id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5045 Modeller sequence mismatch failure yen-li.li@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description I like to build a multichain homology model using Modeller Comparative, but was unable to get output model. The template structure PDB number is 4n9f. The sequence alignment of target sequence and template sequence are open (see attached). The error is shown below: No output models from Modeller; see log for Modeller text output. Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Already try many hours on it but still failed to figure out how to fix it. Could you please give me some instruction? Thank you Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""E:\temp\EM data\4n9f.pdb1"" format pdb Summary of feedback from opening E:\temp\EM data\4n9f.pdb1 --- warnings | Start residue of secondary structure not found: HELIX 35 35 LYS C 18 GLN C 32 1 15 Start residue of secondary structure not found: HELIX 36 36 THR C 36 ASP C 54 1 19 Start residue of secondary structure not found: HELIX 37 37 LYS C 56 SER C 82 1 27 Start residue of secondary structure not found: HELIX 38 38 ASP C 85 LEU C 107 1 23 Start residue of secondary structure not found: HELIX 39 39 PRO C 108 PRO C 110 5 3 680 messages similar to the above omitted Cannot find LINK/SSBOND residue HIS (139 ) Cannot find LINK/SSBOND residue HIS (139 ) Cannot find LINK/SSBOND residue CYS (114 ) Cannot find LINK/SSBOND residue CYS (114 ) Cannot find LINK/SSBOND residue CYS (133 ) 33 messages similar to the above omitted 4n9f.pdb1 title: Crystal structure of the vif-cbfbeta-CUL5-elob-eloc pentameric complex [more info...] Chain information for 4n9f.pdb1 #1 --- Chain | Description U | No description available X | No description available Y | No description available a | No description available b | No description available Non-standard residues in 4n9f.pdb1 #1 --- ZN — zinc ion > hide atoms > show cartoons > delete #1/U > open ""E:/temp/EM data/FL-Hxb2Vif_4n9f-NL43.aln"" Summary of feedback from opening E:/temp/EM data/FL-Hxb2Vif_4n9f-NL43.aln --- notes | Alignment identifier is FL-Hxb2Vif_4n9f-NL43.aln Associated 4n9f.pdb1 chain b to NL43Vif_4n9f with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment FL-Hxb2Vif_4n9f-NL43.aln Opened 2 sequences from FL-Hxb2Vif_4n9f-NL43.aln > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:1 Disassociated 4n9f.pdb1 chain b from NL43Vif_4n9f Associated 4n9f.pdb1 chain b to Hxb2Vif_P69723 with 20 mismatches and/or gaps > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:2 Disassociated 4n9f.pdb1 chain b from Hxb2Vif_P69723 Associated 4n9f.pdb1 chain b to NL43Vif_4n9f with 0 mismatches > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:1 Disassociated 4n9f.pdb1 chain b from NL43Vif_4n9f Associated 4n9f.pdb1 chain b to Hxb2Vif_P69723 with 20 mismatches and/or gaps > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:2 Disassociated 4n9f.pdb1 chain b from Hxb2Vif_P69723 Associated 4n9f.pdb1 chain b to NL43Vif_4n9f with 0 mismatches > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:1 Disassociated 4n9f.pdb1 chain b from NL43Vif_4n9f Associated 4n9f.pdb1 chain b to Hxb2Vif_P69723 with 20 mismatches and/or gaps > open ""E:/temp/EM data/FL-CBFb_4n9f-CBFb.aln"" ""E:/temp/EM data/FL- > ELOB_4n9f-ELOB.aln"" ""E:/temp/EM data/FL-ELOC_4n9f-ELOC.aln"" Summary of feedback from opening E:/temp/EM data/FL-CBFb_4n9f-CBFb.aln --- notes | Alignment identifier is FL-CBFb_4n9f-CBFb.aln Associated 4n9f.pdb1 chain a to CBFb_4n9f with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment FL-CBFb_4n9f-CBFb.aln Summary of feedback from opening E:/temp/EM data/FL-ELOB_4n9f-ELOB.aln --- notes | Alignment identifier is FL-ELOB_4n9f-ELOB.aln Associated 4n9f.pdb1 chain X to ELOB_4n9f with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment FL-ELOB_4n9f-ELOB.aln Summary of feedback from opening E:/temp/EM data/FL-ELOC_4n9f-ELOC.aln --- notes | Alignment identifier is FL-ELOC_4n9f-ELOC.aln Associated 4n9f.pdb1 chain Y to ELOC_4n9f with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment FL-ELOC_4n9f-ELOC.aln Opened 2 sequences from FL-CBFb_4n9f-CBFb.aln Opened 2 sequences from FL-ELOB_4n9f-ELOB.aln Opened 2 sequences from FL-ELOC_4n9f-ELOC.aln > sequence associate /X FL-ELOB_4n9f-ELOB.aln:1 Disassociated 4n9f.pdb1 chain X from ELOB_4n9f Associated 4n9f.pdb1 chain X to ELOB_Q15370 with 0 mismatches > select /a:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select /a:5 7 atoms, 6 bonds, 1 residue, 1 model selected > sequence associate /a FL-CBFb_4n9f-CBFb.aln:1 Disassociated 4n9f.pdb1 chain a from CBFb_4n9f Associated 4n9f.pdb1 chain a to CBFb_Q13951 with 0 mismatches > sequence associate /Y FL-ELOC_4n9f-ELOC.aln:1 Disassociated 4n9f.pdb1 chain Y from ELOC_4n9f Associated 4n9f.pdb1 chain Y to ELOC_Q15369 with 0 mismatches > ui tool show ""Modeller Comparative"" > modeller comparative FL-CBFb_4n9f-CBFb.aln:1 FL-ELOB_4n9f-ELOB.aln:1 FL- > ELOC_4n9f-ELOC.aln:1 FL-Hxb2Vif_4n9f-NL43.aln:1 multichain true numModels 5 > fast false hetPreserve false hydrogens false waterPreserve false Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1628754749123800597657 