![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#6972 closed defect (nonchimerax)
Graphics crash, macOS 12.4, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000000110d8a600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 95 in draw_new_frame
Fatal Python error: Segmentation fault
{"app_name":"ChimeraX","timestamp":"2022-05-27 01:14:51.00 -0400","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"C15A2415-1F23-4D5C-B808-E318746681BF","name":"ChimeraX"}
{
"uptime" : 470000,
"procLaunch" : "2022-05-26 23:31:56.3744 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"procStartAbsTime" : 468203221640309,
"coalitionID" : 1920,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2022-05-27 01:14:24.0111 -0400",
"incident" : "C15A2415-1F23-4D5C-B808-E318746681BF",
"bug_type" : "309",
"pid" : 90273,
"procExitAbsTime" : 474350676690141,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8B4529AF-1CFB-5F11-8E79-0A5644571A50","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A43C6006-34B7-90C4-6BD6-971F9B9BE23A",
"wakeTime" : 26381,
"bridgeVersion" : {"build":"19P5071","train":"6.5"},
"sleepWakeUUID" : "254BDE8C-9D82-4A1A-BF6B-CB4175E21215",
"sip" : "enabled",
"vmRegionInfo" : "0xb8 is not in any region. Bytes before following region: 140737487363912\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff0e000-7ffffff0f000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000b8","rawCodes":[1,184],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000b8"},
"vmregioninfo" : "0xb8 is not in any region. Bytes before following region: 140737487363912\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff0e000-7ffffff0f000 [ 4K] r-x\/r-x SM=ALI ",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"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" : 35,
"threads" : [{"id":4085248,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":525197,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":1},{"imageOffset":518680,"symbol":"__CFRunLoopRun","symbolLocation":1276,"imageIndex":1},{"imageOffset":515676,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":1},{"imageOffset":189926,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":2},{"imageOffset":189258,"symbol":"ReceiveNextEventCommon","symbolLocation":594,"imageIndex":2},{"imageOffset":188645,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":70,"imageIndex":2},{"imageOffset":258557,"symbol":"_DPSNextEvent","symbolLocation":927,"imageIndex":3},{"imageOffset":252090,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1394,"imageIndex":3},{"imageOffset":196457,"symbol":"-[NSApplication run]","symbolLocation":586,"imageIndex":3},{"imageOffset":235055,"symbol":"QCocoaEventDispatcher::processEvents(QFlags)","symbolLocation":2495,"imageIndex":4},{"imageOffset":2050767,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":431,"imageIndex":5},{"imageOffset":2068546,"symbol":"QCoreApplication::exec()","symbolLocation":130,"imageIndex":5},{"imageOffset":2344706,"symbol":"meth_QApplication_exec_(_object*, _object*)","symbolLocation":82,"imageIndex":6},{"imageOffset":503917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":7},{"imageOffset":246141,"symbol":"_PyObject_MakeTpCall","symbolLocation":365,"imageIndex":7},{"imageOffset":1132060,"symbol":"call_function","symbolLocation":876,"imageIndex":7},{"imageOffset":1120947,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25219,"imageIndex":7},{"imageOffset":248136,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":256394,"symbol":"method_vectorcall","symbolLocation":202,"imageIndex":7},{"imageOffset":1131916,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1120947,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25219,"imageIndex":7},{"imageOffset":1135235,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":248017,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1131916,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1121099,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25371,"imageIndex":7},{"imageOffset":1135235,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":1095435,"symbol":"PyEval_EvalCode","symbolLocation":139,"imageIndex":7},{"imageOffset":1082770,"symbol":"builtin_exec","symbolLocation":626,"imageIndex":7},{"imageOffset":501866,"symbol":"cfunction_vectorcall_FASTCALL","symbolLocation":218,"imageIndex":7},{"imageOffset":1131916,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1121099,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25371,"imageIndex":7},{"imageOffset":1135235,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":248017,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1131916,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1121099,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25371,"imageIndex":7},{"imageOffset":1135235,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":248017,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1551904,"symbol":"pymain_run_module","symbolLocation":208,"imageIndex":7},{"imageOffset":1549623,"symbol":"Py_RunMain","symbolLocation":1431,"imageIndex":7},{"imageOffset":1551167,"symbol":"pymain_main","symbolLocation":223,"imageIndex":7},{"imageOffset":1550923,"symbol":"Py_Main","symbolLocation":43,"imageIndex":7},{"imageOffset":3528,"symbol":"main","symbolLocation":120,"imageIndex":8},{"imageOffset":21790,"symbol":"start","symbolLocation":462,"imageIndex":9}]},{"id":4085251,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3377823,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":11},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085252,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3377823,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":11},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085253,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3377823,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":11},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085274,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":45272682,"symbol":"base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*)","symbolLocation":330,"imageIndex":12},{"imageOffset":45272263,"symbol":"base::MessagePumpKqueue::Run(base::MessagePump::Delegate*)","symbolLocation":167,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44829332,"symbol":"base::internal::ServiceThread::Run(base::RunLoop