![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16466 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202405220104 (2024-05-22 01:04:59 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 68000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 2365,
"osVersion" : {
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"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2024-12-12 15:44:11.1660 -0800",
"codeSigningMonitor" : 1,
"incident" : "9A552BE1-44C6-4F65-A833-62D49F69D0D5",
"pid" : 99618,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-12 14:06:04.0100 -0800",
"procStartAbsTime" : 1506193713948,
"procExitAbsTime" : 1647420604167,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.22.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BE8F28B1-79B1-6419-7478-E6376CE6B56E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"IAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1A==","atPC":"AAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1A=="},
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"wakeTime" : 16661,
"sleepWakeUUID" : "6B41DC07-90D5-4F14-BDCA-2C0FFD16E90C",
"sip" : "enabled",
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===== Log before crash start =====
> lighting soft
> set bgColor white
UCSF ChimeraX version: 1.8rc202405220104 (2024-05-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/amberms/Library/CloudStorage/Box-
> Box/NECManuscript/Nature/MapsForFinalStructure/NEC_00923.pdb
Chain information for NEC_00923.pdb #1
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide atoms
> show cartoons
> lighting soft
> open /Users/amberms/Library/CloudStorage/Box-
> Box/NECManuscript/MolCell/StructureStuff/ColoringNEC_#1.cxc
> color #1/A,C #c0c0c0ff
> color #1/E #009051ff
> color #1/G #00fdffff
> color #1/D,H #ffd479ff
> color #1/B #6ec066ff
executed ColoringNEC_#1.cxc
> view name front
> save /Users/amberms/Desktop/NEC.png pixelSize 0.05 transparentBackground
> true
> save /Users/amberms/Desktop/Box/Box-
> Box/NECManuscript/MolCell/StructureStuff/NECPDB.cxs includeMaps true
> open 4PMI
4pmi title:
Crystal structure of Rev and Rev-response-element RNA complex [more info...]
Chain information for 4pmi #2
---
Chain | Description | UniProt
A | Rev-Response-Element RNA |
B C | Protein Rev | REV_HV1H3 1-70
Non-standard residues in 4pmi #2
---
PO4 — phosphate ion
4pmi mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #2/B to #1/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NEC_00923.pdb, chain E (#1) with 4pmi, chain B (#2), sequence
alignment score = 283.1
RMSD between 44 pruned atom pairs is 1.211 angstroms; (across all 53 pairs:
1.542)
> select #2
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> color (#!2 & sel) #424242ff
> color (#!2 & sel) #941100ff
> color (#!2 & sel) #531b93ff
> select clear
> hide #2/A
> hide #2/A cartoons
> hide #2/C,A,D,H,G cartoons
> show #2/A cartoons
> show #2/B cartoons
> hide #2/C cartoons
> hide #2/B cartoons
> hide #2/A cartoons
> show #2/B,C cartoons
> hide #1/A,C,D,H,G cartoons
> hide atoms
> select #2
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #005493ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #005493ff
> select clear
> select #2
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> color (#!2 & sel) #fffb00ff
> select clear
> select #2
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> color (#!2 & sel) #797979ff
> select clear
> view name RevDimers
> save /Users/amberms/Desktop/RevDimers.png pixelSize 0.05
> transparentBackground true
> turn 90 y
Expected an axis vector or a keyword
> turn y 90
> turn x 180
> turn x 90
> view RevDimers
> turn x -90
> save /Users/amberms/Desktop/RevDimers_min90.png pixelSize 0.05
> transparentBackground true
> turn y 30
> turn y -60
> hide #2 cartoons
> view name dimerback
> save /Users/amberms/Desktop/RevDimers_back.png pixelSize 0.05
> transparentBackground true
> view list
Named views: RevDimers, dimerback, front
> view RevDimers
> view dimerback
> view RevDimers
> turn y -60
> turn x -90
> view name RevDimerSide
> save /Users/amberms/Desktop/RevDimers_side.png pixelSize 0.05
> transparentBackground true
> view list
Named views: RevDimerSide, RevDimers, dimerback, front
> view RevDimers
> show #2/B,C cartoons
> view RevDimerSide
> turn y -90
> view RevDimerSide
> turn x -90
> view RevDimerSide
> turn x 90
> save /Users/amberms/Desktop/RevDimers_2.png pixelSize 0.05
> transparentBackground true
> view RevDimerSide
> turn y 90
> hide #2 cartoons
> save /Users/amberms/Desktop/RevDimersRear_2.png pixelSize 0.05
> transparentBackground true
> open /Users/amberms/Library/CloudStorage/Box-
> Box/NECManuscript/Nature/MapsForFinalStructure/NEC_00923.pdb
Chain information for NEC_00923.pdb #3
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide atoms
> show atoms
> hide atoms
> show cartoons
> open /Users/amberms/Library/CloudStorage/Box-
> Box/NECManuscript/MolCell/StructureStuff/ColoringNEC_#3.cxc
> color #3/A,C #c0c0c0ff
> color #3/E #009051ff
> color #3/G #00fdffff
> color #3/D,H #ffd479ff
> color #3/B #6ec066ff
executed ColoringNEC_#3.cxc
> hide #3/A,C,D,H,G cartoons
> hide #1 models
> show #1 models
> hide #1 models
> hide #!2 models
> hide #3 models
> show #3 models
> mmaker #3/B to #1/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NEC_00923.pdb, chain E (#1) with NEC_00923.pdb, chain B (#3),
sequence alignment score = 362.2
RMSD between 41 pruned atom pairs is 1.205 angstroms; (across all 78 pairs:
27.009)
> show #1 models
> hide #1/A,C,D,H,G cartoons
> hide #1/B cartoons
> hide #3/E cartoons
> save /Users/amberms/Desktop/RevONLDimer_2.png pixelSize 0.05
> transparentBackground true
===== Log before crash end =====
Log:
> lighting soft
> set bgColor white
UCSF ChimeraX version: 1.8rc202405220104 (2024-05-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/amberms/Desktop/group/relion_new/Refine3D/job261/run_class001.mrc
Opened run_class001.mrc as #1, grid size 320,320,320, pixel 0.835, shown at
level 0.00768, step 2, values float32
> set bgColor white
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Pro
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: Mac14,9
Model Number: MPHE3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 3 days, 21 hours, 27 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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: 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: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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: 1.2.4
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-ColorActions: 1.0.4
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: 1.8rc202405220104
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-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: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
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: 1.13.4
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: 3.0.7
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: 1.4.1
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: 4.51.0
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: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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: 3.0.43
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
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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