KeyError in floating-tool dict after de-iconfiy

[daysehuang20@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209232318 (2022-09-23 23:18:29 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209232318 (2022-09-23)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/daysehuang/Downloads/ChimeraX/PDB/2h4f.cif

2h4f.cif title:  
Sir2-p53 peptide-NAD+ [more info...]  
  
Chain information for 2h4f.cif #1  
---  
Chain | Description | UniProt  
A | NAD-dependent deacetylase | NPD_THEMA  
D | Cellular tumor antigen p53 | P53_HUMAN  
  
Non-standard residues in 2h4f.cif #1  
---  
NAD — nicotinamide-adenine-dinucleotide  
ZN — zinc ion  
  

> open /Users/daysehuang/Downloads/ChimeraX/PDB/2h4f.cif

2h4f.cif title:  
Sir2-p53 peptide-NAD+ [more info...]  
  
Chain information for 2h4f.cif #2  
---  
Chain | Description | UniProt  
A | NAD-dependent deacetylase | NPD_THEMA  
D | Cellular tumor antigen p53 | P53_HUMAN  
  
Non-standard residues in 2h4f.cif #2  
---  
NAD — nicotinamide-adenine-dinucleotide  
ZN — zinc ion  
  

> close session

> ui tool show "Modeller Comparative"

> open /Users/daysehuang/Downloads/2KDL.fasta

Summary of feedback from opening /Users/daysehuang/Downloads/2KDL.fasta  
---  
note | Alignment identifier is 2KDL.fasta  
  
Opened 1 sequences from 2KDL.fasta  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> open /Users/daysehuang/Downloads/2KDL.fasta

Summary of feedback from opening /Users/daysehuang/Downloads/2KDL.fasta  
---  
notes | Destroying pre-existing alignment with identifier 2KDL.fasta  
Alignment identifier is 2KDL.fasta  
  
Opened 1 sequences from 2KDL.fasta  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> modeller comparative 2KDL.fasta:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment 2KDL.fasta has no associated chains  

> open /Users/daysehuang/Downloads/2KDL.fasta format fasta

Summary of feedback from opening /Users/daysehuang/Downloads/2KDL.fasta  
---  
notes | Destroying pre-existing alignment with identifier 2KDL.fasta  
Alignment identifier is 2KDL.fasta  
  
Opened 1 sequences from 2KDL.fasta  

> ui tool show AlphaFold

Populating font family aliases took 819 ms. Replace uses of missing font
family "Segoe UI" with one that exists to avoid this cost.  

> open /Users/daysehuang/Downloads/2KDL.fasta format fasta

Summary of feedback from opening /Users/daysehuang/Downloads/2KDL.fasta  
---  
notes | Destroying pre-existing alignment with identifier 2KDL.fasta  
Alignment identifier is 2KDL.fasta  
  
Opened 1 sequences from 2KDL.fasta  

> ui tool show "Modeller Comparative"

> modeller comparative 2KDL.fasta:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment 2KDL.fasta has no associated chains  

> alphafold predict TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 3 time(s)]

> open /Users/daysehuang/Downloads/2KDL-clean.pdb

Chain information for 2KDL-clean.pdb #1  
---  
Chain | Description  
A | No description available  
  
Associated 2KDL-clean.pdb chain A to chain A with 0 mismatches  

> color bfactor #1 palette alphafold

919 atoms, 56 residues, atom bfactor range 0 to 0  

> undo

Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 614, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 719, in hide_floating_tools  
tw._mw_set_shown(True)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2199, in _mw_set_shown  
self.__toolkit.shown = shown  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2199, in _mw_set_shown  
self.__toolkit.shown = shown  
  
See log for complete Python traceback.  
  
AlphaFold prediction finished  
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_1  

> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to chain A with 0 mismatches  

> hide #1 models

> Color factor #1 palette alphafold

Unknown command: Color factor #1 palette alphafold  

> color factor #1 palette alphafold

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> show #1 models

> align #1/A:1-56@CA toAtoms #2/A:1-56@CA

RMSD between 56 atom pairs is 4.544 angstroms  

> align #1/A:8-52@CA toAtoms #2/A:8-52@CA

RMSD between 45 atom pairs is 1.302 angstroms  

> save "/Users/daysehuang/Downloads/sequence strcuture 2kdl.pdb"

