![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7349 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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 (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: Segmentation fault
Thread 0x000070001478b000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000113a2bdc0 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [33349]
Path: /Applications/ChimeraX-1.3.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 [33349]
User ID: 573055
Date/Time: 2022-07-29 16:19:40.036 +0200
OS Version: Mac OS X 10.15.7 (19H1615)
Report Version: 12
Bridge OS Version: 6.1 (19P647)
Anonymous UUID: BF10E68F-7EB4-A7BF-BFD0-67ED6F3CDCA0
Time Awake Since Boot: 360000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00006cc00cf6da40
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x6cc00cf6da40:
MALLOC_NANO (reserved) 0000600090000000-00006000a0000000 [256.0M] rw-/rwx SM=NUL reserved VM address space (unallocated)
-->
STACK GUARD 000070000904d000-000070000904e000 [ 4K] ---/rwx SM=NUL stack guard for thread 24
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff711fc33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff712b8e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff7111393e raise + 26
3 libsystem_platform.dylib 0x00007fff712ad5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010df3b06d cfunction_call + 125
6 org.python.python 0x000000010defc6cc _PyObject_Call + 140
7 QtCore.abi3.so 0x00000001132b3957 PyQtSlot::call(_object*, _object*) const + 39
8 QtCore.abi3.so 0x00000001132b3866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9 QtCore.abi3.so 0x00000001132b4455 PyQtSlotProxy::unislot(void**) + 85
10 QtCore.abi3.so 0x00000001132b43ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11 QtCore 0x0000000123c89b9f QObject::event(QEvent*) + 943
12 QtWidgets 0x000000012620b9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13 QtWidgets 0x000000012620ce11 QApplication::notify(QObject*, QEvent*) + 497
14 QtWidgets.abi3.so 0x0000000125dbedb9 sipQApplication::notify(QObject*, QEvent*) + 233
15 QtCore 0x0000000123c5ea34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16 QtCore 0x0000000123c5fd79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17 libqcocoa.dylib 0x0000000134163259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18 libqcocoa.dylib 0x00000001341639c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
19 com.apple.CoreFoundation 0x00007fff37317682 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
20 com.apple.CoreFoundation 0x00007fff37317621 __CFRunLoopDoSource0 + 103
21 com.apple.CoreFoundation 0x00007fff3731743b __CFRunLoopDoSources0 + 209
22 com.apple.CoreFoundation 0x00007fff3731616a __CFRunLoopRun + 927
23 com.apple.CoreFoundation 0x00007fff3731576e CFRunLoopRunSpecific + 462
24 com.apple.HIToolbox 0x00007fff35f41aad RunCurrentEventLoopInMode + 292
25 com.apple.HIToolbox 0x00007fff35f417c5 ReceiveNextEventCommon + 584
26 com.apple.HIToolbox 0x00007fff35f41569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
27 com.apple.AppKit 0x00007fff3458a659 _DPSNextEvent + 883
28 com.apple.AppKit 0x00007fff34588ea0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
29 com.apple.AppKit 0x00007fff3457abae -[NSApplication run] + 658
30 libqcocoa.dylib 0x000000013416262f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31 QtCore 0x0000000123c5aacf QEventLoop::exec(QFlags) + 431
32 QtCore 0x0000000123c5f042 QCoreApplication::exec() + 130
33 QtWidgets.abi3.so 0x0000000125eb0702 meth_QApplication_exec_(_object*, _object*) + 82
34 org.python.python 0x000000010df3b06d cfunction_call + 125
35 org.python.python 0x000000010defc17d _PyObject_MakeTpCall + 365
36 org.python.python 0x000000010dfd461c call_function + 876
37 org.python.python 0x000000010dfd1ab3 _PyEval_EvalFrameDefault + 25219
38 org.python.python 0x000000010defc948 function_code_fastcall + 104
39 org.python.python 0x000000010defe98a method_vectorcall + 202
40 org.python.python 0x000000010dfd458c call_function + 732
41 org.python.python 0x000000010dfd1ab3 _PyEval_EvalFrameDefault + 25219
42 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
43 org.python.python 0x000000010defc8d1 _PyFunction_Vectorcall + 289
44 org.python.python 0x000000010dfd458c call_function + 732
45 org.python.python 0x000000010dfd1b4b _PyEval_EvalFrameDefault + 25371
46 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
47 org.python.python 0x000000010dfcb70b PyEval_EvalCode + 139
48 org.python.python 0x000000010dfc8592 builtin_exec + 626
49 org.python.python 0x000000010df3a86a cfunction_vectorcall_FASTCALL + 218
50 org.python.python 0x000000010dfd458c call_function + 732
51 org.python.python 0x000000010dfd1b4b _PyEval_EvalFrameDefault + 25371
52 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
53 org.python.python 0x000000010defc8d1 _PyFunction_Vectorcall + 289
