Crash in QDialog::exec(

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.5rc202210270150 (2022-10-27 01:50:44 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 110000,
  "procLaunch" : "2023-04-27 00:50:35.2791 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
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  "procStartAbsTime" : 2852960807440,
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  "captureTime" : "2023-04-27 00:51:15.3016 +0200",
  "incident" : "5CE7A14C-BC41-482C-B5BC-34BF99591FB3",
  "bug_type" : "309",
  "pid" : 45843,
  "procExitAbsTime" : 2853920828279,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5-rc2022.10.27.app\/Contents\/MacOS\/ChimeraX",
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  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "0740B69D-04DC-C6BF-9AF3-7717A25208A6",
  "wakeTime" : 12095,
  "sleepWakeUUID" : "158EC56B-5EF4-455C-8207-AE1909167411",
  "sip" : "enabled",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00000001924b3684","rawCodes":[1,6749369988],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
  "termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":45843},
  "ktriageinfo" : "VM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\n",
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Log:
UCSF ChimeraX version: 1.5rc202210270150 (2022-10-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/chand/Alphafold/AF2-Pred/Output/MTR4_PAPOLG_660_690/MTR4_PAPOLG_660_696.cxc

> open
> /Volumes/chand/Alphafold/AF2-Pred/Output/MTR4_PAPOLG_660_690/ranked_*.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_10.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_11.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_12.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_13.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_14.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_15.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_16.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_17.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_18.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_19.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_2.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_20.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_21.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_22.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_23.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_24.pdb #18  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_3.pdb #19  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_4.pdb #20  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_5.pdb #21  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_6.pdb #22  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_7.pdb #23  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_8.pdb #24  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for ranked_9.pdb #25  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> name PAPOLG_660_690 /B

> name MTR4 /A

> color PAPOLG_660_690 dark magenta

> color MTR4 cadet blue

> set bgColor white

> graphics silhouettes true

> lighting depthCue false

> mmaker all & ~#1 to #1/A

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 ranked_0.pdb, chain A (#1) with ranked_12.pdb, chain A (#5),
sequence alignment score = 5316.8  
RMSD between 719 pruned atom pairs is 0.271 angstroms; (across all 1042 pairs:
13.167)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 5372.6  
RMSD between 982 pruned atom pairs is 0.445 angstroms; (across all 1042 pairs:
1.305)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#3),
sequence alignment score = 5340.2  
RMSD between 920 pruned atom pairs is 0.595 angstroms; (across all 1042 pairs:
7.737)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_11.pdb, chain A (#4),
sequence alignment score = 5351  
RMSD between 694 pruned atom pairs is 0.289 angstroms; (across all 1042 pairs:
15.949)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_13.pdb, chain A (#6),
sequence alignment score = 5337.2  
RMSD between 701 pruned atom pairs is 0.301 angstroms; (across all 1042 pairs:
15.218)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#22),
sequence alignment score = 5352.2  
RMSD between 883 pruned atom pairs is 0.824 angstroms; (across all 1042 pairs:
11.234)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_14.pdb, chain A (#7),
sequence alignment score = 5346.8  
RMSD between 925 pruned atom pairs is 0.618 angstroms; (across all 1042 pairs:
5.489)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_15.pdb, chain A (#8),
sequence alignment score = 5324  
RMSD between 714 pruned atom pairs is 0.307 angstroms; (across all 1042 pairs:
10.747)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_16.pdb, chain A (#9),
sequence alignment score = 5348.6  
RMSD between 714 pruned atom pairs is 0.326 angstroms; (across all 1042 pairs:
9.752)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_17.pdb, chain A (#10),
sequence alignment score = 5339.6  
RMSD between 729 pruned atom pairs is 0.319 angstroms; (across all 1042 pairs:
8.718)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_18.pdb, chain A (#11),
sequence alignment score = 5320.4  
RMSD between 721 pruned atom pairs is 0.304 angstroms; (across all 1042 pairs:
11.114)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_19.pdb, chain A (#12),
sequence alignment score = 5319.2  
RMSD between 726 pruned atom pairs is 0.286 angstroms; (across all 1042 pairs:
11.676)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#13),
sequence alignment score = 5375.6  
RMSD between 996 pruned atom pairs is 0.283 angstroms; (across all 1042 pairs:
1.084)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_20.pdb, chain A (#14),
sequence alignment score = 5339.6  
RMSD between 803 pruned atom pairs is 0.550 angstroms; (across all 1042 pairs:
7.600)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_21.pdb, chain A (#15),
sequence alignment score = 5325.2  
RMSD between 731 pruned atom pairs is 0.305 angstroms; (across all 1042 pairs:
8.407)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_22.pdb, chain A (#16),
sequence alignment score = 5346.2  
RMSD between 731 pruned atom pairs is 0.321 angstroms; (across all 1042 pairs:
8.684)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_23.pdb, chain A (#17),
sequence alignment score = 5357  
RMSD between 932 pruned atom pairs is 0.673 angstroms; (across all 1042 pairs:
7.666)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_24.pdb, chain A (#18),
sequence alignment score = 5334.2  
RMSD between 725 pruned atom pairs is 0.322 angstroms; (across all 1042 pairs:
6.130)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#19),
sequence alignment score = 5366  
RMSD between 982 pruned atom pairs is 0.675 angstroms; (across all 1042 pairs:
1.678)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#20),
sequence alignment score = 5368.4  
RMSD between 981 pruned atom pairs is 0.510 angstroms; (across all 1042 pairs:
1.467)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#21),
sequence alignment score = 5336.6  
RMSD between 926 pruned atom pairs is 0.593 angstroms; (across all 1042 pairs:
9.312)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#23),
sequence alignment score = 5352.2  
RMSD between 701 pruned atom pairs is 0.310 angstroms; (across all 1042 pairs:
13.219)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#24),
sequence alignment score = 5352.2  
RMSD between 930 pruned atom pairs is 0.553 angstroms; (across all 1042 pairs:
6.249)  
  
Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#25),
sequence alignment score = 5359.4  
RMSD between 973 pruned atom pairs is 0.774 angstroms; (across all 1042 pairs:
5.328)  
  

> color byelement

> hide /A :1-80 cartoons

executed MTR4_PAPOLG_660_696.cxc  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 6 days 12:59

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210270150
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.5
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0