*)","symbolLocation":20,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085276,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":44869496,"symbol":"base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*)","symbolLocation":56,"imageIndex":12},{"imageOffset":44872016,"symbol":"base::internal::WorkerThread::RunWorker()","symbolLocation":1024,"imageIndex":12},{"imageOffset":44870724,"symbol":"base::internal::WorkerThread::RunBackgroundPooledWorker()","symbolLocation":20,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085277,"name":"Chrome_IOThread","frames":[{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":45272682,"symbol":"base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*)","symbolLocation":330,"imageIndex":12},{"imageOffset":45272263,"symbol":"base::MessagePumpKqueue::Run(base::MessagePump::Delegate*)","symbolLocation":167,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":111124230,"symbol":"content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*)","symbolLocation":102,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085278,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085282,"name":"CompositorTileWorker1","frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":45194776,"symbol":"base::ConditionVariable::Wait()","symbolLocation":104,"imageIndex":12},{"imageOffset":64820728,"symbol":"non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run()","symbolLocation":56,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085283,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":44343823,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":223,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085284,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":45272682,"symbol":"base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*)","symbolLocation":330,"imageIndex":12},{"imageOffset":45272263,"symbol":"base::MessagePumpKqueue::Run(base::MessagePump::Delegate*)","symbolLocation":167,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085285,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085286,"name":"VizCompositorThread","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085294,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085295,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44869482,"symbol":"base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*)","symbolLocation":42,"imageIndex":12},{"imageOffset":44872016,"symbol":"base::internal::WorkerThread::RunWorker()","symbolLocation":1024,"imageIndex":12},{"imageOffset":44870964,"symbol":"base::internal::WorkerThread::RunDedicatedWorker()","symbolLocation":20,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085314,"name":"MemoryInfra","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085343,"name":"NetworkConfigWatcher","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44343771,"symbol":"base::MessagePumpDefault::Run(base::MessagePump::Delegate*)","symbolLocation":171,"imageIndex":12},{"imageOffset":44783147,"symbol":"base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta)","symbolLocation":139,"imageIndex":12},{"imageOffset":44537803,"symbol":"base::RunLoop::Run()","symbolLocation":395,"imageIndex":12},{"imageOffset":44911229,"symbol":"base::Thread::ThreadMain()","symbolLocation":413,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085381,"name":"com.apple.NSEventThread","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":525197,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":1},{"imageOffset":518680,"symbol":"__CFRunLoopRun","symbolLocation":1276,"imageIndex":1},{"imageOffset":515676,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":1},{"imageOffset":1756190,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":3},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4085384,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":45228751,"symbol":"base::WaitableEvent::Wait()","symbolLocation":31,"imageIndex":12},{"imageOffset":44869482,"symbol":"base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*)","symbolLocation":42,"imageIndex":12},{"imageOffset":44871229,"symbol":"base::internal::WorkerThread::RunWorker()","symbolLocation":237,"imageIndex":12},{"imageOffset":44870772,"symbol":"base::internal::WorkerThread::RunBackgroundSharedWorker()","symbolLocation":20,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4088461,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3379947,"symbol":"blas_thread_server","symbolLocation":619,"imageIndex":13},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4088462,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3379947,"symbol":"blas_thread_server","symbolLocation":619,"imageIndex":13},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4088463,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":3379947,"symbol":"blas_thread_server","symbolLocation":619,"imageIndex":13},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114722,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114723,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114724,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114725,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114726,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114727,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114728,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114729,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":518355,"symbol":"OpenMM::threadBody(void*)","symbolLocation":195,"imageIndex":14},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4114730,"frames":[{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":10},{"imageOffset":1147731,"symbol":"threadBody(void*)","symbolLocation":115,"imageIndex":15},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4125426,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":0},{"imageOffset":45229202,"symbol":"base::WaitableEvent::TimedWait(base::TimeDelta const&)","symbolLocation":434,"imageIndex":12},{"imageOffset":44869496,"symbol":"base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*)","symbolLocation":56,"imageIndex":12},{"imageOffset":44872016,"symbol":"base::internal::WorkerThread::RunWorker()","symbolLocation":1024,"imageIndex":12},{"imageOffset":44870868,"symbol":"base::internal::WorkerThread::RunPooledWorker()","symbolLocation":20,"imageIndex":12},{"imageOffset":45211143,"symbol":"base::(anonymous