54 org.python.python 0x000000010dfd458c call_function + 732
55 org.python.python 0x000000010dfd1b4b _PyEval_EvalFrameDefault + 25371
56 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
57 org.python.python 0x000000010defc8d1 _PyFunction_Vectorcall + 289
58 org.python.python 0x000000010e03ae20 pymain_run_module + 208
59 org.python.python 0x000000010e03a537 Py_RunMain + 1431
60 org.python.python 0x000000010e03ab3f pymain_main + 223
61 org.python.python 0x000000010e03aa4b Py_Main + 43
62 edu.ucsf.cgl.ChimeraX 0x000000010deb4dc8 main + 120
63 libdyld.dylib 0x00007fff710b4cc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff711feb96 kevent64 + 10
1 QtWebEngineCore 0x0000000129a06e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000129a06cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012999aa94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299a4778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001299a5150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x00000001299a4c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff711feb96 kevent64 + 10
1 QtWebEngineCore 0x0000000129a06e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000129a06cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012d8d3f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299241db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 5:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x00000001299f3e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x000000012acab5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 6:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000012992420f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 7:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff711feb96 kevent64 + 10
1 QtWebEngineCore 0x0000000129a06e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000129a06cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 8:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000012992420f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299241db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299241db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 11:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299a476a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x00000001299a5150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x00000001299a4d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 12:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299241db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299241db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012998f62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001299537cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001299aea7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 14:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff37317825 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff373162f2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff3731576e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff3472bea4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 15:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299fc2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001299a476a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x00000001299a4e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x00000001299a4c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 16:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010eb98a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 23:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299a4778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001299a5150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x00000001299a4cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 24:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 25:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 27:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 28:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 29:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 30:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 31:
0 libsystem_pthread.dylib 0x00007fff712b4b68 start_wqthread + 0
Thread 32:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60
2 QtWebEngineCore 0x00000001299fc492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001299a4778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001299a4e3d base::internal::WorkerThread::RunWorker() + 237
5 QtWebEngineCore 0x00000001299a4cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x00000001299f7e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 33:
0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698
2 org.python.python 0x000000010e02ad6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010e079a1f acquire_timed + 111
