Opened 5 weeks ago

Closed 5 weeks ago

#19001 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 0x0000700022e8c000 (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 0x0000700021e89000 (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 0x0000700020e86000 (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 0x000070001fe83000 (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 0x000070001ee80000 (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 0x000070001de7d000 (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 0x000070001ce7a000 (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 0x000070001be77000 (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 0x000070001ae74000 (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 0x0000700019e71000 (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 0x0000700018e6e000 (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 0x0000700017e6b000 (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 0x0000700016e68000 (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 0x0000700015e65000 (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 0x0000700014e62000 (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 0x0000700013e5f000 (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 0x0000700012e5c000 (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 0x0000700011e59000 (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 0x0000700010e56000 (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.surface._surface, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mask._mask, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio (total: 56)


{"app_name":"ChimeraX","timestamp":"2025-09-30 10:48:06.00 +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":"586632D4-90DF-4283-A60A-646A57C2DA68"}
{
  "uptime" : 8500000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 573055,
  "deployVersion" : 210,
  "modelCode" : "iMac20,2",
  "coalitionID" : 2030561,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
  },
  "captureTime" : "2025-09-30 10:47:46.0187 +0200",
  "codeSigningMonitor" : 0,
  "incident" : "586632D4-90DF-4283-A60A-646A57C2DA68",
  "pid" : 89153,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-09-26 16:06:32.4152 +0200",
  "procStartAbsTime" : 8225979791617915,
  "procExitAbsTime" : 8552443623951583,
  "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" : {"reasons":["deviceNotCapable"],"state":"unavailable"},
  "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: 4380741632\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1051cd000-1051d1000    [   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":89153},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4380741632\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1051cd000-1051d1000    [   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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    "uuid" : "ae16bb51-bedf-3c8a-9b96-5684b608789d",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    "name" : "_ribbons.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5976498176,
    "size" : 524288,
    "uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    "name" : "mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 6047354880,
    "size" : 442368,
    "uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    "name" : "_mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5949657088,
    "size" : 180224,
    "uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
    "name" : "_pdbio.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703248596992,
    "size" : 248656,
    "uuid" : "dab10aa4-8afa-3d02-9cde-6023554ac858",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703248846848,
    "size" : 48592,
    "uuid" : "a6d1f05a-0743-31b7-9fe2-268f06ccd51a",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703247421440,
    "size" : 560296,
    "uuid" : "19f23df9-b4a5-3be3-8777-5c8f0c5a43c8",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703249088512,
    "size" : 38264,
    "uuid" : "1fb5adb0-059e-3369-9c63-abde93e91499",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703345790976,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 5033928,
    "uuid" : "5614b329-06ef-3851-9d89-9ff5e56c9b74",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703247114240,
    "size" : 291594,
    "uuid" : "a709554b-250f-3213-b4dd-6708dd83f622",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703249317888,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4935667,
    "uuid" : "2f3a4185-6038-37d0-a02b-ec620bcd977b",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "3502.1.401"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703445082112,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3020526,
    "uuid" : "1ed7a7b9-e12f-348a-ac39-834f923795b6",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703310794752,
    "CFBundleShortVersionString" : "6.9",
    "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=13.7G written=303.9M(2%) resident=0K(0%) swapped_out=303.9M(2%) unallocated=13.4G(98%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                          1744K       42 \nColorSync                          296K       38 \nCoreAnimation                     1872K      129 \nCoreGraphics                         8K        2 \nCoreImage                           20K        1 \nCoreUI image data                 5260K       40 \nFoundation                          36K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                            12.3G      250 \nMALLOC guard page                   72K       18 \nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        248K       62 \nStack                            461.5M       63 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      809.9M      354 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            42.3M     1101 \n__DATA_CONST                     121.7M      998 \n__DATA_DIRTY                      2590K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       193.6M      153 \n__OBJC_RO                         61.3M        1 \n__OBJC_RW                         2395K        2 \n__TEXT                             1.4G     1123 \n__TEXT (graphics)                   16K        1 \n__TPRO_CONST                         16        2 \ndyld private memory                532K        7 \nmapped file                      302.0M       72 \nshared memory                     3756K       31 \n===========                     =======  ======= \nTOTAL                             15.8G     4853 \nTOTAL, minus reserved VM space    15.7G     4853 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "f012f69cd83fb9b412fbf7265a9e96c3a530b8f2",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "670ea6eb7a111748a97092a4",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "68cb4f2e5b018b060eb1a0ef"
      },
      "deploymentId" : 240000180
    },
    {
      "rolloutId" : "642da32dea3b2418c750f848",
      "factorPackIds" : {

