Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5rc202211182308 (2022-11-18 23:08:37 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007ff8450a84c0 (most recent call first):
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/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":"2023-03-28 16:21:49.00 +0200","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.0.1 (22A400)","roots_installed":0,"name":"ChimeraX","incident_id":"4B5EB0A7-A438-48CF-96CC-9BD5E89397B9"}
{
  "uptime" : 190000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "coalitionID" : 600,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2023-03-28 16:21:44.4136 +0200",
  "incident" : "4B5EB0A7-A438-48CF-96CC-9BD5E89397B9",
  "pid" : 36396,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-28 14:57:27.3225 +0200",
  "procStartAbsTime" : 194206854517703,
  "procExitAbsTime" : 198885650773273,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3148C109-351E-5669-8FC7-A745D4AE7DAD","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "DAE5A66E-5B02-652B-9AB4-D1348B2E5EC8",
  "wakeTime" : 1750,
  "bridgeVersion" : {"build":"20P420","train":"7.0"},
  "sleepWakeUUID" : "7575CED9-022A-43D2-A85E-7B082A1F9E51",
  "sip" : "enabled",
  "vmRegionInfo" : "0x40 is not in any region.  Bytes before following region: 140737487650752\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7ffffff54000-7ffffff55000 [    4K] r-x\/r-x SM=SHM  ",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
  "vmregioninfo" : "0x40 is not in any region.  Bytes before following region: 140737487650752\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7ffffff54000-7ffffff55000 [    4K] r-x\/r-x SM=SHM  ",
  "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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[46,15,31,132,0,0,0,0,0,15,31,68,0,0,85,72,137,229,72,137,248,72,139,78,48,72,137,15,72,139,86,56,72,137,87,8,72,139,86,64,72,137,87,16,72,133,201,116,4,240,131,1,1,93,195,15,31,128,0,0,0,0,85,72,137,229,65,87,65,86,65,85,65,84,83,72,131,236,40,73,137,254,15,87,192,15,17,7,72,199,71,16,0,0,0,0,76,139,102,64,77,133,228,15,132,213,1,0,0,72,139,70,56,72,137,69,184,73,193,228,3,69,49,255,72,141,93,192,235,39,102,46,15,31,132,0,0,0,0,0,102,144,76,137,247,49,246,49,210,49,201,232,114,4,0,0,73,131,199,8,77,57,252,15,132,153,1,0,0,72,139,69,184,74,139,4,56,72,139,72,88,72,133,201,116,100,139,81,4,133,210,116],"offset":96}},"frames":[{"imageOffset":33550,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":24443,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":279856,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15389,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":185051,"imageIndex":5},{"imageOffset":178541,"imageIndex":5},{"imageOffset":778274,"imageIndex":6},{"imageOffset":554254,"symbol":"QGuiApplicationPrivate::processActivatedEvent(QWindowSystemInterfacePrivate::ActivatedWindowEvent*)","symbolLocation":942,"imageIndex":7},{"imageOffset":916860,"imageIndex":7},{"imageOffset":404183,"imageIndex":5},{"imageOffset":1427454,"symbol":"-[NSWindow _realMakeFirstResponder:]","symbolLocation":364,"imageIndex":8},{"imageOffset":2281161,"symbol":"-[NSWindow(NSEventRouting) _handleMouseDownEvent:isDelayedEvent:]","symbolLocation":3914,"imageIndex":8},{"imageOffset":1714858,"symbol":"-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:]","symbolLocation":2595,"imageIndex":8},{"imageOffset":1711723,"symbol":"-[NSWindow(NSEventRouting) sendEvent:]","symbolLocation":345,"imageIndex":8},{"imageOffset":486223,"imageIndex":5},{"imageOffset":1704410,"symbol":"-[NSApplication(NSEvent) sendEvent:]","symbolLocation":358,"imageIndex":8},{"imageOffset":46090,"imageIndex":5},{"imageOffset":4583433,"symbol":"-[NSApplication _handleEvent:]","symbolLocation":65,"imageIndex":8},{"imageOffset":196632,"symbol":"-[NSApplication run]","symbolLocation":623,"imageIndex":8},{"imageOffset":102572,"imageIndex":5},{"imageOffset":488230,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":6},{"imageOffset":451125,"symbol":"QCoreApplication::exec()","symbolLocation":133,"imageIndex":6},{"imageOffset":2252186,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":90,"imageIndex":9},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":10},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":10},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":10},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":10},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":10},{"imageOffset":269674,"symbol":"method_vectorcall","symbolLocation":202,"imageIndex":10},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":10},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":10},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":10},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":10},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":10},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":10},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":10},{"imageOffset":1109419,"symbol":"PyEval_EvalCode","symbolLocation":139,"imageIndex":10},{"imageOffset":1096722,"symbol":"builtin_exec","symbolLocation":626,"imageIndex":10},{"imageOffset":516131,"symbol":"cfunction_vectorcall_FASTCALL","symbolLocation":195,"imageIndex":10},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":10},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":10},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":10},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":10},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":10},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":10},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":10},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":10},{"imageOffset":1566832,"symbol":"pymain_run_module","symbolLocation":208,"imageIndex":10},{"imageOffset":1564551,"symbol":"Py_RunMain","symbolLocation":1431,"imageIndex":10},{"imageOffset":1566095,"symbol":"pymain_main","symbolLocation":223,"imageIndex":10},{"imageOffset":1565851,"symbol":"Py_Main","symbolLocation":43,"imageIndex":10},{"imageOffset":3528,"symbol":"main","symbolLocation":120,"imageIndex":11},{"imageOffset":25360,"symbol":"start","symbolLocation":2432,"imageIndex":12}],"id":1610475,"triggered":true,"threadState":{"r13":{"value":1},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":11},"rsi":{"value":11},"r8":{"value":140532221566792},"cr2":{"value":140532226642496},"rdx":{"value":0},"r10":{"value":140704286934208,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":12074595879713188763},"r15":{"value":22},"rbx":{"value":140704286934208,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703153017614,"matchesCrashFrame":1},"rbp":{"value":140532221565568},"rsp":{"value":140532221565528},"r12":{"value":259},"rcx":{"value":140532221565528},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain"},{"id":1610489,"frames":[{"imageOffset":16894,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":13},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610490,"frames":[{"imageOffset":16894,