = atom.bondStyles[i];
+                    if(!bstyle.iswire) {
+                        continue;
+                    }
+                    if(bstyle.radius) bondR = bstyle.radius;
+                    if(bstyle.singleBond) singleBond = true;
+                    if(typeof(bstyle.color1) != "undefined") {
+                        c1 = $3Dmol.CC.color(bstyle.color1);
+                    }
+                    if(typeof(bstyle.color2) != "undefined") {
+                        c2 = $3Dmol.CC.color(bstyle.color2);
+                    }
+                }
+
+                var offset = geoGroup.vertices*3;
+                
+                if(atom.bondOrder[i] > 1 && atom.bondOrder[i] < 4 && !singleBond) {
+                    var v = getSideBondV(atom, atom2, i);
+                    var dir = p2.clone();
+                    dir.sub(p1);
+                    
+                    if(atom.bondOrder[i] == 2) { //double
+                        
+                        v.multiplyScalar(.1);
+                           p1a = p1.clone();
+                        p1a.add(v);
+                        p1b = p1.clone();
+                        p1b.sub(v);
+
+                        p2a = p1a.clone();
+                        p2a.add(dir);
+                        p2b = p1b.clone();
+                        p2b.add(dir);
+                        
+                        if(c1 == c2) {
+                            geoGroup.vertices += 4;
+                            addLine(vertexArray, colorArray, offset, p1a, p2a, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, p1b, p2b, c1);                            
+                        }
+                        else {
+                            geoGroup.vertices += 8;
+                            dir.multiplyScalar(0.5);
+                            var mpa = p1a.clone();
+                            mpa.add(dir);
+                            var mpb = p1b.clone();
+                            mpb.add(dir);
+                            
+                            addLine(vertexArray, colorArray, offset, p1a, mpa, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, mpa, p2a, c2);                            
+                            addLine(vertexArray, colorArray, offset+12, p1b, mpb, c1); 
+                            addLine(vertexArray, colorArray, offset+18, mpb, p2b, c2); 
+                        }
+                    }
+                    else if(atom.bondOrder[i] == 3) { //triple
+                        
+                        v.multiplyScalar(.1);
+                           p1a = p1.clone();
+                        p1a.add(v);
+                        p1b = p1.clone();
+                        p1b.sub(v);
+
+                        p2a = p1a.clone();
+                        p2a.add(dir);
+                        p2b = p1b.clone();
+                        p2b.add(dir);
+                        
+                        if(c1 == c2) {
+                            geoGroup.vertices += 6;
+                            addLine(vertexArray, colorArray, offset, p1, p2, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, p1a, p2a, c1);                            
+                            addLine(vertexArray, colorArray, offset+12, p1b, p2b, c1);                            
+                        }
+                        else {
+                            geoGroup.vertices += 12;
+                            dir.multiplyScalar(0.5);
+                            var mpa = p1a.clone();
+                            mpa.add(dir);
+                            var mpb = p1b.clone();
+                            mpb.add(dir);
+
+                            addLine(vertexArray, colorArray, offset, p1, mp, c1);                            
+                            addLine(vertexArray, colorArray, offset+6, mp, p2, c2);
+                            addLine(vertexArray, colorArray, offset+12, p1a, mpa, c1);                            
+                            addLine(vertexArray, colorArray, offset+18, mpa, p2a, c2);                            
+                            addLine(vertexArray, colorArray, offset+24, p1b, mpb, c1); 
+                            addLine(vertexArray, colorArray, offset+30, mpb, p2b, c2); 
+                        }
+                    }
+                }
+                else { //single bond                                    
+                    if(c1 == c2) {
+                        geoGroup.vertices += 2;
+                        addLine(vertexArray, colorArray, offset, p1, p2, c1);
+                    } else {
+                        geoGroup.vertices += 4;
+                        addLine(vertexArray, colorArray, offset, p1, mp, c1);
+                        addLine(vertexArray, colorArray, offset+6, mp, p2, c2);                        
+                    }
+                    
+                }
+            }
+
+        };
+
+        // bonds as cylinders
+        var defaultStickRadius = 0.25;
+
+        /**@typedef SphereStyleSpec
+         * @prop {boolean} hidden - do not show atom
+         * @prop {number} radius - override van der waals radius
+         * @prop {number} scale - scale radius by specified amount
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+         */
+        
+        //sphere drawing
+        //See also: drawCylinder
+        /** 
+         * 
+         * @param {AtomSpec} atom
+         * @param {$3Dmol.Geometry} geo
+         */
+        var drawAtomSphere = function(atom, geo) {
+            
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
+                                                                 
+            var C = $3Dmol.getColorFromStyle(atom, style);
+            
+            var x, y;
+            var radius = getRadiusFromStyle(atom, style);
+            
+            if ((atom.clickable === true) && (atom.intersectionShape !== undefined)) {
+                var center = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                atom.intersectionShape.sphere.push(new $3Dmol.Sphere(center, radius));
+            }
+            
+            $3Dmol.GLDraw.drawSphere(geo, atom, radius, C);    
+            
+        };
+
+        var drawAtomInstanced = function(atom, geo) {
+
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
+
+            var radius = getRadiusFromStyle(atom, style);
+            var C = $3Dmol.getColorFromStyle(atom, style);
+
+            var geoGroup = geo.updateGeoGroup(1);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var radiusArray = geoGroup.radiusArray;
+
+            vertexArray[start] = atom.x;
+            vertexArray[start+1] = atom.y ;
+            vertexArray[start+2] = atom.z;
+
+            var normalArray = geoGroup.normalArray;
+            var colorArray = geoGroup.colorArray;
+            colorArray[start] = C.r;
+            colorArray[start+1] = C.g;
+            colorArray[start+2] = C.b;
+
+            radiusArray[startv] = radius;
+
+            geoGroup.vertices += 1;
+
+        };
+
+        var drawSphereImposter = function(geo, center, radius, C) {
+            //create flat square                                   
+            var geoGroup = geo.updateGeoGroup(4);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            
+            //use center point for each vertex
+            for(var i = 0; i < 4; i++) {
+                vertexArray[start+3*i] = center.x;
+                vertexArray[start+3*i+1] = center.y ;
+                vertexArray[start+3*i+2] = center.z;                           
+            }
+            
+
+            //same colors for all 4 vertices
+            var normalArray = geoGroup.normalArray;
+            var colorArray = geoGroup.colorArray;
+            for(var i = 0; i < 4; i++) {
+                colorArray[start+3*i] = C.r;
+                colorArray[start+3*i+1] = C.g;
+                colorArray[start+3*i+2] = C.b;                
+            }
+            
+            normalArray[start+0] = -radius;
+            normalArray[start+1] = radius;
+            normalArray[start+2] = 0;
+            
+            normalArray[start+3] = -radius;
+            normalArray[start+4] = -radius;
+            normalArray[start+5] = 0;
+            
+            normalArray[start+6] = radius;
+            normalArray[start+7] = -radius;
+            normalArray[start+8] = 0;
+            
+            normalArray[start+9] = radius;
+            normalArray[start+10] = radius;
+            normalArray[start+11] = 0;
+            
+            geoGroup.vertices += 4;
+            
+            //two faces
+            var faceArray = geoGroup.faceArray;
+            var faceoffset = geoGroup.faceidx; //not number faces, but index
+            faceArray[faceoffset+0] = startv;
+            faceArray[faceoffset+1] = startv+1;
+            faceArray[faceoffset+2] = startv+2;
+            faceArray[faceoffset+3] = startv+2;
+            faceArray[faceoffset+4] = startv+3;
+            faceArray[faceoffset+5] = startv;
+            geoGroup.faceidx += 6;
+        };
+        
+        //dkoes -  code for sphere imposters
+        var drawAtomImposter = function(atom, geo) {
+            
+            if (!atom.style.sphere)
+                return;
+            var style = atom.style.sphere;
+            if (style.hidden)
+                return;
+            
+            var radius = getRadiusFromStyle(atom, style);
+            var C = $3Dmol.getColorFromStyle(atom, style);
+            
+            drawSphereImposter(geo, atom, radius, C);            
+        };
+                
+          
+        var drawStickImposter =  function(geo, from, to, radius, color, fromCap, toCap) {
+           //we need the four corners - two have from coord, two have to coord, the normal
+            //is the opposing point, from which we can get the normal and length
+            //also need the radius
+            var geoGroup = geo.updateGeoGroup(4);
+            var startv =  geoGroup.vertices;
+            var start = startv*3;
+            var vertexArray = geoGroup.vertexArray;
+            var colorArray = geoGroup.colorArray;
+            var radiusArray = geoGroup.radiusArray;
+            var normalArray = geoGroup.normalArray;
+            //encode extra bits of information in the color
+            var r = color.r;
+            var g = color.g;
+            var b = color.b;
+            
+            var negateColor = function(c) {
+                //set sign bit
+                var n = -c;
+                if(n == 0) n = -0.0001;
+                return n;
+            };
+            
+            /* for sticks, always draw caps, but we could in theory set caps in color */
+            
+            //4 vertices, distinguish between p1 and p2 with neg blue
+            var pos = start;
+            for(var i = 0; i < 4; i++) {
+                vertexArray[pos] = from.x;
+                normalArray[pos] = to.x;
+                colorArray[pos] = r;
+                pos++;
+                vertexArray[pos] = from.y;
+                normalArray[pos] = to.y;
+                colorArray[pos] = g;
+                pos++;
+                vertexArray[pos] = from.z;
+                normalArray[pos] = to.z;
+                if(i < 2)
+                    colorArray[pos] = b;
+                else
+                    colorArray[pos] = negateColor(b);
+                pos++;
+            }
+
+            geoGroup.vertices += 4;
+
+            radiusArray[startv] = -radius;
+            radiusArray[startv+1] = radius;
+            radiusArray[startv+2] = -radius;
+            radiusArray[startv+3] = radius;      
+                        
+            //two faces
+            var faceArray = geoGroup.faceArray;
+            var faceoffset = geoGroup.faceidx; //not number faces, but index
+            faceArray[faceoffset+0] = startv;
+            faceArray[faceoffset+1] = startv+1;
+            faceArray[faceoffset+2] = startv+2;
+            faceArray[faceoffset+3] = startv+2;
+            faceArray[faceoffset+4] = startv+3;
+            faceArray[faceoffset+5] = startv;
+            geoGroup.faceidx += 6;          
+        };
+        
+        /**@typedef StickStyleSpec
+         * @prop {boolean} hidden - do not show 
+         * @prop {number} radius 
+         * @prop {boolean} singleBonds - draw all bonds as single bonds if set
+         * @prop {ColorschemeSpec} colorscheme - element based coloring
+         * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+         */
+        
+        // draws cylinders and small spheres (at bond radius)
+        var drawBondSticks = function(atom, atoms, geo) {
+            if (!atom.style.stick)
+                return;
+            var style = atom.style.stick;
+            if (style.hidden)
+                return;
+
+            var atomBondR = style.radius || defaultStickRadius;
+            var bondR = atomBondR;
+            var atomSingleBond = style.singleBonds || false;
+            var fromCap = 0, toCap = 0;
+
+            var C1 = $3Dmol.getColorFromStyle(atom, style);
+
+            var mp, mp1, mp2;
+            
+            if (!atom.capDrawn && atom.bonds.length < 4)
+                fromCap = 2;
+            
+            var drawCyl = $3Dmol.GLDraw.drawCylinder; //mesh cylinder
+            if(geo.imposter) 
+                drawCyl = drawStickImposter;
+
+                
+            for (var i = 0; i < atom.bonds.length; i++) {
+                var j = atom.bonds[i]; // our neighbor
+                var atom2 = atoms[j]; //parsePDB, etc should only add defined bonds
+                
+                if (atom.serial < atom2.serial) {// only draw if less, this
+                    // lets us combine
+                    // cylinders of the same
+                    // color
+                    var style2 = atom2.style;
+                    if (!style2.stick)
+                        continue; // don't sweat the details                     
+                   
+                    var C2 = $3Dmol.getColorFromStyle(atom2, style2.stick);
+                    
+                    //support bond specific styles
+                    bondR = atomBondR;                    
+                    var singleBond = atomSingleBond;
+                    if(atom.bondStyles && atom.bondStyles[i]) {
+                        var bstyle = atom.bondStyles[i];
+                        if(bstyle.iswire) {
+                            continue;
+                        }
+                        if(bstyle.radius) bondR = bstyle.radius;
+                        if(bstyle.singleBond) singleBond = true;
+                        if(typeof(bstyle.color1) != "undefined") {
+                            C1 = $3Dmol.CC.color(bstyle.color1);
+                        }
+                        if(typeof(bstyle.color2) != "undefined") {
+                            C2 = $3Dmol.CC.color(bstyle.color2);
+                        }
+                    }
+                    var p1 = new $3Dmol.Vector3(atom.x, atom.y, atom.z);
+                    var p2 = new $3Dmol.Vector3(atom2.x, atom2.y, atom2.z);
+
+                    // draw cylinders
+                    if (atom.bondOrder[i] === 1 || singleBond) {
+
+                        if (!atom2.capDrawn && atom2.bonds.length < 4)
+                            toCap = 2;       
+                                                
+                        if (C1 != C2) {
+                            mp = new $3Dmol.Vector3().addVectors(p1, p2)
+                                    .multiplyScalar(0.5);
+                            drawCyl(geo, p1, mp, bondR, C1, fromCap, 0);
+                            drawCyl(geo, mp, p2, bondR, C2, 0, toCap);
+                        } else {
+                            drawCyl(geo, p1, p2, bondR, C1, fromCap, toCap);
+                        }
+                        
+                        if (atom.clickable || atom2.clickable) {
+                            mp = new $3Dmol.Vector3().addVectors(p1, p2).multiplyScalar(0.5);
+                            if (atom.clickable){
+                                var cylinder1 = new $3Dmol.Cylinder(p1 , mp , bondR);
+                                var sphere1 = new $3Dmol.Sphere(p1 , bondR);
+                                atom.intersectionShape.cylinder.push(cylinder1);   
+                                atom.intersectionShape.sphere.push(sphere1);                             
+                            }
+                            if (atom2.clickable){
+                                var cylinder2 = new $3Dmol.Cylinder(p2 , mp , bondR);
+                                var sphere2 = new $3Dmol.Sphere(p2 , bondR);
+                                atom2.intersectionShape.cylinder.push(cylinder2);
+                                atom2.intersectionShape.sphere.push(sphere2);
+                            }
+
+                        }
+                        
+                    } 
+                    
+                    else if (atom.bondOrder[i] > 1) {
+                        var mfromCap = 0; mtoCap = 0; //multi bond caps
+                        
+                        if(bondR != atomBondR) {
+                            //assume jmol style multiple bonds - the radius doesn't fit within atom sphere
+                            mfromCap = 2;
+                            mtoCap = 2;
+                        }
+                        
+                        var dir = p2.clone();
+                        var v = null;
+                        dir.sub(p1);
+                        
+                        var r, p1a, p1b, p2a, p2b;
+                        var v = getSideBondV(atom, atom2, i);
+                        
+                        if (atom.bondOrder[i] == 2) {
+                            var r = bondR/2.5;
+                            var v = getSideBondV(atom, atom2, i);
+                            
+                            v.multiplyScalar(r*1.5);
+                            p1a = p1.clone();
+                            p1a.add(v);
+                            p1b = p1.clone();
+                            p1b.sub(v);
+
+                            p2a = p1a.clone();
+                            p2a.add(dir);
+                            p2b = p1b.clone();
+                            p2b.add(dir);
+
+                                                                 
+                            if (C1 != C2) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                drawCyl(geo, p1a, mp, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp, p2a, r, C2, 0, mtoCap);
+                                drawCyl(geo, p1b, mp2, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp2, p2b, r, C2, 0, mtoCap);
+                            } else {
+                                drawCyl(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
+                                drawCyl(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
+                            }
+                            if (atom.clickable || atom2.clickable){
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                               .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                                .multiplyScalar(0.5);
+                                if (atom.clickable) {
+                                    cylinder1a = new $3Dmol.Cylinder(p1a , mp , r);
+                                    cylinder1b = new $3Dmol.Cylinder(p1b , mp2 , r);
+                                    atom.intersectionShape.cylinder.push(cylinder1a);
+                                    atom.intersectionShape.cylinder.push(cylinder1b);
+                                }
+                                if (atom2.clickable) {
+                                    cylinder2a = new $3Dmol.Cylinder(p2a , mp , r);
+                                    cylinder2b = new $3Dmol.Cylinder(p2b , mp2 , r);
+                                    atom2.intersectionShape.cylinder.push(cylinder2a);
+                                    atom2.intersectionShape.cylinder.push(cylinder2b);                               
+                                }
+                            }
+                        } 
+                        else if (atom.bondOrder[i] == 3) {
+                            r = bondR / 4;
+                            v.cross(dir);
+                            v.normalize();
+                            v.multiplyScalar(r * 3);
+
+                            p1a = p1.clone();
+                            p1a.add(v);
+                            p1b = p1.clone();
+                            p1b.sub(v);
+
+                            p2a = p1a.clone();
+                            p2a.add(dir);
+                            p2b = p1b.clone();
+                            p2b.add(dir);
+
+                            if (C1 != C2) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
+                                        .multiplyScalar(0.5);
+                                drawCyl(geo, p1a, mp, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp, p2a, r, C2, 0, mtoCap);
+                                drawCyl(geo, p1, mp3, r, C1, fromCap, 0);
+                                drawCyl(geo, mp3, p2, r, C2, 0, toCap);
+                                drawCyl(geo, p1b, mp2, r, C1, mfromCap, 0);
+                                drawCyl(geo, mp2, p2b, r, C2, 0, mtoCap);
+                            } else {
+                                drawCyl(geo, p1a, p2a, r, C1, mfromCap, mtoCap);
+                                drawCyl(geo, p1, p2, r, C1, fromCap, toCap);
+                                drawCyl(geo, p1b, p2b, r, C1, mfromCap, mtoCap);
+
+                            }
+                            if (atom.clickable || atom2.clickable) {
+                                mp = new $3Dmol.Vector3().addVectors(p1a, p2a)
+                                        .multiplyScalar(0.5);
+                                mp2 = new $3Dmol.Vector3().addVectors(p1b, p2b)
+                                        .multiplyScalar(0.5);
+                                mp3 = new $3Dmol.Vector3().addVectors(p1, p2)
+                                        .multiplyScalar(0.5);
+                                                                
+                                if (atom.clickable) {
+                                    cylinder1a = new $3Dmol.Cylinder(p1a.clone(), mp.clone(), r);
+                                    cylinder1b = new $3Dmol.Cylinder(p1b.clone(), mp2.clone(), r);
+                                    cylinder1c = new $3Dmol.Cylinder(p1.clone(), mp3.clone(), r);
+                                    atom.intersectionShape.cylinder.push(cylinder1a);
+                                    atom.intersectionShape.cylinder.push(cylinder1b);
+                                    atom.intersectionShape.cylinder.push(cylinder1c);
+                                } 
+                                if (atom2.clickable) {                               
+                                    cylinder2a = new $3Dmol.Cylinder(p2a.clone(), mp.clone(), r);
+                                    cylinder2b = new $3Dmol.Cylinder(p2b.clone(), mp2.clone(), r);
+                                    cylinder2c = new $3Dmol.Cylinder(p2.clone(), mp3.clone(), r);
+                                    atom2.intersectionShape.cylinder.push(cylinder2a);
+                                    atom2.intersectionShape.cylinder.push(cylinder2b);
+                                    atom2.intersectionShape.cylinder.push(cylinder2c);                                
+                                }
+                            }
+                        }
+                    }
+                     
+                }                   
+                                 
+            }            
+
+            // draw non bonded heteroatoms as spheres
+            var drawSphere = false;
+            var numsinglebonds = 0;
+            var differentradii = false;
+            //also, if any bonds were drawn as multiples, need sphere
+            for(var i = 0; i < atom.bonds.length; i++) {
+                var singleBond = atomSingleBond;
+                if(atom.bondStyles && atom.bondStyles[i]) {
+                    var bstyle = atom.bondStyles[i];
+                    if(bstyle.singleBond) singleBond = true;
+                    if(bstyle.radius && bstyle.radius != atomBondR) {
+                        differentradii = true;
+                    }
+                }
+                if(singleBond || atom.bondOrder[i] == 1) {
+                    numsinglebonds++;
+                }
+            }
+            
+            if(differentradii) { //jmol style double/triple bonds - no sphere
+                if(numsinglebonds > 0) drawSphere = true; //unless needed as a cap
+            }
+            else if(numsinglebonds == 0 && atom.bonds.length > 0) {
+                drawSphere = true;
+            }
+           
+            if (drawSphere) {
+                var savedstyle = atom.style;
+                bondR = atomBondR;
+                //do not use bond style as this can be variable, particularly
+                //with jmol export of double/triple bonds
+                if(geo.imposter) {
+                    drawSphereImposter(geo.sphereGeometry, atom, bondR, C1);
+                }
+                else {
+                    $3Dmol.GLDraw.drawSphere(geo, atom, bondR, C1);
+                }
+            }
+            
+        };
+        
+        
+
+        // go through all the atoms and regenerate their geometries
+        // we try to have one geometry for each style since this is much much
+        // faster
+        // at some point we should optimize this to avoid unnecessary
+        // recalculation
+        /** param {AtomSpec[]} atoms */
+        var createMolObj = function(atoms, options) {
+
+            options = options || {};
+
+            var ret = new $3Dmol.Object3D();
+            var cartoonAtoms = [];
+            var lineGeometries = {};
+            var crossGeometries = {};
+            
+            var drawSphereFunc = drawAtomSphere;
+            var sphereGeometry = null;
+            var stickGeometry = null;
+            if (options.supportsImposters) {
+                drawSphereFunc = drawAtomImposter;
+                sphereGeometry = new $3Dmol.Geometry(true);
+                sphereGeometry.imposter = true;
+                stickGeometry = new $3Dmol.Geometry(true, true);
+                stickGeometry.imposter = true;
+                stickGeometry.sphereGeometry = sphereGeometry; //for caps
+                stickGeometry.drawnCaps = {};
+            }
+            else if (options.supportsAIA) {
+                drawSphereFunc = drawAtomInstanced;
+                sphereGeometry = new $3Dmol.Geometry(false, true,true);
+                sphereGeometry.instanced = true;
+                stickGeometry = new $3Dmol.Geometry(true); //don't actually have instanced sticks
+            }  else {
+                sphereGeometry = new $3Dmol.Geometry(true);
+                stickGeometry = new $3Dmol.Geometry(true);
+            }
+            
+            var i, j, n, testOpacities;
+            var opacities = {};
+            var range = [Number.POSITIVE_INFINITY, Number.NEGATIVE_INFINITY];
+            for (i = 0, n = atoms.length; i < n; i++) {
+                var atom = atoms[i];
+                // recreate gl info for each atom as necessary
+                // set up appropriate intersection spheres for clickable atoms
+
+                if (atom && atom.style) {
+
+                    if (atom.clickable && atom.intersectionShape === undefined)
+                        atom.intersectionShape = {sphere: [], cylinder: [], line: [], triangle : []};
+
+                    testOpacities = {line:undefined, cross:undefined, stick:undefined, sphere:undefined};
+                    for (j in testOpacities)
+                    {
+                        if (atom.style[j])
+                        {
+                            if (atom.style[j].opacity)
+                                testOpacities[j] = parseFloat(atom.style[j].opacity);
+                            else
+                                testOpacities[j] = 1;
+
+                        } else testOpacities[j] = undefined;
+
+                        if (opacities[j])
+                        {
+                            if (testOpacities[j] != undefined && opacities[j] != testOpacities[j])
+                            {
+                                console.log("Warning: " + j + " opacity is ambiguous");
+                                opacities[j] = 1;
+                            }
+
+                        } else opacities[j] = testOpacities[j];
+                    }
+
+                    drawSphereFunc(atom, sphereGeometry);
+                   
+                    drawAtomCross(atom, crossGeometries);
+                    drawBondLines(atom, atoms, lineGeometries);
+                    drawBondSticks(atom, atoms, stickGeometry);
+
+                    if (typeof (atom.style.cartoon) !== "undefined" && !atom.style.cartoon.hidden) {
+                        //gradient color scheme range
+                        if (atom.style.cartoon.color === "spectrum" && typeof(atom.resi) === "number" && !atom.hetflag) {                            
+                            if (atom.resi < range[0])
+                                range[0] = atom.resi;
+                            if (atom.resi > range[1])
+                                range[1] = atom.resi;
+                        }
+
+                        cartoonAtoms.push(atom);
+                    }                   
+                }
+            }
+            // create cartoon if needed - this is a whole model analysis
+            if (cartoonAtoms.length > 0) {
+                var gradientscheme = null;
+                //TODO: Should have an option to choose gradient type
+                if (range[0] < range[1])
+                    gradientscheme = new $3Dmol.Gradient.Sinebow(range[0], range[1]);
+
+                $3Dmol.drawCartoon(ret, cartoonAtoms, gradientscheme);
+
+            }
+
+            // add sphere geometry
+            if (sphereGeometry && sphereGeometry.vertices > 0) {
+                //Initialize buffers in geometry                
+                sphereGeometry.initTypedArrays();                
+                var sphereMaterial = null;
+                
+                //create appropriate material
+                if(sphereGeometry.imposter) {
+                    sphereMaterial = new $3Dmol.SphereImposterMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0
+                    });            
+                }
+                else if(sphereGeometry.instanced) {
+                    var sphere = new $3Dmol.Geometry(true);
+                    $3Dmol.GLDraw.drawSphere(sphere, {x:0, y:0, z:0}, 1, new $3Dmol.Color(0.5, 0.5, 0.5));
+                    sphere.initTypedArrays();
+                    sphereMaterial = new $3Dmol.InstancedMaterial({
+                        sphereMaterial : new $3Dmol.MeshLambertMaterial({
+                            ambient : 0x000000,
+                            vertexColors : true,
+                            reflectivity : 0,
+                        }),
+                        sphere : sphere
+                    });                
+                }
+                else { //regular mesh
+                    var sphereMaterial = new $3Dmol.MeshLambertMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0,
+                    });
+                }
+                if (opacities.sphere < 1 && opacities.sphere >= 0)
+                {
+                    sphereMaterial.transparent = true;
+                    sphereMaterial.opacity = opacities.sphere;
+                }
+                
+                var sphere = new $3Dmol.Mesh(sphereGeometry, sphereMaterial);
+                ret.add(sphere);
+            }
+            
+            // add stick geometry
+            if (stickGeometry.vertices > 0) {
+                
+                if(stickGeometry.imposter) {
+                    var imposterMaterial = new $3Dmol.StickImposterMaterial({
+                        ambient : 0x000000,
+                        vertexColors : true,
+                        reflectivity : 0
+                    });
+                    
+                    //Initialize buffers in geometry                
+                    stickGeometry.initTypedArrays();
+                    
+                    var sticks = new $3Dmol.Mesh(stickGeometry, imposterMaterial);
+                    ret.add(sticks);                    
+                } else {                
+                    var cylinderMaterial = new $3Dmol.MeshLambertMaterial({
+                        vertexColors : true,
+                        ambient : 0x000000,
+                        reflectivity : 0
+                    });
+                    if (opacities.stick < 1 && opacities.stick >= 0)
+                    {
+                        cylinderMaterial.transparent = true;
+                        cylinderMaterial.opacity = opacities.stick;
+                    }
+    
+                    //Initialize buffers in geometry                
+                    stickGeometry.initTypedArrays();
+                    
+                    if (cylinderMaterial.wireframe)
+                        stickGeometry.setUpWireframe();
+                
+                    var sticks = new $3Dmol.Mesh(stickGeometry, cylinderMaterial);
+                    ret.add(sticks);
+                }
+            }
+            
+            //var linewidth;
+            // add any line geometries, distinguished by line width
+            for (i in lineGeometries) {
+                if (lineGeometries.hasOwnProperty(i)) {
+                    var linewidth = i;
+                    var lineMaterial = new $3Dmol.LineBasicMaterial({
+                        linewidth : linewidth,
+                        vertexColors : true
+                    });
+                    if (opacities.line < 1 && opacities.line >= 0)
+                    {
+                        lineMaterial.transparent = true;
+                        lineMaterial.opacity = opacities.line;
+                    }
+                    
+                    lineGeometries[i].initTypedArrays();
+                    
+                    var line = new $3Dmol.Line(lineGeometries[i], lineMaterial,
+                            $3Dmol.LinePieces);
+
+                    ret.add(line);
+                }
+            }
+
+            // add any cross geometries
+            for (i in crossGeometries) {
+                if (crossGeometries.hasOwnProperty(i)) {
+                    var linewidth = i;
+                    var crossMaterial = new $3Dmol.LineBasicMaterial({
+                        linewidth : linewidth,
+                        vertexColors : true
+                    });
+                    if (opacities.cross < 1 && opacities.cross >= 0)
+                    {
+                        crossMaterial.transparent = true;
+                        crossMaterial.opacity = opacities.cross;
+                    }
+
+                    crossGeometries[i].initTypedArrays();
+                    
+                    var cross = new $3Dmol.Line(crossGeometries[i], crossMaterial,
+                            $3Dmol.LinePieces);
+
+                    ret.add(cross);
+                }
+            }
+            
+            //for BIOMT assembly
+            if (dontDuplicateAtoms && modelData.symmetries && modelData.symmetries.length > 0) {
+                var finalRet = new $3Dmol.Object3D();
+                var t;
+                for (t = 0; t < modelData.symmetries.length; t++) {
+                    var transformedRet = new $3Dmol.Object3D();
+                    transformedRet = ret.clone();
+                    transformedRet.matrix.copy(modelData.symmetries[t]);
+                    transformedRet.matrixAutoUpdate = false;
+                    finalRet.add(transformedRet);
+                }
+                return finalRet;
+            }
+
+            return ret;
+        };
+        
+        
+        this.getCrystData = function() {
+            if (modelData.cryst) {
+                return modelData.cryst;
+            }
+            else {
+                return null;
+            }
+        }
+        
+        /**
+         * Returns list of rotational/translational matrices if there is BIOMT data
+         * Otherwise returns a list of just the ID matrix
+         *
+         * @function $3Dmol.GlModel#getSymmetries
+         * @return {Array<$3Dmol.Matrix4>}
+         *
+         */
+        this.getSymmetries = function() {
+            
+            if (typeof(modelData.symmetries) == 'undefined') {
+                modelData.symmetries = [idMatrix];
+            }
+            return modelData.symmetries; 
+        };
+        
+        /**
+         * Sets symmetries based on specified matrices in list
+         *
+         * @function $3Dmol.GlModel#setSymmetries
+         * @param {Array<$3Dmol.Matrix4>} list
+         *
+         */
+        this.setSymmetries = function(list) {
+            if (typeof(list) == "undefined") { //delete sym data
+                modelData.symmetries = [idMatrix];
+            }
+            else {
+                modelData.symmetries = list;
+            }
+        };
+
+        /**
+         * Returns model id number
+         * 
+         * @function $3Dmol.GLModel#getID
+         * @return {number} Model ID
+         */
+        this.getID = function() {
+            return id;
+        };
+        
+        /**
+         * Returns model's frames property, a list of atom lists
+         * 
+         * @function $3Dmol.GLModel#getFrames
+         * @return {Array.<Object>}
+         */
+        this.getFrames = function() {
+            return frames;
+        };
+        
+        /**
+         * Sets model's atomlist to specified frame
+         * Sets to last frame if framenum out of range
+         * 
+         * @function $3Dmol.GLModel#setFrame
+         * @param {number} framenum - model's atoms are set to this index in frames list
+         */
+        this.setFrame = function(framenum) {
+            if (frames.length == 0) {
+                return;
+            }
+            if (framenum >= 0 && framenum < frames.length) {
+                atoms = frames[framenum];
+            }
+            else {
+                atoms = frames[frames.length-1];
+            }
+            molObj = null;
+        };
+        
+        /**
+         * Add atoms as frames of model
+         * 
+         * @function $3Dmol.GLModel#addFrame
+         * @param {AtomSpec} atom - atoms to be added
+         */
+        this.addFrame = function(atoms) {
+            frames.push(atoms);
+        };
+
+        
+        /**
+         * If model atoms have dx, dy, dz properties (in some xyz files), vibrate populates the model's frame property based on parameters.
+         * Model can then be animated
+         * 
+         * @function $3Dmol.GLModel#vibrate
+         * @param {number} numFrames - number of frames to be created, default to 10
+         * @param {number} amplitude - amplitude of distortion, default to 1 (full)
+         */
+        this.vibrate = function(numFrames, amplitude) {
+            var vectors = [];
+            var amplitude = amplitude || 1;
+            var numFrames = numFrames || 10; 
+            for (var i = 0; i < atoms.length; i++) {
+                var vector = new $3Dmol.Vector3(atoms[i].dx, atoms[i].dy, atoms[i].dz);
+                vectors.push(vector);
+            }
+            numFrames--;
+            for (var i = 1; i <= numFrames; i++) {
+                var newAtoms = [];
+                for (var j = 0; j < atoms.length; j++) {
+                    var newVector = new $3Dmol.Vector3(atoms[j].dx, atoms[j].dy, atoms[j].dz);
+                    var starting = new $3Dmol.Vector3(atoms[j].x, atoms[j].y, atoms[j].z);
+                    newVector.sub(starting);
+                    newVector.multiplyScalar((i*amplitude)/numFrames);
+                    starting.add(newVector);
+                    var newAtom = {};
+                    for (var k in atoms[j]) {
+                        newAtom[k] = atoms[j][k];
+                    }
+                    newAtom.x = starting.x;
+                    newAtom.y = starting.y;
+                    newAtom.z = starting.z;
+                    newAtoms.push(newAtom);
+                }
+                frames.push(newAtoms);
+            }
+            frames.unshift(atoms); //add 1st frame
+        };
+        
+        // set default style and colors for atoms
+        this.setAtomDefaults = function(atoms) {
+            for ( var i = 0; i < atoms.length; i++) {
+                var atom = atoms[i];
+                if (atom) {
+                    atom.style = atom.style || defaultAtomStyle;
+                    atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
+                    atom.model = id;
+                    if (atom.clickable)
+                        atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                }
+            }
+        };
+
+        /** add atoms to this model from molecular data string
+         * 
+         * @function $3Dmol.GLModel#addMolData
+         * @param {string|ArrayBuffer} data - atom structure file input data string, for gzipped input use ArrayBuffer
+         * @param {string} format - input file string format (e.g 'pdb', 'sdf', 'sdf.gz', etc.)
+         * @param {Object} options - format dependent options (e.g. 'options.keepH' to keep hydrogens)
+         */
+        this.addMolData = function(data, format, options) {
+            options = options || {};
+            var parsedAtoms = $3Dmol.GLModel.parseMolData(data, format, options);
+            dontDuplicateAtoms = !options.duplicateAssemblyAtoms;
+            var mData = parsedAtoms.modelData;
+            if (mData) {
+                if (Array.isArray(mData)) {
+                    modelData = mData[0];
+                } else {
+                    modelData = mData;
+                }
+            }
+
+            if (frames.length == 0) { //first call
+                for (var i = 0; i < parsedAtoms.length; i++) {
+                    if (parsedAtoms[i].length != 0)
+                        frames.push(parsedAtoms[i]);
+                }
+                if(frames[0])
+                    atoms = frames[0];
+            }
+            
+            else { //subsequent calls
+                if (options.frames) { //add to new frame
+                    for (var i = 0; i < parsedAtoms.length; i++) {
+                        frames.push(parsedAtoms[i]);
+                    }
+                }
+                else { //add atoms to current frame
+                    for (var i = 0; i < parsedAtoms.length; i++) {
+                        this.addAtoms(parsedAtoms[i]); 
+                    }
+                }
+            }
+            
+            for (var i = 0; i < frames.length; i++) {
+                this.setAtomDefaults(frames[i], id);
+            }
+
+        };
+
+        this.setDontDuplicateAtoms = function(dup) {
+            dontDuplicateAtoms = dup;
+        }
+
+        this.setModelData = function(mData) {
+            modelData = mData;
+        }
+        
+        /** given a selection specification, return true if atom is selected
+         * 
+         * @function $3Dmol.GLModel#atomIsSelected
+         * @param {AtomSpec} atom
+         * @param {AtomSelectionSpec} sel
+         * @return {boolean}
+         */
+        this.atomIsSelected = function(atom, sel) {
+            if (typeof (sel) === "undefined")
+                return true; // undef gets all
+            var invert = !!sel.invert;
+            var ret = true;
+            for ( var key in sel) {
+                if(key === 'predicate') { //a user supplied function for evaluating atoms
+                    if(!sel['predicate'](atom) ) {
+                        ret = false;
+                        break;
+                    }
+                }
+                else if(key == "properties" && atom[key]) {
+                    for (var propkey in sel.properties) {
+                        if(typeof(atom.properties[propkey]) === 'undefined') {
+                            ret = false;
+                            break
+                        }
+                        if(atom.properties[propkey] != sel.properties[propkey]) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                }
+                else if (sel.hasOwnProperty(key) && key != "props" && key != "invert" && key != "model" && key != "byres" && key != "expand" && key != "within") {
+
+                    // if something is in sel, atom must have it                    
+                    if (typeof (atom[key]) === "undefined") {
+                        ret = false;
+                        break;
+                    }
+                    var isokay = false;
+                    if(key === "bonds") {
+                        //special case counting number of bonds, for selecting nonbonded mostly
+                        var val = sel[key];
+                        if(val != atom.bonds.length) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                    else if ($.isArray(sel[key])) {
+                        // can be any of the listed values
+                        var valarr = sel[key];
+                        for ( var i = 0; i < valarr.length; i++) {
+                            if (atom[key] == valarr[i]) {
+                                isokay = true;
+                                break;
+                            }
+                        }
+                        if (!isokay) {
+                            ret = false;
+                            break;
+                        }
+                    } else { // single match
+                        var val = sel[key];
+                        if (atom[key] != val) {
+                            ret = false;
+                            break;
+                        }
+                    }
+                }
+            }
+            
+            return invert ? !ret : ret;
+        };
+
+
+        /** return list of atoms selected by sel, this is specific to glmodel
+         * 
+         * @function $3Dmol.GLModel#selectedAtoms
+         * @param {AtomSelectionSpec} sel
+         * @return {Array.<Object>}
+         */
+        this.selectedAtoms = function(sel, from) {
+            var ret = [];
+            sel = sel || {};
+            if (!from) from = atoms;
+            var aLength = from.length;
+            for ( var i = 0; i < aLength; i++) {
+                var atom = from[i];
+                if (atom) {
+                    if (this.atomIsSelected(atom, sel))
+                        ret.push(atom);
+                }
+            }
+
+            // expand selection by some distance
+            if (sel.hasOwnProperty("expand")) {
+
+                // get atoms in expanded bounding box
+
+                var expand = expandAtomList(ret, parseFloat(sel.expand));
+                var retlen = ret.length;
+                for (var i = 0; i < expand.length; i++) {
+                    for (var j = 0; j < retlen; j++) {
+
+                        var dist = squaredDistance(expand[i], ret[j]);
+                        var thresh = Math.pow(sel.expand, 2);
+                        if (dist < thresh && dist > 0) {
+                            ret.push(expand[i]);
+                        }
+                    }
+                }
+            }
+
+            // selection within distance of sub-selection
+            if (sel.hasOwnProperty("within") && sel.within.hasOwnProperty("sel") && sel.within.hasOwnProperty("distance")) {
+
+                // get atoms in second selection
+                var sel2 = this.selectedAtoms(sel.within.sel, atoms);
+                var within = [];
+                for (var i = 0; i < sel2.length; i++) {
+                    for (var j = 0; j < ret.length; j++) {
+
+                        var dist = squaredDistance(sel2[i], ret[j]);
+                        var thresh = Math.pow(parseFloat(sel.within.distance), 2);
+                        if (dist < thresh && dist > 0) {
+                            within.push(ret[j]);
+                        }
+                    }
+                }
+                ret = within;
+            }
+
+            // byres selection flag
+            if (sel.hasOwnProperty("byres")) {
+
+                // Keep track of visited residues, visited atoms, and atom stack
+                var vResis = {};
+                var vAtoms = [];
+                var stack = [];
+
+                for (var i = 0; i < ret.length; i++) {
+                    
+                    // Check if atom is part of a residue, and that the residue hasn't been traversed yet
+                    var atom = ret[i];
+                    var c = atom.chain;
+                    var r = atom.resi;
+                    if (vResis[c] === undefined) vResis[c] = {};
+                    if (atom.hasOwnProperty("resi") && vResis[c][r] === undefined) {
+
+                        // Perform a depth-first search of atoms with the same resi
+                        vResis[c][r] = true;
+                        stack.push(atom);
+                        while(stack.length > 0) {
+                            atom = stack.pop();
+                            c = atom.chain;
+                            r = atom.resi;
+                            if (vAtoms[atom.index] === undefined) {
+                                vAtoms[atom.index] = true;
+                                for (var j = 0; j < atom.bonds.length; j++) {
+                                    var atom2 = atoms[atom.bonds[j]];
+                                    if (vAtoms[atom2.index] === undefined && atom2.hasOwnProperty("resi") && atom2.chain == c && atom2.resi == r) {
+                                        stack.push(atom2);
+                                        ret.push(atom2);
+                                    }
+                                }
+                            }
+                        }
+                    }   
+                }
+            }
+
+            return ret;
+        };
+
+        var squaredDistance = function(atom1, atom2) {
+            var xd = atom2.x - atom1.x;
+            var yd = atom2.y - atom1.y;
+            var zd = atom2.z - atom1.z;
+            return (Math.pow(xd, 2) + Math.pow(yd, 2) + Math.pow(zd, 2));
+        };
+
+        /** returns a list of atoms in the expanded bounding box, but not in the current one
+         *
+         *  Bounding box:
+         *
+         *    [ [ xmin, ymin, zmin ],
+         *      [ xmax, ymax, zmax ],
+         *      [ xctr, yctr, zctr ] ]
+         *
+         **/
+        var expandAtomList = function(atomList, amt) {
+
+            if (amt <= 0) return atomList;
+
+            var pb = $3Dmol.getExtent(atomList); // previous bounding box
+            var nb = [[], [], []]; // expanded bounding box
+
+            for (var i = 0; i < 3; i++)
+            {
+                nb[0][i] = pb[0][i]-amt;
+                nb[1][i] = pb[1][i]+amt;
+                nb[2][i] = pb[2][i];
+            }
+
+            // look in added box "shell" for new atoms
+            var expand = [];
+            for (var i = 0; i < atoms.length; i++) {
+
+                var x = atoms[i].x;
+                var y = atoms[i].y;
+                var z = atoms[i].z;
+
+                if (x >= nb[0][0] && x <= nb[1][0] && y >= nb[0][1] && y <= nb[1][1] && z >= nb[0][2] && z <= nb[1][2]) {
+                    if (!(x >= pb[0][0] && x <= pb[1][0] && y >= pb[0][1] && y <= pb[1][1] && z >= pb[0][2] && z <= pb[1][2])) {
+                        expand.push(atoms[i]);
+                    }
+                }
+            }
+            return expand;
+        };
+        
+        /** Add list of new atoms to model.  Adjusts bonds appropriately.
+         * 
+         * @function $3Dmol.GLModel#addAtoms
+         * @param {type} newatoms
+         */        
+        this.addAtoms = function(newatoms) {
+            molObj = null;
+            var start = atoms.length;
+            var indexmap = [];
+            // mapping from old index to new index
+            var i;
+            for(i = 0; i < newatoms.length; i++) {
+                if(typeof(newatoms[i].index) == "undefined")
+                    newatoms[i].index = i;
+                if(typeof(newatoms[i].serial) == "undefined")
+                    newatoms[i].serial = i;
+                indexmap[newatoms[i].index] = start+i;
+            }
+            
+            // copy and push newatoms onto atoms
+            for(i = 0; i < newatoms.length; i++) {
+                var olda = newatoms[i];
+                var nindex = indexmap[olda.index];
+                var a = $.extend(false, {}, olda);
+                a.index = nindex;
+                a.bonds = [];
+                a.bondOrder = [];
+                a.model = id;
+                a.style = a.style || defaultAtomStyle;
+                if(typeof(a.color) == "undefined")
+                    a.color = ElementColors[a.elem] || defaultColor;                
+                // copy over all bonds contained in selection,
+                // updating indices appropriately
+                var nbonds = olda.bonds ? olda.bonds.length : 0;
+                for(var j = 0; j < nbonds; j++) {
+                    var neigh = indexmap[olda.bonds[j]];
+                    if(typeof(neigh) != "undefined") {
+                        a.bonds.push(neigh);
+                        a.bondOrder.push(olda.bondOrder ? olda.bondOrder[j] : 1);
+                    }                
+                }
+                atoms.push(a);
+            }
+        };
+
+        /** Remove specified atoms from model
+         * 
+         * @function $3Dmol.GLModel#removeAtoms
+         * @param {type} badatoms
+         * @return {removeAtoms}
+         */
+        this.removeAtoms = function(badatoms) {
+            molObj = null;
+            // make map of all baddies
+            var baddies = [];
+            var i;
+            for(i = 0; i < badatoms.length; i++) {
+                baddies[badatoms[i].index] = true;
+            }
+            
+            // create list of good atoms
+            var newatoms = [];
+            for(i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                if(!baddies[a.index])
+                    newatoms.push(a);
+            }
+            
+            // clear it all out
+            atoms = [];
+            // and add back in to get updated bonds
+            this.addAtoms(newatoms);
+        };
+        
+        
+        /** Set atom style of selected atoms
+         * 
+         * @function $3Dmol.GLModel#setStyle
+         * @param {AtomSelectionSpec} sel
+         * @param {AtomStyleSpec} style
+         * @param {boolean} add - if true, add to current style, don't replace
+         */
+        this.setStyle = function(sel, style, add) {
+            
+            if(typeof(style) === 'undefined' && typeof(add) == 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            
+            // report to console if this is not a valid selector
+            var s;
+            for (s in sel) {
+                if(validAtomSelectionSpecs.indexOf(s) === -1) {
+                    console.log('Unknown selector ' + s);
+                }
+            }
+            // report to console if this is not a valid style
+            for (s in style) {
+                if(validAtomStyleSpecs.indexOf(s) === -1) {
+                    console.log('Unknown style ' + s);
+                }
+            }
+
+            var changedAtoms = false;
+            // somethings we only calculate if there is a change in a certain
+            // style, although these checks will only catch cases where both
+            // are either null or undefined
+            
+            var setStyleHelper = function(atomArr) {
+                var selected = that.selectedAtoms(sel, atomArr);
+                for (var i = 0; i < atomArr.length; i++) {
+                    if (atomArr[i]) atomArr[i].capDrawn = false; //reset for proper stick render
+                }
+            
+                for ( var i = 0; i < selected.length; i++) {                
+                    changedAtoms = true;
+                    if (selected[i].clickable) 
+                        selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};                    
+                   
+
+                    if(!add) selected[i].style = {};
+                    for(s in style) {
+                        if(style.hasOwnProperty(s)) {
+                            selected[i].style[s]=selected[i].style[s]||{}; //create distinct object for each atom
+                            for(var prop in style[s]){
+                                selected[i].style[s][prop]=style[s][prop];
+                            }
+                        }
+                    }
+                }
+            }
+            
+            var that = this;
+            setStyleHelper(atoms);
+            for (var i = 0; i < frames.length; i++) {
+                setStyleHelper(frames[i]);
+            }
+            
+            if (changedAtoms)
+                molObj = null; //force rebuild
+            
+        };
+
+        /** Set clickable and callback of selected atoms
+         * 
+         * @function $3Dmol.GLModel#setClickable
+         * @param {AtomSelectionSpec} sel - atom selection to apply clickable settings to
+         * @param {boolean} clickable - whether click-handling is enabled for the selection
+         * @param {function} callback - function called when an atom in the selection is clicked
+         */
+        this.setClickable = function(sel, clickable, callback) {           
+
+            // report to console if this is not a valid selector
+            var s;
+            for (s in sel) {
+                if (validAtomSelectionSpecs.indexOf(s) === -1) {
+                    console.log('Unknown selector ' + s);
+                }
+            }
+
+            // make sure clickable is a boolean
+            clickable = !!clickable;
+
+            // report to console if callback is not a valid function
+            if (callback && typeof callback != "function") {
+                console.log("Callback is not a function");
+                return;
+            }
+
+            var i;
+            var selected = this.selectedAtoms(sel, atoms);
+            var len = selected.length;
+            for (i = 0; i < len; i++) {                
+
+                selected[i].intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+                selected[i].clickable = clickable;
+                if (callback) selected[i].callback = callback;
+
+            }
+
+            if (len > 0) molObj = null; // force rebuild to get correct intersection shapes         
+        };
+        
+        /** given a mapping from element to color, set atom colors
+         * 
+         * @function $3Dmol.GLModel#setColorByElement
+         * @param {type} sel
+         * @param {type} colors
+         */
+        this.setColorByElement = function(sel, colors) {
+            
+            if(molObj !== null && sameObj(colors,lastColors))
+                return; // don't recompute
+            lastColors = colors;
+            var atoms = this.selectedAtoms(sel, atoms);
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            for ( var i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                if(typeof(colors[a.elem]) !== "undefined") {
+                    a.color = colors[a.elem];
+                }
+            }
+        };
+        
+        /**
+         * @function $3Dmol.GLModel.setColorByProperty
+         * @param {type} sel
+         * @param {type} prop
+         * @param {type} scheme
+         */
+        this.setColorByProperty = function(sel, prop, scheme, range) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            lastColors = null; // don't bother memoizing
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            var min =  Number.POSITIVE_INFINITY;
+            var max =  Number.NEGATIVE_INFINITY;
+            var i, a;
+            
+            if(!range) { //no explicit range, get from scheme
+                range = scheme.range();
+            }
+            
+            if(!range) { //no range in scheme, compute the range for this model
+                range = $3Dmol.getPropertyRange(atoms, prop);
+            }
+            // now apply colors using scheme
+            for (i = 0; i < atoms.length; i++) {
+                a = atoms[i];
+                var val = $3Dmol.getAtomProperty(a, prop);
+                if(val != null) {
+                    a.color = scheme.valueToHex(parseFloat(a.properties[prop]), [range[0],range[1]]);
+                }                    
+            }
+        };
+        
+        /**
+         * @function $3Dmol.GLModel.setColorByFunction
+         * @param {type} sel
+         * @param {type} func
+         */
+        this.setColorByFunction = function(sel, colorfun) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            lastColors = null; // don't bother memoizing
+            if(atoms.length > 0)
+                molObj = null; // force rebuild
+            
+            // now apply colorfun
+            for (i = 0; i < atoms.length; i++) {
+                a = atoms[i];
+                a.color = colorfun(a);
+            }
+        };
+
+        /** Convert the model into an object in the format of a ChemDoodle JSON model.
+         *
+         * @function $3Dmol.GLModel#toCDObject