      },
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    }
  ],
  "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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  

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 /Users/jabrilg/Downloads/emd_34359_additional_2.map

Opened emd_34359_additional_2.map as #1, grid size 420,420,420, pixel 1.33,
shown at level 0.18, step 2, values float32  

> volume #1 level 0.0968

> volume #1 level 0.2727

> 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 #2, grid size 512,512,512, pixel 1.05, shown at
level 0.00278, step 2, values float32  

> volume #2 level 0.0008412

> volume #2 level 0.0007637

> volume #2 step 4

> 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 #3, 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 #4, 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 #5, 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 #6, 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 #7, 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 #8, grid size 512,512,512, pixel 1.05, shown
at level 0.00456, step 2, values float32  

> hide #!1 models

> hide #!7 models

> hide #!2 models

> hide #!6 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!8 models

> show #!8 models

> hide #!4 models

> volume #8 level 0.001288

> show #!2 models

> volume #8 level 0.0005333

> hide #!2 models

> volume #8 level 0.001144

> show #!2 models

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,52.388,0,1,0,-167.15,0,0,1,-337.33

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.55048,0.32202,0.77024,-148.34,0.093451,0.89305,-0.44015,-29.526,-0.8296,0.31428,0.46151,-36.614

> view matrix models
> #1,0.74854,-0.043664,0.66165,-81.546,0.66033,0.14009,-0.7378,91.934,-0.060474,0.98918,0.13369,-274.53

> view matrix models
> #1,0.78538,0.21763,0.57949,-123.47,0.58151,0.061478,-0.81121,151.65,-0.21217,0.97409,-0.078272,-168.09

> view matrix models
> #1,0.94408,-0.17933,0.27669,20.279,0.20877,-0.32441,-0.92259,364.01,0.25521,0.92876,-0.26883,-213.57

> view matrix models
> #1,0.96252,-0.13388,0.23586,18.272,0.18,-0.33516,-0.92481,374.16,0.20287,0.9326,-0.2985,-192.36

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.96252,-0.13388,0.23586,-52.385,0.18,-0.33516,-0.92481,501.07,0.20287,0.9326,-0.2985,45.029

> view matrix models
> #1,0.96252,-0.13388,0.23586,-27.481,0.18,-0.33516,-0.92481,542.02,0.20287,0.9326,-0.2985,28.109

> fitmap #1 inMap #8

Fit map emd_34359_additional_2.map in map run_it030_class001.mrc using 62439
points  
correlation = 0.8864, correlation about mean = 0.4125, overlap = 103.4  
steps = 320, shift = 9.07, angle = 29.4 degrees  
  
Position of emd_34359_additional_2.map (#1) relative to run_it030_class001.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.97888599 0.01246413 0.20402662 -61.69361175  
0.20003988 0.14680722 -0.96872684 447.73588220  
-0.04202692 0.98908659 0.14121421 -60.19889181  
Axis 0.98774202 0.12413717 0.09463437  
Axis point 0.00000000 261.99055936 232.86191869  
Rotation angle (degrees) 82.33078505  
Shift along axis -11.05359193  
  

> volume #8 level 0.0004974

> hide #!1 models

> show #!1 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> shape sphere radius 50

> close #9

> shape sphere radius 80

> close #9

> shape sphere radius 120

> select add #9

3 models selected  

> view matrix models
> #1,0.97889,0.012464,0.20403,-52.635,0.20004,0.14681,-0.96873,449.51,-0.042027,0.98909,0.14121,-50.404,#9,1,0,0,9.0585,0,1,0,1.7702,0,0,1,9.795