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":13},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610491,"frames":[{"imageOffset":16894,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":13},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610554,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":44874,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":14},{"imageOffset":66455847,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":65958573,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610556,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66009023,"imageIndex":14},{"imageOffset":66011756,"imageIndex":14},{"imageOffset":66010589,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610557,"name":"Chrome_IOThread","frames":[{"imageOffset":44874,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":14},{"imageOffset":66455847,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":48386978,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610558,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610561,"name":"CompositorTileWorker1","frames":[{"imageOffset":16894,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":66219291,"imageIndex":14},{"imageOffset":100616493,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610562,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610563,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":44874,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":14},{"imageOffset":66455847,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610564,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610565,"name":"VizCompositorThread","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610575,"name":"NetworkService","frames":[{"imageOffset":44874,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":14},{"imageOffset":66455847,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610576,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610577,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66009023,"imageIndex":14},{"imageOffset":66011756,"imageIndex":14},{"imageOffset":66010829,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610602,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610648,"name":"com.apple.NSEventThread","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":519438,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":145,"imageIndex":15},{"imageOffset":513914,"symbol":"__CFRunLoopRun","symbolLocation":1360,"imageIndex":15},{"imageOffset":510896,"symbol":"CFRunLoopRunSpecific","symbolLocation":560,"imageIndex":15},{"imageOffset":1697430,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610673,"name":"MemoryInfra","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66251759,"imageIndex":14},{"imageOffset":65421769,"imageIndex":14},{"imageOffset":65919580,"imageIndex":14},{"imageOffset":65624472,"imageIndex":14},{"imageOffset":66059960,"imageIndex":14},{"imageOffset":66060362,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1610674,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66009023,"imageIndex":14},{"imageOffset":66011034,"imageIndex":14},{"imageOffset":66010637,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1612682,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66009023,"imageIndex":14},{"imageOffset":66011756,"imageIndex":14},{"imageOffset":66010733,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1646159,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":5794,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":63101,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34586,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6537,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":14},{"imageOffset":66009023,"imageIndex":14},{"imageOffset":66011756,"imageIndex":14},{"imageOffset":66010733,"imageIndex":14},{"imageOffset":66222344,"imageIndex":14},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":1646456,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1646754,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1646755,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":1646756,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]}],
  "usedImages" : [
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703152984064,
    "size" : 237560,
    "uuid" : "0c2fd2c9-777c-3355-b70f-7b1b6e9d1b0b",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703153221632,
    "size" : 49144,
    "uuid" : "13b5e252-77d1-31e1-888d-1c5f4426ea87",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703151968256,
    "size" : 561152,
    "uuid" : "5efaf10b-2ec1-32ed-b077-80125e552c8d",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703153405952,
    "size" : 40952,
    "uuid" : "f07558db-8b15-3d96-93f9-3a61bbd52f25",
    "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" : 4726763520,
    "size" : 655360,
    "uuid" : "4bf756eb-ff87-3f7f-8c98-b1eda6463b81",
    "path" : "\/Applications\/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_64",
    "base" : 4544065536,
    "size" : 5259264,
    "uuid" : "35b47b1c-6952-3d39-a5e7-711f3ca228f2",
    "path" : "\/Applications\/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" : 4716670976,
    "size" : 6979584,
    "uuid" : "49d915f7-1c6d-3bbd-b96f-064260e7d998",
    "path" : "\/Applications\/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"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703205400576,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16797687,
    "uuid" : "817d572e-eb8c-3999-b7a0-68e1c4b47266",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4532678656,
    "size" : 2801664,
    "uuid" : "babd94e3-ec19-3110-ab5b-11c39432d8c5",
    "path" : "\/Applications\/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" : 4443398144,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4435296256,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703149875200,
    "size" : 607568,
    "uuid" : "28fd2071-57f3-3873-87bf-e4f674a82de6",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4552257536,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Applications\/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" : 5064687616,
    "size" : 165052416,
    "uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
    "path" : "\/Applications\/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_64h",
    "base" : 140703153623040,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4820992,
    "uuid" : "dbc459f3-81bb-398a-8f74-3f7392392bb7",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.1"
  }
],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "62fe74515312cd4599bd3c80",
      "factorPackIds" : {
        "MYRIAD_BOOSTS" : "62fe74805312cd4599bd3c81"
      },
      "deploymentId" : 240000006
    },
    {
      "rolloutId" : "62699e1ec1ff2978b47f6c3b",
      "factorPackIds" : {
        "SIRI_FIND_MY_CONFIGURATION_FILES" : "631f72d1de559130376df1fb"
      },
      "deploymentId" : 240000023
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/fadlof/Downloads/cryosparc_P202_J200_class_00_00800_volume.mrc

