MediaWiki/Demo

Test for the Jmol Extension for MediaWiki

Pop-up models

A user action will open a popup window with a model.

jmolFile tag The link cyclohexane will open a popup window displaying Chair.cml taken from this wiki <jmolFile text='cyclohexane'>Chair.cml</jmolFile>	jmolMol tag The link in your coffee will open a popup window displaying caffeine. También algo en el café <jmolMol text='something in your coffee'>caffeine</jmolMol> and something in vinegar
jmolSmiles tag The link nitrobenzene will open a popup window displaying nitrobenzene <jmolSmiles text='nitrobenzene'>c1ccccc1[N+](=O)[O-]</jmolSmiles>	jmolPdb tag The link adipocyte lipid binding protein will open a popup window displaying 1ab0.pdb. Esta es una proteína que une lípidos <jmolPdb text='adipocyte lipid binding protein'>1ab0</jmolPdb>

jmolAppletButton tag

jmolAppletLink tag Adipocyte lipid binding protein

Pop-in models

User action will insert a model within the page.

jmolAppletInlineButton tag Using urlContents 1AB0.pdb Murine adipocyte lipid binding protein at pH 4.5✖

jmolAppletInlineLink tag Using uploadedFileContents Cyclohexane Cyclohexane, chair conformation ✖ This is a very favoured conformation

jmolApplet tag with cover image

The JSmol model is inserted when clicking on the image. Here using uploadedFileContents

Cyclohexane, chair conformation

[x]

In-page models

A model is inserted as part of the page at page load time.

