PDB Structure Fully optimized PM7 Geometry Fully optimized PM6 Geometry
Jmol._Canvas2D (Jmol) "jmolAppletPM7_PDB"[x] script 1 started FileManager.getAtomSetCollectionFromFile(../PM7_PDB/Bacteriorhodopsin_(1AP9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_PDB/Bacteriorhodopsin_(1AP9).pdb The Resolver thinks Pdb PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 63 Time for openFile(../PM7_PDB/Bacteriorhodopsin_(1AP9).pdb): 728 ms reading 3579 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 3579 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES found biomolecule 1: A 3601 connections deleted Standard Hbond calculation 182 hydrogen bonds measurementUnits = "angstroms" Jmol 14.4.0_2015.10.14 2015-10-14 19:01 DSSP analysis for model 1.1 - 1AP9 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 65.1.6: 789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345 65.1.5: ....................................................>5555<.................................>5555<...........>5555<.............................>>>55<<<..............................>>555<<..................>5555<....... 65.1.4: ..>>>>XXXXX<<X<>><>XX4<<<....>>>>XXX<XX<4XX>>XXX<XXX4<<<.................>4>><4X<4>X44<X44><44<..>>>>XXXXXXXXXXXXXXXX<<<<.....>>>>XXXXXXXXXXXXX<X<<><>4<4<....>>44X<>>X>XXXXXXX<XXX><<<<..........>>>>XXXXXXXXX<<XX4><<4<.. 65.1.3: >33<...............>33<>33<...........>33<.......>33<......................>33<>33<...................>33<....................>33<..............>33<.>>3<<>33<>>3<<..............>>><<X33<.........>>3<X33<.........>33<... 65.1.1: .TTHHHHHHHHHHHTTHHHHHHHHTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.................TTHHHHTTTHHHH.TTTTTTTT..HHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHTTTTGGG..TT..HHHHTTHHHHHHHHHHHHHHHHHHTTTT........HHHHHHHHHHHHHHHHHHHTT... 65.1.0: RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILL! NOTE: '!' indicates a residue that is missing a backbone carbonyl oxygen atom. SUMMARY: T : A:8_A:9 H : A:10_A:20 T : A:21_A:22 H : A:23_A:30 T : A:31_A:32 H : A:37_A:61 T : A:62_A:63 T : A:81_A:82 H : A:83_A:86 T : A:87_A:89 H : A:90_A:93 T : A:95_A:102 H : A:105_A:126 H : A:134_A:152 T : A:153_A:156 G : A:157_A:159 T : A:162_A:163 H : A:166_A:169 T : A:170_A:171 H : A:172_A:189 T : A:190_A:193 H : A:202_A:220 T : A:221_A:222 hermiteLevel = 4 ribbonAspectRatio = 12 Script completed Jmol script terminated loadClass J.g3d.HermiteRenderer |
Jmol._Canvas2D (Jmol) "jmolAppletPM7_OPT"[x] script 1 started FileManager.getAtomSetCollectionFromFile(../PM7_OPT/Bacteriorhodopsin_(1AP9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM7_OPT/Bacteriorhodopsin_(1AP9).pdb The Resolver thinks Pdb loadClass J.adapter.readers.pdb.PdbReader JSmol exec jmolAppletPM6_OPT start applet null Jmol JavaScript applet jmolAppletPM6_OPT__857261539343628__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM6_OPT__857261539343628__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM6_OPT","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM6_OPT__857261539343628__","codePath":"http://openmopac.net/PM7_accuracy/PM7_proteins/../../jsmol/j2s/","display":"jmolAppletPM6_OPT_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"857261539343628","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).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_OPT (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_OPT__857261539343628__ ready |