Opened cryosparc_P202_J200_class_00_00800_volume.mrc as #1, grid size
32,32,32, pixel 5.9, shown at level 0.889, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J200_class_01_00800_volume.mrc

Opened cryosparc_P202_J200_class_01_00800_volume.mrc as #2, grid size
32,32,32, pixel 5.9, shown at level 0.657, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J200_class_02_00800_volume.mrc

Opened cryosparc_P202_J200_class_02_00800_volume.mrc as #3, grid size
32,32,32, pixel 5.9, shown at level 0.671, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #4, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_01_final_volume.mrc

Opened cryosparc_P202_J209_class_01_final_volume.mrc as #5, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_02_final_volume.mrc

Opened cryosparc_P202_J209_class_02_final_volume.mrc as #6, grid size
64,64,64, pixel 2.95, shown at level 0.305, step 1, values float32  

> tile

6 models tiled  

> volume #1 level 0.3915

> tile

6 models tiled  

> set bgColor white

> lighting full

> volume #2 level 0.2683

> volume #6 level 0.2392

> volume #6 level 0.1548

> volume #5 level 0.2345

> volume #5 level 0.1565

> close #1

> close #2

> close #3

> close #4

> close #5

> close #6

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_00_final_volume.mrc

Opened cryosparc_P202_J75_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.04, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_01_final_volume.mrc

Opened cryosparc_P202_J75_class_01_final_volume.mrc as #2, grid size
128,128,128, pixel 1.77, shown at level 0.101, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #3, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #4, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_01_final_volume.mrc

Opened cryosparc_P202_J209_class_01_final_volume.mrc as #5, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_02_final_volume.mrc

Opened cryosparc_P202_J209_class_02_final_volume.mrc as #6, grid size
64,64,64, pixel 2.95, shown at level 0.305, step 1, values float32  

> volume #3 level 0.05495

> tile

6 models tiled  

> tile

6 models tiled  

> volume #6 level 0.1092

> volume #1 level 0.1447

> volume #3 level 0.1543

> close #1

> close #2

> close #3

> close #4

> close #5

> close #6

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_00_final_volume.mrc

Opened cryosparc_P202_J75_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.04, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_01_final_volume.mrc

Opened cryosparc_P202_J75_class_01_final_volume.mrc as #2, grid size
128,128,128, pixel 1.77, shown at level 0.101, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #3, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_00_final_volume.mrc

Opened cryosparc_P202_J141_class_00_final_volume.mrc as #4, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_01_final_volume.mrc

Opened cryosparc_P202_J141_class_01_final_volume.mrc as #5, grid size
64,64,64, pixel 2.95, shown at level 0.301, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_02_final_volume.mrc

Opened cryosparc_P202_J141_class_02_final_volume.mrc as #6, grid size
64,64,64, pixel 2.95, shown at level 0.242, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #7, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_01_final_volume.mrc

Opened cryosparc_P202_J209_class_01_final_volume.mrc as #8, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_02_final_volume.mrc

Opened cryosparc_P202_J209_class_02_final_volume.mrc as #9, grid size
64,64,64, pixel 2.95, shown at level 0.305, step 1, values float32  

