Crash querying cursor position

[chimerax-bug-report@…]

W{{{
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x000000010db77600 (most recent call first):

File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py", line 514 in _cursor_position
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py", line 472 in mouse_pause_tracking
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 140 in _redraw_timer_callback
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/main.py", line 892 in init
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/main.py", line 1043 in
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main

{"app_name":"ChimeraX","timestamp":"2023-07-30 06:32:44.00 -0400","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.6 (21G646)","incident_id":"D102C30B-44E2-40A3-BD19-78CC535EAA72","name":"ChimeraX"}
{

"uptime" : 1300000,
"procLaunch" : "2023-07-28 10:21:46.2594 -0400",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac19,2",
"procStartAbsTime" : 1316132098938212,
"coalitionID" : 92877,
"osVersion" : {

"train" : "macOS 12.6.6",
"build" : "21G646",
"releaseType" : "User"

},
"captureTime" : "2023-07-30 06:32:22.8140 -0400",
"incident" : "D102C30B-44E2-40A3-BD19-78CC535EAA72",
"bug_type" : "309",
"pid" : 46633,
"procExitAbsTime" : 1339730638892821,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0861E011-4197-5C99-A974-0738D481B05E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BF6DBB31-4673-91A0-29D2-BFBE876A9176",
"wakeTime" : 12,
"sleepWakeUUID" : "F07575B5-B9FB-4F60-984B-A7F472B2C3EE",
"sip" : "enabled",
"vmRegionInfo" : "0x10760b994 is in 0x1075f7000-0x10760f000; bytes after start: 84372 bytes before end: 13931\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n LINKEDIT 1075cb000-1075f7000 [ 176K] r--\/rwx SM=COW ...-39-darwin.so\n---> TEXT 1075f7000-10760f000 [ 96K] r-x\/rwx SM=COW ...-39-darwin.so\n DATA 10760f000-107613000 [ 16K] rw-\/rwx SM=COW ...-39-darwin.so",
"isCorpse" : 1,
"exception" : {"codes":"0x000000000000000a, 0x000000010760b994","rawCodes":[10,4418746772],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010760b994"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x10760b994 is in 0x1075f7000-0x10760f000; bytes after start: 84372 bytes before end: 13931\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n LINKEDIT 1075cb000-1075f7000 [ 176K] r--\/rwx SM=COW ...-39-darwin.so\n---> TEXT 1075f7000-10760f000 [ 96K] r-x\/rwx SM=COW ...-39-darwin.so\n DATA 10760f000-107613000 [ 16K] rw-\/rwx SM=COW ...-39-darwin.so",
"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":12912060,"threadState":{"r13":{"value":8209},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":10},"rsi":{"value":10},"r8":{"value":140362463665992},"cr2":{"value":140705832466976},"rdx":{"value":0},"r10":{"value":4525094400,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":12482339074188576719},"r15":{"value":22},"rbx":{"value":4525094400,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703500931070,"matchesCrashFrame":1},"rbp":{"value":140362463664768},"rsp":{"value":140362463664728},"r12":{"value":259},"rcx":{"value":140362463664728},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":32766,"symbol":"pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25087,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":279256,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15869,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":84151,"symbol":"sipOMAddObject","symbolLocation":55,"imageIndex":5},{"imageOffset":27249,"symbol":"sipSimpleWrapper_init","symbolLocation":353,"imageIndex":5},{"imageOffset":610233,"symbol":"type_call","symbolLocation":345,"imageIndex":6},{"imageOffset":260828,"symbol":"_PyObject_Call","symbolLocation":140,"imageIndex":6},{"imageOffset":86644,"symbol":"sipWrapInstance","symbolLocation":212,"imageIndex":5},{"imageOffset":1106866,"symbol":"meth_QCursor_pos(_object*, _object*)","symbolLocation":178,"imageIndex":7},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":6},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":6},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":6},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":6},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":6},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":6},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":6},{"imageOffset":269746,"symbol":"method_vectorcall","symbolLocation":274,"imageIndex":6},{"imageOffset":1258136,"symbol":"PyQtSlot::call(_object*, _object*) const","symbolLocation":40,"imageIndex":8},{"imageOffset":1257882,"symbol":"PyQtSlot::invoke(void, _object*, void*, bool) const","symbolLocation":362,"imageIndex":8},{"imageOffset":1261989,"symbol":"PyQtSlotProxy::unislot(void)","symbolLocation":85,"imageIndex":8},{"imageOffset":1261850,"symbol":"PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void)","symbolLocation":58,"imageIndex":8},{"imageOffset":774846,"imageIndex":9},{"imageOffset":858122,"symbol":"QTimer::timerEvent(QTimerEvent*)","symbolLocation":202,"imageIndex":9},{"imageOffset":154025,"symbol":"sipQTimer::timerEvent(QTimerEvent*)","symbolLocation":121,"imageIndex":8},{"imageOffset":742701,"symbol":"QObject::event(QEvent*)","symbolLocation":109,"imageIndex":9},{"imageOffset":153642,"symbol":"sipQTimer::event(QEvent*)","symbolLocation":186,"imageIndex