Crash making weak-key dictionary based on bonds

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
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

Current thread 0x00004a28 (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
Windows fatal exception: code 0xc0000374

Thread 0x000013a4 (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 0x00004a28 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\weakref.py", line 506 in update
  File "C:\Program Files\ChimeraX 1.3\bin\lib\weakref.py", line 380 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\build_structure\tool.py", line 92 in _ab_sel_changed
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\build_structure\tool.py", line 200 in _layout_adjust_bonds
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\build_structure\tool.py", line 54 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\build_structure\__init__.py", line 35 in start_tool
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1264 in start_tool
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 554 in start_tool
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\cmd.py", line 219 in ui_tool_show
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2856 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1659 in 
  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\zeman\Documents\MassSpec\\__RQT
> results\HADDOCK_run2\cluster11_1.pdb" format pdb

Summary of feedback from opening C:\Users\zeman\Documents\MassSpec\\__RQT
results\HADDOCK_run2\cluster11_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_343w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_343.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for cluster11_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> lighting simple

> lighting soft

> lighting full

> lighting simple

> set bgColor white

> set bgColor black

> ui tool show XMAS

  
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/20211027_RQT_BS3/results/20PercentLinkFDR_CSM_xiFDR2.1.5.5.csv  
Unique peptide pairs: 338 out of 340  
Unique peptide pairs with pseudobonds: 83  
Pseudobonds are stored in
C:/Users/zeman/Documents/MassSpec/20211027_RQT_BS3/results/20PercentLinkFDR_CSM_xiFDR2.1.5.5_1.pb  
Mapping information is stored in
C:/Users/zeman/Documents/MassSpec/20211027_RQT_BS3/results/20PercentLinkFDR_CSM_xiFDR2.1.5.5_1.tsv  
Please select pseudobonds  

> hide #3 models

> hide #4 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> ~select #2

Nothing selected  

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> show #4 models

> show #2 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> close #2-4

  
Peptide pair mapping of Xi_alternative evidence file:
C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv  
Unique peptide pairs: 341 out of 412  
Unique peptide pairs with pseudobonds: 203  
Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb  
Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
SBP sulfo-SDA/sulfo-
SDA/results/RQT_sulfoSDA_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv  

> ~select #2

Nothing selected  

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> color #2 #ff5500 models transparency 0

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> show #2 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

Please select pseudobonds  

> close #3

> select /A

19339 atoms, 19665 bonds, 116 pseudobonds, 1967 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel sienna

> select /B

6291 atoms, 6380 bonds, 23 pseudobonds, 624 residues, 2 models selected  

> color sel rebecca purple

> select /C

5353 atoms, 5409 bonds, 37 pseudobonds, 530 residues, 2 models selected  

> color sel medium sea green

> color sel medium turquoise

> select /A

19339 atoms, 19665 bonds, 116 pseudobonds, 1967 residues, 2 models selected  

> color sel dark goldenrod

> select #1

30983 atoms, 31454 bonds, 180 pseudobonds, 3121 residues, 2 models selected  

> ~select #2

30983 atoms, 31454 bonds, 3121 residues, 1 model selected  

> select #2

180 pseudobonds, 1 model selected  

> ~select #2

Nothing selected  

> color #2 #b81c00 models transparency 0

> color #2 #b80003 models transparency 0

> color #2 #b80000 models transparency 0

Please select pseudobonds  
Please select pseudobonds  

> ~select #2

Nothing selected  

> select /B

6291 atoms, 6380 bonds, 23 pseudobonds, 624 residues, 2 models selected  

> ui tool show "Build Structure"


===== 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 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1060 3GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP EliteDesk 800 G4 TWR
OS: Microsoft Windows 10 Education (Build 19044)
Memory: 16,948,436,992
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
OSLanguage: en-GB
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-XMAS: 1.1.1
    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
    et-xmlfile: 1.1.0
    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
    openpyxl: 3.0.9
    openvr: 1.16.801
    packaging: 21.3
    pandas: 1.4.2
    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
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    seaborn: 0.11.2
    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