+         * @param {boolean} whether or not to include style information. Defaults to false.
+         * @return {Object}
+         */
+        this.toCDObject = function(includeStyles) {
+            var out = { a:[], b:[] };
+            if (includeStyles) {
+                out.s = [];
+            }
+            for (var i = 0; i < atoms.length; i++) {
+                var atomJSON = {};
+                var atom = atoms[i];
+                atomJSON.x = atom.x;
+                atomJSON.y = atom.y;
+                atomJSON.z = atom.z;
+                if (atom.elem != "C") {
+                    atomJSON.l = atom.elem;
+                }
+                if (includeStyles) {
+                    var s = 0;
+                    while (s < out.s.length &&
+                          (JSON.stringify(atom.style) !== JSON.stringify(out.s[s]))) {
+                        s++;
+                    }
+                    if (s === out.s.length) {
+                        out.s.push(atom.style);
+                    }
+                    if (s !== 0) {
+                        atomJSON.s = s;
+                    }
+                }
+                
+                out.a.push(atomJSON);
+
+                for (var b = 0; b < atom.bonds.length; b++) {
+                    var firstAtom = i;
+                    var secondAtom = atom.bonds[b];
+                    if (firstAtom >= secondAtom)
+                        continue;
+                    var bond = {
+                        b: firstAtom,
+                        e: secondAtom
+                    };
+                    var bondOrder =  atom.bondOrder[b];
+                    if (bondOrder != 1) {
+                        bond.o = bondOrder;
+                    }
+                    out.b.push(bond);
+                }
+            }
+            return out;
+        }
+
+
+        /** manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
+         * 
+         * @function $3Dmol.GLModel#globj
+         * @param {$3Dmol.Object3D} group
+         * @param Object options
+         */
+        this.globj = function(group, options) {
+            var time = new Date();
+            if(molObj === null) { // have to regenerate
+                molObj = createMolObj(atoms, options);
+                var time2 = new Date();
+                //console.log("object creation time: " + (time2 - time));
+                if(renderedMolObj) { // previously rendered, remove
+                    group.remove(renderedMolObj);
+                    renderedMolObj = null;
+                }
+                renderedMolObj = molObj.clone();
+                if(hidden) {
+                    renderedMolObj.setVisible(false);
+                    molObj.setVisible(false);
+                }
+                group.add(renderedMolObj);              
+            }
+        };
+        
+        /** Remove any renderable mol object from scene
+         * 
+         * @function $3Dmol.GLModel#removegl
+         * @param {$3Dmol.Object3D} group
+         */
+        this.removegl = function(group) {
+            if(renderedMolObj) {
+                //dispose of geos and materials
+                if (renderedMolObj.geometry !== undefined) renderedMolObj.geometry.dispose();             
+                if (renderedMolObj.material !== undefined) renderedMolObj.material.dispose();
+                group.remove(renderedMolObj);
+                renderedMolObj = null;
+            }
+            molObj = null;
+        };
+        
+        /** Don't show this model is future renderings.  Keep all styles and state
+         * so it can be efficiencly shown again.
+         * 
+         * @function $3Dmol.GLModel#hide
+         */
+        this.hide = function() {
+            hidden = true;
+            if(renderedMolObj) renderedMolObj.setVisible(false);
+            if(molObj) molObj.setVisible(false);
+        }
+        
+        this.show = function() {
+            hidden = false;
+            if(renderedMolObj) renderedMolObj.setVisible(true);
+            if(molObj) molObj.setVisible(true);
+        }
+        
+        /** Create labels for residues of selected atoms.
+         * Will create a single label at the center of mass of all atoms
+         * with the same chain,resn, and resi.
+         * @function $3Dmol.GLModel#addResLabels
+         * 
+         * @param {AtomSelectionSpec} sel
+         * @param {$3Dmol.GLViewer} viewer
+         */
+        this.addResLabels = function(sel, viewer, style) {
+            var atoms = this.selectedAtoms(sel, atoms);
+            var bylabel = {}
+            //collect by chain:resn:resi
+            for(var i = 0; i < atoms.length; i++) {
+                var a = atoms[i];
+                var c = a.chain;
+                var resn = a.resn;
+                var resi = a.resi;
+                var label =  resn + '' + resi;
+                if(!bylabel[c]) bylabel[c] = {};
+                if(!bylabel[c][label]) bylabel[c][label] = []
+                bylabel[c][label].push(a);
+            }
+            
+            var mystyle = $.extend(true, {}, style);
+            //now compute centers of mass
+            for(var c in bylabel) {
+                if(bylabel.hasOwnProperty(c)) {
+                    var labels = bylabel[c];
+                    for(var label in labels) {
+                        if(labels.hasOwnProperty(label)) {
+                            var atoms = labels[label];
+                            var sum = new $3Dmol.Vector3(0,0,0);
+                            for(var i = 0; i < atoms.length; i++) {
+                                var a = atoms[i];
+                                sum.x += a.x;
+                                sum.y += a.y;
+                                sum.z += a.z;
+                            }
+                            sum.divideScalar(atoms.length);
+                            mystyle.position = sum;
+                            viewer.addLabel(label, mystyle);
+                        }                        
+                    }
+                }
+            }
+        }
+
+    }
+
+    GLModel.parseMolData = function(data, format, options) {
+        format = format || "";
+
+        if (!data)
+            return []; //leave an empty model
+
+        if(/\.gz$/.test(format)) {
+            //unzip gzipped files
+            format = format.replace(/\.gz$/,'');
+            try {
+                data = pako.inflate(data, {to: 'string'});
+            } catch(err) {
+                console.log(err);
+            }
+        }
+
+        if(typeof($3Dmol.Parsers[format]) == "undefined") {
+            //let someone provide a file name and get format from extension
+            format = format.split('.').pop();
+            if(typeof($3Dmol.Parsers[format]) == "undefined") {
+                console.log("Unknown format: "+format);
+                //try to guess correct format from data contents
+                if(data.match(/^@<TRIPOS>MOLECULE/gm)) {
+                    format = "mol2";
+                } else if(data.match(/^HETATM/gm) || data.match(/^ATOM/gm)) {
+                    format = "pdb";
+                } else if(data.match(/^.*\n.*\n.\s*(\d+)\s+(\d+)/gm)){
+                    format = "sdf"; //could look at line 3
+                } else {
+                    format = "xyz";
+                }
+                console.log("Best guess: "+format);
+            }
+        }
+        var parse = $3Dmol.Parsers[format];
+        var parsedAtoms = parse(data, options);
+
+        return parsedAtoms;
+    };
+
+
+    // set default style and colors for atoms
+    GLModel.setAtomDefaults = function(atoms, id) {
+        for ( var i = 0; i < atoms.length; i++) {
+            var atom = atoms[i];
+            if (atom) {
+                atom.style = atom.style || defaultAtomStyle;
+                atom.color = atom.color || ElementColors[atom.elem] || defaultColor;
+                atom.model = id;
+                if (atom.clickable)
+                    atom.intersectionShape = {sphere : [], cylinder : [], line : [], triangle : []};
+            }
+        }
+    };
+
+    return GLModel;
+    
+})();
+/**
+ * A GLShape is a collection of user specified shapes.
+ * 
+ * @constructor $3Dmol.GLShape
+ * @extends {ShapeSpec}
+ * @param {number} sid - Unique identifier
+ * @param {ShapeSpec} stylespec - shape style specification
+ */
+$3Dmol.GLShape = (function() {
+
+    // Marching cube, to match with protein surface generation
+    var ISDONE = 2;
+
+    
+    var finalizeGeo = function(geo) {
+        //to avoid creating a bunch of geometries, we leave geoGroup untruncated
+        //until render is called, at which point we truncate; 
+        //successive called up updateGeo will return a new geometry
+        var geoGroup = geo.updateGeoGroup(0);
+        if(geoGroup.vertices > 0) {
+            geoGroup.truncateArrayBuffers(true, true);
+        }
+    };
+    
+    /**
+     * 
+     * @param {$3Dmol.Geometry}
+     *            geo
+     * @param {$3Dmol.Color |
+     *            colorlike} color
+     */
+    var updateColor = function(geo, color) {
+
+        var C = color || $3Dmol.CC.color(color);
+        geo.colorsNeedUpdate = true;
+        
+        var r,g,b;
+        if(! (color.constructor === Array)) {
+            r = color.r;
+            g = color.g;
+            b = color.b;
+        }
+
+
+        for ( var gg in geo.geometryGroups) {
+
+            var geoGroup = geo.geometryGroups[gg];
+            var colorArr = geoGroup.colorArray;
+
+            for (var i = 0, il = geoGroup.vertices; i < il; ++i) {
+            
+                if( color.constructor === Array) {
+                    var c = color[i];
+                    r = c.r;
+                    g = c.g;
+                    b = c.b;
+                }
+
+                colorArr[i * 3] = r;
+                colorArr[i * 3 + 1] = g;
+                colorArr[i * 3 + 2] = b;
+            }
+        }
+
+    };
+
+
+    /**
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {geometryGroup}
+     *            geoGroup
+     * @param {ArrowSpec}
+     *            spec
+     */
+    var drawArrow = function(shape, geo, spec) {
+
+        var from = spec.start, end = spec.end, radius = spec.radius, radiusRatio = spec.radiusRatio, mid = spec.mid;
+
+        if (!(from && end))
+            return;
+
+        var geoGroup = geo.updateGeoGroup(51);
+
+        // vertices
+
+        var dir = end.clone();
+        dir.sub(from).multiplyScalar(mid);
+        var to = from.clone().add(dir);
+        var negDir = dir.clone().negate();
+
+        shape.intersectionShape.cylinder.push(new $3Dmol.Cylinder(from.clone(),
+                to.clone(), radius));
+        shape.intersectionShape.sphere.push(new $3Dmol.Sphere(from.clone(),
+                radius));
+
+        // get orthonormal vector
+        var nvecs = [];
+        nvecs[0] = dir.clone();
+        if (Math.abs(nvecs[0].x) > 0.0001)
+            nvecs[0].y += 1;
+        else
+            nvecs[0].x += 1;
+        nvecs[0].cross(dir);
+        nvecs[0].normalize();
+
+        nvecs[0] = nvecs[0];
+        // another orth vector
+        nvecs[4] = nvecs[0].clone();
+        nvecs[4].crossVectors(nvecs[0], dir);
+        nvecs[4].normalize();
+        nvecs[8] = nvecs[0].clone().negate();
+        nvecs[12] = nvecs[4].clone().negate();
+
+        // now quarter positions
+        nvecs[2] = nvecs[0].clone().add(nvecs[4]).normalize();
+        nvecs[6] = nvecs[4].clone().add(nvecs[8]).normalize();
+        nvecs[10] = nvecs[8].clone().add(nvecs[12]).normalize();
+        nvecs[14] = nvecs[12].clone().add(nvecs[0]).normalize();
+
+        // eights
+        nvecs[1] = nvecs[0].clone().add(nvecs[2]).normalize();
+        nvecs[3] = nvecs[2].clone().add(nvecs[4]).normalize();
+        nvecs[5] = nvecs[4].clone().add(nvecs[6]).normalize();
+        nvecs[7] = nvecs[6].clone().add(nvecs[8]).normalize();
+        nvecs[9] = nvecs[8].clone().add(nvecs[10]).normalize();
+        nvecs[11] = nvecs[10].clone().add(nvecs[12]).normalize();
+        nvecs[13] = nvecs[12].clone().add(nvecs[14]).normalize();
+        nvecs[15] = nvecs[14].clone().add(nvecs[0]).normalize();
+
+        var start = geoGroup.vertices;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        var faceArray = geoGroup.faceArray;
+        var normalArray = geoGroup.normalArray;
+        var lineArray = geoGroup.lineArray;
+
+        var offset, i, n;
+        // add vertices, opposing vertices paired together
+        for (i = 0, n = nvecs.length; i < n; ++i) {
+            offset = 3 * (start + 3 * i);
+            var bottom = nvecs[i].clone().multiplyScalar(radius).add(from);
+            var top = nvecs[i].clone().multiplyScalar(radius).add(to);
+            var conebase = nvecs[i].clone()
+                    .multiplyScalar(radius * radiusRatio).add(to);
+
+            vertexArray[offset] = bottom.x;
+            vertexArray[offset + 1] = bottom.y;
+            vertexArray[offset + 2] = bottom.z;
+
+            vertexArray[offset + 3] = top.x;
+            vertexArray[offset + 4] = top.y;
+            vertexArray[offset + 5] = top.z;
+
+            vertexArray[offset + 6] = conebase.x;
+            vertexArray[offset + 7] = conebase.y;
+            vertexArray[offset + 8] = conebase.z;
+
+            if (i > 0) {
+                var prev_x = vertexArray[offset - 3];
+                var prev_y = vertexArray[offset - 2];
+                var prev_z = vertexArray[offset - 1];
+
+                var c = new $3Dmol.Vector3(prev_x, prev_y, prev_z);
+                var b = end.clone(), b2 = to.clone();
+                var a = new $3Dmol.Vector3(conebase.x, conebase.y, conebase.z);
+
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(a, b,
+                        c));
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(c
+                        .clone(), b2, a.clone()));
+            }
+        }
+
+        geoGroup.vertices += 48;
+        offset = geoGroup.vertices * 3;
+
+        // caps
+        vertexArray[offset] = from.x;
+        vertexArray[offset + 1] = from.y;
+        vertexArray[offset + 2] = from.z;
+
+        vertexArray[offset + 3] = to.x;
+        vertexArray[offset + 4] = to.y;
+        vertexArray[offset + 5] = to.z;
+
+        vertexArray[offset + 6] = end.x;
+        vertexArray[offset + 7] = end.y;
+        vertexArray[offset + 8] = end.z;
+
+        geoGroup.vertices += 3;
+
+        // now faces
+        var face, norm, faceoffset, lineoffset;
+        var t1, t2, t2b, t3, t3b, t4, t1offset, t2offset, t2boffset, t3offset, t3boffset, t4offset;
+        var n1, n2, n3, n4;
+        var n_vertices = 0;
+        var fromi = geoGroup.vertices - 3, toi = geoGroup.vertices - 2, endi = geoGroup.vertices - 1;
+        var fromoffset = fromi * 3, tooffset = toi * 3, endoffset = endi * 3;
+        for (i = 0, n = nvecs.length - 1; i < n; ++i) {
+
+            var ti = start + 3 * i;
+            offset = ti * 3;
+            faceoffset = geoGroup.faceidx;
+            lineoffset = geoGroup.lineidx;
+
+            t1 = ti;
+            t1offset = t1 * 3;
+            t2 = ti + 1;
+            t2offset = t2 * 3;
+            t2b = ti + 2;
+            t2boffset = t2b * 3;
+            t3 = ti + 4;
+            t3offset = t3 * 3;
+            t3b = ti + 5;
+            t3boffset = t3b * 3;
+            t4 = ti + 3;
+            t4offset = t4 * 3;
+
+            // face = [t1, t2, t4], [t2, t3, t4];
+            // face = [t1, t2, t3, t4];
+
+            norm = [ nvecs[i], nvecs[i], nvecs[i + 1], nvecs[i + 1] ];
+
+            n1 = n2 = nvecs[i];
+            n3 = n4 = nvecs[i + 1];
+
+            normalArray[t1offset] = n1.x;
+            normalArray[t2offset] = n2.x;
+            normalArray[t4offset] = n4.x;
+            normalArray[t1offset + 1] = n1.y;
+            normalArray[t2offset + 1] = n2.y;
+            normalArray[t4offset + 1] = n4.y;
+            normalArray[t1offset + 2] = n1.z;
+            normalArray[t2offset + 2] = n2.z;
+            normalArray[t4offset + 2] = n4.z;
+
+            normalArray[t2offset] = n2.x;
+            normalArray[t3offset] = n3.x;
+            normalArray[t4offset] = n4.x;
+            normalArray[t2offset + 1] = n2.y;
+            normalArray[t3offset + 1] = n3.y;
+            normalArray[t4offset + 1] = n4.y;
+            normalArray[t2offset + 2] = n2.z;
+            normalArray[t3offset + 2] = n3.z;
+            normalArray[t4offset + 2] = n4.z;
+
+            normalArray[t2boffset] = n2.x;
+            normalArray[t3boffset] = n3.x;
+            normalArray[t2boffset + 1] = n2.y;
+            normalArray[t3boffset + 1] = n3.y;
+            normalArray[t2boffset + 2] = n2.z;
+            normalArray[t3boffset + 2] = n3.z;
+
+            // sides
+            faceArray[faceoffset] = t1;
+            faceArray[faceoffset + 1] = t2;
+            faceArray[faceoffset + 2] = t4;
+            faceArray[faceoffset + 3] = t2;
+            faceArray[faceoffset + 4] = t3;
+            faceArray[faceoffset + 5] = t4;
+            // caps
+            faceArray[faceoffset + 6] = t1;
+            faceArray[faceoffset + 7] = t4;
+            faceArray[faceoffset + 8] = fromi;
+            faceArray[faceoffset + 9] = t2b;
+            faceArray[faceoffset + 10] = toi;
+            faceArray[faceoffset + 11] = t3b;
+            // arrowhead
+            faceArray[faceoffset + 12] = t2b;
+            faceArray[faceoffset + 13] = endi;
+            faceArray[faceoffset + 14] = t3b;
+
+            // sides
+            lineArray[lineoffset] = t1;
+            lineArray[lineoffset + 1] = t2;
+            lineArray[lineoffset + 2] = t1;
+            lineArray[lineoffset + 3] = t4;
+            // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
+            lineArray[lineoffset + 4] = t3;
+            lineArray[lineoffset + 5] = t4;
+            // caps
+            lineArray[lineoffset + 6] = t1;
+            lineArray[lineoffset + 7] = t4;
+            // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
+            // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+
+            lineArray[lineoffset + 8] = t2b;
+            lineArray[lineoffset + 9] = t2; // toi
+            lineArray[lineoffset + 10] = t2b;
+            lineArray[lineoffset + 11] = t3b;
+            lineArray[lineoffset + 12] = t3;
+            lineArray[lineoffset + 13] = t3b; // toi
+            // arrowhead
+            lineArray[lineoffset + 14] = t2b;
+            lineArray[lineoffset + 15] = endi;
+            lineArray[lineoffset + 16] = t2b;
+            lineArray[lineoffset + 17] = t3b;
+            lineArray[lineoffset + 18] = endi;
+            lineArray[lineoffset + 19] = t3b;
+
+            geoGroup.faceidx += 15;
+            geoGroup.lineidx += 20;
+
+        }
+        // final face
+
+        face = [ start + 45, start + 46, start + 1, start, start + 47,
+                start + 2 ];
+        norm = [ nvecs[15], nvecs[15], nvecs[0], nvecs[0] ];
+
+        faceoffset = geoGroup.faceidx;
+        lineoffset = geoGroup.lineidx;
+
+        t1 = face[0];
+        t1offset = t1 * 3;
+        t2 = face[1];
+        t2offset = t2 * 3;
+        t2b = face[4];
+        t2boffset = t2b * 3;
+        t3 = face[2];
+        t3offset = t3 * 3;
+        t3b = face[5];
+        t3boffset = t3b * 3;
+        t4 = face[3];
+        t4offset = t4 * 3;
+
+        n1 = n2 = nvecs[15];
+        n3 = n4 = nvecs[0];
+
+        normalArray[t1offset] = n1.x;
+        normalArray[t2offset] = n2.x;
+        normalArray[t4offset] = n4.x;
+        normalArray[t1offset + 1] = n1.y;
+        normalArray[t2offset + 1] = n2.y;
+        normalArray[t4offset + 1] = n4.y;
+        normalArray[t1offset + 2] = n1.z;
+        normalArray[t2offset + 2] = n2.z;
+        normalArray[t4offset + 2] = n4.z;
+
+        normalArray[t2offset] = n2.x;
+        normalArray[t3offset] = n3.x;
+        normalArray[t4offset] = n4.x;
+        normalArray[t2offset + 1] = n2.y;
+        normalArray[t3offset + 1] = n3.y;
+        normalArray[t4offset + 1] = n4.y;
+        normalArray[t2offset + 2] = n2.z;
+        normalArray[t3offset + 2] = n3.z;
+        normalArray[t4offset + 2] = n4.z;
+
+        normalArray[t2boffset] = n2.x;
+        normalArray[t3boffset] = n3.x;
+        normalArray[t2boffset + 1] = n2.y;
+        normalArray[t3boffset + 1] = n3.y;
+        normalArray[t2boffset + 2] = n2.z;
+        normalArray[t3boffset + 2] = n3.z;
+
+        // Cap normals
+        dir.normalize();
+        negDir.normalize();
+        normalArray[fromoffset] = negDir.x;
+        normalArray[tooffset] = normalArray[endoffset] = dir.x;
+        normalArray[fromoffset + 1] = negDir.y;
+        normalArray[tooffset + 1] = normalArray[endoffset + 1] = dir.y;
+        normalArray[fromoffset + 2] = negDir.z;
+        normalArray[tooffset + 2] = normalArray[endoffset + 2] = dir.z;
+
+        // Final side
+        faceArray[faceoffset] = t1;
+        faceArray[faceoffset + 1] = t2;
+        faceArray[faceoffset + 2] = t4;
+        faceArray[faceoffset + 3] = t2;
+        faceArray[faceoffset + 4] = t3;
+        faceArray[faceoffset + 5] = t4;
+        // final caps
+        faceArray[faceoffset + 6] = t1;
+        faceArray[faceoffset + 7] = t4;
+        faceArray[faceoffset + 8] = fromi;
+        faceArray[faceoffset + 9] = t2b;
+        faceArray[faceoffset + 10] = toi;
+        faceArray[faceoffset + 11] = t3b;
+        // final arrowhead
+        faceArray[faceoffset + 12] = t2b;
+        faceArray[faceoffset + 13] = endi;
+        faceArray[faceoffset + 14] = t3b;
+
+        // sides
+        lineArray[lineoffset] = t1;
+        lineArray[lineoffset + 1] = t2;
+        lineArray[lineoffset + 2] = t1;
+        lineArray[lineoffset + 3] = t4;
+        // lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
+        lineArray[lineoffset + 4] = t3;
+        lineArray[lineoffset + 5] = t4;
+        // caps
+        lineArray[lineoffset + 6] = t1;
+        lineArray[lineoffset + 7] = t4;
+        // lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
+        // lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
+
+        lineArray[lineoffset + 8] = t2b;
+        lineArray[lineoffset + 9] = t2; // toi
+        lineArray[lineoffset + 10] = t2b;
+        lineArray[lineoffset + 11] = t3b;
+        lineArray[lineoffset + 12] = t3;
+        lineArray[lineoffset + 13] = t3b; // toi
+        // arrowhead
+        lineArray[lineoffset + 14] = t2b;
+        lineArray[lineoffset + 15] = endi;
+        lineArray[lineoffset + 16] = t2b;
+        lineArray[lineoffset + 17] = t3b;
+        lineArray[lineoffset + 18] = endi;
+        lineArray[lineoffset + 19] = t3b;
+
+        geoGroup.faceidx += 15;
+        geoGroup.lineidx += 20;
+
+    };
+
+    //helper function for adding an appropriately sized mesh
+    var addCustomGeo = function(shape, geo, mesh, color, clickable) {
+        var geoGroup = geo.addGeoGroup();
+        var vertexArr = mesh.vertexArr, normalArr = mesh.normalArr, 
+            faceArr = mesh.faceArr;
+
+        geoGroup.vertices = vertexArr.length;
+        geoGroup.faceidx = faceArr.length;
+
+        var offset, v, a, b, c, i, il;
+        var vertexArray = geoGroup.vertexArray;
+        var colorArray = geoGroup.colorArray;
+        
+        if(! (color.constructor === Array)) {
+            var r = color.r;
+            var g = color.g;
+            var b = color.b;
+        }
+        for (i = 0, il = geoGroup.vertices; i < il; ++i) {
+            offset = i * 3;
+            v = vertexArr[i];
+            vertexArray[offset] = v.x;
+            vertexArray[offset + 1] = v.y;
+            vertexArray[offset + 2] = v.z;
+            
+            if( color.constructor === Array) {
+                var c = color[i];
+                var r = c.r;
+                var g = c.g;
+                var b = c.b;
+            }
+            
+            colorArray[offset] = r;
+            colorArray[offset + 1] = g;
+            colorArray[offset + 2] = b;
+        }
+        
+        if(clickable) {
+            for (i = 0, il = geoGroup.faceidx / 3; i < il; ++i) {
+                offset = i * 3;
+                a = faceArr[offset];
+                b = faceArr[offset + 1];
+                c = faceArr[offset + 2];
+                var vA = new $3Dmol.Vector3(), vB = new $3Dmol.Vector3(), vC = new $3Dmol.Vector3();
+                shape.intersectionShape.triangle.push(new $3Dmol.Triangle(vA
+                        .copy(vertexArr[a]), vB.copy(vertexArr[b]), vC
+                        .copy(vertexArr[c])));
+            }
+        }
+        
+        if(clickable) {
+            
+            var center = new $3Dmol.Vector3(0,0,0);
+            var cnt = 0;
+            for(var g = 0; g < geo.geometryGroups.length; g++) {
+                center.add(geo.geometryGroups[g].getCentroid());
+                cnt++;
+            }
+            center.divideScalar(cnt);
+            
+            
+            updateBoundingFromPoints(shape.boundingSphere, {centroid: center}, vertexArray);
+        }
+
+        geoGroup.faceArray = new Uint16Array(faceArr);
+
+        geoGroup.truncateArrayBuffers(true, true);
+
+        if (normalArr.length < geoGroup.vertices)
+            geoGroup.setNormals();
+        else {
+
+            var normalArray = geoGroup.normalArray = new Float32Array(geoGroup.vertices * 3);
+            var n;
+            for (i = 0, il = geoGroup.vertices; i < il; ++i) {
+                offset = i * 3;
+                n = normalArr[i];
+                normalArray[offset] = n.x;
+                normalArray[offset + 1] = n.y;
+                normalArray[offset + 2] = n.z;
+            }
+        }
+        
+        geoGroup.setLineIndices();
+        geoGroup.lineidx = geoGroup.lineArray.length;
+    };
+    
+
+    
+    // handles custom shape generation from user supplied arrays
+    // May need to generate normal and/or line indices
+    /**
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {geometry}
+     *            geo
+     * @param {CustomSpec}
+     *            customSpec
+     */
+    var drawCustom = function(shape, geo, customSpec) {
+        var mesh = customSpec;
+        var vertexArr = mesh.vertexArr, normalArr = mesh.normalArr, 
+        faceArr = mesh.faceArr;
+        if (vertexArr.length === 0 || faceArr.length === 0) {
+            console
+                    .warn("Error adding custom shape component: No vertices and/or face indices supplied!");
+        }
+
+        var color = customSpec.color;
+        if(typeof(color) == 'undefined') {
+            color = shape.color;
+        }
+        color =  $3Dmol.CC.color(color);
+
+        //var firstgeo = geo.geometryGroups.length;
+        var splits = $3Dmol.splitMesh(mesh);
+        for(var i = 0, n = splits.length; i < n; i++) {
+            addCustomGeo(shape, geo, splits[i], splits[i].colorArr ? splits[i].colorArr : color, customSpec.clickable);
+        } 
+    }; 
+
+    // Update a bounding sphere's position and radius
+    // from list of centroids and new points
+    /**
+     * @param {$3Dmol.Sphere}
+     *            sphere
+     * @param {Object}
+     *            components
+     * @param {Array}
+     *            points
+     */
+    var updateBoundingFromPoints = function(sphere, components, points) {
+
+        sphere.center.set(0, 0, 0);
+
+        var i, il;
+
+        if (components.length > 0) {
+
+            for (i = 0, il = components.length; i < il; ++i) {
+                var centroid = components[i].centroid;
+                sphere.center.add(centroid);
+            }
+
+            sphere.center.divideScalar(components.length);
+        }
+
+        var maxRadiusSq = sphere.radius * sphere.radius;
+
+        for (i = 0, il = points.length / 3; i < il; i++) {
+            var x = points[i * 3], y = points[i * 3 + 1], z = points[i * 3 + 2];
+            var radiusSq = sphere.center.distanceToSquared({
+                x : x,
+                y : y,
+                z : z
+            });
+            maxRadiusSq = Math.max(maxRadiusSq, radiusSq);
+        }
+
+        sphere.radius = Math.sqrt(maxRadiusSq);
+
+    };
+
+    /**
+     * 
+     * @param {$3Dmol.GLShape}
+     *            shape
+     * @param {ShapeSpec}
+     *            stylespec
+     * @returns {undefined}
+     */
+    var updateFromStyle = function(shape, stylespec) {
+        if(typeof(stylespec.color) != 'undefined') {
+            shape.color = stylespec.color || new $3Dmol.Color();
+            if(! (stylespec.color instanceof $3Dmol.Color))
+                shape.color = $3Dmol.CC.color(stylespec.color);
+        }
+        shape.wireframe = stylespec.wireframe ? true : false;
+        //opacity is the preferred nomenclature, support alpha for backwards compat
+        shape.opacity = stylespec.alpha ? $3Dmol.Math.clamp(stylespec.alpha, 0.0,
+                1.0) : 1.0;
+        if(typeof(stylespec.opacity) != 'undefined') {
+            shape.opacity = $3Dmol.Math.clamp(stylespec.opacity, 0.0, 1.0);
+        }
+        shape.side = (stylespec.side !== undefined) ? stylespec.side
+                : $3Dmol.DoubleSide;
+
+        shape.linewidth = typeof(stylespec.linewidth) == 'undefined' ? 1 : stylespec.linewidth;
+        // Click handling
+        shape.clickable = stylespec.clickable ? true : false;
+        shape.callback = typeof (stylespec.callback) === "function" ? stylespec.callback
+                : null;
+        shape.hidden = stylespec.hidden;
+    };
+
+    /**
+     * Custom renderable shape
+     * 
+     * @constructor $3Dmol.GLShape
+     * 
+     * @param {Object}
+     *            stylespec
+     * @returns {$3Dmol.GLShape}
+     */
+    function GLShape(stylespec) {
+
+        stylespec = stylespec || {};
+        $3Dmol.ShapeIDCount++;
+
+        this.boundingSphere = new $3Dmol.Sphere();
+        /** @type {IntersectionShapes} */
+        this.intersectionShape = {
+            sphere : [],
+            cylinder : [],
+            line : [],
+            triangle : []
+        };
+
+        updateFromStyle(this, stylespec);
+
+        // Keep track of shape components and their centroids
+        var components = [];
+        var shapeObj = null;
+        var renderedShapeObj = null;
+
+        var geo = new $3Dmol.Geometry(true);
+        var linegeo = new $3Dmol.Geometry(true);
+
+        /** Update shape with new style specification
+         * @param {ShapeSpec} newspec
+         * @return {$3Dmol.GLShape}
+         */
+        this.updateStyle = function(newspec) {
+
+            for ( var prop in newspec) {
+                stylespec[prop] = newspec[prop];
+            }
+
+            updateFromStyle(this, stylespec);
+        };
+
+        /**
+         * Creates a custom shape from supplied vertex and face arrays
+         * @function $3Dmol.GLShape#addCustom
+         * @param {CustomSpec} customSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCustom = function(customSpec) {
+
+            customSpec.vertexArr = customSpec.vertexArr || [];
+            customSpec.faceArr = customSpec.faceArr || [];
+            customSpec.normalArr = customSpec.normalArr || [];
+
+            var firstgeo = geo.geometryGroups.length;
+            // will split mesh as needed
+            drawCustom(this, geo, customSpec);
+        };
+
+        /**
+         * Creates a sphere shape
+         * @function $3Dmol.GLShape#addSphere
+         * @param {SphereSpec} sphereSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addSphere = function(sphereSpec) {
+
+            sphereSpec.center = sphereSpec.center || {
+                x : 0,
+                y : 0,
+                z : 0
+            };
+            sphereSpec.radius = sphereSpec.radius ? $3Dmol.Math.clamp(
+                    sphereSpec.radius, 0, Infinity) : 1.5;
+            sphereSpec.color = $3Dmol.CC.color(sphereSpec.color);
+            
+            this.intersectionShape.sphere.push(new $3Dmol.Sphere(
+                    sphereSpec.center, sphereSpec.radius));
+
+            $3Dmol.GLDraw.drawSphere(geo, sphereSpec.center,
+                    sphereSpec.radius, sphereSpec.color);
+
+            components.push({
+                centroid : new $3Dmol.Vector3(sphereSpec.center.x,
+                        sphereSpec.center.y, sphereSpec.center.z)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+        };
+
+        /**
+         * Creates a cylinder shape
+         * @function $3Dmol.GLShape#addCylinder
+         * @param {CylinderSpec} cylinderSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCylinder = function(cylinderSpec) {
+
+            cylinderSpec.start = cylinderSpec.start || {};
+            cylinderSpec.end = cylinderSpec.end || {};
+
+            var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
+                    cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
+            var end = new $3Dmol.Vector3(cylinderSpec.end.x,
+                    cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
+        	if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+
+            var radius = cylinderSpec.radius || 0.1;
+            var color = $3Dmol.CC.color(cylinderSpec.color);
+            
+            this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(start, end, radius));
+
+            $3Dmol.GLDraw.drawCylinder(geo, start, end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);            
+            
+            var centroid = new $3Dmol.Vector3();
+            components.push({
+                centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+
+        };
+
+        /**
+         * Creates a line shape
+         * @function $3Dmol.GLShape#addLine         
+         * @param {LineSpec} lineSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addLine = function(lineSpec) {
+            lineSpec.start = lineSpec.start || {};
+            lineSpec.end = lineSpec.end || {};
+
+            var start = new $3Dmol.Vector3(lineSpec.start.x || 0,
+                    lineSpec.start.y || 0, lineSpec.start.z || 0);
+            var end = new $3Dmol.Vector3(lineSpec.end.x,
+                    lineSpec.end.y || 0, lineSpec.end.z || 0);            
+            if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
+
+            var geoGroup = geo.updateGeoGroup(2);
+
+            //make line from start to end
+            //for consistency with rest of shapes, uses vertices and lines rather
+            //than a separate line geometry
+            var vstart = geoGroup.vertices;
+            var i = vstart*3;
+            var vertexArray = geoGroup.vertexArray;
+            vertexArray[i] = start.x;
+            vertexArray[i+1] = start.y;
+            vertexArray[i+2] = start.z;
+            vertexArray[i+3] = end.x;
+            vertexArray[i+4] = end.y;
+            vertexArray[i+5] = end.z;
+            geoGroup.vertices += 2;
+            
+            var lineArray = geoGroup.lineArray;
+            var li =  geoGroup.lineidx;
+            lineArray[li] = vstart;
+            lineArray[li+1] = vstart+1;
+            geoGroup.lineidx += 2;
+            
+        }
+        /**
+         * Creates an arrow shape
+         * @function $3Dmol.GLShape#addArrow        
+         * @param {ArrowSpec} arrowSpec
+         * @return {$3Dmol.GLShape}
+         */
+        this.addArrow = function(arrowSpec) {
+
+            arrowSpec.start = arrowSpec.start || {};
+            arrowSpec.end = arrowSpec.end || {};
+
+            arrowSpec.start = new $3Dmol.Vector3(arrowSpec.start.x || 0,
+                    arrowSpec.start.y || 0, arrowSpec.start.z || 0);
+
+            if (arrowSpec.dir instanceof $3Dmol.Vector3
+                    && arrowSpec.length instanceof number) {
+                var end = arrowSpec.dir.clone().multiplyScalar(arrowSpec.length).add(
+                        start);
+                arrowSpec.end = end;
+            }
+
+            else {
+                arrowSpec.end = new $3Dmol.Vector3(arrowSpec.end.x,
+                        arrowSpec.end.y || 0, arrowSpec.end.z || 0);
+            	if(typeof(arrowSpec.end.x) == 'undefined') arrowSpec.end.x = 3; //show something even if undefined
+            }
+
+            arrowSpec.radius = arrowSpec.radius || 0.1;
+
+            arrowSpec.radiusRatio = arrowSpec.radiusRatio || 1.618034;
+            arrowSpec.mid = (0 < arrowSpec.mid && arrowSpec.mid < 1) ? arrowSpec.mid
+                    : 0.618034;
+
+
+            drawArrow(this, geo, arrowSpec);
+
+            var centroid = new $3Dmol.Vector3();
+            components.push({
+                centroid : centroid.addVectors(arrowSpec.start, arrowSpec.end)
+                        .multiplyScalar(0.5)
+            });
+            var geoGroup = geo.updateGeoGroup(0);
+            updateBoundingFromPoints(this.boundingSphere, components,
+                    geoGroup.vertexArray);
+
+        };
+        
+        /**
+         * Create isosurface from voluemetric data.
+         * @function $3Dmol.GLShape#addIsosurface         
+         * @param {$3Dmol.VolumeData} data - volumetric input data
+         * @param {IsoSurfaceSpec} isoSpec - volumetric data shape specification
+         */
+        this.addIsosurface = function(data, volSpec) {
+            var isoval = (volSpec.isoval !== undefined && typeof (volSpec.isoval) === "number") ? volSpec.isoval
+                    : 0.0;
+            var voxel = (volSpec.voxel) ? true : false;
+            var smoothness = (volSpec.smoothness === undefined) ? 1 : volSpec.smoothness;
+
+            var nX = data.size.x;
+            var nY = data.size.y;
+            var nZ = data.size.z;
+            var vertnums = new Int16Array(nX * nY * nZ);
+            var vals = data.data;
+            var i, il;
+
+            for (i = 0, il = vertnums.length; i < il; ++i)
+                vertnums[i] = -1;
+
+            //mark locations partitioned by isoval
+            var bitdata = new Uint8Array(nX * nY * nZ);
+
+            for (i = 0, il = vals.length; i < il; ++i) {
+                var val = (isoval >= 0) ? vals[i] - isoval : isoval - vals[i];
+
+                if (val > 0)
+                    bitdata[i] |= ISDONE;
+
+            }
+
+            var verts = [], faces = [];
+
+            $3Dmol.MarchingCube.march(bitdata, verts, faces, {
+                fulltable : true,
+                voxel : voxel,
+                unitCube : data.unit,
+                origin : data.origin,
+                nX : nX,
+                nY : nY,
+                nZ : nZ
+            });
+
+            if (!voxel)
+                $3Dmol.MarchingCube.laplacianSmooth(smoothness, verts, faces);
+
+            drawCustom(this, geo, {
+                vertexArr : verts,
+                faceArr : faces,
+                normalArr : [],
+                clickable : volSpec.clickable
+            });
+           
+            this.updateStyle(volSpec);
+            
+            //computing bounding sphere from vertices
+            var origin = new $3Dmol.Vector3(data.origin.x, data.origin.y, data.origin.z);
+            var size = new $3Dmol.Vector3(data.size.x*data.unit.x, data.size.y*data.unit.y, data.size.z*data.unit.z);            
+
+            var total = new $3Dmol.Vector3(0,0,0);
+            var maxv = origin.clone();
+            var minv = origin.clone().add(size);
+            for(var i = 0; i < verts.length; i++) {
+                total.add(verts[i]);
+                maxv.max(verts[i]);
+                minv.min(verts[i]);
+            }
+            total.divideScalar(verts.length);
+            var len1 = total.distanceTo(minv);
+            var len2 = total.distanceTo(maxv);
+            this.boundingSphere.center = total;
+            this.boundingSphere.radius = Math.max(len1,len2);
+           
+        };
+        
+        /** 
+         * @deprecated Use addIsosurface instead
+         * Creates custom shape from volumetric data 
+         * @param {string} data - Volumetric input data 
+         * @param {string} fmt - Input data format (e.g. 'cube' for cube file format)
+         * @param {IsoSurfaceSpec} isoSpec - Volumetric data shape specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addVolumetricData = function(data, fmt, volSpec) {
+            var data = new $3Dmol.VolumeData(data, fmt);
+            this.addIsosurface(data, volSpec);
+        };
+
+        /**
+         * Initialize webgl objects for rendering
+         * @param {$3Dmol.Object3D} group
+         * 
+         */  
+        this.globj = function(group) {
+
+            if (renderedShapeObj) {
+                group.remove(renderedShapeObj);
+                renderedShapeObj = null;
+            }
+            
+            if(this.hidden)
+                return;
+            finalizeGeo(geo);
+            geo.initTypedArrays();
+
+            if(typeof(this.color) != 'undefined')
+                updateColor(geo, this.color);
+
+            shapeObj = new $3Dmol.Object3D();
+            var material = null;
+            if(this.side == $3Dmol.DoubleSide) {
+                var material = new $3Dmol.MeshDoubleLambertMaterial({
+                    wireframe : this.wireframe,
+                    side : this.side,
+                    transparent : (this.opacity < 1) ? true : false,
+                    opacity : this.opacity,
+                    wireframeLinewidth: this.linewidth
+                });
+            } else {
+                var material = new $3Dmol.MeshLambertMaterial({
+                    wireframe : this.wireframe,
+                    side : this.side,
+                    transparent : (this.opacity < 1) ? true : false,
+                    opacity : this.opacity,
+                    wireframeLinewidth: this.linewidth
+                });
+            }
+            
+            var mesh = new $3Dmol.Mesh(geo, material);
+
+            shapeObj.add(mesh);
+            
+            var lineMaterial = new $3Dmol.LineBasicMaterial({
+                linewidth : this.linewidth,
+                color: this.color
+            });
+            var line = new $3Dmol.Line(linegeo, lineMaterial,
+                    $3Dmol.LinePieces);
+            shapeObj.add(line);
+
+            renderedShapeObj = shapeObj.clone();
+            group.add(renderedShapeObj);
+
+        };
+
+        this.removegl = function(group) {
+            if (renderedShapeObj) {
+                // dispose of geos and materials
+                if (renderedShapeObj.geometry !== undefined)
+                    renderedShapeObj.geometry.dispose();
+                if (renderedShapeObj.material !== undefined)
+                    renderedShapeObj.material.dispose();
+                group.remove(renderedShapeObj);
+                renderedShapeObj = null;
+            }
+            shapeObj = null;
+        };
+
+    };
+
+    Object.defineProperty(GLShape.prototype, "position", {
+
+        get : function() {
+            return this.boundingSphere.center;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "x", {
+
+        get : function() {
+            return this.boundingSphere.center.x;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "y", {
+
+        get : function() {
+            return this.boundingSphere.center.y;
+        }
+
+    });
+
+    Object.defineProperty(GLShape.prototype, "z", {
+
+        get : function() {
+            return this.boundingSphere.center.z;
+        }
+
+    });
+
+    return GLShape;
+
+}());
+
+$3Dmol.ShapeIDCount = 0;
+
+
+$3Dmol.splitMesh = function(mesh) {
+	    var MAXVERT = 64000; //webgl only supports 2^16 elements, leave a little breathing room (require at least 2)
+    //peel off 64k vertices rsvh into their own mesh
+    //duplicating vertices and normals as necessary to preserve faces and lines
+	
+        if(mesh.vertexArr.length < MAXVERT) return [mesh]; //typical case
+        
+        var nverts = mesh.vertexArr.length;
+        var slices = [{vertexArr: [], normalArr: [], faceArr: []}];
+        if(mesh.colorArr) slices.colorArr = [];
+        var vertSlice = []; //indexed by original vertex to get current slice
+        var vertIndex =[]; //indexed by original vertex to get index within slice
+        var currentSlice = 0;
+        
+        //for each face, make sure all three vertices (or copies) are in the same slice
+        var faces = mesh.faceArr;
+        var vs = [0,0,0];
+        for(var i = 0, nf = faces.length; i < nf; i += 3) {
+            var slice = slices[currentSlice];
+            for(var j = 0; j < 3; j++) {
+                //process each vertex to make sure it is assigned a slice
+                //all vertices of a face must belong to the same slice
+                var v = faces[i+j];
+                if(vertSlice[v] !== currentSlice) { //true if undefined
+                    vertSlice[v] = currentSlice;
+                    vertIndex[v] = slice.vertexArr.length;
+                    slice.vertexArr.push(mesh.vertexArr[v]);
+                    if(mesh.normalArr && mesh.normalArr[v]) slice.normalArr.push(mesh.normalArr[v]);
+                    if(mesh.colorArr && mesh.colorArr[v]) slice.colorArr.push(mesh.colorArr[v]);
+                }
+                slice.faceArr.push(vertIndex[v]);
+            }
+            
+            if(slice.vertexArr.length >= MAXVERT) {
+                //new slice
+                slices.push({vertexArr: [], normalArr: [], faceArr: []});
+                if(mesh.colorArr) slices.colorArr = [];
+                currentSlice++;
+            }
+        }
+        return slices;
+    }
+//a molecular viewer based on GLMol
+
+
+
+/**
+ * WebGL-based 3Dmol.js viewer
+ * Note: The preferred method of instantiating a GLViewer is through {@link $3Dmol.createViewer} 
+ * 
+ * @constructor 
+ * @param {Object} element HTML element within which to create viewer
+ * @param {function} callback - Callback function to be immediately executed on this viewer
+ * @param {Object} defaultcolors - Object defining default atom colors as atom => color property value pairs for all models within this viewer
+ */
+$3Dmol.GLViewer = (function() {
+    // private class variables
+    var numWorkers = 4; // number of threads for surface generation
+    var maxVolume = 64000; // how much to break up surface calculations
+
+    // private class helper functions
+
+    function GLViewer(element, config) { 
+        // set variables
+        config = config || {};
+        var callback = config.callback;
+        var defaultcolors = config.defaultcolors;    	
+        if(!defaultcolors)
+            defaultcolors = $3Dmol.elementColors.defaultColors;
+        var nomouse = config.nomouse;
+        var bgColor = 0;
+
+        if(typeof(config.backgroundColor) != undefined) {
+            bgColor = $3Dmol.CC.color(config.backgroundColor).getHex();
+        }
+
+        var camerax = 0;
+        if(typeof(config.camerax) != undefined) {
+            camerax = parseFloat(config.camerax);
+        }
+        var _viewer = this;
+        var container = element;
+        var id = container.id;
+        var glDOM = null;
+
+        var models = []; // atomistic molecular models
+        var surfaces = {};
+        var shapes = []; // Generic shapes
+        var labels = [];
+        var clickables = []; //things you can click on
+        
+        var WIDTH = container.width();
+        var HEIGHT = container.height();
+
+        // set dimensions
+        // $(container).width(WIDTH);
+        // $(container).height(HEIGHT);
+
+        var ASPECT = WIDTH / HEIGHT;
+        var NEAR = 1, FAR = 800;
+        var CAMERA_Z = 150;
+        var fov = 20;
+
+        var linkedViewers = [];
+
+        var renderer = new $3Dmol.Renderer({
+            antialias : true,
+            preserveDrawingBuffer: true, //so we can export images
+            premultipliedAlpha : false/* more traditional compositing with background */
+        });
+
+        renderer.domElement.style.width = "100%";
+        renderer.domElement.style.height = "100%";
+        renderer.domElement.style.padding = "0";
+        renderer.domElement.style.position = "absolute"; //TODO: get rid of this
+        renderer.domElement.style.top = "0px";
+        renderer.domElement.style.left = "0px";
+        renderer.domElement.style.zIndex = "0";
+
+        var camera = new $3Dmol.Camera(fov, ASPECT, NEAR, FAR);
+        camera.position = new $3Dmol.Vector3(camerax, 0, CAMERA_Z);
+        var lookingAt = new $3Dmol.Vector3();
+        camera.lookAt(lookingAt);
+
+        var raycaster = new $3Dmol.Raycaster(new $3Dmol.Vector3(0, 0, 0),
+                new $3Dmol.Vector3(0, 0, 0));
+        var projector = new $3Dmol.Projector();
+        var mouseVector = new $3Dmol.Vector3(0, 0, 0);
+
+        var scene = null;
+        var rotationGroup = null; // which contains modelGroup
+        var modelGroup = null;
+
+        var fogStart = 0.4;
+        var slabNear = -50; // relative to the center of rotationGroup
+        var slabFar = 50;
+
+        // UI variables
+        var cq = new $3Dmol.Quaternion(0, 0, 0, 1);
+        var dq = new $3Dmol.Quaternion(0, 0, 0, 1);
+        var animated = false;
+        var isDragging = false;
+        var mouseStartX = 0;
+        var mouseStartY = 0;
+        var touchDistanceStart = 0;
+        var currentModelPos = 0;
+        var cz = 0;
+        var cslabNear = 0;
+        var cslabFar = 0;      
+        
+        var nextSurfID = function() {
+            //compute the next highest surface id directly from surfaces
+            //this is necessary to support linking of model data
+            var max = 0;
+            for (i in surfaces) { // this is an object with possible holes
+                if(!surfaces.hasOwnProperty(i)) continue;
+                if(i > max) max = i;
+            }
+            return max+1;
+        };
+
+        var setSlabAndFog = function() {
+            var center = camera.position.z - rotationGroup.position.z;
+            if (center < 1)
+                center = 1;
+            camera.near = center + slabNear;
+            if (camera.near < 1)
+                camera.near = 1;
+            camera.far = center + slabFar;
+            if (camera.near + 1 > camera.far)
+                camera.far = camera.near + 1;
+            if (camera instanceof $3Dmol.Camera) {
+                camera.fov = fov;
+            } else {
+                camera.right = center * Math.tan(Math.PI / 180 * fov);
+                camera.left = -camera.right;
+                camera.top = camera.right / ASPECT;
+                camera.bottom = -camera.top;
+            }
+            camera.updateProjectionMatrix();
+            scene.fog.near = camera.near + fogStart
+                    * (camera.far - camera.near);
+            // if (scene.fog.near > center) scene.fog.near = center;
+            scene.fog.far = camera.far;
+        };
+
+        // display scene
+        //if nolink is set/true, don't propagate changes to linked viewers
+        var show = function(nolink) {
+            if (!scene)
+                return;
+
+            // var time = new Date();
+            setSlabAndFog();
+            renderer.render(scene, camera);
+            // console.log("rendered in " + (+new Date() - time) + "ms");
+            
+            if(!nolink && linkedViewers.length > 0) {
+                var view = _viewer.getView();
+                for(var i = 0; i < linkedViewers.length; i++) {
+                    var other = linkedViewers[i];
+                    other.setView(view, true);
+                }
+            }
+        };
+
+        var initializeScene = function() {
+
+            scene = new $3Dmol.Scene();
+            scene.fog = new $3Dmol.Fog(bgColor, 100, 200);
+
+            modelGroup = new $3Dmol.Object3D();
+            rotationGroup = new $3Dmol.Object3D();
+            rotationGroup.useQuaternion = true;
+            rotationGroup.quaternion = new $3Dmol.Quaternion(0, 0, 0, 1);
+            rotationGroup.add(modelGroup);
+
+            scene.add(rotationGroup);
+
+            // setup lights
+            var directionalLight = new $3Dmol.Light(0xFFFFFF);
+            directionalLight.position = new $3Dmol.Vector3(0.2, 0.2, 1)
+                    .normalize();
+            directionalLight.intensity = 1.0;
+            scene.add(directionalLight);
+        };
+
+        initializeScene();
+
+        renderer.setClearColorHex(bgColor, 1.0);
+        scene.fog.color = $3Dmol.CC.color(bgColor);
+
+        var clickedAtom = null;
+
+        // enable mouse support
+
+        //regenerate the list of clickables
+        var updateClickables = function() {
+            clickables.splice(0,clickables.length);
+            var i, il;
+
+            for (i = 0, il = models.length; i < il; i++) {
+                var model = models[i];
+                if(model) {
+                    var atoms = model.selectedAtoms({
+                        clickable : true
+                    });
+                    Array.prototype.push.apply(clickables, atoms); //add atoms into clickables
+                }
+            }
+
+            for (i = 0, il = shapes.length; i < il; i++) {
+
+                var shape = shapes[i];
+                if (shape && shape.clickable) {
+                    clickables.push(shape);
+                }
+            }
+        };
+        
+        // Checks for selection intersects on mousedown
+        var handleClickSelection = function(mouseX, mouseY, event) {
+            if(clickables.length == 0) return;
+            var mouse = {
+                x : mouseX,
+                y : mouseY,
+                z : -1.0
+            };
+            mouseVector.set(mouse.x, mouse.y, mouse.z);
+            projector.unprojectVector(mouseVector, camera);
+            mouseVector.sub(camera.position).normalize();
+
+            raycaster.set(camera.position, mouseVector);
+
+            var intersects = [];
+
+            intersects = raycaster.intersectObjects(modelGroup, clickables);
+            if (intersects.length) {
+                var selected = intersects[0].clickable;
+                if (selected.callback !== undefined
+                        && typeof (selected.callback) === "function") {
+                    selected.callback(selected, _viewer, event, container);
+                }
+            }
+        };
+
+        var calcTouchDistance = function(ev) { // distance between first two
+                                                // fingers
+            var xdiff = ev.originalEvent.targetTouches[0].pageX
+                    - ev.originalEvent.targetTouches[1].pageX;
+            var ydiff = ev.originalEvent.targetTouches[0].pageY
+                    - ev.originalEvent.targetTouches[1].pageY;
+            return Math.sqrt(xdiff * xdiff + ydiff * ydiff);
+        }
+        
+        //check targetTouches as well
+        var getXY = function(ev) {
+            var x = ev.pageX, y = ev.pageY;
+            if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches[0]) {
+                x = ev.originalEvent.targetTouches[0].pageX;
+                y = ev.originalEvent.targetTouches[0].pageY;
+            }
+            else if (ev.originalEvent.changedTouches
+                    && ev.originalEvent.changedTouches[0]) {
+                x = ev.originalEvent.changedTouches[0].pageX;
+                y = ev.originalEvent.changedTouches[0].pageY;
+            }            
+            return [x,y];
+        };
+
+        //for a given screen (x,y) displacement return model displacement 
+        var screenXY2model = function(x,y) {
+            var dx = x/WIDTH;
+            var dy = y/HEIGHT;
+            var zpos = rotationGroup.position.z; 
+            var q = rotationGroup.quaternion;                        
+            var t = new $3Dmol.Vector3(0,0,zpos);
+            projector.projectVector(t, camera);
+            t.x += dx*2;
+            t.y -= dy*2;
+            projector.unprojectVector(t, camera);
+            t.z = 0;                            
+            t.applyQuaternion(q);
+            return t;
+        }
+
+        // this event is bound to the body element, not the container,
+        // so no need to put it inside initContainer()
+        $('body').bind('mouseup touchend', function(ev) {
+            // handle selection
+            if(isDragging && scene) { //saw mousedown, haven't moved
+                var xy = getXY(ev);
+                var x = xy[0];
+                var y = xy[1];
+                if(x == mouseStartX && y == mouseStartY) {
+                    var offset = $('canvas',container).offset();
+                    var mouseX = ((x - offset.left) / WIDTH) * 2 - 1;
+                    var mouseY = -((y - offset.top) / HEIGHT) * 2 + 1;
+
+                    handleClickSelection(mouseX, mouseY, ev, container);
+                }
+            }
+            
+            isDragging = false;
+
+        });
+        
+        var _handleMouseDown = this._handleMouseDown = function(ev) {
+            ev.preventDefault();
+            if (!scene)
+                return;
+            var xy = getXY(ev);
+            var x = xy[0];
+            var y = xy[1];
+            
+            if (x === undefined)
+                return;
+            isDragging = true;
+            clickedAtom = null;
+            mouseButton = ev.which;
+            mouseStartX = x;
+            mouseStartY = y;
+            touchDistanceStart = 0;
+            if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 2) {
+                touchDistanceStart = calcTouchDistance(ev);
+            }
+            cq = rotationGroup.quaternion;
+            cz = rotationGroup.position.z;
+            currentModelPos = modelGroup.position.clone();
+            cslabNear = slabNear;
+            cslabFar = slabFar;
+
+        };
+        
+        var _handleMouseScroll  = this._handleMouseScroll = function(ev) { // Zoom
+            ev.preventDefault();
+            if (!scene)
+                return;
+            var scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
+            if (ev.originalEvent.detail) { // Webkit
+                rotationGroup.position.z += scaleFactor
+                        * ev.originalEvent.detail / 10;
+            } else if (ev.originalEvent.wheelDelta) { // Firefox
+                rotationGroup.position.z -= scaleFactor
+                        * ev.originalEvent.wheelDelta / 400;
+            }
+            if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+
+            show();
+        };
+        
+        var _handleMouseMove = this._handleMouseMove = function(ev) { // touchmove
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ev.preventDefault();
+            if (!scene)
+                return;
+            if (!isDragging)
+                return;
+            var mode = 0;
+
+            var xy = getXY(ev);
+            var x = xy[0];
+            var y = xy[1];
+            if (x === undefined)
+                return;
+            var dx = (x - mouseStartX) / WIDTH;
+            var dy = (y - mouseStartY) / HEIGHT;
+            // check for pinch
+            if (touchDistanceStart != 0
+                    && ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 2) {
+                var newdist = calcTouchDistance(ev);
+                // change to zoom
+                mode = 2;
+                dy = (newdist - touchDistanceStart) * 2
+                        / (WIDTH + HEIGHT);
+            } else if (ev.originalEvent.targetTouches
+                    && ev.originalEvent.targetTouches.length == 3) {
+                // translate
+                mode = 1;
+            }
+
+            var r = Math.sqrt(dx * dx + dy * dy);
+            var scaleFactor;
+            if (mode == 3
+                    || (mouseButton == 3 && ev.ctrlKey)) { // Slab
+                slabNear = cslabNear + dx * 100;
+                slabFar = cslabFar + dy * 100;
+            } else if (mode == 2 || mouseButton == 3
+                    || ev.shiftKey) { // Zoom
+                scaleFactor = (CAMERA_Z - rotationGroup.position.z) * 0.85;
+                if (scaleFactor < 80)
+                    scaleFactor = 80;
+                rotationGroup.position.z = cz + dy * scaleFactor;
+                if(rotationGroup.position.z > CAMERA_Z) rotationGroup.position.z = CAMERA_Z*0.999; //avoid getting stuck
+            } else if (mode == 1 || mouseButton == 2
+                    || ev.ctrlKey) { // Translate
+                var t = screenXY2model(x-mouseStartX, y-mouseStartY);
+                modelGroup.position.addVectors(currentModelPos,t);
+                
+            } else if ((mode === 0 || mouseButton == 1)
+                    && r !== 0) { // Rotate
+                var rs = Math.sin(r * Math.PI) / r;
+                dq.x = Math.cos(r * Math.PI);
+                dq.y = 0;
+                dq.z = rs * dx;
+                dq.w = -rs * dy;
+                rotationGroup.quaternion = new $3Dmol.Quaternion(
+                        1, 0, 0, 0);
+                rotationGroup.quaternion.multiply(dq);
+                rotationGroup.quaternion.multiply(cq);
+            }
+            show();
+        };
+        
+        var initContainer = function(element) {
+            container = element;
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ASPECT = WIDTH / HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            container.append(renderer.domElement);
+            glDOM = $(renderer.domElement);
+
+            if (!nomouse) {
+                // user can request that the mouse handlers not be installed
+                glDOM.bind('mousedown touchstart', _handleMouseDown);
+                glDOM.bind('DOMMouseScroll mousewheel', _handleMouseScroll);
+                glDOM.bind('mousemove touchmove', _handleMouseMove);
+                
+                glDOM.bind("contextmenu", function(ev) {
+                    ev.preventDefault();
+                });
+            }
+        };
+        initContainer(container);
+
+        // public methods
+        /**
