Opened 4 months ago

Closed 4 months ago

#18366 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error

Current thread 0x0000000104810580 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-08-05 15:16:04.00 +0800","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F2081)","incident_id":"BA7D482F-B5E8-4403-912F-65FE561D4F6E","name":"ChimeraX"}
{
  "uptime" : 210000,
  "procLaunch" : "2025-08-05 12:48:33.7073 +0800",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "procStartAbsTime" : 4964648119259,
  "coalitionID" : 13552,
  "osVersion" : {
    "train" : "macOS 12.4",
    "build" : "21F2081",
    "releaseType" : "User"
  },
  "captureTime" : "2025-08-05 15:16:00.5900 +0800",
  "incident" : "BA7D482F-B5E8-4403-912F-65FE561D4F6E",
  "bug_type" : "309",
  "pid" : 44331,
  "procExitAbsTime" : 5082551496059,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"77B0E97D-EC9B-5A12-9EEB-B2BE49174AE0","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "8F60DABA-EB3D-19D9-AFF5-E3E8A6C9ECD0",
  "sleepWakeUUID" : "98255FCA-BEAC-42ED-839A-A67ABE89B56B",
  "sip" : "enabled",
  "vmRegionInfo" : "0x6000012a3f50 is in 0x600000000000-0x600008000000;  bytes after start: 19545936  bytes before end: 114671791\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n      GAP OF 0x5f9000000000 BYTES\n--->  MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  \n      MALLOC_NANO              600008000000-600010000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000002, 0x00006000012a3f50","rawCodes":[2,105553135812432],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x00006000012a3f50"},
  "vmregioninfo" : "0x6000012a3f50 is in 0x600000000000-0x600008000000;  bytes after start: 19545936  bytes before end: 114671791\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n      GAP OF 0x5f9000000000 BYTES\n--->  MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  \n      MALLOC_NANO              600008000000-600010000000 [128.0M] rw-\/rwx SM=PRV  ",
  "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" : [{"triggered":true,"id":1726389,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100567192},{"value":99},{"value":119},{"value":1688854353692080},{"value":4132},{"value":9981356118301551444},{"value":9981356114082016980},{"value":14757395258967641293},{"value":4294967286},{"value":5100567122},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8423519872},{"value":0},{"value":10},{"value":4370531712,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":4370531936,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4389275184,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8158301550,"objc-selector":"_updateSurfaceResolution"},{"value":8158642071,"objc-selector":"viewDidChangeBackingProperties:"},{"value":8158087757,"objc-selector":"viewDidChangeBackingProperties"},{"value":105553126035552}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6912884448},"cpsr":{"value":1073745920},"fp":{"value":5100567264},"sp":{"value":5100567232},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6912667032,"matchesCrashFrame":1},"far":{"value":4470652928}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":40344,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":0},{"imageOffset":28384,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":1},{"imageOffset":272000,"symbol":"raise","symbolLocation":32,"imageIndex":2},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":3},{"imageOffset":17572,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":4},{"imageOffset":349380,"imageIndex":5},{"imageOffset":349160,"imageIndex":5},{"imageOffset":440196,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":332,"imageIndex":6},{"imageOffset":9317132,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":240,"imageIndex":6},{"imageOffset":2540084,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":548,"imageIndex":6},{"imageOffset":599504,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":140,"imageIndex":6},{"imageOffset":2539524,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":6},{"imageOffset":606324,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":2256,"imageIndex":6},{"imageOffset":9290552,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":656,"imageIndex":6},{"imageOffset":3964972,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1296,"imageIndex":6},{"imageOffset":4123672,"symbol":"-[NSWindow _displayChangedSoAdjustWindows:]","symbolLocation":116,"imageIndex":6},{"imageOffset":12078852,"symbol":"___NSApplicationPerformScreenInvalidationReactions_block_invoke","symbolLocation":96,"imageIndex":6},{"imageOffset":244056,"symbol":"-[NSApplication