![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17532 closed defect (can't reproduce)
Crash de-iconifying from dock
| 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-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 3800000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 117663,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
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"captureTime" : "2025-05-01 22:54:02.7503 -0400",
"codeSigningMonitor" : 1,
"incident" : "31501F06-4632-4A8A-8603-2D122B372B24",
"pid" : 63280,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-01 22:10:11.2424 -0400",
"procStartAbsTime" : 91165007721565,
"procExitAbsTime" : 91228163623476,
"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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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "216F332D-5F24-FDDF-13EF-8C5782DCD983",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"ARAA1MADX9aQBYCSARAA1MADX9awBYCSARAA1MADX9bQBYCSARAA1A==","atPC":"wANf1vAFgJIBEADUwANf1hAGgJIBEADUwANf1jAGgJIBEADUwANf1g=="},
"sip" : "enabled",
"sroute_id" : 12,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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/shoichitachiyama/Downloads/cryosparc_P3_J561_000_volume_map_sharp.mrc
Opened cryosparc_P3_J561_000_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 1.14, shown at level 0.087, step 2, values float32
> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J561_000_volume_map_sharp.mrc
Opened cryosparc_P3_J561_000_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 1.14, shown at level 0.087, step 2, values float32
> volume #2 level 0.04056
> volume #2 level 0.03168
> surface dust #1 size 11.4
> surface dust #2 size 11.4
> ui tool show "Side View"
> view orient
> turn x 90
> hide #!1 models
> open /Users/shoichitachiyama/Desktop/6ve2.pdb1
6ve2.pdb1 title:
Tetradecameric pilq bound by tsap heptamer from pseudomonas aeruginosa [more
info...]
Chain information for 6ve2.pdb1 #3
---
Chain | Description
A B C D E F G H I J K L M N | No description available
O P Q R S T U | No description available
> volume #2 level 0.05579
> select add #3
30198 atoms, 30177 bonds, 6153 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color #2 #5e5e5eff models
> color #2 #5e5e5e93 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.92892,-0.34564,0.13284,400.45,-0.35165,0.93582,-0.024131,81.982,-0.11597,-0.06913,-0.99084,395.18
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.92892,-0.34564,0.13284,403.06,-0.35165,0.93582,-0.024131,139.64,-0.11597,-0.06913,-0.99084,552.51
> view matrix models
> #3,-0.92892,-0.34564,0.13284,472.87,-0.35165,0.93582,-0.024131,150.65,-0.11597,-0.06913,-0.99084,566.04
> view matrix models
> #3,-0.92892,-0.34564,0.13284,472.53,-0.35165,0.93582,-0.024131,152.04,-0.11597,-0.06913,-0.99084,576.23
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 6ve2.pdb1 (#3) to map cryosparc_P3_J561_000_volume_map_sharp.mrc
(#2) using 30198 atoms
average map value = 0.02912, steps = 296
shifted from previous position = 11.6
rotated from previous position = 9.58 degrees
atoms outside contour = 28679, contour level = 0.055785
Position of 6ve2.pdb1 (#3) relative to
cryosparc_P3_J561_000_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.89157429 -0.45235616 0.02166078 512.42384844
-0.45144296 0.89153883 0.03684788 164.51702479
-0.03597979 0.02307402 -0.99908610 554.75561965
Axis -0.23238999 0.97250064 0.01540746
Axis point 280.08994269 0.00000000 272.08233670
Rotation angle (degrees) 178.30177762
Shift along axis 49.45811706
> volume #2 level 0.04207
> view orient
> color #2 silver models
> color #2 darkgrey models
> view matrix models
> #3,-0.89157,-0.45236,0.021661,502.08,-0.45144,0.89154,0.036848,172.19,-0.03598,0.023074,-0.99909,554.76
> fitmap #3 inMap #2
Fit molecule 6ve2.pdb1 (#3) to map cryosparc_P3_J561_000_volume_map_sharp.mrc
(#2) using 30198 atoms
average map value = 0.0296, steps = 68
shifted from previous position = 4.43
rotated from previous position = 3.26 degrees
atoms outside contour = 23737, contour level = 0.042071
Position of 6ve2.pdb1 (#3) relative to
cryosparc_P3_J561_000_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.87428815 -0.48540724 0.00019910 508.64224702
-0.48540724 0.87428817 0.00000743 184.14309534
-0.00017768 -0.00009015 -0.99999998 551.49734788
Axis -0.25071077 0.96806204 -0.00002140
Axis point 278.19372502 0.00000000 275.72450770
Rotation angle (degrees) 179.98885009
Shift along axis 50.72805067
> select subtract #3
Nothing selected
> hide #3 models
> volume #2 level 0.03708
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> volume #2 level 0.03875
> hide #!2 models
> close #2
> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J561_002_volume_map_sharp.mrc
Opened cryosparc_P3_J561_002_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 1.14, shown at level 0.0889, step 2, values float32
> view orient
> turn x 90
> select add #3
30198 atoms, 30177 bonds, 6153 residues, 1 model selected
> view matrix models
> #3,-0.87429,-0.48541,0.0001991,508.9,-0.48541,0.87429,7.4301e-06,184.14,-0.00017768,-9.0148e-05,-1,544.38
> volume #2 level 0.06947
> view matrix models
> #3,-0.87429,-0.48541,0.0001991,508.86,-0.48541,0.87429,7.4301e-06,184.27,-0.00017768,-9.0148e-05,-1,539.38
> volume #2 level 0.05698
> view matrix models
> #3,-0.87429,-0.48541,0.0001991,508.84,-0.48541,0.87429,7.4301e-06,184.34,-0.00017768,-9.0148e-05,-1,536.87
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #3 inMap #2
Fit molecule 6ve2.pdb1 (#3) to map cryosparc_P3_J561_002_volume_map_sharp.mrc
(#2) using 30198 atoms
average map value = 0.033, steps = 92
shifted from previous position = 9.57
rotated from previous position = 0.965 degrees
atoms outside contour = 27051, contour level = 0.05698
Position of 6ve2.pdb1 (#3) relative to
cryosparc_P3_J561_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.86598702 -0.50006646 0.00013856 509.84278836
-0.50006645 0.86598703 0.00008326 188.39332226
-0.00016162 0.00000281 -0.99999999 546.41568488
Axis -0.25885605 0.96591591 0.00002224
Axis point 280.18715629 0.00000000 273.18464842
Rotation angle (degrees) 179.99109702
Shift along axis 50.00837137
> volume #2 level 0.03243
> view orient
> turn x 90
> molmap #3 10 onGrid #2
Opened 6ve2.pdb1 map 10 as #4, grid size 224,224,224, pixel 2.29, shown at
level 0.056, step 1, values float32
> vop resample #4 ongrid #2
Opened 6ve2.pdb1 map 10 resampled as #5, grid size 448,448,448, pixel 1.14,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/6ve2-mask.mrc models #5
> save /Users/shoichitachiyama/Desktop/PilQ-mode.cxs includeMaps true
> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J564_000_volume_map_sharp.mrc
Opened cryosparc_P3_J564_000_volume_map_sharp.mrc as #6, grid size
448,448,448, pixel 1.14, shown at level 0.083, step 2, values float32
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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
OpenGL renderer: Apple M1 Max
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: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 43 days, 23 hours, 53 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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-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-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-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
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash de-iconifying from dock |
comment:2 by , 6 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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