Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
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 0x8001010d

Thread 0x0000df0c (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 0x00006c40 (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
Fatal Python error: Aborted

Thread 0x00003978 (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 0x00006c40 (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 =====
> select ligand

390 atoms, 405 bonds, 26 residues, 1 model selected  

> show sel cartoons

> hide sel surfaces

> select /A/B/C/D/E

16834 atoms, 17114 bonds, 2 pseudobonds, 2278 residues, 2 models selected  

> hide sel cartoons

> color (#!1 & sel) dark gray

> transparency (#!1 & sel) 70

> hide sel atoms

> transparency (#!1 & sel) 50

> transparency (#!1 & sel) 30

> transparency (#!1 & sel) 80

> color (#!1 & sel) gray

> transparency (#!1 & sel) 80

> show sel cartoons

> hide sel surfaces

> select ligand

390 atoms, 405 bonds, 26 residues, 1 model selected  

> show sel surfaces

> select /A/B/C/D/E

16834 atoms, 17114 bonds, 2 pseudobonds, 2278 residues, 2 models selected  

> hide sel surfaces

> show sel surfaces

> hide sel cartoons

> show sel cartoons

> color (#!1 & sel) cornflower blue

> color (#!1 & sel) gray

> transparency (#!1 & sel) 80

> show sel cartoons

> color (#!1 & sel) cornflower blue

> transparency (#!1 & sel) 80

> color (#!1 & sel) light gray

> transparency (#!1 & sel) 80

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> color (#!1 & sel) dim gray

> transparency (#!1 & sel) 80

> ui tool show "Color Actions"

> color sel light gray

> color sel light steel blue

> transparency (#!1 & sel) 80

> select #1

17224 atoms, 17520 bonds, 2 pseudobonds, 2304 residues, 2 models selected  

> ~select #1

16 models selected  

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-1.bmp" width
> 1003 height 628 supersample 3

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-2.bmp" width
> 1003 height 628 supersample 3

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-1.bmp" width
> 1003 height 628 supersample 3

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-2.bmp" width
> 1003 height 628 supersample 3

> select ligand

390 atoms, 405 bonds, 26 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pink

> lighting soft

> select #1

17224 atoms, 17520 bonds, 2 pseudobonds, 2304 residues, 2 models selected  

> ~select #1

16 models selected  

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-2.bmp" width
> 1003 height 628 supersample 3

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/HPV16-HSPG-1.bmp" width
> 1003 height 628 supersample 3

> open 6BSP format mmcif fromDatabase pdb

6bsp title:  
High-Resolution Structure Analysis of Antibody V5 and U4 Conformational
Epitope on Human Papillomavirus 16 [more info...]  
  
Chain information for 6bsp #2  
---  
Chain | Description | UniProt  
A | U4 Heavy chain |  
B | U4 Light chain |  
C D E F G H | Major capsid protein L1 | VL1_HPV16  
  
6bsp mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> hide #!1 models

> show #!1 models

> select #1

17224 atoms, 17520 bonds, 2 pseudobonds, 2304 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,18.703,0,1,0,18.48,0,0,1,30.654

> view matrix models #1,1,0,0,30.598,0,1,0,-15.251,0,0,1,24.624

> hide #!1 models

> view matrix models #1,1,0,0,-0.69311,0,1,0,-22.37,0,0,1,26.451

> view matrix models #1,1,0,0,-60.841,0,1,0,-15.207,0,0,1,20.762

> view matrix models #1,1,0,0,-141.75,0,1,0,-56.226,0,0,1,9.0855

> ~select #1

16 models selected  

> select #1/A#1/B#1/C#1/D#1/E#2/C#2/D#2/E#2/F#2/G#2/H

38823 atoms, 39706 bonds, 2 pseudobonds, 5078 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel light steel blue

> ui mousemode right translate

> show sel & #2 surfaces

> hide sel & #!2 atoms

> ui tool show "Color Actions"

> color sel light steel blue

> transparency (#!2 & sel) 30

> transparency (#!2 & sel) 40

> volume style surface

No volumes specified  

> lighting soft

> show sel & #!2 cartoons

> select #2/A

851 atoms, 874 bonds, 109 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select #2/B

850 atoms, 871 bonds, 110 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select #2

23690 atoms, 24337 bonds, 3019 residues, 1 model selected  

> ~select #2

6 models selected  

> select #2

23690 atoms, 24337 bonds, 3019 residues, 1 model selected  

> transparency (#!2 & sel) 70

> transparency (#!2 & sel) 30

> transparency (#!2 & sel) 40

> transparency (#!2 & sel) 50

> ~select #2

6 models selected  

> select #2/A

851 atoms, 874 bonds, 109 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select #2/B

850 atoms, 871 bonds, 110 residues, 1 model selected  

> color sel wheat

> select #2

23690 atoms, 24337 bonds, 3019 residues, 1 model selected  

> ~select #2

6 models selected  

> save "C:/Users/13180/Desktop/撰写/figure/20231127 修改/U4-HPV16.bmp" width 1003
> height 628 supersample 3

> open 7DNH format mmcif fromDatabase pdb

7dnh title:  
2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in
complexed with the Fab fragment of 2H3 [more info...]  
  
Chain information for 7dnh #3  
---  
Chain | Description | UniProt  
A B C D E | Major capsid protein L1 | VL1_HPV58  
H | The heavy chain of 2H3 Fab fragment |  
L | The light chain of 2H3 Fab fragment |  
  

> hide #!2 models

> open 6BT3

6bt3 title:  
High-Resolution Structure Analysis of Antibody V5 Conformational Epitope on
Human Papillomavirus 16 [more info...]  
  
Chain information for 6bt3 #4  
---  
Chain | Description | UniProt  
A C E G | V5 Fab Light-chain |  
B D F H | V5 Fab Heavy-chain |  
I J K L M N | Major capsid protein L1 | VL1_HPV16  
  
6bt3 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> hide #3 models

> select #4/I

3675 atoms, 3776 bonds, 468 residues, 1 model selected  

> select
> #1/A#1/B#1/C#1/D#1/E#2/C#2/D#2/E#2/F#2/G#2/H#3/A#3/B#3/C#3/D#3/E#4/I#4/J#4/K#4/L#4/M#4/N

79317 atoms, 81304 bonds, 2 pseudobonds, 10211 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel light steel blue

> hide sel & #4 atoms

> show sel & #4 cartoons

> show sel & #4 surfaces

> color sel light steel blue

> transparency (#!4 & sel) 50

> select #4/B#4/D#4/F#4/H

6700 atoms, 6900 bonds, 892 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> select #4/A#4/C#4/E#4/G

6692 atoms, 6832 bonds, 880 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select #4/B#4/D#4/F#4/H

6700 atoms, 6900 bonds, 892 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pink

> color sel pale green

> select #4/A#4/C#4/E#4/G

6692 atoms, 6832 bonds, 880 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale green


===== 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  




OpenGL version: 3.3.0 - Build 31.0.101.4502
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 14 5410
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,905,961,472
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-11370H @ 3.30GHz
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: 1.31
    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
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    sphinxcontrib-qthelp: 1.0.3
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    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