> volume #3 level 0.06719

> tile

9 models tiled  

> tile

9 models tiled  

> volume #5 level 0.12

> volume #9 level 0.1386

> volume #1 level 0.1213

> volume #3 level 0.1884

> volume #7 level 0.3877

> volume #7 level 0.2566

> volume #9 level 0.1574

> volume #6 level 0.1584

> volume #6 level 0.2273

> close #1

> close #3

> close #2

> close #4

> close #5

> close #6

> close #7

> close #8

> close #9

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_02_final_volume.mrc

Opened cryosparc_P202_J141_class_02_final_volume.mrc as #2, grid size
64,64,64, pixel 2.95, shown at level 0.242, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #3, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> tile

3 models tiled  

> volume #1 level 0.1653

> close #1

> close #2

> close #3

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_00_final_volume.mrc

Opened cryosparc_P202_J75_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.04, step 1, values float32  

> volume #1 level 0.3025

> volume #1 level 0.07263

> close #1

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_01_final_volume.mrc

Opened cryosparc_P202_J75_class_01_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.101, step 1, values float32  

> close #1

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #1, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> volume #1 level 0.1837

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_02_final_volume.mrc

Opened cryosparc_P202_J141_class_02_final_volume.mrc as #2, grid size
64,64,64, pixel 2.95, shown at level 0.242, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #3, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> tile

3 models tiled  

> tile

3 models tiled  

> volume #2 level 0.2824

> volume #3 level 0.3033

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.89795,-0.43457,-0.069549,268.63,-0.40087,0.87284,-0.2783,176.77,0.18165,-0.22202,-0.95797,146.93

> view matrix models
> #3,0.33139,-0.22513,0.91624,40.181,0.50733,-0.77625,-0.37423,255.53,0.79548,0.58886,-0.14303,-64.056

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.33139,-0.22513,0.91624,-18.73,0.50733,-0.77625,-0.37423,231.13,0.79548,0.58886,-0.14303,-91.2

> view matrix models
> #3,0.33139,-0.22513,0.91624,-82.134,0.50733,-0.77625,-0.37423,183.7,0.79548,0.58886,-0.14303,-102.63

> view matrix models
> #3,0.33139,-0.22513,0.91624,-142.97,0.50733,-0.77625,-0.37423,137.21,0.79548,0.58886,-0.14303,-112.74

> view matrix models
> #3,0.33139,-0.22513,0.91624,-160.35,0.50733,-0.77625,-0.37423,124.14,0.79548,0.58886,-0.14303,-115.81

> ui mousemode right select

> select subtract #3

Nothing selected  

> volume #1 level 0.1579

> volume #2 level 0.325

> volume #3 level 0.3507

> ui mousemode right "tape measure"

Drag select of 2 cryosparc_P202_J141_class_02_final_volume.mrc  

> ui mousemode right "tape measure"

> set bgColor black

> ui mousemode right "tape measure"

> select clear

Drag select of 2 cryosparc_P202_J141_class_02_final_volume.mrc  

> marker segment #4 position 58.63,88.16,54.44 toPosition 59.4,70.63,64.57
> color yellow radius 0.7381 label 20.27 labelHeight 2.027 labelColor yellow

> marker segment #4 position 51.57,94.74,49.29 toPosition 7.774,68.49,44.6
> color yellow radius 0.7381 label 51.28 labelHeight 5.128 labelColor yellow

> marker delete #4

> marker segment #4 position 60.5,94.15,67.08 toPosition 7.844,67.34,44.92
> color yellow radius 0.7381 label 63.1 labelHeight 6.31 labelColor yellow

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_00_final_volume.mrc

Opened cryosparc_P202_J159_class_00_final_volume.mrc as #5, grid size
64,64,64, pixel 2.95, shown at level 0.268, step 1, values float32  

> volume #5 level 0.2305

> close #1

> close #2

> close #3

> close #4

> tile

1 model tiled  

> volume #5 level 0.3814

> open /Volumes/pool-schulman-
> share/Frank/AlphaFold/Fbxo7-180-324-PI31-1-151/AF_results/Fbxo7-180-324-PI31-1-151/ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select add #1

4699 atoms, 4745 bonds, 296 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

4699 atoms, 4745 bonds, 296 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,104.34,0,1,0,104.13,0,0,1,65.904

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 124  
shifted from previous position = 35.1  
rotated from previous position = 69.6 degrees  
atoms outside contour = 1958, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70220720 -0.24640462 0.66797442 91.30014113  
0.69284976 0.45248109 -0.56144464 95.99360916  
-0.16390325 0.85705638 0.48845686 94.74280038  
Axis 0.74903558 0.43927072 0.49597070  
Axis point 0.00000000 5.75443656 42.10304412  
Rotation angle (degrees) 71.24194620  
Shift along axis 157.54388914  
  

