Opened 7 months ago

Closed 7 months ago

#17174 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-15.3.2-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 0x0000700028c8d000 (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 0x0000700027c8a000 (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 0x0000700026c87000 (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 0x0000700025c84000 (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 0x0000700024c81000 (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 0x0000700023c7e000 (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 0x0000700022c7b000 (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 0x0000700021c78000 (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 0x0000700020c75000 (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 0x000070001fc72000 (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 0x000070001ec6f000 (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 0x000070001dc6c000 (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 0x000070001cc69000 (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 0x000070001bc66000 (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 0x000070001ac63000 (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 0x0000700019c60000 (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 0x0000700018c5d000 (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 0x0000700017c5a000 (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 0x0000700016c57000 (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 0x00007ff8481e7b00 (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.pdb_lib._load_libs, chimerax.surface._surface, 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, lxml._elementpath, lxml.etree, 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, PIL._imagingmath, PIL._webp (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-03-24 14:09:29.00 +0100","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 15.3.2 (24D81)","roots_installed":0,"name":"ChimeraX","incident_id":"03FAF53B-157D-4242-84D7-56F7A490C0A3"}
{
  "uptime" : 250000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "coalitionID" : 1003,
  "osVersion" : {
    "train" : "macOS 15.3.2",
    "build" : "24D81",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-24 14:08:52.5349 +0100",
  "codeSigningMonitor" : 0,
  "incident" : "03FAF53B-157D-4242-84D7-56F7A490C0A3",
  "pid" : 34762,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-24 09:43:10.9461 +0100",
  "procStartAbsTime" : 241693401052098,
  "procExitAbsTime" : 255450736333536,
  "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":"C4027B15-248B-5659-BACC-6FB29543A4B7","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "8D528D7E-5C72-169F-357F-E09EC31F9564",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bootSessionUUID" : "ECAC3F3E-CD7E-4414-A068-42C10232CC05",
  "wakeTime" : 39,
  "bridgeVersion" : {"build":"22P3060","train":"9.3"},
  "sleepWakeUUID" : "DB7CFAF6-970D-4FED-ADE4-16B7E49EF866",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4507873280\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10cb0b000-10cb0f000    [   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":34762},
  "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\nVM - (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\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: 4507873280\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10cb0b000-10cb0f000    [   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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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebpdemux.2.dylib",
    "name" : "libwebpdemux.2.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5836869632,
    "size" : 32768,
    "uuid" : "bf1dedf6-3f1f-3378-9ec6-c91ecb5c45e3",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libsharpyuv.0.dylib",
    "name" : "libsharpyuv.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703217029120,
    "size" : 245760,
    "uuid" : "c214d771-f6a3-30be-b657-b4e0cb81c9df",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703217274880,
    "size" : 49152,
    "uuid" : "2b452c39-67e1-3f73-87ca-5e07d5f1e90d",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703215857664,
    "size" : 561144,
    "uuid" : "12e8dc9e-ee00-37e7-8830-dc84a6de23b1",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703217508352,
    "size" : 40936,
    "uuid" : "c55810b0-b8d2-3648-9009-570354c94d10",
    "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" : 140703312719872,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 5042162,
    "uuid" : "cd52ebdf-7b39-37d9-9f84-9bb672715b96",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703215550464,
    "size" : 294906,
    "uuid" : "43e79603-edb3-3d9a-995b-91dfc8e49a9c",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703217737728,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4841443,
    "uuid" : "404c409f-d28c-309d-ade3-f0ee6f1ca33d",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "3302.1.400"
  },
  {
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    "arch" : "x86_64",
    "base" : 140703410225152,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3002358,
    "uuid" : "0d3fd4c1-55be-30b9-aa97-225609c52278",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 21999608,
    "uuid" : "e3f76bb8-4950-3c7a-8aa7-8516a93aeeb9",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2575.40.6"
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    "size" : 572544,
    "uuid" : "f2913392-361a-304f-b30d-486be5639e2d",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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    "arch" : "x86_64",
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    "size" : 511996,
    "uuid" : "8323bbd6-c37a-33d4-bd4e-d12bc3b17415",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
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],
  "sharedCache" : {
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  "uuid" : "516bea14-552c-3fc6-ab95-a99ee266aaf3"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=4.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 36.6M        1 \nCG image                           648K       56 \nCG raster data                       8K        1 \nColorSync                          280K       38 \nCoreAnimation                     5948K      229 \nCoreGraphics                        20K        4 \nCoreServices                       620K        2 \nCoreUI image data                 5728K       45 \nDispatch continuations           128.0M        1 \nFoundation                          36K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.9G    11923 \nMALLOC guard page                   48K       12 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        280K       70 \nStack                            488.0M       71 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      350.4M      369 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            41.8M     1099 \n__DATA_CONST                     114.5M      978 \n__DATA_DIRTY                      2569K      341 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5176K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       216.7M      165 \n__OBJC_RO                         76.9M        1 \n__OBJC_RW                         2375K        2 \n__TEXT                             1.4G     1115 \n__TPRO_CONST                       272K        2 \ndyld private memory                276K        5 \nmapped file                      578.1M      101 \nowned unmapped memory            125.2M        1 \nshared memory                     3024K       35 \n===========                     =======  ======= \nTOTAL                              6.5G    16691 \nTOTAL, minus reserved VM space     6.4G    16691 \n",
  "legacyInfo" : {
  "threadTriggered" : {
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},
  "logWritingSignature" : "0cd94223fc2c91e3df682c71721754d0730f484c",
  "trialInfo" : {
  "rollouts" : [
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.09, step 1, values float32  
opened ChimeraX session  