+         * Change the viewer's container element 
+         * Also useful if the original container element was removed from the DOM.
+         * 
+         * @function $3Dmol.GLViewer#resetContainer
+         *
+         * @param {Object | string} element
+         *            Either HTML element or string identifier. Defaults to the element used to initialize the viewer.
+
+         * @example
+         * // Assume there exist HTML divs with ids "gldiv", "gldiv2"
+         * var element = $("#gldiv"), element2 = $("#gldiv2");
+         * // Create GLViewer within 'gldiv'
+         * var myviewer = $3Dmol.createViewer(element);
+         * // Move the canvas to the other div
+         * myviewer.setContainer(element2)
+         *
+         * @example
+         * // Assume there exists an HTML div with id "gldiv"
+         * var element = $("#gldiv");
+         * // Create GLViewer within 'gldiv'
+         * var myviewer = $3Dmol.createViewer(element);
+         * // Remove the element from the DOM, and add a new element
+         * element.remove()
+         * $('body').prepend("<div id='newdiv'></div>")
+         * // Show the canvas in the new element
+         * myviewer.setContainer('newdiv')
+         */
+        this.setContainer = function(element) {
+            if($.type(element) === "string")
+                element = $("#"+element);
+            if(!element) {
+                element = container
+            };
+            initContainer(element);
+            return this;
+        };
+        
+        /**
+         * Set the background color (default white)
+         * 
+         * @function $3Dmol.GLViewer#setBackgroundColor
+         * @param {number}
+         *            hex Hexcode specified background color, or standard color spec
+         * @param {number}
+         *            a Alpha level (default 1.0)
+         * 
+         * @example
+         * 
+         * //Set 'myviewer' background color to white
+         * myviewer.setBackgroundColor(0xffffff)
+         * 
+         */
+        this.setBackgroundColor = function(hex, a) {
+            if(typeof(a) == "undefined") {
+                a = 1.0;
+            }
+            else if(a < 0 || a > 1.0) {
+                a = 1.0;
+            }
+            var c = $3Dmol.CC.color(hex);
+            scene.fog.color = c;
+            bgColor = c.getHex();
+            renderer.setClearColorHex(c.getHex(), a);
+            show();
+            return this;
+        };
+        
+        /**
+         * Enable outline 
+         * @function $eDmol.GLViewer#outline
+         * 
+         * @example
+         * myviewer.outline()
+         * 
+         */
+         this.setViewStyle = function(parameters) {
+            if (parameters["style"] === "outline") {
+                var params = {};
+                if(parameters.color) params.color =  $3Dmol.CC.color(parameters.color);
+                if(parameters.width) params.width = parameters.width;
+                renderer.enableOutline(params);
+            } else {
+                renderer.disableOutline();
+            }
+            return this;
+        }
+         
+        if(config.style) { //enable setting style in constructor
+             this.setViewStyle(config.style);
+        }
+
+        /**
+         * Set viewer width
+         * 
+         * @function $3Dmol.GLViewer#setWidth
+         * @param {number}
+         *            w Width in pixels
+         */
+        this.setWidth = function(w) {
+            WIDTH = w || WIDTH;
+            renderer.setSize(WIDTH, HEIGHT);
+            return this;
+        };
+
+        /**
+         * Set viewer height
+         * 
+         * @function $3Dmol.GLViewer#setHeight
+         * @param {number}
+         *            h Height in pixels
+         */
+        this.setHeight = function(h) {
+            HEIGHT = h || HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            return this;
+        };
+
+        /**
+         * Resize viewer according to containing HTML element's dimensions
+         * 
+         * @function $3Dmol.GLViewer#resize
+         */
+        this.resize = function() {
+            WIDTH = container.width();
+            HEIGHT = container.height();
+            ASPECT = WIDTH / HEIGHT;
+            renderer.setSize(WIDTH, HEIGHT);
+            camera.aspect = ASPECT;
+            camera.updateProjectionMatrix();
+            show();
+            return this;
+        };
+
+        $(window).resize(this.resize);
+
+        /**
+         * Return specified model
+         * 
+         * @function $3Dmol.GLViewer#getModel
+         * @param {number}
+         *            [id=last model id] - Retrieve model with specified id
+         * @default Returns last model added to viewer
+         * @return {GLModel}
+         * 
+         * @example // Retrieve reference to first GLModel added var m =
+         *          glviewer.getModel(0);
+         */
+        this.getModel = function(id) {
+            id = id || models.length - 1;
+            return models[id];
+        };
+
+        /**
+         * Rotate scene by angle degrees around axis
+         * 
+         * @function $3Dmol.GLViewer#rotate
+         * @param {number}
+         *            [angle] - Angle, in degrees, to rotate by.
+         * @param {string}
+         *            [angle] - Axis ("x", "y", or "z") to rotate around.
+         *            Default "y"
+         * 
+         */
+        this.rotate = function(angle, axis) {
+            if (typeof (axis) === "undefined") {
+                axis = "y";
+            }
+            var i = 0, j = 0, k = 0;
+            var rangle = Math.PI * angle / 180.0;
+            var s = Math.sin(rangle / 2.0);
+            var c = Math.cos(rangle / 2.0);
+            if (axis == "x")
+                i = s;
+            if (axis == "y")
+                j = s;
+            if (axis == "z")
+                k = s;
+
+            var q = new $3Dmol.Quaternion(i, j, k, c).normalize();
+            rotationGroup.quaternion.multiply(q);
+            show();
+            return this;
+        };
+
+        /** Returns an array representing the current viewpoint.
+         * Translation, zoom, and rotation quaternion. 
+         * @function $3Dmol.GLViewer#getView
+         * @returns {Array.<number>} arg
+         *  */
+        this.getView = function() {
+            if (!modelGroup)
+                return [ 0, 0, 0, 0, 0, 0, 0, 1 ];
+            var pos = modelGroup.position;
+            var q = rotationGroup.quaternion;
+            return [ pos.x, pos.y, pos.z, rotationGroup.position.z, q.x, q.y,
+                    q.z, q.w ];
+        };
+
+        /** Sets the view to the specified translation, zoom, and rotation.
+         * 
+         * @function $3Dmol.GLViewer#setView
+         * @param {Array.<number>} arg Array formatted identically to the return value of getView */
+        this.setView = function(arg, nolink) {
+
+            if (arg === undefined
+                    || !(arg instanceof Array || arg.length !== 8))
+                return this;
+
+            if (!modelGroup || !rotationGroup)
+                return this;
+            modelGroup.position.x = arg[0];
+            modelGroup.position.y = arg[1];
+            modelGroup.position.z = arg[2];
+            rotationGroup.position.z = arg[3];
+            rotationGroup.quaternion.x = arg[4];
+            rotationGroup.quaternion.y = arg[5];
+            rotationGroup.quaternion.z = arg[6];
+            rotationGroup.quaternion.w = arg[7];
+            if(typeof(arg[8]) != "undefined") {
+                rotationGroup.position.x = arg[8];
+                rotationGroup.position.y = arg[9];
+            }
+            show(nolink);
+            return this;
+        };
+
+        // apply styles, models, etc in viewer
+        /**
+         * Render current state of viewer, after 
+         * adding/removing models, applying styles, etc.
+         * 
+         * @function $3Dmol.GLViewer#render
+         */
+        this.render = function() {
+
+            updateClickables(); //must render for clickable styles to take effect
+            var time1 = new Date();
+            var view = this.getView();
+            
+            var i, n;
+            var exts = renderer.supportedExtensions();
+            for (i = 0; i < models.length; i++) {
+                if (models[i]) {
+                    models[i].globj(modelGroup, exts);
+                }
+            }
+
+            for (i = 0; i < shapes.length; i++) {
+                if (shapes[i]) {
+                    shapes[i].globj(modelGroup, exts);
+                }
+            }
+            
+            for (i in surfaces) { // this is an object with possible holes
+                if(!surfaces.hasOwnProperty(i)) continue;
+                var surfArr = surfaces[i];
+                for (n = 0; n < surfArr.length; n++) {
+                    if (surfArr.hasOwnProperty(n)) {
+                        var geo = surfArr[n].geo;
+                        // async surface generation can cause
+                        // the geometry to be webgl initialized before it is fully
+                        // formed; force various recalculations until full surface
+                        // is
+                        // available
+                        if (!surfArr[n].finished) {
+                            geo.verticesNeedUpdate = true;
+                            geo.elementsNeedUpdate = true;
+                            geo.normalsNeedUpdate = true;
+                            geo.colorsNeedUpdate = true;
+                            geo.buffersNeedUpdate = true;
+                            geo.boundingSphere = null;
+
+                            if (surfArr[n].done)
+                                surfArr[n].finished = true;
+
+                            // remove partially rendered surface
+                            if (surfArr[n].lastGL)
+                                modelGroup.remove(surfArr[n].lastGL);
+
+                            // create new surface
+                            var smesh = null;
+
+                            if(surfArr[n].mat instanceof $3Dmol.LineBasicMaterial) {
+                                //special case line meshes
+                                smesh = new $3Dmol.Line(geo, surfArr[n].mat);
+                            }
+                            else {
+                                smesh = new $3Dmol.Mesh(geo, surfArr[n].mat);
+                            }
+                            if(surfArr[n].mat.transparent && surfArr[n].mat.opacity == 0) {
+                                //don't bother with hidden surfaces
+                                smesh.visible = false;
+                            } else {
+                                smesh.visible = true;
+                            }
+                            if (surfArr[n].symmetries.length > 1 || 
+                            (surfArr[n].symmetries.length == 1 && 
+                            !(surfArr[n].symmetries[n].isIdentity()))) {
+                                var j;
+                                var tmeshes = new $3Dmol.Object3D(); //transformed meshes
+                                for (j = 0; j < surfArr[n].symmetries.length; j++) {
+                                    var tmesh = smesh.clone();
+                                    tmesh.matrix = surfArr[n].symmetries[j];
+                                    tmesh.matrixAutoUpdate = false;
+                                    tmeshes.add(tmesh);
+                                }
+                                surfArr[n].lastGL = tmeshes;
+                                modelGroup.add(tmeshes);
+                            }
+                            else {
+                                surfArr[n].lastGL = smesh;
+                                modelGroup.add(smesh);
+                            }
+                        } // else final surface already there
+                    }
+                }
+            }
+            
+            this.setView(view); // Calls show() => renderer render
+            var time2 = new Date();
+            //console.log("render time: " + (time2 - time1));
+            return this;
+        };
+
+        /**
+         * 
+         * @param {AtomSelectionSpec}
+         *            sel
+         * @return {AtomSpec[]}
+         */
+        function getAtomsFromSel(sel) {
+            var atoms = [];
+            if (typeof (sel) === "undefined")
+                sel = {};
+
+            var ms = [];
+            var i;
+
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+
+            for (i = 0; i < ms.length; i++) {
+                atoms = atoms.concat(ms[i].selectedAtoms(sel));
+            }
+
+            return atoms;
+        }
+
+        /**
+         * 
+         * @param {AtomSpec}
+         *            atom
+         * @param {AtomSpec}
+         *            sel
+         * @return {boolean}
+         */
+        function atomIsSelected(atom, sel) {
+            if (typeof (sel) === "undefined")
+                sel = {};
+
+            var ms = [];
+            var i;
+
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+
+            for (i = 0; i < ms.length; i++) {
+                if (ms[i].atomIsSelected(atom, sel))
+                    return true;
+            }
+
+            return false;
+        }
+
+        
+        /** return list of atoms selected by sel
+         * 
+         * @function $3Dmol.GLViewer#selectedAtoms
+         * @param {AtomSelectionSpec} sel
+         * @return {Array.<Object>}
+         */
+        this.selectedAtoms = function(sel) {
+            return getAtomsFromSel(sel);
+        };
+        
+        /**
+         * Return pdb output of selected atoms (if atoms from pdb input)
+         * 
+         * @function $3Dmol.GLViewer#pdbData  
+         * @param {Object=} [sel] - Selection specification specifying model and atom properties to select.  Default: all atoms in viewer
+         * @return {string} PDB string of selected atoms
+         */
+        this.pdbData = function(sel) {
+            var atoms = getAtomsFromSel(sel);
+            var ret = "";
+            for (var i = 0, n = atoms.length; i < n; ++i) {
+                ret += atoms[i].pdbline + "\n";
+            }
+            return ret;
+        };
+
+        /**
+         * Zoom current view by a constant factor
+         * 
+         * @function $3Dmol.GLViewer#zoom
+         * @param {number}
+         *            [factor] - Magnification factor. Values greater than 1
+         *            will zoom in, less than one will zoom out. Default 2.
+         * 
+         */
+        this.zoom = function(factor) {
+            var factor = factor || 2;
+            var scale = (CAMERA_Z - rotationGroup.position.z) / factor;
+            rotationGroup.position.z = CAMERA_Z - scale;
+            show();
+            return this;
+        };
+        
+        /**
+         * Translate current view by x,y screen coordinates
+         * This pans the camera rather than translating the model.
+         * 
+         * @function $3Dmol.GLViewer#translate
+         * @param {number} x
+         * @param {number} y
+         * 
+         */
+        this.translate = function(x, y) {
+            
+            var dx = x/WIDTH;
+            var dy = y/HEIGHT;
+            var v = new $3Dmol.Vector3(0,0,-CAMERA_Z);
+
+            projector.projectVector(v, camera);
+            v.x -= dx;
+            v.y -= dy;
+            projector.unprojectVector(v, camera);
+            v.z = 0;            
+            lookingAt.add(v);
+            camera.lookAt(lookingAt);
+            show();
+            return this;
+        };
+        
+
+        /**
+         * Zoom to center of atom selection
+         * 
+         * @function $3Dmol.GLViewer#zoomTo
+         * @param {Object}
+         *            [sel] - Selection specification specifying model and atom
+         *            properties to select. Default: all atoms in viewer
+         * @example // Assuming we have created a model of a protein with
+         *          multiple chains (e.g. from a PDB file), focus on atoms in
+         *          chain B glviewer.zoomTo({chain: 'B'});
+         *  // Focus on centroid of all atoms of all models in this
+         * viewer glviewer.zoomTo(); // (equivalent to glviewer.zoomTo({}) )
+         */
+        this.zoomTo = function(sel) {
+            var allatoms, alltmp;
+            sel = sel || {};
+            var atoms = getAtomsFromSel(sel);
+            var tmp = $3Dmol.getExtent(atoms);
+
+            if($.isEmptyObject(sel)) {
+                //include shapes when zooming to full scene
+                //TODO: figure out a good way to specify shapes as part of a selection
+                $.each(shapes, function(i, shape) {
+                	if(shape && shape.boundingSphere && shape.boundingSphere.center)
+                	    var c = shape.boundingSphere.center;
+                	    var r = shape.boundingSphere.radius;
+                	    if(r > 0) {
+                	        //make sure full shape is visible
+                            atoms.push(new $3Dmol.Vector3(c.x+r,c.y,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x-r,c.y,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y+r,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y-r,c.z));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y,c.z+r));
+                            atoms.push(new $3Dmol.Vector3(c.x,c.y,c.z-r));
+                	    } else {
+                            atoms.push(c);
+                	    }
+                });
+                tmp = $3Dmol.getExtent(atoms);
+                allatoms = atoms;
+                alltmp = tmp;
+
+            }
+            else {
+                allatoms = getAtomsFromSel({});
+                alltmp = $3Dmol.getExtent(allatoms);
+            }
+
+            // use selection for center
+            var center = new $3Dmol.Vector3(tmp[2][0], tmp[2][1], tmp[2][2]);
+            modelGroup.position = center.clone().multiplyScalar(-1);
+            // but all for bounding box
+            var x = alltmp[1][0] - alltmp[0][0], y = alltmp[1][1]
+                    - alltmp[0][1], z = alltmp[1][2] - alltmp[0][2];
+
+            var maxD = Math.sqrt(x * x + y * y + z * z);
+            if (maxD < 5)
+                maxD = 5;
+
+            // use full bounding box for slab/fog
+            slabNear = -maxD / 1.9;
+            slabFar = maxD / 2;
+
+            // for zoom, use selection box
+            x = tmp[1][0] - tmp[0][0];
+            y = tmp[1][1] - tmp[0][1];
+            z = tmp[1][2] - tmp[0][2];
+            maxD = Math.sqrt(x * x + y * y + z * z);
+            if (maxD < 5)
+                maxD = 5;
+            
+            //find the farthest atom from center to get max distance needed for view
+            var maxDsq = 25;
+            for (var i = 0; i < atoms.length; i++) {
+                if(atoms[i]) {
+                    var dsq = center.distanceToSquared(atoms[i]);
+                    if(dsq > maxDsq)
+                        maxDsq = dsq;
+                }
+            }
+            
+            var maxD = Math.sqrt(maxDsq)*2;
+
+            rotationGroup.position.z = -(maxD * 0.5
+                    / Math.tan(Math.PI / 180.0 * camera.fov / 2) - CAMERA_Z);
+            show();
+            
+            return this;
+        };
+        
+        /**
+         * Set slab of view (contents outside of slab are clipped). M
+         * Must call render to update.
+         * 
+         * @function $3Dmol.GLViewer#setSlab
+         * @param {near}
+         * @param {far}
+         */
+        this.setSlab = function(near, far) {
+            slabNear = near;
+            slabFar = far;
+        };
+        
+        /**
+         * Get slab of view (contents outside of slab are clipped).
+         * 
+         * @function $3Dmol.GLViewer#setSlab
+         * @return {Object} near/far
+         */
+        this.getSlab = function(sel) {
+            return {near: slabNear, far: slabFar};
+        };
+                
+        /**
+         * Add label to viewer
+         * 
+         * @function $3Dmol.GLViewer#addLabel
+         * @param {string}
+         *            text - Label text
+         * @param {Object}
+         *            data - Label style specification
+         * @return {$3Dmol.Label}
+         * 
+         * @example
+         *  // Assuming glviewer contains a model representing a protein, label
+         * all alpha carbons with their residue name
+         *  // Select all alpha carbons (have property atom : "CA") from last
+         * model added var atoms =
+         * glviewer.getModel().selectedAtoms({atom:"CA"}); var labels = [];
+         * 
+         * for (var a in atoms) { var atom = atoms[a];
+         *  // Create label at alpha carbon's position displaying atom's residue
+         * and residue number var labelText = atom.resname + " " + atom.resi;
+         * 
+         * var l = glviewer.createLabel(labelText, {fontSize: 12, position: {x:
+         * atom.x, y: atom.y, z: atom.z});
+         * 
+         * labels.push(l); }
+
+         *  // Render labels glviewer.render();
+         */
+        this.addLabel = function(text, data) {
+            var label = new $3Dmol.Label(text, data);
+            label.setContext();
+            modelGroup.add(label.sprite);
+            labels.push(label);
+            show();
+            return label;
+        };
+        
+        /** Add residue labels.  This will generate one label per a
+         * residue within the selected atoms.  The label will be at the
+         * centroid of the atoms and styled according to the passed style.
+         * The label text will be [resn][resi]
+         * 
+         * @param {Object} sel
+         * @param {Object} style
+         */
+        this.addResLabels = function(sel, style) {
+            applyToModels("addResLabels", sel, this, style);
+            return this;
+        }
+
+        /**
+         * Remove label from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeLabel
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * 
+         * @example // Remove labels created in [addLabel example]{@link $3Dmol.GLViewer#addLabel}
+         * 
+         * for (var i = 0; i < labels.length; i++) {
+         * glviewer.removeLabel(label); }
+         * 
+         * glviewer.render();
+         */
+        this.removeLabel = function(label) {
+            //todo: don't do the linear search
+            for(var i = 0; i < labels.length; i++) {
+                if(labels[i] == label) {
+                    labels.splice(i,1);
+                    label.dispose();
+                    modelGroup.remove(label.sprite);
+                    break;
+                }
+            }
+            return this;
+        };
+
+        /**
+         * Remove all labels from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeAllLabels
+         */
+        this.removeAllLabels = function() {
+            for (var i = 0; i < labels.length; i++) {
+                modelGroup.remove(labels[i].sprite);
+            }
+            labels.splice(0,labels.length); //don't overwrite in case linked
+            return this;
+        };
+        
+        // Modify label style
+        /**
+         * Modify existing label's style
+         * 
+         * @function $3Dmol.GLViewer#setLabelStyle
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * @param {Object}
+         *            stylespec - Label style specification
+         * @return {$3Dmol.Label}
+         */
+        this.setLabelStyle = function(label, stylespec) {
+            modelGroup.remove(label.sprite);
+            label.dispose();
+            label.stylespec = stylespec;
+            label.setContext();
+            modelGroup.add(label.sprite);
+            show();
+            return label;
+
+        };
+
+        // Change label text
+        /**
+         * Modify existing label's text
+         * 
+         * @function $3Dmol.GLViewer#setLabelText
+         * @param {$3Dmol.Label}
+         *            label - $3Dmol label
+         * @param {String}
+         *            text - Label text
+         * @return {$3Dmol.Label}
+         */
+        this.setLabelText = function(label, text) {
+            modelGroup.remove(label.sprite);
+            label.dispose();
+            label.text = text;
+            label.setContext();
+            modelGroup.add(label.sprite);
+            show();
+            return label;
+
+        };
+
+        /**
+         * Add shape object to viewer 
+         * @see {@link $3Dmol.GLShape}
+         * 
+         * @function $3Dmol.GLViewer#addShape
+         * @param {ShapeSpec} shapeSpec - style specification for label
+         * @return {$3Dmol.GLShape}
+         */
+        this.addShape = function(shapeSpec) {
+            shapeSpec = shapeSpec || {};
+            var shape = new $3Dmol.GLShape(shapeSpec);
+            shape.shapePosition = shapes.length;
+            shapes.push(shape);
+
+            return shape;
+
+        };
+
+        /**
+         * Remove shape object from viewer
+         *
+         * @function $3Dmol.GLViewer#removeShape
+         * @param {$3Dmol.GLShape} shape - Reference to shape object to remove
+         */
+        this.removeShape = function(shape) {
+            if (!shape)
+                return this;
+            shape.removegl(modelGroup);
+            delete shapes[shape.shapePosition];
+            // clear off back of model array
+            while (shapes.length > 0
+                    && typeof (shapes[shapes.length - 1]) === "undefined")
+                shapes.pop();
+            return this;
+        };
+        
+        /**
+         * Remove all shape objects from viewer
+         * @function $3Dmol.GLViewer#removeAllShapes
+         */
+        this.removeAllShapes = function() {
+            for (var i = 0; i < shapes.length; i++) {
+                var shape = shapes[i];
+                shape.removegl(modelGroup);
+            }
+            shapes.splice(0,shapes.length);
+            return this;
+        }
+
+        /**
+         * Create and add sphere shape. This method provides a shorthand 
+         * way to create a spherical shape object
+         * 
+         * @function $3Dmol.GLViewer#addSphere
+         * @param {SphereSpec} spec - Sphere shape style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addSphere = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addSphere(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Create and add arrow shape
+         * 
+         * @function $3Dmol.GLViewer#addArrow
+         * @param {ArrowSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addArrow = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addArrow(spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Create and add cylinder shape
+         * 
+         * @function $3Dmol.GLViewer#addCylinder
+         * @param {CylinderSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCylinder = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addCylinder(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Create and add line shape
+         * 
+         * @function $3Dmol.GLViewer#addLine
+         * @param {LineSpec} spec - Style specification, can specify dashed, dashLength, and gapLength
+         * @return {$3Dmol.GLShape}
+         */
+        this.addLine = function(spec) {
+            spec = spec || {};
+            spec.wireframe = true;
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            if (spec.dashed)
+                s = addLineDashed(spec, s);
+            else
+                s.addLine(spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        
+        /**
+         * Create and add unit cell
+         *
+         * @function $3Dmol.GLViewer#addUnitCell
+         * @param {GLModel} Model with unit cell information (e.g., pdb derived).
+         * @return {$3Dmol.GLShape}  Line shape delineating unit cell.
+         */
+        this.addUnitCell = function(model) {
+
+            var s = new $3Dmol.GLShape({'wireframe' : true});
+            s.shapePosition = shapes.length;
+            var data = model.getCrystData();
+            if (data) {
+                var a = data.a, b = data.b, c = data.c, alpha = data.alpha, beta = data.beta, gamma = data.gamma;
+                alpha = alpha * Math.PI/180.0;
+                beta = beta * Math.PI/180.0;
+                gamma = gamma * Math.PI/180.0;
+            
+                var u, v, w;
+            
+                u = Math.cos(beta);
+                v = (Math.cos(alpha) - Math.cos(beta)*Math.cos(gamma))/Math.sin(gamma);
+                w = Math.sqrt(Math.max(0, 1-u*u-v*v));
+            
+                var matrix = new $3Dmol.Matrix4(a, b*Math.cos(gamma), c*u, 0, 
+                                                0, b*Math.sin(gamma), c*v, 0,
+                                                0, 0,                 c*w, 0,
+                                                0, 0,                 0,   1); 
+         
+                var points = [  new $3Dmol.Vector3(0, 0, 0),
+                                new $3Dmol.Vector3(1, 0, 0),
+                                new $3Dmol.Vector3(0, 1, 0),
+                                new $3Dmol.Vector3(0, 0, 1),
+                                new $3Dmol.Vector3(1, 1, 0),
+                                new $3Dmol.Vector3(0, 1, 1),
+                                new $3Dmol.Vector3(1, 0, 1),
+                                new $3Dmol.Vector3(1, 1, 1)  ];
+                            
+                for (var i = 0; i < points.length; i++) {
+                    points[i] = points[i].applyMatrix4(matrix);
+                }
+            
+                s.addLine({start: points[0], end: points[1]});
+                s.addLine({start: points[0], end: points[2]});
+                s.addLine({start: points[1], end: points[4]});
+                s.addLine({start: points[2], end: points[4]});
+            
+                s.addLine({start: points[0], end: points[3]});
+                s.addLine({start: points[3], end: points[5]});
+                s.addLine({start: points[2], end: points[5]});
+            
+                s.addLine({start: points[1], end: points[6]});
+                s.addLine({start: points[4], end: points[7]});
+                s.addLine({start: points[6], end: points[7]});
+            
+                s.addLine({start: points[3], end: points[6]});
+                s.addLine({start: points[5], end: points[7]});
+            }
+            
+            shapes.push(s);
+            return s;
+        };
+
+        function addLineDashed(spec, s) {
+            spec.dashLength = spec.dashLength || 0.5;
+            spec.gapLength = spec.gapLength || 0.5;
+            spec.start = spec.start || {};
+            spec.end = spec.end || {};
+            
+            var p1 = new $3Dmol.Vector3(spec.start.x || 0,
+        			spec.start.y || 0, spec.start.z || 0)
+        	var p2 = new $3Dmol.Vector3(spec.end.x,
+        			spec.end.y || 0, spec.end.z || 0);
+        			
+            var dir = new $3Dmol.Vector3();
+            var dash = new $3Dmol.Vector3();
+            var gap = new $3Dmol.Vector3();
+            var length, dashAmt, gapAmt;
+            var temp = p1.clone();
+            var drawn = 0;
+
+            dir.subVectors(p2, p1);
+            length = dir.length();
+            dir.normalize();
+            dash = dir.clone();
+            gap = dir.clone();
+            dash.multiplyScalar(spec.dashLength);
+            gap.multiplyScalar(spec.gapLength);
+            dashAmt = dash.length();
+            gapAmt = gap.length();
+
+            while (drawn < length) {
+                if ((drawn + dashAmt) > length) { 
+                    spec.start = p1;
+                    spec.end = p2;
+                    s.addLine(spec);
+                    break;
+                }
+                temp.addVectors(p1, dash); 
+                spec.start = p1;
+                spec.end = temp;
+                s.addLine(spec);
+                p1 = temp.clone();
+                drawn += dashAmt;
+
+                temp.addVectors(p1, gap);
+                p1 = temp.clone();   
+                drawn += gapAmt;
+            }
+        			
+        	return s;
+        }
+
+        /**
+         * Add custom shape component from user supplied function
+         * 
+         * @function $3Dmol.GLViewer#addCustom
+         * @param {CustomSpec} spec - Style specification
+         * @return {$3Dmol.GLShape}
+         */
+        this.addCustom = function(spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addCustom(spec);
+            shapes.push(s);
+
+            return s;
+        };
+
+        /**
+         * Construct isosurface from volumetric data in gaussian cube format
+         * @deprecated
+         * @function $3Dmol.GLViewer#addVolumetricData
+         * @param {String} data - Input file contents 
+         * @param {String} format - Input file format (currently only supports "cube")
+         * @param {IsoSurfaceSpec} spec - Shape style specification
+         * @return {$3Dmol.GLShape}
+         * 
+         * @example
+         * viewer.addVolumetricData(data, "cube", {isoval: 0.01, color: "blue", opacity: 0.95});              
+         * viewer.addVolumetricData(data, "cube", {isoval: -0.01, color: "red", opacity: 0.95}); 
+         */
+        this.addVolumetricData = function(data, format, spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addVolumetricData(data, format, spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Construct isosurface from volumetric data
+         * @function $3Dmol.GLViewer#addIsosurface
+         * @param {$3Dmol.VolumeData} data - volumetric data
+         * @param {IsoSurfaceSpec} spec - Shape style specification
+         * @return {$3Dmol.GLShape}
+         * 
+         * @example
+         * var data = new $3Dmol.VolumeData(str,"cube");
+         * viewer.addIsosurface(data, {isoval: 0.01, color: "blue", opacity: 0.95});              
+         * viewer.addIsosurface(data, {isoval: -0.01, color: "red", opacity: 0.95}); 
+         */
+        this.addIsosurface = function(data,  spec) {
+            spec = spec || {};
+            var s = new $3Dmol.GLShape(spec);
+            s.shapePosition = shapes.length;
+            s.addIsosurface(data, spec);
+            shapes.push(s);
+
+            return s;
+        };
+        
+        /**
+         * Sets the atomlists of all models in the viewer to specified frame
+         * Sets to last frame if framenum out of range
+         * 
+         * @function $3Dmol.GLViewer#setFrame
+         * @param {number} framenum - each model in viewer has their atoms set to this index in frames list
+         */
+        this.setFrame = function(framenum) {
+            for (var i = 0; i < models.length; i++) {
+                models[i].setFrame(framenum);
+            }
+            return this;
+        };
+        
+        /**
+         * Returns the number of frames that the model with the most frames in the viewer has
+         * 
+         * @function $3Dmol.GLViewer#getFrames
+         * @return {number}
+         */
+        this.getFrames = function() {
+            var mostFrames = 0;
+            var modelNum = 0;
+            for (var i = 0; i < models.length; i++) {
+                if (models[i].getFrames().length > mostFrames) {
+                    modelNum = i;
+                    mostFrames = models[i].getFrames().length;
+                }
+            }
+            return mostFrames;
+        };
+        
+
+        /**
+         * Animate all models in viewer from their respective frames
+         * @function $3Dmol.GLViewer#animate
+         * @param {Object} options - can specify interval (speed of animation), loop (direction
+         * of looping, 'backward', 'forward' or 'backAndForth') and reps (numer of repetitions, 0 indicates infinite loop)
+         *      
+         * @example
+         * viewer.addModelAsFrames(data, "pdb");
+         * viewer.animate({interval: 75, loop: "backward", reps: 30});
+         */
+        this.animate = function(options) {
+            animated = true;
+            var interval = 100;
+            var loop = "forward";
+            var reps = 0;
+            options = options || {};
+            if (options.interval) {
+                interval = options.interval;
+            }
+            if (options.loop) {
+                loop = options.loop;
+            }
+            if (options.reps) {
+                reps = options.reps;
+            }
+            var mostFrames = this.getFrames();
+            var that = this;
+            var currFrame = 0;
+            var inc = 1;
+            var displayCount = 0;
+            var displayMax = mostFrames * reps;
+            var display = function(direction) {
+                if (direction == "forward") {
+                    that.setFrame(currFrame);
+                    currFrame = (currFrame + inc) % mostFrames;
+                }
+                else if (direction == "backward") {
+                    that.setFrame((mostFrames-1) - currFrame);
+                    currFrame = (currFrame + inc) % mostFrames;
+                }
+                else { //back and forth
+                    that.setFrame(currFrame);
+                    currFrame += inc;
+                    inc *= (((currFrame % (mostFrames-1)) == 0) ? -1 : 1);
+                }
+                that.render();
+                if (++displayCount == displayMax || !that.isAnimated()) {
+                    clearInterval(intervalID);
+                }
+            };
+            var intervalID = setInterval( function() { display(loop); }, interval);
+            return this;
+        };
+        
+        /**
+         * Stop animation of all models in viewer
+         * @function $3Dmol.GLViewer#stopAnimate
+         */
+        this.stopAnimate = function() {
+            animated = false;
+            return this;
+        };
+        
+        /**
+         * Return true if viewer is currently being animated, false otherwise
+         * @function $3Dmol.GLViewer#isAnimated
+         * @return {boolean}
+         */
+        this.isAnimated = function() {
+            return animated;
+        };
+        
+
+        /**
+         * Create and add model to viewer, given molecular data and its format 
+         * (pdb, sdf, xyz, or mol2)
+         * 
+         * @function $3Dmol.GLViewer#addModel
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addModel = function(data, format, options) {
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+
+            return m;
+        };
+        
+        /**
+         * Given multimodel file and its format, add atom data to the viewer as separate models
+         * and return list of these models
+         * 
+         * @function $3Dmol.GLViewer#addModels
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {Array<$3Dmol.GLModel>}
+         */
+        this.addModels = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.frames = true;
+
+            var modelatoms = $3Dmol.GLModel.parseMolData(data, format, options);
+
+            for (var i = 0; i < modelatoms.length; i++) {
+                var newModel = new $3Dmol.GLModel(models.length, defaultcolors);
+                newModel.setAtomDefaults(modelatoms[i]);
+                newModel.addFrame(modelatoms[i]);
+                newModel.setFrame(0);
+                newModel.setModelData(modelatoms.modelData[i]);
+                newModel.setDontDuplicateAtoms(!options.duplicateAssemblyAtoms);
+                models.push(newModel);
+            }
+            
+            return models;
+        };
+        
+        /**
+         * Create and add model to viewer. Given multimodel file and its format, 
+         * different atomlists are stored in model's frame
+         * property and model's atoms are set to the 0th frame
+         * 
+         * @function $3Dmol.GLViewer#addModelsAsFrames
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addModelsAsFrames = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.frames = true;
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+
+            return m;
+        };
+        
+        /**
+         * Create and add model to viewer. Given multimodel file and its format,
+         * all atoms are added to one model
+         * 
+         * @function $3Dmol.GLViewer#addAsOneMolecule
+         * @param {string} data - Input data
+         * @param {string} format - Input format ('pdb', 'sdf', 'xyz', or 'mol2')
+         * @return {$3Dmol.GLModel}
+         */
+        this.addAsOneMolecule = function(data, format, options) {
+            options = options || {};
+            options.multimodel = true;
+            options.onemol = true;
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            m.addMolData(data, format, options);
+            models.push(m);
+            
+            return m;
+        };
+        
+
+        /**
+         * Delete specified model from viewer
+         * 
+         * @function $3Dmol.GLViewer#removeModel
+         * @param {$3Dmol.GLModel} model
+         */
+        this.removeModel = function(model) {
+            if (!model)
+                return;
+            model.removegl(modelGroup);
+            delete models[model.getID()];
+            // clear off back of model array
+            while (models.length > 0
+                    && typeof (models[models.length - 1]) === "undefined")
+                models.pop();
+            return this;
+        };
+
+        /** 
+         * Delete all existing models
+         * @function $3Dmol.GLViewer#removeAllModels
+         */
+        this.removeAllModels = function() {
+            for (var i = 0; i < models.length; i++) {
+                var model = models[i];
+                model.removegl(modelGroup);
+
+            }
+            models.splice(0,models.length); //don't simply overwrite array in case linked
+            return this;
+        };
+
+        /**
+         * Export one or all of the loaded models into ChemDoodle compatible JSON.
+         * @function $3Dmol.GLViewer#exportJSON
+         * @param {boolean} includeStyles - Whether or not to include style information.
+         * @param {number} modelID - Optional parameter for which model to export. If left out, export all of them.
+         * @return {string}
+         */
+        this.exportJSON = function(includeStyles, modelID) {
+            var object = {};
+            if (modelID === undefined) {
+                object.m = models.map(function(model) {
+                    return model.toCDObject(includeStyles);
+                });
+            } else {
+                object.m = [ model[modelID].toCDObject() ];
+            }
+            return JSON.stringify(object);
+        }
+
+        /**
+         * Create a new model from atoms specified by sel.
+         * If extract, removes selected atoms from existing models 
+         * 
+         * @function $3Dmol.GLViewer#createModelFrom
+         * @param {Object} sel - Atom selection specification
+         * @param {boolean=} extract - If true, remove selected atoms from existing models
+         * @return {$3Dmol.GLModel}
+         */
+        this.createModelFrom = function(sel, extract) {
+            var m = new $3Dmol.GLModel(models.length, defaultcolors);
+            for (var i = 0; i < models.length; i++) {
+                if (models[i]) {
+                    var atoms = models[i].selectedAtoms(sel);
+                    m.addAtoms(atoms);
+                    if (extract)
+                        models[i].removeAtoms(atoms);
+                }
+            }
+            models.push(m);
+            return m;
+        };
+
+        function applyToModels(func, sel, value1, value2) {
+            
+            //apply func to all models that are selected by sel with value1 and 2
+            var ms = []
+            if (typeof sel.model === "undefined") {
+                for (i = 0; i < models.length; i++) {
+                    if (models[i])
+                        ms.push(models[i]);
+                }
+            } else { // specific to some models
+                ms = sel.model;
+                if (!$.isArray(ms))
+                    ms = [ ms ];
+            }
+            
+            
+            for (var i = 0; i < ms.length; i++) {
+                if (ms[i]) {
+                    ms[i][func](sel, value1, value2);
+                }
+            }
+        }
+
+        /**
+         * Set style properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#setStyle
+         * @param {AtomSelectionSpec} sel - Atom selection specification
+         * @param {AtomStyleSpec} style - Style spec to apply to specified atoms
+         * 
+         * @example
+         * viewer.setStyle({}, {stick:{}}); //set all atoms to stick
+         * viewer.setStyle({chain: 'B'}, {cartoon: {color: 'spectrum'}}); //set chain B to rainbow cartoon
+         */
+        this.setStyle = function(sel, style) {
+            if(typeof(style) === 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            
+            applyToModels("setStyle", sel, style, false);
+            return this;
+        };
+
+        /**
+         * Add style properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#addStyle
+         * @param {AtomSelectionSpec} sel - Atom selection specification
+         * @param {AtomStyleSpec} style - style spec to add to specified atoms
+         */
+        this.addStyle = function(sel, style) {
+            if(typeof(style) === 'undefined') {
+                //if a single argument is provided, assume it is a style and select all
+                style = sel;
+                sel = {};
+            }
+            applyToModels("setStyle", sel, style, true);
+            return this;
+        };
+
+        /**
+         * Set click-handling properties to all selected atoms
+         * 
+         * @function $3Dmol.GLViewer#setClickable
+         * @param {AtomSelectionSpec} sel - atom selection to apply clickable settings to
+         * @param {boolean} clickable - whether click-handling is enabled for the selection
+         * @param {function} callback - function called when an atom in the selection is clicked
+         * 
+         * @example
+         * viewer.setClickable({}, false); // disable click-handling for entire viewer
+         * viewer.setClickable({chain: 'B'}, true, function(){ console.log(this.elem); }); // chain B prints the clicked element to console
+         */
+        this.setClickable = function(sel, clickable, callback) {
+            applyToModels("setClickable", sel, clickable, callback);
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#setColorByProperty
+         * @param {AtomSelectionSpec} sel
+         * @param {type} prop
+         * @param {type} scheme
+         */
+        this.setColorByProperty = function(sel, prop, scheme) {
+            applyToModels("setColorByProperty", sel, prop, scheme);
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#setColorByElement
+         * @param {AtomSelectionSpec} sel
+         * @param {type} colors
+         */
+        this.setColorByElement = function(sel, colors) {
+            applyToModels("setColorByElement", sel, colors);
+            return this;
+        };
+
+        /**
+         * 
+         * @param {AtomSpec[]} atomlist
+         * @param {Array}
+         *            extent
+         * @return {Array}
+         */
+        var getAtomsWithin = function(atomlist, extent) {
+            var ret = [];
+
+            for (var i = 0; i < atomlist.length; i++) {
+                var atom = atomlist[i];
+                if (typeof (atom) == "undefined")
+                    continue;
+
+                if (atom.x < extent[0][0] || atom.x > extent[1][0])
+                    continue;
+                if (atom.y < extent[0][1] || atom.y > extent[1][1])
+                    continue;
+                if (atom.z < extent[0][2] || atom.z > extent[1][2])
+                    continue;
+                ret.push(i);
+            }
+            return ret;
+        };
+
+        // return volume of extent
+        var volume = function(extent) {
+            var w = extent[1][0] - extent[0][0];
+            var h = extent[1][1] - extent[0][1];
+            var d = extent[1][2] - extent[0][2];
+            return w * h * d;
+        }; // volume
+        /*
+         * Break up bounding box/atoms into smaller pieces so we can parallelize
+         * with webworkers and also limit the size of the working memory Returns
+         * a list of bounding boxes with the corresponding atoms. These extents
+         * are expanded by 4 angstroms on each side.
+         */
+        /**
+         * 
+         * @param {Array}
+         *            extent
+         * @param {AtomSpec[]} atomlist
+         * @param {AtomSpec[]} atomstoshow
+         * @return {Array}
+         */
+        var carveUpExtent = function(extent, atomlist, atomstoshow) {
+            var ret = [];
+
+            var copyExtent = function(extent) {
+                // copy just the dimensions
+                var ret = [];
+                ret[0] = [ extent[0][0], extent[0][1], extent[0][2] ];
+                ret[1] = [ extent[1][0], extent[1][1], extent[1][2] ];
+                return ret;
+            }; // copyExtent
+            var splitExtentR = function(extent) {
+                // recursively split until volume is below maxVol
+                if (volume(extent) < maxVolume) {
+                    return [ extent ];
+                } else {
+                    // find longest edge
+                    var w = extent[1][0] - extent[0][0];
+                    var h = extent[1][1] - extent[0][1];
+                    var d = extent[1][2] - extent[0][2];
+
+                    var index;
+
+                    if (w > h && w > d) {
+                        index = 0;
+                    } else if (h > w && h > d) {
+                        index = 1;
+                    } else {
+                        index = 2;
+                    }
+
+                    // create two halves, splitting at index
+                    var a = copyExtent(extent);
+                    var b = copyExtent(extent);
+                    var mid = (extent[1][index] - extent[0][index]) / 2
+                            + extent[0][index];
+                    a[1][index] = mid;
+                    b[0][index] = mid;
+
+                    var alist = splitExtentR(a);
+                    var blist = splitExtentR(b);
+                    return alist.concat(blist);
+                }
+            }; // splitExtentR
+
+            // divide up extent
+            var splits = splitExtentR(extent);
+            // now compute atoms within expanded (this could be more efficient)
+            var off = 6; // enough for water and 2*r, also depends on scale
+            // factor
+            for (var i = 0, n = splits.length; i < n; i++) {
+                var e = copyExtent(splits[i]);
+                e[0][0] -= off;
+                e[0][1] -= off;
+                e[0][2] -= off;
+                e[1][0] += off;
+                e[1][1] += off;
+                e[1][2] += off;
+
+                var atoms = getAtomsWithin(atomlist, e);
+                var toshow = getAtomsWithin(atomstoshow, splits[i]);
+
+                // ultimately, divide up by atom for best meshing
+                ret.push({
+                    extent : splits[i],
+                    atoms : atoms,
+                    toshow : toshow
+                });
+            }
+
+            return ret;
+        };
+
+        // create a mesh defined from the passed vertices and faces and material
+        // Just create a single geometry chunk - broken up whether sync or not
+        /**
+         * 
+         * @param {AtomSpec[]} atoms
+         * @param {{vertices:number,faces:number}}
+         *            VandF
+         * @param {$3Dmol.MeshLambertMaterial}
+         *            mat
+         * @return {$3Dmol.Mesh}
+         */
+        var generateSurfaceMesh = function(atoms, VandF, mat) {
+            var geo = new $3Dmol.Geometry(true);
+            // Only one group per call to generate surface mesh (addSurface
+            // should split up mesh render)
+            var geoGroup = geo.updateGeoGroup(0);
+
+            // set colors for vertices
+            var colors = [];
+            for (i = 0, il = atoms.length; i < il; i++) {
+                var atom = atoms[i];
+                if (atom) {
+                    if (typeof (atom.surfaceColor) != "undefined") {
+                        colors[i] = atom.surfaceColor;
+                    } else if (atom.color) // map from atom
+                        colors[i] = $3Dmol.CC.color(atom.color);
+                }
+            }
+            
+            var vertexArray = geoGroup.vertexArray;
+
+            // reconstruct vertices and faces
+            var v = VandF['vertices'];
+            var offset;
+            var i, il;
+            for (i = 0, il = v.length; i < il; i++) {
+                offset = geoGroup.vertices * 3;
+                vertexArray[offset] = v[i].x;
+                vertexArray[offset + 1] = v[i].y;
+                vertexArray[offset + 2] = v[i].z;
+                geoGroup.vertices++;                
+            }
+
+            //set colorArray of there are per-atom colors
+            var colorArray = geoGroup.colorArray;
+            
+            if(mat.voldata && mat.volscheme) {
+                //convert volumetric data into colors
+                var scheme = mat.volscheme;
+                var voldata = mat.voldata;
+                var range = scheme.range() || [-1,1];
+                for (i = 0, il = v.length; i < il; i++) {
+                    var val = voldata.getVal(v[i].x,v[i].y,v[i].z);
+                    var col =  $3Dmol.CC.color(scheme.valueToHex(val, range));
+                    var offset = i * 3;
+                    colorArray[offset] = col.r;
+                    colorArray[offset + 1] = col.g;
+                    colorArray[offset + 2] = col.b;
+                }
+            }
+            else if(colors.length > 0) { //have atom colors
+                for (i = 0, il = v.length; i < il; i++) {
+                    var A = v[i].atomid;
+                    var offsetA = i * 3;
+
+                    colorArray[offsetA] = colors[A].r;
+                    colorArray[offsetA + 1] = colors[A].g;
+                    colorArray[offsetA + 2] = colors[A].b;
+                }
+            }
+            
+            var faces = VandF['faces'];
+            geoGroup.faceidx = faces.length;// *3;
+            geo.initTypedArrays();
+
+            var verts = geoGroup.vertexArray;
+            var normalArray = geoGroup.normalArray;
+            var vA, vB, vC, norm;
+
+            // Setup colors, faces, and normals
+            for (i = 0, il = faces.length; i < il; i += 3) {
+
+                // var a = faces[i].a, b = faces[i].b, c = faces[i].c;
+                var a = faces[i], b = faces[i + 1], c = faces[i + 2];
+                var A = v[a]['atomid'];
+                var B = v[b]['atomid'];
+                var C = v[c]['atomid'];
+
+                var offsetA = a * 3, offsetB = b * 3, offsetC = c * 3;
+
+                // setup Normals
+                // todo - calculate normals in parallel code
+                vA = new $3Dmol.Vector3(verts[offsetA], verts[offsetA + 1],
+                        verts[offsetA + 2]);
+                vB = new $3Dmol.Vector3(verts[offsetB], verts[offsetB + 1],
+                        verts[offsetB + 2]);
+                vC = new $3Dmol.Vector3(verts[offsetC], verts[offsetC + 1],
+                        verts[offsetC + 2]);
+
+                vC.subVectors(vC, vB);
+                vA.subVectors(vA, vB);
+                vC.cross(vA);
+
+                // face normal
+                norm = vC;
+                norm.normalize();
+
+                normalArray[offsetA] += norm.x;
+                normalArray[offsetB] += norm.x;
+                normalArray[offsetC] += norm.x;
+                normalArray[offsetA + 1] += norm.y;
+                normalArray[offsetB + 1] += norm.y;
+                normalArray[offsetC + 1] += norm.y;
+                normalArray[offsetA + 2] += norm.z;
+                normalArray[offsetB + 2] += norm.z;
+                normalArray[offsetC + 2] += norm.z;
+
+            }
+            geoGroup.faceArray = new Uint16Array(faces);
+            var mesh = new $3Dmol.Mesh(geo, mat);
+            mesh.doubleSided = true;        
+            return mesh;
+        };
+
+        // do same thing as worker in main thread
+        /**
+         * 
+         * @param {$3Dmol.SurfaceType}
+         *            type
+         * @param {Array}
+         *            expandedExtent
+         * @param {Array}
+         *            extendedAtoms
+         * @param {Array}
+         *            atomsToShow
+         * @param {AtomSpec[]} atoms
+         * @param {number}
+         *            vol
+         * @return {Object}
+         */
+        var generateMeshSyncHelper = function(type, expandedExtent,
+                extendedAtoms, atomsToShow, atoms, vol) {
+            var time = new Date();
+            var ps = new $3Dmol.ProteinSurface();
+            ps.initparm(expandedExtent, (type === 1) ? false : true, vol);
+
+            var time2 = new Date();
+            //console.log("initialize " + (time2 - time) + "ms");
+
+            ps.fillvoxels(atoms, extendedAtoms);
+
+            var time3 = new Date();
+            //console.log("fillvoxels " + (time3 - time2) + "  " + (time3 - time) + "ms");
+
+            ps.buildboundary();
+
+            if (type == $3Dmol.SurfaceType.SES) {
+                ps.fastdistancemap();
+                ps.boundingatom(false);
+                ps.fillvoxelswaals(atoms, extendedAtoms);
+            }
+
+            var time4 = new Date();
+            //console.log("buildboundaryetc " + (time4 - time3) + "  " + (time4 - time) + "ms");
+
+            ps.marchingcube(type);
+
+            var time5 = new Date();
+            //console.log("marching cube " + (time5 - time4) + "  "+ (time5 - time) + "ms");
+
+            return ps.getFacesAndVertices(atomsToShow);
+        };
+
+        /**
+         * 
+         * @param {matSpec}
+         *            style
+         * @return {$3Dmol.MeshLambertMaterial}
+         */
+        function getMatWithStyle(style) {
+            var mat = new $3Dmol.MeshLambertMaterial();
+            mat.vertexColors = $3Dmol.VertexColors;
+
+            for ( var prop in style) {
+                if (prop === "color" || prop === "map") {
+                    // ignore
+                } else if (style.hasOwnProperty(prop))
+                    mat[prop] = style[prop];
+            }
+            if (style.opacity !== undefined) {
+                if (style.opacity === 1)
+                    mat.transparent = false;
+                else
+                    mat.transparent = true;
+            }
+
+            return mat;
+        }
+
+        
+        /**
+         * Adds an explicit mesh as a surface object.
+         * 
+         * @param {$3Dmol.Mesh}
+         *            mesh
+         * @param {Object}
+         *            style
+         * @returns {Number} surfid
+         */
+        this.addMesh = function(mesh) {
+            var surfobj = {
+                geo : mesh.geometry,
+                mat : mesh.material,
+                done : true,
+                finished : false //the rendered finishes surfaces when they are done
+            };
+            var surfid = nextSurfID();
+            surfaces[surfid] = surfobj;
+            return surfid;
+        }
+
+        //return a shallow copy of list l, e.g., for atoms so we can
+        //ignore superficial changes (ie surfacecolor, position) that happen
+        //while we're surface building
+        var shallowCopy = function(l) {
+            var ret = [];
+            $.each(l, function(k,v) {
+                ret[k] = $.extend({},v);
+            });
+            return ret;
+        }
+        /**
+         * Add surface representation to atoms
+         *  @function $3Dmol.GLViewer#addSurface
+         * @param {$3Dmol.SurfaceType} type - Surface type
+         * @param {SurfaceStyleSpec} style - optional style specification for surface material (e.g. for different coloring scheme, etc)
+         * @param {AtomSelectionSpec} atomsel - Show surface for atoms in this selection
+         * @param {AtomSelectionSpec} allsel - Use atoms in this selection to calculate surface; may be larger group than 'atomsel' 
+         * @param {AtomSelectionSpec} focus - Optionally begin rendering surface specified atoms
+         * 
+         * @return {number} surfid - Identifying number for this surface
+         */
+        this.addSurface = function(type, style, atomsel, allsel, focus) {
+            // type 1: VDW 3: SAS 4: MS 2: SES
+            // if sync is true, does all work in main thread, otherwise uses
+            // workers
+            // with workers, must ensure group is the actual modelgroup since
+            // surface
+            // will get added asynchronously
+            // all atoms in atomlist are used to compute surfaces, but only the
+            // surfaces
+            // of atomsToShow are displayed (e.g., for showing cavities)
+            // if focusSele is specified, will start rending surface around the
+            // atoms specified by this selection
+            var atomlist = null, focusSele = null;
+            //TODO: currently generating a shallow copy to avoid problems when atoms are chagned
+            //during surface generation - come up with a better solution
+            var atomsToShow = shallowCopy(getAtomsFromSel(atomsel));