":8},{"imageOffset":43463,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":10},{"imageOffset":47372,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":508,"imageIndex":10},{"imageOffset":1282438,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":230,"imageIndex":11},{"imageOffset":450858,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":9},{"imageOffset":2063393,"symbol":"QTimerInfoList::activateTimers()","symbolLocation":993,"imageIndex":9},{"imageOffset":88741,"imageIndex":12},{"imageOffset":524635,"symbol":"CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION","symbolLocation":17,"imageIndex":13},{"imageOffset":524483,"symbol":"CFRunLoopDoSource0","symbolLocation":180,"imageIndex":13},{"imageOffset":523837,"symbol":"CFRunLoopDoSources0","symbolLocation":242,"imageIndex":13},{"imageOffset":518232,"symbol":"CFRunLoopRun","symbolLocation":892,"imageIndex":13},{"imageOffset":515612,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":13},{"imageOffset":189926,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":14},{"imageOffset":189258,"symbol":"ReceiveNextEventCommon","symbolLocation":594,"imageIndex":14},{"imageOffset":188645,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":70,"imageIndex":14},{"imageOffset":257901,"symbol":"_DPSNextEvent","symbolLocation":927,"imageIndex":15},{"imageOffset":251434,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1394,"imageIndex":15},{"imageOffset":195801,"symbol":"-[NSApplication run]","symbolLocation":586,"imageIndex":15},{"imageOffset":91987,"imageIndex":12},{"imageOffset":488630,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":9},{"imageOffset":452389,"symbol":"QCoreApplication::exec()","symbolLocation":133,"imageIndex":9},{"imageOffset":2250058,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":90,"imageIndex":11},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":6},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":6},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":6},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":6},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":6},{"imageOffset":269674,"symbol":"method_vectorcall","symbolLocation":202,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":6},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":6},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":6},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":6},{"imageOffset":1109419,"symbol":"PyEval_EvalCode","symbolLocation":139,"imageIndex":6},{"imageOffset":1096722,"symbol":"builtin_exec","symbolLocation":626,"imageIndex":6},{"imageOffset":516131,"symbol":"cfunction_vectorcall_FASTCALL","symbolLocation":195,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":6},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":6},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":6},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":6},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":6},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":6},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":6},{"imageOffset":1566832,"symbol":"pymain_run_module","symbolLocation":208,"imageIndex":6},{"imageOffset":1564551,"symbol":"Py_RunMain","symbolLocation":1431,"imageIndex":6},{"imageOffset":1566095,"symbol":"pymain_main","symbolLocation":223,"imageIndex":6},{"imageOffset":1565851,"symbol":"Py_Main","symbolLocation":43,"imageIndex":6},{"imageOffset":3528,"symbol":"main","symbolLocation":120,"imageIndex":16},{"imageOffset":21806,"symbol":"start","symbolLocation":462,"imageIndex":17}]},{"id":12915422,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":43194,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":72176586,"imageIndex":18},{"imageOffset":72176239,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71838381,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915423,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71893079,"imageIndex":18},{"imageOffset":71891853,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915424,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71893079,"imageIndex":18},{"imageOffset":71891709,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915425,"name":"Chrome_IOThread","frames":[{"imageOffset":43194,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":72176586,"imageIndex":18},{"imageOffset":72176239,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":30119282,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915426,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915431,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915432,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":43194,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":72176586,"imageIndex":18},{"imageOffset":72176239,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":118470786,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915433,"name":"CompositorTileWorker1","frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":72117794,"imageIndex":18},{"imageOffset":108041477,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915434,"name":"ThreadPoolSingleThreadSharedForeground0","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71893079,"imageIndex":18},{"imageOffset":71891901,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915435,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