Opened 2 months ago

Closed 2 months ago

#18771 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-15.5-x86_64-i386-64bit
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

Thread 0x000070002bc8e000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070002ac8b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700029c88000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700028c85000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700027c82000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700026c7f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700025c7c000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700024c79000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700023c76000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700022c73000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700021c70000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700020c6d000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001fc6a000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001ec67000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001dc64000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001cc61000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001bc5e000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001ac5b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700019c58000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007ff848cb4dc0 (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, PIL._imagingmath, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mask._mask (total: 54)


{"app_name":"ChimeraX","timestamp":"2025-09-12 09:40:20.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"F45FA137-8915-4D3B-808F-21ADE3F90FCC"}
{
  "uptime" : 6900000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 573055,
  "deployVersion" : 210,
  "modelCode" : "iMac20,2",
  "coalitionID" : 2030561,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
  },
  "captureTime" : "2025-09-12 09:39:48.9961 +0200",
  "codeSigningMonitor" : 0,
  "incident" : "F45FA137-8915-4D3B-808F-21ADE3F90FCC",
  "pid" : 6604,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-09-08 10:38:16.2208 +0200",
  "procStartAbsTime" : 6651131506471128,
  "procExitAbsTime" : 6993212219867330,
  "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":"779C63CD-13F5-56E9-8E6A-A12AEF46EFBB","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BF10E68F-7EB4-A7BF-BFD0-67ED6F3CDCA0",
  "appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "68F55CCD-537A-4DC7-A4F2-8C8E14EDDEA3",
  "bridgeVersion" : {"build":"22P5072","train":"9.5"},
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4486905856\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10b70c000-10b710000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6604},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4486905856\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10b70c000-10b710000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 22356791,
    "uuid" : "c26f6f9e-8230-3c1f-8c48-02d9de58fbc8",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2575.60.5"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703245021184,
    "size" : 632104,
    "uuid" : "3771ea6a-0fe5-3b63-961d-c09e01d5e680",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703247982592,
    "size" : 520192,
    "uuid" : "e9b27e7e-c40d-3405-a371-a753e116f54f",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703216578560,
  "size" : 30064771072,
  "uuid" : "57b0c2b8-36d6-3cf0-8bd0-0ac6133ec8b3"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=6.5G written=68.0M(1%) resident=0K(0%) swapped_out=68.0M(1%) unallocated=6.4G(99%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           384K       38 \nColorSync                          276K       33 \nCoreAnimation                     1480K      111 \nCoreGraphics                         8K        2 \nCoreUI image data                 2756K       23 \nFoundation                          16K        1 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             5.6G      182 \nMALLOC guard page                   72K       18 \nMach message                        76K        6 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        272K       68 \nStack                            464.5M       69 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      279.9M      255 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            41.9M     1094 \n__DATA_CONST                     121.2M      996 \n__DATA_DIRTY                      2589K      341 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       193.0M      152 \n__OBJC_RO                         61.3M        1 \n__OBJC_RW                         2395K        2 \n__TEXT                             1.4G     1117 \n__TEXT (graphics)                  752K        1 \n__TPRO_CONST                         16        2 \ndyld private memory                404K        5 \nmapped file                      261.9M       58 \nshared memory                     3648K       30 \n===========                     =======  ======= \nTOTAL                              8.6G     4620 \nTOTAL, minus reserved VM space     8.5G     4620 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "f012f69cd83fb9b412fbf7265a9e96c3a530b8f2",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "64628732bf2f5257dedc8988",
      "factorPackIds" : {

      },
      "deploymentId" : 240000001
    },
    {
      "rolloutId" : "670ea6eb7a111748a97092a4",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "689d2ab82518847024529994"
      },
      "deploymentId" : 240000173
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "28060e10-d4e5-4163-aa2b-d8bd088d5cbf",
      "experimentId" : "6685b283afc7c17197d69eec",
      "deploymentId" : 400000012
    }
  ]
}
}

System Profile:
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Thunderbolt Bus: iMac, Apple Inc., 58.2
Boot Volume File System Type: apfs
Memory Module: Slot 2 (Channel A / DIMM 0), 16 GB, DDR4, 2667 MHz, 029E, CMSA64GX4M4A2666C18
Memory Module: Slot 4 (Channel B / DIMM 0), 16 GB, DDR4, 2667 MHz, 029E, CMSA64GX4M4A2666C18
USB Device: USB31Bus
USB Device: USB Laser Mouse
USB Device: T2Bus
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Display: iMac, Retina 5K (5120 x 2880), Main, MirrorOff, Online
Display: ROG PG278QR, 2048 x 1152, MirrorOff, Online
Model: iMac20,2, BootROM 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0), 8 processors, 8-Core Intel Core i7, 3,8 GHz, 32 GB, SMC 
Graphics: AMD Radeon Pro 5700, AMD Radeon Pro 5700, PCIe, 8 GB
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x7BF), wl0: Jul 26 2024 22:36:01 version 9.30.514.0.32.5.94 FWID 01-68d7ff80
AirPort: 
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

still retrieving bundle list from toolshed  

> isolde shorthand

Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand  
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
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_it014_half2_class001.mrc