> undo

> select subtract #1

1 model selected  

> show #!8 models

> view matrix models #9,1,0,0,182.61,0,1,0,141.76,0,0,1,212.84

> view matrix models #9,1,0,0,253.1,0,1,0,263.95,0,0,1,129.09

> view matrix models #9,1,0,0,292.97,0,1,0,244.42,0,0,1,91.053

> view matrix models #9,1,0,0,294.93,0,1,0,244.13,0,0,1,91.134

> volume #8 level 3.04e-05

> hide #!1 models

> hide #9 models

> show #!8 models

> set bgColor black

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

> volume #8 style surface region 0,0,0,511,511,511 step 1

> volume #8 change image level -0.0005871,0 level 0.004556,0.8 level 0.0157,1

> volume #8 level 0.0003194

> volume #8 level 0.0004639

> volume #8 level 0.0003194

> volume #8 level 0.0001026

> volume #8 level -7.796e-05

> volume #8 level 6.652e-05

> volume #8 level 0.0004639

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_sphere3.mrc

Opened j64_recent_sphere3.mrc as #10, grid size 512,512,512, pixel 1.05, shown
at level 0.0002, step 2, values int8  

> select subtract #9

Nothing selected  

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!10 models

> show #!10 models

> show #9 models

> hide #9 models

> show #!2 models

> color #10 #e7142bff models

> view #10 clip false

No displayed objects specified.  

> hide #!2 models

> view #10 clip false

No displayed objects specified.  

> view #10 clip false

No displayed objects specified.  

> show #!10 target m

> show #!2 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_sphere2.mrc

Opened j64_recent_sphere2.mrc as #11, grid size 512,512,512, pixel 1.05, shown
at level 5e-05, step 2, values int8  

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!10 models

> show #!10 models

> show #!2 models

> 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 #!11 models

> hide #!2 models

> show #!2 models

> show #!11 models

> hide #!10 models

> hide #!2 models

> show #!11 target m

> view #11 clip false

> show #!10 models

> hide #!11 models

> view #10 clip false

No displayed objects specified.  

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_sphere.mrc

Opened j64_recent_sphere.mrc as #12, grid size 512,512,512, pixel 1.05, shown
at level 5e-05, step 2, values int8  

> hide #!10 models

> view #12 clip false

> show #!2 models

> show #!11 models

> hide #!2 models

> show #!2 models

> shape sphere radius 10

> select add #13

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #13,1,0,0,403.55,0,1,0,239.97,0,0,1,230.83

> view matrix models #13,1,0,0,334.6,0,1,0,264.26,0,0,1,210.32

> view matrix models #13,1,0,0,326.72,0,1,0,252.43,0,0,1,206.13

> color #2 #ffffb298 models

> color #2 #ffffb299 models

> view matrix models #13,1,0,0,320.02,0,1,0,247.46,0,0,1,203.09

> view matrix models #13,1,0,0,316.61,0,1,0,239.4,0,0,1,207.26

> volume #2 change image level -0.0006188,0 level 0.002774,0.8 level 0.03277,1

> volume #2 level 0.001621

> view matrix models #13,1,0,0,290.27,0,1,0,242.96,0,0,1,207.78

> view matrix models #13,1,0,0,289.76,0,1,0,255.57,0,0,1,196.21

> show #!8 models

> hide #!2 models

> volume #8 level 0.0007889

> hide #!12 models

> hide #!11 models

> color #8 #e5bf99a2 models

> color #8 #e5bf99a3 models

> volume #8 level 0.0003555

> view matrix models #13,1,0,0,294.79,0,1,0,253.17,0,0,1,188.78

> view matrix models #13,1,0,0,294.07,0,1,0,253.68,0,0,1,190.87

> volume onesmask #13

Opened mask masked as #14, grid size 101,101,101, pixel 0.2, shown at step 1,
values int8  

> hide #13 models

> select subtract #13

Nothing selected  

> volume #8 level 0.0008612

> volume #8 level 0.001186

> volume #8 level -0.0001863

> volume #8 level -4.184e-05

> volume #8 level 0.0002471

> vop resample #14 ongrid #2

Opened mask masked resampled as #15, grid size 512,512,512, pixel 1.05, shown
at step 1, values int8  

> save /Users/jabrilg/Desktop/j64_recent_sphere4.mrc models #15

> volume #8 level 0.001006

> volume #10 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 255,255,255 imageMode orthoplanes