> close session

> open /Users/daysehuang/Downloads/2KDM.fasta

Error processing trigger "new alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Summary of feedback from opening /Users/daysehuang/Downloads/2KDM.fasta  
---  
notes | Alignment identifier is 2KDM.fasta  
Traceback (most recent call last):  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
  
return self._func(self._name, data)  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
  
  
  
Opened 1 sequences from 2KDM.fasta  

> open /Users/daysehuang/Downloads/2KDM.fasta format fasta

Error processing trigger "destroy alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Error processing trigger "new alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Summary of feedback from opening /Users/daysehuang/Downloads/2KDM.fasta  
---  
notes | Destroying pre-existing alignment with identifier 2KDM.fasta  
Traceback (most recent call last):  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
  
return self._func(self._name, data)  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
  
Alignment identifier is 2KDM.fasta  
Traceback (most recent call last):  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
  
return self._func(self._name, data)  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
  
  
  
Opened 1 sequences from 2KDM.fasta  

> ui tool show AlphaFold

> alphafold predict TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE

Running AlphaFold prediction  

> alphafold predict TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2  

> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to chain A with 0 mismatches  
AlphaFold prediction finished  
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2  

> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to chain A with 0 mismatches  

> open /Users/daysehuang/Downloads/2KDM-clean.pdb

Chain information for 2KDM-clean.pdb #3  
---  
Chain | Description  
A | No description available  
  
Associated 2KDM-clean.pdb chain A to chain A with 0 mismatches  

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain A (#1) with 2KDM-clean.pdb, chain A (#3),
sequence alignment score = 280.1  
RMSD between 51 pruned atom pairs is 1.026 angstroms; (across all 56 pairs:
1.307)  
  

> align #1/A:1-56@CA toAtoms #2/A:1-56@CA

RMSD between 56 atom pairs is 0.000 angstroms  
Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
Error processing trigger "destroy alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  

> hide #1 models

> save "/Users/daysehuang/Downloads/sequence 2kdm.pdb"

> close session

> open "/Users/daysehuang/Downloads/sequence strcuture 2kdl.pdb" format pdb

Chain information for sequence strcuture 2kdl.pdb  
---  
Chain | Description  
1.1/A 1.2/A | No description available  
  

> open "/Users/daysehuang/Downloads/sequence strcuture 2kdl.pdb"

Chain information for sequence strcuture 2kdl.pdb  
---  
Chain | Description  
2.1/A 2.2/A | No description available  
  

> close session

> open /Users/daysehuang/Downloads/2KDM-clean.pdb format pdb

Chain information for 2KDM-clean.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/daysehuang/Downloads/2KDL-clean.pdb

Chain information for 2KDL-clean.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2KDM-clean.pdb, chain A (#1) with 2KDL-clean.pdb, chain A (#2),
sequence alignment score = 115.3  
RMSD between 5 pruned atom pairs is 1.065 angstroms; (across all 56 pairs:
15.446)  
  

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 312, in set_value  
self.widget.setChecked(value)  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 312, in set_value  
self.widget.setChecked(value)  
  
See log for complete Python traceback.  
  

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2KDM-clean.pdb, chain A (#1) with 2KDL-clean.pdb, chain A (#2),
sequence alignment score = 115.3  
Alignment identifier is 1  
Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
Error processing trigger "new alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
Error processing trigger "destroy alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Traceback (most recent call last):  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
Error processing trigger "new alignment":  
RuntimeError: wrapped C/C++ object of type AlignmentListWidget has been
deleted  
  
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/DCAC8711-3CC2-4BBC-A5F9-C58686E419B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/widgets.py", line 34, in _items_change  
self.alignments_changed.emit(self.session.alignments.alignments)  
  
See log for complete Python traceback.  
  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 2KDM-clean.pdb #1/A, 2KDL-
clean.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 5 pruned atom pairs is 1.065 angstroms; (across all 56 pairs:
15.446)  
  




OpenGL version: 4.1 INTEL-16.5.9
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.6.5 (20G527)
      Kernel Version: Darwin 20.6.0
      Time since boot: 1 day 6:23

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209232318
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

[Eric Pettersen]

Hi Dayse,

Thanks for reporting this problem. I have committed a fix for the issue which will be in tomorrow's daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

fix: ​https://github.com/RBVI/ChimeraX/commit/7fc6d5376d96c4c97970a30897a53becdc5d00cc