User:Bduke

Interested in Jmol in general and in particular right now about adding Jmol images to Wikis, particularly Wikipedia.

Tests of Jmol incorporated into a MediaWiki wiki.

urlContent Test from this server - does not work

Jmol._Canvas2D (Jmol) "JSmol_ethane"[x] script 1 started pdbGetHeader = true loadScript /extensions/Jmol/j2s/core/coretext.z.js JSmol exec JSmol_1CRN start applet null Jmol JavaScript applet JSmol_1CRN__3666101591788067__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_1CRN__3666101591788067__) vwrOptions: { "name":"JSmol_1CRN","applet":true,"documentBase":"http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke","platform":"J.awtjs2d.Platform","fullName":"JSmol_1CRN__3666101591788067__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_1CRN_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3666101591788067","bgcolor":"blue" } setting document base to "http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 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:JSmol_1CRN (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor blue backgroundColor = "blue" 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 JSmol_1CRN__3666101591788067__ ready

urlContent Test from a different server - does not work

Jmol._Canvas2D (Jmol) "JSmol_1CRN"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_asprin start applet null Jmol JavaScript applet JSmol_asprin__3666101591788067__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_asprin__3666101591788067__) vwrOptions: { "name":"JSmol_asprin","applet":true,"documentBase":"http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke","platform":"J.awtjs2d.Platform","fullName":"JSmol_asprin__3666101591788067__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_asprin_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3666101591788067","bgcolor":"green" } setting document base to "http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 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:JSmol_asprin (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor green backgroundColor = "green" 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 JSmol_asprin__3666101591788067__ ready

Alchemy file - does not work

Jmol._Canvas2D (Jmol) "JSmol_asprin"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_ethane-s start applet null Jmol JavaScript applet JSmol_ethane-s__3666101591788067__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_ethane-s__3666101591788067__) vwrOptions: { "name":"JSmol_ethane-s","applet":true,"documentBase":"http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke","platform":"J.awtjs2d.Platform","fullName":"JSmol_ethane-s__3666101591788067__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_ethane-s_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3666101591788067","bgcolor":"palegreen" } setting document base to "http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 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:JSmol_ethane-s (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor palegreen backgroundColor = "palegreen" 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 JSmol_ethane-s__3666101591788067__ ready

Staggered and eclipsed ethane

These are pdb files generated by Sybyl for staggered and eclipsed ethane. Use the buttons and the menu that comes up by right mouse clicking on the image to manipulate the images. The left mouse can be used to move the image.

Jmol._Canvas2D (Jmol) "JSmol_ethane-s"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_ethane-e start applet null Jmol JavaScript applet JSmol_ethane-e__3666101591788067__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_ethane-e__3666101591788067__) vwrOptions: { "name":"JSmol_ethane-e","applet":true,"documentBase":"http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke","platform":"J.awtjs2d.Platform","fullName":"JSmol_ethane-e__3666101591788067__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_ethane-e_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3666101591788067","bgcolor":"skyblue" } setting document base to "http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 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:JSmol_ethane-e (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor skyblue backgroundColor = "skyblue" 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 JSmol_ethane-e__3666101591788067__ ready

Jmol._Canvas2D (Jmol) "JSmol_ethane-e"[x] loadScript /extensions/Jmol/j2s/core/package.js loadScript /extensions/Jmol/j2s/core/corejmol.z.js loadScript /extensions/Jmol/j2s/J/translation/PO.js loadScript /extensions/Jmol/j2s/core/corescript.z.js JSmol exec JSmol_ethane start applet null Jmol JavaScript applet JSmol_ethane__3666101591788067__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_ethane__3666101591788067__) vwrOptions: { "name":"JSmol_ethane","applet":true,"documentBase":"http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke","platform":"J.awtjs2d.Platform","fullName":"JSmol_ethane__3666101591788067__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_ethane_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3666101591788067","bgcolor":"red" } setting document base to "http://wiki.jmol.org/index.php?diff=prev&oldid=2142&title=User%3ABduke" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 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:JSmol_ethane (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor red backgroundColor = "red" 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 JSmol_ethane__3666101591788067__ ready script 1 started pdbGetHeader = true Loading...|Please wait. platformSpeed = 5      FileManager.getAtomSetCollectionFromFile(http://orion.vcp.monash.edu.au/pictures/1CRN.pdb) FileManager opening url http://orion.vcp.monash.edu.au/pictures/1CRN.pdb Time for openFile(http://orion.vcp.monash.edu.au/pictures/1CRN.pdb): 1381 ms File Error:unrecognized file format for file http://orion.vcp.monash.edu.au/pictures/1CRN.pdb                                    script ERROR: unrecognized file format for file http://orion.vcp.monash.edu.au/pictures/1CRN.pdb                                    ---- load <<<<"http://orion.vcp.monash.edu.au/pictures/1CRN.pdb" Script completed Jmol script terminated platformSpeed = 5 loadScript /extensions/Jmol/j2s/core/corescriptcmd.z.js The Resolver thinks Alchemy loadScript /extensions/Jmol/j2s/J/adapter/readers/simple/AlchemyReader.js reading 21 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 21 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Time for creating model: 7 ms loadScript /extensions/Jmol/j2s/JV/DataManager.js loadScript /extensions/Jmol/j2s/J/api/JmolDataManager.js Script completed Jmol script terminated platformSpeed = 5 The Resolver thinks Pdb loadScript /extensions/Jmol/j2s/core/corebio.z.js PROTEIN 19-OCT-95 reading 8 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 8 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Time for creating model: 6 ms PROTEIN 19-OCT-95      spinX = 10 loadScript /extensions/Jmol/j2s/J/thread/SpinThread.js Script completed Jmol script terminated Loading...|Please wait. platformSpeed = 5 The Resolver thinks Pdb PROTEIN 19-OCT-95 reading 8 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 8 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Time for creating model: 2 ms PROTEIN 19-OCT-95      spinX = 10 Script completed Jmol script terminated platformSpeed = 5      FileManager.getAtomSetCollectionFromFile(http://wiki.jmol.org/User:Bduke/ethane-s.pdb) FileManager opening url http://wiki.jmol.org/User:Bduke/ethane-s.pdb Time for openFile(http://wiki.jmol.org/User:Bduke/ethane-s.pdb): 101 ms File Error:unrecognized file format for file http://wiki.jmol.org/User:Bduke/ethane-s.pdb      <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN" >      <html><head>      <title>404 Not Found</title>                script ERROR: unrecognized file format for file http://wiki.jmol.org/User:Bduke/ethane-s.pdb      <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN" >      <html><head>      <title>404 Not Found</title>                ---- load <<<<"/User:Bduke/ethane-s.pdb" Script completed Jmol script terminated spinFPS is set too fast (30) -- can't keep up! spinFPS is set too fast (30) -- can't keep up!

Contributors

Bduke, AngelHerraez, NicolasVervelle