Opened 2 years ago

Closed 2 years ago

#9221 closed defect (can't reproduce)

Crash after opening session file

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045-SP0
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.
Windows fatal exception: code 0x800706ba

Thread 0x00000c50 (most recent call first):
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x800706ba

Thread 0x00000c50 (most recent call first):
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x800706ba

Thread 0x00000c50 (most recent call first):
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\WindowsApps\UCSF-ChimeraX-1.3-ENG-x64-R1_1.3.0.0_x64__rz2y3e1z92nne\VFS\ProgramFilesX64\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  

> ui tool show Registration

Registration server unavailable. Please try again later.  

> open "C:/Users/k2032116/Downloads/NIHMS1683160-supplement-1 (4).txt"

Unrecognized file suffix '.txt'  

> open "C:/Users/k2032116/Downloads/NIHMS1683160-supplement-1 (4).pdb"

Chain information for NIHMS1683160-supplement-1 (4).pdb #1  
---  
Chain | Description  
A B C D E F G H | No description available  
I J | No description available  
K L M N | No description available  
  

> select /J

600 atoms, 605 bonds, 74 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select /J:191

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 14 atom styles  

> select /J:194

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 8 atom styles  

> color sel red

> select /J:198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel red

> select /J:192-210

154 atoms, 154 bonds, 19 residues, 1 model selected  

> style sel stick

Changed 154 atom styles  

> style sel ball

Changed 154 atom styles  

> show sel atoms

> select /I

600 atoms, 605 bonds, 74 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select /I:192

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select /I:191

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 14 atom styles  

> select/I :194

Unknown command: select/I :194  

> select /I :194

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel atom

Expected a keyword  

> style sel stick

Changed 8 atom styles  

> colour sel red

> select /I 198

Expected a keyword  

> select /I:198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /I:198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel red

> save "C:/Users/k2032116/OneDrive - King's College London/My
> Documents/chimera sessions/Tm TnI lehman 2022.cxs"

> select /I

600 atoms, 605 bonds, 74 residues, 1 model selected  

> select /I,J

1200 atoms, 1210 bonds, 148 residues, 1 model selected  

> select ~sel

29200 atoms, 29724 bonds, 8 pseudobonds, 3700 residues, 2 models selected  

> hide sel atoms

> select /I:154-155

16 atoms, 15 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 16 atom styles  

> show sel atoms

> undo

> open "C:\Users\k2032116\OneDrive - King's College London\My Documents\TnI
> 168 175.cxs" format session

No such file/path: C:\Users\k2032116\OneDrive - King's College London\My
Documents\TnI 168 175.cxs  

> open "C:\Users\k2032116\OneDrive - King's College London\My Documents\TnI
> 168 175.cxs" format session

No such file/path: C:\Users\k2032116\OneDrive - King's College London\My
Documents\TnI 168 175.cxs  

> open "C:/Users/k2032116/OneDrive - King's College London/My
> Documents/chimera sessions/TnI 168 175.cxs"

opened ChimeraX session  

> log metadata #1

No models had metadata

> log chains #1

> view clip false

> log metadata #1

No models had metadata

> log chains #1

> show target m

> hide target m

> show target m

> select /b

1374 atoms, 1384 bonds, 170 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> open "C:\Users\k2032116\OneDrive - King's College London\My
> Documents\chimera sessions\Tm TnI lehman 2022.cxs" format session

opened ChimeraX session  

> select /I 190-210

Expected a keyword  

> select /I :190-210

176 atoms, 178 bonds, 21 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /I ILE 195 CD  

> select /I :195-210

126 atoms, 126 bonds, 16 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /I ILE 195 CD  

> select /I :196-210

118 atoms, 118 bonds, 15 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /I ILE 195 CD  

> hide sel surfaces

> style sel ball

Changed 118 atom styles  

> show sel atoms

> color (#!1 & sel) byelement

> select /g

2965 atoms, 3029 bonds, 1 pseudobond, 377 residues, 2 models selected  

> style sel sphere

Changed 2965 atom styles  

> color (#!1 & sel) byelement

> hbonds sel reveal true

376 hydrogen bonds found  
Alignment identifier is 1/G  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select /g, /b

Expected an objects specifier or a keyword  

> select /g, b

5930 atoms, 6058 bonds, 352 pseudobonds, 754 residues, 3 models selected  

> select /g, b:196-210

250 atoms, 252 bonds, 10 pseudobonds, 30 residues, 2 models selected  

> select /g, I:196-210

243 atoms, 244 bonds, 10 pseudobonds, 30 residues, 2 models selected  

> select /g:, I:196-210

Expected an objects specifier or a keyword  

> select /g:0-370, I:196-210

2889 atoms, 2950 bonds, 332 pseudobonds, 370 residues, 2 models selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hbonds sel reveal true

376 hydrogen bonds found  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /G ILE 289 CD  

> show sel surfaces

> mlp sel

Map values for surface "NIHMS1683160-supplement-1 (4).pdb_G SES surface":
minimum -30.7, mean -4.599, maximum 21.72  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /G ILE 289 CD  

> ui windowfill toggle

> open "C:\Users\k2032116\OneDrive - King's College London\My
> Documents\chimera sessions\TnI 168 175.cxs" format session

opened ChimeraX session  

> open "C:\Users\k2032116\OneDrive - King's College London\My
> Documents\chimera sessions\Tm TnI lehman 2022.cxs" format session

opened ChimeraX session  


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

Log:
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: certificate has expired (_ssl.c:1129)  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Registration




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7080
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 8,286,973,952
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10500 CPU @ 3.10GHz
OSLanguage: en-US
Locale: ('en_GB', '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 (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash after opening session file

comment:2 by Eric Pettersen, 2 years ago

Component: Core → Sessions
Resolution: → can't reproduce
Status: accepted → closed
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