-
Notifications
You must be signed in to change notification settings - Fork 0
/
screw.spt
297 lines (276 loc) · 8.13 KB
/
screw.spt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
# Jmol state version 14.31.0 2020-05-27 14:50;
function _setWindowState() {
# width 500;
# height 500;
stateVersion = 1431000;
background [xffffff];
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
set ambientPercent 45;
set diffusePercent 84;
set specular true;
set specularPercent 22;
set specularPower 40;
set specularExponent 6;
set celShading false;
set celShadingPower 10;
set zShadePower 3;
}
function _setFileState() {
set allowEmbeddedScripts false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set autoBond true;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultLattice {0.0 0.0 0.0};
set defaultLoadFilter "";
set defaultLoadScript "";
set defaultStructureDssp true;
set defaultVDW Auto;
set forceAutoBond false;
#set defaultDirectory "C:/WINDOWS/system32";
#set loadFormat "https://files.rcsb.org/download/%FILE.pdb";
#set loadLigandFormat "https://files.rcsb.org/ligands/download/%FILE.cif";
#set smilesUrlFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=true";
#set nihResolverFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE";
#set pubChemFormat "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
set bondingVersion 0;
set legacyAutoBonding false;
set legacyAutoBonding false;
set legacyHAddition false;
set legacyJavaFloat false;
set minBondDistance 0.4;
set minimizationCriterion 0.001;
set minimizationSteps 100;
set multipleBondBananas false;
set pdbAddHydrogens false;
set pdbGetHeader false;
set pdbSequential false;
set percentVdwAtom 23;
set smallMoleculeMaxAtoms 40000;
set smartAromatic true;
load /*file*/"http://lampx.tugraz.at/~hadley/ss1/crystalstructure/structures/bcc/bcc.cif" /*options*/ {555.0 555.0 -1.0} PACKED;
}
function _setParameterState() {
set defaultanglelabel "%VALUE %UNITS";
set defaultcolorscheme "jmol";
set defaultdistancelabel "%VALUE %UNITS";
set defaultdrawarrowscale 0.5;
set defaultlabelpdb "%m%r";
set defaultlabelxyz "%a";
set defaultlattice "{0.0 0.0 0.0}";
set defaultloadfilter "";
set defaultloadscript "";
set defaulttorsionlabel "%VALUE %UNITS";
set defaulttranslucent 0.5;
set defaultvdw "Auto";
set allowembeddedscripts true;
set allowmoveatoms false;
set allowrotateselected false;
set animationmode "once";
set appletproxy "";
set applysymmetrytobonds false;
set atomtypes "";
set autobond true;
set autofps false;
set axes unitcell;
set axesmode 2;
set axesoffset 0.0;
set axesscale 2.0;
set bondmodeor false;
set bondradiusmilliangstroms 150;
set bondtolerance 0.45;
set cartoonbaseedges false;
set cartoonblockheight 0.5;
set cartoonblocks false;
set cartoonfancy false;
set cartoonladders false;
set cartoonrockets false;
set cartoonsfancy false;
set cartoonsteps false;
set chaincasesensitive false;
set dataseparator "~~~";
set defaultstructuredssp true;
set delaymaximumms 0;
set dipolescale 1.0;
set disablepopupmenu false;
set displaycellparameters true;
set dotdensity 3;
set dotscale 1;
set dotsselectedonly false;
set dotsurface true;
set dragselected false;
set drawfontsize 14.0;
set drawhover false;
set dsspcalculatehydrogenalways true;
set ellipsoidarcs false;
set ellipsoidarrows false;
set ellipsoidaxes false;
set ellipsoidaxisdiameter 0.02;
set ellipsoidball true;
set ellipsoiddotcount 200;
set ellipsoiddots false;
set ellipsoidfill false;
set energyunits "kJ";
set forceautobond false;
set gestureswipefactor 1.0;
set greyscalerendering false;
set hbondsbackbone false;
set hbondsrasmol true;
set hbondssolid false;
set helixstep 1;
set helppath "https://chemapps.stolaf.edu/jmol/docs/index.htm";
set hermitelevel 0;
set hiddenlinesdashed false;
set hidenameinpopup false;
set hidenavigationpoint false;
set highresolution false;