namespace)::ThreadFunc(void*)","symbolLocation":87,"imageIndex":12},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]},{"id":4131761,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":10}]},{"id":4132254,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":10}]},{"id":4132551,"frames":[{"imageOffset":8008,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":10}]},{"triggered":true,"id":4134441,"instructionState":{"instructionStream":{"bytes":[139,131,184,0,0,0,255,192,137,131,184,0,0,0,72,139,187,192,0,0,0,72,133,255,116,45,102,144,72,139,71,248,72,139,79,8,72,139,73,48,72,131,224,252,72,137,131,192,0,0,0,255,209,72,139,187,192,0,0,0,72,133,255,117,219,139,131,184,0,0,0,255,200,137,131,184,0,0,0,72,131,196,8,91,93,195,102,15,31,68,0,0,85,72,137,229,139,135,184,0,0,0,131,248,50,124,47,72,141,5,242,243,35,0,72,139,128,104,2,0,0,72,139,78,248,72,131,225,3,72,11,136,192,0,0,0,72,137,78,248,72,137,176,192,0,0,0,184,1,0,0,0,93,195,255,192,137,135,184,0,0,0,49,192,93,195,102,15,31,68,0,0,85,72,137,229,83,80,139,135,184,0,0,0,255,200,137,135,184,0,0,0],"offset":96}},"threadState":{"r13":{"value":140530131943344},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":11},"rsi":{"value":11},"r8":{"value":123145416842408},"cr2":{"value":184},"rdx":{"value":0},"r10":{"value":123145416847360},"r9":{"value":4658073197460650614},"r15":{"value":22},"rbx":{"value":123145416847360},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703392489486,"matchesCrashFrame":1},"rbp":{"value":123145416841184},"rsp":{"value":123145416841144},"r12":{"value":211039},"rcx":{"value":123145416841144},"flavor":"x86_THREAD_STATE","rdi":{"value":211039}},"queue":"opencl_runtime","frames":[{"imageOffset":32782,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25087,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":10},{"imageOffset":279256,"symbol":"raise","symbolLocation":26,"imageIndex":16},{"imageOffset":15869,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":17},{"imageOffset":18,"imageIndex":18},{"imageOffset":349627,"symbol":"frame_dealloc","symbolLocation":91,"imageIndex":7},{"imageOffset":1493151,"symbol":"dump_traceback","symbolLocation":527,"imageIndex":7},{"imageOffset":1493619,"symbol":"_Py_DumpTracebackThreads","symbolLocation":339,"imageIndex":7},{"imageOffset":1901128,"symbol":"faulthandler_fatal_error","symbolLocation":232,"imageIndex":7},{"imageOffset":15869,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":17},{"imageOffset":4435943424,"imageIndex":18},{"imageOffset":531748,"symbol":"abort","symbolLocation":123,"imageIndex":16},{"imageOffset":5679,"symbol":"gpusGenerateCrashLog","symbolLocation":157,"imageIndex":19},{"imageOffset":13433129,"symbol":"gpusKillClientExt","symbolLocation":9,"imageIndex":20},{"imageOffset":8160,"symbol":"gpusQueueSubmitDataBuffers","symbolLocation":162,"imageIndex":19},{"imageOffset":1659122,"symbol":"IntelCLCommandBuffer::getNew(GLDQueueRec*)","symbolLocation":32,"imageIndex":20},{"imageOffset":1658867,"symbol":"intelSubmitCLCommands(GLDQueueRec*, unsigned int)","symbolLocation":69,"imageIndex":20},{"imageOffset":1658688,"symbol":"CHAL_INTEL::ChalContext::ChalFlush()","symbolLocation":82,"imageIndex":20},{"imageOffset":1642275,"symbol":"CHAL_INTEL::ChalContext::SetupFixedFunctionKernelExecute(CHAL_INTEL::tagCHALCommandPacket*, unsigned long*)","symbolLocation":503,"imageIndex":20},{"imageOffset":1641706,"symbol":"CHAL_INTEL::ChalContext::ChalExecuteCopyBufferData(GLDBufferImageRegionRec*, GLDBufferRec*, GLDBufferImageRegionRec*, GLDBufferRec*, GLDFenceRec*)","symbolLocation":1558,"imageIndex":20},{"imageOffset":1640040,"symbol":"gldCopyBufferDataWithQueue","symbolLocation":268,"imageIndex":20},{"imageOffset":72187,"imageIndex":21},{"imageOffset":176224,"imageIndex":21},{"imageOffset":183534,"imageIndex":21},{"imageOffset":13079,"symbol":"_dispatch_client_callout","symbolLocation":8,"imageIndex":22},{"imageOffset":67566,"symbol":"_dispatch_lane_barrier_sync_invoke_and_complete","symbolLocation":60,"imageIndex":22},{"imageOffset":183162,"imageIndex":21},{"imageOffset":172607,"imageIndex":21},{"imageOffset":137466,"symbol":"clEnqueueReadBuffer","symbolLocation":749,"imageIndex":21},{"imageOffset":16470,"symbol":"OpenMM::OpenCLArray::download(void*, bool) const","symbolLocation":118,"imageIndex":15},{"imageOffset":1309560,"symbol":"OpenMM::IntegrationUtilities::getLastStepSize()","symbolLocation":136,"imageIndex":15},{"imageOffset":950540,"symbol":"OpenMM::CommonIntegrateVariableLangevinStepKernel::execute(OpenMM::ContextImpl&, OpenMM::VariableLangevinIntegrator const&, double)","symbolLocation":1212,"imageIndex":15},{"imageOffset":521905,"symbol":"OpenMM::VariableLangevinIntegrator::step(int)","symbolLocation":161,"imageIndex":14},{"imageOffset":15326,"symbol":"isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long, bool)","symbolLocation":494,"imageIndex":23},{"imageOffset":34541,"symbol":"void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long, bool), isolde::OpenMM_Thread_Handler*, unsigned long, bool> >(void*)","symbolLocation":77,"imageIndex":23},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":10},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":10}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703392456704,
"size" : 229376,
"uuid" : "61711d11-e776-3bc3-b9a2-6f9f37cb8499",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703393001472,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "f8e45ef9-9fd2-3331-bb1b-703d5dacdaf1",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1863"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703540813824,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3096576,
"uuid" : "04544f53-a387-3ac3-a85d-f8adfc0bc69e",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703437557760,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15265792,
"uuid" : "832ad371-d3b8-3061-b4e2-1c4e0cffce0b",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.50.132"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4733501440,
"size" : 1503232,
"uuid" : "d4ab240b-4535-3aec-b72b-5ffc4750e4e5",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4676722688,
"size" : 5705728,
"uuid" : "c723812a-f7a5-3001-98d5-e60e8daa6ffb",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtCore.framework\/Versions\/5\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4714209280,