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1628754749123800597657 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service1628754749123800597657 finished Modeller error output Traceback (most recent call last): File ""/usr/local/opal-local/bin/modeller9v8.py"", line 322, in main() File ""/usr/local/opal-local/bin/modeller9v8.py"", line 24, in main VersionMap[cf[""version""]](cf) File ""/usr/local/opal-local/bin/modeller9v8.py"", line 34, in v2_run execfile(fn) File ""ModellerModelling.py"", line 67, in a.make() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 133, in make self.homcsr(exit_stage) File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 595, in homcsr aln = self.read_alignment() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 556, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File ""/usr/lib64/python2.7/site-packages/modeller/alignment.py"", line 80, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one- letter code matches (e.g. B to N, Z to Q). Modeller run output MODELLER 9.22, 2019/06/19, r11413 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2019 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu 3.10.0-1160.36.2.el7.x86_64 x86_64 Date and time of compilation : 2019/06/19 14:00:54 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2021/08/12 00:52:29 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269801 263.478 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 284893 278.216 0.272 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300293 293.255 0.286 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331093 323.333 0.316 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489 0.375 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 515893 503.802 0.492 openf___224_> Open ./4n9f.pdb1_1.pdb get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Alignment sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPEMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPNEVNFREIPSHVLSKVCMYFTY KVRYTNSSTEIPEFPIAPEIALELLMAANFLDRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQ NACRDGRSEIAFVATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDE ERAQQEDALAQQAFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYEST NPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRN TILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED PDB sequence matching range provided in alignment: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPERVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAF VATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQ AFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPL GDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRNTILGRIVSPRCE YQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED No output models from Modeller; see log for Modeller text output. > sequence associate /b FL-Hxb2Vif_4n9f-NL43.aln:2 Disassociated 4n9f.pdb1 chain b from Hxb2Vif_P69723 Associated 4n9f.pdb1 chain b to NL43Vif_4n9f with 0 mismatches > sequence associate /a FL-CBFb_4n9f-CBFb.aln:2 Disassociated 4n9f.pdb1 chain a from CBFb_Q13951 Associated 4n9f.pdb1 chain a to CBFb_4n9f with 0 mismatches > sequence associate /X FL-ELOB_4n9f-ELOB.aln:2 Disassociated 4n9f.pdb1 chain X from ELOB_Q15370 Associated 4n9f.pdb1 chain X to ELOB_4n9f with 0 mismatches > sequence associate /Y FL-ELOC_4n9f-ELOC.aln:2 Disassociated 4n9f.pdb1 chain Y from ELOC_Q15369 Associated 4n9f.pdb1 chain Y to ELOC_4n9f with 0 mismatches > ui tool show ""Modeller Comparative"" > modeller comparative FL-CBFb_4n9f-CBFb.aln:1 FL-ELOB_4n9f-ELOB.aln:1 FL- > ELOC_4n9f-ELOC.aln:1 FL-Hxb2Vif_4n9f-NL43.aln:1 multichain true numModels 5 > fast false hetPreserve false hydrogens false waterPreserve false Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service16287548655501857557318 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service16287548655501857557318 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service16287548655501857557318 finished Modeller error output Traceback (most recent call last): File ""/usr/local/opal-local/bin/modeller9v8.py"", line 322, in main() File ""/usr/local/opal-local/bin/modeller9v8.py"", line 24, in main VersionMap[cf[""version""]](cf) File ""/usr/local/opal-local/bin/modeller9v8.py"", line 34, in v2_run execfile(fn) File ""ModellerModelling.py"", line 67, in a.make() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 133, in make self.homcsr(exit_stage) File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 595, in homcsr aln = self.read_alignment() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 556, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File ""/usr/lib64/python2.7/site-packages/modeller/alignment.py"", line 80, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one- letter code matches (e.g. B to N, Z to Q). Modeller run output MODELLER 9.22, 2019/06/19, r11413 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2019 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu 3.10.0-1160.36.2.el7.x86_64 x86_64 Date and time of compilation : 2019/06/19 14:00:54 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2021/08/12 00:54:25 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269801 263.478 