Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5045 closed defect (fixed)

Modeller sequence mismatch failure

Reported by: yen-li.li@… Owned by: pett
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 <module>  
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 <module>  
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 <module>  
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 <module>  
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 <module>  
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 <module>  
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

Modeller Comparative Error.png​

Attachments (1)

Modeller Comparative Error.png​ (252.8 KB ) - added by yen-li.li@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (8)

by yen-li.li@…, 4 years ago

Attachment: Modeller Comparative Error.png​ added

Added by email2trac

comment:1 by pett, 4 years ago

Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller sequence mismatch failure

comment:2 by pett, 4 years ago

I am in communication with the Modeller group, and it's still a little unclear at this point whether this is a Modeller problem or a ChimeraX problem. Until this is fixed, I believe you have to delete parts of the complex that are not being used as templates. I don't know if the resulting models will be satisfactory or not -- but I believe the job will run.

in reply to:  4 comment:3 by Yen-Li.Li@…, 4 years ago 

Thank you for your help, Eric. I would like to build a homology model for a tetrameric complex. I could build homology models using two proteins as templates, but the other two proteins always have issues. I'm looking forward to hearing that if the issue can be resolved in the future. Thank you.

Yen-Li
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 13, 2021 6:12 PM
Cc: PETTERSEN, ERIC <pett@cgl.ucsf.edu>; Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5045: Modeller sequence mismatch failure

#5045: Modeller sequence mismatch failure
----------------------------------+----------------------------
          Reporter:  yen-li.li@…  |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  accepted
          Priority:  normal       |  Milestone:
         Component:  Sequence     |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------

Comment (by Eric Pettersen):

 I am in communication with the Modeller group, and it's still a little
 unclear at this point whether this is a Modeller problem or a ChimeraX
 problem.  Until this is fixed, I believe you have to delete parts of the
 complex that are not being used as templates.  I don't know if the
 resulting models will be satisfactory or not -- but I believe the job will
 run.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5045#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Tomorrow's daily build should work without the delete-chains hocus pocus I mentioned before.

in reply to:  6 comment:5 by Yen-Li.Li@…, 4 years ago 

Hi Eric,

Thank you for the update. Is it possible to renumber the residue number of chains in Chimera X? After building homology model for two proteins (chain A: 182 residues; chain B: 192 residues) with modeller comparative, these two proteins were combined into a single model file and chain B was renumbered from 183-374. I would like to make chain B residues starting from 1 to 192.
Thank you

Yen-Li
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 16, 2021 3:27 PM
Cc: PETTERSEN, ERIC <pett@cgl.ucsf.edu>; Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5045: Modeller sequence mismatch failure

#5045: Modeller sequence mismatch failure
----------------------------------+----------------------------
          Reporter:  yen-li.li@…  |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Sequence     |    Version:
        Resolution:  fixed        |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Tomorrow's daily build should work without the delete-chains hocus pocus I
 mentioned before.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5045#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:6 by pett, 4 years ago

There is no command for renumbering residues in ChimeraX yet. It is really easy to do in ChimeraX's Python shell if you know Python. If you do know Python, let me know and I'll send instructions.

--Eric

in reply to:  8 comment:7 by Yen-Li.Li@…, 4 years ago 

Hi Eric,

Thank you for your email. I used chimera to renumber the residue and then imported the file to chimera X for subsequent work.

Best,
Yen-Li
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, August 25, 2021 11:20 AM
Cc: PETTERSEN, ERIC <pett@cgl.ucsf.edu>; Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5045: Modeller sequence mismatch failure

#5045: Modeller sequence mismatch failure
----------------------------------+----------------------------
          Reporter:  yen-li.li@…  |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Sequence     |    Version:
        Resolution:  fixed        |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------

Comment (by Eric Pettersen):

 There is no command for renumbering residues in ChimeraX yet.  It is
 really easy to do in ChimeraX's Python shell if you know Python.  If you
 do know Python, let me know and I'll send instructions.

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5045#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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