"size" : 2691072,
"uuid" : "259274fb-9944-3b14-95c0-acb6f7b3f7d7",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4439560192,
"CFBundleShortVersionString" : "3.9.6, (c) 2001-2019 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2510848,
"uuid" : "7fdc4a6b-e70b-3c9e-a72e-cd15ddf0d90f",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.6"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4434759680,
"CFBundleShortVersionString" : "1.3.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.3.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4577075200,
"size" : 442368,
"uuid" : "b70ce1ec-b902-3852-8268-05de00bfa8d5",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703392686080,
"size" : 49152,
"uuid" : "bc574849-1aae-31e7-b350-916dda999d97",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4577828864,
"size" : 62603264,
"uuid" : "9112000d-375c-34f0-9a66-9d68f91a12cd",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4936847360,
"size" : 131002368,
"uuid" : "86651daf-3bff-3a6f-b313-e84d303e55eb",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6109794304,
"size" : 61087744,
"uuid" : "6286b1a0-1fc3-3620-a830-7af7902ead7f",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4812521472,
"size" : 2195456,
"uuid" : "b75e2a1b-22bb-388f-bebd-91ae10f2b866",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/lib\/libOpenMM.7.6.dylib",
"name" : "libOpenMM.7.6.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4809310208,
"size" : 1929216,
"uuid" : "a07ecf21-6a6b-35be-a77f-9d4fd3c7c0ff",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/lib\/plugins\/libOpenMMOpenCL.dylib",
"name" : "libOpenMMOpenCL.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703391440896,
"size" : 561152,
"uuid" : "d9ba0660-744d-3f84-9f80-afb51d450512",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703392784384,
"size" : 40960,
"uuid" : "f6cad74b-ec4d-3ff9-80f3-b066753f9fab",
"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" : 140707961081856,
"size" : 45056,
"uuid" : "5fcec882-890c-3c7a-a3dd-6e82f716199a",
"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
"name" : "libGPUSupportMercury.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712281427968,
"CFBundleShortVersionString" : "18.7.4",
"CFBundleIdentifier" : "com.apple.driver.AppleIntelICLGraphicsGLDriver",
"size" : 15745024,
"uuid" : "acbc46a1-4939-3eb3-bc5b-665821985db7",
"path" : "\/System\/Library\/Extensions\/AppleIntelICLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelICLGraphicsGLDriver",
"name" : "AppleIntelICLGraphicsGLDriver",
"CFBundleVersion" : "18.0.7"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712423026688,
"CFBundleShortVersionString" : "4.7",
"CFBundleIdentifier" : "com.apple.opencl",
"size" : 360448,
"uuid" : "cd768dfd-f8e1-3ea8-9082-7b7b79f386ff",
"path" : "\/System\/Library\/Frameworks\/OpenCL.framework\/Versions\/A\/OpenCL",
"name" : "OpenCL",
"CFBundleVersion" : "4.7"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703390900224,
"size" : 290816,
"uuid" : "534511b9-b3b0-33a7-b1ea-402595d28bda",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5655531520,
"size" : 81920,
"uuid" : "722da143-5bec-3fd3-b9c5-0663a0843da2",
"path" : "\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/libopenmm.dylib",
"name" : "libopenmm.dylib"
}
],
"sharedCache" : {
"base" : 140703389429760,
"size" : 15220686848,
"uuid" : "398acfb4-57f6-31e0-bc82-e9959e5c92ce"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=9.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=9.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2768K 8 \nCG image 568K 44 \nColorSync 232K 27 \nCoreAnimation 5076K 145 \nCoreGraphics 16K 3 \nCoreUI image data 5460K 53 \nFoundation 40K 2 \nKernel Alloc Once 8K 1 \nMALLOC 8.5G 48611 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 640K 2 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nObjC additional data 15K 1 \nOpenCL 172.0M 81 \nOpenCL (reserved) 60K 11 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 56.1M 36 \nStack 138.3M 36 \nVM_ALLOCATE 293.3M 278 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 45.1M 762 \n__DATA_CONST 32.4M 338 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 755.8M 217 \n__TEXT 893.3M 741 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 496.3M 64 \nshared memory 3100K 27 \n=========== ======= ======= \nTOTAL 11.5G 51732 \nTOTAL, minus reserved VM space 11.3G 51732 \n",
"legacyInfo" : {
"threadTriggered" : {
"queue" : "opencl_runtime"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "61301e3a61217b3110231469",
"factorPackIds" : {
"SIRI_FIND_MY_CONFIGURATION_FILES" : "6216ae152a40e71046e16225"
},
"deploymentId" : 240000016
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/tatyanabodrug/Downloads/cryosparc_P19_J1031_003_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 1.17, shown at level 0.587, step 2, values float32
> volume flip #1
Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip as #2, grid size
400,400,400, pixel 1.17, shown at step 1, values float32
> ui mousemode right "map eraser"
> volume erase #2 center 233.13,216.03,244.03 radius 139 outside true
Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip copy as #4, grid
size 400,400,400, pixel 1.17, shown at step 1, values float32
> volume erase #4 center 237.71,112.06,242.16 radius 42.987
> volume erase #4 center 220.37,112.78,212.69 radius 42.987
> volume erase #4 center 213.35,112.19,226.22 radius 54.732
> volume erase #4 center 133.34,145.63,223.4 radius 54.732
> volume erase #4 center 352.73,214.22,232.39 radius 54.732
> volume erase #4 center 345.23,140.71,199.15 radius 54.732
> volume erase #4 center 352.35,246.24,299.65 radius 54.732
> volume erase #4 center 333.2,133.35,305.16 radius 54.732
> volume erase #4 center 112.23,229.69,299.25 radius 54.732
> volume erase #4 center 120.39,256.71,262.35 radius 54.732
> volume erase #4 center 294.02,285.71,374.51 radius 54.732
> volume erase #4 center 96.424,197.37,165.69 radius 54.732
> volume erase #4 center 303.3,101.49,228.24 radius 54.732
> surface dust #4 size 11.7
> surface dust #4 size 3
> surface dust #4 size 4
> surface dust #4 size 5
> close #1
> close #2
> open /Users/tatyanabodrug/Desktop/model_fitting/pdbs/6tnt.pdb
6tnt.pdb title:
Sumoylated apoapc/C with repositioned APC2 WHB domain [more info...]