enumerateWindowsWithOptions:usingBlock:]","symbolLocation":288,"imageIndex":6},{"imageOffset":12077456,"symbol":"___NSApplicationReactToScreenInvalidation_block_invoke","symbolLocation":640,"imageIndex":6},{"imageOffset":12076172,"symbol":"_NSApplicationReactToScreenInvalidation","symbolLocation":288,"imageIndex":6},{"imageOffset":12076680,"symbol":"-[NSApplication(ScreenHandling) _reactToDisplayChanges:]","symbolLocation":408,"imageIndex":6},{"imageOffset":7482820,"symbol":"_NSCGSDisplayConfigurationUpdateAndInvokeObservers","symbolLocation":456,"imageIndex":6},{"imageOffset":7483784,"symbol":"_NSCGSDisplayConfigurationDidReconfigureNotificationHandler","symbolLocation":328,"imageIndex":6},{"imageOffset":50096,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":860,"imageIndex":7},{"imageOffset":3161128,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":228,"imageIndex":7},{"imageOffset":3160868,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":28,"imageIndex":7},{"imageOffset":9712,"symbol":"_dispatch_call_block_and_release","symbolLocation":32,"imageIndex":8},{"imageOffset":16820,"symbol":"_dispatch_client_callout","symbolLocation":20,"imageIndex":8},{"imageOffset":75468,"symbol":"_dispatch_main_queue_drain","symbolLocation":928,"imageIndex":8},{"imageOffset":74524,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":44,"imageIndex":8},{"imageOffset":813596,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":16,"imageIndex":9},{"imageOffset":539816,"symbol":"__CFRunLoopRun","symbolLocation":2532,"imageIndex":9},{"imageOffset":535332,"symbol":"CFRunLoopRunSpecific","symbolLocation":600,"imageIndex":9},{"imageOffset":205624,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":10},{"imageOffset":204980,"symbol":"ReceiveNextEventCommon","symbolLocation":564,"imageIndex":10},{"imageOffset":204392,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":72,"imageIndex":10},{"imageOffset":268172,"symbol":"_DPSNextEvent","symbolLocation":860,"imageIndex":6},{"imageOffset":262276,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1328,"imageIndex":6},{"imageOffset":205392,"symbol":"-[NSApplication run]","symbolLocation":596,"imageIndex":6},{"imageOffset":88376,"imageIndex":5},{"imageOffset":572692,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":540,"imageIndex":11},{"imageOffset":534620,"symbol":"QCoreApplication::exec()","symbolLocation":112,"imageIndex":11},{"imageOffset":2477972,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":96,"imageIndex":12},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":3},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":3},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":3},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":3},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":3},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":3},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":3},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":3},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":3},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":3},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":3},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":3},{"imageOffset":15700,"symbol":"main","symbolLocation":128,"imageIndex":13},{"imageOffset":20620,"symbol":"start","symbolLocation":520,"imageIndex":14}]},{"id":1726479,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":54104,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":71187368,"imageIndex":15},{"imageOffset":71186848,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70856668,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726480,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902644,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726481,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902696,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726482,"name":"Chrome_IOThread","frames":[{"imageOffset":54104,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":71187368,"imageIndex":15},{"imageOffset":71186848,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":45328188,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726483,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70677152,"imageIndex":15},{"imageOffset":70343492,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726484,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902644,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726485,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902644,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726486,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70343392,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726487,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":54104,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":71187368,"imageIndex":15},{"imageOffset":71186848,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":114048632,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726488,"name":"CompositorTileWorker1","frames":[{"imageOffset":21104,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30780,"symbol":"_pthread_cond_wait","symbolLocation":1236,"imageIndex":1},{"imageOffset":71055056,"imageIndex":15},{"imageOffset":104344336,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726489,"name":"ThreadPoolSingleThreadSharedForeground0","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70903324,"imageIndex":15},{"imageOffset":70902728,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726490,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70677152,"imageIndex":15},{"imageOffset":70343492,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726491,"name":"VizCompositorThread","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70343392,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726492,"name":"NetworkService","frames":[{"imageOffset":54104,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":71187368,"imageIndex":15},{"imageOffset":71186848,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726493,"name":"NetworkNotificationThreadMac","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":545456,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":372,"imageIndex":9},{"imageOffset":538464,"symbol":"__CFRunLoopRun","symbolLocation":1180,"imageIndex":9},{"imageOffset":535332,"symbol":"CFRunLoopRunSpecific","symbolLocation":600,"imageIndex":9},{"imageOffset":409904,"symbol":"-[NSRunLoop(NSRunLoop) runMode:beforeDate:]","symbolLocation":236,"imageIndex":16},{"imageOffset":71382916,"imageIndex":15},{"imageOffset":71377136,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726494,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70677152,"imageIndex":15},{"imageOffset":70343492,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726495,"name":"ThreadPoolSingleThreadForegroundBlocking1","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902712,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726514,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70677152,"imageIndex":15},{"imageOffset":70343492,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726535,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70904380,"imageIndex":15},{"imageOffset":70902644,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726545,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70903324,"imageIndex":15},{"imageOffset":70902696,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726547,"name":"MemoryInfra","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70677152,"imageIndex":15},{"imageOffset":70343492,"imageIndex":15},{"imageOffset":70809656,"imageIndex":15},{"imageOffset":70544784,"imageIndex":15},{"imageOffset":70952276,"imageIndex":15},{"imageOffset":70952656,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726548,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":71161832,"imageIndex":15},{"imageOffset":70677284,"imageIndex":15},{"imageOffset":70900888,"imageIndex":15},{"imageOffset":70903324,"imageIndex":15},{"imageOffset":70902760,"imageIndex":15},{"imageOffset":71057880,"imageIndex":15},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1726566,"name":"com.apple.NSEventThread","frames":[{"imageOffset":6320,"symbol":"mach_msg_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":7456,"symbol":"mach_msg","symbolLocation":76,"imageIndex":0},{"imageOffset":545456,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":372,"imageIndex":9},{"imageOffset":538464,"symbol":"__CFRunLoopRun","symbolLocation":1180,"imageIndex":9},{"imageOffset":535332,"symbol":"CFRunLoopRunSpecific","symbolLocation":600,"imageIndex":9},{"imageOffset":1762164,"symbol":"_NSEventThread","symbolLocation":196,"imageIndex":6},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1732778,"queue":"com.apple.root.user-initiated-qos","frames":[{"imageOffset":14600,"symbol":"__ulock_wake","symbolLocation":8,"imageIndex":0},{"imageOffset":8676,"symbol":"_os_unfair_lock_unlock_slow","symbolLocation":56,"imageIndex":4},{"imageOffset":38972,"imageIndex":17},{"imageOffset":16820,"symbol":"_dispatch_client_callout","symbolLocation":20,"imageIndex":8},{"imageOffset":30320,"symbol":"_dispatch_continuation_pop","symbolLocation":500,"imageIndex":8},{"imageOffset":108768,"symbol":"_dispatch_source_invoke","symbolLocation":1596,"imageIndex":8},{"imageOffset":93336,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":648,"imageIndex":8},{"imageOffset":13152,"symbol":"_pthread_wqthread","symbolLocation":288,"imageIndex":1},{"imageOffset":8320,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":1}]},{"id":1733928,"name":"QFileInfoGatherer","frames":[{"imageOffset":21104,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30780,"symbol":"_pthread_cond_wait","symbolLocation":1236,"imageIndex":1},{"imageOffset":2118012,"imageIndex":11},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":11},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":18},{"imageOffset":2063036,"imageIndex":11},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1733933,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1733992,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1734210,"name":"QFileInfoGatherer","frames":[{"imageOffset":21104,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30780,"symbol":"_pthread_cond_wait","symbolLocation":1236,"imageIndex":1},{"imageOffset":2118012,"imageIndex":11},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":11},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":18},{"imageOffset":2063036,"imageIndex":11},{"imageOffset":29292,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":8332,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":1734212,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1734213,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1734434,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1734435,"frames":[{"imageOffset":8312,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]}],
  "usedImages" : [
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6912626688,
    "size" : 229376,