Opened run_it014_half2_class001.mrc as #1, grid size 512,512,512, pixel 1.05,
shown at level 0.00282, step 2, values float32  

> volume #1 level 0.001956

> volume #1 level 0.00149

> volume #1 level 0.0008918

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_it024_half2_class001.mrc

Opened run_it024_half2_class001.mrc as #2, grid size 512,512,512, pixel 1.05,
shown at level 0.00282, step 2, values float32  

> volume #2 level 0.0009973

> ui tool show "Map Filter"

> volume bin #2 binSize 2

Opened run_it024_half2_class001.mrc binned as #3, grid size 256,256,256, pixel
2.1, shown at step 1, values float32  

> volume #3 level 0.001055

> close #3

> volume bin #2 binSize 8

Opened run_it024_half2_class001.mrc binned as #3, grid size 64,64,64, pixel
8.4, shown at step 1, values float32  

> volume #3 level 0.0004786

> volume #3 level 0.0002436

> volume #3 level 0.0001497

> set bgColor black

> set bgColor white

> set bgColor black

> volume #3 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #3 style surface

> volume #3 change image level -0.0004297,0 level 0.003037,0.8 level 0.0116,1

> volume #3 level 0.0004551

> close session

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class006.mrc

Opened run_it030_class006.mrc as #1, grid size 512,512,512, pixel 1.05, shown
at level 0.0002, step 2, values float32  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class005.mrc

Opened run_it030_class005.mrc as #2, grid size 512,512,512, pixel 1.05, shown
at level 0.0026, step 2, values float32  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class004.mrc

Opened run_it030_class004.mrc as #3, grid size 512,512,512, pixel 1.05, shown
at level 0.075, step 2, values float32  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class003.mrc

Opened run_it030_class003.mrc as #4, grid size 512,512,512, pixel 1.05, shown
at level 1.8, step 2, values float32  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class002.mrc

Opened run_it030_class002.mrc as #5, grid size 512,512,512, pixel 1.05, shown
at level 0.0663, step 2, values float32  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class001.mrc

Opened run_it030_class001.mrc as #6, grid size 512,512,512, pixel 1.05, shown
at level 0.00456, step 2, values float32  

> tile

5 models tiled  

> volume #6 level 0.001683

> volume #6 level 0.0007488

> volume #2 level 0.0008627

> volume #6 level 0.0005333

> volume #6 level 0.00021

> volume #6 level 0.0004974

> volume #2 level 0.0004776

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> ~tile

> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #2 style surface region 0,0,0,511,511,511 step 1

> hide #!6 models

> show #!6 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #6 level 0.001539

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #6 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #6 style surface region 0,0,0,511,511,511 step 1

> volume #6 change image level -0.0005871,0 level 0.004556,0.8 level 0.0157,1

> volume #6 level 0.001359

> volume #6 level 0.0008889

> volume #6 level 0.0006361

> volume #6 level 0.0007444

> volume #6 level 0.001431

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_class001.mrc

Opened run_class001.mrc as #7, grid size 512,512,512, pixel 1.05, shown at
level 0.00278, step 2, values float32  

> ~tile

> hide #!7 models

> show #!7 models

> hide #!6 models

> show #!6 models

> volume #7 level 0.000704

> volume #7 level 0.0003846

> volume #6 level 0.001178

> volume #6 level 0.0008889

> volume #6 level 0.0004194

> shape sphere radius 5

> select add #8

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,292.66,0,1,0,74.965,0,0,1,318.35

> view matrix models #8,1,0,0,249.06,0,1,0,227.64,0,0,1,426.39

> view matrix models #8,1,0,0,296.94,0,1,0,260.04,0,0,1,418.89

> view matrix models #8,1,0,0,308.83,0,1,0,259.28,0,0,1,399.22

> volume #6 level 0.0007444

> view matrix models #8,1,0,0,340.95,0,1,0,246.69,0,0,1,397.34

> view matrix models #8,1,0,0,340.28,0,1,0,247.29,0,0,1,392.2

> select subtract #8

Nothing selected  

> show #!7 models

> hide #!7 models

> volume onesmask #8

Opened mask masked as #9, grid size 101,101,101, pixel 0.1, shown at step 1,
values int8  

> hide #8 models

> vop resample #9 ongrid #7

Opened mask masked resampled as #10, grid size 512,512,512, pixel 1.05, shown
at step 1, values int8  

> save /Users/jabrilg/Desktop/j64_recent_sphere.mrc models #10

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map.mrc

Opened j64_recent_map.mrc as #11, grid size 512,512,512, pixel 1.05, shown at
level 0.00279, step 2, values float32  

> volume #11 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #11 style surface region 0,0,0,511,511,511 step 1

> hide #!6 models

> volume #11 change image level -0.0005418,0 level 0.002786,0.8 level
> 0.03411,1

> close session

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_class001.mrc

Opened run_class001.mrc as #1, grid size 512,512,512, pixel 1.05, shown at
level 0.00278, step 2, values float32  

