![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15841 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-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.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002075d4f40 (most recent call first):
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, chimerax.map._map, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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{
"uptime" : 46000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 4477,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-08-29 13:04:52.4662 +0100",
"codeSigningMonitor" : 1,
"incident" : "82AB1069-3D45-409B-BEDF-B7353D03F566",
"pid" : 17009,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-29 09:52:46.7331 +0100",
"procStartAbsTime" : 856725353287,
"procExitAbsTime" : 1108771295084,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"D6D41503-67AF-5CBE-B0C8-CB4C04D71465","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AC256AE6-F04D-8CD8-A858-DD32AC0AFFE1",
"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=="},
"sleepWakeUUID" : "FACE5180-6663-439C-8B89-632D13815D95",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4366581400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10444c000-104450000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17009},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4366581400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10444c000-104450000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
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/naito/Downloads/cryosparc_P106_J266_class_02_final_volume.mrc
Opened cryosparc_P106_J266_class_02_final_volume.mrc as #1, grid size
180,180,180, pixel 1.38, shown at level 0.0506, step 1, values float32
> open /Users/naito/Downloads/cryosparc_P106_J115_009_volume_map_sharp.mrc
Opened cryosparc_P106_J115_009_volume_map_sharp.mrc as #2, grid size
180,180,180, pixel 1.38, shown at level 0.0602, step 1, values float32
> set bgColor white
> lighting soft
> graphics silhouettes true
> hide #!1 models
> volume #2 level 0.2386
> show #!1 models
> hide #!2 models
> volume #1 level 0.1449
> open /Users/naito/Library/CloudStorage/OneDrive-
> ImperialCollegeLondon/rMRP2/04_Cisplatine-
> glutathione/cryosparc_P29_J24_005_volume_map_sharp.mrc
Opened cryosparc_P29_J24_005_volume_map_sharp.mrc as #3, grid size
180,180,180, pixel 2.38, shown at level 0.115, step 1, values float32
> hide #!1 models
> open /Users/naito/Library/CloudStorage/OneDrive-
> ImperialCollegeLondon/rMRP2/03_Vinblastin-
> glutathione/cryosparc_P28_J27_006_volume_map_sharp.mrc
Opened cryosparc_P28_J27_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.68, shown at level 0.048, step 1, values float32
> hide #!4 models
> open /Users/naito/Library/CloudStorage/OneDrive-
> ImperialCollegeLondon/rMRP2/05_Sulindac/cryosparc_P30_J32_005_volume_map_sharp.mrc
Opened cryosparc_P30_J32_005_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.68, shown at level 0.0417, step 1, values float32
> hide #!5 models
> show #!4 models
> hide #!3 models
> volume #4 level 0.1545
> show #!5 models
> hide #!4 models
> volume #5 level 0.1379
> show #!3 models
> hide #!5 models
> volume #3 level 0.3585
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> /Users/naito/Library/CloudStorage/Dropbox/UK_Project/MRP2/Phenix/rMRP2-MK517/rMRP2_MK_J22-coot-1.pdb
> format pdb
Summary of feedback from opening
/Users/naito/Library/CloudStorage/Dropbox/UK_Project/MRP2/Phenix/rMRP2-MK517/rMRP2_MK_J22-coot-1.pdb
---
warning | Start residue of secondary structure not found: HELIX 34 34 ARG A 900 SER A 912 1 13
Chain information for rMRP2_MK_J22-coot-1.pdb #6
---
Chain | Description
A | No description available
> select add #6
11137 atoms, 11374 bonds, 2 pseudobonds, 1402 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.96347,-0.20551,-0.17175,68.71,-0.187,-0.97526,0.11793,326.11,-0.19174,-0.081502,-0.97806,388.24
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.96347,-0.20551,-0.17175,130.76,-0.187,-0.97526,0.11793,384.15,-0.19174,-0.081502,-0.97806,404.06
> view matrix models
> #6,0.96347,-0.20551,-0.17175,112.76,-0.187,-0.97526,0.11793,394.55,-0.19174,-0.081502,-0.97806,418.08
> show #!4 models
> hide #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.99014,0.13896,-0.017573,362.41,0.13379,0.97543,0.17504,19.335,0.041464,0.17096,-0.9844,339.4
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.99014,0.13896,-0.017573,361.77,0.13379,0.97543,0.17504,0.059394,0.041464,0.17096,-0.9844,338.73
> fitmap #6 inMap #4
Fit molecule rMRP2_MK_J22-coot-1.pdb (#6) to map
cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) using 11137 atoms
average map value = 0.3362, steps = 64
shifted from previous position = 4.91
rotated from previous position = 5.85 degrees
atoms outside contour = 2629, contour level = 0.15454
Position of rMRP2_MK_J22-coot-1.pdb (#6) relative to
cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99788207 0.05938548 0.02654723 366.12256504
0.06378206 0.97341231 0.22000078 4.97978977
-0.01277655 0.22122807 -0.97513841 342.40108694
Axis 0.03100166 0.99333018 0.11105876
Axis point 184.65942373 0.00000000 169.10645919