jmolApplet tag

Using uploadedFileContents A model stored in a file in this wiki Jmol._Canvas2D (Jmol) "JSmol_B"[x] script 1 started pdbGetHeader = true loadScript /extensions/Jmol/j2s/core/coretext.z.js JSmol exec JSmol_BB start applet null Jmol JavaScript applet JSmol_BB__915590356388607__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_BB__915590356388607__) vwrOptions: { "name":"JSmol_BB","applet":true,"documentBase":"http://wiki.jmol.org./index.php/MediaWiki/Demo","platform":"J.awtjs2d.Platform","fullName":"JSmol_BB__915590356388607__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_BB_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"915590356388607","bgcolor":"blueTint" } setting document base to "http://wiki.jmol.org./index.php/MediaWiki/Demo" (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_BB (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor blueTint backgroundColor = "blueTint" 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_BB__915590356388607__ ready Chair conformation of cyclohexane	Using urlContents A file retrieved from the PDB Jmol._Canvas2D (Jmol) "JSmol_BB"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_C start applet null Jmol JavaScript applet JSmol_C__915590356388607__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_C__915590356388607__) vwrOptions: { "name":"JSmol_C","applet":true,"documentBase":"http://wiki.jmol.org./index.php/MediaWiki/Demo","platform":"J.awtjs2d.Platform","fullName":"JSmol_C__915590356388607__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_C_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"915590356388607","bgcolor":"lightGray" } setting document base to "http://wiki.jmol.org./index.php/MediaWiki/Demo" (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_C (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor lightGray backgroundColor = "lightGray" 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_C__915590356388607__ ready Murine adipocyte lipid binding protein at pH 4.5 (1AB0.pdb)
Using inlineContents Jmol._Canvas2D (Jmol) "JSmol_C"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_D start applet null Jmol JavaScript applet JSmol_D__915590356388607__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_D__915590356388607__) vwrOptions: { "name":"JSmol_D","applet":true,"documentBase":"http://wiki.jmol.org./index.php/MediaWiki/Demo","platform":"J.awtjs2d.Platform","fullName":"JSmol_D__915590356388607__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_D_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"915590356388607","bgcolor":"yellowtint" } setting document base to "http://wiki.jmol.org./index.php/MediaWiki/Demo" (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_D (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor yellowtint backgroundColor = "yellowtint" 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_D__915590356388607__ ready This is 1-propanol ball and stickspincolor CPKbluegreencolor CPK blue green	Using wikiPageContents This is 2-propanol Jmol._Canvas2D (Jmol) "JSmol_D"[x] script 1 started pdbGetHeader = true Loading...|Please wait. JSmol exec JSmol_A start applet null Jmol JavaScript applet JSmol_A__915590356388607__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_A__915590356388607__) vwrOptions: { "name":"JSmol_A","applet":true,"documentBase":"http://wiki.jmol.org./index.php/MediaWiki/Demo","platform":"J.awtjs2d.Platform","fullName":"JSmol_A__915590356388607__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_A_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"915590356388607","bgcolor":"blueTint" } setting document base to "http://wiki.jmol.org./index.php/MediaWiki/Demo" (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_A (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor blueTint backgroundColor = "blueTint" 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_A__915590356388607__ ready Data read from the page Models/2-propanol
Using script This box has a message, but might hold a 3D model Jmol._Canvas2D (Jmol) "JSmol_A"[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_B start applet null Jmol JavaScript applet JSmol_B__915590356388607__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_B__915590356388607__) vwrOptions: { "name":"JSmol_B","applet":true,"documentBase":"http://wiki.jmol.org./index.php/MediaWiki/Demo","platform":"J.awtjs2d.Platform","fullName":"JSmol_B__915590356388607__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_B_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"915590356388607","bgcolor":"greenTint" } setting document base to "http://wiki.jmol.org./index.php/MediaWiki/Demo" (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_B (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor greenTint backgroundColor = "greenTint" 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_B__915590356388607__ ready script 1 started pdbGetHeader = true Loading...|Please wait. platformSpeed = 2 platformSpeed = 2 loadScript /extensions/Jmol/j2s/core/corescriptcmd.z.js The Resolver thinks Mol C3H8O 1-propanol APtclcactv02181912073D 0 0.00000 0.00000           C3H8O 1-propanol reading 12 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 12 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 C3H8O 1-propanol      Script completed Jmol script terminated platformSpeed = 2 loadScript /extensions/Jmol/j2s/core/corescriptmath.z.js loadScript /extensions/Jmol/j2s/J/bspt/PointIterator.js FileManager opening url http://wiki.jmol.org./index.php?title=Models/2-propanol&action=raw Loading...|Please wait. platformSpeed = 2 Hi there! Script completed Jmol script terminated Viewer cachePut cache://localLOAD_https://files.rcsb.org/download/1ab0.pdb.gz Viewer cachePut https://files.rcsb.org/download/1ab0.pdb.gz      FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/1ab0.pdb.gz) The Resolver thinks Pdb loadScript /extensions/Jmol/j2s/core/corebio.z.js FATTY ACID BINDING PROTEIN 30-JAN-97 1AB0 C1G/V32D/F57H MUTANT OF MURINE ADIPOCYTE LIPID BINDING PROTEIN 4.5 found biomolecule 1: A biomolecule 1: number of transforms: 2 Setting space group name to P 43 21 2 1AB0 Time for openFile(https://files.rcsb.org/download/1ab0.pdb.gz): 1044 ms reading 1044 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 Jmol 1044 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Time for creating model: 47 ms FATTY ACID BINDING PROTEIN 30-JAN-97 1AB0 C1G/V32D/F57H MUTANT OF MURINE ADIPOCYTE LIPID BINDING PROTEIN 4.5 found biomolecule 1: A 1AB0      Script completed Jmol script terminated The Resolver thinks Mol 2-propanol APtclcactv02271914333D 0 0.00000 0.00000           2-propanol Time for openFile(@modelData): 5 ms reading 12 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 12 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Time for creating model: 2 ms 2-propanol      Script completed Jmol script terminated platformSpeed = 5      FileManager.getAtomSetCollectionFromFile(http://wiki.jmol.org./images/f/f1/Chair.cml) FileManager opening url http://wiki.jmol.org./images/f/f1/Chair.cml The Resolver thinks XmlCml loadScript /extensions/Jmol/j2s/J/adapter/readers/xml/XmlReader.js loadScript /extensions/Jmol/j2s/J/adapter/readers/xml/XmlCmlReader.js chair.mol Time for openFile(http://wiki.jmol.org./images/f/f1/Chair.cml): 3223 ms reading 18 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 18 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Time for creating model: 3 ms chair.mol      Script completed Jmol script terminated

Contributors

AngelHerraez, Jaime Prilusky