diff --git a/doc.md b/doc.md
index 2ef0765b3..f84fef50d 100644
--- a/doc.md
+++ b/doc.md
@@ -15,20 +15,21 @@
3Dmol.js is an object-oriented, WebGL based JavaScript library for online molecular visualization - No Java required!
-With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Features include:
+With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications.
-* support for pdb, sdf, mol2, xyz, and cube formats
-* parallelized molecular surface computation
-* sphere, stick, line, cross, cartoon, and surface styles
-* atom property based selection and styling
-* labels
-* clickable interactivity with molecular data
-* geometric shapes including spheres and arrows
+Features include:
+
+- Support for pdb, sdf, mol2, xyz, and cube formats
+- Parallelized molecular surface computation
+- Sphere, stick, line, cross, cartoon, and surface styles
+- Atom property based selection and styling
+- Labels
+- Clickable interactivity with molecular data
+- Geometric shapes including spheres and arrows
## Getting Started
-Molecular data can be shared and visualized without writing any HTML
- using only a declarative URL specification and our hosted viewer (see {@tutorial url}).
+Molecular data can be shared and visualized without writing any HTML using only a declarative URL specification and our hosted viewer (see {@tutorial url}).
Viewers can be quickly embedded in any HTML document using just two lines of source code (see {@tutorial embeddable}).
diff --git a/jsdoc.conf.json b/jsdoc.conf.json
index a5396fa6a..c8f186ef4 100644
--- a/jsdoc.conf.json
+++ b/jsdoc.conf.json
@@ -2,13 +2,17 @@
"tags": {
"allowUnknownTags": true
},
- "plugins": ["plugins/markdown",
- "../../node_modules/better-docs/typescript",
- "../../node_modules/better-docs/category"],
+ "plugins": [
+ "plugins/markdown",
+ "../../node_modules/better-docs/typescript",
+ "../../node_modules/better-docs/category"
+ ],
+ "recurseDepth": 10,
"source": {
"includePattern": "\\.(jsx|js|ts|tsx)$"
},
"templates": {
+ "search": true,
"cleverLinks": true,
"monospaceLinks": false,
"footer": "",
@@ -16,30 +20,53 @@
"linenums" : true,
"collapseSymbols" : false,
"inverseNav" : true,
- "highlightTutorialCode" : true,
- "better-docs": {
- "name": "3Dmol.js",
- "title": "3Dmol.js Documentation",
- "css": "../tutorials/style.css",
- "navLinks": [
- {
- "label": "Github",
- "href": "https://github.com/3dmol/3Dmol.js"
- }
- ]
- }
+ "highlightTutorialCode" : true
},
"markdown" : {
- "parser" : "gfm",
- "hardwrap" : true
+ "hardwrap": true,
+ "idInHeadings": true
},
"opts":{
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"encoding": "utf8",
- "template": "./node_modules/better-docs",
- "destination": "doc",
- "tutorials": "tutorials",
- "search": true
- },
- "tutorials": "tutorials/"
+ "destination": "doc/",
+ "recurse": true,
+ "verbose": true,
+ "template": "./node_modules/clean-jsdoc-theme",
+ "copyright": "3Dmol.js © 2019-2023",
+ "theme_opts": {
+ "default_theme": "light",
+ "includeFilesListInHomepage": true,
+ "homepageTitle": "3Dmol.js",
+ "displayModuleHeader": true,
+ "footer":"3Dmol.js © 2019-2023 | University of Pittsburgh | License",
+ "title": "3Dmol.js",
+ "create_style": "article ul li { list-style: disc}",
+ "menu": [
+ {
+ "title": " Documentation",