+            if(!allsel) {
+                atomlist = atomsToShow;
+            }
+            else {
+                atomlist = shallowCopy(getAtomsFromSel(allsel));
+            }
+            
+            var symmetries = false;
+            var n;
+            for (n = 0; n < models.length; n++) { 
+                if(models[n]) {
+                    var symMatrices = models[n].getSymmetries();
+                    if (symMatrices.length > 1 || (symMatrices.length == 1 && !(symMatrices[0].isIdentity()))) {
+                        symmetries = true;
+                        break;
+                    }
+                }
+            }
+
+            var addSurfaceHelper = function addSurfaceHelper(surfobj, atomlist, atomsToShow) {
+            
+                if(!focus) {
+                    focusSele = atomsToShow;
+                } else {
+                    focusSele = shallowCopy(getAtomsFromSel(focus));
+                }
+
+                var atom;
+                var time = new Date();
+                var extent = $3Dmol.getExtent(atomsToShow, true);
+
+                var i, il;
+                if (style['map'] && style['map']['prop']) {
+                    // map color space using already set atom properties
+                    /** @type {AtomSpec} */
+                    var prop = style['map']['prop'];
+                    /** @type {Gradient} */
+                    var scheme = style['map']['scheme'] || style['map']['gradient'] || new $3Dmol.Gradient.RWB();
+                    var range = scheme.range();
+                    if (!range) {
+                        range = $3Dmol.getPropertyRange(atomsToShow, prop);
+                    }
+                    style.colorscheme = {prop: prop, gradient: scheme};
+
+                }
+                
+                //cache surface color on each atom
+                for (i = 0, il = atomlist.length; i < il; i++) {
+                    atom = atomlist[i];
+                    atom.surfaceColor = $3Dmol.getColorFromStyle(atom, style);
+                }                
+
+                var totalVol = volume(extent); // used to scale resolution
+                var extents = carveUpExtent(extent, atomlist, atomsToShow);
+
+                if (focusSele && focusSele.length && focusSele.length > 0) {
+                    var seleExtent = $3Dmol.getExtent(focusSele, true);
+                    // sort by how close to center of seleExtent
+                    var sortFunc = function(a, b) {
+                        var distSq = function(ex, sele) {
+                            // distance from e (which has no center of mass) and
+                            // sele which does
+                            var e = ex.extent;
+                            var x = e[1][0] - e[0][0];
+                            var y = e[1][1] - e[0][1];
+                            var z = e[1][2] - e[0][2];
+                            var dx = (x - sele[2][0]);
+                            dx *= dx;
+                            var dy = (y - sele[2][1]);
+                            dy *= dy;
+                            var dz = (z - sele[2][2]);
+                            dz *= dz;
+
+                            return dx + dy + dz;
+                        };
+                        var d1 = distSq(a, seleExtent);
+                        var d2 = distSq(b, seleExtent);
+                        return d1 - d2;
+                    };
+                    extents.sort(sortFunc);
+                }
+
+                //console.log("Extents " + extents.length + "  "+ (+new Date() - time) + "ms");
+
+
+                var reducedAtoms = [];
+                // to reduce amount data transfered, just pass x,y,z,serial and elem
+                for (i = 0, il = atomlist.length; i < il; i++) {
+                    atom = atomlist[i];
+                    reducedAtoms[i] = {
+                        x : atom.x,
+                        y : atom.y,
+                        z : atom.z,
+                        serial : i,
+                        elem : atom.elem
+                    };
+                }
+
+                var sync = !!($3Dmol.syncSurface);
+                if (sync) { // don't use worker, still break up for memory purposes
+
+                    // to keep the browser from locking up, call through setTimeout
+                    var callSyncHelper = function callSyncHelper(i) {
+                        if (i >= extents.length)
+                            return;
+
+                        var VandF = generateMeshSyncHelper(type, extents[i].extent,
+                                extents[i].atoms, extents[i].toshow, reducedAtoms,
+                                totalVol);
+                        var mesh = generateSurfaceMesh(atomlist, VandF, mat);
+                        $3Dmol.mergeGeos(surfobj.geo, mesh);
+                        _viewer.render();
+
+                        setTimeout(callSyncHelper, 1, i + 1);
+                    }
+
+                    setTimeout(callSyncHelper, 1, 0);
+
+                    // TODO: Asynchronously generate geometryGroups (not separate
+                    // meshes) and merge them into a single geometry
+                } else { // use worker
+
+                    var workers = [];
+                    if (type < 0)
+                        type = 0; // negative reserved for atom data
+                    for (i = 0, il = numWorkers; i < il; i++) {
+                        // var w = new Worker('3Dmol/SurfaceWorker.js');
+                        var w = new Worker($3Dmol.SurfaceWorker);
+                        workers.push(w);
+                        w.postMessage({
+                            'type' : -1,
+                            'atoms' : reducedAtoms,
+                            'volume' : totalVol
+                        });
+                    }
+                    var cnt = 0;
+
+                    var rfunction = function(event) {
+                        var VandFs = $3Dmol.splitMesh({vertexArr:event.data.vertices,
+							                           faceArr:event.data.faces});
+					    for(var i=0,vl=VandFs.length;i<vl;i++){
+                            var VandF={vertices:VandFs[i].vertexArr,
+								       faces:VandFs[i].faceArr};
+                            var mesh = generateSurfaceMesh(atomlist, VandF, mat);
+                            $3Dmol.mergeGeos(surfobj.geo, mesh);
+                            _viewer.render();
+						}
+
+                    //    console.log("async mesh generation " + (+new Date() - time) + "ms");
+                        cnt++;
+                        if (cnt == extents.length)
+                            surfobj.done = true;
+                    };
+
+                    var efunction = function(event) {
+                        console.log(event.message + " (" + event.filename + ":" + event.lineno + ")");
+                    };
+
+                    for (i = 0; i < extents.length; i++) {
+                        var worker = workers[i % workers.length];
+                        worker.onmessage = rfunction;
+
+                        worker.onerror = efunction;
+
+                        worker.postMessage({
+                            'type' : type,
+                            'expandedExtent' : extents[i].extent,
+                            'extendedAtoms' : extents[i].atoms,
+                            'atomsToShow' : extents[i].toshow
+                        });
+                    }
+                }
+
+                // NOTE: This is misleading if 'async' mesh generation - returns
+                // immediately
+                //console.log("full mesh generation " + (+new Date() - time) + "ms");
+            }
+            
+            style = style || {};
+            var mat = getMatWithStyle(style);
+            var surfobj = [];
+            
+            if (symmetries) { //do preprocessing
+                var modelsAtomList = {};
+                var modelsAtomsToShow = {};
+                for (n = 0; n < models.length; n++) {
+                    modelsAtomList[n] = [];
+                    modelsAtomsToShow[n] = [];
+                }
+                for (n = 0; n < atomlist.length; n++) {
+                    modelsAtomList[atomlist[n].model].push(atomlist[n]);
+                }
+                for (n = 0; n < atomsToShow.length; n++) {
+                    modelsAtomsToShow[atomsToShow[n].model].push(atomsToShow[n]);
+                }
+                for (n = 0; n < models.length; n++) {
+                    surfobj.push({
+                        geo : new $3Dmol.Geometry(true),
+                        mat : mat,
+                        done : false,
+                        finished : false,
+                        symmetries : models[n].getSymmetries()
+                    // also webgl initialized
+                    });
+                    addSurfaceHelper(surfobj[n], modelsAtomList[n], modelsAtomsToShow[n]);
+                }
+            }
+            else {
+                surfobj.push({
+                    geo : new $3Dmol.Geometry(true),
+                    mat : mat,
+                    done : false,
+                    finished : false,
+                    symmetries : [new $3Dmol.Matrix4()]
+                });
+                addSurfaceHelper(surfobj[surfobj.length-1], atomlist, atomsToShow);
+            } 
+            var surfid = nextSurfID();
+            surfaces[surfid] = surfobj;
+            
+            return surfid;
+
+        };
+
+        /**
+         * Set the surface material to something else, must render change
+         * 
+         * @param {number} surf - Surface ID to apply changes to
+         * @param {matSpec} style - new material style specification
+         */ 
+        this.setSurfaceMaterialStyle = function(surf, style) {
+            if (surfaces[surf]) {
+                surfArr = surfaces[surf];
+                for (var i = 0; i < surfArr.length; i++) {
+                    surfArr[i].mat = getMatWithStyle(style);
+                    surfArr[i].mat.side = $3Dmol.FrontSide;
+                    surfArr[i].finished = false; // trigger redraw
+                }
+            }
+            return this;
+        };
+
+        /**
+         * Remove surface with given ID
+         * 
+         * @param {number} surf - surface id
+         */
+        this.removeSurface = function(surf) {
+            var surfArr = surfaces[surf];
+            for (var i = 0; i < surfArr.length; i++) {
+                if (surfArr[i] && surfArr[i].lastGL) {
+                    if (surfArr[i].geo !== undefined)
+                        surfArr[i].geo.dispose();
+                    if (surfArr[i].mat !== undefined)
+                        surfArr[i].mat.dispose();
+                    modelGroup.remove(surfArr[i].lastGL); // remove from scene
+                }
+            }
+            delete surfaces[surf];
+            show();
+            return this;
+        };
+        
+        /** Remove all surfaces.
+         * @function $3Dmol.GLViewer#removeAllSurfaces */
+        this.removeAllSurfaces = function() {
+            for (n in  surfaces) {
+                if(!surfaces.hasOwnProperty(n)) continue;
+                var surfArr = surfaces[n];
+                for(var i = 0; i < surfArr.length; i++) {
+                    if (surfArr[i] && surfArr[i].lastGL) {
+                        if (surfArr[i].geo !== undefined)
+                            surfArr[i].geo.dispose();
+                        if (surfArr[i].mat !== undefined)
+                            surfArr[i].mat.dispose();
+                        modelGroup.remove(surfArr[i].lastGL); // remove from scene
+                    }
+                }
+                delete surfaces[n];
+            }
+            show();
+            return this;
+        };
+
+        /** return Jmol moveto command to position this scene */
+        this.jmolMoveTo = function() {
+            var pos = modelGroup.position;
+            // center on same position
+            var ret = "center { " + (-pos.x) + " " + (-pos.y) + " " + (-pos.z)
+                    + " }; ";
+            // apply rotation
+            var q = rotationGroup.quaternion;
+            ret += "moveto .5 quaternion { " + q.x + " " + q.y + " " + q.z
+                    + " " + q.w + " };";
+            // zoom is tricky.. maybe i would be best to let callee zoom on
+            // selection?
+            // can either do a bunch of math, or maybe zoom to the center with a
+            // fixed
+            // but reasonable percentage
+
+            return ret;
+        };
+
+        /** Clear scene of all objects 
+         * @function $3Dmol.GLViewer#clear
+         * */
+        this.clear = function() {
+            this.removeAllSurfaces();
+            this.removeAllModels();
+            this.removeAllLabels();
+            this.removeAllShapes();
+            show();
+            return this;
+        };
+
+        // props is a list of objects that select certain atoms and enumerate
+        // properties for those atoms
+        /**
+         * @function $3Dmol.GLViewer#mapAtomProperties
+         * Add specified properties to all atoms matching input argument
+         * @function $3Dmol.GLViewer#mapAtomProperties
+         * @param {Object} props, either array of atom selectors with associated props, or function that takes atom and sets its properties
+         * @param {AtomSelectionSpec} sel
+         */
+        this.mapAtomProperties = function(props, sel) {
+            sel = sel || {};
+            var atoms = getAtomsFromSel(sel);
+            
+            if(typeof(props) == "function") {
+                for (var a = 0, numa = atoms.length; a < numa; a++) {
+                    var atom = atoms[a];
+                    props(atom);
+                }
+            }
+            else {
+                for (var a = 0, numa = atoms.length; a < numa; a++) {
+                    var atom = atoms[a];
+                    for (var i = 0, n = props.length; i < n; i++) {
+                        var prop = props[i];
+                        if (prop.props) {
+                            for ( var p in prop.props) {
+                                if (prop.props.hasOwnProperty(p)) {
+                                    // check the atom
+                                    if (atomIsSelected(atom, prop)) {
+                                        if (!atom.properties)
+                                            atom.properties = {};
+                                        atom.properties[p] = prop.props[p];
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+            return this;
+        };
+
+        /**
+         * @function $3Dmol.GLViewer#linkViewer
+         * Synchronize this view matrix of this viewer to the passed viewer.
+         * When the viewpoint of this viewer changes, the other viewer will
+         * be set to this viewer's view.
+         * @function $3Dmol.GLViewer#linkViewer
+         */
+        this.linkViewer = function(otherviewer) {
+           linkedViewers.push(otherviewer);
+           return this;
+        };
+        
+
+        try {
+            if (typeof (callback) === "function")
+                callback(this);
+        } catch (e) {
+            // errors in callback shouldn't invalidate the viewer
+            console.log("error with glviewer callback: " + e);
+        }
+    }
+
+    return GLViewer;
+
+})();
+
+$3Dmol['glmolViewer'] = $3Dmol.GLViewer;
+//color scheme mappings
+var $3Dmol = $3Dmol || {};
+
+/** Color mapping gradiens
+ * @interface
+ * @param {number} min
+ * @param {number} max
+ */
+$3Dmol.Gradient = function(min, max) {};
+
+/**
+ * Map value to hex color
+ * @param {number} val
+ * @param {number} range
+ * @returns {number}
+ */
+$3Dmol.Gradient.valueToHex = function(val, range) {};
+//return range used for color mapping, null if none set
+$3Dmol.Gradient.range = function() {};
+
+
+
+/**
+ * Color scheme red to white to blue, for charges
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.RWB = function(min, max,mid) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+        
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val; //reverse if necessary
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(val === undefined)
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var middle = (hi+lo)/2;
+        if(typeof(mid) != 'undefined')
+            middle = mid; //allow user to specify midpoint
+        var scale, color;
+        
+        //scale bottom from red to white
+        if(val <= middle) {
+            scale = Math.floor(255*Math.sqrt((val-lo)/(middle-lo)));
+            color = 0xff0000 + 0x100*scale + scale;
+            return color;
+        }
+        else { //form white to blue
+            scale = Math.floor(255*Math.sqrt((1-(val-middle)/(hi-middle))));
+            color =  0x10000*scale+0x100*scale+0xff;
+            return color;
+        }
+    };
+    
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+
+/**
+ * rainbow gradient, but without purple to match jmol
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.ROYGB = function(min, max) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+    
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val;
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(typeof(val) == "undefined")
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var mid = (lo+hi)/2;
+        var q1 = (lo+mid)/2;
+        var q3 = (mid+hi)/2;
+        
+        var scale, color;
+        
+        if(val < q1) { //scale green up, red up, blue down
+            scale = Math.floor(255*Math.sqrt((val-lo)/(q1-lo)));
+            color = 0xff0000 + 0x100*scale + 0;
+            return color;
+        }
+        else if(val < mid) { //scale red down, green up, blue down
+            scale = Math.floor(255*Math.sqrt((1-(val-q1)/(mid-q1))));
+            color =  0x010000*scale+0xff00+0x0;
+            return color;
+        }
+        else if(val < q3) { //scale blue up, red down, green up
+            scale = Math.floor(255*Math.sqrt((val-mid)/(q3-mid)));
+            color = 0x000000 + 0xff00 + 0x1*scale;
+            return color;
+        }
+        else { //scale green down, blue up, red down
+            scale = Math.floor(255*Math.sqrt((1-(val-q3)/(hi-q3))));
+            color =  0x000000+0x0100*scale+0xff;
+            return color;
+        }        
+    };
+   
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+
+/**
+ * rainbow gradient with constant saturation, all the way to purple!
+ * @constructor
+ * @implements {$3Dmol.Gradient}
+ */
+$3Dmol.Gradient.Sinebow = function(min, max) {
+    var mult = 1.0;
+    if(typeof(max) == 'undefined' && $.isArray(min) && min.length >= 2) {
+        //we were passed a single range
+        max = min[1];
+        min = min[0];
+    }
+    if(max < min) { //reverse the order
+        mult = -1.0;
+        min *= -1.0;
+        max *= -1.0;
+    }
+    //map value to hex color, range is provided
+    this.valueToHex = function(val, range) {
+        var lo, hi;
+        val = mult*val;
+        if(range) {
+            lo = range[0];
+            hi = range[1];
+        }
+        else {
+            lo = min;
+            hi = max;
+        }
+    
+        if(typeof(val) == "undefined")
+            return 0xffffff;
+        
+        if(val < lo) val = lo;
+        if(val > hi) val = hi;
+        
+        var scale = (val-lo)/(hi-lo);
+        var h = (5*scale/6.0+0.5);
+        var r = Math.sin(Math.PI*h);
+        r *= r*255;
+        var g = Math.sin(Math.PI*(h+1/3.0));
+        g *= g*255;
+        var b = Math.sin(Math.PI*(h+2/3.0));
+        b *= b*255;
+        
+        return 0x10000*Math.floor(r)+0x100*Math.floor(b)+0x1*Math.floor(g);
+    };
+    
+
+    //return range used for color mapping, null if none set
+    this.range = function() {
+        if(typeof(min) != "undefined" && typeof(max) != "undefined") {
+            return [min,max];
+        }
+        return null;
+    };
+
+};
+//Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
+
+$3Dmol.LabelCount = 0;
+
+/**
+ * Renderable labels
+ * @constructor $3Dmol.Label
+ * @param {string} tag - Label text
+ * @param {LabelSpec} parameters Label style and font specifications
+ */
+$3Dmol.Label = function(text, parameters) {
+
+    this.id = $3Dmol.LabelCount++;
+    this.stylespec = parameters || {};
+
+    this.canvas = document.createElement('canvas');
+    //todo: implement resizing canvas..
+    this.canvas.width = 134;
+    this.canvas.height = 35;
+    this.context = this.canvas.getContext('2d');
+    this.sprite = new $3Dmol.Sprite();
+    this.text = text;
+
+};
+
+$3Dmol.Label.prototype = {
+
+    constructor : $3Dmol.Label,
+
+    getStyle : function () { return this.stylespec; }, 
+    
+    setContext : function() {
+        // function for drawing rounded rectangles - for Label drawing
+        var roundRect = function(ctx, x, y, w, h, r, drawBorder) {
+
+            ctx.beginPath();
+            ctx.moveTo(x + r, y);
+            ctx.lineTo(x + w - r, y);
+            ctx.quadraticCurveTo(x + w, y, x + w, y + r);
+            ctx.lineTo(x + w, y + h - r);
+            ctx.quadraticCurveTo(x + w, y + h, x + w - r, y + h);
+            ctx.lineTo(x + r, y + h);
+            ctx.quadraticCurveTo(x, y + h, x, y + h - r);
+            ctx.lineTo(x, y + r);
+            ctx.quadraticCurveTo(x, y, x + r, y);
+            ctx.closePath();
+            ctx.fill();
+            if(drawBorder)
+                ctx.stroke();
+
+        };
+        
+        //do all the checks to figure out what color is desired
+        var getColor = function(style, stylealpha, init) {
+            var ret = init;
+            if(typeof(style) != 'undefined') {
+                //convet regular colors
+                 if(style instanceof $3Dmol.Color) 
+                     ret = style.scaled();
+                 else //hex or name
+                    ret = $3Dmol.CC.color(style).scaled();                    
+            }
+            if(typeof(stylealpha) != 'undefined') {
+                ret.a = parseFloat(stylealpha);
+            }
+            return ret;
+        }
+
+        /**
+         * Label type specification
+         * @typedef LabelSpec
+         * @struct
+         * @prop {string} font - font name, default sans-serif
+         * @prop {number} fontSize - height of text, default 18
+         * @prop {ColorSpec} fontColor - font color, default white
+         * @prop {number} fontOpacity - font opacity, default 1
+         * @prop {number} borderThickness - line width of border around label, default 0
+         * @prop {ColorSpec} borderColor - color of border, default backgroundColor
+         * @prop {string} borderOpacity - color of border
+         * @prop {ColorSpec} backgroundColor - color of background, default black
+         * @prop {string} backgroundOpacity - opacity of background, default 1
+         * @prop {Object} position - x,y,z coordinates for label
+         * @prop {boolean} inFront - always put labels in from of model
+         * @prop {boolean} showBackground - show background rounded rectangle, default true
+         */
+        return function() {
+            
+            var style = this.stylespec;
+            var useScreen =  typeof(style.useScreen) == "undefined" ? false : style.useScreen;
+            
+            var showBackground = style.showBackground;
+            if(showBackground === '0' || showBackground === 'false') showBackground = false;
+            if(typeof(showBackground) == "undefined") showBackground = true; //default
+            var font = style.font ? style.font : "sans-serif";
+
+            var fontSize = parseInt(style.fontSize) ? parseInt(style.fontSize) : 18;
+
+            var fontColor = getColor(style.fontColor, style.fontOpacity,
+                     {
+                        r : 255,
+                        g : 255,
+                        b : 255,
+                        a : 1.0
+                    });
+
+            var padding = style.padding ? style.padding : 4;
+            var borderThickness = style.borderThickness ? style.borderThickness
+                    : 0;
+    
+            var backgroundColor = getColor(style.backgroundColor, style.backgroundOpacity, 
+                     {
+                        r : 0,
+                        g : 0,
+                        b : 0,
+                        a : 1.0
+                    });
+                    
+            var borderColor = getColor(style.borderColor, style.borderOpacity, backgroundColor);
+
+                    
+            var position = style.position ? style.position
+                    : {
+                        x : -10,
+                        y : 1,
+                        z : 1
+                    };
+                    
+            // Should labels always be in front of model?
+            var inFront = (style.inFront !== undefined) ? style.inFront    : true;
+            if(inFront === 'false' || inFront === '0') inFront = false;
+
+            // clear canvas
+
+            var spriteAlignment = style.alignment || $3Dmol.SpriteAlignment.topLeft;
+
+            var bold = "";
+            if(style.bold)
+                bold = "bold ";
+            this.context.font = bold+fontSize + "px  " + font;
+
+            var metrics = this.context.measureText(this.text);
+            var textWidth = metrics.width;
+            
+            if(!showBackground) borderThickness = 0;
+        
+            var width = textWidth+2.5*borderThickness +2*padding;
+            var height = fontSize*1.25+2*borderThickness+2*padding;            // 1.25 is extra height factor for text below baseline: g,j,p,q.
+
+            
+            if(style.backgroundImage) {
+                var img = style.backgroundImage;
+                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
+                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
+                if(w > width) width = w;
+                if(h > height) height = h;
+            }
+
+            this.canvas.width = width;
+            this.canvas.height = height;
+            this.context.clearRect(0, 0, this.canvas.width, this.canvas.height);
+
+            var bold = "";
+            if(style.bold)
+                bold = "bold ";
+            this.context.font = bold+fontSize + "px  " + font;
+
+            // background color
+            this.context.fillStyle = "rgba(" + backgroundColor.r + ","
+                    + backgroundColor.g + "," + backgroundColor.b
+                    + "," + backgroundColor.a + ")";
+            // border color
+            this.context.strokeStyle = "rgba(" + borderColor.r + ","
+                    + borderColor.g + "," + borderColor.b + ","
+                    + borderColor.a + ")";
+
+            this.context.lineWidth = borderThickness;
+            if(showBackground) {
+                roundRect(this.context, borderThickness,borderThickness , width-2*borderThickness,height-2*borderThickness, 6, borderThickness > 0);
+            }
+            
+            if(style.backgroundImage) {
+                var img = style.backgroundImage;
+                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
+                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
+                this.context.drawImage(img,0,0, w, h);
+            }
+            
+
+            // text color
+            this.context.fillStyle = "rgba(" + fontColor.r + ","
+                    + fontColor.g + "," + fontColor.b + ","
+                    + fontColor.a + ")";
+            
+            this.context.fillText(this.text, borderThickness+padding,
+                    fontSize + borderThickness+padding, textWidth);
+
+            // canvas contents will be used for a texture
+            var texture = new $3Dmol.Texture(this.canvas);
+            texture.needsUpdate = true;
+            this.sprite.material = new $3Dmol.SpriteMaterial({
+                map : texture,
+                useScreenCoordinates : useScreen,
+                alignment : spriteAlignment,
+                depthTest : !inFront
+            });
+
+            this.sprite.scale.set(1,1,1);
+
+            this.sprite.position.set(position.x, position.y, position.z);
+        };
+
+    }(),
+
+    // clean up material and texture
+    dispose : function() {
+
+        if (this.sprite.material.map !== undefined)
+            this.sprite.material.map.dispose();
+        if (this.sprite.material !== undefined)
+            this.sprite.material.dispose();
+    }
+
+};
+
+$3Dmol = $3Dmol || {};
+//Encapsulate marching cube algorithm for isosurface generation
+// (currently used by protein surface rendering and generic volumetric data reading)
+$3Dmol.MarchingCubeInitializer = function() {
+    
+    //Marching cube algorithm - assume data has been pre-treated so isovalue is 0 
+    // (i.e. select points greater than 0)
+    //origin -  vector of origin of volumetric data (default is (0,0,0))
+    // nX, nY, nZ - specifies number of voxels in each dimension
+    // scale - cube diagonal unit vector scale (3Dmol vector) (specifying distance between data points); diagonal of cube
+    // - default is 1 - assumes unit cube (1,1,1) diag)
+    // fulltable - if true, use full marching cubes and tritables - else use trimmed table (e.g. surf render)
+    // voxel - if true, draws with a blocky voxel style (default false)
+    // verts, faces - vertex and face arrays to fill up
+    
+    //to match with protein surface...
+    var ISDONE = 2;
+    var my = {};
+    
+    my.march = function(data, verts, faces, spec) {
+
+        var fulltable = !!(spec.fulltable);
+        var origin = (spec.hasOwnProperty('origin') && spec.origin.hasOwnProperty('x')) ? spec.origin : {x:0, y:0, z:0};
+        var voxel = !!(spec.voxel);
+        
+        var nX = spec.nX || 0;
+        var nY = spec.nY || 0;
+        var nZ = spec.nZ || 0;
+        
+        var scale = spec.scale || 1.0;
+        var unitCube = null;
+        if(spec.unitCube) {
+            unitCube = spec.unitCube;
+        } else {
+            unitCube = {x:scale,y:scale,z:scale};
+        }
+        
+        //keep track of calculated vertices to avoid repeats
+        var vertnums = new Int32Array(nX*nY*nZ);
+        
+        var i, il;
+        
+        for (i = 0, il = vertnums.length; i < il; ++i)
+            vertnums[i] = -1;
+
+        // create (or retrieve) a vertex at the appropriate point for
+        // the edge (p1,p2)
+        
+        var getVertex = function(i, j, k, code, p1, p2) {
+            var pt = {x: origin.x, y: origin.y, z: origin.z};
+            var val1 = !!(code & (1 << p1));
+            var val2 = !!(code & (1 << p2));
+             
+            // p1 if they are the same or if !val1
+            var p = p1;
+            if (!val1 && val2)
+                p = p2;
+            
+            // adjust i,j,k by p
+            if (p & 1)
+                k++;
+            if (p & 2)
+                j++;
+            if (p & 4)
+                i++;
+    
+            pt.x += unitCube.x*i;
+            pt.y += unitCube.y*j;
+            pt.z += unitCube.z*k;
+    
+            var index = ((nY * i) + j) * nZ + k;
+            
+            //Have to add option to do voxels
+            if (!voxel) {
+            
+                if (vertnums[index] < 0) // not created yet
+                {
+                    vertnums[index] = verts.length;
+                    verts.push( pt );
+                }
+                return vertnums[index];
+            
+            }
+            
+            else {
+                verts.push(pt);
+                return verts.length - 1;
+            }
+            
+        };
+            
+        var intersects = new Int32Array(12);
+        
+        var etable = (fulltable) ? edgeTable2 : edgeTable;
+        var tritable = (fulltable) ? triTable2 : triTable;
+                
+        //Run marching cubes algorithm
+        for (i = 0; i < nX-1; ++i) {
+            
+            for (var j = 0; j < nY-1; ++j){
+                
+                for (var k = 0; k < nZ-1; ++k){
+                    
+                    var code = 0;
+                    
+                    for (var p = 0; p < 8; ++p) {
+                        var index = ((nY * (i + ((p & 4) >> 2))) + j + ((p & 2) >> 1)) *
+                                        nZ + k + (p & 1);
+
+                        //TODO: Need to fix vpBits in protein surface for this to work
+                        var val = !!(data[index] & ISDONE);
+                        //var val = !!(data[index] > 0);   
+                        
+                        code |= val << p;                        
+                    }
+                    
+                    if (code === 0 || code === 255)
+                        continue;
+                    
+                    var ecode = etable[code];
+                    
+                    if (ecode === 0)
+                        continue;
+                        
+                    var ttable = tritable[code];                        
+                    
+                    if (ecode & 1)
+                        intersects[0] = getVertex(i, j, k, code, 0, 1);
+                    if (ecode & 2)
+                        intersects[1] = getVertex(i, j, k, code, 1, 3);
+                    if (ecode & 4)
+                        intersects[2] = getVertex(i, j, k, code, 3, 2);
+                    if (ecode & 8)
+                        intersects[3] = getVertex(i, j, k, code, 2, 0);
+                    if (ecode & 16)
+                        intersects[4] = getVertex(i, j, k, code, 4, 5);
+                    if (ecode & 32)
+                        intersects[5] = getVertex(i, j, k, code, 5, 7);
+                    if (ecode & 64)
+                        intersects[6] = getVertex(i, j, k, code, 7, 6);
+                    if (ecode & 128)
+                        intersects[7] = getVertex(i, j, k, code, 6, 4);
+                    if (ecode & 256)
+                        intersects[8] = getVertex(i, j, k, code, 0, 4);
+                    if (ecode & 512)
+                        intersects[9] = getVertex(i, j, k, code, 1, 5);
+                    if (ecode & 1024)
+                        intersects[10] = getVertex(i, j, k, code, 3, 7);
+                    if (ecode & 2048)
+                        intersects[11] = getVertex(i, j, k, code, 2, 6);       
+
+                    for (var t = 0; t < ttable.length; t += 3) {
+                        
+                        var a = intersects[ttable[t]],
+                            b = intersects[ttable[t+1]],
+                            c = intersects[ttable[t+2]];         
+                                           
+                        if (voxel && t >= 3) {
+                            verts.push(verts[a]); a = verts.length - 1;
+                            verts.push(verts[b]); b = verts.length - 1;
+                            verts.push(verts[c]); c = verts.length - 1;
+                        }
+
+                        
+                        faces.push(a); faces.push(b); faces.push(c);                               
+                    }              
+                    
+                }
+                
+            }
+            
+        }
+             
+        
+    };
+
+    my.laplacianSmooth = function(numiter, verts, faces) {
+            var tps = new Array(verts.length);
+            var i, il, j, jl, k, kl;
+            for (i = 0, il = verts.length; i < il; i++)
+                    tps[i] = {
+                        x : 0,
+                        y : 0,
+                        z : 0
+                    };
+            var vertdeg = new Array(20);
+            var flagvert;
+            for (i = 0; i < 20; i++)
+                    vertdeg[i] = new Array(verts.length);
+            for (i = 0, il = verts.length; i < il; i++)
+                    vertdeg[0][i] = 0;
+            for (i = 0, il = faces.length / 3; i < il; i++) {
+                var aoffset = i*3, boffset = i*3 + 1, coffset = i*3 + 2;
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
+                    if (faces[boffset] == vertdeg[j + 1][faces[aoffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[aoffset]]++;
+                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[boffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[aoffset]]; j < jl; j++) {
+                    if (faces[coffset] == vertdeg[j + 1][faces[aoffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[aoffset]]++;
+                    vertdeg[vertdeg[0][faces[aoffset]]][faces[aoffset]] = faces[coffset];
+                }
+                // b
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
+                    if (faces[aoffset] == vertdeg[j + 1][faces[boffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[boffset]]++;
+                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[aoffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[boffset]]; j < jl; j++) {
+                    if (faces[coffset] == vertdeg[j + 1][faces[boffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[boffset]]++;
+                    vertdeg[vertdeg[0][faces[boffset]]][faces[boffset]] = faces[coffset];
+                }
+                // c
+                flagvert = true;
+                for (j = 0; j < vertdeg[0][faces[coffset]]; j++) {
+                    if (faces[aoffset] == vertdeg[j + 1][faces[coffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[coffset]]++;
+                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[aoffset];
+                }
+                flagvert = true;
+                for (j = 0, jl = vertdeg[0][faces[coffset]]; j < jl; j++) {
+                    if (faces[boffset] == vertdeg[j + 1][faces[coffset]]) {
+                        flagvert = false;
+                        break;
+                    }
+                }
+                if (flagvert) {
+                    vertdeg[0][faces[coffset]]++;
+                    vertdeg[vertdeg[0][faces[coffset]]][faces[coffset]] = faces[boffset];
+                }
+            }
+
+            var wt = 1.00;
+            var wt2 = 0.50;
+            var ssign;
+            var scaleFactor = 1;
+            var outwt = 0.75 / (scaleFactor + 3.5); // area-preserving
+            for (k = 0; k < numiter; k++) {
+                    for (i = 0, il = verts.length; i < il; i++) {
+                            if (vertdeg[0][i] < 3) {
+                                    tps[i].x = verts[i].x;
+                                    tps[i].y = verts[i].y;
+                                    tps[i].z = verts[i].z;
+                            } else if (vertdeg[0][i] == 3 || vertdeg[0][i] == 4) {
+                                    tps[i].x = 0;
+                                    tps[i].y = 0;
+                                    tps[i].z = 0;
+                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
+                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
+                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
+                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
+                                    }
+                                    tps[i].x += wt2 * verts[i].x;
+                                    tps[i].y += wt2 * verts[i].y;
+                                    tps[i].z += wt2 * verts[i].z;
+                                    tps[i].x /= wt2 + vertdeg[0][i];
+                                    tps[i].y /= wt2 + vertdeg[0][i];
+                                    tps[i].z /= wt2 + vertdeg[0][i];
+                            } else {
+                                    tps[i].x = 0;
+                                    tps[i].y = 0;
+                                    tps[i].z = 0;
+                                    for (j = 0, jl = vertdeg[0][i]; j < jl; j++) {
+                                            tps[i].x += verts[vertdeg[j + 1][i]].x;
+                                            tps[i].y += verts[vertdeg[j + 1][i]].y;
+                                            tps[i].z += verts[vertdeg[j + 1][i]].z;
+                                    }
+                                    tps[i].x += wt * verts[i].x;
+                                    tps[i].y += wt * verts[i].y;
+                                    tps[i].z += wt * verts[i].z;
+                                    tps[i].x /= wt + vertdeg[0][i];
+                                    tps[i].y /= wt + vertdeg[0][i];
+                                    tps[i].z /= wt + vertdeg[0][i];
+                            }
+                    }
+                    for (i = 0, il = verts.length; i < il; i++) {
+                            verts[i].x = tps[i].x;
+                            verts[i].y = tps[i].y;
+                            verts[i].z = tps[i].z;
+                    }
+                    /*
+                     * computenorm(); for (var i = 0; i < vertnumber; i++) { if
+                     * (verts[i].inout) ssign = 1; else ssign = -1; verts[i].x += ssign *
+                     * outwt * verts[i].pn.x; verts[i].y += ssign * outwt *
+                     * verts[i].pn.y; verts[i].z += ssign * outwt * verts[i].pn.z; }
+                     */
+            }
+    };
+
+
+    /*
+     * These tables are based off those by Paul Bourke and Geoffrey Heller:
+     * http://paulbourke.net/geometry/polygonise/
+     * http://paulbourke.net/geometry/polygonise/table2.txt
+     * 
+     * However, they have been substantially modified to reflect a more 
+     * sensible corner numbering scheme and the discrete nature of our voxel data
+     * (resulting in fewer faces).
+     */
+    my.edgeTable = [ 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
+            0xb00, 0x0, 0x0, 0x0, 0x700, 0x0, 0xd00, 0xe00, 0xf00, 0x0, 0x0, 0x0,
+            0x8a, 0x0, 0x15, 0x0, 0x86, 0x0, 0x0, 0x0, 0x28c, 0x0, 0x813, 0xf19,
+            0xe10, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x0, 0x0, 0x126, 0x0, 0x0, 0x15, 0x1c,
+            0x0, 0xf23, 0x419, 0xd20, 0x0, 0xa8, 0xa2, 0xaa, 0x0, 0x285, 0x9ab,
+            0x8a2, 0x0, 0x2af, 0x125, 0xac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x0, 0x0,
+            0x0, 0x0, 0x0, 0x45, 0x0, 0x384, 0x0, 0x0, 0x0, 0x700, 0x8a, 0x83,
+            0x648, 0x780, 0x0, 0x51, 0x0, 0x81a, 0x54, 0x55, 0x54, 0x56, 0x0, 0x51,
+            0x0, 0xe5c, 0x14a, 0x451, 0x759, 0x650, 0x0, 0x0, 0x0, 0x2a, 0x0, 0x45,
+            0x0, 0x1f6, 0x0, 0x0, 0x15, 0xdfc, 0x8a, 0x7f3, 0x4f9, 0x5f0, 0xb00,
+            0x68, 0x921, 0x6a, 0x348, 0x245, 0x16f, 0x66, 0xb00, 0xe6f, 0xd65,
+            0xc6c, 0x76a, 0x663, 0x569, 0x460, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
+            0xf46, 0x0, 0x0, 0x45, 0x24c, 0x2a, 0x823, 0x29, 0xb40, 0x0, 0x0, 0x0,
+            0x6ba, 0x0, 0x8f5, 0xfff, 0xef6, 0x0, 0xff, 0x2f5, 0x2fc, 0x9ea, 0x8f3,
+            0xbf9, 0xaf0, 0x0, 0x0, 0x51, 0x152, 0x0, 0xf55, 0x45f, 0xd56, 0x54,
+            0x357, 0x55, 0x154, 0x852, 0xb53, 0x59, 0x950, 0x700, 0x2c8, 0xc2,
+            0x48a, 0xfc4, 0xec5, 0xdcf, 0xcc6, 0x2c4, 0x2cf, 0xc5, 0xcc, 0xbca,
+            0xac3, 0x9c9, 0x8c0, 0x0, 0x0, 0x0, 0x0, 0xa8, 0x1a4, 0xa8, 0x7a6,
+            0xa2, 0xa2, 0x2a4, 0xbac, 0xaa, 0xa3, 0x2a8, 0x3a0, 0xd00, 0xc18,
+            0xd00, 0xe3a, 0x34, 0x35, 0x73f, 0x636, 0x924, 0x83f, 0xb35, 0xa3c,
+            0x12a, 0x33, 0x339, 0x230, 0xe00, 0xe00, 0xc12, 0xd9a, 0x684, 0x795,
+            0x49f, 0x596, 0x92, 0xb9f, 0x815, 0x99c, 0x9a, 0x393, 0x99, 0x190,
+            0xf00, 0xe08, 0xd01, 0xc0a, 0x704, 0x605, 0x50f, 0x406, 0xb02, 0xa0f,
+            0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
+    
+    var edgeTable = new Uint32Array(my.edgeTable);
+    
+    var triTable = my.triTable = [ [], [], [], [], [], [], [], [ 11, 9, 8 ], [], [], [],
+            [ 8, 10, 9 ], [], [ 10, 8, 11 ], [ 9, 11, 10 ],
+            [ 8, 10, 9, 8, 11, 10 ], [], [], [], [ 1, 7, 3 ], [], [ 4, 2, 0 ], [],
+            [ 2, 1, 7 ], [], [], [], [ 2, 7, 3, 2, 9, 7 ], [],
+            [ 1, 4, 11, 1, 0, 4 ], [ 3, 8, 0, 11, 9, 4, 11, 10, 9 ],
+            [ 4, 11, 9, 11, 10, 9 ], [], [], [], [ 5, 3, 1 ], [], [], [],
+            [ 2, 5, 8, 2, 1, 5 ], [], [], [ 2, 4, 0 ], [ 3, 2, 4 ], [],
+            [ 0, 9, 1, 8, 10, 5, 8, 11, 10 ], [ 3, 4, 0, 3, 10, 4 ],
+            [ 5, 8, 10, 8, 11, 10 ], [], [ 3, 5, 7 ], [ 7, 1, 5 ],
+            [ 1, 7, 3, 1, 5, 7 ], [], [ 9, 2, 0, 9, 7, 2 ],
+            [ 0, 3, 8, 1, 7, 11, 1, 5, 7 ], [ 11, 1, 7, 1, 5, 7 ], [],
+            [ 9, 1, 0, 5, 3, 2, 5, 7, 3 ], [ 8, 2, 5, 8, 0, 2 ],
+            [ 2, 5, 3, 5, 7, 3 ], [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
+            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
+            [ 11, 5, 7, 11, 10, 5 ], [], [], [], [], [], [ 0, 6, 2 ], [],
+            [ 7, 2, 9, 7, 9, 8 ], [], [], [], [ 8, 10, 9 ], [ 7, 1, 3 ],
+            [ 7, 1, 0 ], [ 6, 9, 3, 6, 10, 9 ], [ 7, 10, 8, 10, 9, 8 ], [],
+            [ 6, 0, 4 ], [], [ 11, 1, 4, 11, 3, 1 ], [ 2, 4, 6 ],
+            [ 2, 0, 4, 2, 4, 6 ], [ 2, 4, 6 ], [ 1, 4, 2, 4, 6, 2 ], [],
+            [ 6, 0, 4 ], [], [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ], [ 8, 6, 1, 8, 1, 3 ],
+            [ 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
+            [ 10, 4, 6, 10, 9, 4 ], [], [], [], [ 5, 3, 1 ], [], [ 0, 6, 2 ], [],
+            [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ], [], [], [ 2, 4, 0 ],
+            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ], [ 7, 1, 3 ],
+            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
+            [ 10, 5, 6, 4, 8, 7 ], [ 9, 11, 8 ], [ 3, 5, 6 ],
+            [ 0, 5, 11, 0, 11, 8 ], [ 6, 3, 5, 3, 1, 5 ], [ 3, 9, 6, 3, 8, 9 ],
+            [ 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
+            [ 1, 6, 2, 1, 5, 6 ], [ 9, 11, 8 ], [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ],
+            [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ], [ 3, 2, 11, 10, 5, 6 ],
+            [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ], [ 0, 9, 1, 5, 6, 10 ],
+            [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ], [], [], [], [], [], [], [],
+            [ 1, 10, 2, 9, 11, 6, 9, 8, 11 ], [], [], [ 6, 0, 2 ],
+            [ 3, 6, 9, 3, 2, 6 ], [ 3, 5, 1 ], [ 0, 5, 1, 0, 11, 5 ], [ 0, 3, 5 ],
+            [ 6, 9, 11, 9, 8, 11 ], [], [], [], [ 4, 5, 9, 7, 1, 10, 7, 3, 1 ], [],
+            [ 11, 6, 7, 2, 4, 5, 2, 0, 4 ],
+            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
+            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [],
+            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ], [ 9, 4, 5, 0, 6, 7, 0, 2, 6 ],
+            [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ], [ 6, 7, 11, 5, 3, 8, 5, 1, 3 ],
+            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
+            [ 9, 4, 5, 7, 11, 6 ], [], [], [ 0, 6, 4 ], [ 8, 6, 4, 8, 1, 6 ], [],
+            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
+            [ 10, 2, 1, 6, 0, 3, 6, 4, 0 ], [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ],
+            [ 4, 2, 6 ], [ 1, 0, 9, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
+            [ 8, 2, 4, 2, 6, 4 ], [ 11, 4, 1, 11, 6, 4 ],
+            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 3, 6, 0, 6, 4, 0 ],
+            [ 8, 6, 4, 8, 11, 6 ], [ 10, 8, 9 ], [ 6, 3, 9, 6, 7, 3 ], [ 6, 7, 1 ],
+            [ 10, 7, 1, 7, 3, 1 ], [ 7, 11, 6, 8, 10, 2, 8, 9, 10 ],
+            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
+            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2 ],
+            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 7, 0, 6, 0, 2, 6 ],
+            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
+            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ], [], [], [],
+            [], [ 5, 3, 7 ], [ 8, 5, 2, 8, 7, 5 ], [ 5, 3, 7 ],
+            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 1, 7, 5 ], [ 1, 7, 5 ],
+            [ 9, 2, 7, 9, 7, 5 ], [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ],
+            [ 1, 3, 7, 1, 7, 5 ], [ 0, 7, 1, 7, 5, 1 ], [ 9, 3, 5, 3, 7, 5 ],
+            [ 9, 7, 5, 9, 8, 7 ], [ 8, 10, 11 ], [ 3, 4, 10, 3, 10, 11 ],
+            [ 8, 10, 11 ], [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ], [ 2, 4, 5 ],
+            [ 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
+            [ 2, 1, 10, 9, 4, 5 ], [ 2, 8, 5, 2, 11, 8 ],
+            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
+            [ 11, 3, 2, 9, 4, 5 ], [ 8, 5, 3, 5, 1, 3 ], [ 5, 0, 4, 5, 1, 0 ],
+            [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ], [ 11, 9, 10 ], [ 11, 9, 10 ],
+            [ 1, 11, 4, 1, 10, 11 ], [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
+            [ 2, 7, 9, 2, 9, 10 ], [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ],
+            [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ], [ 10, 2, 1, 8, 7, 4 ], [ 1, 7, 4 ],
+            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 11, 4, 2, 4, 0, 2 ],
+            [ 2, 11, 3, 7, 4, 8 ], [ 4, 1, 7, 1, 3, 7 ], [ 1, 0, 9, 8, 7, 4 ],
+            [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ], [ 8, 9, 10, 8, 10, 11 ],
+            [ 3, 9, 11, 9, 10, 11 ], [ 0, 10, 8, 10, 11, 8 ],
+            [ 10, 3, 1, 10, 11, 3 ], [ 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
+            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 1, 11, 9, 11, 8, 9 ],
+            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
+            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
+     
+    var edgeTable2 = [ 0x0, 0x109, 0x203, 0x30a, 0x80c, 0x905, 0xa0f,
+            0xb06, 0x406, 0x50f, 0x605, 0x70c, 0xc0a, 0xd03, 0xe09, 0xf00, 0x190,
+            0x99, 0x393, 0x29a, 0x99c, 0x895, 0xb9f, 0xa96, 0x596, 0x49f, 0x795,
+            0x69c, 0xd9a, 0xc93, 0xf99, 0xe90, 0x230, 0x339, 0x33, 0x13a, 0xa3c,
+            0xb35, 0x83f, 0x936, 0x636, 0x73f, 0x435, 0x53c, 0xe3a, 0xf33, 0xc39,
+            0xd30, 0x3a0, 0x2a9, 0x1a3, 0xaa, 0xbac, 0xaa5, 0x9af, 0x8a6, 0x7a6,
+            0x6af, 0x5a5, 0x4ac, 0xfaa, 0xea3, 0xda9, 0xca0, 0x8c0, 0x9c9, 0xac3,
+            0xbca, 0xcc, 0x1c5, 0x2cf, 0x3c6, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x4ca,
+            0x5c3, 0x6c9, 0x7c0, 0x950, 0x859, 0xb53, 0xa5a, 0x15c, 0x55, 0x35f,
+            0x256, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x55a, 0x453, 0x759, 0x650, 0xaf0,
+            0xbf9, 0x8f3, 0x9fa, 0x2fc, 0x3f5, 0xff, 0x1f6, 0xef6, 0xfff, 0xcf5,
+            0xdfc, 0x6fa, 0x7f3, 0x4f9, 0x5f0, 0xb60, 0xa69, 0x963, 0x86a, 0x36c,
+            0x265, 0x16f, 0x66, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x76a, 0x663, 0x569,
+            0x460, 0x460, 0x569, 0x663, 0x76a, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x66,
+            0x16f, 0x265, 0x36c, 0x86a, 0x963, 0xa69, 0xb60, 0x5f0, 0x4f9, 0x7f3,
+            0x6fa, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x1f6, 0xff, 0x3f5, 0x2fc, 0x9fa,
+            0x8f3, 0xbf9, 0xaf0, 0x650, 0x759, 0x453, 0x55a, 0xe5c, 0xf55, 0xc5f,
+            0xd56, 0x256, 0x35f, 0x55, 0x15c, 0xa5a, 0xb53, 0x859, 0x950, 0x7c0,
+            0x6c9, 0x5c3, 0x4ca, 0xfcc, 0xec5, 0xdcf, 0xcc6, 0x3c6, 0x2cf, 0x1c5,
+            0xcc, 0xbca, 0xac3, 0x9c9, 0x8c0, 0xca0, 0xda9, 0xea3, 0xfaa, 0x4ac,
+            0x5a5, 0x6af, 0x7a6, 0x8a6, 0x9af, 0xaa5, 0xbac, 0xaa, 0x1a3, 0x2a9,
+            0x3a0, 0xd30, 0xc39, 0xf33, 0xe3a, 0x53c, 0x435, 0x73f, 0x636, 0x936,
+            0x83f, 0xb35, 0xa3c, 0x13a, 0x33, 0x339, 0x230, 0xe90, 0xf99, 0xc93,
+            0xd9a, 0x69c, 0x795, 0x49f, 0x596, 0xa96, 0xb9f, 0x895, 0x99c, 0x29a,
+            0x393, 0x99, 0x190, 0xf00, 0xe09, 0xd03, 0xc0a, 0x70c, 0x605, 0x50f,
+            0x406, 0xb06, 0xa0f, 0x905, 0x80c, 0x30a, 0x203, 0x109, 0x0 ];
+     
+    var triTable2 = [ [], [ 8, 3, 0 ], [ 9, 0, 1 ], [ 8, 3, 1, 8, 1, 9 ],
+            [ 11, 2, 3 ], [ 11, 2, 0, 11, 0, 8 ], [ 11, 2, 3, 0, 1, 9 ],
+            [ 2, 1, 11, 1, 9, 11, 11, 9, 8 ], [ 10, 1, 2 ], [ 8, 3, 0, 1, 2, 10 ],
+            [ 9, 0, 2, 9, 2, 10 ], [ 3, 2, 8, 2, 10, 8, 8, 10, 9 ],
+            [ 10, 1, 3, 10, 3, 11 ], [ 1, 0, 10, 0, 8, 10, 10, 8, 11 ],
+            [ 0, 3, 9, 3, 11, 9, 9, 11, 10 ], [ 8, 10, 9, 8, 11, 10 ], [ 8, 4, 7 ],
+            [ 3, 0, 4, 3, 4, 7 ], [ 1, 9, 0, 8, 4, 7 ],
+            [ 9, 4, 1, 4, 7, 1, 1, 7, 3 ], [ 2, 3, 11, 7, 8, 4 ],
+            [ 7, 11, 4, 11, 2, 4, 4, 2, 0 ], [ 3, 11, 2, 4, 7, 8, 9, 0, 1 ],
+            [ 2, 7, 11, 2, 1, 7, 1, 4, 7, 1, 9, 4 ], [ 10, 1, 2, 8, 4, 7 ],
+            [ 2, 10, 1, 0, 4, 7, 0, 7, 3 ], [ 4, 7, 8, 0, 2, 10, 0, 10, 9 ],
+            [ 2, 7, 3, 2, 9, 7, 7, 9, 4, 2, 10, 9 ],
+            [ 8, 4, 7, 11, 10, 1, 11, 1, 3 ],
+            [ 11, 4, 7, 1, 4, 11, 1, 11, 10, 1, 0, 4 ],
+            [ 3, 8, 0, 7, 11, 4, 11, 9, 4, 11, 10, 9 ],
+            [ 7, 11, 4, 4, 11, 9, 11, 10, 9 ], [ 9, 5, 4 ], [ 3, 0, 8, 4, 9, 5 ],
+            [ 5, 4, 0, 5, 0, 1 ], [ 4, 8, 5, 8, 3, 5, 5, 3, 1 ],
+            [ 11, 2, 3, 9, 5, 4 ], [ 9, 5, 4, 8, 11, 2, 8, 2, 0 ],
+            [ 3, 11, 2, 1, 5, 4, 1, 4, 0 ],
+            [ 8, 5, 4, 2, 5, 8, 2, 8, 11, 2, 1, 5 ], [ 2, 10, 1, 9, 5, 4 ],
+            [ 0, 8, 3, 5, 4, 9, 10, 1, 2 ], [ 10, 5, 2, 5, 4, 2, 2, 4, 0 ],
+            [ 3, 4, 8, 3, 2, 4, 2, 5, 4, 2, 10, 5 ],
+            [ 5, 4, 9, 1, 3, 11, 1, 11, 10 ],
+            [ 0, 9, 1, 4, 8, 5, 8, 10, 5, 8, 11, 10 ],
+            [ 3, 4, 0, 3, 10, 4, 4, 10, 5, 3, 11, 10 ],
+            [ 4, 8, 5, 5, 8, 10, 8, 11, 10 ], [ 9, 5, 7, 9, 7, 8 ],
+            [ 0, 9, 3, 9, 5, 3, 3, 5, 7 ], [ 8, 0, 7, 0, 1, 7, 7, 1, 5 ],
+            [ 1, 7, 3, 1, 5, 7 ], [ 11, 2, 3, 8, 9, 5, 8, 5, 7 ],
+            [ 9, 2, 0, 9, 7, 2, 2, 7, 11, 9, 5, 7 ],
+            [ 0, 3, 8, 2, 1, 11, 1, 7, 11, 1, 5, 7 ],
+            [ 2, 1, 11, 11, 1, 7, 1, 5, 7 ], [ 1, 2, 10, 5, 7, 8, 5, 8, 9 ],
+            [ 9, 1, 0, 10, 5, 2, 5, 3, 2, 5, 7, 3 ],
+            [ 5, 2, 10, 8, 2, 5, 8, 5, 7, 8, 0, 2 ],
+            [ 10, 5, 2, 2, 5, 3, 5, 7, 3 ],
+            [ 3, 9, 1, 3, 8, 9, 7, 11, 10, 7, 10, 5 ],
+            [ 9, 1, 0, 10, 7, 11, 10, 5, 7 ], [ 3, 8, 0, 7, 10, 5, 7, 11, 10 ],
+            [ 11, 5, 7, 11, 10, 5 ], [ 11, 7, 6 ], [ 0, 8, 3, 11, 7, 6 ],
+            [ 9, 0, 1, 11, 7, 6 ], [ 7, 6, 11, 3, 1, 9, 3, 9, 8 ],
+            [ 2, 3, 7, 2, 7, 6 ], [ 8, 7, 0, 7, 6, 0, 0, 6, 2 ],
+            [ 1, 9, 0, 3, 7, 6, 3, 6, 2 ], [ 7, 6, 2, 7, 2, 9, 2, 1, 9, 7, 9, 8 ],
+            [ 1, 2, 10, 6, 11, 7 ], [ 2, 10, 1, 7, 6, 11, 8, 3, 0 ],
+            [ 11, 7, 6, 10, 9, 0, 10, 0, 2 ],
+            [ 7, 6, 11, 3, 2, 8, 8, 2, 10, 8, 10, 9 ],
+            [ 6, 10, 7, 10, 1, 7, 7, 1, 3 ],
+            [ 6, 10, 1, 6, 1, 7, 7, 1, 0, 7, 0, 8 ],
+            [ 9, 0, 3, 6, 9, 3, 6, 10, 9, 6, 3, 7 ],
+            [ 6, 10, 7, 7, 10, 8, 10, 9, 8 ], [ 8, 4, 6, 8, 6, 11 ],
+            [ 11, 3, 6, 3, 0, 6, 6, 0, 4 ], [ 0, 1, 9, 4, 6, 11, 4, 11, 8 ],
+            [ 1, 9, 4, 11, 1, 4, 11, 3, 1, 11, 4, 6 ],
+            [ 3, 8, 2, 8, 4, 2, 2, 4, 6 ], [ 2, 0, 4, 2, 4, 6 ],
+            [ 1, 9, 0, 3, 8, 2, 2, 8, 4, 2, 4, 6 ], [ 9, 4, 1, 1, 4, 2, 4, 6, 2 ],
+            [ 10, 1, 2, 11, 8, 4, 11, 4, 6 ],
+            [ 10, 1, 2, 11, 3, 6, 6, 3, 0, 6, 0, 4 ],
+            [ 0, 2, 10, 0, 10, 9, 4, 11, 8, 4, 6, 11 ],
+            [ 2, 11, 3, 6, 9, 4, 6, 10, 9 ],
+            [ 8, 4, 6, 8, 6, 1, 6, 10, 1, 8, 1, 3 ],
+            [ 1, 0, 10, 10, 0, 6, 0, 4, 6 ], [ 8, 0, 3, 9, 6, 10, 9, 4, 6 ],
+            [ 10, 4, 6, 10, 9, 4 ], [ 9, 5, 4, 7, 6, 11 ],
+            [ 4, 9, 5, 3, 0, 8, 11, 7, 6 ], [ 6, 11, 7, 4, 0, 1, 4, 1, 5 ],
+            [ 6, 11, 7, 4, 8, 5, 5, 8, 3, 5, 3, 1 ], [ 4, 9, 5, 6, 2, 3, 6, 3, 7 ],
+            [ 9, 5, 4, 8, 7, 0, 0, 7, 6, 0, 6, 2 ],
+            [ 4, 0, 1, 4, 1, 5, 6, 3, 7, 6, 2, 3 ], [ 7, 4, 8, 5, 2, 1, 5, 6, 2 ],
+            [ 6, 11, 7, 1, 2, 10, 9, 5, 4 ],
+            [ 11, 7, 6, 8, 3, 0, 1, 2, 10, 9, 5, 4 ],
+            [ 11, 7, 6, 10, 5, 2, 2, 5, 4, 2, 4, 0 ],
+            [ 7, 4, 8, 2, 11, 3, 10, 5, 6 ],
+            [ 4, 9, 5, 6, 10, 7, 7, 10, 1, 7, 1, 3 ],
+            [ 5, 6, 10, 0, 9, 1, 8, 7, 4 ], [ 5, 6, 10, 7, 0, 3, 7, 4, 0 ],
+            [ 10, 5, 6, 4, 8, 7 ], [ 5, 6, 9, 6, 11, 9, 9, 11, 8 ],
+            [ 0, 9, 5, 0, 5, 3, 3, 5, 6, 3, 6, 11 ],
+            [ 0, 1, 5, 0, 5, 11, 5, 6, 11, 0, 11, 8 ],
+            [ 11, 3, 6, 6, 3, 5, 3, 1, 5 ], [ 9, 5, 6, 3, 9, 6, 3, 8, 9, 3, 6, 2 ],
+            [ 5, 6, 9, 9, 6, 0, 6, 2, 0 ], [ 0, 3, 8, 2, 5, 6, 2, 1, 5 ],
+            [ 1, 6, 2, 1, 5, 6 ], [ 1, 2, 10, 5, 6, 9, 9, 6, 11, 9, 11, 8 ],
+            [ 1, 0, 9, 6, 10, 5, 11, 3, 2 ], [ 6, 10, 5, 2, 8, 0, 2, 11, 8 ],
+            [ 3, 2, 11, 10, 5, 6 ], [ 10, 5, 6, 9, 3, 8, 9, 1, 3 ],
+            [ 0, 9, 1, 5, 6, 10 ], [ 8, 0, 3, 10, 5, 6 ], [ 10, 5, 6 ],
+            [ 10, 6, 5 ], [ 8, 3, 0, 10, 6, 5 ], [ 0, 1, 9, 5, 10, 6 ],
+            [ 10, 6, 5, 9, 8, 3, 9, 3, 1 ], [ 3, 11, 2, 10, 6, 5 ],
+            [ 6, 5, 10, 2, 0, 8, 2, 8, 11 ], [ 1, 9, 0, 6, 5, 10, 11, 2, 3 ],
+            [ 1, 10, 2, 5, 9, 6, 9, 11, 6, 9, 8, 11 ], [ 1, 2, 6, 1, 6, 5 ],
+            [ 0, 8, 3, 2, 6, 5, 2, 5, 1 ], [ 5, 9, 6, 9, 0, 6, 6, 0, 2 ],
+            [ 9, 6, 5, 3, 6, 9, 3, 9, 8, 3, 2, 6 ], [ 11, 6, 3, 6, 5, 3, 3, 5, 1 ],
+            [ 0, 5, 1, 0, 11, 5, 5, 11, 6, 0, 8, 11 ],
+            [ 0, 5, 9, 0, 3, 5, 3, 6, 5, 3, 11, 6 ],
+            [ 5, 9, 6, 6, 9, 11, 9, 8, 11 ], [ 10, 6, 5, 4, 7, 8 ],
+            [ 5, 10, 6, 7, 3, 0, 7, 0, 4 ], [ 5, 10, 6, 0, 1, 9, 8, 4, 7 ],
+            [ 4, 5, 9, 6, 7, 10, 7, 1, 10, 7, 3, 1 ],
+            [ 7, 8, 4, 2, 3, 11, 10, 6, 5 ],
+            [ 11, 6, 7, 10, 2, 5, 2, 4, 5, 2, 0, 4 ],
+            [ 11, 6, 7, 8, 0, 3, 1, 10, 2, 9, 4, 5 ],
+            [ 6, 7, 11, 1, 10, 2, 9, 4, 5 ], [ 7, 8, 4, 5, 1, 2, 5, 2, 6 ],
+            [ 4, 1, 0, 4, 5, 1, 6, 7, 3, 6, 3, 2 ],
+            [ 9, 4, 5, 8, 0, 7, 0, 6, 7, 0, 2, 6 ], [ 4, 5, 9, 6, 3, 2, 6, 7, 3 ],
+            [ 6, 7, 11, 4, 5, 8, 5, 3, 8, 5, 1, 3 ],
+            [ 6, 7, 11, 4, 1, 0, 4, 5, 1 ], [ 4, 5, 9, 3, 8, 0, 11, 6, 7 ],
+            [ 9, 4, 5, 7, 11, 6 ], [ 10, 6, 4, 10, 4, 9 ],
+            [ 8, 3, 0, 9, 10, 6, 9, 6, 4 ], [ 1, 10, 0, 10, 6, 0, 0, 6, 4 ],
+            [ 8, 6, 4, 8, 1, 6, 6, 1, 10, 8, 3, 1 ],
+            [ 2, 3, 11, 6, 4, 9, 6, 9, 10 ],
+            [ 0, 10, 2, 0, 9, 10, 4, 8, 11, 4, 11, 6 ],
+            [ 10, 2, 1, 11, 6, 3, 6, 0, 3, 6, 4, 0 ],
+            [ 10, 2, 1, 11, 4, 8, 11, 6, 4 ], [ 9, 1, 4, 1, 2, 4, 4, 2, 6 ],
+            [ 1, 0, 9, 3, 2, 8, 2, 4, 8, 2, 6, 4 ], [ 2, 4, 0, 2, 6, 4 ],
+            [ 3, 2, 8, 8, 2, 4, 2, 6, 4 ],
+            [ 1, 4, 9, 11, 4, 1, 11, 1, 3, 11, 6, 4 ],
+            [ 0, 9, 1, 4, 11, 6, 4, 8, 11 ], [ 11, 6, 3, 3, 6, 0, 6, 4, 0 ],
+            [ 8, 6, 4, 8, 11, 6 ], [ 6, 7, 10, 7, 8, 10, 10, 8, 9 ],
+            [ 9, 3, 0, 6, 3, 9, 6, 9, 10, 6, 7, 3 ],
+            [ 6, 1, 10, 6, 7, 1, 7, 0, 1, 7, 8, 0 ],
+            [ 6, 7, 10, 10, 7, 1, 7, 3, 1 ],
+            [ 7, 11, 6, 3, 8, 2, 8, 10, 2, 8, 9, 10 ],
+            [ 11, 6, 7, 10, 0, 9, 10, 2, 0 ], [ 2, 1, 10, 7, 11, 6, 8, 0, 3 ],
+            [ 1, 10, 2, 6, 7, 11 ], [ 7, 2, 6, 7, 9, 2, 2, 9, 1, 7, 8, 9 ],
+            [ 1, 0, 9, 3, 6, 7, 3, 2, 6 ], [ 8, 0, 7, 7, 0, 6, 0, 2, 6 ],
+            [ 2, 7, 3, 2, 6, 7 ], [ 7, 11, 6, 3, 9, 1, 3, 8, 9 ],
+            [ 9, 1, 0, 11, 6, 7 ], [ 0, 3, 8, 11, 6, 7 ], [ 11, 6, 7 ],
+            [ 11, 7, 5, 11, 5, 10 ], [ 3, 0, 8, 7, 5, 10, 7, 10, 11 ],
+            [ 9, 0, 1, 10, 11, 7, 10, 7, 5 ],
+            [ 3, 1, 9, 3, 9, 8, 7, 10, 11, 7, 5, 10 ],
+            [ 10, 2, 5, 2, 3, 5, 5, 3, 7 ],
+            [ 5, 10, 2, 8, 5, 2, 8, 7, 5, 8, 2, 0 ],
+            [ 9, 0, 1, 10, 2, 5, 5, 2, 3, 5, 3, 7 ],
+            [ 1, 10, 2, 5, 8, 7, 5, 9, 8 ], [ 2, 11, 1, 11, 7, 1, 1, 7, 5 ],
+            [ 0, 8, 3, 2, 11, 1, 1, 11, 7, 1, 7, 5 ],
+            [ 9, 0, 2, 9, 2, 7, 2, 11, 7, 9, 7, 5 ],
+            [ 11, 3, 2, 8, 5, 9, 8, 7, 5 ], [ 1, 3, 7, 1, 7, 5 ],
+            [ 8, 7, 0, 0, 7, 1, 7, 5, 1 ], [ 0, 3, 9, 9, 3, 5, 3, 7, 5 ],
+            [ 9, 7, 5, 9, 8, 7 ], [ 4, 5, 8, 5, 10, 8, 8, 10, 11 ],
+            [ 3, 0, 4, 3, 4, 10, 4, 5, 10, 3, 10, 11 ],
+            [ 0, 1, 9, 4, 5, 8, 8, 5, 10, 8, 10, 11 ],
+            [ 5, 9, 4, 1, 11, 3, 1, 10, 11 ],
+            [ 3, 8, 4, 3, 4, 2, 2, 4, 5, 2, 5, 10 ],
+            [ 10, 2, 5, 5, 2, 4, 2, 0, 4 ], [ 0, 3, 8, 5, 9, 4, 10, 2, 1 ],
+            [ 2, 1, 10, 9, 4, 5 ], [ 8, 4, 5, 2, 8, 5, 2, 11, 8, 2, 5, 1 ],
+            [ 3, 2, 11, 1, 4, 5, 1, 0, 4 ], [ 9, 4, 5, 8, 2, 11, 8, 0, 2 ],
+            [ 11, 3, 2, 9, 4, 5 ], [ 4, 5, 8, 8, 5, 3, 5, 1, 3 ],
+            [ 5, 0, 4, 5, 1, 0 ], [ 3, 8, 0, 4, 5, 9 ], [ 9, 4, 5 ],
+            [ 7, 4, 11, 4, 9, 11, 11, 9, 10 ],
+            [ 3, 0, 8, 7, 4, 11, 11, 4, 9, 11, 9, 10 ],
+            [ 11, 7, 4, 1, 11, 4, 1, 10, 11, 1, 4, 0 ],
+            [ 8, 7, 4, 11, 1, 10, 11, 3, 1 ],
+            [ 2, 3, 7, 2, 7, 9, 7, 4, 9, 2, 9, 10 ],
+            [ 4, 8, 7, 0, 10, 2, 0, 9, 10 ], [ 2, 1, 10, 0, 7, 4, 0, 3, 7 ],
+            [ 10, 2, 1, 8, 7, 4 ], [ 2, 11, 7, 2, 7, 1, 1, 7, 4, 1, 4, 9 ],
+            [ 3, 2, 11, 4, 8, 7, 9, 1, 0 ], [ 7, 4, 11, 11, 4, 2, 4, 0, 2 ],
+            [ 2, 11, 3, 7, 4, 8 ], [ 9, 1, 4, 4, 1, 7, 1, 3, 7 ],
+            [ 1, 0, 9, 8, 7, 4 ], [ 3, 4, 0, 3, 7, 4 ], [ 8, 7, 4 ],
+            [ 8, 9, 10, 8, 10, 11 ], [ 0, 9, 3, 3, 9, 11, 9, 10, 11 ],
+            [ 1, 10, 0, 0, 10, 8, 10, 11, 8 ], [ 10, 3, 1, 10, 11, 3 ],
+            [ 3, 8, 2, 2, 8, 10, 8, 9, 10 ], [ 9, 2, 0, 9, 10, 2 ],
+            [ 8, 0, 3, 1, 10, 2 ], [ 10, 2, 1 ], [ 2, 11, 1, 1, 11, 9, 11, 8, 9 ],
+            [ 11, 3, 2, 0, 9, 1 ], [ 11, 0, 2, 11, 8, 0 ], [ 11, 3, 2 ],
+            [ 8, 1, 3, 8, 9, 1 ], [ 9, 1, 0 ], [ 8, 0, 3 ], [] ];
             