4 org.python.python 0x000000010e079b30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010df04e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x000000010dfd458c call_function + 732
7 org.python.python 0x000000010dfd1a92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010defc8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010dfd458c call_function + 732
11 org.python.python 0x000000010dfd1a92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x000000010dfd5283 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010defc8d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010dfd458c call_function + 732
15 org.python.python 0x000000010dfd1a92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010defc948 function_code_fastcall + 104
17 org.python.python 0x000000010dfd458c call_function + 732
18 org.python.python 0x000000010dfd1a92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x000000010defc948 function_code_fastcall + 104
20 org.python.python 0x000000010dfd458c call_function + 732
21 org.python.python 0x000000010dfd1a92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x000000010defc948 function_code_fastcall + 104
23 org.python.python 0x000000010defe9d2 method_vectorcall + 274
24 org.python.python 0x000000010e0793c6 t_bootstrap + 70
25 org.python.python 0x000000010e02a8c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000113a2bdc0 rcx: 0x00007fbc50047a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fbc50047a80 rsp: 0x00007fbc50047a58
r8: 0x00007fbc50047f48 r9: 0xeacfa29f790d5013 r10: 0x0000000113a2bdc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x000060000194aa00 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff711fc33a rfl: 0x0000000000000246 cr2: 0x00000001139fe048
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x10e860000 - 0x1124126ef +libopenblas.0.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libopenblas.0.dylib
0x1126b0000 - 0x1127c7ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x112835000 - 0x11286bfff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x11287f000 - 0x112894ff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x1128a4000 - 0x1128b3fff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x1128c4000 - 0x1128dbfff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x1128ec000 - 0x1128fbff3 +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x112914000 - 0x112916fff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x11291f000 - 0x112923ff7 +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
0x11292d000 - 0x11293eff7 +_ctypes.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so
0x112955000 - 0x112958ffb +lapack_lite.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/lapack_lite.cpython-39-darwin.so
0x112965000 - 0x112980ff3 +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
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0x1129b8000 - 0x112a2bffb +mtrand.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/mtrand.cpython-39-darwin.so
0x112a8e000 - 0x112aadfff +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
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0x112b35000 - 0x112b8dfff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.1.1.dylib
0x112bbc000 - 0x112dd2f4f +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
0x112e70000 - 0x112e76ff7 +_blake2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_blake2.cpython-39-darwin.so
0x112e80000 - 0x112ed3fff +_bounded_integers.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_bounded_integers.cpython-39-darwin.so
0x112f03000 - 0x112f12ff3 +_mt19937.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_mt19937.cpython-39-darwin.so
0x112f25000 - 0x112f34ff7 +_philox.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_philox.cpython-39-darwin.so
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0x112f81000 - 0x11300cfff +_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_generator.cpython-39-darwin.so
0x113077000 - 0x113077fff +_opcode.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_opcode.cpython-39-darwin.so
0x11307f000 - 0x11307ffff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x113086000 - 0x113127ff7 +libarrays.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x11314b000 - 0x113169ff3 +_geometry.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/geometry/_geometry.cpython-39-darwin.so
0x11317e000 - 0x1132ddff7 +QtCore.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtCore.abi3.so
0x1134bb000 - 0x1134d2ff7 +sip.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/sip.cpython-39-darwin.so
0x1134e9000 - 0x113652ff3 +QtGui.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtGui.abi3.so
0x1137ff000 - 0x113820fff +QtWebEngineWidgets.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtWebEngineWidgets.abi3.so
0x113852000 - 0x113875ff7 +QtWebEngineWidgets (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWebEngineWidgets.framework/Versions/5/QtWebEngineWidgets
