id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18752	ISOLDE simulation running: crash in OpenMM::CustomBondForce::~CustomBondForce()	chimerax-bug-report@…	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so"",
    ""name"" : ""QtOpenGLWidgets.abi3.so""
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    ""base"" : 13344538624,
    ""size"" : 49152,
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    ""base"" : 13342081024,
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    ""uuid"" : ""05196fb3-fabb-39f7-809e-aeb67fcfe6b1"",
    ""path"" : ""\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/_map_mask.cpython-311-darwin.so"",
    ""name"" : ""_map_mask.cpython-311-darwin.so""
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    ""uuid"" : ""3e76f489-07a8-3155-976d-31b548d0885d"",
    ""path"" : ""\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/contour_thread.cpython-311-darwin.so"",
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    ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/contourpy\/_contourpy.cpython-311-darwin.so"",
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    ""path"" : ""\/usr\/lib\/dyld"",
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    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
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  ""experiments"" : [
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/garrettskidds/Desktop/Building/PCCoat/coatvertexrecentered-1.mrc
> format mrc

No such file/path:
/Users/garrettskidds/Desktop/Building/PCCoat/coatvertexrecentered-1.mrc  

> open /Users/garrettskidds/Desktop/Building/PCCoat/CoatC5map.mrc format mrc

Opened CoatC5map.mrc as #1, grid size 576,576,576, pixel 0.92, shown at level
5.24, step 4, values float32  

> open
> /Users/garrettskidds/Desktop/Building/PCCoat/CoatHexamerAdjacentPortal_1Isolde.pdb
> format pdb

Chain information for CoatHexamerAdjacentPortal_1Isolde.pdb #2  
---  
Chain | Description  
A B C D E F | No description available  
L M N O P Q | No description available  
  

> hide atoms

> show cartoons

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #2 to IUPAC-IUB
standards.  
Chain information for CoatHexamerAdjacentPortal_1Isolde.pdb  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E 2.2/F | No description available  
2.2/L 2.2/M 2.2/N 2.2/O 2.2/P 2.2/Q | No description available  
  

> clipper associate #1 toModel #2

Opened CoatC5map.mrc as #2.1.1.1, grid size 576,576,576, pixel 0.92, shown at
step 1, values float32  

> isolde sim start /A,L,B,M,C,N,D,O,E,P,F,Q

ISOLDE: started sim  

> ui tool show ""Ramachandran Plot""

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close session

> open
> /Users/garrettskidds/phenix-1.21.2-5419/Phenix-1.21.2-5419.app/Contents/Resources/PCPortalScaffCoat250520/Autosharpen_1/Autosharpen_4/sharpened_mapC1Vertex557PostProcess.ccp4
> format ccp4

Opened sharpened_mapC1Vertex557PostProcess.ccp4 as #1, grid size 576,576,576,
pixel 0.92, shown at level 5.19, step 4, values float32  

> open /Users/garrettskidds/Desktop/PortalPCCoattrimer.pdb format pdb

Chain information for PortalPCCoattrimer.pdb #2  
---  
Chain | Description  
0 9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV | No description available  
1 2 3 4 5 D E F G H I J K L M R S b c d e f g n o p q r s z | No description available  
  

> hide atoms

> show cartoons

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 22 residues in model #2 to IUPAC-IUB
standards.  
Chain information for PortalPCCoattrimer.pdb  
---  
Chain | Description  
2.2/0 2.2/9 2.2/AA 2.2/AB 2.2/AC 2.2/AD 2.2/AE 2.2/AF 2.2/AG 2.2/AH 2.2/AI 2.2/AJ 2.2/AK 2.2/AL 2.2/AM 2.2/AN 2.2/AO 2.2/AP 2.2/AQ 2.2/AR 2.2/AS 2.2/AT 2.2/AU 2.2/AV | No description available  
2.2/1 2.2/2 2.2/3 2.2/4 2.2/5 2.2/D 2.2/E 2.2/F 2.2/G 2.2/H 2.2/I 2.2/J 2.2/K 2.2/L 2.2/M 2.2/R 2.2/S 2.2/b 2.2/c 2.2/d 2.2/e 2.2/f 2.2/g 2.2/n 2.2/o 2.2/p 2.2/q 2.2/r 2.2/s 2.2/z | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
o405-r405; 9173-AL173; 0153-AA153; AH173-AS173; 0283-AA283; AD516-AO516;
0173-AA173; 0516-AA516; AJ283-AU283; c405-f405; AK173-AV173; AB153-AM153;
R405-S405; z405-5405; AG516-AR516; AF153-AQ153; d405-g405; AE153-AP153;
AG283-AR283; 9283-AL283; 9516-AL516; AF283-AQ283; AC283-AN283; AI283-AT283;
AD283-AO283; AD173-AO173; AB173-AM173; AG173-AR173; D405-G405; AH283-AS283;
AH516-AS516; AK153-AV153; AI153-AT153; AK283-AV283; 2405-4405; AC153-AN153;
AI173-AT173; AJ173-AU173; AE283-AP283; AJ516-AU516; p405-s405; AE516-AP516;
AC173-AN173; F405-I405; AF173-AQ173; AB516-AM516; AG153-AR153; J405-L405;
AE173-AP173; AB283-AM283; n405-q405; AC516-AN516; 9153-AL153; 1405-3405;
AF516-AQ516; AI516-AT516; K405-M405; E405-H405; AJ153-AU153; b405-e405;
AD153-AO153; AK516-AV516; AH153-AS153  

> clipper associate #1 toModel #2

Opened sharpened_mapC1Vertex557PostProcess.ccp4 as #2.1.1.1, grid size
576,576,576, pixel 0.92, shown at step 1, values float32  

> isolde sim start /D-F,J-K,R,b-d,n-p,z,1-2,9,0,AB-
> AK,G-I,L-M,S,e-g,q-s,5,3-4,AL,AA,AM-AV

ISOLDE: started sim  

> ui tool show ""Ramachandran Plot""


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,1
      Model Number: MW2U3LL/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 5 days, 12 hours, 47 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
}}}
"	defect	assigned	normal		Third Party								all	ChimeraX