+ "link": "https://3dmol.org/doc/index.html"
+ },
+ {
+ "title": "Tutorials",
+ "link": "tutorial-home.html"
+ },
+ {
+ "title": "GitHub",
+ "link": "https://github.com/3dmol/3Dmol.js",
+ "target": "_blank"
+ }
+ ],
+ "meta": [
+ {
+ "name": "Author",
+ "content": "David Koes & 3Dmoljs Contributors"
+ },
+ {
+ "name": "Description",
+ "content": "A modern, object-oriented JavaScript library for visualizing molecular data"
+ }
+ ]
+ },
+ "tutorials": "tutorials/"
+ }
}
diff --git a/package-lock.json b/package-lock.json
index f4c83d1c1..115b19eea 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,6 +10,7 @@
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"license": "BSD-3-Clause",
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"pako": "^2.1.0",
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@@ -3323,6 +3309,15 @@
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"dependencies": {
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}
@@ -7671,7 +7758,6 @@
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- "dev": true,
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"@jsdoc/salty": "^0.2.1",
@@ -7700,7 +7786,6 @@
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- "dev": true,
"engines": {
"node": ">=8"
}
@@ -7805,6 +7890,25 @@
"node": ">=6"
}
},
+ "node_modules/jsonfile": {
+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/jsonfile/-/jsonfile-6.1.0.tgz",
+ "integrity": "sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==",
+ "dependencies": {
+ "universalify": "^2.0.0"
+ },
+ "optionalDependencies": {
+ "graceful-fs": "^4.1.6"
+ }
+ },
+ "node_modules/jsonfile/node_modules/universalify": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/universalify/-/universalify-2.0.0.tgz",
+ "integrity": "sha512-hAZsKq7Yy11Zu1DE0OzWjw7nnLZmJZYTDZZyEFHZdUhV8FkH5MCfoU1XMaxXovpyW5nq5scPqq0ZDP9Zyl04oQ==",
+ "engines": {
+ "node": ">= 10.0.0"
+ }
+ },
"node_modules/jstransformer": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/jstransformer/-/jstransformer-1.0.0.tgz",
@@ -7828,11 +7932,18 @@
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- "dev": true,
"dependencies": {
"graceful-fs": "^4.1.9"
}
},
+ "node_modules/klaw-sync": {
+ "version": "6.0.0",
+ "resolved": "https://registry.npmjs.org/klaw-sync/-/klaw-sync-6.0.0.tgz",
+ "integrity": "sha512-nIeuVSzdCCs6TDPTqI8w1Yre34sSq7AkZ4B3sfOBbI2CgVSB4Du4aLQijFU2+lhAFCwt9+42Hel6lQNIv6AntQ==",
+ "dependencies": {
+ "graceful-fs": "^4.1.11"
+ }
+ },
"node_modules/kleur": {
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/kleur/-/kleur-3.0.3.tgz",
@@ -7874,7 +7985,6 @@
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/linkify-it/-/linkify-it-3.0.3.tgz",
"integrity": "sha512-ynTsyrFSdE5oZ/O9GEf00kPngmOfVwazR5GKDq6EYfhlpFug3J2zybX56a2PRRpc9P+FuSoGNAwjlbDs9jJBPQ==",
- "dev": true,
"dependencies": {
"uc.micro": "^1.0.1"
}
@@ -7920,8 +8030,7 @@
"node_modules/lodash": {
"version": "4.17.21",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
- "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==",
- "dev": true
+ "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg=="
},
"node_modules/lodash.get": {
"version": "4.4.2",
@@ -7953,6 +8062,14 @@
"loose-envify": "cli.js"
}
},