0x1138ad000 - 0x1138d8ff7 +QtPrintSupport (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtPrintSupport.framework/Versions/5/QtPrintSupport
0x113906000 - 0x11391fff3 +QtWebChannel (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWebChannel.framework/Versions/5/QtWebChannel
0x113936000 - 0x113942ffb +QtQuickWidgets (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQuickWidgets.framework/Versions/5/QtQuickWidgets
0x113960000 - 0x1139f2267 dyld (750.7) /usr/lib/dyld
0x123a66000 - 0x123fd67df +QtCore (0) /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
0x125c74000 - 0x125f04ff7 +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtWidgets.abi3.so
0x1261fb000 - 0x126641fff +QtWidgets (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWidgets.framework/Versions/5/QtWidgets
0x12683e000 - 0x126d27fff +QtGui (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtGui.framework/Versions/5/QtGui
0x126eda000 - 0x12ebc8f4f +QtWebEngineCore (0) /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
0x133242000 - 0x133586ff7 +QtQuick (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQuick.framework/Versions/5/QtQuick
0x1337aa000 - 0x133802ff3 +QtQmlModels (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQmlModels.framework/Versions/5/QtQmlModels
0x133843000 - 0x133b9bffb +QtQml (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQml.framework/Versions/5/QtQml
0x133d0f000 - 0x133e1ffff +QtNetwork (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtNetwork.framework/Versions/5/QtNetwork
0x133ead000 - 0x133f13fff +QtPositioning (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtPositioning.framework/Versions/5/QtPositioning
0x133f45000 - 0x133f4aff7 +QtWebChannel.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtWebChannel.abi3.so
0x133f55000 - 0x133fb6fff +QtNetwork.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtNetwork.abi3.so
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0x7fff705d5000 - 0x7fff705e7ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff70e96000 - 0x7fff70e9bff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff70e9c000 - 0x7fff70ea7fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff70ea8000 - 0x7fff70eaffff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff70eb0000 - 0x7fff70eb9ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff70eba000 - 0x7fff70f4cfdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff71059000 - 0x7fff71099ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff7109a000 - 0x7fff710d0fff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff710d1000 - 0x7fff710d1ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff710d2000 - 0x7fff710deff3 libkxld.dylib (6153.141.50) /usr/lib/system/libkxld.dylib
0x7fff710df000 - 0x7fff710dfff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff710e0000 - 0x7fff710e5ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff710e6000 - 0x7fff710e8ff3 libquarantine.dylib (110.40.5) /usr/lib/system/libquarantine.dylib
0x7fff710e9000 - 0x7fff710eaff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff710eb000 - 0x7fff71102ff3 libsystem_asl.dylib (377.60.3) /usr/lib/system/libsystem_asl.dylib
0x7fff71103000 - 0x7fff71103ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff71104000 - 0x7fff7118bfff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff7118c000 - 0x7fff7118fffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff71190000 - 0x7fff71193fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff71194000 - 0x7fff7119cfff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff7119d000 - 0x7fff711a4fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff711a5000 - 0x7fff711a6ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff711a7000 - 0x7fff711f4ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff711f5000 - 0x7fff71221ff7 libsystem_kernel.dylib (6153.141.50) /usr/lib/system/libsystem_kernel.dylib
0x7fff71222000 - 0x7fff71269fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff7126a000 - 0x7fff71291fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff71292000 - 0x7fff7129fffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff712a0000 - 0x7fff712a9ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff712aa000 - 0x7fff712b2fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff712b3000 - 0x7fff712bdfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff712be000 - 0x7fff712c2ff3 libsystem_sandbox.dylib (1217.141.7) /usr/lib/system/libsystem_sandbox.dylib
0x7fff712c3000 - 0x7fff712c5fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff712c6000 - 0x7fff712cdffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff712ce000 - 0x7fff712e4ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff712e6000 - 0x7fff712ebff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff712ec000 - 0x7fff71321ffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 2191
