Opened 4 years ago

Closed 4 years ago

#6353 closed defect (duplicate)

model loops: chain not in match maps

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chrismuriel/Downloads/lcl_V.fischeri x lcl_V.cholera.aln"

Cannot open files: Syntax error in ALN file 'lcl_V.fischeri x
lcl_V.cholera.aln': First non-blank line does not start with 'CLUSTAL'  

> open "/Users/chrismuriel/Downloads/lcl_V.fischeri x lcl_V.cholera.aln"

Cannot open files: Syntax error in ALN file 'lcl_V.fischeri x
lcl_V.cholera.aln': First non-blank line does not start with 'CLUSTAL'  

> open "/Users/chrismuriel/Downloads/model1_5m7nA (1).pdb"

Summary of feedback from opening /Users/chrismuriel/Downloads/model1_5m7nA
(1).pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3348 messages similar to the above omitted  
  
Chain information for model1_5m7nA (1).pdb #1  
---  
Chain | Description  
Q | No description available  
T | No description available  
  

> open "/Users/chrismuriel/Downloads/AF-Q9KN48-F1-model_v2 (1).pdb"

AF-Q9KN48-F1-model_v2 (1).pdb title:  
Alphafold monomer V2.0 prediction for transcriptional regulator vash (Q9KN48)
[more info...]  
  
Chain information for AF-Q9KN48-F1-model_v2 (1).pdb #2  
---  
Chain | Description | UniProt  
A | transcriptional regulator vash | VASH_VIBCH  
  

> select #1

11706 atoms, 11832 bonds, 972 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #1

11706 atoms, 11832 bonds, 972 residues, 1 model selected  

> ~select #1

Nothing selected  

> color bynucleotide

> show atoms

[Repeated 1 time(s)]

> hide atoms

> log metadata #1

The model has no metadata

> log chains #1

Chain information for model1_5m7nA (1).pdb #1  
---  
Chain | Description  
Q | No description available  
T | No description available  
  

> open "/Users/chrismuriel/Desktop/vasH/VasH_V.cholerae prediction
> model/model1_1ny5B.pdb"

Summary of feedback from opening
/Users/chrismuriel/Desktop/vasH/VasH_V.cholerae prediction
model/model1_1ny5B.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3094 messages similar to the above omitted  
  
Chain information for model1_1ny5B.pdb #3  
---  
Chain | Description  
Q | No description available  
T | No description available  
  

> hide #1 models

> show #1 models

> hide #1 models

> view #3 clip false

[Repeated 1 time(s)]

> show #3 target m

> style #2-3 sphere

Changed 15625 atom styles  

> set bgColor white

> set bgColor black

> lighting simple

> lighting soft

> lighting full

Alignment identifier is 1  
Alignment identifier is 1/T  
Alignment identifier is 3/T  

> select #3/T:214

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/T:214-219

36 atoms, 36 bonds, 6 residues, 1 model selected  

> sequence associate #2/A 3/T

Associated AF-Q9KN48-F1-model_v2 (1).pdb chain A to chain T with 272
mismatches and/or gaps  

> sequence associate #2/A 3/T

Disassociated AF-Q9KN48-F1-model_v2 (1).pdb chain A from chain T  
Associated AF-Q9KN48-F1-model_v2 (1).pdb chain A to chain T with 272
mismatches and/or gaps  

> show #3 target m

> style sel sphere

Changed 36 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> rainbow sel

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for model1_1ny5B.pdb_T SES surface #3.1: minimum, -16.92,
mean -1.33, maximum 15.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> ui tool show "Model Loops"

<QNSWindow: 0x7fadacba3fa0; contentView=<QNSView: 0x7fadae1148f0;
QCocoaWindow(0x7fadae18cc50, window=QWidgetWindow(0x7fadab2e7ef0,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
<QNSWindow: 0x7fadc8980970; contentView=<QNSView: 0x7fadac8b19e0;
QCocoaWindow(0x7fadab195070, window=QWidgetWindow(0x7fadc4433320,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast true
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast true
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol standard

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

> modeller refine 1/T:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol standard

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

> modeller refine 1/T:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol standard

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

> modeller refine 1/T:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol standard

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

> ui tool show "Model Loops"

<QNSWindow: 0x7fadc5fecb20; contentView=<QNSView: 0x7fadc40c4a20;
QCocoaWindow(0x7fadc0a78ad0, window=QWidgetWindow(0x7fadc5fe9b90,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
<QNSWindow: 0x7fadc5d2d350; contentView=<QNSView: 0x7fadc15fccb0;
QCocoaWindow(0x7fadab5d2970, window=QWidgetWindow(0x7fadc61b8ea0,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast true
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

> modeller refine 1/T:1:all-missing 3/T:1:all-missing numModels 5 fast true
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller  
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
KeyError: <chimerax.atomic.molobject.Chain object at 0x7fadbf946a90>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model  
mmap = seq.match_maps[chain]  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook
      Model Identifier: MacBook10,1
      Processor Name: Dual-Core Intel Core m3
      Processor Speed: 1.2 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 447.80.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.42f13

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 2 days 22:41

Graphics/Displays:

    Intel HD Graphics 615:

      Chipset Model: Intel HD Graphics 615
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591e
      Revision ID: 0x0002
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2304 x 1440 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Prediction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → model loops: chain not in match maps

comment:2 by pett, 4 years ago

Resolution: → duplicate
Status: accepted → closed
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