Modeller sequence/structure mismatch

[chimerax-bug-report@…]

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
(Describe the actions that caused this problem to occur here)

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 6JX7

Summary of feedback from opening 6JX7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6jx7 from
http://files.rcsb.org/download/6jx7.cif  
Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif  
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
  
6jx7 title:  
Cryo-EM structure of spike protein of feline infectious peritonitis virus
strain UU4 [more info...]  
  
Chain information for 6jx7 #1  
---  
Chain | Description  
A B C | Feline Infectious Peritonitis Virus Spike Protein  
  
Non-standard residues in 6jx7 #1  
---  
BMA — beta-D-mannopyranose  
FUC — alpha-L-fucopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"

2811 atoms, 2943 bonds, 219 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /A

9768 atoms, 10007 bonds, 2 pseudobonds, 1245 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select /C

9768 atoms, 10007 bonds, 2 pseudobonds, 1245 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> open "C:/Users/panan/OneDrive/Documents/Andi
> Pan/Scripps/Course&workshop/Structural bio
> bootcamp/exercise/canine_coronavirus.fasta"

Summary of feedback from opening C:/Users/panan/OneDrive/Documents/Andi
Pan/Scripps/Course&workshop/Structural bio
bootcamp/exercise/canine_coronavirus.fasta  
---  
note | Alignment identifier is canine_coronavirus.fasta  
  
Opened 1 sequences from canine_coronavirus.fasta  

> blastprotein canine_coronavirus.fasta:1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1629928712237-1153447976  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1629928712237-1153447976  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> ui tool show "Modeller Comparative"

> modeller comparative canine_coronavirus.fasta:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Alignment canine_coronavirus.fasta has no associated chains  

> modeller comparative canine_coronavirus.fasta:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Alignment canine_coronavirus.fasta has no associated chains  

> close session

> open 6NQD

Summary of feedback from opening 6NQD fetched from pdb  
---  
note | Fetching compressed mmCIF 6nqd from
http://files.rcsb.org/download/6nqd.cif  
  
6nqd title:  
Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195
Fab [more info...]  
  
Chain information for 6nqd #1  
---  
Chain | Description  
A E I | T/F100 Env gp120  
B F J | T/F100 Env gp41  
C G K | 8ANC195 G52K5 heavy chain, IG gamma-1 chain  
D H L | 8ANC195 G52K5 light chain  
  
Non-standard residues in 6nqd #1  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
Drag select of 20175 atoms, 18 pseudobonds, 1980 bonds  

> hide sel cartoons

> style sel stick

Changed 20175 atom styles  

> style sel ball

Changed 20175 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> hide sel atoms

> show sel atoms

> undo

> undo

> undo

> undo

> undo

> select clear

> select ::name="BMA"::name="MAN"::name="NAG"

1839 atoms, 1917 bonds, 141 residues, 1 model selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete ~sel

> undo

> delete sel

> select clear

> select clear

> select clear

Drag select of 1837 atoms, 1916 bonds  

> delete sel

> close session

> open 6NQD format mmcif fromDatabase pdb

6nqd title:  
Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195
Fab [more info...]  
  
Chain information for 6nqd #1  
---  
Chain | Description  
A E I | T/F100 Env gp120  
B F J | T/F100 Env gp41  
C G K | 8ANC195 G52K5 heavy chain, IG gamma-1 chain  
D H L | 8ANC195 G52K5 light chain  
  
Non-standard residues in 6nqd #1  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> select ::name="BMA"::name="MAN"::name="NAG"

1839 atoms, 1917 bonds, 141 residues, 1 model selected  

> delete sel

> ui tool show "Modeller Comparative"

> open "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Protein production/Immunogen/poor eCD4
> binder/homology modeling/CNE8gp120.fasta"

Summary of feedback from opening C:/Users/panan/OneDrive/Documents/Andi
Pan/Scripps/Farzan lab/B cell editing in vivo evolution/eCD4/Protein
production/Immunogen/poor eCD4 binder/homology modeling/CNE8gp120.fasta  
---  
notes | Alignment identifier is CNE8gp120.fasta  
Associated 6nqd chain A to pdb|6NQD|A Chain A, T/F100 Env gp120 with 0
mismatches  
Associated 6nqd chain E to pdb|6NQD|A Chain A, T/F100 Env gp120 with 0
mismatches  
Associated 6nqd chain I to pdb|6NQD|A Chain A, T/F100 Env gp120 with 0
mismatches  
  