+ "node_modules/lower-case": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/lower-case/-/lower-case-2.0.2.tgz",
+ "integrity": "sha512-7fm3l3NAF9WfN6W3JOmf5drwpVqX78JtoGJ3A6W0a6ZnldM41w2fV5D490psKFTpMds8TJse/eHLFFsNHHjHgg==",
+ "dependencies": {
+ "tslib": "^2.0.3"
+ }
+ },
"node_modules/lru-cache": {
"version": "5.1.1",
"resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-5.1.1.tgz",
@@ -8008,7 +8125,6 @@
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"resolved": "https://registry.npmjs.org/markdown-it/-/markdown-it-12.3.2.tgz",
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- "dev": true,
"dependencies": {
"argparse": "^2.0.1",
"entities": "~2.1.0",
@@ -8024,7 +8140,6 @@
"version": "8.6.7",
"resolved": "https://registry.npmjs.org/markdown-it-anchor/-/markdown-it-anchor-8.6.7.tgz",
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- "dev": true,
"peerDependencies": {
"@types/markdown-it": "*",
"markdown-it": "*"
@@ -8033,14 +8148,12 @@
"node_modules/markdown-it/node_modules/argparse": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz",
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- "dev": true
+ "integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q=="
},
"node_modules/marked": {
"version": "4.3.0",
"resolved": "https://registry.npmjs.org/marked/-/marked-4.3.0.tgz",
"integrity": "sha512-PRsaiG84bK+AMvxziE/lCFss8juXjNaWzVbN5tXAm4XjeaS9NAHhop+PjQxz2A9h8Q4M/xGmzP8vqNwy6JeK0A==",
- "dev": true,
"bin": {
"marked": "bin/marked.js"
},
@@ -8051,8 +8164,7 @@
"node_modules/mdurl": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/mdurl/-/mdurl-1.0.1.tgz",
- "integrity": "sha512-/sKlQJCBYVY9Ers9hqzKou4H6V5UWc/M59TH2dvkt+84itfnq7uFOMLpOiOS4ujvHP4etln18fmIxA5R5fll0g==",
- "dev": true
+ "integrity": "sha512-/sKlQJCBYVY9Ers9hqzKou4H6V5UWc/M59TH2dvkt+84itfnq7uFOMLpOiOS4ujvHP4etln18fmIxA5R5fll0g=="
},
"node_modules/merge-stream": {
"version": "2.0.0",
@@ -8195,7 +8307,6 @@
"version": "1.0.4",
"resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz",
"integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==",
- "dev": true,
"bin": {
"mkdirp": "bin/cmd.js"
},
@@ -8234,7 +8345,6 @@
"version": "3.3.6",
"resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.6.tgz",
"integrity": "sha512-BGcqMMJuToF7i1rt+2PWSNVnWIkGCU78jBG3RxO/bZlnZPK2Cmi2QaffxGO/2RvWi9sL+FAiRiXMgsyxQ1DIDA==",
- "dev": true,
"funding": [
{
"type": "github",
@@ -8268,6 +8378,15 @@
"iobuffer": "^5.2.1"
}
},
+ "node_modules/no-case": {
+ "version": "3.0.4",
+ "resolved": "https://registry.npmjs.org/no-case/-/no-case-3.0.4.tgz",
+ "integrity": "sha512-fgAN3jGAh+RoxUGZHTSOLJIqUc2wmoBwGR4tbpNAKmmovFoWq0OdRkb0VkldReO2a2iBT/OEulG9XSUc10r3zg==",
+ "dependencies": {
+ "lower-case": "^2.0.2",
+ "tslib": "^2.0.3"
+ }
+ },
"node_modules/node-dir": {
"version": "0.1.17",
"resolved": "https://registry.npmjs.org/node-dir/-/node-dir-0.1.17.tgz",
@@ -8541,6 +8660,15 @@
"resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz",
"integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug=="
},
+ "node_modules/param-case": {
+ "version": "3.0.4",
+ "resolved": "https://registry.npmjs.org/param-case/-/param-case-3.0.4.tgz",
+ "integrity": "sha512-RXlj7zCYokReqWpOPH9oYivUzLYZ5vAPIfEmCTNViosC78F8F0H9y7T7gG2M39ymgutxF5gcFEsyZQSph9Bp3A==",
