Opened 2 years ago

Closed 2 years ago

#9993 closed defect (can't reproduce)

Crash in coulombic in assign_charges()

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-valve37-1-neptune-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202308212127 (2023-08-21 21:27:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f34c17fe640 (most recent call first):
  File "/app/lib/python3.11/threading.py", line 324 in wait
  File "/app/lib/python3.11/threading.py", line 622 in wait
  File "/app/lib/python3.11/threading.py", line 1392 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f35e43b8740 (most recent call first):
  Garbage-collecting
  File "/app/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 150 in 
  File "/app/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 150 in __iter__
  File "/app/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 66 in assign_charges
  File "/app/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 88 in cmd_coulombic
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 513 in run
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 570 in run_expanded_command
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 61 in func_plus_tip
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 327 in run
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 408 in run_shortcut
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 390 in try_shortcut
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1355 in run_provider
  File "/app/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 55 in run_provider
  File "/app/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1291 in run_provider
  File "/app/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
  File "/app/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
  File "/app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 52)
===== Log before crash start =====
UCSF ChimeraX version: 1.7.dev202308212127 (2023-08-21)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/deck/Documents/Ülikool/1hew.pdb format pdb

1hew.pdb title:  
Refinement of an enzyme complex with inhibitor bound At partial occupancy. Hen
egg-white lysozyme and tri-N-acetylchitotriose At 1.75 angstroms resolution
[more info...]  
  
Chain information for 1hew.pdb #1  
---  
Chain | Description | UniProt  
A | hen egg white lysozyme | LYC_CHICK 1-129  
  
Non-standard residues in 1hew.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 1147 atom styles  

> style sphere

Changed 1147 atom styles  

> undo

> style ball

Changed 1147 atom styles  

> color bynucleotide

> color byhetero

> color bynucleotide

> color byhetero

> color bychain

> color bynucleotide

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1hew.pdb_A SES surface #1.1: minimum, -10.83, mean 1.95,
maximum 10.75  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow

> color bynucleotide

> color bfactor

1147 atoms, 235 residues, 1 surfaces, atom bfactor range 0.01 to 151  

> nucleotides slab

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color bynucleotide

> view

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting full

> lighting soft

> lighting simple

> lighting soft

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> volume hide

No volumes specified  

> open /home/deck/Documents/Ülikool/1hew.pdb

1hew.pdb title:  
Refinement of an enzyme complex with inhibitor bound At partial occupancy. Hen
egg-white lysozyme and tri-N-acetylchitotriose At 1.75 angstroms resolution
[more info...]  
  
Chain information for 1hew.pdb #2  
---  
Chain | Description | UniProt  
A | hen egg white lysozyme | LYC_CHICK 1-129  
  
Non-standard residues in 1hew.pdb #2  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> close session

> open /home/deck/Documents/Ülikool/1hew.pdb format pdb

1hew.pdb title:  
Refinement of an enzyme complex with inhibitor bound At partial occupancy. Hen
egg-white lysozyme and tri-N-acetylchitotriose At 1.75 angstroms resolution
[more info...]  
  
Chain information for 1hew.pdb #1  
---  
Chain | Description | UniProt  
A | hen egg white lysozyme | LYC_CHICK 1-129  
  
Non-standard residues in 1hew.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> show atoms

> hide atoms

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show atoms

> hide atoms

> show cartoons

> style stick

Changed 1147 atom styles  

> hide cartoons

> style sphere

Changed 1147 atom styles  

> show atoms

> style stick

Changed 1147 atom styles  

> style ball

Changed 1147 atom styles  

> style sphere

Changed 1147 atom styles  

> hide atoms

> show cartoons

> set bgColor black

> set bgColor white

> set bgColor black

> lighting soft

> lighting simple

> lighting soft

> lighting full

> ui tool show "Selection Inspector"

> color bynucleotide

> show atoms

> hide cartoons

> color bynucleotide

> nucleotides tube/slab shape ellipsoid

> nucleotides stubs

> nucleotides ladder

> color bynucleotide

> color byhetero

> color bychain

> color bypolymer

> rainbow

> coulombic


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

Log:
UCSF ChimeraX version: 1.7.dev202308212127 (2023-08-21)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 23.1.8 (git-4baea976bb)
OpenGL renderer: AMD Custom GPU 0405 (vangogh, LLVM 15.0.7, DRM 3.45, 5.13.0-valve37-1-neptune)
OpenGL vendor: AMD

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma-steamos-oneshot
XDG_SESSION_DESKTOP=KDE (One-Time Launch)
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:99.0
Manufacturer: Valve
Model: Jupiter
OS: Freedesktop SDK 22.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 8 AMD Custom APU 0405
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            14Gi       9.2Gi       537Mi       748Mi       4.7Gi       4.2Gi
	Swap:          1.0Gi       1.0Gi       2.0Mi

Graphics:
	04:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] VanGogh [AMD Custom GPU 0405] [1002:163f] (rev ae)	
	Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Device [1002:0123]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.47.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202308212127
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.10
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.2
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    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: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7.post1
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.7
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.5
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.2
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (2)

comment:1 by Tom Goddard, 2 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in coulombic in assign_charges()

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed

Crash is in "for o_a, c_a in zip(struct.atoms, charged_struct.atoms):" which in turn may be creating Python Atom instances from C++ pointers. At any rate, works for me on PDB 1hew.

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