Opened 1 sequences from CNE8gp120.fasta  

> modeller comparative CNE8gp120.fasta:1 multichain true numModels 4 fast
> false hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1629930289664-63533501  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629930289664-63533501  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1629930289664-63533501 finished  
  
Modeller error output  
Traceback (most recent call last):  
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, 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 141, in make  
self.homcsr(exit_stage)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr  
aln = self.read_alignment()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment  
aln.append(file=self.alnfile, align_codes=codes)  
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 82, in
append  
allow_alternates)  
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not
match that in PDB file: 1 ./6nqd_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  
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****  
check_lice_E> Invalid license key: xxx  
Go to https://salilab.org/modeller/ to get a license key,  
and then set the 'license' variable to it in the file  
/usr/lib/modeller10.1/modlib/modeller/config.py  
  
**** END IGNORED MESSAGE ****  
  
MODELLER 10.1, 2021/03/12, r12156  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2021 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 : 2021/03/12 00:18:43  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2021/08/25 15:24:49  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v1}/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 ${MODINSTALL10v1}/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 ${MODINSTALL10v1}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v1}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/xs4.mat  
rdrrwgh_268_> Number of residue types: 21  
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead  
openf___224_> Open alignment.ali  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806
0.269  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544
0.284  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583
0.298  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661
0.328  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817
0.387  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528517 516.130
0.504  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 774917 756.755
0.739  
openf___224_> Open ./6nqd_1.pdb  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 784465 766.079
0.748  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 794013 775.403
0.757  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 803561 784.728
0.766  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 813109 794.052
0.775  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 822657 803.376
0.785  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 832205 812.700
0.794  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 841753 822.024
0.803  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 851301 831.349
0.812  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 860849 840.673
0.821  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 870397 849.997
0.830  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 879945 859.321
0.839  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 889493 868.646
0.848  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 899041 877.970
0.857  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 908589 887.294
0.866  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 918137 896.618
0.876  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 927685 905.942
0.885  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 937233 915.267
0.894  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 946781 924.591
0.903  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 956329 933.915
0.912  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 965877 943.239
0.921  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 975425 952.563
0.930  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 984973 961.888
0.939  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 994521 971.212
0.948  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1004069 980.536
0.958  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1013617 989.860
0.967  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1023165 999.185
0.976  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6nqd_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:  
ATNNLWVTVYYGVPVWRDADTTLFCASDAKATEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQE  
DVISLWDQSLKPCVKLTPLCVTLNCTSATDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDNFSEYRLINCNT  
SVIKQACPKVSFDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIR  
SENLTNNAKTIIVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKL  
KEHFNNKTIVFKPSSGGDPEITMHHFNCRGEFFYCNTTKLFNSTWGTRDNGTITIPCRIKQIINMWQGVGQAMYA  
PPIKGVIKCLSNITGILLTRDGGNNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRATNNLWVTVYY  
GVPVWRDADTTLFCASDAKATEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQEDVISLWDQSLK  
PCVKLTPLCVTLNCTSATDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDNFSEYRLINCNTSVIKQACPKVS  
FDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIRSENLTNNAKTI  
IVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVF  
KPSSGGDPEITMHHFNCRGEFFYCNTTKLFNSTWGTRDNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLS  
NITGILLTRDGGNNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRATNNLWVTVYYGVPVWRDADTT  
LFCASDAKATEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVT  
LNCTSATDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDNFSEYRLINCNTSVIKQACPKVSFDPIPIHYCTP  
AGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIRSENLTNNAKTIIVHFNESVKIN  
CTRPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVFKPSSGGDPEIT  
MHHFNCRGEFFYCNTTKLFNSTWGTRDNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLSNITGILLTRDG  
GNNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRR  
  