> volume #10 style surface

> volume #8 style image region 0,0,0,511,511,511 step 2 orthoplanes xyz
> positionPlanes 255,255,255 imageMode orthoplanes

> volume #8 region 0,0,254,511,511,254 step 1 colorMode auto8 imageMode "full
> region"

> volume #8 region 0,0,0,511,511,511 step 2

> volume #8 region 0,0,0,511,511,511 step 1 colorMode opaque8 imageMode "box
> faces"

> volume #8 style surface

> show #!14 models

> hide #!15 models

> select add #14

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #14,1,0,0,-0.34637,0,1,0,0.85475,0,0,1,12.195

> vop resample #14 ongrid #2

Opened mask masked resampled as #16, grid size 512,512,512, pixel 1.05, shown
at step 1, values int8  

> save /Users/jabrilg/Desktop/j64_recent_sphere4.mrc models #16

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map3.mrc

Opened j64_recent_map3.mrc as #17, grid size 512,512,512, pixel 1.05, shown at
level 0.00281, step 2, values float32  

> volume #17 level 0.0007902

> hide #!8 models

> volume #17 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #17 style surface region 0,0,0,511,511,511 step 1

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!17 models

> hide #!16 models

> show #!14 models

> volume #8 region 0,0,0,511,511,511

> ui mousemode right "translate selected models"

> view matrix models #14,1,0,0,2.4041,0,1,0,-1.2817,0,0,1,27.81

> view matrix models #14,1,0,0,-18.739,0,1,0,-0.7759,0,0,1,28.413

> view matrix models #14,1,0,0,-18.713,0,1,0,-8.5654,0,0,1,22.626

> vop resample #14 ongrid #2

Opened mask masked resampled as #18, grid size 512,512,512, pixel 1.05, shown
at step 1, values int8  

> save /Users/jabrilg/Desktop/j64_recent_sphere5.mrc models #18

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map4.mrc

Opened j64_recent_map4.mrc as #19, grid size 512,512,512, pixel 1.05, shown at
level 0.0028, step 2, values float32  

> volume #8 level -0.02118

> volume #8 level 0.0121

> volume #8

> hide #!19 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> volume #8 style image region 0,0,0,511,511,511 step 2

> volume #8 style surface region 0,0,0,511,511,511 step 1

> volume #8 level 0.0004292

> show #!19 models

> volume #19 level 0.0009493

> hide #!8 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!17 models

> open EMD-34359

'EMD-34359' has no suffix  

> open EMD:34359

No such database 'emd'  

> open EMDB:34359

Summary of feedback from opening 34359 fetched from emdb  
---  
notes | Fetching compressed map 34359 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34359/map/emd_34359.map.gz  
Fetching map header 34359 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34359/header/emd-34359.xml  
  
Opened emdb 34359 as #20, grid size 420,420,420, pixel 1.33, shown at level
0.156, step 2, values float32, fit PDB 8gxq  

> select subtract #14

Nothing selected  

> hide #!17 models

> hide #!19 models

> volume #20 level 0.1362

> volume #20 level 0.1494

> volume #20 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #20 style surface region 0,0,0,419,419,419 step 1

> show #!19 models

> hide #!19 models

> volume #20 change image level 0.0001237,0 level 0.3982,0.8 level 2.545,1

> volume #20 level 0.1288

> hide #!20 models

> show #!20 models

> show #!19 models

> hide #!20 models

> show #!8 models

> hide #!19 models

> volume #19 level 0.001479

> hide #!19 models

> volume #8 level 0.0008265

> ui mousemode right "tape measure"

> marker segment #21 position 291.8,133.3,76.18 toPosition 238.7,340.3,431.2
> color yellow radius 0.2625 label 414.4 labelHeight 41.44 labelColor yellow

> marker segment #21 position 360.3,133.6,74.37 toPosition 167.2,300.1,442.4
> color yellow radius 0.2625 label 447.7 labelHeight 44.77 labelColor yellow

> hide #!21 models

> show #!21 models

> marker delete #21

> ui mousemode right "tape measure"

> ui mousemode right "crop volume"

> ui mousemode right "tape measure"