> volume #1 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #1 style surface region 0,0,0,511,511,511 step 1

> shape sphere radius 2

> select add #2

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,326.26,0,1,0,36.382,0,0,1,160.15

> volume #1 change image level -0.0006178,0 level 0.002778,0.8 level 0.03544,1

> volume #1 level 0.001282

> view matrix models #2,1,0,0,380.91,0,1,0,187.68,0,0,1,122.21

> view matrix models #2,1,0,0,360.27,0,1,0,225.12,0,0,1,196.55

> view matrix models #2,1,0,0,366.36,0,1,0,226.03,0,0,1,197.98

> view matrix models #2,1,0,0,366.94,0,1,0,254.74,0,0,1,180.11

> view matrix models #2,1,0,0,375.3,0,1,0,251.96,0,0,1,175.52

> volume onesmask #2

Opened mask masked as #3, grid size 101,101,101, pixel 0.04, shown at step 1,
values int8  

> vop resample #3 ongrid #1

Opened mask masked resampled as #4, grid size 512,512,512, pixel 1.05, shown
at step 1, values int8  

> save /Users/jabrilg/Desktop/j64_recent_sphere2.mrc models #4

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map.mrc

Opened j64_recent_map.mrc as #5, grid size 512,512,512, pixel 1.05, shown at
level 0.00279, step 2, values float32  

> volume #5 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #5 style surface region 0,0,0,511,511,511 step 1

> show #!1 models

> select subtract #2

Nothing selected  

> color #5 #ffb3ff8a models

> color #5 #ffb3ff74 models

> hide #!5 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map2.mrc

Opened j64_recent_map2.mrc as #6, grid size 512,512,512, pixel 1.05, shown at
level 0.00279, step 2, values float32  

> hide #!6 models

> show #!6 models

> hide #!1 models

> show #!1 models

> volume #6 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #6 style surface region 0,0,0,511,511,511 step 1

> hide #!1 models

> volume #6 change image level -0.000458,0 level 0.002789,0.8 level 0.03283,1

> volume #6 level 0.0013

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map_corrected.mrc

Opened j64_recent_map_corrected.mrc as #7, grid size 512,512,512, pixel 1.05,
shown at level 0.000631, step 2, values float32  

> close #7

> show #!5 models

> hide #!5 models

> show #!1 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map2.mrc

Opened j64_recent_map2.mrc as #7, grid size 512,512,512, pixel 1.05, shown at
level 0.00279, step 2, values float32  

> hide #!6 models

> show #!6 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map_2p1px_box256.mrc

Opened j64_recent_map_2p1px_box256.mrc as #8, grid size 256,256,256, pixel
2.1, shown at level 0.00279, step 1, values float32  

> hide #!6 models

> hide #!4 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> hide #!1 models

> show #!1 models

> volume #8 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #8 style surface

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #8 style image colorMode auto8 imageMode "full region"

> volume #8 level -0.0004495,0 level 0.002787,0.8 level 0.03422,1

> volume #8 level -0.004304,0.04615 level 0.002787,0.8 level 0.03422,1

> volume #8 style surface

> ui tool show "Map Coordinates"

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job067/run_class001.mrc

Opened run_class001.mrc as #9, grid size 256,256,256, pixel 2.1, shown at
level 0.0246, step 1, values float32  

> volume #9 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #9 style surface

> volume #9 change image level -0.0008415,0 level 0.02455,0.8 level 0.1633,1

> volume #9 level 0.006645

> volume #9 level 0.001376

> volume #9 level 0.002781

> close session

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job067/run_class001.mrc

Opened run_class001.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.0246, step 1, values float32  

> volume #1 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #1 style surface

> volume #1 change image level -0.0008415,0 level 0.02455,0.8 level 0.1633,1

> volume #1 level 0.006136

> volume #1 level 0.02661

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job068/run_it003_half2_class001.mrc

Opened run_it003_half2_class001.mrc as #2, grid size 256,256,256, pixel 2.1,
shown at level 0.0261, step 1, values float32  

> volume #2 level 0.005503

> volume #2 level 0.001999

> volume #2 level 0.002954

> volume #2 level 0.0106


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

still retrieving bundle list from toolshed  

> isolde shorthand

Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand  
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 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.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: iMac
      Model Identifier: iMac20,2
      Processor Name: 8-Core Intel Core i7
      Processor Speed: 3,8 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
      OS Loader Version: 583~1350

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 80 days, 22 hours, 34 minutes

Graphics/Displays:

    AMD Radeon Pro 5700:

      Chipset Model: AMD Radeon Pro 5700
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x731b
      Revision ID: 0x0040
      ROM Revision: 113-D1820Q-231
      VBIOS Version: 113-D182A2XG-013
      Option ROM Version: 113-D182A2XG-013
      EFI Driver Version: 01.01.231
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        ROG PG278QR:
          Resolution: 2048 x 1152
          UI Looks like: 2048 x 1152 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: #ASOT2TO5phXd
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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, 2 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 Eric Pettersen, 2 months ago

Resolution: → duplicate
Status: assigned → closed
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