Chain information for 6tnt.pdb #1
---
Chain | Description | UniProt
A | anaphase-promoting complex subunit 1 | APC1_HUMAN
B | anaphase-promoting complex subunit 11 | APC11_HUMAN
C | cell division cycle protein 23 homolog | CDC23_HUMAN
D | APC15 | APC15_HUMAN
E | anaphase-promoting complex subunit 16 | APC16_HUMAN
F | cell division cycle protein 27 homolog | CDC27_HUMAN
G | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN
H | cell division cycle protein 27 homolog | CDC27_HUMAN
I | anaphase-promoting complex subunit 4 | APC4_HUMAN
J | cell division cycle protein 16 homolog | CDC16_HUMAN
K | cell division cycle protein 16 homolog | CDC16_HUMAN
L | anaphase-promoting complex subunit 10 | APC10_HUMAN
M | anaphase-promoting complex subunit 13 | APC13_HUMAN
N | anaphase-promoting complex subunit 2 | ANC2_HUMAN
O | anaphase-promoting complex subunit 5 | APC5_HUMAN
P | cell division cycle protein 23 homolog | CDC23_HUMAN
T | unidentified peptide |
W | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN
X | anaphase-promoting complex subunit 7 | APC7_HUMAN
Y | anaphase-promoting complex subunit 7 | APC7_HUMAN
Non-standard residues in 6tnt.pdb #1
---
ZN — zinc ion
> hide atoms
> show cartoons
> select #1
63822 atoms, 65192 bonds, 41 pseudobonds, 8112 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98934,0.069816,-0.12781,13.01,-0.14563,0.4781,-0.86615,275.72,0.00063494,0.87553,0.48317,-59.205
> view matrix models
> #1,-0.032966,0.9527,0.30213,-30.982,-0.21706,0.28826,-0.93263,334.19,-0.9756,-0.096326,0.19729,342.89
> view matrix models
> #1,-0.23443,0.93103,-0.2797,115.83,-0.40982,-0.35555,-0.84002,465.5,-0.88153,-0.082305,0.4649,274.4
> view matrix models
> #1,-0.18775,0.92135,-0.34038,119.95,0.010581,-0.34462,-0.93868,403.97,-0.98216,-0.17984,0.054954,384.6
> view matrix models
> #1,-0.3406,0.81359,-0.47123,190.8,-0.059458,-0.51883,-0.85281,431.74,-0.93833,-0.26245,0.22509,360.01
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.3406,0.81359,-0.47123,190.91,-0.059458,-0.51883,-0.85281,432.46,-0.93833,-0.26245,0.22509,359.84
> view matrix models
> #1,-0.3406,0.81359,-0.47123,222.67,-0.059458,-0.51883,-0.85281,489.98,-0.93833,-0.26245,0.22509,410.39
> view matrix models
> #1,-0.3406,0.81359,-0.47123,224.35,-0.059458,-0.51883,-0.85281,491.46,-0.93833,-0.26245,0.22509,417.56
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.052021,0.95688,-0.28579,112.31,-0.041632,-0.28801,-0.95672,466.71,-0.99778,-0.037872,0.05482,420.23
> view matrix models
> #1,0.057421,0.96397,-0.25976,86.139,-0.03022,-0.25839,-0.96557,461.03,-0.99789,0.063294,0.014294,409.94
> view matrix models
> #1,-0.10978,0.95098,-0.28912,124.6,-0.07566,-0.29803,-0.95155,473.8,-0.99107,-0.082583,0.10467,417.75
> fitmap #1 inMap #4
Fit molecule 6tnt.pdb (#1) to map cryosparc_P19_J1031_003_volume_map_sharp.mrc
z flip copy (#4) using 63822 atoms
average map value = 0.7218, steps = 116
shifted from previous position = 7.8
rotated from previous position = 7.71 degrees
atoms outside contour = 28283, contour level = 0.58682
Position of 6tnt.pdb (#1) relative to
cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip copy (#4) coordinates:
Matrix rotation and translation
0.01239040 0.96583206 -0.25887235 100.02477482
-0.12270284 -0.25546698 -0.95899981 478.17787139
-0.99236611 0.04364676 0.11534500 388.31731970
Axis 0.60702707 0.44407529 -0.65902600
Axis point 417.38692737 334.01584219 0.00000000
Rotation angle (degrees) 124.32356702
Shift along axis 17.15351501
> volume #4 color #73fdff
> volume #4 color #73fdff32
> volume #4 level 0.9882
> ~select #1
Nothing selected
> isolde start
> set selectionWidth 4
Removed all altlocs in #1 and reset associated occupancies to 1.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 546 residues in model #1 to IUPAC-IUB
standards.
6tnt.pdb title:
Sumoylated apoapc/C with repositioned APC2 WHB domain [more info...]
Chain information for 6tnt.pdb
---
Chain | Description | UniProt
1.2/A | anaphase-promoting complex subunit 1 | APC1_HUMAN
1.2/B | anaphase-promoting complex subunit 11 | APC11_HUMAN
1.2/C | cell division cycle protein 23 homolog | CDC23_HUMAN
1.2/D | APC15 | APC15_HUMAN
1.2/E | anaphase-promoting complex subunit 16 | APC16_HUMAN
1.2/F | cell division cycle protein 27 homolog | CDC27_HUMAN
1.2/G | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN
1.2/H | cell division cycle protein 27 homolog | CDC27_HUMAN
1.2/I | anaphase-promoting complex subunit 4 | APC4_HUMAN
1.2/J | cell division cycle protein 16 homolog | CDC16_HUMAN
1.2/K | cell division cycle protein 16 homolog | CDC16_HUMAN
1.2/L | anaphase-promoting complex subunit 10 | APC10_HUMAN
1.2/M | anaphase-promoting complex subunit 13 | APC13_HUMAN