+ "dependencies": {
+ "dot-case": "^3.0.4",
+ "tslib": "^2.0.3"
+ }
+ },
"node_modules/parent-module": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz",
@@ -8610,6 +8738,15 @@
"url": "https://github.com/fb55/entities?sponsor=1"
}
},
+ "node_modules/pascal-case": {
+ "version": "3.1.2",
+ "resolved": "https://registry.npmjs.org/pascal-case/-/pascal-case-3.1.2.tgz",
+ "integrity": "sha512-uWlGT3YSnK9x3BQJaOdcZwrnV6hPpd8jFH1/ucpiLRPh/2zCVJKS19E4GvYHvaCcACn3foXZ0cLB9Wrx1KGe5g==",
+ "dependencies": {
+ "no-case": "^3.0.4",
+ "tslib": "^2.0.3"
+ }
+ },
"node_modules/path-exists": {
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
@@ -9523,6 +9660,14 @@
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"dev": true
},
+ "node_modules/relateurl": {
+ "version": "0.2.7",
+ "resolved": "https://registry.npmjs.org/relateurl/-/relateurl-0.2.7.tgz",
+ "integrity": "sha512-G08Dxvm4iDN3MLM0EsP62EDV9IuhXPR6blNz6Utcp7zyV3tr4HVNINt6MpaRWbxoOHT3Q7YN2P+jaHX8vUbgog==",
+ "engines": {
+ "node": ">= 0.10"
+ }
+ },
"node_modules/require-directory": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -9557,7 +9702,6 @@
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"resolved": "https://registry.npmjs.org/requizzle/-/requizzle-0.2.4.tgz",
"integrity": "sha512-JRrFk1D4OQ4SqovXOgdav+K8EAhSB/LJZqCz8tbX0KObcdeM15Ss59ozWMBWmmINMagCwmqn4ZNryUGpBsl6Jw==",
- "dev": true,
"dependencies": {
"lodash": "^4.17.21"
}
@@ -9825,6 +9969,29 @@
"node": ">=8"
}
},
+ "node_modules/showdown": {
+ "version": "2.1.0",
+ "resolved": "https://registry.npmjs.org/showdown/-/showdown-2.1.0.tgz",
+ "integrity": "sha512-/6NVYu4U819R2pUIk79n67SYgJHWCce0a5xTP979WbNp0FL9MN1I1QK662IDU1b6JzKTvmhgI7T7JYIxBi3kMQ==",
+ "dependencies": {
+ "commander": "^9.0.0"
+ },
+ "bin": {
+ "showdown": "bin/showdown.js"
+ },
+ "funding": {
+ "type": "individual",
+ "url": "https://www.paypal.me/tiviesantos"
+ }
+ },
+ "node_modules/showdown/node_modules/commander": {
+ "version": "9.5.0",
+ "resolved": "https://registry.npmjs.org/commander/-/commander-9.5.0.tgz",
+ "integrity": "sha512-KRs7WVDKg86PWiuAqhDrAQnTXZKraVcCc6vFdL14qrZ/DcWwuRo7VoiYXalXO7S5GKpqYiVEwCbgFDfxNHKJBQ==",
+ "engines": {
+ "node": "^12.20.0 || >=14"
+ }
+ },
"node_modules/signal-exit": {
"version": "3.0.7",
"resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz",
@@ -9898,7 +10065,6 @@
"version": "0.6.1",
"resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
"integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==",
- "dev": true,
"engines": {
"node": ">=0.10.0"
}
@@ -9916,7 +10082,6 @@
"version": "0.5.21",
"resolved": "https://registry.npmjs.org/source-map-support/-/source-map-support-0.5.21.tgz",
"integrity": "sha512-uBHU3L3czsIyYXKX88fdrGovxdSCoTGDRZ6SYXtSRxLZUzHg5P/66Ht6uoUlHu9EZod+inXhKo3qQgwXUT/y1w==",
- "dev": true,
"dependencies": {
"buffer-from": "^1.0.0",
"source-map": "^0.6.0"
@@ -10068,7 +10233,6 @@
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
"integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig==",
- "dev": true,
"engines": {
"node": ">=8"
},
@@ -10227,7 +10391,6 @@
"version": "5.18.2",
"resolved": "https://registry.npmjs.org/terser/-/terser-5.18.2.tgz",
"integrity": "sha512-Ah19JS86ypbJzTzvUCX7KOsEIhDaRONungA4aYBjEP3JZRf4ocuDzTg4QWZnPn9DEMiMYGJPiSOy7aykoCc70w==",