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: 33343813
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)
Writable regions: Total=10.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=10.7G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 2420K 5
CG image 832K 37
CoreAnimation 4092K 79
CoreGraphics 8K 1
CoreImage 36K 5
CoreUI image data 3944K 35
Foundation 28K 2
Kernel Alloc Once 8K 1
MALLOC 8.6G 797
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 1.1G 13 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 24K 2
OpenGL GLSL 384K 4
STACK GUARD 132K 33
Stack 160.3M 34
Stack Guard 56.0M 1
VM_ALLOCATE 203.8M 151
VM_ALLOCATE (reserved) 352.0M 2 reserved VM address space (unallocated)
__DATA 66.3M 641
__DATA_CONST 132K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 494.6M 211
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 642.8M 581
__UNICODE 564K 1
mapped file 424.1M 84
shared memory 2844K 25
=========== ======= =======
TOTAL 12.4G 2772
TOTAL, minus reserved VM space 10.7G 2772
===== Log before crash start =====
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
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/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/chimera_lres.cxs"
Error opening map "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images
for figures/chimera_lres.cxs": File chimera_lres.cxs, format mrc
MRC data value type (119742531) is not 8 or 16 bit integers or 32 bit floats
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened run_class001.mrc as #10, grid size 400,400,400, pixel 1.05, shown at
level 0.00637, step 1, values float32
Opened run_class001.mrc as #12, grid size 400,400,400, pixel 1.05, shown at
level 0.00654, step 1, values float32
Opened Gauss_Mask.mrc as #11, grid size 400,400,400, pixel 1.05, shown at
level 0.791, step 1, values float32
Opened run_it060_class001.mrc copy as #7, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class002.mrc copy as #13, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class003.mrc copy as #14, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class004.mrc copy as #15, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class001.mrc copy as #19, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class002.mrc copy as #20, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class003.mrc copy as #21, grid size 400,400,400, pixel 1.05,
shown at level 0.0095, step 1, values float32
Opened run_it060_class001.mrc as #2, grid size 400,400,400, pixel 1.05, shown
at level 0.01, step 1, values float32
Opened run_it060_class003.mrc as #4, grid size 400,400,400, pixel 1.05, shown
at level 0.01, step 1, values float32
Opened run_it060_class001.mrc as #3, grid size 400,400,400, pixel 1.05, shown
at level 0.008, step 1, values float32
Opened run_it060_class002.mrc as #5, grid size 400,400,400, pixel 1.05, shown
at level 0.008, step 1, values float32
Opened run_it060_class003.mrc as #16, grid size 400,400,400, pixel 1.05, shown
at level 0.008, step 1, values float32
Opened run_it060_class004.mrc as #17, grid size 400,400,400, pixel 1.05, shown
at level 0.008, step 1, values float32
Opened run_it060_class001.mrc as #18, grid size 400,400,400, pixel 1.05, shown
at level 0.012, step 1, values float32
Opened run_it060_class002.mrc as #22, grid size 400,400,400, pixel 1.05, shown
at level 0.012, step 1, values float32
Opened run_it060_class003.mrc as #23, grid size 400,400,400, pixel 1.05, shown
at level 0.012, step 1, values float32
Opened run_it060_class004.mrc as #24, grid size 400,400,400, pixel 1.05, shown
at level 0.012, step 1, values float32
Opened postprocess.mrc as #25, grid size 250,250,250, pixel 1.05, shown at
level 0.015, step 1, values float32
Opened run_class001.mrc as #26, grid size 400,400,400, pixel 1.05, shown at
level 0.0083, step 1, values float32
Opened j662_cPIC_rec_lres_sharpened_map.ccp4 copy as #28, grid size
300,300,300, pixel 1.05, shown at level 3.5, step 1, values float32
Opened postprocess_masked.mrc as #27, grid size 200,200,200, pixel 1.05, shown
at level 0.021, step 1, values float32
Opened NCP_postprocess.mrc as #29, grid size 200,200,200, pixel 1.05, shown at
level 0.025, step 1, values float32
Opened j665_cPIC-high_rec_lres_sharpened_map.ccp4 copy as #31, grid size
300,300,300, pixel 1.05, shown at level 2.8, step 1, values float32
Opened j803_cPIC-NCP_lres_sharpened.ccp4 as #30, grid size 400,400,400, pixel
1.05, shown at level 4.13, step 1, values float32
Opened postprocess.mrc as #32, grid size 300,300,300, pixel 1.05, shown at
level 0.016, step 1, values float32
Opened postprocess.mrc as #33, grid size 300,300,300, pixel 1.05, shown at
level 0.01, step 1, values float32
Opened run_half1_class001_unfil.mrc as #34, grid size 300,300,300, pixel 1.05,