-            var showBackground = style.showBackground;
-            if(showBackground === '0' || showBackground === 'false') showBackground = false;
-            if(typeof(showBackground) == "undefined") showBackground = true; //default
-            var font = style.font ? style.font : "sans-serif";
-
-            var fontSize = parseInt(style.fontSize) ? parseInt(style.fontSize) : 18;
+            return my;
+};
 
-            var fontColor = getColor(style.fontColor, style.fontOpacity,
-                     {
-                        r : 255,
-                        g : 255,
-                        b : 255,
-                        a : 1.0
-                    });
+//each webworker needs its own marching cube object
+$3Dmol.MarchingCube  = $3Dmol.MarchingCubeInitializer();    
 
-            var padding = style.padding ? style.padding : 4;
-            var borderThickness = style.borderThickness ? style.borderThickness
-                    : 0;
-    
-            var backgroundColor = getColor(style.backgroundColor, style.backgroundOpacity, 
-                     {
-                        r : 0,
-                        g : 0,
-                        b : 0,
-                        a : 1.0
-                    });
-                    
-            var borderColor = getColor(style.borderColor, style.borderOpacity, backgroundColor);
 
-                    
-            var position = style.position ? style.position
-                    : {
-                        x : -10,
-                        y : 1,
-                        z : 1
-                    };
-                    
-            // Should labels always be in front of model?
-            var inFront = (style.inFront !== undefined) ? style.inFront    : true;
-            if(inFront === 'false' || inFront === '0') inFront = false;
 