915436,"name":"VizCompositorThread","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915441,"name":"NetworkService","frames":[{"imageOffset":43194,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":72176586,"imageIndex":18},{"imageOffset":72176239,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915442,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915443,"name":"ThreadPoolSingleThreadForegroundBlocking1","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71893079,"imageIndex":18},{"imageOffset":71891949,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915452,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915501,"name":"com.apple.NSEventThread","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":525133,"symbol":"CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":13},{"imageOffset":518616,"symbol":"CFRunLoopRun","symbolLocation":1276,"imageIndex":13},{"imageOffset":515612,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":13},{"imageOffset":1755534,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":15},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915507,"name":"MemoryInfra","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":72148767,"imageIndex":18},{"imageOffset":71278185,"imageIndex":18},{"imageOffset":71786483,"imageIndex":18},{"imageOffset":71490098,"imageIndex":18},{"imageOffset":71944792,"imageIndex":18},{"imageOffset":71945194,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12915508,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71892236,"imageIndex":18},{"imageOffset":71891757,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12917304,"frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":19},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12917305,"frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":19},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12917306,"frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":19},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12917307,"frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":19},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12917308,"frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":19},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":12926659,"name":"QFileInfoGatherer","frames":[{"imageOffset":17370,"symbol":"psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":1},{"imageOffset":2108299,"imageIndex":9},{"imageOffset":2108158,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":94,"imageIndex":9},{"imageOffset":4640285,"symbol":"QFileInfoGatherer::run()","symbolLocation":125,"imageIndex":20},{"imageOffset":2067843,"imageIndex":9},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":13148555,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71893079,"imageIndex":18},{"imageOffset":71891853,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":13149231,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":13149268,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":13149298,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":13149693,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6506,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7384,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":72149299,"imageIndex":18},{"imageOffset":71890095,"imageIndex":18},{"imageOffset":71892236,"imageIndex":18},{"imageOffset":71891853,"imageIndex":18},{"imageOffset":72123480,"imageIndex":18},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":13149905,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]}],
"usedImages" : [
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703500898304,
"size" : 229376,
"uuid" : "35a199f3-e389-3202-916b-d6662a391f7e",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703501127680,
"size" : 49152,
"uuid" : "e5d44afd-2577-3cee-8711-9d8d426229e0",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703499882496,
"size" : 561152,
"uuid" : "e42e9d7a-03b4-340b-b61e-dcd45fd4acc0",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703501225984,
"size" : 40960,
"uuid" : "a8a33774-6d44-35e9-ad2a-bad9e4d5192a",
"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" : 4418662400,
"size" : 98304,
"uuid" : "f511de72-2757-3ff5-8524-716ba83b7953",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/sip.cpython-39-darwin.so",
"name" : "sip.cpython-39-darwin.so"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4411183104,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4519575552,
"size" : 1490944,
"uuid" : "9c3eb0df-69a3-3b03-ab77-80606e4891d2",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtGui.abi3.so",
"name" : "QtGui.abi3.so"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4507680768,
"size" : 1605632,
"uuid" : "5590e5eb-1a53-3bf0-9ffc-71d23992c730",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4500512768,
"size" : 5210112,
"uuid" : "6238782e-d1aa-3245-81ef-2925bf1a4c96",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4762996736,
"size" : 4931584,
"uuid" : "5bfaef33-ce47-32bf-acb3-03cbe9e68a6f",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4756836352,
"size" : 2834432,
"uuid" : "951581e2-ae51-392a-82d9-fdf83e162d11",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4771688448,
"size" : 638976,
"uuid" : "7175bc4c-ca2f-30b6-9734-062b84bd0ae2",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"

