Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.4rc202205180015 (2022-05-18 00:15:17 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x0000187c (most recent call first):
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\threading.py", line 316 in wait
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\threading.py", line 574 in wait
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\threading.py", line 1297 in run
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00000a88 (most recent call first):
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\site-packages\ChimeraX_main.py", line 870 in init
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\site-packages\ChimeraX_main.py", line 1021 in 
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\runpy.py", line 87 in _run_code
  File "F:\software\ChimeraX 1.4rc202205180015\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open F:\Data\CYP文章数据整理\AlfaFold\CypAHL.cxs format session

opened ChimeraX session  

> open
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_1_model_2.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_2_model_3.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_3_model_5.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_4_model_4.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_5_model_1.pdb

Chain information for af834_relaxed_rank_1_model_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_2_model_3.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_3_model_5.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_4_model_4.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_5_model_1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close

> open
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_1_model_2.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_2_model_3.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_3_model_5.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_4_model_4.pdb
> C:/Users/13296/Downloads/ChimeraX/AlphaFold/prediction_11/af834_relaxed_rank_5_model_1.pdb

Chain information for af834_relaxed_rank_1_model_2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_2_model_3.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_3_model_5.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_4_model_4.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for af834_relaxed_rank_5_model_1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> color #1 #16b48c transparency 0

> color #1 #160b8c transparency 0

> color #1 #16718c transparency 0

> color #1 #167101 transparency 0

> color #1 #1671b1 transparency 0

> color #1 #1671b1fe

> color #1 #1671b1f7

> color #1 #1671b1c8

> color #1 #1671b1 transparency 0

> color #2 #ffceeb transparency 0

> color #2 #ff7feb transparency 0

> color #2 #ff7f0d transparency 0

> color #3 #02a0dd transparency 0

> color #3 #23a0dd transparency 0

> color #3 #239cdd transparency 0

> color #3 #239c23 transparency 0

> color #4 #d7ee90 transparency 0

> color #4 #d72990 transparency 0

> color #4 #d72929 transparency 0

> color #5 #958072 transparency 0

> color #5 #950172 transparency 0

> color #5 #956872 transparency 0

> color #5 #956801 transparency 0

> color #5 #9568bd transparency 0

> select #1/A#2/A#3/A#4/A#5/A

45045 atoms, 45495 bonds, 2920 residues, 5 models selected  

> delete atoms sel

> delete bonds sel

> select #1/C#2/C#3/C#4/C#5/C

4470 atoms, 4505 bonds, 320 residues, 5 models selected  

> delete atoms sel

> delete bonds sel

> open F:/Data/CYP文章数据整理/202211/AlphaFold/CypL-AF-E5KIB8-F1-model_v4.pdb

CypL-AF-E5KIB8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (E5KIB8) [more
info...]  
  
Chain information for CypL-AF-E5KIB8-F1-model_v4.pdb #6  
---  
Chain | Description | UniProt  
A | uncharacterized protein | E5KIB8_9ACTN  
  

> color #6 #949494 transparency 0

> ui tool show Matchmaker

> matchmaker #2-5 to #6

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 CypL-AF-E5KIB8-F1-model_v4.pdb, chain A (#6) with
af834_relaxed_rank_2_model_3.pdb, chain B (#2), sequence alignment score = 949  
RMSD between 100 pruned atom pairs is 0.970 angstroms; (across all 186 pairs:
16.832)  
  
Matchmaker CypL-AF-E5KIB8-F1-model_v4.pdb, chain A (#6) with
af834_relaxed_rank_3_model_5.pdb, chain B (#3), sequence alignment score = 949  
RMSD between 94 pruned atom pairs is 0.908 angstroms; (across all 186 pairs:
16.867)  
  
Matchmaker CypL-AF-E5KIB8-F1-model_v4.pdb, chain A (#6) with
af834_relaxed_rank_4_model_4.pdb, chain B (#4), sequence alignment score = 949  
RMSD between 97 pruned atom pairs is 0.936 angstroms; (across all 186 pairs:
16.825)  
  
Matchmaker CypL-AF-E5KIB8-F1-model_v4.pdb, chain A (#6) with
af834_relaxed_rank_5_model_1.pdb, chain B (#5), sequence alignment score = 937  
RMSD between 98 pruned atom pairs is 0.954 angstroms; (across all 186 pairs:
16.903)  
  

> close #6

> ui tool show Matchmaker

> matchmaker #2-5 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 af834_relaxed_rank_1_model_2.pdb, chain B (#1) with
af834_relaxed_rank_2_model_3.pdb, chain B (#2), sequence alignment score =
941.8  
RMSD between 180 pruned atom pairs is 0.525 angstroms; (across all 186 pairs:
1.109)  
  
Matchmaker af834_relaxed_rank_1_model_2.pdb, chain B (#1) with
af834_relaxed_rank_3_model_5.pdb, chain B (#3), sequence alignment score =
941.8  
RMSD between 180 pruned atom pairs is 0.549 angstroms; (across all 186 pairs:
0.750)  
  
Matchmaker af834_relaxed_rank_1_model_2.pdb, chain B (#1) with
af834_relaxed_rank_4_model_4.pdb, chain B (#4), sequence alignment score =
941.8  
RMSD between 182 pruned atom pairs is 0.563 angstroms; (across all 186 pairs:
0.676)  
  
Matchmaker af834_relaxed_rank_1_model_2.pdb, chain B (#1) with
af834_relaxed_rank_5_model_1.pdb, chain B (#5), sequence alignment score =
956.2  
RMSD between 182 pruned atom pairs is 0.524 angstroms; (across all 186 pairs:
0.669)  
  


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

Log:
UCSF ChimeraX version: 1.4rc202205180015 (2022-05-18)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 23.20.16.4849
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Timi
Model: TM1607
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 4,172,386,304
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) m3-7Y30 CPU @ 1.00GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205180015
    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: 1.1
    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: 1.2
    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: 1.1.1
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    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: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
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    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1