> volume #5 color #b2b2ff95

> set bgColor white

> lighting full

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 64  
shifted from previous position = 3.54  
rotated from previous position = 0.0424 degrees  
atoms outside contour = 1960, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70240018 -0.24694620 0.66757141 91.34215036  
0.69280698 0.45231042 -0.56163492 96.00641179  
-0.16325590 0.85699059 0.48878897 94.73519107  
Axis 0.74914894 0.43874397 0.49626564  
Axis point 0.00000000 5.84408081 42.15372900  
Rotation angle (degrees) 71.23122301  
Shift along axis 157.56493048  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 48  
shifted from previous position = 0.0736  
rotated from previous position = 0.105 degrees  
atoms outside contour = 1961, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70216055 -0.24547257 0.66836652 91.27340918  
0.69265420 0.45292174 -0.56133062 95.98578675  
-0.16492647 0.85709108 0.48805138 94.74468472  
Axis 0.74899215 0.44001717 0.49537425  
Axis point 0.00000000 5.61598677 42.03651133  
Rotation angle (degrees) 71.24229328  
Shift along axis 157.53253842  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 40  
shifted from previous position = 0.0149  
rotated from previous position = 0.0417 degrees  
atoms outside contour = 1958, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70222444 -0.24607753 0.66807687 91.28717273  
0.69274689 0.45266785 -0.56142104 95.98993871  
-0.16426382 0.85705174 0.48834386 94.74442476  
Axis 0.74903289 0.43952239 0.49575175  
Axis point 0.00000000 5.70308278 42.08538870  
Rotation angle (degrees) 71.23919280  
Shift along axis 157.53653680  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 40  
shifted from previous position = 0.0404  
rotated from previous position = 0.0438 degrees  
atoms outside contour = 1962, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70241884 -0.24666082 0.66765727 91.32586171  
0.69270122 0.45254255 -0.56157837 95.99962449  
-0.16362395 0.85695023 0.48873666 94.74282475  
Axis 0.74912445 0.43899932 0.49607676  
Axis point 0.00000000 5.78872073 42.13610873  
Rotation angle (degrees) 71.22521721  
Shift along axis 157.55791950  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 40  
shifted from previous position = 0.0501  
rotated from previous position = 0.0873 degrees  
atoms outside contour = 1960, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70223130 -0.24538434 0.66832458 91.27797553  
0.69257385 0.45295634 -0.56140184 95.98918240  
-0.16496264 0.85709806 0.48802690 94.74311766  
Axis 0.74904431 0.44002051 0.49529242  
Axis point 0.00000000 5.60851453 42.04276866  
Rotation angle (degrees) 71.23984639  
Shift along axis 157.53400450  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 44  
shifted from previous position = 0.00633  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 1961, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70220543 -0.24559120 0.66827577 91.27602124  
0.69263889 0.45290496 -0.56136305 95.98312482  
-0.16479960 0.85706597 0.48813833 94.74209149  
Axis 0.74901147 0.43991134 0.49543903  
Axis point 0.00000000 5.63108349 42.04631956  
Rotation angle (degrees) 71.23881218  
Shift along axis 157.52978164  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 40  
shifted from previous position = 0.0751  
rotated from previous position = 0.129 degrees  
atoms outside contour = 1961, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70234004 -0.24742151 0.66745867 91.34445993  
0.69299992 0.45196186 -0.56167749 96.00959310  
-0.16269477 0.85703739 0.48889399 94.73596977  
Axis 0.74915532 0.43836424 0.49659148  
Axis point 0.00000000 5.91752333 42.18860369  
Rotation angle (degrees) 71.24041064  
Shift along axis 157.56343594  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 48  
shifted from previous position = 0.0611  
rotated from previous position = 0.142 degrees  
atoms outside contour = 1957, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70211381 -0.24539756 0.66844316 91.28875778  
0.69268742 0.45289012 -0.56131515 95.98942673  
-0.16498594 0.85712927 0.48796420 94.74123302  
Axis 0.74898192 0.44007599 0.49533748  
Axis point 0.00000000 5.61421255 42.01917088  
Rotation angle (degrees) 71.24730162  
Shift along axis 157.54515369  
  

> fitmap #1 inMap #5

Fit molecule ranked_0.pdb (#1) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 4699 atoms  
average map value = 0.426, steps = 44  
shifted from previous position = 0.0553  
rotated from previous position = 0.121 degrees  
atoms outside contour = 1957, contour level = 0.38142  
  
Position of ranked_0.pdb (#1) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.70237255 -0.24721110 0.66750242 91.33938059  
0.69284721 0.45244409 -0.56147761 96.00035458  
-0.16320404 0.85684364 0.48906383 94.75515394  
Axis 0.74903949 0.43871016 0.49646072  
Axis point 0.00000000 5.84935076 42.15235578  
Rotation angle (degrees) 71.21969739  
Shift along axis 157.57534529  
  

> volume #5 level 0.4534

> open /Users/fadlof/Downloads/Chimera/PDB/4ouh_PI31-FP_dimer.pdb

4ouh_PI31-FP_dimer.pdb title:  
Crystal structure of the FP domain of human Π31 proteasome inhibitor [more
info...]  
  