> ui mousemode right distance

> ui mousemode right "tape measure"

> marker segment #21 position 192.4,140.1,266 toPosition 102.7,497.2,51.41
> color yellow radius 0.2625 label 426.1 labelHeight 42.61 labelColor yellow

> marker delete #21

> volume #8 level -0.001305

> marker segment #21 position -0.525,36.43,279.5 toPosition -75.22,528.2,280.5
> color yellow radius 0.2625 label 497.4 labelHeight 49.74 labelColor yellow

> marker segment #21 position 10.48,33.64,537.1 toPosition 529.8,532.5,537.1
> color yellow radius 0.2625 label 720.1 labelHeight 72.01 labelColor yellow

> marker segment #21 position 1.723,3.206,537.1 toPosition 1.448,536.8,537.1
> color yellow radius 0.2625 label 533.5 labelHeight 53.35 labelColor yellow

> volume #8 level 0.0009349

> marker delete #21

> marker segment #21 position 161.9,320.1,421.8 toPosition 332.3,133.9,40.2
> color yellow radius 0.2625 label 457.5 labelHeight 45.75 labelColor yellow

> open 8gxs

8gxs title:  
PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state [more
info...]  
  
Chain information for 8gxs #22  
---  
Chain | Description | UniProt  
BA | Transcription initiation factor IIB | TF2B_HUMAN 1-316  
DA | Transcription initiation factor TFIID subunit 1 | TAF1_HUMAN 1-1872  
DB | Transcription initiation factor TFIID subunit 2 | TAF2_HUMAN 1-1199  
DD Dd | Transcription initiation factor TFIID subunit 4 | TAF4_HUMAN 1-1085  
DE De | Transcription initiation factor TFIID subunit 5 | TAF5_HUMAN 1-800  
DF Df | Transcription initiation factor TFIID subunit 6 | TAF6_HUMAN 1-677  
DG | Transcription initiation factor TFIID subunit 7 | TAF7_HUMAN 1-349  
DH | Transcription initiation factor TFIID subunit 8 | TAF8_HUMAN 1-310  
DI Di | Transcription initiation factor TFIID subunit 9 | TAF9_HUMAN 1-264  
DJ Dj | Transcription initiation factor TFIID subunit 10 | TAF10_HUMAN 1-218  
DL Dl | Transcription initiation factor TFIID subunit 12 | TAF12_HUMAN 1-161  
DO | Transcription initiation factor IIA subunit 2 | T2AG_HUMAN 1-109  
DP | TATA-box-binding protein | TBP_HUMAN 1-339  
DQ | Transcription initiation factor IIA subunit 1 | TF2AA_HUMAN 1-376  
Dc | Transcription initiation factor TFIID subunit 3 | TAF3_HUMAN 1-929  
Dk | Transcription initiation factor TFIID subunit 11 | TAF11_HUMAN 1-211  
Dm | Transcription initiation factor TFIID subunit 13 | TAF13_HUMAN 1-124  
EA | General transcription factor IIE subunit 1 | T2EA_HUMAN 1-439  
EB | Transcription initiation factor IIE subunit beta | T2EB_HUMAN 1-291  
FA | General transcription factor IIF subunit 1 | T2FA_HUMAN 1-517  
FB | General transcription factor IIF subunit 2 | T2FB_HUMAN 1-249  
HA | General transcription and DNA repair factor IIH helicase subunit XPD | ERCC2_HUMAN 1-760  
HB | General transcription factor IIH subunit 1 | TF2H1_HUMAN 1-548  
HC | General transcription factor IIH subunit 4 | TF2H4_HUMAN 1-462  
HD | CDK-activating kinase assembly factor MAT1 | MAT1_HUMAN 1-309  
HE | General transcription factor IIH subunit 3 | TF2H3_HUMAN 1-308  
HF | General transcription factor IIH subunit 5 | TF2H5_HUMAN 1-71  
HG | General transcription factor IIH subunit 2 | TF2H2_HUMAN 1-395  
HH | General transcription and DNA repair factor IIH helicase subunit XPB | ERCC3_HUMAN 1-782  
HI | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346  
