![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#8530 closed defect (fixed)
Crash clearing aniso_u6
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard, Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.2-arm64-arm-64bit
ChimeraX Version: 1.6.dev202302180254 (2023-02-18 02:54:55 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
It crashed when I chose the model for ISOLDE
Fatal Python error: Segmentation fault
Current thread 0x00000001027d8580 (most recent call first):
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 853 in _set_aniso_u6
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py", line 670 in _anisou_sanity_check
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py", line 639 in add_model
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py", line 597 in __init__
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py", line 815 in _change_selected_model
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py", line 771 in change_selected_model
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py", line 434 in selected_model
File "/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/ui/main_win.py", line 157 in _set_selected_model
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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"version" : 2,
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"bug_type" : "309",
"pid" : 31833,
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"procPath" : "\/Users\/USER\/Desktop\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"sleepWakeUUID" : "AD5A3816-4510-461B-ABB9-DEBCBEC88543",
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"uuid" : "0c98ecde-c21a-3501-9c98-fc9d3dd5bb12",
"path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore",
"name" : "QuartzCore",
"CFBundleVersion" : "962.63"
},
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"source" : "P",
"arch" : "arm64e",
"base" : 6861291520,
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"size" : 4120576,
"uuid" : "90321a38-43a5-3767-9a9c-2c631338b9bc",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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"size" : 19300352,
"uuid" : "5431bff3-be1a-3fe5-a552-bcdbb3e0536e",
"path" : "\/Users\/USER\/Desktop\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblasp-r0.3.20.dylib",
"name" : "libopenblasp-r0.3.20.dylib"
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"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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"sharedCache" : {
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"size" : 3091218432,
"uuid" : "b90241b2-e425-3982-b3f6-26c4567cbb49"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=15.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=15.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 4032K 4 \nCG image 192K 10 \nColorSync 624K 27 \nCoreAnimation 304K 16 \nCoreGraphics 32K 2 \nCoreUI image data 3760K 25 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 12.7G 240 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 984.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1008K 63 \nStack 198.6M 64 \nStack Guard 56.0M 1 \nVM_ALLOCATE 309.1M 860 \nVM_ALLOCATE (reserved) 512.0M 3 reserved VM address space (unallocated)\n__AUTH 2570K 308 \n__AUTH_CONST 19.7M 500 \n__DATA 27.0M 794 \n__DATA_CONST 29.7M 784 \n__DATA_DIRTY 1787K 215 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 623.1M 284 \n__OBJC_CONST 3569K 273 \n__OBJC_RO 82.1M 1 \n__OBJC_RW 3104K 1 \n__TEXT 777.7M 803 \n__UNICODE 588K 1 \ndyld private memory 1072K 3 \nmapped file 193.3M 47 \nshared memory 3168K 26 \n=========== ======= ======= \nTOTAL 16.8G 5388 \nTOTAL, minus reserved VM space 15.0G 5388 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202302180254 (2023-02-18)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/siqiong/Desktop/crosslinking/2811,4.26/Crosslinking_NF5_IMP-
> FL4.26.pdb
Summary of feedback from opening
/Users/siqiong/Desktop/crosslinking/2811,4.26/Crosslinking_NF5_IMP-FL4.26.pdb
---
warning | Start residue of secondary structure not found: HELIX 1 1 PRO A 9
GLN A 11 1 3
Chain information for Crosslinking_NF5_IMP-FL4.26.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
Populating font family aliases took 184 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.1 to IUPAC-IUB
standards.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.dev202302180254 (2023-02-18)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 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 (21D49)
Kernel Version: Darwin 21.3.0
Time since boot: 1 day 12:34
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.11.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.0.1
ChimeraX-AddCharge: 1.5.8
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.8
ChimeraX-AtomicLibrary: 10.0.4
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.1
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-Clipper: 0.20.0
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: 1.6.dev202302180254
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: 1.1
ChimeraX-DistMonitor: 1.3.3
ChimeraX-DockPrep: 1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-ExperimentalCommands: 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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.dev0
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: 1.1.4
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: 2.0.11
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.8
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.6.13
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-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
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: 2.8.2
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: 1.10.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.27.1
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
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: 0.1.2
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.0.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.4
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.2.0
jupyterlab-widgets: 3.0.5
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.0.0
prompt-toolkit: 3.0.36
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.2
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.2
python-dateutil: 2.8.2
pytz: 2022.7.1
pyzmq: 25.0.0
qtconsole: 5.4.0
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.0.2
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.14
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.5
zipp: 3.14.0
Change History (6)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash clearing aniso_u6 |
comment:2 by , 3 years ago
| Status: | assigned → feedback |
|---|
Hi Siqiong,
Thanks for reporting this problem. Does it happen every time you choose a model in ISOLDE, or was it only one time?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
follow-up: 3 comment:3 by , 3 years ago
Hi Siqiong, We’ve had about a dozen reports of this so far, all on M1 Macs. Unfortunately I’ve had no success replicating it on my own machine. If it’s happening reproducibly for you, I’d be very grateful if you could help out by running a few tests to help diagnose the problem. Please let me know if you’re willing, and I’ll get back to you with details. Thanks, Tristan On Tue, 21 Feb 2023 at 17:17, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:4 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
Fix will be in tomorrow's daily build.
follow-up: 5 comment:5 by , 3 years ago
Ah - nice detective work! On Thu, Mar 2, 2023 at 8:51 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:6 by , 3 years ago
The fact that it was ARM only made me suspicious that it was a library-calling issue, which made me look at the call itself more closely, and voila.
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Reported by Siqiong Zheng