> volume #4 level 0.08

> hide #13/J,L atoms

> hide #13/K:6-46 atoms

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif" width 1984 height
> 1210 supersample 3

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> volume #4 level 0.06

> show #13/A:83,85 atoms

> show #13/K:39-40 atoms

> show #13/L:6-7 atoms

> select clear

> show #13/L,J #13/K:7-46 atoms

> color #13/L light gray

> color #13/K dim gray

> color #13/J dark red

> color #13/I rebecca purple

> color #13/B forest green

> color #13/C,D,E,F,G,H khaki

> color #13/A steel blue

> color #13/A:232-350 dark turquoise

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif" width 1984 height
> 1210 supersample 3

> color #13/A. byhet

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #13/A byhetero

> ui tool show "Side View"

> hide #13/K:7-46 #13/L cartoons

> hide #13/K:7-46 #13/L atoms

> show #13/K:39-40 #13/L:6-7 atoms

> ui tool show Distances

> show #!11 models

Exactly two atoms must be selected!  

> hide #!4 models

> show #13/K:39-41 #13/L:6-7 atoms

> select #13/A:83@OD1

1 atom, 1 residue, 1 model selected  

> select add #13/K:40@N2

2 atoms, 2 residues, 1 model selected  

> distance #13/A:83@OD1 #13/K:40@N2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and /K DG 40 N2: 3.013Å  

> distance style color black

> ui tool show "Color Actions"

> distance style color dimgrey

> select #13/A:85@NZ

1 atom, 1 residue, 1 model selected  

> select add #13/K:41@O2

2 atoms, 2 residues, 1 model selected  

> distance #13/A:85@NZ #13/K:41@O2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /K DC 41 O2: 3.020Å  

> select #13/A:85@NZ

1 atom, 1 residue, 1 model selected  

> select add #13/L:6@N2

2 atoms, 2 residues, 1 model selected  

> distance #13/A:85@NZ #13/L:6@N2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /L DG 6 N2: 3.258Å  

> select #13/A:83@OD1

1 atom, 1 residue, 1 model selected  

> select add #13/A:85@NZ

2 atoms, 2 residues, 1 model selected  

> distance #13/A:83@OD1 #13/A:85@NZ

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and LYS 85 NZ: 2.939Å  

> select add #11

2 atoms, 12 pseudobonds, 2 residues, 3 models selected  

> color sel dim gray

> select clear

> select add #13/A:85

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

> select add #13/A:83

17 atoms, 15 bonds, 2 residues, 1 model selected  

> color sel steel blue

> color sel byhetero

> color sel dim gray

> select clear

> show #!4 models

> volume #4 level 0.08

> volume #4 level 0.07

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3

> hide #!4 models

> hide #13/K:39 atoms

> show #!4 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3

> show #11.1 models

> distance style decimalPlaces 1

> hide #11.1 models

> view #13/L

> volume #4 level 0.06

> show #13/k,l cartoons

> show #13/k:7-46 #13/l atoms

> hide #!4 models

> select #13/A:178

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #13/A:193

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

> show sel atoms

> show #!4 models

> hide #!11 models

> hide #13/A:83,85 atoms

> select clear

> surface dust #4 size 7.25

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3

> show #13/A:191 atoms

> select #13/A:193@OD1

1 atom, 1 residue, 1 model selected  

> select add #13/L:9@N2

2 atoms, 2 residues, 1 model selected  

> distance #13/A:193@OD1 #13/L:9@N2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1
and /L DG 9 N2: 2.6Å  