1.2/N | anaphase-promoting complex subunit 2 | ANC2_HUMAN
1.2/O | anaphase-promoting complex subunit 5 | APC5_HUMAN
1.2/P | cell division cycle protein 23 homolog | CDC23_HUMAN
1.2/T | unidentified peptide |
1.2/W | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN
1.2/X | anaphase-promoting complex subunit 7 | APC7_HUMAN
1.2/Y | anaphase-promoting complex subunit 7 | APC7_HUMAN
Non-standard residues in 6tnt.pdb #1.2
---
ZN — zinc ion
Done loading forcefield
> addh
Summary of feedback from adding hydrogens to 6tnt.pdb #1.2
---
warnings | Not adding hydrogens to /A LYS 71 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A GLU 82 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ILE 83 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 109 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 135 CB because it is missing heavy-atom bond
partners
402 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /N PRO 16 N; /A PRO 515 N; /N PRO 33 N; /A PRO 993 N; /A PRO
651 N; /D PRO 23 N; /F PRO 700 N; /B PRO 40 N; /L PRO 171 N; /A PRO 206 N
notes | No usable SEQRES records for 6tnt.pdb (#1.2) chain A; guessing termini
instead
No usable SEQRES records for 6tnt.pdb (#1.2) chain B; guessing termini instead
No usable SEQRES records for 6tnt.pdb (#1.2) chain C; guessing termini instead
No usable SEQRES records for 6tnt.pdb (#1.2) chain D; guessing termini instead
No usable SEQRES records for 6tnt.pdb (#1.2) chain E; guessing termini instead
15 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 11, /B MET 1, /C PHE
26, /D SER 2, /E ARG 52, /F GLN 5, /G MET 1, /H GLN 5, /I THR 6, /J ASN 2, /K
ASN 2, /L THR 3, /M MET 1, /N ARG 15, /O GLY 25, /P PHE 26, /T ALA 1, /W MET
1, /X ASN 36, /Y ASN 36
Chain-initial residues that are not actual N termini: /A LYS 71, /A PRO 206,
/A SER 234, /A SER 362, /A ILE 403, /A GLU 422, /A GLN 579, /A ASP 704, /A LEU
747, /A SER 892, /A VAL 923, /A GLU 1011, /A SER 1347, /A LEU 1452, /A SER
1908, /C GLU 509, /F GLN 455, /F THR 691, /H ALA 451, /I ASN 160, /I GLU 473,
/J SER 124, /K SER 127, /M GLU 48, /N PRO 50, /N TRP 232, /N ASN 319, /N SER
474, /N SER 499, /N GLU 750, /O PRO 206, /O VAL 458, /P VAL 146, /P THR 511,
/X LEU 132, /Y LEU 132
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A LEU 1936, /A ALA 34, /A
ALA 193, /A LYS 226, /A VAL 281, /A ASN 375, /A THR 416, /A PRO 515, /A THR
678, /A SER 731, /A LEU 887, /A THR 900, /A PRO 993, /A HIS 1333, /A ILE 1439,
/A PRO 1902, /B GLU 84, /C ARG 557, /C CYS 500, /D LYS 56, /E PRO 107, /F LEU
755, /F THR 171, /F LEU 682, /G ASP 25, /H ASP 767, /H ASN 175, /I SER 757, /I
PRO 146, /I ASN 457, /J TYR 533, /J MET 95, /K ILE 527, /K LEU 93, /L ARG 184,
/M GLU 67, /M PRO 39, /N LEU 817, /N PRO 33, /N GLY 191, /N PHE 304, /N THR
443, /N ASP 486, /N ILE 730, /O LEU 755, /O LYS 167, /O GLU 452, /P ALA 538,
/P THR 134, /P CYS 500, /T ALA 15, /W LEU 26, /X PRO 540, /X LEU 110, /Y MET
552, /Y LEU 110
6602 hydrogen bonds
Adding 'H' to /A LYS 71
Adding 'H' to /A SER 234
Adding 'H' to /A SER 362
Adding 'H' to /A ILE 403
Adding 'H' to /A GLU 422
28 messages similar to the above omitted
/A LEU 1936 is not terminus, removing H atom from 'C'
/B GLU 84 is not terminus, removing H atom from 'C'
/C ARG 557 is not terminus, removing H atom from 'C'
/D LYS 56 is not terminus, removing H atom from 'C'
/E PRO 107 is not terminus, removing H atom from 'C'
15 messages similar to the above omitted
62845 hydrogens added
> set silhouettes false
> view
> delete ~protein
> hide HC
> select #1
126755 atoms, 128138 bonds, 36 pseudobonds, 8109 residues, 9 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> select /G:1-25
453 atoms, 454 bonds, 25 residues, 1 model selected
> select /D:2-56
843 atoms, 854 bonds, 55 residues, 1 model selected
> select /E:52-107
888 atoms, 897 bonds, 56 residues, 1 model selected
> select /E
888 atoms, 897 bonds, 56 residues, 1 model selected
> isolde sim start sel
Populating font family aliases took 370 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
ISOLDE: started sim
> view
> view sel
> hide ~@CA
ISOLDE: paused sim
> sequence chain #1.2/E
Alignment identifier is 1.2/E
> select /E:107
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /E:86-107
365 atoms, 370 bonds, 21 pseudobonds, 22 residues, 2 models selected
> select /E:72
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /E:72-84
203 atoms, 203 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /E:89-90
34 atoms, 33 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /E:73-90
285 atoms, 284 bonds, 17 pseudobonds, 18 residues, 2 models selected
> select /E:73-90
285 atoms, 284 bonds, 17 pseudobonds, 18 residues, 2 models selected
> isolde sim start sel
Simulation already running!
