![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Last modified 13 months ago
#16046 accepted defect
OpenCommands script crashes ChimeraX
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard, Tony Schaefer | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Steps to reproduce:
- install the OpenCommands plugin
- configure it such that any time a PDB file is opened, the following commands are run: "~show protein; ribbon; contacts ligand reveal true; style stick; color byhet; ~show HC; ~contacts"
- if the last "~contacts" command is included, ChimeraX crashes when a PDB is opened; without the last "~contacts" command, there is no crash
Fatal Python error: Segmentation fault
Current thread 0x00000001ff4dcf40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 106 in get_prop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 174 in get_prop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/pbgroup.py", line 108 in get_selected
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py", line 40 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py", line 40 in models
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 247 in _fill_tree
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 218 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, lxml._elementpath, lxml.etree, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, chimerax.graphics._graphics, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast (total: 57)
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{
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"procRole" : "Foreground",
"version" : 2,
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"coalitionID" : 11797,
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"captureTime" : "2024-09-30 14:16:25.5147 -0700",
"codeSigningMonitor" : 1,
"incident" : "A4617C5C-0B34-4EE8-AE01-5A4F85BEDFCC",
"pid" : 47831,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-30 14:14:09.8702 -0700",
"procStartAbsTime" : 1426938461045,
"procExitAbsTime" : 1430193470123,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "AF060895-CCDA-EE7D-51D0-A1E9291202B4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 9191,
"sleepWakeUUID" : "4B5BF3FE-37CE-4DC6-B424-096F5F61F724",
"sip" : "enabled",
"vmRegionInfo" : "0xf55cdc57f60 is not in any region. Bytes after previous region: 16380162572129 Bytes before following region: 88691917357216\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor white
> lighting soft
> clipper init
> cofr centerOfView showPivot true
> camera ortho
> lighting simple
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
> FL Baculovirus.pdb" format pdb
Summary of feedback from opening
/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
FL Baculovirus.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7709 version_1 2023.12.11
STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb title:
Structure of SAMR1 FL Baculovirus bound to G01979294.1-1 at 1.98 A re
solution. [more info...]
Chain information for STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
Chain | Description
A B C D E F G H | No description available
Non-standard residues in STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
DRG — (DRG)
NAD — (NAD)
> ~contacts
> close
> open
> "/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
> FL Baculovirus.pdb" format pdb
Summary of feedback from opening
/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
FL Baculovirus.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7709 version_1 2023.12.11
STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb title:
Structure of SAMR1 FL Baculovirus bound to G01979294.1-1 at 1.98 A re
solution. [more info...]
Chain information for STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
Chain | Description
A B C D E F G H | No description available
Non-standard residues in STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
DRG — (DRG)
NAD — (NAD)
> ~show protein
> ribbon
> contacts ligand reveal true
1418 contacts
> style stick
Changed 30902 atom styles
> color byhetero
> ~show HC
> close
> open
> "/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
> FL Baculovirus.pdb" format pdb
Summary of feedback from opening
/Users/rohoua/work/Genentech/SARM1/SARM1_NAD_G01979294/STR7709.G01979294.1-1.SAMR1
FL Baculovirus.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STR7709 version_1 2023.12.11
STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb title:
Structure of SAMR1 FL Baculovirus bound to G01979294.1-1 at 1.98 A re
solution. [more info...]
Chain information for STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
Chain | Description
A B C D E F G H | No description available
Non-standard residues in STR7709.G01979294.1-1.SAMR1 FL Baculovirus.pdb #1
---
DRG — (DRG)
NAD — (NAD)
> ~show protein
> ribbon
> contacts ligand reveal true
1418 contacts
> style stick
Changed 30902 atom styles
> color byhetero
> ~show HC
> ~contacts
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor white
> lighting soft
> clipper init
> cofr centerOfView showPivot true
> camera ortho
> lighting simple
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16T0006PLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 3 days, 5 hours, 32 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL P4317Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 3840 x 2160 @ 30.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-Clipper: 0.23.1
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
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-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-OpenCommands: 1.2
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Attachments (1)
Change History (9)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → OpenCommands script crashes ChimeraX |
comment:3 by , 13 months ago
Is it a hard crash on mac? I'm getting an error message on windows when I
try this with 1brr with all the commands (including ~contacts) in
OpenCommands:
```
Traceback (most recent call last):
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\core\triggerset.py",
line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\model_panel\tool.py",
line 218, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\model_panel\tool.py",
line 247, in _fill_tree
all_selected_models = self.session.selection.models(all_selected=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\core\selection.py",
line 40, in models
return [m for m in self._all_models if
m.get_selected(include_children=True, fully=True)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\core\selection.py",
line 40, in <listcomp>
return [m for m in self._all_models if
m.get_selected(include_children=True, fully=True)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\atomic\pbgroup.py",
line 108, in get_selected
if self.pseudobonds.num_selected < self.num_pseudobonds:
^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\atomic\molc.py",
line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\atomic\molc.py",
line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
OSError: exception: access violation writing 0x0000000000002B2B
Error processing trigger "new frame":
OSError: exception: access violation writing 0x0000000000002B2B
File
"C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-packages\chimerax\atomic\molc.py",
line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
```
The ~contacts will delete the pseudobonds child of 1brr. There might be
some interaction with OpenCommands deleting the model between when ChimeraX
figures out it needs to add the model to the model panel and when ChimeraX
tries adding the pseudobonds child to the model panel. I can see the
structure without any contacts shown, but it isn't listed in the model
panel. If I try to open something else (not mmCIF or PDB), I get basically
the same error as long as this structure is open. I'll try adding a short
delay between when the model is opened and when OpenCommands does stuff to
see if that fixes it.
Best,
Tony
On Tue, Oct 1, 2024 at 11:57 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
>
>
>
>
comment:4 by , 13 months ago
It is a hard crash on Mac. The traceback is helpful. I had narrowed it down to somewhere in the routine where the model-panel table gets rebuilt, but from the traceback you sent I see it's the selection manager not screening out deleted models from its return value. I'll see if fixing that solves the problem.
comment:5 by , 13 months ago
As a temporary workaround, I've attached a version of OpenCommands that adds a one second delay between opening a model and running ChimeraX commands. With this version, I'm able to open 1brr and run the commands including ~contacts. To install 1. uninstall the current version of OpenCommands (toolshed uninstall ChimeraX_OpenCommands) 2. restart ChimeraX 3. install the attached .whl file (e.g. toolshed install ~/Downloads/ChimeraX_OpenCommands-1.2.1a1-py3-none-any.whl) 4. restart ChimeraX again for the OpenCommands options to appear in the settings/preferences Best, Tony On Tue, Oct 1, 2024 at 12:43 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > >
by , 13 months ago
| Attachment: | ChimeraX_OpenCommands-1.2.1a1-py3-none-any.whl added |
|---|
Added by email2trac
comment:6 by , 13 months ago
comment:7 by , 13 months ago
Thanks - I downloaded a daily build and can confirm that I can use OpenCommand as intended! On Tue, Oct 1, 2024 at 2:34 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > >
Note:
See TracTickets
for help on using tickets.
Using 1brr as a test case, I can reproduce this. Unfortunately, I get different stack traces each time, probably making this challenging to debug. Also, the participation of OpenCommands seems to be needed -- if I do "open 1brr for pdb; the-same-open-commands-used-before" then there is no crash.