shown at level 0.0145, step 1, values float32
Opened upstr_post.mrc as #35, grid size 300,300,300, pixel 1.05, shown at
level 0.018, step 2, values float32
Opened relion_locres_filtered.mrc as #6, grid size 300,300,300, pixel 1.05,
shown at level 0.0181, step 1, values float32
Opened relion_locres.mrc as #37, grid size 300,300,300, pixel 1.05, shown at
level 23.5, step 2, values float32
Opened relion_locres_filtered.mrc as #39, grid size 400,400,400, pixel 1.05,
shown at level 0.0135, step 1, values float32
Opened relion_locres.mrc as #40, grid size 400,400,400, pixel 1.05, shown at
level 24.7, step 2, values float32
Opened relion_locres_filtered.mrc as #41, grid size 300,300,300, pixel 1.05,
shown at level 0.0184, step 1, values float32
Opened relion_locres.mrc as #42, grid size 300,300,300, pixel 1.05, shown at
level 24.2, step 2, values float32
Opened relion_locres_filtered.mrc copy as #44, grid size 300,300,300, pixel
1.05, shown at level 0.0184, step 1, values float32
Opened relion_locres_filtered.mrc as #43, grid size 200,200,200, pixel 1.05,
shown at level 0.0213, step 1, values float32
Opened relion_locres.mrc as #45, grid size 200,200,200, pixel 1.05, shown at
level 34.5, step 1, values float32
Opened relion_locres_filtered.mrc as #46, grid size 250,250,250, pixel 1.05,
shown at level 0.0263, step 1, values float32
Opened relion_locres.mrc as #47, grid size 250,250,250, pixel 1.05, shown at
level 43.8, step 1, values float32
Opened relion_locres_filtered.mrc as #48, grid size 400,400,400, pixel 1.05,
shown at level 0.0152, step 1, values float32
Opened relion_locres.mrc as #49, grid size 400,400,400, pixel 1.05, shown at
level 24.7, step 2, values float32
Opened relion_locres_filtered.mrc as #50, grid size 200,200,200, pixel 1.05,
shown at level 0.0196, step 1, values float32
Opened relion_locres.mrc as #51, grid size 200,200,200, pixel 1.05, shown at
level 22, step 1, values float32
opened ChimeraX session
> close #1-35,37
> close #39-51
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/sub2/j605/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #1, grid size 200,200,200, pixel 1.05,
shown at level 0.0247, step 1, values float32
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/sub2/j605/relion_locres.mrc
Opened relion_locres.mrc as #2, grid size 200,200,200, pixel 1.05, shown at
level 22.9, step 1, values float32
> view matrix camera
> -0.11555,-0.53815,0.83489,954.04,-0.54025,0.73938,0.40181,562.5,-0.83352,-0.40464,-0.37617,-157.57
> volume #1 level 0.02644
> volume #1 level 0.01737
> surface dust #1 size 10.5
> ui tool show "Color Zone"
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.37, mean 3.873, maximum 7.275
> key rainbow :3.37 :4.35 :5.32 :6.30 :7.28 showTool true
> ui mousemode right "color key"
> key colorTreatment distinct
> key colorTreatment blended
> ui mousemode right translate
> volume #1 level 0.01562
> surface dust #1 size 10.5
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.37, mean 3.904, maximum 7.366
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.37, mean 3.904, maximum 7.366
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.37, mean 3.904, maximum 7.366
> volume #1 level 0.01795
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.37, mean 3.864, maximum 7.253
> volume #1 level 0.02555
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.371, mean 3.796, maximum 7.018
> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.371, mean 3.796, maximum 7.018
> key rainbow :3.37 :4.28 :5.19 :6.11 :7.02 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j605_NCP_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> hide #!1 models
> show #!1 models
> hide #!1 models
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j306/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #3, grid size 200,200,200, pixel 1.05,
shown at level 0.0328, step 1, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j306/relion_locres.mrc
Opened relion_locres.mrc as #4, grid size 200,200,200, pixel 1.05, shown at
level 26.3, step 1, values float32
> volume #3 level 0.04208
> volume #3 level 0.03716
> surface dust #3 size 10.5
> surface dust #4 size 10.5
> volume #3 level 0.03497
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j306/postprocess.mrc
Opened postprocess.mrc as #5, grid size 200,200,200, pixel 1.05, shown at
level 0.0214, step 1, values float32
> volume #5 level 0.02334
> close #5
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j306/postprocess_masked.mrc
Opened postprocess_masked.mrc as #5, grid size 200,200,200, pixel 1.05, shown
at level 0.0209, step 1, values float32
> volume #5 level 0.02243
> surface dust #4 size 10.5
> surface dust #5 size 10.5
> volume #5 level 0.02049
> volume #5 level 0.01777
> color sample #5.1 map #4 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.22, mean 3.957, maximum 7.406