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /E:73-90
285 atoms, 284 bonds, 18 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> hide ~@CA
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /E:74
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /E:52-74
347 atoms, 350 bonds, 23 residues, 1 model selected
> select /E:82-83
29 atoms, 28 bonds, 2 residues, 1 model selected
> select /E:57-83
439 atoms, 441 bonds, 27 residues, 1 model selected
> select /E:57-83
439 atoms, 441 bonds, 27 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> hide ~@CA
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /E:76-77
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /E:59-77
305 atoms, 307 bonds, 19 residues, 1 model selected
> select /E:73
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /E:55-73
294 atoms, 296 bonds, 19 residues, 1 model selected
> select /E:55-73
294 atoms, 296 bonds, 19 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> hide ~@CA
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /G:1-25
453 atoms, 454 bonds, 25 residues, 1 model selected
> view
> select /E:52-107
888 atoms, 897 bonds, 56 residues, 1 model selected
> select /F:5-755
7083 atoms, 7170 bonds, 2 pseudobonds, 460 residues, 2 models selected
> select /Y:36-552
7781 atoms, 7841 bonds, 1 pseudobond, 496 residues, 2 models selected
> sequence chain #1.2/Y
Alignment identifier is 1.2/Y
> select /Y:276-327
809 atoms, 815 bonds, 52 residues, 1 model selected
> select /Y:276-552
4333 atoms, 4364 bonds, 277 residues, 1 model selected
> select /Y:36-37
32 atoms, 31 bonds, 2 residues, 1 model selected
> select /Y:36-274
3441 atoms, 3469 bonds, 1 pseudobond, 218 residues, 2 models selected
> select /Y:36-274
3441 atoms, 3469 bonds, 1 pseudobond, 218 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> view sel
> hide ~@CA
> select /Y:170-174
89 atoms, 88 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:170-226
853 atoms, 856 bonds, 56 pseudobonds, 57 residues, 2 models selected
> select /Y:228-236
139 atoms, 141 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:228-245
292 atoms, 298 bonds, 17 pseudobonds, 18 residues, 2 models selected
> select /Y:330-335
107 atoms, 107 bonds, 3 pseudobonds, 6 residues, 2 models selected
> select /Y:321-335
235 atoms, 235 bonds, 3 pseudobonds, 15 residues, 2 models selected
> select /Y:37-44
133 atoms, 133 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:37-54
271 atoms, 272 bonds, 17 pseudobonds, 18 residues, 2 models selected
> select /Y:52-60
152 atoms, 151 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:52-67
255 atoms, 254 bonds, 15 pseudobonds, 16 residues, 2 models selected
> select /Y:69-70
34 atoms, 33 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /Y:69-85
284 atoms, 289 bonds, 16 pseudobonds, 17 residues, 2 models selected
> select /Y:86-95
175 atoms, 177 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:86-110
422 atoms, 425 bonds, 24 pseudobonds, 25 residues, 2 models selected
> select /Y:134-140
119 atoms, 119 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:134-156
379 atoms, 380 bonds, 22 pseudobonds, 23 residues, 2 models selected
> select /Y:157-158
29 atoms, 28 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /Y:157-178
355 atoms, 356 bonds, 21 pseudobonds, 22 residues, 2 models selected
> select /Y:179-181
65 atoms, 65 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:179-206
452 atoms, 455 bonds, 27 pseudobonds, 28 residues, 2 models selected
> select /Y:199-203
73 atoms, 73 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:199-206
114 atoms, 114 bonds, 7 pseudobonds, 8 residues, 2 models selected
> view sel
> select /Y:194-200
116 atoms, 116 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:194-204
176 atoms, 176 bonds, 10 pseudobonds, 11 residues, 2 models selected
> select /Y:207-211
75 atoms, 74 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:207-229
290 atoms, 289 bonds, 22 pseudobonds, 23 residues, 2 models selected
> view sel
> select /Y:230-238
145 atoms, 147 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:230-256
426 atoms, 433 bonds, 26 pseudobonds, 27 residues, 2 models selected
> select /Y:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /Y:249-256
108 atoms, 107 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:246-248
47 atoms, 47 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:246-250
66 atoms, 66 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:242-246
77 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:242-247
94 atoms, 96 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:237-239
51 atoms, 52 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:237-243
123 atoms, 125 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:220-224
59 atoms, 58 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:220-226
82 atoms, 81 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:228-232
65 atoms, 65 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:224-232
114 atoms, 114 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:235-239
94 atoms, 97 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:235-244
176 atoms, 180 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:249-252
44 atoms, 43 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:249-256
108 atoms, 107 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:257-260
55 atoms, 54 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:257-276
316 atoms, 315 bonds, 19 pseudobonds, 20 residues, 2 models selected
> view sel
> select /Y:273-280
116 atoms, 115 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:273-293
328 atoms, 329 bonds, 20 pseudobonds, 21 residues, 2 models selected
> view
> select /Y:266-271
104 atoms, 103 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:266-276
172 atoms, 171 bonds, 10 pseudobonds, 11 residues, 2 models selected
> select /Y:260-265
100 atoms, 99 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:260-269
174 atoms, 173 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:271-275
73 atoms, 72 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:271-287
252 atoms, 253 bonds, 16 pseudobonds, 17 residues, 2 models selected
> view sel
> select /Y:262-269
144 atoms, 143 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:257-269
218 atoms, 217 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /Y:281-287
108 atoms, 109 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:281-292
190 atoms, 191 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:295-302
121 atoms, 121 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:291-302
198 atoms, 199 bonds, 11 pseudobonds, 12 residues, 2 models selected
> view
> view orient
> select /Y:267-307
654 atoms, 658 bonds, 40 pseudobonds, 41 residues, 2 models selected
> select /Y:307-335
429 atoms, 431 bonds, 11 pseudobonds, 29 residues, 2 models selected
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /Y
7781 atoms, 7841 bonds, 1 pseudobond, 496 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> hide ~@CA
> select /Y:322-323
27 atoms, 26 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /Y:322-340
287 atoms, 288 bonds, 18 pseudobonds, 19 residues, 2 models selected
> select /Y:311-312
28 atoms, 28 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /Y:311-320
142 atoms, 143 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:295-301
107 atoms, 106 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:295-306
202 atoms, 203 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:271-279
125 atoms, 124 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:271-289
288 atoms, 289 bonds, 18 pseudobonds, 19 residues, 2 models selected
> select /Y:257-262
89 atoms, 88 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:257-268
206 atoms, 205 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:203-244
601 atoms, 606 bonds, 41 pseudobonds, 42 residues, 2 models selected
> select /Y:244-256
185 atoms, 186 bonds, 12 pseudobonds, 13 residues, 2 models selected
> view sel
> select /Y:236-246
188 atoms, 191 bonds, 10 pseudobonds, 11 residues, 2 models selected
> select /Y:236-247
