Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5921 closed defect (can't reproduce)

Crash after running MatchMaker

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x000022a4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000287c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000039b8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00005564 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
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 "C:/Users/camrh/OneDrive/Documents/488-Computational Protein
> Design/pila.fasta.fasta"

Summary of feedback from opening
C:/Users/camrh/OneDrive/Documents/488-Computational Protein
Design/pila.fasta.fasta  
---  
note | Alignment identifier is pila.fasta.fasta  
  
Opened 1 sequences from pila.fasta.fasta  

> open "C:\Users\camrh\OneDrive\Documents\488-Computational Protein
> Design\pila.fasta.fasta" format fasta

Summary of feedback from opening
C:\Users\camrh\OneDrive\Documents\488-Computational Protein
Design\pila.fasta.fasta  
---  
notes | Destroying pre-existing alignment with identifier pila.fasta.fasta  
Alignment identifier is pila.fasta.fasta  
  
Opened 1 sequences from pila.fasta.fasta  

> open "C:\Users\camrh\OneDrive\Documents\488-Computational Protein
> Design\pila.fasta.fasta" format fasta

Summary of feedback from opening
C:\Users\camrh\OneDrive\Documents\488-Computational Protein
Design\pila.fasta.fasta  
---  
notes | Destroying pre-existing alignment with identifier pila.fasta.fasta  
Alignment identifier is pila.fasta.fasta  
  
Opened 1 sequences from pila.fasta.fasta  

> open "C:\Users\camrh\OneDrive\Documents\488-Computational Protein
> Design\pila.fasta.fasta" format fasta

Summary of feedback from opening
C:\Users\camrh\OneDrive\Documents\488-Computational Protein
Design\pila.fasta.fasta  
---  
notes | Destroying pre-existing alignment with identifier pila.fasta.fasta  
Alignment identifier is pila.fasta.fasta  
  
Opened 1 sequences from pila.fasta.fasta  

> open C:/Users/camrh/Downloads/1oqw_swiss.pdb

1oqw_swiss.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design
[more info...]  
  
Chain information for 1oqw_swiss.pdb #1  
---  
Chain | Description  
A | No description available  
  
Associated 1oqw_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA
[Pseudomonas aeruginosa PAO1] with 0 mismatches  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open C:/Users/camrh/Downloads/1dzo.pdb

1dzo.pdb title:  
Truncated pak pilin from pseudomonas aeruginosa [more info...]  
  
Chain information for 1dzo.pdb #2  
---  
Chain | Description | UniProt  
A | type IV pilin | FMPA_PSEAE  
  

> rainbow

> ui tool show Matchmaker

> 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 1oqw_swiss.pdb, chain A (#1) with 1dzo.pdb, chain A (#2), sequence
alignment score = 349.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  

> 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 1oqw_swiss.pdb, chain A (#1) with 1dzo.pdb, chain A (#2), sequence
alignment score = 349.1  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  

> color byattribute seq_conservation key true noValueColor gray

> key blue-white-red :-1.12 :-0.12 :0.88 showTool true

> ui mousemode right "color key"

2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884  

> color byattribute seq_conservation key true noValueColor gray palette
> rainbow

> key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true

2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884  

> ui mousemode right translate

> color byattribute seq_conservation palette rainbow key true noValueColor
> gray

> key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true

> ui mousemode right "color key"

2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884  

> ui mousemode right translate

> color byattribute seq_rmsd palette rainbow key true noValueColor gray

> key rainbow :0.03 :1.45 :2.88 :4.31 :5.74 showTool true

> ui mousemode right "color key"

2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74  

> color byattribute seq_rmsd key true noValueColor gray

> key blue-white-red :0.03 :2.88 :5.74 showTool true

2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74  

> color byattribute seq_rmsd palette rainbow key true noValueColor gray

> key rainbow :0.03 :1.45 :2.88 :4.31 :5.74 showTool true

2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74  

> save "C:/Chimera/1dzo homology modeling with correct seq.cxs"

> ui mousemode right translate

> move #1 x 5

Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 1043
atoms  

> move x 5 #1

Expected an integer >= 1 or a keyword  

> move x 5 #2

Expected an integer >= 1 or a keyword  

> help move

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

> move x 5 models #1

> open C:/Users/camrh/Downloads/1x6r_swiss.pdb
> C:/Users/camrh/Downloads/5kua_swiss.pdb

1x6r_swiss.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design
[more info...]  
  