-            // clear canvas
+/**
+ * $3Dmol.Parsers stores functions for parsing molecular data. They all take a string of molecular data
+ * and options. The default behavior is to only read the first model in the case of multimodel files, and
+ * all parsers return a list of atom list(s)
+ * 
+ * $3Dmol.Parsers.<ext> corresponds to the parsers for files with extension ext
+ */
+$3Dmol.Parsers = (function() {
+    var parsers = {};
 
-            var spriteAlignment = style.alignment || $3Dmol.SpriteAlignment.topLeft;
+    /**
+     * @param {AtomSpec[]}
+     *            atomsarray
+     */
+    var assignBonds = function(atoms) {
+        // assign bonds - yuck, can't count on connect records
 
-            var bold = "";
-            if(style.bold)
-                bold = "bold ";
-            this.context.font = bold+fontSize + "px  " + font;
+        for (var i = 0, n = atoms.length; i < n; i++) {
+            // Don't reindex if atoms are already indexed
+            if (!atoms[i].index)
+                atoms[i].index = i;
+        }
 
-            var metrics = this.context.measureText(this.text);
-            var textWidth = metrics.width;
-            
-            if(!showBackground) borderThickness = 0;
-        
-            var width = textWidth+2.5*borderThickness +2*padding;
-            var height = fontSize*1.25+2*borderThickness+2*padding;            // 1.25 is extra height factor for text below baseline: g,j,p,q.
+        var grid = {};
+        var MAX_BOND_LENGTH = 4.95; // (largest bond length, Cs) 2.25 * 2 * 1.1 (fudge factor)
 
-            
-            if(style.backgroundImage) {
-                var img = style.backgroundImage;
-                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
-                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
-                if(w > width) width = w;
-                if(h > height) height = h;
+        for (var index = 0; index < atoms.length; index++) {
+            var atom = atoms[index];
+            var x = Math.floor(atom.x / MAX_BOND_LENGTH);
+            var y = Math.floor(atom.y / MAX_BOND_LENGTH);
+            var z = Math.floor(atom.z / MAX_BOND_LENGTH);
+            if (!grid[x]) {
+                grid[x] = {};
             }
-
-            this.canvas.width = width;
-            this.canvas.height = height;
-            this.context.clearRect(0, 0, this.canvas.width, this.canvas.height);
-
-            var bold = "";
-            if(style.bold)
-                bold = "bold ";
-            this.context.font = bold+fontSize + "px  " + font;
-
-            // background color
-            this.context.fillStyle = "rgba(" + backgroundColor.r + ","
-                    + backgroundColor.g + "," + backgroundColor.b
-                    + "," + backgroundColor.a + ")";
-            // border color
-            this.context.strokeStyle = "rgba(" + borderColor.r + ","
-                    + borderColor.g + "," + borderColor.b + ","
-                    + borderColor.a + ")";
-
-            this.context.lineWidth = borderThickness;
-            if(showBackground) {
-                roundRect(this.context, borderThickness,borderThickness , width-2*borderThickness,height-2*borderThickness, 6, borderThickness > 0);
+            if (!grid[x][y]) {
+                grid[x][y] = {};
             }
-            
-            if(style.backgroundImage) {
-                var img = style.backgroundImage;
-                var w = style.backgroundWidth ? style.backgroundWidth : img.width;
-                var h = style.backgroundHeight ? style.backgroundHeight : img.height;
-                this.context.drawImage(img,0,0, w, h);
+            if (!grid[x][y][z]) {
+                grid[x][y][z] = [];
             }
-            
-
-            // text color
-            this.context.fillStyle = "rgba(" + fontColor.r + ","
-                    + fontColor.g + "," + fontColor.b + ","
-                    + fontColor.a + ")";
-            
-            this.context.fillText(this.text, borderThickness+padding,
-                    fontSize + borderThickness+padding, textWidth);
-
-            // canvas contents will be used for a texture
-            var texture = new $3Dmol.Texture(this.canvas);
-            texture.needsUpdate = true;
-            this.sprite.material = new $3Dmol.SpriteMaterial({
-                map : texture,
-                useScreenCoordinates : useScreen,
-                alignment : spriteAlignment,
-                depthTest : !inFront
-            });
-
-            this.sprite.scale.set(1,1,1);
-
-            this.sprite.position.set(position.x, position.y, position.z);
-        };
 
-    }(),
+            grid[x][y][z].push(atom);
+        }
 
-    // clean up material and texture
-    dispose : function() {
+        var findConnections = function(points, otherPoints) {
+            for (var i = 0; i < points.length; i++) {
+                var atom1 = points[i];
+                for (var j = 0; j < otherPoints.length; j++) {
+                    var atom2 = otherPoints[j];
+
+                    if (areConnected(atom1, atom2)) {
+                        if (atom1.bonds.indexOf(atom2.index) == -1) {
+                            atom1.bonds.push(atom2.index);
+                            atom1.bondOrder.push(1);
+                            atom2.bonds.push(atom1.index);
+                            atom2.bondOrder.push(1);
+                        }
+                    }
+                }
+            }
+        }
 
-        if (this.sprite.material.map !== undefined)
-            this.sprite.material.map.dispose();
-        if (this.sprite.material !== undefined)
-            this.sprite.material.dispose();
-    }
 
-};
+        /*const*/ var OFFSETS = [
+            {x: 0, y: 0, z: 1},
+            {x: 0, y: 1, z:-1},
+            {x: 0, y: 1, z: 0},
+            {x: 0, y: 1, z: 1},
+            {x: 1, y:-1, z:-1},
+            {x: 1, y:-1, z: 0},
+            {x: 1, y:-1, z: 1},
+            {x: 1, y: 0, z:-1},
+            {x: 1, y: 0, z: 0},
+            {x: 1, y: 0, z: 1},
+            {x: 1, y: 1, z:-1},
+            {x: 1, y: 1, z: 0},
+            {x: 1, y: 1, z: 1}
+        ];
+        for (var x in grid) {
+            x = parseInt(x);
+            for (var y in grid[x]) {
+                y = parseInt(y);
+                for (var z in grid[x][y]) {
+                    z = parseInt(z);
+                    var points = grid[x][y][z];
+
+                    for (var i = 0; i < points.length; i++) {
+                        var atom1 = points[i];
+                        for (var j = i + 1; j < points.length; j++) {
+                            var atom2 = points[j];
+                            if (areConnected(atom1, atom2)) {
+                                if (atom1.bonds.indexOf(atom2.index) == -1) {
+                                    atom1.bonds.push(atom2.index);
+                                    atom1.bondOrder.push(1);
+                                    atom2.bonds.push(atom1.index);
+                                    atom2.bondOrder.push(1);
+                                }
+                            }
+                        }
+                    }
 
-/**
- * $3Dmol.Parsers stores functions for parsing molecular data.
- * The all take an atom list (which gets filled out) and a string.
- * 
- * $3Dmol.Parsers.<ext> corresponds to the parsers for files with extension ext
- */
-$3Dmol.Parsers = (function() {
-    var parsers = {};
-    
-     /** @param {AtomSpec[]} atomsarray */
-    var assignBonds = function(atomsarray) {
-        // assign bonds - yuck, can't count on connect records
-        var atoms = atomsarray.slice(0);
-        var i, j, n;
-        for (i = 0, n = atomsarray.length; i < n; i++)
-        {
-            //Don't reindex if atoms are already indexed 
-            if (!atomsarray[i].index)
-                atomsarray[i].index = i;
-        }
-        
-        atoms.sort(function(a, b) {
-            return a.z - b.z;
-        });
-        for (i = 0, n = atoms.length; i < n; i++) {
-            var ai = atoms[i];
+                    for (var o = 0; o < OFFSETS.length; o++) {
+                        var offset = OFFSETS[o];
+                        if (!grid[x+offset.x]
+                            || !grid[x+offset.x][y+offset.y]
+                            || !grid[x+offset.x][y+offset.y][z+offset.z]) continue;
 
-            for (j = i + 1; j < n; j++) {
-                var aj = atoms[j];
-                if (aj.z - ai.z > 1.9) // can't be connected
-                    break;
-                if (areConnected(ai, aj)) {
-                    if (ai.bonds.indexOf(aj.index) == -1) {
-                        // only add if not already there
-                        ai.bonds.push(aj.index);
-                        ai.bondOrder.push(1);
-                        aj.bonds.push(ai.index);
-                        aj.bondOrder.push(1);
+                        var otherPoints = grid[x + offset.x][y + offset.y][z + offset.z];
+                        findConnections(points, otherPoints);
                     }
                 }
             }
         }
     };
-    
+
     // this is optimized for proteins where it is assumed connected
     // atoms are on the same or next residue
-    /** @param {AtomSpec[]} atomsarray */
+    /**
+     * @param {AtomSpec[]}
+     *            atomsarray
+     */
     var assignPDBBonds = function(atomsarray) {
         // assign bonds - yuck, can't count on connect records
         var protatoms = [];
-        var hetatoms = [];        
+        var hetatoms = [];
         var i, n;
         for (i = 0, n = atomsarray.length; i < n; i++) {
             var atom = atomsarray[i];
             atom.index = i;
-            if(atom.hetflag)
+            if (atom.hetflag)
                 hetatoms.push(atom);
             else
                 protatoms.push(atom);
         }
 
         assignBonds(hetatoms);
-        
+
         // sort by resid
         protatoms.sort(function(a, b) {
-            if(a.chain != b.chain)
+            if (a.chain != b.chain)
                 return a.chain < b.chain ? -1 : 1;
             return a.resi - b.resi;
         });
-        
-        //for identifying connected residues
+
+        // for identifying connected residues
         var currentResi = -1;
         var reschain = -1;
         var lastResConnected;
-        
+
         for (i = 0, n = protatoms.length; i < n; i++) {
             var ai = protatoms[i];
-            
+
             if (ai.resi !== currentResi) {
                 currentResi = ai.resi;
                 if (!lastResConnected)
                     reschain++;
-                    
+
                 lastResConnected = false;
             }
-            
+
             ai.reschain = reschain;
 
-            for ( var j = i + 1; j < protatoms.length; j++) {
+            for (var j = i + 1; j < protatoms.length; j++) {
                 var aj = protatoms[j];
-                if(aj.chain != ai.chain)
+                if (aj.chain != ai.chain)
                     break;
                 if (aj.resi - ai.resi > 1) // can't be connected
                     break;
@@ -24027,14 +30583,14 @@ $3Dmol.Parsers = (function() {
                         aj.bonds.push(ai.index);
                         aj.bondOrder.push(1);
                     }
-                    
-                    if (ai.resi !== aj.resi) 
-                        lastResConnected = true;                   
-                        
+
+                    if (ai.resi !== aj.resi)
+                        lastResConnected = true;
+
                 }
             }
         }
-        
+
     };
 
     // this will identify all hydrogen bonds between backbone
@@ -24052,7 +30608,7 @@ $3Dmol.Parsers = (function() {
             if (!atom.hetflag && (atom.atom === "N" || atom.atom === "O")) {
                 atoms.push(atom);
                 atom.hbondOther = null;
-                atom.hbondDistanceSq = Number.POSITIVE_INFINITY;                
+                atom.hbondDistanceSq = Number.POSITIVE_INFINITY;
             }
         }
 
@@ -24068,692 +30624,895 @@ $3Dmol.Parsers = (function() {
                 if (zdiff > maxlength) // can't be connected
                     break;
                 if (aj.atom == ai.atom)
-                    continue; //can't be connected, but later might be    
+                    continue; // can't be connected, but later might be
                 var ydiff = Math.abs(aj.y - ai.y);
-                if( ydiff > maxlength)
+                if (ydiff > maxlength)
                     continue;
                 var xdiff = Math.abs(aj.x - ai.x);
-                if(xdiff > maxlength)
+                if (xdiff > maxlength)
                     continue;
-                var dist = xdiff*xdiff+ydiff*ydiff+zdiff*zdiff;
-                if (dist >  maxlengthSq)
+                var dist = xdiff * xdiff + ydiff * ydiff + zdiff * zdiff;
+                if (dist > maxlengthSq)
                     continue;
 
-                if(aj.chain == ai.chain && Math.abs(aj.resi - ai.resi) < 4)
-                    continue; //ignore bonds between too close residues
-                //select closest hbond
+                if (aj.chain == ai.chain && Math.abs(aj.resi - ai.resi) < 4)
+                    continue; // ignore bonds between too close residues
+                // select closest hbond
                 if (dist < ai.hbondDistanceSq) {
                     ai.hbondOther = aj;
                     ai.hbondDistanceSq = dist;
                 }
-                if(dist < aj.hbondDistanceSq) {
+                if (dist < aj.hbondDistanceSq) {
                     aj.hbondOther = ai;
                     aj.hbondDistanceSq = dist;
                 }
             }
         }
-    };
+    };
+
+    var computeSecondaryStructure = function(atomsarray) {
+        assignBackboneHBonds(atomsarray);
+
+        // compute, per residue, what the secondary structure is
+        var chres = {}; // lookup by chain and resid
+        var i, il, c, r;
+        var atom, val;
+
+        //identify helices first
+        for (i = 0, il = atomsarray.length; i < il; i++) {
+            atom = atomsarray[i];
+
+            if (typeof (chres[atom.chain]) === "undefined")
+                chres[atom.chain] = [];
+            
+            if (isFinite(atom.hbondDistanceSq)) {
+                var other = atom.hbondOther;
+                if (typeof (chres[other.chain]) === "undefined")
+                    chres[other.chain] = [];
+                
+                if (Math.abs(other.resi - atom.resi) === 4) {
+                    // helix
+                    chres[atom.chain][atom.resi] = 'h';
+                } 
+            }
+        }
+        
+        // plug gaps in helices
+        for (c in chres) {
+            for (r = 1; r < chres[c].length - 1; r++) {
+                var valbefore = chres[c][r - 1];
+                var valafter = chres[c][r + 1];
+                val = chres[c][r];
+                if (valbefore == 'h' && valbefore == valafter && val != valbefore) {
+                    chres[c][r] = valbefore;
+                }
+            }
+        }
+        
+        //now potential sheets - but only if mate not part of helix
+        for (i = 0, il = atomsarray.length; i < il; i++) {
+            atom = atomsarray[i];
 
-    var computeSecondaryStructure = function(atomsarray) {
-        assignBackboneHBonds(atomsarray);
+            if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] != 'h' && atom.ss != 'h') {
+                chres[atom.chain][atom.resi] = 'maybesheet';
+            }
+        }
         
-        // compute, per residue, what the secondary structure is
-        var chres = {}; // lookup by chain and resid
-        var i, il, c, r;
-        var atom, val;
         
+        //sheets must bond to other sheets
         for (i = 0, il = atomsarray.length; i < il; i++) {
             atom = atomsarray[i];
-            
-            if (typeof(chres[atom.chain]) === "undefined")
-                chres[atom.chain] = [];
-            
-            if (isFinite(atom.hbondDistanceSq)) {
+
+            if (isFinite(atom.hbondDistanceSq) && chres[atom.chain][atom.resi] == 'maybesheet') {
                 var other = atom.hbondOther;
-                if (Math.abs(other.resi - atom.resi) === 4) { 
-                    // helix
-                    chres[atom.chain][atom.resi] = 'h';
-                }
-                else { // otherwise assume sheet
+                var otherval = chres[other.chain][other.resi];
+                if (otherval == 'maybesheet' || otherval == 's') {
+                    // true sheet
                     chres[atom.chain][atom.resi] = 's';
+                    chres[other.chain][other.resi] = 's';
                 }
             }
         }
         
-        // plug gaps and remove singletons
+        // plug gaps in sheets and remove singletons
         for (c in chres) {
-            for (r = 1; r < chres[c].length-1; r++) {
-                var valbefore = chres[c][r-1];
-                var valafter = chres[c][r+1];
+            for (r = 1; r < chres[c].length - 1; r++) {
+                var valbefore = chres[c][r - 1];
+                var valafter = chres[c][r + 1];
                 val = chres[c][r];
-                if(valbefore == valafter && val != valbefore) {
+                if (valbefore == 's' && valbefore == valafter && val != valbefore) {
                     chres[c][r] = valbefore;
                 }
             }
             for (r = 0; r < chres[c].length; r++) {
                 val = chres[c][r];
                 if (val == 'h' || val == 's') {
-                    if (chres[c][r-1] != val && chres[c][r+1] != val)
+                    if (chres[c][r - 1] != val && chres[c][r + 1] != val)
                         delete chres[c][r];
                 }
             }
         }
+
         