Jmol._Canvas2D (Jmol) "jmolAppletPM6_OPT"[x] loadClass core.package loadClass java.lang.String loadClass core.package JSmol exec jmolAppletPM7_PDB start applet null Jmol JavaScript applet jmolAppletPM7_PDB__857261539343628__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_PDB__857261539343628__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_PDB","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_PDB__857261539343628__","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":"857261539343628","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).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_OPT start applet null Jmol JavaScript applet jmolAppletPM7_OPT__857261539343628__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolAppletPM7_OPT__857261539343628__) nographics false nographics false headless false vwrOptions: { "name":"jmolAppletPM7_OPT","applet":true,"documentBase":"http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).html","platform":"J.awtjs2d.Platform","fullName":"jmolAppletPM7_OPT__857261539343628__","codePath":"http://openmopac.net/PM7_accuracy/PM7_proteins/../../jsmol/j2s/","display":"jmolAppletPM7_OPT_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"857261539343628","bgcolor":"#000000" } setting document base to "http://openmopac.net/PM7_accuracy/PM7_proteins/Bacteriorhodopsin_(1AP9).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_OPT (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_OPT__857261539343628__ ready script 1 started FileManager.getAtomSetCollectionFromFile(../PM6_OPT/Bacteriorhodopsin_(1AP9).pdb) FileManager opening url http://openmopac.net/PM7_accuracy/PM6_OPT/Bacteriorhodopsin_(1AP9).pdb The Resolver thinks Pdb PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 63 Time for openFile(../PM6_OPT/Bacteriorhodopsin_(1AP9).pdb): 151 ms reading 3579 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 3579 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES found biomolecule 1: A loadClass JS.MathExt loadClass JS.CmdExt 3601 connections deleted Standard Hbond calculation 289 hydrogen bonds measurementUnits = "angstroms" Jmol 14.4.0_2015.10.14 2015-10-14 19:01 DSSP analysis for model 1.1 - 1AP9 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 65.1.6: 789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345 65.1.5: ....................................>5555<..........>5555<......>5555<.....................>5555<..............................................>>555<<..........>5555<...............>>555<<..................>5555<....... 65.1.4: ..>>>>XXXXX<XX<>XX4XX<4<<....>>>>XXX<XX<>XX>XXXXXXXX<<<<.................>>>>XXX<<XX>>XXXXX<<<<..>>>>XXXXXXXXXX<XXX4X<<4<.....>>>>XXXXXXXXXXXXXXX<<XX>4<<<...>>>>XXXXXXXXXXXXXX<XXX>XX<<<<.......>>>>XXXXXXXX<X<<>X4><<4<.. 65.1.3: >3><3<.........>33<>>3<X33X33X>><<<............>33<..>33<...............>>><<<....>33<...>33X33<.>33<...............>33<......>33<........................>33X33<.............>>3<<..............>33<.........>33X33X33<... 65.1.1: .TTHHHHHHHHHHHHHHHHHHHHHTT.TT.HHHHHHHHHHHHHHHHHHHHHHHHHTT...B....TTTT..B.THHHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHTT.......HHHHHHHHHHHHHHHHHHHHHHHHHH..TT.HHHHHHHHHHHHHHHHHHHHHHHHHHHTT.......HHHHHHHHHHHHHHTTHHHHTT... 65.1.0: RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILL! NOTE: '!' indicates a residue that is missing a backbone carbonyl oxygen atom. SUMMARY: T : A:8_A:9 H : A:10_A:30 T : A:31_A:32 T : A:34_A:35 H : A:37_A:61 T : A:62_A:63 B : A:67_A:67 T : A:72_A:75 B : A:78_A:78 T : A:80_A:80 H : A:81_A:100 T : A:101_A:102 H : A:105_A:124 T : A:125_A:126 H : A:134_A:159 T : A:162_A:163 H : A:165_A:191 T : A:192_A:193 H : A:201_A:214 T : A:215_A:216 H : A:217_A:220 T : A:221_A:222 hermiteLevel = 4 ribbonAspectRatio = 12 Script completed Jmol script terminated PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES found biomolecule 1: A biomolecule 1: number of transforms: 3 Setting space group name to P 63 Time for openFile(../PM7_OPT/Bacteriorhodopsin_(1AP9).pdb): 1934 ms reading 3579 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 3579 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically PHOTORECEPTOR 26-JUL-97 1AP9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES 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__857261539343628__ ready |