set hoverdelay 0.5;
set infofontsize 20;
set isosurfacekey false;
set isosurfacepropertysmoothing true;
set isosurfacepropertysmoothingpower 7;
set justifymeasurements false;
set loadatomdatatolerance 0.01;
set measureallmodels false;
set measurementlabels true;
set meshscale 1;
set messagestylechime false;
set minbonddistance 0.4;
set minimizationcriterion 0.001;
set minimizationrefresh true;
set minimizationsilent false;
set minimizationsteps 100;
set minpixelselradius 6;
set modulationscale 1.0;
set monitorenergy false;
set multiplebondbananas false;
set multiplebondradiusfactor 0.0;
set multiplebondspacing -1.0;
set navigationperiodic false;
set navigationspeed 5.0;
set nbocharges true;
set nmrpredictformat "http://www.nmrdb.org/service/predictor?POST?molfile=";
set nmrurlformat "http://www.nmrdb.org/new_predictor?POST?molfile=";
set partialdots false;
set particleradius 20.0;
set pdbaddhydrogens false;
set pdbgetheader false;
set pdbsequential false;
set percentvdwatom 23;
set pickingspinrate 10;
set pointgroupdistancetolerance 0.2;
set pointgrouplineartolerance 8.0;
set propertyatomnumbercolumncount 0;
set propertyatomnumberfield 0;
set propertycolorscheme "roygb";
set propertydatacolumncount 0;
set propertydatafield 0;
set quaternionframe "p";
set rangeselected false;
set ribbonaspectratio 16;
set ribbonborder false;
set rocketbarrels false;
set sheetsmoothing 1.0;
set showhiddenselectionhalos false;
set showhydrogens true;
set showmeasurements true;
set showmodulationvectors false;
set showmultiplebonds true;
set shownavigationpointalways false;
set showunitcelldetails true;
set slabbyatom false;
set slabbymolecule false;
set smallmoleculemaxatoms 40000;
set smartaromatic true;
set solventprobe false;
set solventproberadius 1.2;
set ssbondsbackbone false;
set starwidth 0.05;
set stereodegrees -5.0;
set strandcountformeshribbon 7;
set strandcountforstrands 5;
set strutdefaultradius 0.3;
set strutlengthmaximum 7.0;
set strutsmultiple false;
set strutspacing 6;
set tracealpha true;
set translucent true;
set twistedsheets false;
set usenumberlocalization true;
set vectorscale 1.0;
set vectorscentered false;
set vectorsymmetry false;
set vectortrail 0;
set vibrationscale 1.0;
set waitformoveto true;
set wireframerotation false;
set zdepth 0;
set zoomheight false;
set zoomlarge true;
set zslab 50;
}
function _setModelState() {
select ({0:8});
Spacefill 0.522;
select ({2});
color atoms opaque [xff0000];
draw delete;
draw ID "draw1" ARROW {1.0726 0.0 3.2179} {1.0726 4.2906 3.2179};
draw ID "draw1" fill noMesh noDots notFrontOnly fullylit;
color draw opaque [xffd700];
unitcell on;
font unitcell 14.0 SansSerif Plain;
unitcell on;
font unitcell 14.0 SansSerif Plain;
axes on;
font axes 14.0 SansSerif Plain;
axes scale 2.0;
frank on;
font frank 16.0 SansSerif Plain;
select *;
unitcell on;
font unitcell 14.0 SansSerif Plain;
unitcell on;
font unitcell 14.0 SansSerif Plain;
select *;
set fontScaling false;
}
function _setPerspectiveState() {
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth false;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {0.0 0.0 0.0} {4.2906003 4.2906003 4.2906} # volume = 78.986725;
center {2.1453001 2.1453001 2.1453};
moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {2.1453001 2.1453001 2.1453} 5.985769 {0 0 0} 0 0 0 3.0 0.0 0.0;
save orientation "default";
moveto 0.0 { 698 716 3 20.11} 100.0 0.0 0.0 {2.1453001 2.1453001 2.1453} 5.985769 {0 0 0} 0 0 0 3.0 0.0 0.0;;
slab 100;depth 0;
set slabRange 0.0;
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10;
}
function _setSelectionState() {
select ({2});
set hideNotSelected false;
SelectionHalos ON;
}
function _setState() {
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setParameterState;
_setModelState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
}
_setState;