},
{

"source" : "P",
"arch" : "x86_64h",
"base" : 140703501443072,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "70b99b27-1b5b-33c4-b401-2ecdb80f3303",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1866"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703649292288,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3096576,
"uuid" : "06fdecd6-9f69-397b-b1e2-a8226c0ba7ed",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 140703545982976,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15269888,
"uuid" : "1a1a9da7-da66-31da-92cd-51b9cf968145",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.60.148"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4402556928,
"CFBundleShortVersionString" : "1.6.1",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.6.1.0"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4524568576,
"size" : 442368,
"uuid" : "2517e9fe-884a-3855-8532-92bffba3f81c",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 5119410176,
"size" : 174571520,
"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4525322240,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"

},
{

"source" : "P",
"arch" : "x86_64",
"base" : 4511219712,
"size" : 7094272,
"uuid" : "cf0b9ade-9377-380e-9a84-904983d7bb60",
"path" : "\/Volumes\/NETWORK\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"

}

],

"sharedCache" : {
"base" : 140703497871360,
"size" : 19331678208,
"uuid" : "f2ce8b0d-f2e7-3c14-88fa-430ab7913380"

},

"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 896K 7 \nActivity Tracing 256K 1 \nCG backing stores 3792K 8 \nCG image 640K 56 \nColorSync 236K 28 \nCoreAnimation 3172K 76 \nCoreGraphics 16K 3 \nCoreServices 72K 1 \nCoreUI image data 5164K 51 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 1364K 4 \nMALLOC 538.4M 710 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 165.7M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 206.5M 234 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\nCTF 756 1 \nDATA 57.3M 682 \nDATA_CONST 31.3M 346 \nDATA_DIRTY 1659K 217 \nFONT_DATA 4K 1 \nGLSLBUILTINS 5176K 1 \nLINKEDIT 674.9M 145 \nTEXT 817.6M 676 \nUNICODE 592K 1 \ndyld private memory 1056K 2 \nmapped file 228.5M 54 \nshared memory 3028K 30 \n=========== ======= ======= \nTOTAL 3.2G 3420 \nTOTAL, minus reserved VM space 2.8G 3420 \n",
"legacyInfo" : {
"threadTriggered" : {

"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"

}

},

"trialInfo" : {
"rollouts" : [

{

"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {

},
"deploymentId" : 240000055

},
{

"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {

},
"deploymentId" : 240000021

}

],
"experiments" : [

]

}
}

Log before crash start

UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open /Users/emilieleroy/Desktop/complex_clean_map1.mrc format mrc

No such file/path: /Users/emilieleroy/Desktop/complex_clean_map1.mrc

open /Users/emilieleroy/Desktop/JAK2-LNK_MAPs_Models/complex_clean_map1.mrc

Opened complex_clean_map1.mrc as #1, grid size 78,99,87, pixel 1.67, shown at
level 0.577, step 1, values float32

open /Volumes/eleroy/MAP.mrc

Opened MAP.mrc as #2, grid size 78,99,87, pixel 0.822,0.822,0.822, shown at
level 0.577, step 1, values float32

close #2

close #1

open
/Users/emilieleroy/Desktop/JAK2-LNK_MAPs_Models/complex_clean_072823.mrc

Opened complex_clean_072823.mrc as #1, grid size 78,99,87, pixel 1.67, shown
at level 0.577, step 1, values float32

molmap #0 15

No atoms specified

vop add #0

resample #1 onGrid #0

Unknown command: resample #1 onGrid #0

resample #1 onGrid #1

Unknown command: resample #1 onGrid #1

vop resample #1 ongrid #1

Opened complex_clean_072823.mrc resampled as #2, grid size 78,99,87, pixel
1.67, shown at step 1, values float32

ui tool show "Volume Viewer"