205 atoms, 209 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:229-236
132 atoms, 134 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:229-239
183 atoms, 187 bonds, 10 pseudobonds, 11 residues, 2 models selected
ISOLDE: paused sim
ISOLDE: resumed sim
> select /Y:239-243
96 atoms, 98 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:237-243
123 atoms, 125 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:239-247
159 atoms, 163 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:238-247
175 atoms, 179 bonds, 9 pseudobonds, 10 residues, 2 models selected
ISOLDE: paused sim
ISOLDE: resumed sim
> view sel
> view
> select /Y:250-254
71 atoms, 70 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:250-256
101 atoms, 100 bonds, 6 pseudobonds, 7 residues, 2 models selected
> view sel
> select /Y:215-257
609 atoms, 616 bonds, 42 pseudobonds, 43 residues, 2 models selected
> select /Y:257-272
260 atoms, 259 bonds, 15 pseudobonds, 16 residues, 2 models selected
> select /Y:266-275
161 atoms, 160 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:266-278
201 atoms, 200 bonds, 12 pseudobonds, 13 residues, 2 models selected
> view sel
> select /Y:275-289
222 atoms, 223 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:275-293
290 atoms, 291 bonds, 18 pseudobonds, 19 residues, 2 models selected
> view sel
> select /Y:282
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /Y:275-282
119 atoms, 120 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:282-291
150 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:282-293
191 atoms, 191 bonds, 11 pseudobonds, 12 residues, 2 models selected
> view sel
> select /Y:275-280
78 atoms, 77 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:275-283
143 atoms, 144 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:288-292
82 atoms, 81 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:288-302
245 atoms, 246 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:307-316
149 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:307-326
285 atoms, 286 bonds, 19 pseudobonds, 20 residues, 2 models selected
> view sel
> select /Y:251-297
739 atoms, 741 bonds, 46 pseudobonds, 47 residues, 2 models selected
> select /Y:297-306
170 atoms, 171 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:278-280
41 atoms, 40 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:278-285
123 atoms, 124 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:287
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /Y:287-297
180 atoms, 180 bonds, 10 pseudobonds, 11 residues, 2 models selected
> select /Y:301-304
66 atoms, 67 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:301-306
107 atoms, 108 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:307
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /Y:307-316
149 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:318-320
38 atoms, 37 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:318-332
229 atoms, 229 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:334-337
59 atoms, 58 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:334-343
155 atoms, 158 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:331-338
129 atoms, 130 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:331-341
168 atoms, 170 bonds, 10 pseudobonds, 11 residues, 2 models selected
> select /Y:344-350
93 atoms, 94 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:344-356
203 atoms, 206 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /Y:357-363
110 atoms, 110 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:357-369
211 atoms, 211 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /Y:371-375
68 atoms, 67 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:371-389
295 atoms, 294 bonds, 18 pseudobonds, 19 residues, 2 models selected
> select /Y:356-392
570 atoms, 570 bonds, 36 pseudobonds, 37 residues, 2 models selected
> select /Y:392-406
255 atoms, 257 bonds, 14 pseudobonds, 15 residues, 2 models selected
> view sel
> select /Y:407-411
78 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:407-428
336 atoms, 337 bonds, 21 pseudobonds, 22 residues, 2 models selected
> view sel
> select /Y:399-401
53 atoms, 52 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select /Y:399-406
131 atoms, 131 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:407-411
78 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:400-411
199 atoms, 200 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:410-419
157 atoms, 158 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:407-419
199 atoms, 200 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /Y:418-432
221 atoms, 220 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:418-437
313 atoms, 313 bonds, 19 pseudobonds, 20 residues, 2 models selected
> select /Y:438-447
136 atoms, 135 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:438-452
206 atoms, 205 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:441-442
27 atoms, 26 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /Y:438-442
51 atoms, 50 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /Y:384-392
144 atoms, 143 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:384-393
163 atoms, 162 bonds, 9 pseudobonds, 10 residues, 2 models selected
> select /Y:398-406
146 atoms, 146 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:398-406
146 atoms, 146 bonds, 8 pseudobonds, 9 residues, 2 models selected
ISOLDE: paused sim
ISOLDE: resumed sim
> select /Y:407-412
85 atoms, 85 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:407-422
235 atoms, 236 bonds, 15 pseudobonds, 16 residues, 2 models selected
> select /Y:426-432
98 atoms, 97 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:426-439
207 atoms, 207 bonds, 13 pseudobonds, 14 residues, 2 models selected
> select /Y:441-444
60 atoms, 59 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:441-452
182 atoms, 181 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:457-463
114 atoms, 113 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:457-471
246 atoms, 245 bonds, 14 pseudobonds, 15 residues, 2 models selected
> select /Y:468-476
133 atoms, 134 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:468-485
285 atoms, 286 bonds, 17 pseudobonds, 18 residues, 2 models selected
> select /Y:479-484
101 atoms, 100 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select /Y:479-485
120 atoms, 119 bonds, 6 pseudobonds, 7 residues, 2 models selected
> view sel
> select /Y:433-490
912 atoms, 915 bonds, 57 pseudobonds, 58 residues, 2 models selected
> select /Y:433-495
989 atoms, 993 bonds, 62 pseudobonds, 63 residues, 2 models selected
> select /Y:483
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /Y:483-496
226 atoms, 226 bonds, 13 pseudobonds, 14 residues, 2 models selected
> view sel
> select /Y:499-506
127 atoms, 126 bonds, 7 pseudobonds, 8 residues, 2 models selected
> select /Y:490-506
269 atoms, 269 bonds, 16 pseudobonds, 17 residues, 2 models selected
> select /Y:507-513
110 atoms, 110 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:507-519
206 atoms, 207 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select /Y:517-523
107 atoms, 107 bonds, 6 pseudobonds, 7 residues, 2 models selected
> select /Y:517-535
292 atoms, 294 bonds, 18 pseudobonds, 19 residues, 2 models selected
> select /Y:524-527
68 atoms, 68 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /Y:524-535
185 atoms, 186 bonds, 11 pseudobonds, 12 residues, 2 models selected
> select /Y:537-545
132 atoms, 132 bonds, 8 pseudobonds, 9 residues, 2 models selected
> select /Y:537-552
246 atoms, 246 bonds, 15 pseudobonds, 16 residues, 2 models selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
OS Loader Version: 540.120.3~6
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 9 days 9:50
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP 27er:
Resolution: 1600 x 900
UI Looks like: 1600 x 900 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 3CM6160MVY
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c1
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 12.4, Intel Iris Plus Graphics |
Note:
See TracTickets
for help on using tickets.
Apple graphics driver crash.