Rotation angle (degrees) 178.86581819
Shift along axis 54.32362029
> save /Users/naito/desktop/240829_rMRP2_Vinblastine-Glu.pdb #6
> select subtract #6
Nothing selected
> hide #!6 models
> open /Users/naito/Desktop/240829_rMRP2_Vinblastine-Glu-coot-0.pdb
Chain information for 240829_rMRP2_Vinblastine-Glu-coot-0.pdb #7
---
Chain | Description
A | No description available
> volume #4 level 0.3061
> volume #4 level 0.1955
> volume zone #7/A:1601 range 5
Missing required "near_atoms" argument
> volume zone #4 nearAtoms #7/A:1601 range 5 newMap map true
Invalid "newMap" argument: Expected true or false (or 1 or 0)
> volume zone #4 nearAtoms #7/A:1601 range 5 newMap true
Opened cryosparc_P28_J27_006_volume_map_sharp.mrc zone as #8, grid size
256,256,256, pixel 1.68, shown at step 1, values float32
> transparency #7-8 50
> volume #8 level 0.2351
> ui tool show "Side View"
> color #7 #0019cdff
> color #7/A:1601 orange
> select #7/A:1601
59 atoms, 70 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #7
11196 atoms, 11444 bonds, 2 pseudobonds, 1403 residues, 2 models selected
> select subtract #7
Nothing selected
> color #8 #929292ff models
> transparency #7-8 50
> color #!7 byhetero
> save /Users/naito/Desktop/image13.png supersample 3
> save /Users/naito/Desktop/image14.png supersample 3
> open /Users/naito/Library/CloudStorage/OneDrive-
> ImperialCollegeLondon/rMRP2/01_MK-571/Model_Map_080824/PDB_file/rMRP2_MK_local_J056-coot-1.pdb
Chain information for rMRP2_MK_local_J056-coot-1.pdb #9
---
Chain | Description
A | No description available
> hide #!8 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!7 to #9/A pairing bs
Parameters
---
Chain pairing | bs
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 rMRP2_MK_local_J056-coot-1.pdb, chain A (#9) with
240829_rMRP2_Vinblastine-Glu-coot-0.pdb, chain A (#7), sequence alignment
score = 7288.3
RMSD between 1402 pruned atom pairs is 0.018 angstroms; (across all 1402
pairs: 0.018)
> undo
> hide #!9 models
> show #!9 models
> hide #!8 models
> color #9/A:1600-1603 magenta
> color #!7,9 byhetero
> ui tool show "Side View"
> save /Users/naito/Desktop/image15.png supersample 3
> lighting simple
> lighting full
> lighting soft
> save /Users/naito/Desktop/image16.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/naito/Desktop/movie1.mp4
Movie saved to /Users/naito/Desktop/movie1.mp4
> hide #!7 models
> hide #!9 models
> show #!7 models
> show #!4 models
> ui mousemode right "rotate selected models"
> select add #7
11196 atoms, 11444 bonds, 2 pseudobonds, 1403 residues, 2 models selected
> view matrix models
> #7,0.88025,-0.36556,0.30254,-2.2953,0.25214,0.90046,0.35441,-154.81,-0.40198,-0.23569,0.8848,124.24
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.88025,-0.36556,0.30254,2.7605,0.25214,0.90046,0.35441,-93.807,-0.40198,-0.23569,0.8848,163.38
> view matrix models
> #7,0.88025,-0.36556,0.30254,10.486,0.25214,0.90046,0.35441,-94.83,-0.40198,-0.23569,0.8848,141.93
> view matrix models
> #7,0.88025,-0.36556,0.30254,44.476,0.25214,0.90046,0.35441,-96.317,-0.40198,-0.23569,0.8848,151.08
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.96806,-0.12476,0.21745,-6.9629,0.091171,0.98319,0.15822,-39.122,-0.23354,-0.13335,0.96316,77.861
> view matrix models
> #7,0.96822,-0.13721,0.20908,-2.6577,0.1236,0.98935,0.076914,-30.463,-0.21741,-0.048629,0.97487,54.278
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.96822,-0.13721,0.20908,-4.2342,0.1236,0.98935,0.076914,-37.289,-0.21741,-0.048629,0.97487,60.976
> fitmap #7 inMap #4
Fit molecule 240829_rMRP2_Vinblastine-Glu-coot-0.pdb (#7) to map
cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) using 11196 atoms
average map value = 0.3363, steps = 96
shifted from previous position = 3.09
rotated from previous position = 14.9 degrees
atoms outside contour = 3239, contour level = 0.1955
Position of 240829_rMRP2_Vinblastine-Glu-coot-0.pdb (#7) relative to
cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999996 -0.00017468 -0.00021665 0.09518558
0.00017474 0.99999995 0.00026926 -0.12121246
0.00021661 -0.00026930 0.99999994 0.02611168
Axis -0.69535836 -0.55940720 0.45115445
Axis point 0.00000000 74.42087296 422.34775449
Rotation angle (degrees) 0.02218775
Shift along axis 0.01339944
> select subtract #7
Nothing selected
> transparency #4,7 50
> volume #4 level 0.3184
> transparency #4,7 0
> save /Users/naito/Desktop/image17.png supersample 3
> transparency #4,7 30
> volume #4 level 0.3225
> save /Users/naito/Desktop/image18.png supersample 3
===== Log before crash end =====
Log:
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 M1 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: MacBookPro18,3
Model Number: Z15H000XGJ/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 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: 1日 4時間 9分
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 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
DELL P2422HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 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 , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties, probably connecting or disconnecting a display or sleeping.