         // assign to all atoms in residue, keep track of start
         var curres = null;
         for (i = 0, il = atomsarray.length; i < il; i++) {
             atom = atomsarray[i];
             val = chres[atom.chain][atom.resi];
-            if(typeof(val) == "undefined")
+            if (typeof (val) == "undefined" || val == 'maybesheet')
                 continue;
             atom.ss = val;
-            if(chres[atom.chain][atom.resi-1] != val)
+            if (chres[atom.chain][atom.resi - 1] != val)
                 atom.ssbegin = true;
-            if(chres[atom.chain][atom.resi+1] != val)
+            if (chres[atom.chain][atom.resi + 1] != val)
                 atom.ssend = true;
         }
     };
-    
+
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.cube = parsers.CUBE  = function(atoms, str, options) {
-        var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
-        
+    parsers.cube = parsers.CUBE = function(str, options) {
+        var atoms = [[]];
+        var lines = str.replace(/^\s+/, "").split(/\n\r|\r+/);
+
         if (lines.length < 6)
-            return;
-            
-        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");       
-          
-        var natoms = Math.abs(parseFloat(lineArr[0]));        
-        
+            return atoms;
+
+        var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                " ");
+
+        var natoms = Math.abs(parseFloat(lineArr[0]));
+
         lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-        
-        //might have to convert from bohr units to angstroms
+
+        // might have to convert from bohr units to angstroms
         var convFactor = (parseFloat(lineArr[0]) > 0) ? 0.529177 : 1;
-        
-        //Extract atom portion; send to new GLModel...
+
+        // Extract atom portion; send to new GLModel...
         lines = lines.splice(6, natoms);
-       
-        var start = atoms.length;
+
+        var start = atoms[atoms.length-1].length;
         var end = start + lines.length;
-        
+
         for (var i = start; i < end; ++i) {
             var atom = {};
             atom.serial = i;
             var line = lines[i - start];
             var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
                     " ");
-            
-            if (tokens[0] == 6) 
+
+            if (tokens[0] == 6)
                 atom.elem = "C";
-                        
-            else if (tokens[0] == 1) 
+
+            else if (tokens[0] == 1)
                 atom.elem = "H";
-            
+
             else if (tokens[0] == 8)
                 atom.elem = "O";
-                
+
             else if (tokens[0] == 17)
-                atom.elem = "CL";
-                
+                atom.elem = "Cl";
+
             atom.x = parseFloat(tokens[2]) * convFactor;
             atom.y = parseFloat(tokens[3]) * convFactor;
             atom.z = parseFloat(tokens[4]) * convFactor;
-            
+
             atom.hetflag = true;
             atom.bonds = [];
             atom.bondOrder = [];
             atom.properties = {};
-            atoms.push(atom);
-            
-        }   
-        
-        assignBonds(atoms);
-        
-        return true; 
+            atoms[atoms.length-1].push(atom);
+
+        }
+        for (var i = 0; i < atoms.length; i++)
+            assignBonds(atoms[i]);
+
+        return atoms;
     };
-        
-    // read an XYZ file from str and put the result in atoms
+
+    // read an XYZ file from str and return result
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.xyz = parsers.XYZ = function(atoms, str, options) {
+    parsers.xyz = parsers.XYZ = function(str, options) {
+        
+        var atoms = [[]];
+        var lines = str.split(/\r?\n|\r/);
+        while (lines.length > 0) {
+            if (lines.length < 3)
+                break;
+            var atomCount = parseInt(lines[0]);
+            if (isNaN(atomCount) || atomCount <= 0)
+                break;
+            if (lines.length < atomCount + 2)
+                break;
+            var offset = 2;
+            var start = atoms[atoms.length-1].length;
+            var end = start + atomCount;
+            for (var i = start; i < end; i++) {
+                var line = lines[offset++];
+                var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                        " ");
+                var atom = {};
+                atom.serial = i;
+                var elem = tokens[0];
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                atom.x = parseFloat(tokens[1]);
+                atom.y = parseFloat(tokens[2]);
+                atom.z = parseFloat(tokens[3]);
+                atom.hetflag = true;
+                atom.bonds = [];
+                atom.bondOrder = [];
+                atom.properties = {};
+                atoms[atoms.length-1][i] = atom;
+                if (tokens.length >= 7) {
+                    atom.dx = parseFloat(tokens[4]);
+                    atom.dy = parseFloat(tokens[5]);
+                    atom.dz = parseFloat(tokens[6]);
+                }
+            }
 
-        var lines = str.split("\n");
-        if (lines.length < 3)
-            return;
-        var atomCount = parseInt(lines[0].substr(0, 3));
-        if (isNaN(atomCount) || atomCount <= 0)
-            return;
-        if (lines.length < atomCount + 2)
-            return;
-        var offset = 2;
-        var start = atoms.length;
-        var end = start + atomCount;
-        for ( var i = start; i < end; i++) {
-            var line = lines[offset++];
-            var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
-                    " ");
-            var atom = {};
-            atom.serial = i;
-            atom.atom = atom.elem = tokens[0];
-            atom.x = parseFloat(tokens[1]);
-            atom.y = parseFloat(tokens[2]);
-            atom.z = parseFloat(tokens[3]);
-            atom.hetflag = true;
-            atom.bonds = [];
-            atom.bondOrder = [];
-            atom.properties = {};
-            atoms[i] = atom;
+            if (options.multimodel) {
+                atoms.push([]);
+                lines.splice(0, offset);
+            }
+            else {
+                break;
+            }
+        }
+        
+        for (var i = 0; i < atoms.length; i++) {
+            assignBonds(atoms[i]);
+        }
+        
+        if (options.onemol) {
+            var temp = atoms;
+            atoms = [];
+            atoms.push(temp[0]);
+            for (var i = 1; i < temp.length; i++) {
+                var offset = atoms[0].length;
+                for (var j = 0; j < temp[i].length; j++) {
+                    var a = temp[i][j];
+                    for (var k = 0; k < a.bonds.length; k++) {
+                        a.bonds[k] = a.bonds[k] + offset;
+                    }
+                    a.index = atoms[0].length;
+                    a.serial = atoms[0].length;
+                    atoms[0].push(a);
+                }
+            }
         }
-        assignBonds(atoms);
 
-        return true;
+         return atoms;
     };
 
     // put atoms specified in sdf fromat in str into atoms
     // adds to atoms, does not replace
-    /** 
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+    /**
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.sdf = parsers.SDF = function(atoms, str, options) {
+    parsers.sdf = parsers.SDF = function(str, options) {
 
+        var atoms = [[]];
         var noH = false;
-        if(typeof options.keepH !== "undefined") 
+        if (typeof options.keepH !== "undefined")
             noH = !options.keepH;
-        var lines = str.split("\n");
-        if (lines.length < 4)
-            return;
-        var atomCount = parseInt(lines[3].substr(0, 3));
-        if (isNaN(atomCount) || atomCount <= 0)
-            return;
-        var bondCount = parseInt(lines[3].substr(3, 3));
-        var offset = 4;
-        if (lines.length < 4 + atomCount + bondCount)
-            return;
+        var lines = str.split(/\r?\n|\r/);
         
-        // serial is atom's index in file; index is atoms index in 'atoms'
-        var serialToIndex = [];
-        var start = atoms.length;
-        var end = start + atomCount;
-        var i, line;
-        for (i = start; i < end; i++) {
-            line = lines[offset];
-            offset++;
-            var atom = {};
-            atom.atom = atom.elem = line.substr(31, 3).replace(/ /g, "");
+        while(lines.length > 0) { 
+            if (lines.length < 4)
+                break;
+            var atomCount = parseInt(lines[3].substr(0, 3));
+            if (isNaN(atomCount) || atomCount <= 0)
+                break;
+            var bondCount = parseInt(lines[3].substr(3, 3));
+            var offset = 4;
+            if (lines.length < 4 + atomCount + bondCount)
+                break;
 
-            if (atom.elem != 'H' || !noH) {
-                atom.serial = i;
-                serialToIndex[i] = atoms.length;
-                atom.x = parseFloat(line.substr(0, 10));
-                atom.y = parseFloat(line.substr(10, 10));
-                atom.z = parseFloat(line.substr(20, 10));
-                atom.hetflag = true;
-                atom.bonds = [];
-                atom.bondOrder = [];
-                atom.properties = {};
-                atoms.push(atom);
+            // serial is atom's index in file; index is atoms index in 'atoms'
+            var serialToIndex = [];
+            var start = atoms[atoms.length-1].length;
+            var end = start + atomCount;
+            var i, line;
+            for (i = start; i < end; i++,offset++) {
+                line = lines[offset];
+                var atom = {};
+                var elem = line.substr(31, 3).replace(/ /g, "");
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+
+                if (atom.elem != 'H' || !noH) {
+                    atom.serial = i;
+                    serialToIndex[i] = atoms[atoms.length-1].length;
+                    atom.x = parseFloat(line.substr(0, 10));
+                    atom.y = parseFloat(line.substr(10, 10));
+                    atom.z = parseFloat(line.substr(20, 10));
+                    atom.hetflag = true;
+                    atom.bonds = [];
+                    atom.bondOrder = [];
+                    atom.properties = {};
+                    atom.index = atoms[atoms.length-1].length;
+                    atoms[atoms.length-1].push(atom);
+                }
             }
-        }
-        
-        for (i = 0; i < bondCount; i++) {
-            line = lines[offset];
-            offset++;
-            var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
-            var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
-            var order = parseInt(line.substr(6, 3));      
-            if(typeof(from) != 'undefined' && typeof(to) != 'undefined') {
-                atoms[from].bonds.push(to);
-                atoms[from].bondOrder.push(order);
-                atoms[to].bonds.push(from);
-                atoms[to].bondOrder.push(order);
+
+            for (i = 0; i < bondCount; i++,offset++) {
+                line = lines[offset];
+                var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
+                var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
+                var order = parseInt(line.substr(6, 3));
+                if (typeof (from) != 'undefined' && typeof (to) != 'undefined') {
+                    atoms[atoms.length-1][from].bonds.push(to);
+                    atoms[atoms.length-1][from].bondOrder.push(order);
+                    atoms[atoms.length-1][to].bonds.push(from);
+                    atoms[atoms.length-1][to].bondOrder.push(order);
+                }
+            }
+            if (options.multimodel) {
+                if (!options.onemol)
+                    atoms.push([]);
+                while (lines[offset] != "$$$$")
+                    offset++
+                lines.splice(0, ++offset);
+            }
+            else {
+                break;
             }
         }
 
-        return true;
+        return atoms;
     };
 
+    // This parses the ChemDoodle json file format. Although this is registered
+    // for the json file extension, other chemical json file formats exist that
+    // this can not parse. Check which one you have and do not assume that
+    // .json can be parsed
+    parsers.cdjson = parsers.json = function(str, options) {
+        var atoms = [[]];
+        if (typeof str === "string") { // Str is usually automatically parsed by JQuery
+            str = JSON.parse(str);
+        }
+        var molecules = str.m;
+        var atomsInFile = molecules[0].a; // Assumes there is at least one
+        var bondsInFile = molecules[0].b; // molecule and ignores any more
+                                          // Ignores any shapes
+        var styles = molecules[0].s;
+        var parseStyle = options !== undefined && options.parseStyle !== undefined ? options.parseStyle : styles !== undefined;
+        
+        var offset = atoms[atoms.length-1].length; // When adding atoms their index will be
+                                   // Offset by the number of existing atoms
+        
+        for (var i = 0; i < atomsInFile.length; i++) {
+            var currentAtom = atomsInFile[i];
+            var atom = {};
+            atom.id = currentAtom.i; // Probably won't exist. Doesn't seem to
+                                     // break anything.
+            atom.x = currentAtom.x;
+            atom.y = currentAtom.y;
+            atom.z = currentAtom.z || 0; // Default value if file is 2D
+
+            atom.bonds = [];
+            atom.bondOrder = [];
+            
+            var elem = currentAtom.l || 'C';
+            atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+
+            atom.serial = atoms[atoms.length-1].length;
+            if (parseStyle) {
+                atom.style = styles[currentAtom.s || 0];
+            }
+            atoms[atoms.length-1].push(atom);
+        }
+        for (var i = 0; i < bondsInFile.length; i++) {
+            var currentBond = bondsInFile[i];
+            var beginIndex = currentBond.b + offset;
+            var endIndex = currentBond.e + offset;
+            var bondOrder = currentBond.o || 1;
+            
+            var firstAtom = atoms[atoms.length-1][beginIndex];
+            var secondAtom = atoms[atoms.length-1][endIndex];
+
+            firstAtom.bonds.push(endIndex);
+            firstAtom.bondOrder.push(bondOrder);
+            secondAtom.bonds.push(beginIndex);
+            secondAtom.bondOrder.push(bondOrder);
+        }
+        return atoms;
+    }
+
     // puts atoms specified in mmCIF fromat in str into atoms
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.mcif = parsers.cif = function(atoms, str, options) {
+    parsers.mcif = parsers.cif = function(str, options) {
+        var atoms = [];
+        var noAssembly = !options.doAssembly; // don't assemble by default
+        var copyMatrix = !options.duplicateAssemblyAtoms;
+        var modelData = atoms.modelData = [];
 
-        //Used to handle quotes correctly
+        // Used to handle quotes correctly
         function splitRespectingQuotes(string, separator) {
             var sections = [];
             var sectionStart = 0;
             var sectionEnd = 0;
             while (sectionEnd < string.length) {
-                while (string.substr(sectionEnd, separator.length) !== separator && sectionEnd < string.length) {
-                    //currently does not support escaping quotes
+                while (string.substr(sectionEnd, separator.length) !== separator
+                        && sectionEnd < string.length) {
+                    // currently does not support escaping quotes
                     if (string[sectionEnd] === "'") {
                         sectionEnd++;
-                        while (sectionEnd < string.length && string[sectionEnd] !== "'") {
+                        while (sectionEnd < string.length
+                                && string[sectionEnd] !== "'") {
                             sectionEnd++;
                         }
-                    }
-                    else if (string[sectionEnd] === '"') {
+                    } else if (string[sectionEnd] === '"') {
                         sectionEnd++;
-                        while (sectionEnd < string.length && string[sectionEnd] !== '"') {
+                        while (sectionEnd < string.length
+                                && string[sectionEnd] !== '"') {
                             sectionEnd++;
                         }
                     }
                     sectionEnd++;
-                    
+
                 }
-                sections.push(string.substr(sectionStart, sectionEnd - sectionStart));
+                sections.push(string.substr(sectionStart, sectionEnd
+                        - sectionStart));
                 sectionStart = sectionEnd = sectionEnd + separator.length;
             }
             return sections;
         }
 
-        //Parser puts all of the data in the file in an object
-        //uses getDataItem() to get an array for the category and data item given
-        //The possible categories and data items in each category are defined in
-        //the mmCIF specification
-        function getDataItem(categoryName, dataItemName) {
-            if (! (categoryName in mmCIF)) {
-                mmCIF[categoryName] = {};
-            }
-            var category = mmCIF[categoryName];
-            if (! (dataItemName in category)) {
-                category[dataItemName] = [];
-            }
-            var dataItem = category[dataItemName];
-            return dataItem;
-        }
 
-        var lines = str.split("\n");
-        //Filter text to remove comments, trailing spaces, and empty lines
+        var lines = str.split(/\r?\n|\r/);
+        // Filter text to remove comments, trailing spaces, and empty lines
         var linesFiltered = [];
         var trimDisabled = false;
         for (var lineNum = 0; lineNum < lines.length; lineNum++) {
-            //first remove comments
-            //incorrect if #'s are allowed in strings
-            //comments might only be allowed at beginning of line, not sure
+            // first remove comments
+            // incorrect if #'s are allowed in strings
+            // comments might only be allowed at beginning of line, not sure
             var line = lines[lineNum].split('#')[0];
 
-            //inside data blocks, the string must be left verbatim
-            //datablocks are started with a ';' at the beginning of a line
-            //and ended with a ';' on its own line.
+            // inside data blocks, the string must be left verbatim
+            // datablocks are started with a ';' at the beginning of a line
+            // and ended with a ';' on its own line.
             if (trimDisabled) {
                 if (line[0] === ';') {
                     trimDisabled = false;
                 }
-            }
-            else {
+            } else {
                 if (line[0] === ';') {
                     trimDisabled = true;
                 }
             }
 
-            if (trimDisabled) {
+            if (trimDisabled || line !== "") {
+                if (!trimDisabled) {
+                    line = line.trim();
+                    if (line[0] === '_') {
+                        // Replace dot separating category from data item with underscore. Dots aren't guarenteed, to makes
+                        // files consistent.
+                        var dot = line.split(/\s/)[0].indexOf('.');
+                        if (dot > -1) {
+                            line[dot] = '_';
+                            line = line.substr(0,dot) + '_' + line.substr(dot + 1)
+                        }
+                    }
+                }
                 linesFiltered.push(line);
             }
-            else if (line !== "") {
-                linesFiltered.push(line.trim());
-            }
         }
 
-        //Process the lines and puts all of the data into an object.
-        var mmCIF = {};
         var lineNum = 0;
         while (lineNum < linesFiltered.length) {
-            if (linesFiltered[lineNum][0] === undefined) {
+            while (! linesFiltered[lineNum].startsWith("data_") ||
+                   linesFiltered[lineNum] === "data_global") {
                 lineNum++;
             }
-            else if (linesFiltered[lineNum][0] === '_') {
-                var categoryName = (linesFiltered[lineNum].split('.')[0]).toLowerCase();
-                var dataItemName = (linesFiltered[lineNum].split('.')[1].split(/\s/)[0]).toLowerCase();
-                var dataItem = getDataItem(categoryName, dataItemName);
-                
+            lineNum++;
 
-                //if nothing left on the line go to the next one
-                var restOfLine = linesFiltered[lineNum].substr(linesFiltered[lineNum].indexOf(dataItemName) + dataItemName.length);
-                if (restOfLine === "") {
+            // Process the lines and puts all of the data into an object.
+            var mmCIF = {};
+            while (lineNum < linesFiltered.length &&
+                   ! linesFiltered[lineNum].startsWith("data_")) {
+                if (linesFiltered[lineNum][0] === undefined) {
                     lineNum++;
-                    if (linesFiltered[lineNum][0] === ';') {
-                        var dataBlock = linesFiltered[lineNum].substr(1);
+                } else if (linesFiltered[lineNum][0] === '_') {
+                    var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
+                    var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
+
+                    // if nothing left on the line go to the next one
+                    var restOfLine = linesFiltered[lineNum]
+                        .substr(linesFiltered[lineNum].indexOf(dataItemName)
+                                + dataItemName.length);
+                    if (restOfLine === "") {
                         lineNum++;
-                        while (linesFiltered[lineNum] !== ';') {
-                            dataBlock = dataBlock + '\n' + linesFiltered[lineNum];
+                        if (linesFiltered[lineNum][0] === ';') {
+                            var dataBlock = linesFiltered[lineNum].substr(1);
                             lineNum++;
+                            while (linesFiltered[lineNum] !== ';') {
+                                dataBlock = dataBlock + '\n'
+                                            + linesFiltered[lineNum];
+                                lineNum++;
+                            }
+                            dataItem.push(dataBlock);
+                        } else {
+                            dataItem.push(linesFiltered[lineNum]);
                         }
-                        dataItem.push(dataBlock);
+                    } else {
+                        dataItem.push(restOfLine.trim());
                     }
-                    else {
-                        dataItem.push(linesFiltered[lineNum]);
+                    lineNum++;
+                } else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
+                    lineNum++;
+                    var dataItems = [];
+                    while (linesFiltered[lineNum] === ""
+                           || linesFiltered[lineNum][0] === '_') {
+                        if (linesFiltered[lineNum] !== "") {
+                            var dataItemName = (linesFiltered[lineNum].split(/\s/)[0]).toLowerCase();
+                            var dataItem = (mmCIF[dataItemName] = mmCIF[dataItemName] || []);
+                            dataItems.push(dataItem);
+                        }
+                        lineNum++;
+                    }
+
+                    var currentDataItem = 0;
+                    while (lineNum < linesFiltered.length
+                           && linesFiltered[lineNum][0] !== '_'
+                           && !linesFiltered[lineNum].startsWith("loop_")
+                           && !linesFiltered[lineNum].startsWith("data_")) {
+                        var line = splitRespectingQuotes(linesFiltered[lineNum], " ");
+                        for (var field = 0; field < line.length; field++) {
+                            if (line[field] !== "") {
+                                dataItems[currentDataItem].push(line[field]);
+                                currentDataItem = (currentDataItem + 1) % dataItems.length;
+                            }
+                        }
+                        lineNum++;
                     }
+                } else {
+                    lineNum++;
+                }
+            }
+
+            modelData.push({symmetries:[]});
+
+            // Pulls atom information out of the data
+            atoms.push([]);
+            var currentIndex = 0;
+            var atomCount = mmCIF._atom_site_id !== undefined ? mmCIF._atom_site_id.length
+                : mmCIF._atom_site_label.length;
+            function sqr(n) {
+                return n*n;
+            }
+            var conversionMatrix;
+            if (mmCIF._cell_length_a !== undefined) {
+                var a = parseFloat(mmCIF._cell_length_a);
+                var b = parseFloat(mmCIF._cell_length_b);
+                var c = parseFloat(mmCIF._cell_length_c);
+                var alpha_deg = parseFloat(mmCIF._cell_angle_alpha) || 90;
+                var beta_deg = parseFloat(mmCIF._cell_angle_beta) || 90;
+                var gamma_deg = parseFloat(mmCIF._cell_angle_gamma) || 90;
+                var alpha = alpha_deg * Math.PI / 180;
+                var beta = beta_deg * Math.PI / 180;
+                var gamma = gamma_deg * Math.PI / 180;
+                var cos_alpha = Math.cos(alpha);
+                var cos_beta = Math.cos(beta);
+                var cos_gamma = Math.cos(gamma);
+                var sin_gamma = Math.sin(gamma);
+                conversionMatrix = [
+                    [a, b*cos_gamma, c*cos_beta],
+                    [0, b*sin_gamma, c*(cos_alpha-cos_beta*cos_gamma)/sin_gamma],
+                    [0, 0, c*Math.sqrt(1-sqr(cos_alpha)-sqr(cos_beta)-sqr(cos_gamma)+2*cos_alpha*cos_beta*cos_gamma)/sin_gamma]
+                ];
+                modelData[modelData.length-1].cryst = {'a' : a, 'b' : b, 'c' : c, 'alpha' : alpha_deg, 'beta' : beta_deg, 'gamma' : gamma_deg};
+            }
+            function fractionalToCartesian(a, b, c) {
+                var x = conversionMatrix[0][0]*a + conversionMatrix[0][1]*b + conversionMatrix[0][2]*c;
+                var y = conversionMatrix[1][0]*a + conversionMatrix[1][1]*b + conversionMatrix[1][2]*c;
+                var z = conversionMatrix[2][0]*a + conversionMatrix[2][1]*b + conversionMatrix[2][2]*c;
+                return {x:x, y:y, z:z};
+            }
+            for (var i = 0; i < atomCount; i++) {
+                if (mmCIF._atom_site_group_pdb !== undefined && mmCIF._atom_site_group_pdb[i] === "TER")
+                    continue;
+                var atom = {};
+                if (mmCIF._atom_site_cartn_x !== undefined) {
+                    atom.x = parseFloat(mmCIF._atom_site_cartn_x[i]);
+                    atom.y = parseFloat(mmCIF._atom_site_cartn_y[i]);
+                    atom.z = parseFloat(mmCIF._atom_site_cartn_z[i]);
                 }
                 else {
-                    dataItem.push(restOfLine.trim());
+                    var coords = fractionalToCartesian(
+                        parseFloat(mmCIF._atom_site_fract_x[i]),
+                        parseFloat(mmCIF._atom_site_fract_y[i]),
+                        parseFloat(mmCIF._atom_site_fract_z[i]));
+                    atom.x = coords.x;
+                    atom.y = coords.y;
+                    atom.z = coords.z;
                 }
-                lineNum++;
+                atom.chain = mmCIF._atom_site_auth_asym_id ? mmCIF._atom_site_auth_asym_id[i] : undefined;
+                atom.resi = mmCIF._atom_site_auth_seq_id ? parseInt(mmCIF._atom_site_auth_seq_id[i]) : undefined;
+                atom.resn = mmCIF._atom_site_auth_comp_id ? mmCIF._atom_site_auth_comp_id[i].trim() : undefined;
+                atom.atom = mmCIF._atom_site_auth_atom_id ? mmCIF._atom_site_auth_atom_id[i].replace(/"/gm,'')  : undefined; //"primed" names are in quotes
+                atom.hetflag = !mmCIF._atom_site_group_pdb || mmCIF._atom_site_group_pdb[i] === "HETA" || mmCIF._atom_site_group_pdb[i] === "HETATM";
+                var elem = mmCIF._atom_site_type_symbol[i];
+                atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                atom.bonds = [];
+                atom.ss = 'c';
+                atom.serial = i;
+                atom.bondOrder = [];
+                atom.properties = {};
+                atoms[atoms.length-1].push(atom);
             }
-            else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
-                lineNum++;
-                var dataItems = [];
-                var dataItemNames = []
-                while (linesFiltered[lineNum] === "" || linesFiltered[lineNum][0] === '_') {
-                    if (linesFiltered[lineNum] !== "") {
-                        var categoryName = (linesFiltered[lineNum].split('.')[0]).toLowerCase();
-                        var dataItemName = (linesFiltered[lineNum].split('.')[1].split(/\s/)[0]).toLowerCase();
-                        var dataItem = getDataItem(categoryName, dataItemName);
-                        dataItems.push(dataItem);
-                        dataItemNames.push(dataItemName);
-                    }
-                    lineNum++;
-                }
 
-                var currentDataItem = 0;
-                while (lineNum < linesFiltered.length && linesFiltered[lineNum][0] !== '_' && linesFiltered[lineNum].substr(0,5) !== "loop_") {
-                    var line = splitRespectingQuotes(linesFiltered[lineNum], " ");
-                    for (var field = 0; field < line.length; field++) {
-                        if (line[field] !== "") {
-                            dataItems[currentDataItem].push(line[field]);
-                            currentDataItem = (currentDataItem + 1) % dataItems.length;
+            if (mmCIF._pdbx_struct_oper_list_id !== undefined && !noAssembly) {
+                for (var i = 0; i < mmCIF._pdbx_struct_oper_list_id.length; i++) {
+                    var matrix11 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][1]'][i]);
+                    var matrix12 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][2]'][i]);
+                    var matrix13 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[1][3]'][i]);
+                    var vector1 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[1]'][i]);
+                    var matrix21 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][1]'][i]);
+                    var matrix22 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][2]'][i]);
+                    var matrix23 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[2][3]'][i]);
+                    var vector2 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[2]'][i]);
+                    var matrix31 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][1]'][i]);
+                    var matrix32 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][2]'][i]);
+                    var matrix33 = parseFloat(mmCIF['_pdbx_struct_oper_list_matrix[3][3]'][i]);
+                    var vector3 = parseFloat(mmCIF['_pdbx_struct_oper_list_vector[3]'][i]);
+
+                    var matrix = new $3Dmol.Matrix4(matrix11, matrix12, matrix13, vector1,
+                                                    matrix21, matrix22, matrix23, vector2,
+                                                    matrix31, matrix32, matrix33, vector3);
+                    modelData[modelData.length-1].symmetries.push(matrix);
+                }
+                for (var i = 0; i < atoms.length; i++) {
+                    processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[i]);
+                }
+            }
+            function parseTerm(term){
+                var negative = term.match('-');
+                term = term.replace(/[-xyz]/g, "");
+                var fractionParts = term.split('/');
+
+                var numerator, denominator;
+                if (fractionParts[1] === undefined) {
+                    denominator = 1;
+                }
+                else {
+                    denominator = parseInt(fractionParts[1]);
+                }
+                if (fractionParts[0] === "") {
+                    numerator = 1;
+                }
+                else {
+                    numerator = parseInt(fractionParts[0]);
+                }
+                return numerator / denominator * (negative ? -1 : 1);
+            }
+            if (mmCIF._symmetry_equiv_pos_as_xyz !== undefined) {
+                for (var sym = 0; sym < mmCIF._symmetry_equiv_pos_as_xyz.length; sym++) {
+                    var transform = mmCIF._symmetry_equiv_pos_as_xyz[sym].replace(/["' ]/g,"");
+                    var componentStrings = transform.split(',').map(
+                        function(val){
+                            return val.replace(/-/g,"+-");
+                        });
+                    var matrix = new $3Dmol.Matrix4(0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,1);
+                    for (var coord = 0; coord < 3; coord++) {
+                        var terms = componentStrings[coord].split('+');
+                        var constant = 0, xTerm = 0, yTerm = 0, zTerm = 0;
+                        for (var t = 0; t < terms.length; t++) {
+                            var term = terms[t];
+                            if (term === "")
+                                continue;
+                            var coefficient = parseTerm(term);
+                            if (term.match('x')) {
+                                matrix.elements[coord + 0] = coefficient;
+                            }
+                            else if (term.match('y')) {
+                                matrix.elements[coord + 4] = coefficient;
+                            }
+                            else if (term.match('z')) {
+                                matrix.elements[coord + 8] = coefficient;
+                            }
+                            else {
+                                matrix.elements[coord + 12] = coefficient;
+                            }
                         }
                     }
-                    lineNum++;
+                    var conversionMatrix4 = new $3Dmol.Matrix4(
+                        conversionMatrix[0][0], conversionMatrix[0][1], conversionMatrix[0][2], 0,
+                        conversionMatrix[1][0], conversionMatrix[1][1], conversionMatrix[1][2], 0,
+                        conversionMatrix[2][0], conversionMatrix[2][1], conversionMatrix[2][2], 0);
+                    var conversionInverse = (new $3Dmol.Matrix4()).getInverse(conversionMatrix4, true);
+                    matrix = (new $3Dmol.Matrix4()).multiplyMatrices(matrix, conversionInverse);
+                    matrix = (new $3Dmol.Matrix4()).multiplyMatrices(conversionMatrix4, matrix);
+                    modelData[modelData.length-1].symmetries.push(matrix);
                 }
             }
-            else {
-                lineNum++;
-            }
+        }
+        for (var i = 0; i < atoms.length; i++) {
+            assignBonds(atoms[i]);
+            computeSecondaryStructure(atoms[i]);
+            processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[i]);
         }
 
-        //Pulls atom information out of the data
-        var atomsPreBonds = {};
-        for (var i = 0; i < mmCIF._atom_site.id.length; i++) {
-        if (mmCIF._atom_site.group_pdb[i] === "TER") continue;
-            var atom = {};
-            atom.id = parseFloat(mmCIF._atom_site.id[i]);
-            atom.x = parseFloat(mmCIF._atom_site.cartn_x[i]);
-            atom.y = parseFloat(mmCIF._atom_site.cartn_y[i]);
-            atom.z = parseFloat(mmCIF._atom_site.cartn_z[i]);
-            atom.hetflag = mmCIF._atom_site.group_pdb[i] === "HETA";
-            atom.elem = mmCIF._atom_site.type_symbol[i];
-            atom.bonds = [];
-            atom.bondOrder = [];
-            atom.properties = {};
-            atomsPreBonds[atom.id] = atom;
-        }
-        var atomsIndexed = [];
-        var currentIndex = 0;
-        for (var id in atomsPreBonds) {
-            var atom = atomsPreBonds[id];
-            atom.index = currentIndex;
-            atomsIndexed[currentIndex] = atom;
-            currentIndex++;
-        }
-
-        //create a hash table of the atoms using label and sequence as keys
-        var atomHashTable = {};
-        for (var i = 0; i < mmCIF._atom_site.id.length; i++) {
-            var label_alt = mmCIF._atom_site.label_alt_id[i];
-            if (label_alt === undefined) {
-                label_alt = '.';
-            }
-            var label_asym = mmCIF._atom_site.label_asym_id[i];
-            if (label_asym === undefined) {
-                label_asym = '.';
-            }
-            var label_atom = mmCIF._atom_site.label_atom_id[i];
-            if (label_atom === undefined) {
-                label_atom = '.';
-            }
-            var label_seq = mmCIF._atom_site.label_seq_id[i];
-            if (label_seq === undefined) {
-                label_seq = '.';
-            }
-            var id = mmCIF._atom_site.id[i]; //If file is sorted, id will be i+1
-
-            if (atomHashTable[label_alt] === undefined) {
-                atomHashTable[label_alt] = {};
-            }
-            if (atomHashTable[label_alt][label_asym] === undefined) {
-                atomHashTable[label_alt][label_asym] = {};
-            }
-            if (atomHashTable[label_alt][label_asym][label_atom] === undefined) {
-                atomHashTable[label_alt][label_asym][label_atom] = {};
-            }
-        
-            atomHashTable[label_alt][label_asym][label_atom][label_seq] = id;
-        }
-
-        for (var i = 0; i < mmCIF._struct_conn.id.length; i++) {
-	        var offset = atoms.length;
-	        
-	        var alt = (mmCIF._struct_conn.ptnr1_label_alt_id || [])[i];
-	        if (alt === undefined) {
-	            alt = ".";
-	        }
-	        var asym = (mmCIF._struct_conn.ptnr1_label_asym_id || [])[i];
-	        if (asym === undefined) {
-	            asym = ".";
-	        }
-	        var atom = (mmCIF._struct_conn.ptnr1_label_atom_id || [])[i];
-	        if (atom === undefined) {
-	            atom = ".";
-	        }
-	        var seq = (mmCIF._struct_conn.ptnr1_label_seq_id || [])[i];
-	        if (seq === undefined) {
-	            seq = ".";
-	        }
-	        
-            var id1 = atomHashTable[alt][asym][atom][seq];
-            //if (atomsPreBonds[id1] === undefined) continue;
-            var index1 = atomsPreBonds[id1].index;
-            
-            var alt = (mmCIF._struct_conn.ptnr2_label_alt_id || [])[i];
-	    if (alt === undefined) {
-	        alt = ".";
-	    }
-	    var asym = (mmCIF._struct_conn.ptnr2_label_asym_id || [])[i];
-	    if (asym === undefined) {
-	        asym = ".";
-	    }
-	    var atom = (mmCIF._struct_conn.ptnr2_label_atom_id || [])[i];
-	    if (atom === undefined) {
-	        atom = ".";
-	    }
-	    var seq = (mmCIF._struct_conn.ptnr2_label_seq_id || [])[i];
-	    if (seq === undefined) {
-	        seq = ".";
-	    }
-
-            var id2 = atomHashTable[mmCIF._struct_conn.ptnr2_label_alt_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_asym_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_atom_id[i]]
-                                   [mmCIF._struct_conn.ptnr2_label_seq_id[i]];
-            if (atomsPreBonds[id2] === undefined) continue;
-            var index2 = atomsPreBonds[id2].index;
-
-            atomsPreBonds[id1].bonds.push(index2 + offset);
-            atomsPreBonds[id1].bondOrder.push(1);
-            atomsPreBonds[id2].bonds.push(index1 + offset);
-            atomsPreBonds[id2].bondOrder.push(1);
-            console.log("connected " + index1 + " and " + index2);
-        }
-
-        //atoms = atoms.concat(atomsPreBonds);
-        for (var i = 0; i < atomsIndexed.length; i++) {
-            delete atomsIndexed[i].index;
-            atoms.push(atomsIndexed[i]);
-        }
-
-        assignBonds(atoms);
-	
-    	var matrices = [];
-    	if (mmCIF._pdbx_struct_oper_list !== undefined) {    // transformations may not exist.
-            for (var i = 0; i < mmCIF._pdbx_struct_oper_list.id.length; i++) {
-           	var matrix11 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][1]']);
-           	var matrix12 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][2]']);
-           	var matrix13 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[1][3]']);
-           	var vector1  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[1]'   ]);
-           	var matrix21 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][1]']);
-           	var matrix22 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][2]']);
-           	var matrix23 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[2][3]']);
-           	var vector2  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[2]'   ]);
-           	var matrix31 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][1]']);
-           	var matrix32 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][2]']);
-           	var matrix33 = parseFloat(mmCIF._pdbx_struct_oper_list['matrix[3][3]']);
-           	var vector3  = parseFloat(mmCIF._pdbx_struct_oper_list['vector[3]'   ]);
-           	
-    	        var matrix = new $3Dmol.Matrix4(
-    	                matrix11, matrix12, matrix13, vector1,
-    	                matrix21, matrix22, matrix23, vector2,
-    	                matrix31, matrix32, matrix33, vector3
-    	        );
-    	        matrices.push(matrix);
-    	    }
-    	}
+        return atoms;
     }
 
     // parse SYBYL mol2 file from string - assumed to only contain one molecule
     // tag
-    // TODO: Figure out how to handle multi molecule files (for SDF, too)
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options - keepH (do not strip hydrogens)
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options
      */
-    parsers.mol2 = parsers.MOL2 = function(atoms, str, options) {
-        
+    parsers.mol2 = parsers.MOL2 = function(str, options) {
+
+        var atoms = [[]];
         var noH = false;
-        if(typeof options.keepH !== "undefined") 
+        if (typeof options.keepH !== "undefined")
             noH = !options.keepH;
-        
-        // Note: these regex's work, though they don't match '<TRIPOS>'
-        // correctly - something to do with angle brackets
-        var mol_pos = str.search(/@<TRIPOS>MOLECULE/);
-        var atom_pos = str.search(/@<TRIPOS>ATOM/);
-        
-        // Assuming both Molecule and Atom sections exist
-        if (mol_pos == -1 || atom_pos == -1)
-            return;
-        
-        // serial is atom's index in file; index is atoms index in 'atoms'
-        var serialToIndex = [];
-        
 
         // assert (mol_pos < atom_pos), "Unexpected formatting of mol2 file
         // (expected 'molecule' section before 'atom' section)";
-        
 
-        var lines = str.substr(mol_pos, str.length).split("\n");
-        var tokens = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-        var natoms = parseInt(tokens[0]);
-        var nbonds = 0;
-        
-        if (tokens.length > 1)
-            nbonds = parseInt(tokens[1]); 
-        
-        var offset = 4;
-        var i;
-        // Continue until 'Atom' section
-        for (i = 3; i < lines.length; i++)
-        {
-            if (lines[i] == "@<TRIPOS>ATOM")
-            {
-                offset = i+1;
-                break;
-            }
-        }
-        
-        var start = atoms.length;
-        var end = start + natoms;
-        var line;
-        // Process ATOMS
-        for (i = start; i < end; i++) {
-            line = lines[offset++];
-            tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-            var atom = {};
-            //get element
-            atom.atom = atom.elem = tokens[5].split('.')[0];
-            if (atom.elem == 'H' && noH) {
-                //ignore
-            }
-            else {
-                // 'index' is this atom's index in 'atoms'; 'serial' is this atom's
-                // serial id in mol2 file
-                var index = atoms.length;
-                var serial = parseInt(tokens[0]);
-                atom.serial = serial;
-                // atom.serial = i;
-                
-                atom.x = parseFloat(tokens[2]);
-                atom.y = parseFloat(tokens[3]);
-                atom.z = parseFloat(tokens[4]);
-                atom.atom = tokens[5];
-                var charge = parseFloat(tokens[8]);
-                
-                atom.bonds = [];
-                atom.bondOrder = [];
-                atom.properties = {'charge': charge, 'partialCharge': charge};
-                serialToIndex[serial] = index;
-                
-                atoms.push(atom);
-            }
-        }
+        var lines = str.substr(mol_pos, str.length).split(/\r?\n|\r/);
         
-        // Process BONDS
-        var bonds_found = false;
-        while (offset < lines.length)
-        {
-            if (lines[offset++] == "@<TRIPOS>BOND")
-            {
-                bonds_found = true;
-                break;            
-            }        
-        }
+        while(lines.length > 0) { 
         
-        if (bonds_found && nbonds)
-        {
-            for (i = 0; i < nbonds; i++)
-            {
+            // Note: these regex's work, though they don't match '<TRIPOS>'
+            // correctly - something to do with angle brackets
+            var mol_pos = str.search(/@<TRIPOS>MOLECULE/);
+            var atom_pos = str.search(/@<TRIPOS>ATOM/);
+
+            // Assuming both Molecule and Atom sections exist
+            if (mol_pos == -1 || atom_pos == -1)
+                break;
+        
+            // serial is atom's index in file; index is atoms index in 'atoms'
+            var serialToIndex = []; 
+            var tokens = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(
+                    " ");
+            var natoms = parseInt(tokens[0]);
+            var nbonds = 0;
+
+            if (tokens.length > 1)
+                nbonds = parseInt(tokens[1]);
+
+            var offset = 4;
+            var i;
+            // Continue until 'Atom' section
+            for (i = 3; i < lines.length; i++) {
+                if (lines[i] == "@<TRIPOS>ATOM") {
+                    offset = i + 1;
+                    break;
+                }
+            }
+        
+            var start = atoms[atoms.length-1].length;
+            var end = start + natoms;
+            var line;
+            // Process ATOMS
+            for (i = start; i < end; i++) {
                 line = lines[offset++];
+                tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+                var atom = {};
+                // get element
+                var elem = tokens[5].split('.')[0];
+                atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
+                if (atom.elem == 'H' && noH) {
+                    // ignore
+                } else {
+                    // 'index' is this atom's index in 'atoms'; 'serial' is this
+                    // atom's
+                    // serial id in mol2 file
+                    var index = atoms[atoms.length-1].length;
+                    var serial = parseInt(tokens[0]);
+                    atom.serial = serial;
+                    // atom.serial = i;
+
+                    atom.x = parseFloat(tokens[2]);
+                    atom.y = parseFloat(tokens[3]);
+                    atom.z = parseFloat(tokens[4]);
+                    atom.atom = tokens[5];
+                    var charge = parseFloat(tokens[8]);
+                    
+                    atom.index = index;
+                    atom.bonds = [];
+                    atom.bondOrder = [];
+                    atom.properties = {
+                        'charge' : charge,
+                        'partialCharge' : charge
+                    };
+                    serialToIndex[serial] = index;
+
+                    atoms[atoms.length-1].push(atom);
+                }
+            }
 
