ioChem-BD Browse module - Item page
Item metadata and files
Jmol._Canvas2D (Jmol) "jmolApplet"[x]
loadScript /browse/xslt/jsmol/j2s/core/package.js
loadScript /browse/xslt/jsmol/j2s/core/corejmol.z.js
loadScript /browse/xslt/jsmol/j2s/J/translation/PO.js
loadScript /browse/xslt/jsmol/j2s/core/corescript.z.js
JSmol exec jmolApplet start applet null
Jmol JavaScript applet jmolApplet__7223905564386617__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue allowjavascript null
AppletRegistry.checkIn(jmolApplet__7223905564386617__)
vwrOptions:
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setting document base to "https://iochem-bd.matter.toronto.edu/browse/handle/100/14"
(C) 2015 Jmol Development
Jmol Version: 14.29.25 2018-10-10 10:57
java.vendor: Java2Script (HTML5)
java.version: 2018-01-28 23:38:52 (JSmol/j2s)
os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
Access: ALL
memory: 0.0/0.0
processors available: 1
useCommandThread: false
appletId:jmolApplet (signed)
Jmol getValue emulate null
defaults = "Jmol"
Jmol getValue boxbgcolor null
Jmol getValue bgcolor #FFFFFF
backgroundColor = "#FFFFFF"
Jmol getValue ANIMFRAMECallback null
Jmol getValue APPLETREADYCallback Jmol._readyCallback
APPLETREADYCallback = "Jmol._readyCallback"
callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY
Jmol getValue ATOMMOVEDCallback null
Jmol getValue AUDIOCallback null
Jmol getValue CLICKCallback null
Jmol getValue DRAGDROPCallback null
Jmol getValue ECHOCallback null
Jmol getValue ERRORCallback null
Jmol getValue EVALCallback null
Jmol getValue HOVERCallback null
Jmol getValue IMAGECallback null
Jmol getValue LOADSTRUCTCallback null
Jmol getValue MEASURECallback null
Jmol getValue MESSAGECallback null
Jmol getValue MINIMIZATIONCallback null
Jmol getValue SERVICECallback null
Jmol getValue PICKCallback null
Jmol getValue RESIZECallback null
Jmol getValue SCRIPTCallback null
Jmol getValue SYNCCallback null
Jmol getValue STRUCTUREMODIFIEDCallback null
Jmol getValue doTranslate null
language=en_US
Jmol getValue popupMenu null
Jmol getValue script null
Jmol getValue loadInline null
Jmol getValue load null
Jmol applet jmolApplet__7223905564386617__ ready
script 1 started
loadScript /browse/xslt/jsmol/j2s/JV/StateCreator.js
loadScript /browse/xslt/jsmol/j2s/JV/JmolStateCreator.js
FileManager.getAtomSetCollectionFromFile(https://iochem-bd.matter.toronto.edu:443/browse/bitstream/100/14/6/geometry.cml)
FileManager opening url https://iochem-bd.matter.toronto.edu:443/browse/bitstream/100/14/6/geometry.cml
The Resolver thinks XmlCml
loadScript /browse/xslt/jsmol/j2s/J/adapter/readers/xml/XmlReader.js
loadScript /browse/xslt/jsmol/j2s/J/adapter/readers/xml/XmlCmlReader.js
molecule
Time for openFile(https://iochem-bd.matter.toronto.edu:443/browse/bitstream/100/14/6/geometry.cml): 150 ms
reading 97 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
97 atoms created
ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation
Time for creating model: 9 ms
molecule
loadScript /browse/xslt/jsmol/j2s/core/corescriptcmd.z.js
Script completed
Jmol script terminated
Code snippets
Metadata:
| Title: | /workflow/mol_1/opt S1 |
| Authors: | Garcia, Sergio |
| Issue Date: | 4-Aug-2023 |
| Publisher: | Matter Lab University of Toronto |
| Description: | S1 |
| URI: | https://iochem-bd.matter.toronto.edu/browse/handle/100/14 |
| Appears in Collections: | ChemOS2_0 |
Please use this identifier to cite or link to this item:
https://iochem-bd.matter.toronto.edu/browse/handle/100/14
Item files in Browse 
HTML5 resume (see conditions inside)
Geometry
Standalone HTML page code snippet
<!DOCTYPE html>
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<head>
<meta charset="utf-8" />
<meta http-equiv="x-ua-compatible" content="ie=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title></title>
<link rel="icon" href="https://iochem-bd.matter.toronto.edu:443/browse/images/favicon.png" />
</head>
<body>
<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.4.0/3Dmol-min.js"></script>
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<span style="display:inline-block;z-index:1;position: absolute;bottom: 0px;right: 0px;font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;">Source at <a target="_blank" href="https://iochem-bd.matter.toronto.edu:443/browse/handle/100/14" style="">ioChem-BD</a></span>
</div>
<script>
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var viewer_first = $3Dmol.createViewer("iochembdGeometry", {backgroundColor:"white"});
viewer_first.addModel(data,"xyz");
viewer_first.setStyle({"sphere": {"radius": 0.3}});
viewer_first.addStyle({"stick": {"radius": 0.2}});
viewer_first.zoomTo();
viewer_first.render();
</script>
</body>
</html>
Authorea code snippet
<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.4.0/3Dmol-min.js"></script>
<div id="iochembdGeometry" style="height: 400px; width: 400px; position: relative;" data-backgroundcolor='0xffffff'>
<span style="display:inline-block;z-index:1;position: absolute;bottom: 0px;right: 0px;font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;">Source at <a target="_blank" href="https://iochem-bd.matter.toronto.edu:443/browse/handle/100/14" style="">ioChem-BD</a></span>
</div>
<script>
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viewer_first.addModel(data,"xyz");
viewer_first.setStyle({"sphere": {"radius": 0.3}});
viewer_first.addStyle({"stick": {"radius": 0.2}});
viewer_first.zoomTo();
viewer_first.render();
</script>