> show #!11 models

> select #13/K:39

19 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> hide #!4 models

> select #13/K:39@OP1

1 atom, 1 residue, 1 model selected  

> select add #13/A:191@OG

2 atoms, 2 residues, 1 model selected  

> distance #13/K:39@OP1 #13/A:191@OG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1
and /A SER 191 OG: 2.9Å  

> show sel cartoons

> show #!4 models

> color sel dim gray

> select clear

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!13 models

> show #!13 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #4 level 0.09

> volume #4 level 0.05

> volume #4 level 0.06

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3

> hide #!4 models

> show #!4 models

> hide #!11 models

> select #13/K:4

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

> select add #13/K:3

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select add #13/K:2

45 atoms, 47 bonds, 3 residues, 1 model selected  

> select up

886 atoms, 986 bonds, 45 residues, 1 model selected  

> select down

45 atoms, 47 bonds, 3 residues, 1 model selected  

> hide #!4 models

> select add #13/K:1

54 atoms, 56 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #13/K:3@P

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

886 atoms, 986 bonds, 45 residues, 1 model selected  

> select down

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #13/K:2@O3'

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select up

41 atoms, 45 bonds, 2 residues, 1 model selected  

> color sel byhetero

> select clear

> select #13/K:6

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #13/A:295

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

> select add #13/I:140

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

> show sel atoms

> show #!4 models

> hide #!4 models

> select #13/K:6

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #13/K:7

42 atoms, 45 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show #!4 models

> volume #4 level 0.09

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

22 atoms, 24 bonds, 1 residue, 1 model selected  

> hide #!4 models

> select subtract #13/K:6@O3'

21 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #!4 models

> hide #!4 models

> select #13/K:7@OP1

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select #13/K:6@O3'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show #!4 models

> hide #!4 models

> select #13/I:50

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

> select add #13/I:51

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

> show sel atoms

> show #!4 models

> volume #4 level 0.06

> volume #4 level 0.08

> select #13/I:51@CD

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

11 atoms, 9 bonds, 2 residues, 1 model selected  

> select up

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

> hide sel atoms

> select clear

> volume #4 level 0.1

> color #13/i byhetero

> select clear

> select #13/K:7

20 atoms, 21 bonds, 1 residue, 1 model selected  

> volume #4 level 0.07

> select clear

> volume #4 level 0.09

> show #!2 models

> hide #!2 models

> hide #!4 models

> select #13/A:295@SG

1 atom, 1 residue, 1 model selected  

> select add #13/I:140@SG

2 atoms, 2 residues, 1 model selected  

> distance #13/A:295@SG #13/I:140@SG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG
and /I CYS 140 SG: 3.9Å  

> show #!11 models

> color sel dim gray

> select clear

> hide #13/A:230-350 atoms

> hide #13/o atoms

> select #13/A:295

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

> show sel atoms

> select clear

> show #!4 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif" width
> 1984 height 1210 supersample 3

> hide #!4 models

> show #11.1 models

> hide #11.1 models

> show #!2 models

> select #2/E:706@CG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/E:706@CD

1 atom, 1 residue, 1 model selected  

> select up

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

> show sel atoms

> select clear

> select #2/E:706@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select #2/E:707@CD1

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select clear

> select #13/I:140@SG

1 atom, 1 residue, 1 model selected  

> select add #13/A:295@SG

2 atoms, 2 residues, 1 model selected  

> select up

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

> hide sel atoms

> select clear

> show #13/A:305,304,280,328

> select #2/E:718

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

> select add #13/A:319

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> show #13/O

> select clear

> hide #!11 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif" width 1984
> height 1210 supersample 3

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"

> hide #!2 models

> hide #!13 models


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

OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 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: 16 GB
      System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0)
      OS Loader Version: 582~3311

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 7 days, 53 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02QM2AXF2GC
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          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
    biopython: 1.84
    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
    DiffFit: 0.2
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    fsspec: 2024.6.1
    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
    joblib: 1.4.2
    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
    mpmath: 1.3.0
    mrcfile: 1.5.1
    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
    scikit-learn: 1.5.1
    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
    sympy: 1.13.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    threadpoolctl: 3.5.0
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    torch: 2.2.2
    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 pett, 7 months ago

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

comment:2 by Tom Goddard, 7 months ago

Resolution: → duplicate
Status: assigned → closed
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