Chain information for 4ouh_PI31-FP_dimer.pdb #2  
---  
Chain | Description | UniProt  
A B | HPI31 | PSMF1_HUMAN  
  

> select add #5

4699 atoms, 4745 bonds, 296 residues, 3 models selected  

> select subtract #1

2 models selected  

> select add #2

2615 atoms, 2383 bonds, 2 pseudobonds, 577 residues, 4 models selected  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 436  
shifted from previous position = 126  
rotated from previous position = 147 degrees  
atoms outside contour = 1462, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04748182 0.96000060 -0.27594267 113.93997204  
-0.12535988 -0.27979717 -0.95183951 199.20698172  
-0.99097447 -0.01060293 0.13363085 83.22101945  
Axis 0.58653369 0.44557368 -0.67634483  
Axis point 150.61740250 106.32774437 0.00000000  
Rotation angle (degrees) 126.64277525  
Shift along axis 99.30491456  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 104  
shifted from previous position = 20.4  
rotated from previous position = 0.0638 degrees  
atoms outside contour = 1464, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04701370 0.95979427 -0.27673939 114.02765011  
-0.12474175 -0.28051824 -0.95170848 199.19208818  
-0.99107479 -0.01022239 0.13291463 83.29219428  
Axis 0.58695302 0.44533990 -0.67613499  
Axis point 150.70420735 106.33327226 0.00000000  
Rotation angle (degrees) 126.67738641  
Shift along axis 99.32029002  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4168, steps = 48  
shifted from previous position = 0.0571  
rotated from previous position = 0.0914 degrees  
atoms outside contour = 1463, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04762777 0.95986542 -0.27638741 113.99624462  
-0.12616950 -0.28026629 -0.95159449 199.18308588  
-0.99086471 -0.01045067 0.13445421 83.18284746  
Axis 0.58641929 0.44518516 -0.67669978  
Axis point 150.59946818 106.23173331 0.00000000  
Rotation angle (degrees) 126.63533876  
Shift along axis 99.23313629  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 48  
shifted from previous position = 0.069  
rotated from previous position = 0.0995 degrees  
atoms outside contour = 1466, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04682836 0.95980221 -0.27674329 114.02001979  
-0.12467130 -0.28049675 -0.95172405 199.19994973  
-0.99109243 -0.01006574 0.13279500 83.29327451  
Axis 0.58703662 0.44533043 -0.67606865  
Axis point 150.72047810 106.34465070 -0.00000000  
Rotation angle (degrees) 126.67427171  
Shift along axis 99.33175497  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 44  
shifted from previous position = 0.0058  
rotated from previous position = 0.0293 degrees  
atoms outside contour = 1465, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04707388 0.95987975 -0.27643254 113.98881610  
-0.12499725 -0.28022462 -0.95176145 199.20158493  
-0.99103974 -0.01024981 0.13317361 83.25848767  
Axis 0.58683483 0.44540755 -0.67619302  
Axis point 150.67799687 106.33252031 0.00000000  
Rotation angle (degrees) 126.65979948  
Shift along axis 99.31968802  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 68  
shifted from previous position = 11.7  
rotated from previous position = 0.0789 degrees  
atoms outside contour = 1465, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04779645 0.96011231 -0.27549931 113.89133723  
-0.12570106 -0.27940342 -0.95191018 199.21471003  
-0.99091613 -0.01086738 0.13404164 83.16761735  
Axis 0.58627985 0.44571242 -0.67647348  
Axis point 150.55632236 106.32190151 0.00000000  
Rotation angle (degrees) 126.62528574  
Shift along axis 99.30397894  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 40  
shifted from previous position = 0.0166  
rotated from previous position = 0.0159 degrees  
atoms outside contour = 1461, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04765601 0.96007485 -0.27565416 113.91059308  
-0.12551755 -0.27953613 -0.95189543 199.21081954  
-0.99094615 -0.01076411 0.13382783 83.20635069  
Axis 0.58639097 0.44567719 -0.67640038  
Axis point 150.59114769 106.33045906 0.00000000  
Rotation angle (degrees) 126.63264225  
Shift along axis 99.29905482  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4168, steps = 48  
shifted from previous position = 0.0542  
rotated from previous position = 0.0417 degrees  
atoms outside contour = 1464, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04724226 0.96021525 -0.27523600 113.86734843  
-0.12594294 -0.27907061 -0.95197583 199.22371628  
-0.99091199 -0.01030946 0.13411627 83.22509977  
Axis 0.58640735 0.44567553 -0.67638727  
Axis point 150.64244007 106.33457399 -0.00000000  
Rotation angle (degrees) 126.59096677  
Shift along axis 99.26938686  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 44  
shifted from previous position = 0.0739  
rotated from previous position = 0.147 degrees  
atoms outside contour = 1464, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04736512 0.95951510 -0.27764609 114.12556128  
-0.12527685 -0.28146964 -0.95135722 199.15957412  
-0.99099055 -0.01027853 0.13353689 83.21594514  
Axis 0.58688457 0.44486275 -0.67650841  
Axis point 150.64575034 106.22238798 0.00000000  
Rotation angle (degrees) 126.70169983  
Shift along axis 99.28092028  
  

