Opened 12 months ago

Closed 11 months ago

#16389 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-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000036eeaf000 (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 0x000000036dea3000 (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 0x000000036ce97000 (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 0x000000036be8b000 (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 0x000000036ae7f000 (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 0x0000000369e73000 (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 0x0000000368e67000 (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 0x0000000367e5b000 (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 0x0000000366e4f000 (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 0x0000000365e43000 (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 0x0000000364e37000 (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 0x0000000363e2b000 (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 0x0000000362e1f000 (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 0x0000000361e13000 (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 0x0000000360e07000 (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 0x00000001e9ed0f40 (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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, 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.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 107)


{"app_name":"ChimeraX","timestamp":"2024-11-28 15:40:21.00 +0000","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","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 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"2B67208F-7EB1-478F-88D7-E7167856787A"}
{
  "uptime" : 840000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 26497,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2024-11-28 15:40:17.6958 +0000",
  "codeSigningMonitor" : 1,
  "incident" : "2B67208F-7EB1-478F-88D7-E7167856787A",
  "pid" : 78342,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-11-28 10:34:52.5033 +0000",
  "procStartAbsTime" : 19941201650102,
  "procExitAbsTime" : 20343679753260,
  "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":"24620DA0-5988-5B23-9E82-940A82D06194","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "E13F26CC-2B73-1C1F-F7BF-9C3A2414B42E",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 10,
  "sleepWakeUUID" : "E1E9B716-64A0-4DA9-9B87-59EAF0FC2A74",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4307369623\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100bd4000-100bd8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78342},
  "vmregioninfo" : "0x169 is not in any region.  Bytes before following region: 4307369623\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100bd4000-100bd8000    [   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":1},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6159499608},{"value":99},{"value":103},{"value":2305843023165301776},{"value":956},{"value":10079063415208758585},{"value":10079063420202271353},{"value":14757395258967641293},{"value":4294967286},{"value":6159499537},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8394712296},{"value":0},{"value":11},{"value":8219594560,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8219594784,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4330456624,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6476536864},"cpsr":{"value":1073745920},"fp":{"value":6159499680},"sp":{"value":6159499648},"esr":{"value":1442840704,"description":" 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=8.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           720K       38 \nColorSync                          656K       31 \nCoreAnimation                     2320K      110 \nCoreGraphics                        96K        6 \nCoreServices                       624K        2 \nCoreUI image data                 5456K       43 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             7.4G      184 \nMALLOC guard page                  192K       12 \nMALLOC_LARGE (reserved)          100.0M        1         reserved VM address space (unallocated)\nMach message                        96K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       57.0M       66 \nStack                            409.7M       66 \nVM_ALLOCATE                      401.7M      458 \nVM_ALLOCATE (reserved)           608.0M        5         reserved VM address space (unallocated)\n__AUTH                            2210K      407 \n__AUTH_CONST                      31.9M      625 \n__CTF                               824        1 \n__DATA                            25.0M      865 \n__DATA_CONST                      44.0M      866 \n__DATA_DIRTY                      2032K      234 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       567.5M      236 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2200K        1 \n__TEXT                           994.5M      883 \ndyld private memory                592K        6 \nmapped file                      572.1M       83 \nshared memory                     3184K       28 \n===========                     =======  ======= \nTOTAL                             11.2G     5274 \nTOTAL, minus reserved VM space    10.5G     5274 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "6adeb57a55f13df3622dee06b3c3cc10cf749019",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6297d96be2c9387df974efa4",
      "factorPackIds" : {

      },
      "deploymentId" : 240000032
    },
    {
      "rolloutId" : "642da32dea3b2418c750f848",
      "factorPackIds" : {

      },
      "deploymentId" : 240000004
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
      "experimentId" : "6643969b3099cf28e049862f",
      "deploymentId" : 400000007
    }
  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/SMARCA/M-32792/Prelim-DataQC.cxs format session

Opened cryosparc_P150_J139_005_volume_map.mrc gaussian as #4, grid size
360,360,360, pixel 0.648, shown at level 0.0206, step 1, values float32  
Opened cryosparc_P150_J133_006_volume_map.mrc as #3, grid size 360,360,360,
pixel 0.648, shown at level 0.00704, step 2, values float32  
Opened cryosparc_P150_J133_006_volume_map.mrc gaussian as #5, grid size
360,360,360, pixel 0.648, shown at level 0.0198, step 1, values float32  
Opened E3_ligase_complex_AMPH-19559_final_map.mrc as #6, grid size
300,300,300, pixel 0.731, shown at level 0.136, step 2, values float32  
Opened E3_ligase_complex_AMPH-19559_final_map.mrc gaussian as #7, grid size
300,300,300, pixel 0.731, shown at level 0.0455, step 1, values float32  
Opened cryosparc_P150_J139_005_volume_map.mrc as #8, grid size 360,360,360,
pixel 0.648, shown at level 0.00757, step 2, values float32  
opened ChimeraX session  