Chain information for 1x6r_swiss.pdb #4  
---  
Chain | Description  
A | No description available  
  
5kua_swiss.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design
[more info...]  
  
Chain information for 5kua_swiss.pdb #5  
---  
Chain | Description  
A | No description available  
  
Associated 1x6r_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA
[Pseudomonas aeruginosa PAO1] with 0 mismatches  
Associated 5kua_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA
[Pseudomonas aeruginosa PAO1] with 0 mismatches  
Associated 1x6r_swiss.pdb chain A to 1oqw_swiss.pdb, chain A with 0 mismatches  
Associated 5kua_swiss.pdb chain A to 1oqw_swiss.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A, 1x6r_swiss.pdb #4/A, 5kua_swiss.pdb #5/A  

> move y 5 models #4

> move y 30 models #4

> move y 10 models #4

> move x 50 models #3

> move x -50 models #3

> move x 60 models #5

> move x -10 models #5

> rainbow

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> hide #4 models

> hide #5 models

> ui tool show Matchmaker

> matchmaker #1 to #2 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence
alignment score = 349.1  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  

> matchmaker #1 to #2 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence
alignment score = 349.1  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  

> color byattribute seq_conservation palette rainbow key true noValueColor
> gray

> key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true

> ui mousemode right "color key"

3241 atoms, 562 residues, atom seq_conservation range -1.12 to 0.884  

> ui mousemode right translate

> color byattribute seq_conservation key true noValueColor gray

> key blue-white-red :-1.12 :-0.12 :0.88 showTool true

> ui mousemode right "color key"

3241 atoms, 562 residues, atom seq_conservation range -1.12 to 0.884  

> ui mousemode right translate

> move x 30 models #1

> move x 10 models #1

> move y 30 models #3

> move y 3 models #3

> color byattribute seq_rmsd palette rainbow key true noValueColor gray

> key rainbow :18.3 :29.9 :41.5 :53.1 :64.7 showTool true

> ui mousemode right "color key"

3241 atoms, 562 residues, atom seq_rmsd range 18.3 to 64.7  

> ui mousemode right translate

> ui tool show Matchmaker

> matchmaker #1 to #2 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence
alignment score = 349.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  

> matchmaker #1 to #2 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence
alignment score = 349.1  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  


===== Log before crash end =====

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 C:/Users/camrh/Downloads/1oqw_swiss.pdb

1oqw_swiss.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design
[more info...]  
  
Chain information for 1oqw_swiss.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open C:/Users/camrh/Downloads/1dzo.pdb

1dzo.pdb title:  
Truncated pak pilin from pseudomonas aeruginosa [more info...]  
  
Chain information for 1dzo.pdb #2  
---  
Chain | Description | UniProt  
A | type IV pilin | FMPA_PSEAE  
  

> color gray

> ui tool show Matchmaker

> matchmaker #1 to #2 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence
alignment score = 349.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs:
2.078)  
  




OpenGL version: 3.3.13521 Core Profile Forward-Compatible Context 24.20.11001.8003
OpenGL renderer: Radeon RX Vega M GL Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: XPS 15 9575
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 16,982,163,456
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8705G CPU @ 3.10GHz
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: 2021.10.8
    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
    comtypes: 1.1.10
    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: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    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
    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
    pywin32: 228
    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
    tables: 3.6.1
    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
    WMI: 1.5.1

Change History (5)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash after running MatchMaker

comment:2 by pett, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed

comment:3 by Tom Goddard, 4 years ago

It crashed in the Qt event loop. Here's a complete guess. The user had run matchmaker several times with "showAlignment true". Maybe it crashed when the closed a sequence panel by clicking the close button on the title bar. That doesn't get logged. It seems that matchmaker worked fine, its output is in the log.

Maybe we should have closing any tool using its title bar close button log a "tool close xxx" command that actually does the closing. It would in general be useful to see when the user closes tools to better understand what they were doing in these crash reports.

comment:4 by Tom Goddard, 4 years ago

Crash after matchmaker #5916, also in the event loop, does not use the "showAlignment true" option throwing some water on my idea that closing a sequence panel caused the crash. Curiously this crash is in ChimeraX 1.3 from Dec 8, 2021 and #5916 is in ChimeraX 1.4 from Dec 8, 2021.

comment:5 by pett, 4 years ago

Yeah, if the close button were involved you would get a Python stack trace similar to that AlphoFold one -- the stack would be in our code that handles close-button clicks, not just in the event loop.

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