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/Bacteriorhodopsin_(1AT9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_PDB/Bacteriorhodopsin_(1AT9).pdb The Resolver thinks Pdb PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 3 Time for openFile(../PM7_PDB/Bacteriorhodopsin_(1AT9).pdb): 322 ms reading 3667 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 3667 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A 3716 connections deleted Standard Hbond calculation 254 hydrogen bonds measurementUnits = "angstroms" Jmol 14.4.0_2015.10.14 2015-10-14 19:01 DSSP analysis for model 1.1 - 1AT9 W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at http://swift.cmbi.ru.nl/gv/dssp All bioshapes have been deleted and must be regenerated. NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis. Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation. ------------------------------ 65.1.8: 1 2 65.1.7: 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 65.1.6: 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 65.1.5: ................................................................................................>5555<..............................................>>>>5<<<<.....................................................>>>55<<<............ 65.1.4: .......>>>>XXXXXXXXXXXXXXXX<<<<...>>>>XXXXXX<XXX>XXXXXXXX<<<<.................>>>>XXX<XXX>XXXXXXX<<<<.>>>>XXXXXXXXXXXXXXXXX<<<<.>>>>XXXXXXXXXXXXXXXXX<XXX4X<<4<...>>>>XXXXXXXXXXXXXX<XXX>XX<<<X>44<<..>>>>XXXXXXXXXX<XXX>XXXX<<<<..... 65.1.3: .....>>><<<.............>33X33<...>33<......>33<.>33<>33X33<.>33<............>>><<<.......>>3<<.......>33<..............>33<>33<>33<..>33<................>33<.....................>>3<<.>33<..................>33<.............>>3<<. 65.1.1: ......TTHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHH..TT..............THHHHHHHHHHHHHHHHHHHHHT..HHHHHHHHHHHHHHHHHHHHHHHT..HHHHHHHHHHHHHHHHHHHHHHHHHHHTT.....HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHH....HHHHHHHHHHHHHHHHHHHHHHHHH.GGG.. 65.1.0: AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG SUMMARY: T : A:7_A:8 H : A:9_A:30 H : A:36_A:60 T : A:63_A:64 T : A:79_A:79 H : A:80_A:100 T : A:101_A:101 H : A:104_A:126 T : A:127_A:127 H : A:130_A:156 T : A:157_A:158 H : A:164_A:190 H : A:192_A:195 H : A:200_A:224 G : A:226_A:228 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/Bacteriorhodopsin_(1AT9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_3/Bacteriorhodopsin_(1AT9).pdb The Resolver thinks Pdb loadClass J.adapter.readers.pdb.PdbReader JSmol exec jmolAppletPM6_3 start applet null Jmol JavaScript applet jmolAppletPM6_3__1095486555607712__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM6_3__1095486555607712__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM6_3","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM6_3__1095486555607712__","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":"1095486555607712","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_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__1095486555607712__ 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__1095486555607712__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_PDB__1095486555607712__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_PDB","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_PDB__1095486555607712__","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":"1095486555607712","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_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__1095486555607712__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_3__1095486555607712__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_3","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_3.html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_3__1095486555607712__","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":"1095486555607712","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AT9)_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__1095486555607712__ ready script 1 started FileManager.getAtomSetCollectionFromFile(../PM6_3/Bacteriorhodopsin_(1AT9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM6_3/Bacteriorhodopsin_(1AT9).pdb The Resolver thinks Pdb PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 3 Time for openFile(../PM6_3/Bacteriorhodopsin_(1AT9).pdb): 391 ms reading 3667 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 3667 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A loadClass JS.CmdExt 3716 connections deleted Standard Hbond calculation 294 hydrogen bonds measurementUnits = "angstroms" Jmol 14.4.0_2015.10.14 2015-10-14 19:01 DSSP analysis for model 1.1 - 1AT9 W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at http://swift.cmbi.ru.nl/gv/dssp All bioshapes have been deleted and must be regenerated. NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis. Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation. ------------------------------ 65.1.8: 1 2 65.1.7: 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 65.1.6: 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 65.1.5: ..............................................>5555<.....>5555<.................................>5555<>5>55<5<...>5>55<5<......>5555<...............>5>>5<5<<........>555><555<..........>5555X5555<.>555><555<.>55>><55<<............ 65.1.4: ......>>>>XXXXXXX<XXX>XXXXX<<<<...>>>>XXXXXX<XXX>XXXXXXXX<<<<................>>>><X<<4<>>>>XXXXXX<<<<.>>>>XXXXXXXXXXXXXXXX<X<<4<>>>>XXXXXXXXXXXXXXXXX<<<<.........>>>>XXXXXXXXXX<XXX4XXX>X<<<<........>4>>X>XXXXXXXX<<XX>>XX<<<<...... 65.1.3: .....>>3<<.................>3><3<.>33<........>33<........>33<.......>33<........>>3<<................>33<.................>33<.>33<..............................>33<..............>33<......>33<......>>3<<......>33<...>33X33X33<.. 65.1.1: ......THHHHHHHHHHHHHHHHHHHHHHHTT...HHHHHHHHHHHHHHHHHHHHHHHHHTT..EEEEEETTEEEEEEHHHHHHTT..HHHHHHHHHHHHT..HHHHHHHHHHHHHHHHHHHHHHTT.THHHHHHHHHHHHHHHHHHHHHHHTTTT.......HHHHHHHHHHHHHHHHHHHHHHHHHHTEETTT..EETTHHHHHHHHHHHHHHHHHHHHHHT.TT... 65.1.0: AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG SUMMARY: T : A:7_A:7 H : A:8_A:30 T : A:31_A:32 H : A:36_A:60 T : A:61_A:62 E : A:65_A:70 T : A:71_A:72 E : A:73_A:78 H : A:79_A:84 T : A:85_A:86 H : A:89_A:100 T : A:101_A:101 H : A:104_A:125 T : A:126_A:127 T : A:129_A:129 H : A:130_A:152 T : A:153_A:156 H : A:164_A:189 T : A:190_A:190 E : A:191_A:192 T : A:193_A:195 E : A:198_A:199 T : A:200_A:201 H : A:202_A:223 T : A:224_A:224 T : A:226_A:227 hermiteLevel = 4 ribbonAspectRatio = 12 Script completed Jmol script terminated PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 3 Time for openFile(../PM7_3/Bacteriorhodopsin_(1AT9).pdb): 3775 ms reading 3667 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 3667 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 20-AUG-97 1AT9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY found biomolecule 1: A 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__1095486555607712__ ready |