![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17715 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-14.3.1-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 0x00000001e3ff5c40 (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.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55)
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{
"uptime" : 420000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,7",
"coalitionID" : 3961,
"osVersion" : {
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"build" : "23D60",
"releaseType" : "User"
},
"captureTime" : "2025-05-17 20:27:23.6919 -0400",
"codeSigningMonitor" : 1,
"incident" : "FB3E0B2E-EAE8-4435-A24F-EAC986459388",
"pid" : 43556,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-17 19:22:34.0658 -0400",
"procStartAbsTime" : 10009906880715,
"procExitAbsTime" : 10090154323389,
"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":"256931BF-D996-5535-81AA-A5BE22491F96","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A85DA2DE-3B89-EC80-603B-10B8749149BC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "0BA38F4B-FD57-45A7-B41D-BC643BAA0F9F",
"sip" : "enabled",
"vmRegionInfo" : "0x706609381ad8 is not in any region. Bytes after previous region: 18028279896793 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000706609381ad8","rawCodes":[1,123583543646936],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000706609381ad8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43556},
"vmregioninfo" : "0x706609381ad8 is not in any region. Bytes after previous region: 18028279896793 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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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/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_apix1.4053.mrc
Opened J203_005_volume_map_apix1.4053.mrc as #1, grid size 400,400,400, pixel
1.41, shown at level 0.21, step 2, values float32
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb
Chain information for
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb #2
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
F G I M | No description available
H J K L | No description available
> style stick
Changed 42808 atom styles
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> transparency 50
> set bgColor white
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> combine #2
> split #3
Split copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb
(#3) into 13 models
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb F #3.6
---
Chain | Description
F | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb G #3.7
---
Chain | Description
G | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb H #3.8
---
Chain | Description
H | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb I #3.9
---
Chain | Description
I | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb J #3.10
---
Chain | Description
J | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb K #3.11
---
Chain | Description
K | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb L #3.12
---
Chain | Description
L | No description available
Chain information for copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb M #3.13
---
Chain | Description
M | No description available
> fitmap #3/E inMap #1
Fit molecule copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E (#3.5) to
map J203_005_volume_map_apix1.4053.mrc (#1) using 2132 atoms
average map value = 0.2901, steps = 60
shifted from previous position = 0.00344
rotated from previous position = 0.00696 degrees
atoms outside contour = 655, contour level = 0.20953
Position of copy of
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E (#3.5)
relative to J203_005_volume_map_apix1.4053.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00008055 -0.00004656 -0.02231135
-0.00008055 0.99999999 0.00007821 0.00081140
0.00004657 -0.00007821 1.00000000 0.01806129
Axis -0.64346642 -0.38308710 -0.66271807
Axis point 19.92730800 260.39244332 0.00000000
Rotation angle (degrees) 0.00696413
Shift along axis 0.00207622
Drag select of 1 J203_005_volume_map_apix1.4053.mrc , 1246 atoms, 1272 bonds
> select clear
Drag select of 1 J203_005_volume_map_apix1.4053.mrc , 2 atoms, 4 bonds
> select clear
> ui mousemode right zoom
> volume #1 level 0.08111
> surface dust #1 size 14.1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Map Coordinates"
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203_005_volume_map_deepem_highRes.mrc
Opened J203_005_volume_map_deepem_highRes.mrc as #4, grid size 400,400,400,
pixel 1.43, shown at level 0.128, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #4 inMap #1
Fit map J203_005_volume_map_deepem_highRes.mrc in map
J203_005_volume_map_apix1.4053.mrc using 639777 points
correlation = 0.9107, correlation about mean = 0.6523, overlap = 7.268e+04
steps = 44, shift = 0.022, angle = 0.00245 degrees
Position of J203_005_volume_map_deepem_highRes.mrc (#4) relative to
J203_005_volume_map_apix1.4053.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00003258 0.00001198 0.00273694
-0.00003258 1.00000000 0.00002501 0.00764531
-0.00001198 -0.00002501 1.00000000 0.02454574
Axis -0.58453587 0.27994224 -0.76154459
Axis point 390.64156626 241.69018473 0.00000000
Rotation angle (degrees) 0.00245111
Shift along axis -0.01815227
> color #4 darkgray
> transparency 50
> volume #4 level 0.0797
> fitmap #2 inMap #4
Fit molecule 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb
