PDB Structure PM7 Geometry with 3 Kcal/Angstrom^2 constraint PM6 Geometry with 3 Kcal/Angstrom^2 constraint
Jmol._Canvas2D (Jmol) "jmolAppletPM7_PDB"[x] script 1 started FileManager.getAtomSetCollectionFromFile(../PM7_PDB/Silk_(Poly-(Gly-Ala)).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_PDB/Silk_(Poly-(Gly-Ala)).pdb The Resolver thinks Pdb Time for openFile(../PM7_PDB/Silk_(Poly-(Gly-Ala)).pdb): 796 ms reading 136 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 136 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically null loadClass JS.CmdExt 132 connections deleted Standard Hbond calculation 6 hydrogen bonds measurementUnits = "angstroms" hermiteLevel = 4 ribbonAspectRatio = 12 Script completed Jmol script terminated loadClass J.g3d.HermiteRenderer |
Jmol._Canvas2D (Jmol) "jmolAppletPM7_3"[x] script 1 started FileManager.getAtomSetCollectionFromFile(../PM7_3/Silk_(Poly-(Gly-Ala)).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_3/Silk_(Poly-(Gly-Ala)).pdb The Resolver thinks Pdb loadClass J.adapter.readers.pdb.PdbReader JSmol exec jmolAppletPM6_3 start applet null Jmol JavaScript applet jmolAppletPM6_3__3926979974300049__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM6_3__3926979974300049__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM6_3","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM6_3__3926979974300049__","codePath":"http://openmopac.net/PM7_accuracy/PM7_proteins/../../jsmol/j2s/","display":"jmolAppletPM6_3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3926979974300049","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html" (C) 2015 Jmol Development Jmol Version: 14.4.0_2015.10.14 2015-10-14 19:01 java.vendor: Java2Script (HTML5) java.version: 2015-09-19 23:29:54 (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:jmolAppletPM6_3 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #000000 backgroundColor = "#000000" 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 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 jmolAppletPM6_3__3926979974300049__ ready |
Jmol._Canvas2D (Jmol) "jmolAppletPM6_3"[x] loadClass core.package loadClass java.lang.String loadClass core.package JSmol exec jmolAppletPM7_PDB start applet null Jmol JavaScript applet jmolAppletPM7_PDB__3926979974300049__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_PDB__3926979974300049__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_PDB","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_PDB__3926979974300049__","codePath":"http://openmopac.net/PM7_accuracy/PM7_proteins/../../jsmol/j2s/","display":"jmolAppletPM7_PDB_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3926979974300049","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html" (C) 2015 Jmol Development Jmol Version: 14.4.0_2015.10.14 2015-10-14 19:01 java.vendor: Java2Script (HTML5) java.version: 2015-09-19 23:29:54 (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:jmolAppletPM7_PDB (signed) loadClass JS.ScriptManager JSmol exec jmolAppletPM7_3 start applet null Jmol JavaScript applet jmolAppletPM7_3__3926979974300049__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_3__3926979974300049__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_3","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_3__3926979974300049__","codePath":"http://openmopac.net/PM7_accuracy/PM7_proteins/../../jsmol/j2s/","display":"jmolAppletPM7_3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3926979974300049","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Silk_(Poly-(Gly-Ala))_3.html" (C) 2015 Jmol Development Jmol Version: 14.4.0_2015.10.14 2015-10-14 19:01 java.vendor: Java2Script (HTML5) java.version: 2015-09-19 23:29:54 (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:jmolAppletPM7_3 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #000000 backgroundColor = "#000000" 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 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 jmolAppletPM7_3__3926979974300049__ ready script 1 started FileManager.getAtomSetCollectionFromFile(../PM6_3/Silk_(Poly-(Gly-Ala)).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM6_3/Silk_(Poly-(Gly-Ala)).pdb The Resolver thinks Pdb Time for openFile(../PM6_3/Silk_(Poly-(Gly-Ala)).pdb): 1022 ms reading 136 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 136 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically null Time for openFile(../PM7_3/Silk_(Poly-(Gly-Ala)).pdb): 2628 ms reading 136 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 136 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically null Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #000000 backgroundColor = "#000000" 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 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 jmolAppletPM7_PDB__3926979974300049__ ready |