![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5776 closed defect (can't reproduce)
Crash processing event
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Eric Pettersen, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110191144 (2021-10-19 11:44:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [72753]
Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [72753]
User ID: 1673611984
Date/Time: 2021-12-13 15:59:14.221 -0500
OS Version: Mac OS X 10.15.7 (19H1323)
Report Version: 12
Anonymous UUID: 0F18A509-2CB7-99E1-BF68-E73E1E554599
Time Awake Since Boot: 9000000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff70eca33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff70f86e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff70de193e raise + 26
3 libsystem_platform.dylib 0x00007fff70f7b5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010833706d cfunction_call + 125
6 org.python.python 0x00000001082f86cc _PyObject_Call + 140
7 QtCore.abi3.so 0x00000001157ad957 PyQtSlot::call(_object*, _object*) const + 39
8 QtCore.abi3.so 0x00000001157ad866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9 QtCore.abi3.so 0x00000001157ae455 PyQtSlotProxy::unislot(void**) + 85
10 QtCore.abi3.so 0x00000001157ae3ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11 QtCore 0x0000000115b89b9f QObject::event(QEvent*) + 943
12 QtWidgets 0x000000011817d9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13 QtWidgets 0x000000011817ee11 QApplication::notify(QObject*, QEvent*) + 497
14 QtWidgets.abi3.so 0x0000000117d30db9 sipQApplication::notify(QObject*, QEvent*) + 233
15 QtCore 0x0000000115b5ea34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16 QtCore 0x0000000115b5fd79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17 libqcocoa.dylib 0x0000000126548259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18 libqcocoa.dylib 0x00000001265489c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
19 com.apple.CoreFoundation 0x00007fff36cc27e2 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
20 com.apple.CoreFoundation 0x00007fff36cc2781 __CFRunLoopDoSource0 + 103
21 com.apple.CoreFoundation 0x00007fff36cc259b __CFRunLoopDoSources0 + 209
22 com.apple.CoreFoundation 0x00007fff36cc12ca __CFRunLoopRun + 927
23 com.apple.CoreFoundation 0x00007fff36cc08ce CFRunLoopRunSpecific + 462
24 com.apple.HIToolbox 0x00007fff358ecabd RunCurrentEventLoopInMode + 292
25 com.apple.HIToolbox 0x00007fff358ec7d5 ReceiveNextEventCommon + 584
26 com.apple.HIToolbox 0x00007fff358ec579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
27 com.apple.AppKit 0x00007fff33f33739 _DPSNextEvent + 883
28 com.apple.AppKit 0x00007fff33f31f80 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
29 com.apple.AppKit 0x00007fff33f23c8e -[NSApplication run] + 658
30 libqcocoa.dylib 0x000000012654762f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31 QtCore 0x0000000115b5aacf QEventLoop::exec(QFlags) + 431
32 QtCore 0x0000000115b5f042 QCoreApplication::exec() + 130
33 QtWidgets.abi3.so 0x0000000117e22702 meth_QApplication_exec_(_object*, _object*) + 82
34 org.python.python 0x000000010833706d cfunction_call + 125
35 org.python.python 0x00000001082f817d _PyObject_MakeTpCall + 365
36 org.python.python 0x00000001083d061c call_function + 876
37 org.python.python 0x00000001083cdab3 _PyEval_EvalFrameDefault + 25219
38 org.python.python 0x00000001082f8948 function_code_fastcall + 104
39 org.python.python 0x00000001082fa98a method_vectorcall + 202
40 org.python.python 0x00000001083d058c call_function + 732
41 org.python.python 0x00000001083cdab3 _PyEval_EvalFrameDefault + 25219
42 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
43 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
44 org.python.python 0x00000001083d058c call_function + 732
45 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
46 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
47 org.python.python 0x00000001083c770b PyEval_EvalCode + 139
48 org.python.python 0x00000001083c4592 builtin_exec + 626
49 org.python.python 0x000000010833686a cfunction_vectorcall_FASTCALL + 218
50 org.python.python 0x00000001083d058c call_function + 732
51 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
52 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
53 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
54 org.python.python 0x00000001083d058c call_function + 732
55 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
56 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
57 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
58 org.python.python 0x0000000108436e20 pymain_run_module + 208
59 org.python.python 0x0000000108436537 Py_RunMain + 1431
60 org.python.python 0x0000000108436b3f pymain_main + 223
61 org.python.python 0x0000000108436a4b Py_Main + 43
62 edu.ucsf.cgl.ChimeraX 0x00000001082aedc8 main + 120
63 libdyld.dylib 0x00007fff70d82cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011bcd0a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011bcdac44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011fc09f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 8:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011bcdacd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 9:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011bd29e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x000000011cfe15f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 10:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bc5a20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 11:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 12:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bc5a20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 15:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bcda76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x000000011bcdad34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 16:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 17:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 18:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff36cc2985 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff36cc1452 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff36cc08ce CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff340d4f74 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 19:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bcda76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011bcdae3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x000000011bcdac74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 20:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 21:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdae3d base::internal::WorkerThread::RunWorker() + 237
5 QtWebEngineCore 0x000000011bcdacd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 24:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 25:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 26:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 org.python.python 0x0000000108426d6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x0000000108475a1f acquire_timed + 111
4 org.python.python 0x0000000108475b30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000108300e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x00000001083d058c call_function + 732
7 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
9 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001083d058c call_function + 732
11 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
13 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x00000001083d058c call_function + 732
15 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x00000001082f8948 function_code_fastcall + 104
17 org.python.python 0x00000001083d058c call_function + 732
18 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x00000001082f8948 function_code_fastcall + 104
20 org.python.python 0x00000001083d058c call_function + 732
21 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x00000001082f8948 function_code_fastcall + 104
23 org.python.python 0x00000001082fa9d2 method_vectorcall + 274
24 org.python.python 0x00000001084753c6 t_bootstrap + 70
25 org.python.python 0x00000001084268c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010f482dc0 rcx: 0x00007fb5e015fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fb5e015fa80 rsp: 0x00007fb5e015fa58
r8: 0x00007fb5e015ff48 r9: 0xc7c2c9a3e05cf30e r10: 0x000000010f482dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000600000de5e30 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff70eca33a rfl: 0x0000000000000246 cr2: 0x000000010d023000
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff6fc14000 - 0x7fff6fc4afff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff6fc8a000 - 0x7fff6fc98ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6fc99000 - 0x7fff6fc9cff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff6fc9d000 - 0x7fff6fc9ffff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff6fcce000 - 0x7fff6fce6fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6fce8000 - 0x7fff6fd2cff7 libsandbox.1.dylib (1217.141.3) /usr/lib/libsandbox.1.dylib
0x7fff6fd40000 - 0x7fff6fd41ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6fd42000 - 0x7fff6ff2cff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff70122000 - 0x7fff7017cff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff7017d000 - 0x7fff70180ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff70181000 - 0x7fff7018eff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff70194000 - 0x7fff70276fff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib
0x7fff7027a000 - 0x7fff702a2fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff702a3000 - 0x7fff702b5ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff70b64000 - 0x7fff70b69ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff70b6a000 - 0x7fff70b75fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff70b76000 - 0x7fff70b7dfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff70b7e000 - 0x7fff70b87ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff70b88000 - 0x7fff70c1afdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff70d27000 - 0x7fff70d67ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff70d68000 - 0x7fff70d9efff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff70d9f000 - 0x7fff70d9fffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff70da0000 - 0x7fff70dacff3 libkxld.dylib (6153.141.35) /usr/lib/system/libkxld.dylib
0x7fff70dad000 - 0x7fff70dadff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff70dae000 - 0x7fff70db3ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff70db4000 - 0x7fff70db6ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff70db7000 - 0x7fff70db8ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff70db9000 - 0x7fff70dd0ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff70dd1000 - 0x7fff70dd1ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff70dd2000 - 0x7fff70e59fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff70e5a000 - 0x7fff70e5dffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff70e5e000 - 0x7fff70e61fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff70e62000 - 0x7fff70e6afff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff70e6b000 - 0x7fff70e72fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff70e73000 - 0x7fff70e74ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff70e75000 - 0x7fff70ec2ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff70ec3000 - 0x7fff70eefff7 libsystem_kernel.dylib (6153.141.35) /usr/lib/system/libsystem_kernel.dylib