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

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/protein.pdb

Chain information for protein.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close #10

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_ligandPose1.sdf

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_ligandPose2.sdf

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_protein2.pdb

Chain information for state1_protein2.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close #10-11#12

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_protein1.pdb

Chain information for state1_protein1.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> show #!1 models

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_ligandPose1.sdf

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_protein2.pdb

Chain information for state1_protein2.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_ligandPose2.sdf

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_1/state2_protein1.pdb

Chain information for state2_protein1.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_1/state2_ligandPose1.sdf

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/state2_protein2.pdb

Chain information for state2_protein2.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/state2_ligandPose2.sdf

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!5 models

> hide #!14 models

> hide #15 models

> hide #!16 models

> hide #17 models

> hide #!1 models

> hide #!10 models

> hide #!12 models

> volume #4 level 0.01566

> show #!1 models

> hide #!4 models

> select up

20 atoms, 17 bonds, 4 residues, 2 models selected  

> select up

24 atoms, 22 bonds, 4 residues, 2 models selected  

> select up

154 atoms, 156 bonds, 22 residues, 2 models selected  

> select up

2474 atoms, 2548 bonds, 314 residues, 2 models selected  

> select down

154 atoms, 156 bonds, 22 residues, 2 models selected  

> select down

24 atoms, 22 bonds, 4 residues, 2 models selected  

> select down

20 atoms, 17 bonds, 4 residues, 2 models selected  

> select ~sel & ##selected

16240 atoms, 16559 bonds, 14 pseudobonds, 2051 residues, 5 models selected  

> select ~sel & ##selected

20 atoms, 17 bonds, 4 residues, 2 models selected  

> select ~sel

97587 atoms, 98711 bonds, 59 pseudobonds, 7156 residues, 36 models selected  

> select ~sel

20 atoms, 17 bonds, 4 residues, 2 models selected  

> select ~sel & ##selected

16240 atoms, 16559 bonds, 14 pseudobonds, 2051 residues, 5 models selected  

> select ~sel & ##selected

20 atoms, 17 bonds, 4 residues, 2 models selected  

> ui mousemode right select

> select #1/B:179

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:178

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #1/B:179

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add #1/B:56

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select add #1/B:55

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select subtract #1/B:56

21 atoms, 18 bonds, 3 residues, 1 model selected  

> show #!4 models

> hide #!4 models

> select add #1/B:181

35 atoms, 33 bonds, 4 residues, 1 model selected  

> select add #1/B:52

43 atoms, 40 bonds, 5 residues, 1 model selected  

> select subtract #1/B:52

35 atoms, 33 bonds, 4 residues, 1 model selected  

> style sel ball

Changed 35 atom styles  

> style sel ball

Changed 35 atom styles  

> select add #1/B:177

41 atoms, 38 bonds, 5 residues, 1 model selected  

> style sel ball

Changed 41 atom styles  

> select add #1/B:182

49 atoms, 45 bonds, 6 residues, 1 model selected  

> select add #1/B:56

56 atoms, 51 bonds, 7 residues, 1 model selected  

> style sel ball

Changed 56 atom styles  

> select #1/B:180

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #1/B:181

18 atoms, 18 bonds, 2 residues, 1 model selected  

> style sel ball

Changed 18 atom styles  

> style sel ball

Changed 18 atom styles  

> style sel stick

Changed 18 atom styles  

> style sel stick

Changed 18 atom styles  

> show sel atoms

> show #!4 models

> hide #!4 models

> select add #1/B:184

27 atoms, 26 bonds, 3 residues, 1 model selected  

> show sel atoms

> show #!4 models

> hide #!4 models

> select add #1/B:59

35 atoms, 33 bonds, 4 residues, 1 model selected  

> show sel atoms

> show #!4 models

> hide #11 models

> hide #13 models

> hide #!4 models

> select add #1/C:1407

44 atoms, 41 bonds, 5 residues, 1 model selected  

> show #!4 models

> hide #!4 models

> select add #1/B:55

53 atoms, 49 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 53 atom styles  