No map chosen to save

close #1

save /Users/emilieleroy/test1.mrc models #2

vop resample #1 ongrid #0

open
/Users/emilieleroy/Downloads/cryosparc_P205_J215_class_02_final_volume.mrc
format mrc

Opened cryosparc_P205_J215_class_02_final_volume.mrc as #1, grid size
128,128,128, pixel 1.64, shown at level 0.11, step 1, values float32

vop resample #1 ongrid #2

Opened cryosparc_P205_J215_class_02_final_volume.mrc resampled as #3, grid
size 78,99,87, pixel 1.67, shown at step 1, values float32

volume #3 level 0.003298

volume #3 level 0.0006552

ui tool show "Volume Viewer"

close #3

ui tool show "Map Coordinates"

ui tool show "Model Panel"

select add #1

2 models selected

ui mousemode right "move picked models"

ui mousemode right "translate selected atoms"

ui mousemode right "rotate selected models"

view matrix models
#1,​0.97538,-0.20965,0.068355,17.722,0.18494,0.94657,0.26421,-40.09,-0.12009,-0.24507,0.96204,42.019

view matrix models
#1,​0.78216,0.56827,-0.25553,-11.529,-0.55355,0.82202,0.13366,62.548,0.28601,0.036908,0.95752,-29.2

ui mousemode right "move picked models"

view matrix models
#1,​0.78216,0.56827,-0.25553,-105.9,-0.55355,0.82202,0.13366,-43.846,0.28601,0.036908,0.95752,-105.43

view matrix models
#1,​0.78216,0.56827,-0.25553,-104.22,-0.55355,0.82202,0.13366,-51.588,0.28601,0.036908,0.95752,-113.11

view matrix models #2,​1,​0,​0,​4.7536,0,1,0,0.87004,0,0,1,-0.14601

view matrix models #2,​1,​0,​0,​39.498,0,1,0,49.796,0,0,1,85.848

view matrix models
#1,​0.78216,0.56827,-0.25553,-83.091,-0.55355,0.82202,0.13366,13.544,0.28601,0.036908,0.95752,-40.455

ui mousemode right "rotate selected models"

view matrix models
#1,-0.081929,0.16436,-0.98299,121.96,0.6948,0.71654,0.061898,-97.302,0.71453,-0.67791,-0.1729,104.09

ui mousemode right "move picked models"

view matrix models
#1,-0.081929,0.16436,-0.98299,129.67,0.6948,0.71654,0.061898,-103.18,0.71453,-0.67791,-0.1729,108.01

view matrix models
#1,-0.081929,0.16436,-0.98299,136.55,0.6948,0.71654,0.061898,-104.78,0.71453,-0.67791,-0.1729,102.18

view matrix models
#1,-0.081929,0.16436,-0.98299,134.85,0.6948,0.71654,0.061898,-102.95,0.71453,-0.67791,-0.1729,105.11

ui mousemode right "rotate selected models"

view matrix models
#1,-0.35635,0.097549,-0.92925,164.86,0.018333,0.99507,0.097429,-65.832,0.93417,0.017683,-0.35639,27.681

ui mousemode right "move picked models"

view matrix models
#1,-0.35635,0.097549,-0.92925,168.11,0.018333,0.99507,0.097429,-66.732,0.93417,0.017683,-0.35639,28.314

view matrix models
#1,-0.35635,0.097549,-0.92925,166.65,0.018333,0.99507,0.097429,-63.09,0.93417,0.017683,-0.35639,31.272

