Modeller: UnboundLocalError: local variable 'target_name'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202011130655 (2020-11-13 06:55:07 UTC)
Description
Trying to run modeller using uniprot fetched sequence oprd_human and 4kdl as a template that I associated with the sequence.

Log:
UCSF ChimeraX version: 1.2.dev202011130655 (2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open oprd_human fromDatabase uniprot

Summary of feedback from opening oprd_human fetched from uniprot  
---  
note | Alignment identifier is oprd_human  
  
Opened UniProt oprd_human  

> open 4dkl

4dkl title:  
Crystal structure of the mu-opioid receptor bound to a morphinan antagonist
[more info...]  
  
Chain information for 4dkl #1  
---  
Chain | Description  
A | Mu-type opioid receptor, lysozyme chimera  
  
Non-standard residues in 4dkl #1  
---  
1PE — pentaethylene glycol (PEG400)  
BF0 — methyl
4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate
(beta-funaltrexamine, bound form)  
CL — chloride ion  
CLR — cholesterol  
MPG — [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate  
SO4 — sulfate ion  
  
4dkl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sequence associate /A oprd_human:1

Associated 4dkl chain A to oprd_human with 166 mismatches and/or gaps  

> ui tool show "Modeller Comparative"

Traceback (most recent call last):  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 515, in <lambda>  
% (fmt.nicknames[0], StringArg.unparse(self.alignment.ident))))  
AttributeError: 'bool' object has no attribute 'nicknames'  
  
AttributeError: 'bool' object has no attribute 'nicknames'  
  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 515, in  
% (fmt.nicknames[0], StringArg.unparse(self.alignment.ident))))  
  
See log for complete Python traceback.  
  

> modeller comparative oprd_human:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> modeller comparative oprd_human:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> modeller comparative oprd_human: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: appModeller9v8Service1606366360648-2101771674  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1606366360648-2101771674  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1606366360648-2101771674 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 ./4dkl_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 watson.cgl.ucsf.edu
3.10.0-1127.19.1.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): 2020/11/25 20:52:40  
  
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  
openf___224_> Open ./4dkl_1.pdb  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 402241 392.813
0.384  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 411789 402.138
0.393  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./4dkl_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:  
MVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNIL  
CKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGS  
IDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRGTWDAYEKDRNLRRITRMVLVVVAVF  
IVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCI  
  
PDB sequence matching range provided in alignment:  
MVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNIL  
CKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGS  
IDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRNIFEMLRIDEGLRLKIYKNTEGYYTI  
GIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINM  
VFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYEKDRNLRRITRMVLVV  
VAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCI  
  
No output models from Modeller; see log for Modeller text output.  

> ui tool show "Modeller Comparative"

> ui tool show "Modeller Comparative"

> modeller comparative oprd_human:1 multichain false numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/cmd.py", line 34, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 215, in model  
pir_target = Sequence(name=target_name)  
UnboundLocalError: local variable 'target_name' referenced before assignment  
  
UnboundLocalError: local variable 'target_name' referenced before assignment  
  
File "/Users/goddard/ucsf/chimerax-
pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 215, in model  
pir_target = Sequence(name=target_name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

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Software:

    System Software Overview:

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Locale: ('en_US', 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
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    wheel: 0.35.1

[goddard@…]

First I ran modeller with default basic settings and it said modeller produced no models and modeller output said "Alignment sequence does not match that in PDB file: 1 ./4dkl_1.pdb".  I am not sure if that is an error and the reason for not producing any models.

Then I unclicked the "Make multichain model..." checkbutton and ran modeller again and got the traceback.

[Eric Pettersen]

Currently I cannot open any UniProt entries in Chimera or ChimeraX due to what looks like a failure/bug in the UniProt web site. I can still work on the problem in this ticket using my own alignment though.

[Eric Pettersen]

I have poked the UniProt people.

[Eric Pettersen]

Have committed.a fix for this problem as exhibited by my sequence-alignment test case.

[Eric Pettersen]

Need to wait for UniProt to come "back online" to verify that the problems in the ticket are also resolved.

[Eric Pettersen]

The fix isn't sufficient to get the case in this ticket to work (though undoubtedly also necessary). So, needs more work...