HJ | Cyclin-H | CCNH_HUMAN 1-323  
NA NE | Histone H3 | A0A310TTQ1_XENLA 400-535 600-735  
NB NF | Histone H4 | H4_XENLA 0-102 200-302  
NC NG | HISTONE H2A.Z |   
ND NH | Histone H2B | A0A8J0U496_XENLA 1197-1322 1397-1522  
NX | DNA (162-mer) |   
NY | DNA (162-mer) |   
PA | DNA-directed RNA polymerase subunit | A0A8D1DPV6_PIG 1-1970  
PB | DNA-directed RNA polymerase subunit beta | A0A4X1TVZ5_PIG 1-1174  
PC | DNA-directed RNA polymerase II subunit RPB3 | I3LCH3_PIG 1-275  
PD | DNA-directed RNA polymerase II subunit RPB4 | A0A481BYI6_PIG 1-142  
PE | DNA-directed RNA polymerase II subunit E | A0A4X1VTX4_PIG 1-210  
PF | DNA-directed RNA polymerase II subunit F | A0A4X1VEK9_PIG 1-127  
PG | DNA-directed RNA polymerase II subunit RPB7 | A0A4X1VKG7_PIG 1-172  
PH | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | A0A4X1ULF2_PIG 1-150  
PI | DNA-directed RNA polymerase II subunit RPB9 | RPB9_PIG 1-125  
PJ | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | A0A493TD97_ANAPP 1-67  
PK | RNA_pol_L_2 domain-containing protein | A0A4X1UK25_PIG 1-117  
PL | RPB12 | A0A4X1TRS6_PIG 1-58  
X | DNA (228-mer) |   
Y | DNA (228-mer) |   
a | Mediator of RNA polymerase II transcription subunit 1 | MED1_HUMAN 1-1581  
b | Mediator of RNA polymerase II transcription subunit 29 | MED29_HUMAN 1-200  
c | Mediator of RNA polymerase II transcription subunit 27 | MED27_HUMAN 1-311  
d | Mediator of RNA polymerase II transcription subunit 4 | MED4_HUMAN 1-270  
e | Mediator of RNA polymerase II transcription subunit 28 | MED28_HUMAN 1-178  
f | Mediator of RNA polymerase II transcription subunit 6 | MED6_HUMAN 1-246  
g | Mediator of RNA polymerase II transcription subunit 7 | MED7_HUMAN 1-233  
h | Isoform 2 of Mediator of RNA polymerase II transcription subunit 8 | MED8_HUMAN 1-268  
i | Mediator of RNA polymerase II transcription subunit 9 | MED9_HUMAN 1-146  
j | Mediator of RNA polymerase II transcription subunit 10 | MED10_HUMAN 1-135  
k | Mediator of RNA polymerase II transcription subunit 11 | MED11_HUMAN 1-117  
l | Mediator of RNA polymerase II transcription subunit 30 | MED30_HUMAN 1-178  
m | Mediator of RNA polymerase II transcription subunit 31 | MED31_HUMAN 1-131  
n | Mediator of RNA polymerase II transcription subunit 14 | MED14_HUMAN 1-1454  
o | Mediator of RNA polymerase II transcription subunit 15 | MED15_HUMAN 1-788  
p | Isoform 2 of Mediator of RNA polymerase II transcription subunit 16 | MED16_HUMAN 1-841  
q | Mediator of RNA polymerase II transcription subunit 17 | MED17_HUMAN 1-651  
r | Mediator of RNA polymerase II transcription subunit 18 | MED18_HUMAN 1-208  
s | Mediator of RNA polymerase II transcription subunit 19 | MED19_HUMAN 1-244  
t | Mediator of RNA polymerase II transcription subunit 20 | MED20_HUMAN 1-212  
u | Mediator of RNA polymerase II transcription subunit 21 | MED21_HUMAN 1-144  
v | Mediator of RNA polymerase II transcription subunit 22 | MED22_HUMAN 1-200  
w | Mediator of RNA polymerase II transcription subunit 23 | MED23_HUMAN 1-1368  
x | Mediator of RNA polymerase II transcription subunit 24 | MED24_HUMAN 1-989  
y | Mediator of RNA polymerase II transcription subunit 25 | MED25_HUMAN 1-747  
z | Mediator of RNA polymerase II transcription subunit 26 | MED26_HUMAN 1-600  
  
