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Opened 2 years ago
Closed 2 years ago
#9368 closed defect (can't reproduce)
Crash converting to Hybrid-36
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000317a1e000 (most recent call first):
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py", line 306 in wait
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py", line 558 in wait
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py", line 1252 in run
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py", line 932 in _bootstrap_inner
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py", line 890 in _bootstrap
Current thread 0x0000000204ba7280 (most recent call first):
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 953 in to_h36
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 1023 in _h_name
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 888 in new_hydrogen
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862 in add_altloc_hyds
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895 in _attach_hydrogens
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214 in add_hydrogens
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170 in hbond_add_hydrogens
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63 in cmd_addh
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 74 in assign_charges
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90 in cmd_coulombic
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36 in run
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 511 in run
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 568 in run_expanded_command
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 61 in func_plus_tip
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 326 in run
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 407 in run_shortcut
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 389 in try_shortcut
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/shortcuts.py", line 1333 in run_provider
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/shortcuts/__init__.py", line 52 in run_provider
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/toolshed/__init__.py", line 1285 in run_provider
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/toolshed/info.py", line 379 in run_provider
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/toolbar/tool.py", line 202 in callback
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.2.5 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 194 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-07-13 12:38:42.00 +0900","app_version":"1.2.5","slice_uuid":"74b1c996-e1f3-331c-8c86-116411356099","build_version":"1.2.5.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.4.1 (22F82)","roots_installed":0,"name":"ChimeraX","incident_id":"72583FB1-01DF-4669-B195-D6A7A39595A5"}
{
"uptime" : 780000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Macmini9,1",
"coalitionID" : 3217,
"osVersion" : {
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"build" : "22F82",
"releaseType" : "User"
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"captureTime" : "2023-07-13 12:38:29.4513 +0900",
"incident" : "72583FB1-01DF-4669-B195-D6A7A39595A5",
"pid" : 47771,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-13 12:33:56.5577 +0900",
"procStartAbsTime" : 18772633047895,
"procExitAbsTime" : 18779182368536,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.2.5 2.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.2.5","CFBundleVersion":"1.2.5.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5787265E-9D52-5835-9B07-B090677CF2F7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FFB266ED-B826-2332-D62F-74FBD28FCDA9",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722860998487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc98244000-7ffca7378000 [241.2M] r-x\/r-x SM=COW ...ct_id=369dc5f",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722860998487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc98244000-7ffca7378000 [241.2M] r-x\/r-x SM=COW ...ct_id=369dc5f",
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"faultingThread" : 0,
"threads" : 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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini9,1
Model Number: Z12P000JGJ/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (22F82)
Kernel Version: Darwin 22.5.0
Time since boot: 9日 1時間 21分
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
EV3237:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 30.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash converting to Hybrid-36 |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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