> fitmap #2 inMap #5

Fit molecule 4ouh_PI31-FP_dimer.pdb (#2) to map
cryosparc_P202_J159_class_00_final_volume.mrc (#5) using 2615 atoms  
average map value = 0.4169, steps = 44  
shifted from previous position = 0.0528  
rotated from previous position = 0.115 degrees  
atoms outside contour = 1462, contour level = 0.4534  
  
Position of 4ouh_PI31-FP_dimer.pdb (#2) relative to
cryosparc_P202_J159_class_00_final_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.04779179 0.95999612 -0.27590474 113.93472113  
-0.12612333 -0.27980934 -0.95173507 199.20344363  
-0.99086269 -0.01068710 0.13445051 83.17064678  
Axis 0.58628101 0.44542497 -0.67666179  
Axis point 150.56911015 106.26968582 0.00000000  
Rotation angle (degrees) 126.62501399  
Shift along axis 99.24955288  
  

> select subtract #5

2615 atoms, 2383 bonds, 2 pseudobonds, 577 residues, 2 models selected  

> select add #5

2615 atoms, 2383 bonds, 2 pseudobonds, 577 residues, 4 models selected  

> hide #!5 models

> select subtract #2

2 models selected  

> select subtract #5

Nothing selected  

> select add #2

2615 atoms, 2383 bonds, 2 pseudobonds, 577 residues, 2 models selected  

> view matrix models
> #2,0.62846,0.577,0.52164,27.711,0.76058,-0.59634,-0.25671,121.49,0.16295,0.55808,-0.81363,167.26

> view matrix models
> #2,0.62846,0.577,0.52164,14.84,0.76058,-0.59634,-0.25671,104.05,0.16295,0.55808,-0.81363,156.11

> view matrix models
> #2,0.62846,0.577,0.52164,4.1092,0.76058,-0.59634,-0.25671,98.176,0.16295,0.55808,-0.81363,150.45

> view matrix models
> #2,0.62846,0.577,0.52164,-7.5665,0.76058,-0.59634,-0.25671,89.832,0.16295,0.55808,-0.81363,143.46

> view matrix models
> #2,0.64657,0.24743,0.72161,-28.152,0.64603,-0.68066,-0.34546,99.94,0.4057,0.68955,-0.59994,118.79

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.58652,0.71175,0.38653,7.0178,0.62077,-0.70157,0.34993,23.782,0.52024,0.034709,-0.85332,148.77

> view matrix models
> #2,0.64414,0.75347,-0.13178,63.577,0.59643,-0.38688,0.70327,-16.119,0.47891,-0.5316,-0.6986,134.05

> view matrix models
> #2,0.63638,0.23088,0.73601,-29.642,0.6497,-0.67478,-0.35008,100.41,0.41582,0.70098,-0.57942,116.47

> view matrix models
> #2,0.60195,0.22027,0.76755,-32.968,0.63316,-0.71736,-0.29069,94.104,0.48658,0.66096,-0.57129,115.53

> ui mousemode right "rotate selected models"

> ui mousemode right select

> select add #5

2615 atoms, 2383 bonds, 2 pseudobonds, 577 residues, 4 models selected  

> select subtract #2

2 models selected  

> select add #1

4699 atoms, 4745 bonds, 296 residues, 3 models selected  

> select subtract #5

4699 atoms, 4745 bonds, 296 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #!5 models

> hide #!5 models

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_02_final_volume.mrc

Opened cryosparc_P202_J209_class_02_final_volume.mrc as #3, grid size
64,64,64, pixel 2.95, shown at level 0.305, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_00_final_volume.mrc

Opened cryosparc_P202_J75_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.77, shown at level 0.04, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_01_final_volume.mrc