PDB sequence matching range provided in alignment:  
ATNNLWVTVYYGVPVWRDADTTLFCASDAKATEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQE  
DVISLWDQSLKPCVKLTPLCVTLNCTSATDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDNFSEYRLINCNT  
SVIKQACPKVSFDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIR  
SENLTNNAKTIIVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKL  
KEHFNNKTIVFKPSSGGDPEITMHHFNCRGEFFYCNTTKLFNSTWGTRDNGTITIPCRIKQIINMWQGVGQAMYA  
PPIKGVIKCLSNITGILLTRDGGNNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRGLGAMIFGFLG  
AAGSTMGAASITLTVQARQLLSGIGIKQLQARVLAVERYLQDQKFLGLWGCSGKIICCTAVPWNSSWSNKTFEEI  
WNNMTWIEWEREISNYTSQIYDILTISQTQQEKNEKDLQIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNW  
VRQAPGQSLEYIGQIWRWKSSASHHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDRWSGLH  
HDGVMAFSSWGQGTLISVDIQMTQSPSTLSASTGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLG  
GVPSRFRGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKATNNLWVTVYYGVPVWRDADTTLF  
CASDAKATEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVTLN  
CTSATDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDNFSEYRLINCNTSVIKQACPKVSFDPIPIHYCTPAG  
YAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIRSENLTNNAKTIIVHFNESVKINCT  
RPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVFKPSSGGDPEITMH  
HFNCRGEFFYCNTTKLFNSTWGTRDNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLSNITGILLTRDGGN  
NETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRGLGAMIFGFLGAAGSTMGAASITLTVQARQLLSGI  
GIKQLQARVLAVERYLQDQKFLGLWGCSGKIICCTAVPWNSSWSNKTFEEIWNNMTWIEWEREISNYTSQIYDIL  
TISQTQQEKNEKDLQIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSASH  
HFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDRWSGLHHDGVMAFSSWGQGTLISVDIQMTQ  
SPSTLSASTGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVPSRFRGSAAGTDFTLTIGNLQA  
EDFGTFYCQQYDTYPGTFGQGTKVEVKATNNLWVTVYYGVPVWRDADTTLFCASDAKATEVHNVWATHACVPTDP  
NPQEMHLKNVTENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVTLNCTSATDDVRNCSFNMTTELRDKQQ  
KVYALFYKLDIVPIDNFSEYRLINCNTSVIKQACPKVSFDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQ  
CTHGIKPVVSTQLLLNGSLAEEGIIIRSENLTNNAKTIIVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGDI  
IGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVFKPSSGGDPEITMHHFNCRGEFFYCNTTKLFNSTWGTR  
DNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLSNITGILLTRDGGNNETFRPGGGNIKDNWRNELYKYKV  
VQIEPLGIAPTKCKRRGLGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIGIKQLQARVLAVERYLQDQKFLGL  
WGCSGKIICCTAVPWNSSWSNKTFEEIWNNMTWIEWEREISNYTSQIYDILTISQTQQEKNEKDLQIHLVQSGTE  
VKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSASHHFRGRVLISAVDLTGSSPPISSLE  
IKNLTSDDTAVYFCTTTSTYDRWSGLHHDGVMAFSSWGQGTLISVDIQMTQSPSTLSASTGDTVRISCRASQSIT  
GNWVAWYQQRPGKAPRLLIYRGAALLGGVPSRFRGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKV  
EVK  
  
No output models from Modeller; see log for Modeller text output.  

> ui tool show "Modeller Comparative"

> modeller comparative CNE8gp120.fasta:1 multichain true numModels 4 fast
> false hetPreserve false hydrogens false tempPath C:/Users/panan/OneDrive/桌面
> waterPreserve false

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\tool.py", line 140, in launch_modeller  
run(self.session, "modeller comparative %s multichain %s numModels %d fast %s
hetPreserve %s"  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 34, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 279, in model  
save_pdb(session, pdb_file_name, models=[structure],
polymeric_res_names=ATOM_res_names)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
OSError: Unable to open file
'C:/Users/panan/OneDrive/桌面\template_struc\6nqd_1.pdb' for writing  
  
OSError: Unable to open file
'C:/Users/panan/OneDrive/桌面\template_struc\6nqd_1.pdb' for writing  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 442.70
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,204,307,456
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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

[Eric Pettersen]

Apparently fixed in the daily build.