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 284893 278.216 0.272 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300293 293.255 0.286 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331093 323.333 0.316 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489 0.375 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 515893 503.802 0.492 openf___224_> Open ./4n9f.pdb1_1.pdb get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Alignment sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPEMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPNEVNFREIPSHVLSKVCMYFTY KVRYTNSSTEIPEFPIAPEIALELLMAANFLDRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQ NACRDGRSEIAFVATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDE ERAQQEDALAQQAFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYEST NPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRN TILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED PDB sequence matching range provided in alignment: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPERVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAF VATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQ AFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPL GDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRNTILGRIVSPRCE YQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED No output models from Modeller; see log for Modeller text output. > help help:user > select clear > help help:user > ui tool show ""Modeller Comparative"" > modeller comparative FL-CBFb_4n9f-CBFb.aln:1 FL-ELOB_4n9f-ELOB.aln:1 FL- > ELOC_4n9f-ELOC.aln:1 FL-Hxb2Vif_4n9f-NL43.aln:1 multichain true numModels 5 > fast false hetPreserve false hydrogens false waterPreserve false Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service16287559492801691508076 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service16287559492801691508076 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service16287559492801691508076 finished Modeller error output Traceback (most recent call last): File ""/usr/local/opal-local/bin/modeller9v8.py"", line 322, in main() File ""/usr/local/opal-local/bin/modeller9v8.py"", line 24, in main VersionMap[cf[""version""]](cf) File ""/usr/local/opal-local/bin/modeller9v8.py"", line 34, in v2_run execfile(fn) File ""ModellerModelling.py"", line 67, in a.make() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 133, in make self.homcsr(exit_stage) File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 595, in homcsr aln = self.read_alignment() File ""/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py"", line 556, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File ""/usr/lib64/python2.7/site-packages/modeller/alignment.py"", line 80, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one- letter code matches (e.g. B to N, Z to Q). Modeller run output MODELLER 9.22, 2019/06/19, r11413 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2019 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu 3.10.0-1160.36.2.el7.x86_64 x86_64 Date and time of compilation : 2019/06/19 14:00:54 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2021/08/12 01:12:29 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269801 263.478 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 284893 278.216 0.272 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300293 293.255 0.286 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331093 323.333 0.316 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489 0.375 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 515893 503.802 0.492 openf___224_> Open ./4n9f.pdb1_1.pdb get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4n9f.pdb1_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). Alignment sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPEMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPNEVNFREIPSHVLSKVCMYFTY KVRYTNSSTEIPEFPIAPEIALELLMAANFLDRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQ NACRDGRSEIAFVATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDE ERAQQEDALAQQAFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYEST NPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRN TILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED PDB sequence matching range provided in alignment: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATV GLAFDTFEALCIEPFSSPPERVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAF VATGTNLSLQFFPASWREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQ AFEEARRRTREFEDRDMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPL GDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRNTILGRIVSPRCE YQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTED No output models from Modeller; see log for Modeller text output. OpenGL version: 3.3.0 NVIDIA 461.92 OpenGL renderer: GeForce RTX 2060 SUPER/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Home (Build 19042) Memory: 34,261,569,536 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-US Locale: ('zh_TW', 'cp950') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 File attachment: Modeller Comparative Error.png }}} [attachment:""Modeller Comparative Error.png""] " defect closed normal Sequence fixed all ChimeraX