Load SMILES

Loading a SMILES string into Jmol requires conversion of the SMILES string to a 3D model. This is done in an external web server (which in few occasions might fail temporarily).

The load command is given in a script tag as part of an applet, checkbox, menu, etc. tag.

Jmol._Canvas2D (Jmol) "JSmol_1"[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_1 start applet null Jmol JavaScript applet JSmol_1__2602731000046026__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_1__2602731000046026__) vwrOptions: { "name":"JSmol_1","applet":true,"documentBase":"http://wiki.jmol.org./index.php/Load_SMILES","platform":"J.awtjs2d.Platform","fullName":"JSmol_1__2602731000046026__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"2602731000046026","bgcolor":"black" } setting document base to "http://wiki.jmol.org./index.php/Load_SMILES" (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_1 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor black backgroundColor = "black" 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_1__2602731000046026__ ready script 1 started pdbGetHeader = true loadScript /extensions/Jmol/j2s/core/coretext.z.js Loading...|Please wait. platformSpeed = 5      FileManager.getAtomSetCollectionFromFile(https://cactus.nci.nih.gov/chemical/structure/NC(Cl)(C)O/file?format=sdf&get3d=true) FileManager opening url https://cactus.nci.nih.gov/chemical/structure/NC(Cl)(C)O/file?format=sdf&get3d=true The Resolver thinks Mol C2H6ClNO APtclcactv04132521513D 0 0.00000 0.00000           C2H6ClNO Time for openFile(https://cactus.nci.nih.gov/chemical/structure/NC(Cl)(C)O/file?format=sdf&get3d=true): 1342 ms reading 11 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 11 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Time for creating model: 7 ms C2H6ClNO      Script completed Jmol script terminated

..choose..CCC(C)CNC(C)C(O)=Oc1ccccc1

Contributors

AngelHerraez