    "uuid" : "1be1d0f8-afac-33ab-9216-b31ea1f310d5",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6912856064,
    "size" : 53248,
    "uuid" : "f8f3aea3-7895-3394-896f-ae56e42b9942",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6911574016,
    "size" : 532480,
    "uuid" : "fdc5ba0c-aa45-306f-a9d5-688db72611e6",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4384997376,
    "CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 3948544,
    "uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.11.4"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6912962560,
    "size" : 32768,
    "uuid" : "c9a39c11-bb8c-3974-b13c-9d77e1df066a",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5053759488,
    "size" : 655360,
    "uuid" : "fab03cd7-ccd1-33ab-bc97-91ce7e4911a2",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6958960640,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15433728,
    "uuid" : "d9f2e03b-6eab-3655-bc8d-5926d9b81f96",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.50.132"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6998544384,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 4034560,
    "uuid" : "4bf7a93f-e7d4-31c3-b581-4d8c63164de4",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6911016960,
    "size" : 290816,
    "uuid" : "0f0f4d87-b03d-3677-9bce-1c0e94fbec08",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6913179648,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5533696,
    "uuid" : "0f32d600-0dc9-3be0-af41-35041dacc92a",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1863"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7060557824,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "c8e06e2d-9e83-3898-8583-e943b6a512d3",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4481105920,
    "size" : 4603904,
    "uuid" : "5e316915-192d-32ae-b085-7c0986279324",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4486594560,
    "size" : 3080192,
    "uuid" : "ac9bb37f-d5ad-31aa-8307-d081879d1aef",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4368564224,
    "CFBundleShortVersionString" : "1.9.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "17982d98-65bc-3327-8526-577ec996453c",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.9.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 4370038784,
    "size" : 393216,
    "uuid" : "63780851-f9a8-3a99-97ec-47b511339c9f",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 10921967616,
    "size" : 173883392,
    "uuid" : "309d9313-74e8-3f16-8acc-0f13b36d8e00",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6928924672,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.Foundation",
    "size" : 4136960,
    "uuid" : "380aeaf4-0aa6-3e56-82ca-ac70c5f6c771",
    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    "name" : "Foundation",
    "CFBundleVersion" : "1863"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6958563328,
    "size" : 65536,
    "uuid" : "4a67b60e-0586-315e-9501-0de0fb54267f",
    "path" : "\/usr\/lib\/system\/libsystem_notify.dylib",
    "name" : "libsystem_notify.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5242372096,
    "size" : 6635520,
    "uuid" : "3efe39e7-026f-3417-94b4-be4f2ec95e51",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 6909558784,
  "size" : 3143073792,
  "uuid" : "d5e72daa-1b10-3742-a464-d09152bd6e2c"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 5056K        8 \nCG image                           944K       42 \nColorSync                          640K       28 \nCoreAnimation                      768K       26 \nCoreGraphics                        48K        3 \nCoreServices                       624K        2 \nCoreUI image data                 4720K       34 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                           814.4M      139 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         816.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        512K       32 \nStack                            189.6M       33 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      258.8M      245 \nVM_ALLOCATE (reserved)           160.0M        2         reserved VM address space (unallocated)\n__AUTH                            2684K      343 \n__AUTH_CONST                      21.4M      555 \n__CTF                               756        1 \n__DATA                            25.4M      737 \n__DATA_CONST                      30.3M      743 \n__DATA_DIRTY                      1968K      243 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       612.9M      187 \n__OBJC_CONST                      4018K      320 \n__OBJC_RO                         83.0M        1 \n__OBJC_RW                         3168K        1 \n__TEXT                           797.9M      761 \n__UNICODE                          592K        1 \ndyld private memory               1072K        3 \nmapped file                      685.7M       92 \nshared memory                     3152K       25 \n===========                     =======  ======= \nTOTAL                              4.7G     4642 \nTOTAL, minus reserved VM space     3.5G     4642 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000614
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> ui tool show clix