Opened cryosparc_P202_J75_class_01_final_volume.mrc as #6, grid size
128,128,128, pixel 1.77, shown at level 0.101, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #7, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_00_final_volume.mrc

Opened cryosparc_P202_J141_class_00_final_volume.mrc as #8, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_01_final_volume.mrc

Opened cryosparc_P202_J141_class_01_final_volume.mrc as #9, grid size
64,64,64, pixel 2.95, shown at level 0.301, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_02_final_volume.mrc

Opened cryosparc_P202_J141_class_02_final_volume.mrc as #10, grid size
64,64,64, pixel 2.95, shown at level 0.242, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_00_final_volume.mrc

Opened cryosparc_P202_J159_class_00_final_volume.mrc as #11, grid size
64,64,64, pixel 2.95, shown at level 0.268, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_01_final_volume.mrc

Opened cryosparc_P202_J159_class_01_final_volume.mrc as #12, grid size
64,64,64, pixel 2.95, shown at level 0.315, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_02_final_volume.mrc

Opened cryosparc_P202_J159_class_02_final_volume.mrc as #13, grid size
64,64,64, pixel 2.95, shown at level 0.268, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #14, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_01_final_volume.mrc

Opened cryosparc_P202_J209_class_01_final_volume.mrc as #15, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> close #5

> close #3

> close #4

> close #6

> close #7

> close #8

> close #9

> close #10

> close #11

> close #12

> close #13

> close #14

> close #15

> close

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_02_final_volume.mrc

Opened cryosparc_P202_J209_class_02_final_volume.mrc as #1, grid size
64,64,64, pixel 2.95, shown at level 0.305, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_00_final_volume.mrc

Opened cryosparc_P202_J75_class_00_final_volume.mrc as #2, grid size
128,128,128, pixel 1.77, shown at level 0.04, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_01_final_volume.mrc

Opened cryosparc_P202_J75_class_01_final_volume.mrc as #3, grid size
128,128,128, pixel 1.77, shown at level 0.101, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J75_class_02_final_volume.mrc

Opened cryosparc_P202_J75_class_02_final_volume.mrc as #4, grid size
128,128,128, pixel 1.77, shown at level 0.0255, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_00_final_volume.mrc

Opened cryosparc_P202_J141_class_00_final_volume.mrc as #5, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_01_final_volume.mrc

Opened cryosparc_P202_J141_class_01_final_volume.mrc as #6, grid size
64,64,64, pixel 2.95, shown at level 0.301, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J141_class_02_final_volume.mrc

Opened cryosparc_P202_J141_class_02_final_volume.mrc as #7, grid size
64,64,64, pixel 2.95, shown at level 0.242, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_00_final_volume.mrc

Opened cryosparc_P202_J159_class_00_final_volume.mrc as #8, grid size
64,64,64, pixel 2.95, shown at level 0.268, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_01_final_volume.mrc

Opened cryosparc_P202_J159_class_01_final_volume.mrc as #9, grid size
64,64,64, pixel 2.95, shown at level 0.315, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J159_class_02_final_volume.mrc

Opened cryosparc_P202_J159_class_02_final_volume.mrc as #10, grid size
64,64,64, pixel 2.95, shown at level 0.268, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_00_final_volume.mrc

Opened cryosparc_P202_J209_class_00_final_volume.mrc as #11, grid size
64,64,64, pixel 2.95, shown at level 0.235, step 1, values float32  

> open /Users/fadlof/Downloads/cryosparc_P202_J209_class_01_final_volume.mrc

Opened cryosparc_P202_J209_class_01_final_volume.mrc as #12, grid size
64,64,64, pixel 2.95, shown at level 0.253, step 1, values float32  

> tile

12 models tiled  

> volume #1 level 0.2185

> volume #2 level 0.169

> volume #3 level 0.1623

> volume #4 level 0.1505

> volume #1 level 0.3336

> volume #1 level 0.2232

> volume #1 level 0.2279

> volume #1 level 0.1269

> volume #2 level 0.08597

> select clear

> volume #3 level 0.05453

> volume #6 level 0.1991

> volume #3 level 0.1489

> volume #1 level 0.2655

> select clear

> volume #7 level 0.1981

> close #1

> close #2

> close #3

> close #5

> close #6

> close #9

> close #10

> close #12

> tile

4 models tiled  

> set bgColor black

> volume #4 level 0.2

> volume #7 level 0.2

> volume #8 level 0.2

> volume #11 level 0.2

> volume #4 level 0.1


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

Log:
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.2.44
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2,7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
      OS Loader Version: 564.40.4~27

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 5 Tage und 3 Stunden

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2718Q:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: FN84K91L0H2L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7,55


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202211182308
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.0.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.32
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0