- "dev": true,
"dependencies": {
"@jridgewell/source-map": "^0.3.3",
"acorn": "^8.8.2",
@@ -10609,8 +10772,7 @@
"node_modules/tslib": {
"version": "2.6.0",
"resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.0.tgz",
- "integrity": "sha512-7At1WUettjcSRHXCyYtTselblcHl9PJFFVKiCAy/bY97+BPZXSQ2wbq0P9s8tK2G7dFQfNnlJnPAiArVBVBsfA==",
- "dev": true
+ "integrity": "sha512-7At1WUettjcSRHXCyYtTselblcHl9PJFFVKiCAy/bY97+BPZXSQ2wbq0P9s8tK2G7dFQfNnlJnPAiArVBVBsfA=="
},
"node_modules/type-check": {
"version": "0.4.0",
@@ -10661,8 +10823,7 @@
"node_modules/uc.micro": {
"version": "1.0.6",
"resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-1.0.6.tgz",
- "integrity": "sha512-8Y75pvTYkLJW2hWQHXxoqRgV7qb9B+9vFEtidML+7koHUFapnVJAZ6cKs+Qjz5Aw3aZWHMC6u0wJE3At+nSGwA==",
- "dev": true
+ "integrity": "sha512-8Y75pvTYkLJW2hWQHXxoqRgV7qb9B+9vFEtidML+7koHUFapnVJAZ6cKs+Qjz5Aw3aZWHMC6u0wJE3At+nSGwA=="
},
"node_modules/unbzip2-stream": {
"version": "1.4.3",
@@ -10677,8 +10838,7 @@
"node_modules/underscore": {
"version": "1.13.6",
"resolved": "https://registry.npmjs.org/underscore/-/underscore-1.13.6.tgz",
- "integrity": "sha512-+A5Sja4HP1M08MaXya7p5LvjuM7K6q/2EaC0+iovj/wOcMsTzMvDFbasi/oSapiwOlt252IqsKqPjCl7huKS0A==",
- "dev": true
+ "integrity": "sha512-+A5Sja4HP1M08MaXya7p5LvjuM7K6q/2EaC0+iovj/wOcMsTzMvDFbasi/oSapiwOlt252IqsKqPjCl7huKS0A=="
},
"node_modules/universalify": {
"version": "0.2.0",
@@ -11536,8 +11696,7 @@
"node_modules/xmlcreate": {
"version": "2.0.4",
"resolved": "https://registry.npmjs.org/xmlcreate/-/xmlcreate-2.0.4.tgz",
- "integrity": "sha512-nquOebG4sngPmGPICTS5EnxqhKbCmz5Ox5hsszI2T6U5qdrJizBc+0ilYSEjTSzU0yZcmvppztXe/5Al5fUwdg==",
- "dev": true
+ "integrity": "sha512-nquOebG4sngPmGPICTS5EnxqhKbCmz5Ox5hsszI2T6U5qdrJizBc+0ilYSEjTSzU0yZcmvppztXe/5Al5fUwdg=="
},
"node_modules/y18n": {
"version": "5.0.8",
diff --git a/package.json b/package.json
index 03f1268aa..e8f46a0f2 100644
--- a/package.json
+++ b/package.json
@@ -22,6 +22,10 @@
"text"
]
},
+ "engines": {
+ "npm": ">=8.11",
+ "node": ">=16.16.0"
+ },
"license": "BSD-3-Clause",
"main": "build/3Dmol.js",
"types": "build/types/index.d.ts",
@@ -40,13 +44,10 @@
"generate:glcheck": "python3 ./tests/glcheck/generate_glcheck_render_tests.py -min",
"generate:jest": "python3 tests/jest/generate_jest_render_tests.py",
"cover": "npm run generate:jest && npx jest --coverage",
- "doc": "npx jsdoc -c jsdoc.conf.json src doc.md"
- },
- "engines": {
- "npm": ">=8.11",
- "node": ">=16.16.0"
+ "doc": "rm -rf doc/ && npx jsdoc -c jsdoc.conf.json src doc.md"
},
"dependencies": {
+ "clean-jsdoc-theme": "^4.2.9",
"iobuffer": "^5.3.1",
"netcdfjs": "^2.0.2",
"pako": "^2.1.0",
diff --git a/tutorials/embeddable.md b/tutorials/embeddable.md
index 2f09b9385..b4eeae322 100644
--- a/tutorials/embeddable.md
+++ b/tutorials/embeddable.md
@@ -30,7 +30,9 @@ The contents of the viewer can be set and manipulated through the use of `data-`
- **data-ui** If set will show the UI for the viewer.
Multiple selections, styles, residue labels, and surfaces can be provided by appending a suffix
- each tag. For example.
+ each tag.
+
+For example:
```{@lang xml}
Once created, the 3Dmol viewer can be accessed using the id of the container div in `$3Dmol.viewers`.