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/wangxiang/Downloads/20250804-SCD1-YTX465-final/20250804-SCD1-YTX465-final_refined_053.pdb

Chain information for 20250804-SCD1-YTX465-final_refined_053.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> set bgColor white

> select /A

3218 atoms, 3324 bonds, 392 residues, 1 model selected  

> select /B

3218 atoms, 3324 bonds, 392 residues, 1 model selected  

> open
> /Users/wangxiang/Downloads/20250804-SCD1-YTX465-final/cryosparc_P1_J1418_006_volume_map_sharp.mrc

Opened cryosparc_P1_J1418_006_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.75, shown at level 0.0566, step 2, values float32  

> select #1/A:501

34 atoms, 38 bonds, 1 residue, 1 model selected  

> hide #1 cartoons, atoms

> volume #2 level 0.14 transparency 0.5 style surface color green

> volume zone #2 nearAtoms sel range 2

> select #1/A:501

34 atoms, 38 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel byhetero

> select sel : style sel stick

Changed 228 atom styles  

> show sel atoms

> color sel byhetero

> select sel : show (sel-residues & sidechain) target ab

> undo

> select #1/A:501

34 atoms, 38 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 34 atom styles  

> select sel : hide sel atoms

> show (sel-residues & sidechain) target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> volume #2 step 1

> volume #2 level 0.09198

> volume #2 level 0.09936

> volume #2 level 0.1104

> view sel

> ui tool show "Side View"

> volume #2 level 0.1028

> select #1/A:501

34 atoms, 38 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 34 atom styles  

> ui tool show H-Bonds

> hbonds sel color #4533fa showDist true select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 20250804-SCD1-YTX465-final_refined_053.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select #1/A:501

34 atoms, 38 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #4533fa showDist true select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 20250804-SCD1-YTX465-final_refined_053.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> volume #2 level 0.08763

> volume #2 level 0.09523

> volume #2 level 0.1028

> ui tool show "Side View"

> save /Users/wangxiang/Desktop/SCD1-pocket.png width 1800 height 1434
> supersample 3

> save /Users/wangxiang/Downloads/SCD1.cxs


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

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

> ui tool show clix

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/wangxiang/Downloads/20250228_HMG2_fluvastatin-
> final/20250228_HMG2_fluvastatin_refined_028-final.pdb

Chain information for 20250228_HMG2_fluvastatin_refined_028-final.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open /Users/wangxiang/Downloads/20250228_HMG2_fluvastatin-
> final/cryosparc_P23_J737_004_volume_map_sharp.mrc

Opened cryosparc_P23_J737_004_volume_map_sharp.mrc as #2, grid size
180,180,180, pixel 1.1, shown at level 0.268, step 1, values float32  

> set bgColor white

> color bychain

> color byhetero

> select ::name="115"

120 atoms, 128 bonds, 4 residues, 1 model selected  

> style sel ball

Changed 120 atom styles  

> select /C:1101@C9

1 atom, 1 residue, 1 model selected  

> select /C:1101

30 atoms, 32 bonds, 1 residue, 1 model selected  

> select sel :< 5 & ~sel

187 atoms, 175 bonds, 25 residues, 1 model selected  

> show sel atoms

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 7459.121.3
      OS Loader Version: 7459.121.3

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F2081)
      Kernel Version: Darwin 21.5.0
      Time since boot: 6 days 1:22

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        S27B80P:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-clix: 0.1.10
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LigandRecognizer: 0.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.2.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.13.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.2.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 4 months ago

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

comment:2 by Eric Pettersen, 4 months ago

Resolution: → duplicate
Status: assigned → closed
Note: See TracTickets for help on using tickets.