> style sel stick

Changed 53 atom styles  

> show #!4 models

> hide #!4 models

> select add #1/B:47

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

> style sel stick

Changed 59 atom styles  

> style sel stick

Changed 59 atom styles  

> select add #1/B:48

66 atoms, 61 bonds, 8 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 66 atom styles  

> style sel ball

Changed 66 atom styles  

> style sel ball

Changed 66 atom styles  

> style sel stick

Changed 66 atom styles  

> select clear

> select #1/B:178

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:177@CA

1 atom, 1 residue, 1 model selected  

> select #1/B:178@CA

1 atom, 1 residue, 1 model selected  

> select add #1/B:178@CB

2 atoms, 1 residue, 1 model selected  

> select clear

> select #1/B:178

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #1/B:177@CA

7 atoms, 5 bonds, 2 residues, 1 model selected  

> select add #1/B:179@CB

8 atoms, 6 bonds, 3 residues, 1 model selected  

> select add #1/B:179@SG

9 atoms, 6 bonds, 3 residues, 1 model selected  

> select add #1/B:177@SG

10 atoms, 6 bonds, 3 residues, 1 model selected  

> select add #1/B:177@CB

11 atoms, 6 bonds, 3 residues, 1 model selected  

> color sel byhetero

> show #!4 models

> save
> /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CryoEM_QC_DockedCompounds.cxs

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!12 models

> hide #!12 models

> select clear

> ui tool show Matchmaker

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

> matchmaker #!10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker BDup_fit_J139.pdb, chain A (#1) with state1_protein1.pdb, chain A
(#10), sequence alignment score = 3750.7  
RMSD between 740 pruned atom pairs is 0.193 angstroms; (across all 740 pairs:
0.193)  
  

> matchmaker #12 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker BDup_fit_J139.pdb, chain A (#1) with state1_protein2.pdb, chain A
(#12), sequence alignment score = 3750.7  
RMSD between 740 pruned atom pairs is 0.193 angstroms; (across all 740 pairs:
0.193)  
  

> show #!10 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #11 models

> hide #11 models

> show #13 models

> hide #!10 models

> show #!10 models

> show #11 models

> show #!1 models

> hide #!10 models

> hide #11 models

> hide #13 models

> show #13 models

> show #11 models

> hide #11 models

> hide #13 models

> show #11 models

> show #15 models

> hide #!1 models

> hide #!4 models

> hide #15 models

> show #15 models

> show #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #15 models

> show #13 models

Drag select of 4 cryosparc_P150_J139_005_volume_map.mrc gaussian , 2 bonds, 1
atoms  

> select clear

> show #!2 models

> hide #!1 models

> show #15 models

> show #!5 models

> hide #!4 models

> hide #13 models

> hide #15 models

> hide #11 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tarunnarwani/Desktop/movie1.mp4

Movie saved to /Users/tarunnarwani/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tarunnarwani/Desktop/movie2.mp4

Movie saved to /Users/tarunnarwani/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tarunnarwani/Desktop/movie3.mp4

Movie saved to /Users/tarunnarwani/Desktop/movie3.mp4  
  

> save /Users/tarunnarwani/Desktop/image1.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tarunnarwani/Desktop/movie4.mp4

Movie saved to /Users/tarunnarwani/Desktop/movie4.mp4  
  

> volume #3 level 0.02074

> ui mousemode right windowing

> ui mousemode right "contour level"

> ui mousemode right "play map series"

> ui mousemode right "contour level"

> ui mousemode right "move planes"

> ui mousemode right "rotate slab"

> ui mousemode right "play map series"

Drag select of 3 cryosparc_P150_J133_006_volume_map.mrc  

> ui mousemode right "play map series"

> volume #3 level 0.002471

> volume #3 level 0.004131

> volume #3 level 0.01534

> ui mousemode right "crop volume"

> ui mousemode right "tape measure"

> ui mousemode right "mark maximum"

> ui tool show "Side View"

> show #!1 models

> ui mousemode right select

> volume #3 level 0.009529

> volume #3 level 0.0003946

> volume #3 level 0.002886

> volume #3 level 0.01493

> show #11 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 - 88.1
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: Mac15,6
      Model Number: Z1AY0010LB/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 39 days, 16 hours, 52 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: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    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-ISOLDE: 1.8
    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-QScore: 1.1
    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-StarMap: 1.2.15
    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
    pyqtgraph: 0.13.7
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.8.12
    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, 11 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, 11 months ago

Resolution: → duplicate
Status: assigned → closed
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