volume #1 level 0.07359

select subtract #1

Nothing selected

open /Volumes/eleroy/test1newbox.mrc

Opened test1newbox.mrc as #3, grid size 40,40,40, pixel 1.67, shown at level
0.742, step 1, values float32

volume #3 level 0.2567

open /Volumes/eleroy/test1newbox1.mrc

Opened test1newbox1.mrc as #4, grid size 80,80,80, pixel 1.67, shown at level
0.618, step 1, values float32

open /Volumes/eleroy/test1newbox2.mrc

Opened test1newbox2.mrc as #5, grid size 160,160,160, pixel 1.67, shown at
level 0.116, step 1, values float32

view matrix models #5,​1,​0,​0,-10.863,0,1,0,-36.66,0,0,1,-62.418

volume #5 level 0.5508

hide #2.1 models

hide #1.1 models

open /Volumes/eleroy/MAP.mrc

Opened MAP.mrc as #6, grid size 78,99,87, pixel 0.822,0.822,0.822, shown at
level 0.577, step 1, values float32

view matrix models #6,​1,​0,​0,​67.833,0,1,0,-17.689,0,0,1,97.988

open /Volumes/eleroy/MAPnewbox.mrc

Opened MAPnewbox.mrc as #7, grid size 160,160,160, pixel 0.822,0.822,0.822,
shown at level 0.116, step 1, values float32

view matrix models #7,​1,​0,​0,​17.55,0,1,0,-9.9591,0,0,1,10.784

view matrix models #7,​1,​0,​0,​39.528,0,1,0,-27.269,0,0,1,28.318

view matrix models #7,​1,​0,​0,​29.076,0,1,0,-58.9,0,0,1,-8.7401

volume #7 level 0.5218

view matrix models #7,​1,​0,​0,​30.909,0,1,0,-78.329,0,0,1,-7.3066

view matrix models #7,​1,​0,​0,-1.6388,0,1,0,-93.294,0,0,1,22.536

view matrix models #7,​1,​0,​0,​3.358,0,1,0,-93.499,0,0,1,23.384

Log before crash end

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open
/Users/emilieleroy/Downloads/cryosparc_P205_J282_class_02_final_volume.mrc

Opened cryosparc_P205_J282_class_02_final_volume.mrc as #1, grid size
128,128,128, pixel 2.31, shown at level 0.0613, step 1, values float32

OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

Hardware Overview:

Model Name: iMac
Model Identifier: iMac19,2
Processor Name: 6-Core Intel Core i7
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.120.12.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.47f3

Software:

System Software Overview:

System Version: macOS 12.6.6 (21G646)
Kernel Version: Darwin 21.6.0
Time since boot: 49 days 4:57

Graphics/Displays:

Radeon Pro 560X:

Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C981AA-042
VBIOS Version: 113-C9819A1X-009
EFI Driver Version: 01.B1.042
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:

iMac:

Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal

ASUS VG236:

Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: B4LMTF077013
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00

Installed Packages:

alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0

}}}

[Tom Goddard]

We've seen the crash in this line of code calling one of two Qt functions to find the cursor position when the mouse is hovered over the graphics window.

        p = self.graphics_window.mapFromGlobal(QCursor.pos())

This may be a PyQt reference counting or garbage collection issue where an object that was still referenced got deleted. The crash stack traces shows it crashes in QCursor_pos() in PyQt.

{"imageOffset":84151,"symbol":"sipOMAddObject","symbolLocation":55,"imageIndex":5},{"imageOffset":27249,"symbol":"sipSimpleWrapper_init","symbolLocation":353,"imageIndex":5},{"imageOffset":610233,"symbol":"type_call","symbolLocation":345,"imageIndex":6},{"imageOffset":260828,"symbol":"_PyObject_Call","symbolLocation":140,"imageIndex":6},{"imageOffset":86644,"symbol":"sipWrapInstance","symbolLocation":212,"imageIndex":5},{"imageOffset":1106866,"symbol":"meth_QCursor_pos(_object*, _object*)","symbolLocation":178,"imageIndex":7},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":6},