0x7fff70ef0000 - 0x7fff70f37fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff70f38000 - 0x7fff70f5ffff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff70f60000 - 0x7fff70f6dffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff70f6e000 - 0x7fff70f77ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff70f78000 - 0x7fff70f80fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff70f81000 - 0x7fff70f8bfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff70f8c000 - 0x7fff70f90ff3 libsystem_sandbox.dylib (1217.141.3) /usr/lib/system/libsystem_sandbox.dylib
0x7fff70f91000 - 0x7fff70f93fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff70f94000 - 0x7fff70f9bffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff70f9c000 - 0x7fff70fb2ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff70fb4000 - 0x7fff70fb9ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff70fba000 - 0x7fff70fefffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 94
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 918098070
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 1760K 2
CG image 2564K 25
CoreAnimation 3224K 68
CoreGraphics 8K 1
CoreImage 24K 2
CoreServices 124K 1
CoreUI image data 3204K 29
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 947.9M 186
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 248.0M 4 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 24K 4
OpenGL GLSL 384K 4
STACK GUARD 104K 26
Stack 156.7M 27
Stack Guard 56.0M 1
VM_ALLOCATE 204.5M 180
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 64.0M 547
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 482.1M 150
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 553.8M 511
__UNICODE 564K 1
mapped file 393.0M 55
shared memory 2836K 22
=========== ======= =======
TOTAL 3.4G 1874
TOTAL, minus reserved VM space 2.8G 1874
System Profile:
Network Service: Ethernet, Ethernet, en0
Thunderbolt Bus: iMac, Apple Inc., 41.4
Boot Volume File System Type: apfs
Memory Module: BANK 1/DIMM0, 16 GB, DDR4 SO-DIMM, 2400 MHz, 0x00, -
Memory Module: BANK 1/DIMM1, 16 GB, DDR4 SO-DIMM, 2400 MHz, 0x00, -
USB Device: USB 3.0 Bus
USB Device: USB Laser Mouse
USB Device: Bluetooth USB Host Controller
USB Device: FaceTime HD Camera (Built-in)
USB Device: Expansion
Serial ATA Device: APPLE HDD ST2000DM001, 2 TB
Model: iMac18,3, BootROM 429.140.8.0.0, 4 processors, Quad-Core Intel Core i5, 3.4 GHz, 32 GB, SMC 2.41f2
Graphics: kHW_AMDRadeonPro570Item, Radeon Pro 570, spdisplays_pcie_device, 4 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x16F), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.4)
Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.3.dev202110191144 (2021-10-19)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/dynamic_information/job61/20210119_extra_domain-
> coot-1.pdb"
Summary of feedback from opening /Users/xiang.feng/OneDrive - Van Andel
Institute/NiFeABCSL/dynamic_information/job61/20210119_extra_domain-coot-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 14
ASN A 18 1 5
Start residue of secondary structure not found: HELIX 2 2 THR A 44 GLN A 47 1
4
Start residue of secondary structure not found: SHEET 1 1 1 TYR A 2 VAL A 4 0
Start residue of secondary structure not found: SHEET 2 2 2 ILE A 54 LYS A 56
0
Chain information for 20210119_extra_domain-coot-1.pdb #1
---
Chain | Description
B | No description available
OpenGL version: 4.1 ATI-3.10.22
OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
Boot ROM Version: 429.140.8.0.0
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 105 days 1:38
Graphics/Displays:
Radeon Pro 570:
Chipset Model: Radeon Pro 570
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1L-025
EFI Driver Version: 01.00.931
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
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: 1.30.2
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
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: 2.1.1
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.dev202110191144
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
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-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-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: 2.0.3
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: 1.2.2
ChimeraX-ModelPanel: 1.2
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: 2.6.4
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
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
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: 2.4.5
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 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: 1.13.6
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: 0.10.0
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: 3.4.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
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: 4.8.1
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: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
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: 2.4.7
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: 1.11.2
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: 2.1.0
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: 5.1.0
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 , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash processing event |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash was caused by the Qt window toolkit calling a Python routine in response to some event, but apparently the Python routine had been deleted. There is no indication of what the event was or what Python routine it was trying to call, so no information which would help debug it. It seems likely to be a PyQt bug where somehow Qt holds a reference to a Python callback but did not add a reference count to the Python callback.
Note:
See TracTickets
for help on using tickets.
Reported by Xiang Feng, seemingly the same as for #5775