Non-standard residues in 8gxs #22  
---  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> hide #!21 models

> hide #!22 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!22 models

> ui mousemode right distance

> distance #22/n:931@CG #22/NY:-118@C5'

Distance between 8gxs #22/n ARG 931 CG and /NY DG -118 C5': 373.038Å  

> show #!8 models

> select add #22

185972 atoms, 190592 bonds, 773 pseudobonds, 22937 residues, 5 models selected  

> select clear

> select add #22

185972 atoms, 190592 bonds, 773 pseudobonds, 22937 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #22,1,0,0,116.23,0,1,0,-152.63,0,0,1,-315.11,#23,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.9625,0.12936,0.23846,21.173,0.13782,0.52398,-0.84051,187.38,-0.23368,0.84185,0.4865,-387.66,#23,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #22,0.94177,0.1938,0.2748,-3.637,0.17075,0.42838,-0.88732,221.64,-0.28968,0.88257,0.37034,-353.4,#23,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.94177,0.1938,0.2748,-112.63,0.17075,0.42838,-0.88732,362.79,-0.28968,0.88257,0.37034,-18.844,#23,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #22,0.94177,0.1938,0.2748,-108.77,0.17075,0.42838,-0.88732,365.83,-0.28968,0.88257,0.37034,-24.898,#23,1,0,0,0,0,1,0,0,0,0,1,0

> fitmap #22 inMap #8

Fit molecule 8gxs (#22) to map run_it030_class001.mrc (#8) using 185972 atoms  
average map value = 0.00327, steps = 388  
shifted from previous position = 28.2  
rotated from previous position = 19.5 degrees  
atoms outside contour = 72520, contour level = 0.00093486  
  
Position of 8gxs (#22) relative to run_it030_class001.mrc (#8) coordinates:  
Matrix rotation and translation  
0.98958682 0.04012463 0.13823149 -53.06098352  
0.12974024 0.16723732 -0.97734290 459.69529692  
-0.06233298 0.98509984 0.16029006 -61.44742674  
Axis 0.99379304 0.10156708 0.04538190  
Axis point 0.00000000 268.59891914 242.40520901  
Rotation angle (degrees) 80.87684503  
Shift along axis -8.83032743  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> ui mousemode right distance

> distance #22/NX:113@P #22/n:1275@CD

Distance between 8gxs #22/NX DC 113 P and /n PRO 1275 CD: 378.435Å  

> hide #!22 models

> hide #!23 models

> hide #23.1 models

> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_box600.mrc

Opened j64_box600.mrc as #24, grid size 600,600,600, pixel 1.05, shown at
level 0.00197, step 4, values float32  

> ui tool show "Map Coordinates"

> volume #24 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"

> volume #24 style surface region 0,0,0,599,599,599 step 1

> show #!2 models

> hide #!2 models

> show #!8 models

> hide #!8 models

> volume #24 change image level -0.0005017,0 level 0.001966,0.8 level
> 0.03277,1

> volume #24 level 0.0006826

> show #!8 models

> hide #!8 models

> ui mousemode right "tape measure"

> marker delete #21

> marker segment #21 position 327,344.5,68.22 toPosition 336.1,413.1,259.4
> color yellow radius 0.2625 label 203.3 labelHeight 20.33 labelColor yellow

> marker delete #21

> marker segment #21 position 436,219.5,95.87 toPosition 493.7,355.2,183 color
> yellow radius 0.2625 label 171.2 labelHeight 17.12 labelColor yellow

> marker delete #21

> marker segment #21 position 435.2,220.5,101 toPosition 233.2,431.4,506 color
> yellow radius 0.2625 label 499.3 labelHeight 49.93 labelColor yellow

> hide #!21 models

> show #!22 models

> hide #!24 models

> show #!24 models

> hide #!22 models

> hide #!20 models

> show #!20 models

> hide #!24 models

> show #!24 models

> hide #!24 models

> show #!24 models


===== 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: 100 days, 1 hour, 12 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, 5 weeks 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, 5 weeks ago

Resolution: → duplicate
Status: assigned → closed
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