(#2) to map J203_005_volume_map_deepem_highRes.mrc (#4) using 42808 atoms
average map value = 0.3434, steps = 40
shifted from previous position = 0.0492
rotated from previous position = 0.0148 degrees
atoms outside contour = 6987, contour level = 0.079697
Position of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb
(#2) relative to J203_005_volume_map_deepem_highRes.mrc (#4) coordinates:
Matrix rotation and translation
0.99999999 0.00004656 -0.00016220 0.02803223
-0.00004659 0.99999997 -0.00022013 0.07544607
0.00016219 0.00022013 0.99999996 -0.09485844
Axis 0.79363906 -0.58475785 -0.16791456
Axis point 0.00000000 435.50241357 326.90624144
Rotation angle (degrees) 0.01589195
Shift along axis -0.00594210
> volume #4 level 0.04216
Drag select of 484 atoms, 488 bonds, 4 J203_005_volume_map_deepem_highRes.mrc
Drag select of 4 J203_005_volume_map_deepem_highRes.mrc
> select clear
> volume #4 level 0.07594
> volume #4 level 0.01588
> close #2
> close #3
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250517_TOG5_MT_forPDB-
> coot-0.pdb
Summary of feedback from opening
/Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250517_TOG5_MT_forPDB-
coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 113 113 GLY F 10 HIS F 28 1 19
Start residue of secondary structure not found: HELIX 114 114 SER F 48 THR F
51 1 4
Start residue of secondary structure not found: HELIX 115 115 THR F 73 THR F
80 1 8
Start residue of secondary structure not found: HELIX 116 116 PRO F 89 GLN F
91 1 3
Start residue of secondary structure not found: HELIX 117 117 TYR F 103 THR F
109 1 7
299 messages similar to the above omitted
Cannot find LINK/SSBOND residue MG (502 )
Cannot find LINK/SSBOND residue MG (502 )
Cannot find LINK/SSBOND residue MG (502 )
Cannot find LINK/SSBOND residue MG (502 )
Cannot find LINK/SSBOND residue MG (502 )
11 messages similar to the above omitted
Chain information for 20250517_TOG5_MT_forPDB-coot-0.pdb #2
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
> show cartoons
> hide atoms
> show atoms
> style stick
Changed 15708 atom styles
> color byhetero
Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 670 atoms, 178
residues, 567 bonds
> select #4
2 models selected
> select clear
> hide atoms
> select #2/E
2132 atoms, 2169 bonds, 1 pseudobond, 264 residues, 2 models selected
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel restrict cross distanceOnly 5.0 interModel false intraMol false
> ignoreHiddenModels true select true makePseudobonds false reveal true
463 distances
> select clear
Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 5 atoms, 9 residues,
3 bonds
> select #4
2 models selected
> select clear
> select #2/E
2132 atoms, 2169 bonds, 1 pseudobond, 264 residues, 2 models selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel radius 0.1 interModel false distSlop 1.5 intraMol false intraRes
> false reveal true
16 hydrogen bonds found
> select clear
Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 29 residues
> select #4
2 models selected
> select clear
> ui tool show "Side View"
> ui mousemode right "map eraser"
> volume erase #4 center 263.72,398.15,270.64 radius 82.666 outside true
Opened J203_005_volume_map_deepem_highRes.mrc copy as #5, grid size
400,400,400, pixel 1.41, shown at step 1, values float32
> ui mousemode right zoom
> ui tool show "Side View"
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb
Chain information for
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
F G I M | No description available
H J K L | No description available
> style stick
Changed 58516 atom styles
> show cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #4
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_sharp_apix1.4053.mrc
Opened J203_005_volume_map_sharp_apix1.4053.mrc as #4, grid size 400,400,400,
pixel 1.41, shown at level 0.299, step 2, values float32
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> color #4 darkgray
> transparency 50
===== 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
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/TOG5_MT_Phenix/RealSpaceRefine_99/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9_real_space_refined_099.pdb
Chain information for
20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9_real_space_refined_099.pdb
#1
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
F G I M | No description available
H J K L | No description available
> open
> /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_apix1.4053.mrc
Opened J203_005_volume_map_apix1.4053.mrc as #2, grid size 400,400,400, pixel
1.41, shown at level 0.21, step 2, values float32
> style stick
Changed 42808 atom styles
> transparency 50
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> color byhetero
> select /A:414@CD
1 atom, 1 residue, 1 model selected
> select /A:414@CD
1 atom, 1 residue, 1 model selected
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 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: Mac15,7
Model Number: Z1AJ0018XLL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 24 days, 2 hours, 20 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
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
DELL SE2719H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
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-maskChains: 1.4
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 on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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