Opened 3 years ago

Closed 3 years ago

#7866 closed defect (can't reproduce)

Crash in event loop after MatchMaker

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core 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-10-10.0.22000
ChimeraX Version: 1.4.dev202201020113 (2022-01-02 01:13:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x0000d1f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x0000b5f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\site-packages\chimerax\ui\gui.py", line 316 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202201020113\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open C:/Users/zhiyi/Desktop/SARS-
> COV-2/5514_5840_Omicron_s6p/5840_5514_global_model-
> coot-3_real_space_refined.pdb

Chain information for 5840_5514_global_model-coot-3_real_space_refined.pdb #1  
---  
Chain | Description  
A C H | No description available  
B D G | No description available  
E | No description available  
F | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select clear

> ui mousemode right select

Drag select of 127 atoms, 3898 residues, 20 pseudobonds, 125 bonds  

> color (#!1 & sel) light gray

> select clear

> open C:/Users/zhiyi/Desktop/pdb.cif

Summary of feedback from opening C:/Users/zhiyi/Desktop/pdb.cif  
---  
warnings | Unknown polymer entity '1' near line 37  
Unknown polymer entity '2' near line 2080  
Skipping residue with duplicate label_seq_id 52 in chain B  
Skipping residue with duplicate label_seq_id 82 in chain B  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for pdb.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain A (#1)
with pdb.cif, chain B (#2), sequence alignment score = 244.3  
RMSD between 72 pruned atom pairs is 1.188 angstroms; (across all 110 pairs:
2.875)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain B (#1)
with pdb.cif, chain A (#2), sequence alignment score = 296.3  
RMSD between 92 pruned atom pairs is 1.012 angstroms; (across all 105 pairs:
1.638)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain A (#1)
with pdb.cif, chain B (#2), sequence alignment score = 244.3  
RMSD between 72 pruned atom pairs is 1.188 angstroms; (across all 110 pairs:
2.875)  
  

> ui mousemode right select

Drag select of 168 atoms, 4325 residues, 20 pseudobonds, 160 bonds  

> hide sel atoms

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain B (#1)
with pdb.cif, chain A (#2), sequence alignment score = 296.3  
RMSD between 92 pruned atom pairs is 1.012 angstroms; (across all 105 pairs:
1.638)  
  

> open C:/Users/zhiyi/Desktop/pdb.cif

Summary of feedback from opening C:/Users/zhiyi/Desktop/pdb.cif  
---  
warnings | Unknown polymer entity '1' near line 37  
Unknown polymer entity '2' near line 2080  
Skipping residue with duplicate label_seq_id 52 in chain B  
Skipping residue with duplicate label_seq_id 82 in chain B  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for pdb.cif #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #3 to #1/G pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain G (#1)
with pdb.cif, chain A (#3), sequence alignment score = 296.3  
RMSD between 92 pruned atom pairs is 1.012 angstroms; (across all 105 pairs:
1.638)  
  

> ui tool show Matchmaker

> matchmaker #3 to #1/H pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain H (#1)
with pdb.cif, chain B (#3), sequence alignment score = 244.3  
RMSD between 72 pruned atom pairs is 1.188 angstroms; (across all 110 pairs:
2.875)  
  

> ui mousemode right select

Drag select of 4752 residues, 20 pseudobonds, 41 atoms, 35 bonds  

> hide sel atoms

> select clear

> ui tool show Matchmaker

> matchmaker #3 to #1/G pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain G (#1)
with pdb.cif, chain A (#3), sequence alignment score = 296.3  
RMSD between 92 pruned atom pairs is 1.012 angstroms; (across all 105 pairs:
1.638)  
  

> open C:/Users/zhiyi/Desktop/pdb.cif

Summary of feedback from opening C:/Users/zhiyi/Desktop/pdb.cif  
---  
warnings | Unknown polymer entity '1' near line 37  
Unknown polymer entity '2' near line 2080  
Skipping residue with duplicate label_seq_id 52 in chain B  
Skipping residue with duplicate label_seq_id 82 in chain B  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for pdb.cif #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #4 to #1/C pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain C (#1)
with pdb.cif, chain B (#4), sequence alignment score = 244.3  
RMSD between 72 pruned atom pairs is 1.188 angstroms; (across all 110 pairs:
2.875)  
  

> ui tool show Matchmaker

> matchmaker #4 to #1/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain D (#1)
with pdb.cif, chain A (#4), sequence alignment score = 296.3  
RMSD between 92 pruned atom pairs is 1.012 angstroms; (across all 105 pairs:
1.638)  
  

> ui mousemode right select

Drag select of 5179 residues, 20 pseudobonds, 41 atoms, 35 bonds  

> hide sel atoms

> select clear

> cartoon style thickness 0.7

> lighting soft

> ui tool show Matchmaker

> matchmaker #4 to #1/C pairing bs

Parameters  
---  
Chain pairing | bs  
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 5840_5514_global_model-coot-3_real_space_refined.pdb, chain C (#1)
with pdb.cif, chain B (#4), sequence alignment score = 244.3  
RMSD between 72 pruned atom pairs is 1.188 angstroms; (across all 110 pairs:
2.875)  
  


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

Log:
UCSF ChimeraX version: 1.4.dev202201020113 (2022-01-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 512.36
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82JQ
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 17,024,741,376
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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: 1.32.1
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    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: 1.4.dev202201020113
    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-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: 1.1.5
    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: 2.0.5
    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: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    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: 1.8
    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: 1.7.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    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: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.15.2
    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: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.0
    docutils: 0.17.1
    entrypoints: 0.3
    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: 6.6.0
    ipython: 7.30.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.1
    jupyter-client: 7.1.0
    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
    nest-asyncio: 1.5.4
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.24
    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: 5.2.2
    QtPy: 2.0.0
    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: 3.7.0
    tifffile: 2021.4.8
    tinyarray: 1.2.4
    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 (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop after MatchMaker

comment:2 by Eric Pettersen, 3 years ago

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