-                tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
+            // Process BONDS
+            var bonds_found = false;
+            while (offset < lines.length) {
+                if (lines[offset++] == "@<TRIPOS>BOND") {
+                    bonds_found = true;
+                    break;
+                }
+            }
+
+            if (bonds_found && nbonds) {
+                for (i = 0; i < nbonds; i++) {
+                    line = lines[offset++];
+
+                    tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
                             " ");
-                var from = parseInt(tokens[1]);
-                fromAtom = atoms[serialToIndex[from]];
-                var to = parseInt(tokens[2]);
-                toAtom = atoms[serialToIndex[to]];              
-                    
-                // Won't be able to read aromatic bonds correctly...
-                var order = parseInt(tokens[3]);
-                if (isNaN(order))
-                    order = 1;
-                
-                if (fromAtom !== undefined && toAtom !== undefined){
-                    fromAtom.bonds.push(serialToIndex[to]);
-                    fromAtom.bondOrder.push(order);
-                    toAtom.bonds.push(serialToIndex[from]);
-                    toAtom.bondOrder.push(order);
-                }    
+                    var from = parseInt(tokens[1]);
+                    fromAtom = atoms[atoms.length-1][serialToIndex[from]];
+                    var to = parseInt(tokens[2]);
+                    toAtom = atoms[atoms.length-1][serialToIndex[to]];
 
-                
+                    // Won't be able to read aromatic bonds correctly...
+                    var order = parseInt(tokens[3]);
+                    if (isNaN(order))
+                        order = 1;
 
+                    if (fromAtom !== undefined && toAtom !== undefined) {
+                        fromAtom.bonds.push(serialToIndex[to]);
+                        fromAtom.bondOrder.push(order);
+                        toAtom.bonds.push(serialToIndex[from]);
+                        toAtom.bondOrder.push(order);
+                    }
+
+                }
+            }
+            if (options.multimodel) {
+                if (!options.onemol)
+                    atoms.push([])
+                lines.splice(0, offset);
+                str = lines.join("\n"); //update for str.search
+                continue;
+            }
+            else {
+                break;
             }
         }
-        
-        return true;
-        
+        return atoms;
+
     };
-    
 
+    var bondTable = {
+            H :0.37,                                                                                                                                He:0.32,
+            Li:1.34,Be:0.90,                                                                                B :0.82,C :0.77,N :0.75,O :0.73,F :0.71,Ne:0.69,
+            Na:1.54,Mg:1.30,                                                                                Al:1.18,Si:1.11,P :1.06,S :1.02,Cl:0.99,Ar:0.97,
+            K :1.96,Ca:1.74,Sc:1.44,Ti:1.56,V :1.25,/* Cr */Mn:1.39,Fe:1.25,Co:1.26,Ni:1.21,Cu:1.38,Zn:1.31,Ga:1.26,Ge:1.22,/* As */Se:1.16,Br:1.14,Kr:1.10,
+            Rb:2.11,Sr:1.92,Y :1.62,Zr:1.48,Nb:1.37,Mo:1.45,Tc:1.56,Ru:1.26,Rh:1.35,Pd:1.31,Ag:1.53,Cd:1.48,In:1.44,Sn:1.41,Sb:1.38,Te:1.35,I :1.33,Xe:1.30,
+            Cs:2.25,Ba:1.98,Lu:1.60,Hf:1.50,Ta:1.38,W :1.46,Re:1.59,Os:1.44,Ir:1.37,Pt:1.28,Au:1.44,Hg:1.49,Tl:1.48,Pb:1.47,Bi:1.46,/* Po *//* At */Rn:1.45,
+
+            // None of the boottom row or any of the Lanthanides have bond lengths
+    }
+    var bondLength = function(elem) {
+        return bondTable[elem] || 1.6;
+    }
     // return true if atom1 and atom2 are probably bonded to each other
     // based on distance alone
     var areConnected = function(atom1, atom2) {
-        var maxsq = 3.6;
+        var maxsq = bondLength(atom1.elem) + bondLength(atom2.elem);
+        maxsq += 0.25;// fudge factor, especially important for md frames, also see 1i3d
+        maxsq *= maxsq;
 
         var xdiff = atom1.x - atom2.x;
         xdiff *= xdiff;
@@ -24772,35 +31531,83 @@ $3Dmol.Parsers = (function() {
 
         if (isNaN(distSquared))
             return false;
-        if (distSquared < 0.5)
+        else if (distSquared < 0.5)
             return false; // maybe duplicate position.
-
-        if (distSquared > 1.3 && (atom1.elem == 'H' || atom2.elem == 'H' || atom1.elem == 'D' || atom2.elem == 'D'))
+        else if (distSquared > maxsq)
             return false;
-        if (distSquared < 3.6 && (atom1.elem == 'S' || atom2.elem == 'S'))
+        else
             return true;
-        if (distSquared > 2.78)
-            return false;
-        return true;
     };
-    
+
+    //adds symmetry info to either duplicate and rotate/translate biological unit later or add extra atoms now
+    var processSymmetries = function(copyMatrices, copyMatrix, atoms) {
+        var end = atoms.length;
+        var offset = end;
+        var t, l, n;
+        if (!copyMatrix) { // do full assembly
+            for (t = 0; t < copyMatrices.length; t++) {
+                if (!copyMatrices[t].isIdentity()) {
+                    var xyz = new $3Dmol.Vector3();
+                    for (n = 0; n < end; n++) {
+                        var bondsArr = [];
+                        for (l = 0; l < atoms[n].bonds.length; l++) {
+                            bondsArr.push(atoms[n].bonds[l] + offset);
+                        }
+                        xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
+                        xyz.applyMatrix4(copyMatrices[t]);
+                        var newAtom = {};
+                        for (var i in atoms[n]) {
+                            newAtom[i] = atoms[n][i];
+                        }
+                        newAtom.x = xyz.x;
+                        newAtom.y = xyz.y;
+                        newAtom.z = xyz.z;
+                        newAtom.bonds = bondsArr;
+                        atoms.push(newAtom);
+                    }
+                    offset = atoms.length;
+                }
+            }
+        }
+        else if(copyMatrices.length > 1) {
+            for (t = 0; t < atoms.length; t++) {
+                var symmetries = [];
+                for (l = 0; l < copyMatrices.length; l++) {
+                    if (!copyMatrices[l].isIdentity()) {
+                        var newXYZ = new $3Dmol.Vector3();
+                        newXYZ.set(atoms[t].x, atoms[t].y, atoms[t].z);
+                        newXYZ.applyMatrix4(copyMatrices[l]);
+                        symmetries.push(newXYZ);
+                    }
+                }
+                atoms[t].symmetries = symmetries;
+            }
+        }
+    }
+
+
     // parse pdb file from str and create atoms
-    //if computeStruct is true will always perform secondary structure analysis,
-    //otherwise only do analysis of SHEET/HELIX comments are missing
+    // if computeStruct is true will always perform secondary structure
+    // analysis,
+    // otherwise only do analysis of SHEET/HELIX comments are missing
     /**
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options - keepH (do not strip hydrogens), noSecondaryStructure (do not compute ss)
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options - keepH (do not strip hydrogens), noSecondaryStructure
+     *            (do not compute ss)
      */
-    parsers.pdb = parsers.PDB = parsers.pdbqt = parsers.PDBQT = function(atoms, str, options, copyMatrices) {
+    parsers.pdb = parsers.PDB = parsers.pdbqt = parsers.PDBQT = function(str, options) {
 
+        var atoms = [[]];
         var atoms_cnt = 0;
         var noH = !options.keepH; // suppress hydrogens by default
         var computeStruct = !options.noSecondaryStructure;
-        var noAssembly = !options.doAssembly; //don't assemble by default
-        var copyMatrix = !options.duplicateAssemblyAtoms; //if not specified, default to copyMatrix true
-        var allMatrices = [];
-        var start = atoms.length;
+        var noAssembly = !options.doAssembly; // don't assemble by default
+        var copyMatrix = !options.duplicateAssemblyAtoms; //default true
+        var modelData = atoms.modelData = [{symmetries:[]}];
+
+        var start = atoms[atoms.length-1].length;
         var atom;
         var protein = {
             sheet : [],
@@ -24809,20 +31616,35 @@ $3Dmol.Parsers = (function() {
 
         var hasStruct = false;
         var serialToIndex = []; // map from pdb serial to index in atoms
-        var lines = str.split("\n");
+        var lines = str.split(/\r?\n|\r/);
         var i, j, k, line;
+        var seenbonds = {}; //sometimes connect records are duplicated as an unofficial means of relaying bond orders
         for (i = 0; i < lines.length; i++) {
             line = lines[i].replace(/^\s*/, ''); // remove indent
             var recordName = line.substr(0, 6);
             var startChain, startResi, endChain, endResi;
-            if (recordName == 'ATOM  ' || recordName == 'HETATM') {
+            
+            if(recordName.indexOf("END") == 0) {
+                if (options.multimodel) {
+                    if (!options.onemol) {
+                        atoms.push([]);
+                        modelData.push({symmetries:[]});
+                    }
+                    continue;
+                }
+                else {
+                    break;
+                }
+            }
+
+            else if (recordName == 'ATOM  ' || recordName == 'HETATM') {
                 var resn, chain, resi, icode, x, y, z, hetflag, elem, serial, altLoc, b;
                 altLoc = line.substr(16, 1);
                 if (altLoc != ' ' && altLoc != 'A')
                     continue; // FIXME: ad hoc
                 serial = parseInt(line.substr(6, 5));
                 atom = line.substr(12, 4).replace(/ /g, "");
-                resn = line.substr(17, 3);
+                resn = line.substr(17, 3).replace(/ /g, "");
                 chain = line.substr(21, 1);
                 resi = parseInt(line.substr(22, 4));
                 icode = line.substr(26, 1);
@@ -24831,17 +31653,32 @@ $3Dmol.Parsers = (function() {
                 z = parseFloat(line.substr(46, 8));
                 b = parseFloat(line.substr(60, 8));
                 elem = line.substr(76, 2).replace(/ /g, "");
-                if (elem === '') { // for some incorrect PDB files
+                if (elem === '' || typeof(bondTable[elem]) === 'undefined') { // for some incorrect PDB files
                     elem = line.substr(12, 2).replace(/ /g, "");
+                    if(elem.length > 0 && elem[0] == 'H' && elem != 'Hg') {
+                        elem = 'H'; //workaround weird hydrogen names from MD, note mercury must use lowercase
+                    }
+                    if(elem.length > 1) {
+                        elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();   
+                        if(typeof(bondTable[elem]) === 'undefined') {
+                            //not a known element, probably should just use first letter
+                            elem = elem[0];
+                        } else if(line[0] == 'A' && elem == 'Ca') { //alpha carbon, not calcium
+                            elem = "C";
+                        }
+                    }
+                } else {
+                    elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();                    
                 }
-                if((elem == 'H' || elem == 'HH' || elem == 'HD') && noH)
+
+                if(elem == 'H' && noH)
                     continue;
                 if (line[0] == 'H')
                     hetflag = true;
                 else
                     hetflag = false;
-                serialToIndex[serial] = atoms.length;
-                atoms.push({
+                serialToIndex[serial] = atoms[atoms.length-1].length;
+                atoms[atoms.length-1].push({
                     'resn' : resn,
                     'x' : x,
                     'y' : y,
@@ -24851,10 +31688,10 @@ $3Dmol.Parsers = (function() {
                     'chain' : chain,
                     'resi' : resi,
                     'icode' : icode,
-                    'rescode': resi + (icode != ' ' ? "^"+icode: ""), // combo
-                                                                        // resi
-                                                                        // and
-                                                                        // icode
+                    'rescode' : resi + (icode != ' ' ? "^" + icode : ""), // combo
+                    // resi
+                    // and
+                    // icode
                     'serial' : serial,
                     'atom' : atom,
                     'bonds' : [],
@@ -24877,16 +31714,33 @@ $3Dmol.Parsers = (function() {
                 // also
                 // described in CONECT. But what about 2JYT???
                 var from = parseInt(line.substr(6, 5));
-                var fromAtom = atoms[serialToIndex[from]];
+                var fromindex = serialToIndex[from];
+                var fromAtom = atoms[atoms.length-1][fromindex];
                 for (j = 0; j < 4; j++) {
                     var to = parseInt(line.substr([ 11, 16, 21, 26 ][j], 5));
-                    var toAtom = atoms[serialToIndex[to]];
+                    var toindex = serialToIndex[to];
+                    var toAtom = atoms[atoms.length-1][toindex];
                     if (fromAtom !== undefined && toAtom !== undefined) {
-                        //minimal cleanup here - pymol likes to output duplicated conect records
-                        var toindex = serialToIndex[to];
-                        if(fromAtom.bonds[fromAtom.bonds.length-1] != toindex) {
-                            fromAtom.bonds.push(toindex);
-                            fromAtom.bondOrder.push(1);
+                        // duplicated conect records indicate bond order
+                        if(!seenbonds[ [fromindex,toindex] ]) {
+                            seenbonds[ [fromindex,toindex] ] = 1;
+                            if (fromAtom.bonds.length == 0 || fromAtom.bonds[fromAtom.bonds.length - 1] != toindex) {
+                                fromAtom.bonds.push(toindex);
+                                fromAtom.bondOrder.push(1);
+                            }
+                        } else { //update bond order
+                            seenbonds[ [fromindex,toindex] ] += 1;
+                            
+                            for(var bi = 0; bi < fromAtom.bonds.length; bi++) {
+                                if(fromAtom.bonds[bi] == toindex) {
+                                    var newbo = seenbonds[ [fromindex,toindex] ];
+                                    if(newbo >= 4) { //aromatic
+                                        fromAtom.bondOrder[bi] = 1;
+                                    } else {
+                                        fromAtom.bondOrder[bi] = newbo;
+                                    }
+                                }
+                            }
                         }
                     }
                 }
@@ -24898,20 +31752,28 @@ $3Dmol.Parsers = (function() {
                 endResi = parseInt(line.substr(33, 4));
                 protein.helix
                         .push([ startChain, startResi, endChain, endResi ]);
-            } else if ((!noAssembly) && (recordName == 'REMARK') && (line.substr(13, 5) == 'BIOMT')) {
+            } else if ((!noAssembly) && (recordName == 'REMARK')
+                    && (line.substr(13, 5) == 'BIOMT')) {
                 var n;
-                var matrix = new $3Dmol.Matrix4();
+                var matrix = new $3Dmol.Matrix4(); 
                 for (n = 1; n <= 3; n++) {
                     line = lines[i].replace(/^\s*/, '');
-                    if (parseInt(line.substr(18, 1)) == n) { //check for all three lines by matching # @ end of "BIOMT" to n
-                        matrix.elements[(n-1)] = parseFloat(line.substr(23, 10));
-                        matrix.elements[(n-1)+4] = parseFloat(line.substr(33, 10));
-                        matrix.elements[(n-1)+8] = parseFloat(line.substr(43, 10));
-                        matrix.elements[(n-1)+12] = parseFloat(line.substr(53));
+                    if (parseInt(line.substr(18, 1)) == n) { // check for all
+                                                                // three lines
+                                                                // by matching #
+                                                                // @ end of
+                                                                // "BIOMT" to n
+                        matrix.elements[(n - 1)] = parseFloat(line.substr(23,
+                                10));
+                        matrix.elements[(n - 1) + 4] = parseFloat(line.substr(
+                                33, 10));
+                        matrix.elements[(n - 1) + 8] = parseFloat(line.substr(
+                                43, 10));
+                        matrix.elements[(n - 1) + 12] = parseFloat(line
+                                .substr(53));
                         i++;
-                    }
-                    else {
-                        while(line.substr(13, 5) == 'BIOMT') { //increase "i" until you leave the REMARKs
+                    } else {
+                        while (line.substr(13, 5) == 'BIOMT') {
                             i++;
                             line = lines[i].replace(/^\s*/, '');
                         }
@@ -24921,173 +31783,145 @@ $3Dmol.Parsers = (function() {
                 matrix.elements[7] = 0;
                 matrix.elements[11] = 0;
                 matrix.elements[15] = 1;
-                allMatrices.push(matrix);
-                copyMatrices.push(matrix);
-                
-                i--; //set i back
+                modelData[modelData.length-1].symmetries.push(matrix);
+                i--; // set i back
+            } else if (recordName == 'CRYST1') {
+                var a, b, c, alpha, beta, gamma;
+                a = parseFloat(line.substr(7, 8));
+                b = parseFloat(line.substr(16, 8));
+                c = parseFloat(line.substr(25, 8));
+                alpha = parseFloat(line.substr(34, 6));
+                beta = parseFloat(line.substr(41, 6));
+                gamma = parseFloat(line.substr(48, 6));
+                modelData[modelData.length-1].cryst = {'a' : a, 'b' : b, 'c' : c, 'alpha' : alpha, 'beta' : beta, 'gamma' : gamma};
             }
-
         }
 
         var starttime = (new Date()).getTime();
-        // assign bonds - yuck, can't count on connect records
-        assignPDBBonds(atoms);
-        //console.log("bond connecting " + ((new Date()).getTime() - starttime));
-        
-        var end = atoms.length;
-        var offset = end;
-        var t, l, n;
-        if(!copyMatrix) { //do full assembly
-            for (t = 0; t < allMatrices.length; t++) {
-                if (!allMatrices[t].isIdentity()) {
-                    var xyz = new $3Dmol.Vector3();
-                    for (n = 0; n < end; n++) {
-                        var bondsArr = [];
-                        for (l = 0; l < atoms[n].bonds.length; l++) {
-                            bondsArr.push(atoms[n].bonds[l] + offset);
-                        }
-                        xyz.set(atoms[n].x, atoms[n].y, atoms[n].z);
-                        xyz.applyMatrix4(allMatrices[t]);
-                        atoms.push({
-                            'resn' : atoms[n].resn,
-                            'x' : xyz.x,
-                            'y' : xyz.y,
-                            'z' : xyz.z,
-                            'elem' : atoms[n].elem,
-                            'hetflag' : atoms[n].hetflag,
-                            'chain' : atoms[n].chain,
-                            'resi' : atoms[n].resi,
-                            'icode' : atoms[n].icode,
-                            'rescode': atoms[n].rescode,
-                            'serial' : atoms[n].serial,
-                            'atom' : atoms[n].atom,
-                            'bonds' : bondsArr,
-                            'ss' : atoms[n].ss,
-                            'bondOrder' : atoms[n].bondOrder,
-                            'properties' : atoms[n].properties,
-                            'b' : atoms[n].b,
-                            'pdbline' : atoms[n].pdbline,
-                        });
-                    }
-                    offset = atoms.length;
-                }
-            }
-        }
-        //ELSE give all atoms a pointer to their symmetries 
-        else {
-            for (t = 0; t < atoms.length; t++) {
-                var symmetries = [];
-                for (l = 0; l < copyMatrices.length; l++) {
-                    if (!copyMatrices[l].isIdentity()) {
-                        var newXYZ = new $3Dmol.Vector3();
-                        newXYZ.set(atoms[t].x, atoms[t].y, atoms[t].z);
-                        newXYZ.applyMatrix4(copyMatrices[l]);
-                        symmetries.push(newXYZ);
-                    }
-                }
-                atoms[t].symmetries = symmetries;
-            }
-        }
-                
         
-        if(computeStruct || !hasStruct) {
-            starttime = (new Date()).getTime();
-            computeSecondaryStructure(atoms);
-            //console.log("secondary structure " + ((new Date()).getTime() - starttime));
-        }
+        for (var n = 0; n < atoms.length; n++) {
+            // assign bonds - yuck, can't count on connect records
+            assignPDBBonds(atoms[n]);
+            // console.log("bond connecting " + ((new Date()).getTime() -
+            // starttime));
         
-        // Assign secondary structures from pdb file
-        for (i = start; i < atoms.length; i++) {
-            atom = atoms[i];
-            if (atom === undefined)
-                continue;
+            if (!noAssembly)
+                processSymmetries(modelData[modelData.length-1].symmetries, copyMatrix, atoms[n]);
 
-            var found = false;
-            // MEMO: Can start chain and end chain differ?
-            for (j = 0; j < protein.sheet.length; j++) {
-                if (atom.chain != protein.sheet[j][0])
-                    continue;
-                if (atom.resi < protein.sheet[j][1])
-                    continue;
-                if (atom.resi > protein.sheet[j][3])
-                    continue;
-                atom.ss = 's';
-                if (atom.resi == protein.sheet[j][1])
-                    atom.ssbegin = true;
-                if (atom.resi == protein.sheet[j][3])
-                    atom.ssend = true;
-            }
-            for (j = 0; j < protein.helix.length; j++) {
-                if (atom.chain != protein.helix[j][0])
-                    continue;
-                if (atom.resi < protein.helix[j][1])
-                    continue;
-                if (atom.resi > protein.helix[j][3])
+            if (computeStruct || !hasStruct) {
+                starttime = (new Date()).getTime();
+                computeSecondaryStructure(atoms[n]);
+                // console.log("secondary structure " + ((new Date()).getTime() -
+                // starttime));
+            }
+
+            // Assign secondary structures from pdb file
+            for (i = start; i < atoms[n].length; i++) {
+                atom = atoms[n][i];
+                if (atom === undefined)
                     continue;
-                atom.ss = 'h';
-                if (atom.resi == protein.helix[j][1])
-                    atom.ssbegin = true;
-                else if (atom.resi == protein.helix[j][3])
-                    atom.ssend = true;
+
+                var found = false;
+                // MEMO: Can start chain and end chain differ?
+                for (j = 0; j < protein.sheet.length; j++) {
+                    if (atom.chain != protein.sheet[j][0])
+                        continue;
+                    if (atom.resi < protein.sheet[j][1])
+                        continue;
+                    if (atom.resi > protein.sheet[j][3])
+                        continue;
+                    atom.ss = 's';
+                    if (atom.resi == protein.sheet[j][1])
+                        atom.ssbegin = true;
+                    if (atom.resi == protein.sheet[j][3])
+                        atom.ssend = true;
+                }
+                for (j = 0; j < protein.helix.length; j++) {
+                    if (atom.chain != protein.helix[j][0])
+                        continue;
+                    if (atom.resi < protein.helix[j][1])
+                        continue;
+                    if (atom.resi > protein.helix[j][3])
+                        continue;
+                    atom.ss = 'h';
+                    if (atom.resi == protein.helix[j][1])
+                        atom.ssbegin = true;
+                    else if (atom.resi == protein.helix[j][3])
+                        atom.ssend = true;
+                }
             }
         }
-        return true;
-    };
-
         
-    /** Parse a pqr file from str and create atoms.  A pqr file is assumed
-     * to be a whitespace delimited PDB with charge and radius fields.
+        return atoms;
+    };
 
-     * 
-     * @param {AtomSpec[]} atoms
-     * @param {string} str
-     * @param {Object} options -  noSecondaryStructure (do not compute ss)
+    /**
+     * Parse a pqr file from str and create atoms. A pqr file is assumed to be a
+     * whitespace delimited PDB with charge and radius fields.
+     *
+     * @param {string}
+     *            str
+     * @param {Object}
+     *            options - noSecondaryStructure (do not compute ss)
      */
-    parsers.pqr = parsers.PQR = function(atoms, str, options) {
+    parsers.pqr = parsers.PQR = function(str, options) {
 
+        var atoms = [[]];
         var atoms_cnt = 0;
-        var start = atoms.length;
+        var start = atoms[atoms.length-1].length;
         var atom;
         var computeStruct = !options.noSecondaryStructure;
 
         var serialToIndex = []; // map from pdb serial to index in atoms
-        var lines = str.split("\n");
+        var lines = str.split(/\r?\n|\r/);
         var i, j, k, line;
         for (i = 0; i < lines.length; i++) {
             line = lines[i].replace(/^\s*/, ''); // remove indent
             var recordName = line.substr(0, 6);
             var startChain, startResi, endChain, endResi;
-            if (recordName == 'ATOM  ' || recordName == 'HETATM') {
-                    //I would have liked to split based solely on whitespace, but
-                //it seems that there is no guarantee that all the fields will
-                //be filled out (e.g. the chain) so this doesn't work
+            
+            if (recordName.indexOf("END") == 0) {
+                if (options.multimodel) {
+                    if (!options.onemol)
+                        atoms.push([]);
+                    continue;
+                }
+                else {
+                    break;
+                }
+            }
+            else if (recordName == 'ATOM  ' || recordName == 'HETATM') {
+                // I would have liked to split based solely on whitespace, but
+                // it seems that there is no guarantee that all the fields will
+                // be filled out (e.g. the chain) so this doesn't work
                 var serial = parseInt(line.substr(6, 5));
                 var atom = line.substr(12, 4).replace(/ /g, "");
                 var resn = line.substr(17, 3);
                 var chain = line.substr(21, 1);
                 var resi = parseInt(line.substr(22, 4));
-                //however let's split the coordinates, charge and radius by whitespace
-                //to support extra precision
+                // however let's split the coordinates, charge and radius by
+                // whitespace
+                // to support extra precision
                 var vals = line.substr(30).trim().split(/\s+/);
                 var x = parseFloat(vals[0]);
                 var y = parseFloat(vals[1]);
                 var z = parseFloat(vals[2]);
                 var charge = parseFloat(vals[3]);
                 var radius = parseFloat(vals[4]);
-                
+
                 var elem = atom[0];
-                if(atom.length > 1 && atom[1].toUpperCase() != atom[1]) {
-                    //slight hack - identify two character elements by the
-                    //second character in the atom name being lowercase
-                    elem = atom.substr(0,2);
+                if (atom.length > 1 && atom[1].toUpperCase() != atom[1]) {
+                    // slight hack - identify two character elements by the
+                    // second character in the atom name being lowercase
+                    elem = atom.substr(0, 2);
                 }
 
                 if (line[0] == 'H')
                     hetflag = true;
                 else
                     hetflag = false;
-                serialToIndex[serial] = atoms.length;
-                atoms.push({
+                serialToIndex[serial] = atoms[atoms.length-1].length;
+                atoms[atoms.length-1].push({
                     'resn' : resn,
                     'x' : x,
                     'y' : y,
@@ -25101,7 +31935,11 @@ $3Dmol.Parsers = (function() {
                     'bonds' : [],
                     'ss' : 'c',
                     'bondOrder' : [],
-                    'properties' : {'charge': charge, 'partialCharge': charge, 'radius': radius},
+                    'properties' : {
+                        'charge' : charge,
+                        'partialCharge' : charge,
+                        'radius' : radius
+                    },
                     'pdbline' : line
                 });
             } else if (recordName == 'CONECT') {
@@ -25109,10 +31947,10 @@ $3Dmol.Parsers = (function() {
                 // also
                 // described in CONECT. But what about 2JYT???
                 var from = parseInt(line.substr(6, 5));
-                var fromAtom = atoms[serialToIndex[from]];
+                var fromAtom = atoms[atoms.length-1][serialToIndex[from]];
                 for (j = 0; j < 4; j++) {
                     var to = parseInt(line.substr([ 11, 16, 21, 26 ][j], 5));
-                    var toAtom = atoms[serialToIndex[to]];
+                    var toAtom = atoms[atoms.length-1][serialToIndex[to]];
                     if (fromAtom !== undefined && toAtom !== undefined) {
                         fromAtom.bonds.push(serialToIndex[to]);
                         fromAtom.bondOrder.push(1);
@@ -25122,15 +31960,15 @@ $3Dmol.Parsers = (function() {
         }
 
         // assign bonds - yuck, can't count on connect records
-        assignPDBBonds(atoms);
-        if(computeStruct)
-            computeSecondaryStructure(atoms);
+        for (var i = 0; i < atoms.length; i++) {
+            assignPDBBonds(atoms[i]);
+            if (computeStruct)
+                computeSecondaryStructure(atoms[i]);
+        }
         
-        return true;
+        return atoms;
     };
 
-    
-    
     return parsers;
 })();
 var $3Dmol = $3Dmol || {};
@@ -25324,7 +32162,7 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  * @typedef ViewerSpec
  * @prop {Object} defaultcolors - map of elements to colors
  * @prop {boolean} nomouse - if true, disable handling of mouse events
- * @prop {string} backgroundColor - color of background
+ * @prop {ColorSpec} backgroundColor - color of background
  */
 
 /**
@@ -25334,8 +32172,8 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  * @prop {number} x - Atom's x coordinate
  * @prop {number} y - Atom's y coordinate
  * @prop {number} z - Atom's z coordinate
- * @prop {number} color - Atom's color, as hex code
- * @prop {number} surfaceColor - Hex code for color to be used for surface patch over this atom
+ * @prop {ColorSpec} color - Atom's color, as hex code or built-in color string
+ * @prop {ColorSpec} surfaceColor - Hex code for color to be used for surface patch over this atom
  * @prop {string} elem - Element abbreviation (e.g. 'H', 'Ca', etc)
  * @prop {boolean} hetflag - Set to true if atom is a heteroatom
  * @prop {string} chain - Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)
@@ -25405,9 +32243,11 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 /** 
  * @typedef SurfaceStyleSpec
  * @prop {number} opacity - sets the transparency: 0 to hide, 1 for fully opaque
- * @prop {string} colorscheme - element based coloring
- * @prop {string} color - fixed coloring, overrides colorscheme
- * @prop {Object} map - specifies a numeric atom property (prop) and color mapping (scheme) such as {@link $3Dmol.Gradient.RWB}
+ * @prop {ColorschemeSpec} colorscheme - element based coloring
+ * @prop {ColorSpec} color - fixed coloring, overrides colorscheme
+ * @prop {$3Dmol.VolumeData} voldata - volumetric data for vertex coloring
+ * @prop {$3Dmol.Gradient} volscheme - coloring scheme for mapping volumetric data to vertex color
+ * @prop {Object} map - specifies a numeric atom property (prop) and color mapping (scheme) such as {@link $3Dmol.Gradient.RWB}.  Deprecated, use colorscheme instead.
  * 
  * @example
  * viewer.addSurface($3Dmol.SurfaceType.MS, {map:{prop:'partialCharge',scheme:new $3Dmol.Gradient.RWB(-.6,.6)}, opacity:0.85});
@@ -25415,14 +32255,15 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  */
 
 /** 
- * Volumetric data style specification
- * @typedef VolSpec
+ * Isosurface style specification
+ * @typedef IsoSurfaceSpec
  * @prop {number} isoval - specifies the isovalue to draw surface at
  * @propr {boolean} voxel - if true uses voxel style rendering
- * @prop {string} color - solid color
- * @prop {number} alpha - transparency
+ * @prop {ColorSpec} color - solid color
+ * @prop {number} opacity - transparency, between 0 and 1
  * @prop {boolean} wireframe - draw as wireframe, not surface
  * @prop {number} linewidth - width of line for wireframe rendering
+ * @prop {number} smoothness - amount to smooth surface (default 1)
  * @prop {boolean} clickable - if true, user can click on object to trigger callback
  * @prop {function} callback - function to call on click 
  */
@@ -25430,7 +32271,7 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 /** 
  * GLShape style specification
  * @typedef ShapeSpec
- * @prop {string} color - solid color
+ * @prop {ColorSpec} color - solid color
  * @prop {number} alpha - transparency
  * @prop {boolean} wireframe - draw as wireframe, not surface
  * @prop {number} linewidth - width of line for wireframe rendering
@@ -25440,9 +32281,13 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
 
 
 /**
- * Specification for adding custom shape
+ * Specification for adding custom shape. Extends {@link ShapeSpec}.
  * @typedef CustomShapeSpec
  * @augments ShapeSpec
+ * @prop {Array.<$3Dmol.Vector3>} vertexArr - List of vertex positions
+ * @prop {Array.<$3Dmol.Vector3>} normalArr - List of normal vectors for each vertex
+ * @prop {Array.<number>} faceArr - List of triangles to build the custom shape. Each triangle is defined by the indices of 3 vertices in vertexArr, so the array length should be 3 times the number of faces.
+ * @prop {ColorSpec | Array.<ColorSpec>} color - Either a single color for the whole object or an array specifying the color at each vertex.
  */
 
 /**
@@ -25484,3 +32329,251 @@ $3Dmol.applyPartialCharges = function(atom, keepexisting) {
  */
 
 });
+/**
+ * $3Dmol.VolumeData stores volumetric data. This includes file parsing
+ * functionality.
+ * 
+ * @class
+ * @param {string} str - volumetric data
+ * @param {string} format - format of supplied data (cube)
+ */
+$3Dmol.VolumeData = function(str, format) {
+
+    this.unit = {
+        x : 1,
+        y : 1,
+        z : 1
+    }; // scale of each voxel
+    this.origin = {
+        x : 0,
+        y : 0,
+        z : 0
+    }; // origin (bottom "left", not center)
+    this.size = {
+        x : 0,
+        y : 0,
+        z : 0
+    }; // number of voxels in each direction
+    this.data = new Float32Array([]); // actual floating point data, arranged
+                                        // x->y->z
+
+    format = format.toLowerCase();
+    if (this[format]) {
+        this[format](str);
+    }
+};
+
+/**
+ * @function $3Dmol.VolumeData.getVal
+ * @param {number} x,y,z - the coordinates
+ * @returns - value closest to provided coordinate; zero if coordinate invalid
+ */
+$3Dmol.VolumeData.prototype.getVal = function(x,y,z) {
+    x -= this.origin.x;
+    y -= this.origin.y;
+    z -= this.origin.z;
+    
+    x /= this.unit.x;
+    y /= this.unit.y;
+    z /= this.unit.z;
+    
+    x = Math.round(x);
+    y = Math.round(y);
+    z = Math.round(z);
+    
+    if(x < 0 || x >= this.size.x) return 0;
+    if(y < 0 || y >= this.size.y) return 0;
+    if(z < 0 || z >= this.size.z) return 0;
+    
+    return this.data[x*this.size.y*this.size.z + y*this.size.z + z];
+};
+
+// parse cube data
+$3Dmol.VolumeData.prototype.cube = function(str) {
+    var lines = str.replace(/^\s+/, "").split(/[\n\r]+/);
+
+    if (lines.length < 6)
+        return;
+
+    var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+
+    var atomsnum = parseFloat(lineArr[0]); //includes sign, which indicates presence of oribital line in header
+    var natoms = Math.abs(atomsnum);
+
+    var origin = this.origin = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]));
+
+    lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+
+    // might have to convert from bohr units to angstroms
+    // there is a great deal of confusion here:
+    // n>0 means angstroms: http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm
+    // n<0 means angstroms: http://paulbourke.net/dataformats/cube/
+    // always assume bohr: openbabel source code
+    // always assume angstrom: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
+    // we are going to go with n<0 means angstrom - note this is just the first n
+    var convFactor = (lineArr[0] > 0) ? 0.529177 : 1;
+    origin.multiplyScalar(convFactor);
+
+    var nX = Math.abs(lineArr[0]);
+    var xVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+    var nY = Math.abs(lineArr[0]);
+    var yVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
+    var nZ = Math.abs(lineArr[0]);
+    var zVec = new $3Dmol.Vector3(parseFloat(lineArr[1]),
+            parseFloat(lineArr[2]), parseFloat(lineArr[3]))
+            .multiplyScalar(convFactor);
+
+    this.size = {x:nX, y:nY, z:nZ};
+    this.unit = new $3Dmol.Vector3(xVec.x, yVec.y, zVec.z);
+    
+    if (xVec.y != 0 || xVec.z != 0 || yVec.x != 0 || yVec.z != 0 || zVec.x != 0
+            || zVec.y != 0)
+        console
+                .log("Warning: Cube file is not axis aligned.  This isn't going to look right.");   
+    var headerlines = 6;
+    if(atomsnum < 0) headerlines++; //see: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
+    var raw = lines.splice(natoms + headerlines).join(" ");
+    raw = raw.replace(/^\s+/,'');
+    raw = raw.split(/[\s\r]+/);
+    this.data = new Float32Array(raw);
+
+};
+
+//parse cp4 files
+$3Dmol.VolumeData.prototype.ccp4 = function(bin) {
+
+    // http://www.ccp4.ac.uk/html/maplib.html#description
+        
+        var header = {};
+
+        var intView = new Int32Array( bin, 0, 56 );
+        var floatView = new Float32Array( bin, 0, 56 );
+
+           //# of columns (fastest changing),rows, sections (slowest changing)
+        header.NX = intView[ 0 ];
+        header.NY = intView[ 1 ];
+        header.NZ = intView[ 2 ];
+
+        // mode
+        //  0 image : signed 8-bit bytes range -128 to 127
+        //  1 image : 16-bit halfwords
+        //  2 image : 32-bit reals
+        //  3 transform : complex 16-bit integers
+        //  4 transform : complex 32-bit reals
+        //  6 image : unsigned 16-bit range 0 to 65535
+        // 16 image: unsigned char * 3 (for rgb data, non-standard)
+        header.MODE = intView[ 3 ];
+
+        //position of first column, first row, and first section (voxel grid units)
+        header.NCSTART = intView[ 4 ];
+        header.NRSTART = intView[ 5 ];
+        header.NSSTART = intView[ 6 ];
+
+        //intervals per unit cell repeat along X,Y Z
+        header.MX = Math.abs(intView[ 7 ]);
+        header.MY = Math.abs(intView[ 8 ]);
+        header.MZ = Math.abs(intView[ 9 ]);
+
+       //Map lengths along X,Y,Z in Ångstroms
+        header.xlen =  floatView[ 10 ]; 
+        header.ylen = floatView[ 11 ];  
+        header.zlen = floatView[ 12 ];  
+
+        //single voxel lengths
+        xVox = header.xlen / header.NX; 
+        yVox = header.ylen / header.NY; 
+        zVox = header.zlen / header.NZ;
+
+        // cell angle
+        header.alpha = floatView[ 13 ];
+        header.beta  = floatView[ 14 ];
+        header.gamma = floatView[ 15 ];
+
+        //relationship of X,Y,Z axes to columns, rows, sections
+        header.MAPC = intView[ 16 ];
+        switch (header.MAPC){
+            case 1: header.NXSTART = header.NCSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NCSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NCSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+        header.MAPR = intView[ 17 ];
+        switch (header.MAPR){
+            case 1: header.NXSTART = header.NRSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NRSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NRSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+        header.MAPS = intView[ 18 ];
+         switch (header.MAPS){
+            case 1: header.NXSTART = header.NSSTART; header.NYSTART = 0; header.NZSTART = 0; break;
+            case 2: header.NYSTART = header.NSSTART; header.NXSTART = 0; header.NZSTART = 0; break;
+            case 3: header.NZSTART = header.NSSTART; header.NXSTART = 0; header.NYSTART = 0; break;
+        }
+
+        //Origin Position
+        this.origin = new $3Dmol.Vector3(header.NXSTART, header.NYSTART, header.NZSTART);
+
+        //Minimum, maximum, average density
+        header.DMIN  = floatView[ 19 ];
+        header.DMAX  = floatView[ 20 ];
+        header.DMEAN = floatView[ 21 ];
+
+        // space group number 0 or 1 (default=0)
+        header.ISPG = intView[ 22 ];
+
+        // number of bytes used for symmetry data (0 or 80)
+        header.NSYMBT = intView[23];
+
+        // machine stamp
+        header.ARMS = floatView[54];
+
+        this.size = {x:header.MX, y:header.MY, z:header.MZ};
+        this.unit = new $3Dmol.Vector3(xVox, yVox, zVox ); 
+        var byteData = new Int8Array(bin); 
+        this.data = new Float32Array(bin, 1024 + header.NSYMBT);
+          
+};
+//Hackish way to create webworker (independent of $3Dmol namespace) within minified file
+$3Dmol.workerString = function(){
+
+    self.onmessage = function(oEvent) {
+        var obj = oEvent.data;
+        var type = obj.type;
+        if (type < 0) // sending atom data, initialize
+        {
+            self.atomData = obj.atoms;
+            self.volume = obj.volume;
+            self.ps = new ProteinSurface();
+        } else {
+            var ps = self.ps;
+            ps.initparm(obj.expandedExtent, (type == 1) ? false : true, self.volume);
+            ps.fillvoxels(self.atomData, obj.extendedAtoms);
+            ps.buildboundary();
+            if (type === 4 || type === 2) {
+                ps.fastdistancemap();
+                ps.boundingatom(false);
+                ps.fillvoxelswaals(self.atomData, obj.extendedAtoms);    
+            }        
+            ps.marchingcube(type);
+            var VandF = ps.getFacesAndVertices(obj.atomsToShow);
+            self.postMessage(VandF);
+        }
+    };
+    
+}.toString().replace(/(^.*?\{|\}$)/g, "");
+
+$3Dmol.workerString += "; var ProteinSurface=" + $3Dmol.ProteinSurface.toString().replace(/\$3Dmol.MarchingCube./g, "MarchingCube.");
+$3Dmol.workerString += ",MarchingCube=("+$3Dmol.MarchingCubeInitializer.toString() +")();";
+
+$3Dmol.SurfaceWorker = window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type: 'text/javascript'}));
+
+$3Dmol['workerString'] = $3Dmol.workerString;
+$3Dmol['SurfaceWorker'] = $3Dmol.SurfaceWorker;
diff --git a/tests/testgl.html b/tests/testgl.html
index 2c80eccf5..31a19d5d1 100644
--- a/tests/testgl.html
+++ b/tests/testgl.html
@@ -126,8 +126,9 @@
                     viewer.addSurface($3Dmol.SurfaceType.SAS, {color: 'white', opacity: 0.75}, {bonds: 0, invert: true});
                 });*/   
                 
-                /*
+                
                 $.get('./test_structs/4v99.cif', function(data) {
+                    console.profile("label for profile");
                    glviewer.clear();
                    glviewer.addModel(data, 'cif');
                    glviewer.zoomTo();
@@ -144,8 +145,10 @@
                        console.log("Rotate: "+(new Date() - time));
 
                    }
+                        console.profileEnd();
+
                 });
-                */
+                
                  
                            
         });