Opened 13 months ago

Closed 13 months ago

#15948 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… 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-12.6-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 0x0000000100230580 (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, lxml._elementpath, lxml.etree, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath (total: 59)


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{
  "uptime" : 1400000,
  "procLaunch" : "2024-09-12 11:59:01.4327 -0500",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,4",
  "procStartAbsTime" : 33454282779294,
  "coalitionID" : 51317,
  "osVersion" : {
    "train" : "macOS 12.6",
    "build" : "21G115",
    "releaseType" : "User"
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  "captureTime" : "2024-09-13 09:27:12.3859 -0500",
  "incident" : "04FB61F1-A3C0-49C8-B33F-7430894E2DD1",
  "bug_type" : "309",
  "pid" : 36019,
  "procExitAbsTime" : 33988893478519,
  "translated" : false,
  "cpuType" : "ARM-64",
  "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":"B515EC6E-A45D-5537-B0EB-24C9680664BC","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "6E18411F-7A47-2429-34AF-D37C8C26E794",
  "wakeTime" : 49,
  "sleepWakeUUID" : "1E49D50C-EAEB-4A3E-BB47-21141C8A261A",
  "sip" : "enabled",
  "vmRegionInfo" : "0x3d9e41dbb28 is not in any region.  Bytes after previous region: 3753333603113  Bytes before following region: 101318746326232\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x000083d9e41dbb28","rawCodes":[1,144971858295592],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000083d9e41dbb28 -> 0x000003d9e41dbb28 (possible pointer authentication failure)"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0x3d9e41dbb28 is not in any region.  Bytes after previous region: 3753333603113  Bytes before following region: 101318746326232\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
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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/toddgreen/Desktop/personnel/novak/iga1_protease/cryosparc/cryosparc_P8_J198_006_volume_map_sharp.mrc

Opened cryosparc_P8_J198_006_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.73, shown at level 0.039, step 2, values float32  

> open
> /Users/toddgreen/Desktop/personnel/novak/iga1_protease/cryosparc/082024/rebuilt_composite_083124_v4.pdb

Chain information for rebuilt_composite_083124_v4.pdb #2  
---  
Chain | Description  
A | No description available  
  

> volume #1 level 0.081

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> select /A:718

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:718-1136

3224 atoms, 3269 bonds, 419 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select /A:1137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1137-1652

4161 atoms, 4249 bonds, 516 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel coral

> select /A:1653

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1653-1999

2841 atoms, 2901 bonds, 347 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel plum

> select /A:1137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1137-1652

4161 atoms, 4249 bonds, 516 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark sea green

> ui tool show "Surface Color"

> ui tool show "Color Zone"

> color zone #1 near #2 distance 4.38

> open
> /Users/toddgreen/Desktop/personnel/novak/iga1_protease/cryosparc/082024/rebuilt_composite_083124_v4.pdb

Chain information for rebuilt_composite_083124_v4.pdb #3  
---  
Chain | Description  
A | No description available  
  

> select add #2

10226 atoms, 10421 bonds, 1282 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:1136

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:718-1136

3224 atoms, 3269 bonds, 419 residues, 1 model selected  

> color sel cornflower blue

> select #3/A:1138

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:1138-1652

4154 atoms, 4242 bonds, 515 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium sea green

> select #3/A:1653-1654

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:1653-1999

2841 atoms, 2901 bonds, 347 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel indian red

> open
> /Users/toddgreen/Desktop/personnel/novak/iga1_protease/cryosparc/cryosparc_P8_J198_006_volume_map_sharp.mrc

Opened cryosparc_P8_J198_006_volume_map_sharp.mrc as #4, grid size
480,480,480, pixel 0.73, shown at level 0.039, step 2, values float32  