-
-
-
-
diff --git a/tutorials/home.json b/tutorials/home.json
new file mode 100644
index 000000000..d24fde8ef
--- /dev/null
+++ b/tutorials/home.json
@@ -0,0 +1,3 @@
+{
+ "title" : "3Dmol Tutorials - Home"
+}
diff --git a/tutorials/home.md b/tutorials/home.md
new file mode 100644
index 000000000..533f9aab2
--- /dev/null
+++ b/tutorials/home.md
@@ -0,0 +1,7 @@
+
+This guide helps you with learning how to,
+
+- [Use 3Dmol within your code](tutorial-code.html)
+- [Embedding a 3Dmol Viewer](tutorial-embeddable.html)
+- [Active Learning with 3Dmol.js](tutorial-learning_environment.html)
+- [Hosted 3Dmol.js viewer](tutorial-url.html)
\ No newline at end of file
diff --git a/tutorials/learning_environment.md b/tutorials/learning_environment.md
index 0577489d7..dae9ba740 100644
--- a/tutorials/learning_environment.md
+++ b/tutorials/learning_environment.md
@@ -49,6 +49,3 @@ ProxyPassReverse /socket.io http://localhost:5000/socket.io
The [flask-SocketIO documentation](https://flask-socketio.readthedocs.io/en/latest/) provides more information for running in other setups such as gunicorn, uwsgi, and nginx.
-
-
-
diff --git a/tutorials/url.md b/tutorials/url.md
index 6d86160ab..31e81d6aa 100644
--- a/tutorials/url.md
+++ b/tutorials/url.md
@@ -1,19 +1,19 @@
-
You can view a PDB structure immediately by visiting the 3Dmol.js server. Simply type `https://3Dmol.org/viewer.html` with an appropriately formatted [URL query string](http://en.wikipedia.org/wiki/Query_string) into your browser.
A 3Dmol viewer URL takes the form `https://3Dmol.org/viewer.html?[query string]`, where the `query string` specifies a structure (i.e. a PDB ID) and specific 3Dmol styles to apply. Click the URL below for an example.
-[`https://3Dmol.org/viewer.html?pdb=1YCR&select=chain:A&style=cartoon;stick:radius~0.1&surface=opacity:0.8;colorscheme:whiteCarbon&select=chain:B&style=cartoon;line&select=resi:19,23,26;chain:B&style=stick&labelres=backgroundOpacity:0.8;fontSize:14`](../viewer.html?pdb=1YCR&select=chain:A&style=cartoon;stick:radius~0.1&surface=opacity:0.8;colorscheme:whiteCarbon&select=chain:B&style=cartoon;line&select=resi:19,23,26;chain:B&style=cartoon;stick&labelres=backgroundOpacity:0.8;fontSize:14)
+https://3Dmol.org/viewer.html?pdb=1YCR&select=chain:A&style=cartoon;stick:radius~0.1&surface=opacity:0.8;colorscheme:whiteCarbon&select=chain:B&style=cartoon;line&select=resi:19,23,26;chain:B&style=stick&labelres=backgroundOpacity:0.8;fontSize:14
+
#### Mouse Controls ####
-Movement | | Mouse Input | | Touch Input
----------|-|:------------|------------
-Rotation | | Primary Mouse Button | | Single touch
-Translation | | Middle Mouse Button or Ctrl+Primary | | Triple touch
-Zoom | | Scroll Wheel or Second Mouse Button or Shift+Primary | | Pinch (double touch)
-Slab | | Ctrl+Second | | Not Available
+| Movement | Mouse Input | Touch Input |
+| ----------- | ---------------------------------------------------- | -------------------- |
+| Rotation | Primary Mouse Button | Single touch |
+| Translation | Middle Mouse Button or Ctrl+Primary | Triple touch |
+| Zoom | Scroll Wheel or Second Mouse Button or Shift+Primary | Pinch (double touch) |
+| Slab | Ctrl+Second | Not Available |
### Building a Query String ###
@@ -22,7 +22,6 @@ The URL query can be composed of three types of specifiers: a single **structure
Specifiers are read in the order they are added, and are separated by an '&' character.
-
#### Specifying a Structure ####
The **structure identifier** portion of the URL is a single selector formatted as `pdb=[PDB ID]`, `cid=[PubChem CID]`, or `url=[URL]`
@@ -45,7 +44,6 @@ Be default, the file format will be inferred by any extension (e.g., `.sdf`) pre
manually specified using the type parameter, as shown above.
-
#### Selecting atoms ####