> volume #4 level 0.08055

> color zone #4 near #3 distance 4.38

> color zone #4 near #3 distance 4.48

> color zone #4 near #3 distance 4.58

> color zone #4 near #3 distance 4.68

> color zone #4 near #3 distance 4.78

> color zone #4 near #3 distance 4.88

> color zone #4 near #3 distance 4.98

> color zone #4 near #3 distance 5.08

> color zone #4 near #3 distance 5.18

> color zone #4 near #3 distance 5.28

> color zone #4 near #3 distance 5.38

> color zone #4 near #3 distance 5.48

> color zone #4 near #3 distance 5.38

> surface dust #4 size 7.3

> hide #2 models

> show #2 models

> hide #2 models

> select add #3

10226 atoms, 10421 bonds, 1282 residues, 1 model selected  

> hide #!4 models

> select subtract #3

Nothing selected  

> show #!4 models

> color zone #4 near #3 distance 5.48

> color zone #4 near #3 distance 5.58

> color zone #4 near #3 distance 5.68

> color zone #4 near #3 distance 5.78

> color zone #4 near #3 distance 5.88

> color zone #4 near #3 distance 5.98

> color zone #4 near #3 distance 6.08

> color zone #4 near #3 distance 6.18

> color zone #4 near #3 distance 6.28

> color zone #4 near #3 distance 6.38

> color zone #4 near #3 distance 6.48

> color zone #4 near #3 distance 6.58

> color zone #4 near #3 distance 6.68

> color zone #4 near #3 distance 6.78

> color zone #4 near #3 distance 6.88

> color zone #4 near #3 distance 6.98

> color zone #4 near #3 distance 7.08

> color zone #4 near #3 distance 7.18

> color zone #4 near #3 distance 7.28

> color zone #4 near #3 distance 7.38

> color zone #4 near #3 distance 7.48

> color zone #4 near #3 distance 7.58

> color zone #4 near #3 distance 7.68

> color zone #4 near #3 distance 7.78

> color zone #4 near #3 distance 7.88

> color zone #1 near #2 distance 4.48

> color zone #1 near #2 distance 4.58

> color zone #1 near #2 distance 4.68

> color zone #1 near #2 distance 4.78

> color zone #1 near #2 distance 4.88

> color zone #1 near #2 distance 4.98

> color zone #1 near #2 distance 5.08

> color zone #1 near #2 distance 5.18

> color zone #1 near #2 distance 5.28

> color zone #1 near #2 distance 5.38

> color zone #1 near #2 distance 5.48

> color zone #1 near #2 distance 5.58

> color zone #1 near #2 distance 5.68

> color zone #1 near #2 distance 5.78

> color zone #1 near #2 distance 5.88

> color zone #1 near #2 distance 5.98

> color zone #1 near #2 distance 6.08

> color zone #1 near #2 distance 6.18

> set bgColor white

> hide #!4 models

> show #!4 models

> hide #!4 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:1136

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:718-1136

3224 atoms, 3269 bonds, 419 residues, 1 model selected  

> color sel cornflower blue

> select #3/A:1137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:1137-1652

4161 atoms, 4249 bonds, 516 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale green

> color sel light green

> color sel medium sea green

> select add #3

10226 atoms, 10421 bonds, 1282 residues, 1 model selected  

> select subtract #3

Nothing selected  

> show #!4 models

> color zone #4 near #3 distance 7.88

> color zone #4 near #3 distance 7.78

> color zone #4 near #3 distance 7.68

> color zone #4 near #3 distance 7.58

> color zone #4 near #3 distance 7.48

> color zone #4 near #3 distance 7.38

> color zone #4 near #3 distance 7.28

> color zone #4 near #3 distance 7.18

> color zone #4 near #3 distance 7.08

> color zone #4 near #3 distance 6.98

> color zone #4 near #3 distance 6.88

> color zone #4 near #3 distance 6.78

> color zone #4 near #3 distance 6.68

> color zone #4 near #3 distance 6.58

> color zone #4 near #3 distance 6.48

> color zone #4 near #3 distance 6.38

> color zone #4 near #3 distance 6.28

> color zone #4 near #3 distance 6.18

> color zone #4 near #3 distance 6.08

> color zone #4 near #3 distance 5.98

> color zone #4 near #3 distance 5.88

> color zone #4 near #3 distance 5.78

> color zone #4 near #3 distance 5.68

> color zone #4 near #3 distance 5.58

> color zone #4 near #3 distance 5.48

> color zone #4 near #3 distance 5.38

> color zone #4 near #3 distance 5.28

> color zone #4 near #3 distance 5.18

> color zone #4 near #3 distance 5.08

> color zone #4 near #3 distance 4.98

> color zone #4 near #3 distance 4.88

> color zone #4 near #3 distance 4.78

> color zone #4 near #3 distance 4.88

> color zone #4 near #3 distance 4.98

> color zone #4 near #3 distance 5.08

> color zone #4 near #3 distance 5.18

> color zone #4 near #3 distance 5.28

> color zone #4 near #3 distance 5.38

> color zone #4 near #3 distance 5.48

> color zone #4 near #3 distance 5.58

> color zone #4 near #3 distance 5.68

> color zone #4 near #3 distance 5.78

> color zone #4 near #3 distance 5.88

> color zone #4 near #3 distance 5.98

> color zone #4 near #3 distance 6.08

> color zone #4 near #3 distance 6.18

> color zone #4 near #3 distance 6.28

> color zone #4 near #3 distance 6.18

> color zone #4 near #3 distance 6.08

> color zone #4 near #3 distance 5.98

> color zone #4 near #3 distance 5.88

> color zone #4 near #3 distance 5.78

> surface dust #4 size 7.3

> volume #4 level 0.09463

> save
> /Users/toddgreen/Desktop/personnel/novak/iga1_protease/cryosparc/198_surface.cxs

> select add #3

10226 atoms, 10421 bonds, 1282 residues, 1 model selected  

> ui tool show "Model Panel"

> select #3/A:1999

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1995-1999

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select #3/A:812

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:812-818

54 atoms, 53 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select #3/A:1140

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1140-1143

27 atoms, 26 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select #3/A:1924-1925

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/A:1924-1940

142 atoms, 146 bonds, 17 residues, 1 model selected  

> hide sel cartoons

> select #3/A:1875

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:1875-1881

56 atoms, 56 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select #3/A:1999

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1997-1999

20 atoms, 19 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select add #3

10226 atoms, 10421 bonds, 1282 residues, 1 model selected  

> select subtract #3

Nothing selected  

> hide #!4 models

> show #!4 models

> volume #4 level 0.09816

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> ui tool show "Side View"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #3 models

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> show #!1 models

> surface dust #1 size 7.3

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models


===== 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 - 76.3
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: MacBook Pro
      Model Identifier: MacBookPro18,4
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 38 days 11:17

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        PHL 226E9Q:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          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: 1.6.4
    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 Eric Pettersen, 13 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Tom Goddard, 13 months ago

Resolution: → duplicate
Status: assigned → closed

Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties. Probably connecting or disconnecting a display or waking from sleep.

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