> key rainbow :3.22 :4.27 :5.31 :6.36 :7.41 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j306_CAK_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j394/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #6, grid size 250,250,250, pixel 1.05,
shown at level 0.0231, step 1, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j394/relion_locres.mrc
Opened relion_locres.mrc as #7, grid size 250,250,250, pixel 1.05, shown at
level 38.8, step 1, values float32
> hide #!7 models
> view matrix camera
> -0.11555,-0.53815,0.83489,954.04,-0.54025,0.73938,0.40181,562.5,-0.83352,-0.40464,-0.37617,-157.57
> volume #6 level 0.02832
> color sample #6.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.11, mean 5.138, maximum 7.246
> key rainbow :4.11 :4.89 :5.68 :6.46 :7.25 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j394/postprocess.mrc
Opened postprocess.mrc as #8, grid size 250,250,250, pixel 1.05, shown at
level 0.0126, step 1, values float32
> volume #8 level 0.01543
> color sample #8.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.11, mean 5.247, maximum 8.458
> color sample #6.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.11, mean 5.138, maximum 7.246
> key rainbow :4.11 :4.89 :5.68 :6.46 :7.25 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> surface dust #6 size 10.5
> volume #6 level 0.02411
> color sample #6.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.111, mean 5.195, maximum 7.543
> key rainbow :4.11 :4.97 :5.83 :6.68 :7.54 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> view matrix camera
> -0.11555,-0.53815,0.83489,954.04,-0.54025,0.73938,0.40181,562.5,-0.83352,-0.40464,-0.37617,-157.57
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j429/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #9, grid size 250,250,250, pixel 1.05,
shown at level 0.0165, step 1, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j429/relion_locres.mrc
Opened relion_locres.mrc as #10, grid size 250,250,250, pixel 1.05, shown at
level 37.7, step 1, values float32
> hide #!10 models
> hide #!6 models
> volume #9 level 0.02429
> color sample #9.1 map #10 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.772, mean 4.342, maximum 6.909
> volume #9 level 0.02871
> volume #9 level 0.03042
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j431/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #11, grid size 250,250,250, pixel 1.05,
shown at level 0.0192, step 1, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j431/relion_locres.mrc
Opened relion_locres.mrc as #12, grid size 250,250,250, pixel 1.05, shown at
level 43.8, step 1, values float32
> hide #!12 models
> volume #11 level 0.02879
> color sample #11.1 map #12 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.43, mean 5.378, maximum 7.704
> volume #11 level 0.03201
> show #!10 models
> hide #!10 models
> show #!9 models
> surface dust #9 size 10.5
> surface dust #11 size 10.5
> hide #!11 models
> hide #!9 models
> show #!6 models
> color sample #6.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.111, mean 5.195, maximum 7.543
> key rainbow :4.11 :4.97 :5.83 :6.68 :7.54 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j394_TFIIH_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> hide #!6 models
> show #!9 models
> color sample #9.1 map #10 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.772, mean 4.297, maximum 6.614
> key rainbow :3.77 :4.48 :5.19 :5.90 :6.61 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j429_XPB_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> color sample #11.1 map #12 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.431, mean 5.349, maximum 7.638
> key rainbow :4.43 :5.23 :6.03 :6.84 :7.64 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> volume #11 level 0.02967
> color sample #11.1 map #12 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 4.431, mean 5.369, maximum 7.686
> key rainbow :4.43 :5.24 :6.06 :6.87 :7.69 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j431_XPD_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> hide #!11 models
> open
> /Users/jabrilg/Desktop/18W_processing/fRef/sub/j612/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #13, grid size 300,300,300, pixel 1.05,
shown at level 0.019, step 2, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j612/relion_locres.mrc
Opened relion_locres.mrc as #14, grid size 300,300,300, pixel 1.05, shown at
level 24.2, step 2, values float32
> hide #!14 models
> volume #13 step 1
> volume #13 level 0.01758
> volume #13 level 0.01403
> ui mousemode right "map eraser"
> volume erase #13 center 151.25,177.99,42.687 radius 34.426
Opened relion_locres_filtered.mrc copy as #16, grid size 300,300,300, pixel
1.05, shown at step 1, values float32
> volume erase #16 center 168.9,212.14,48.317 radius 34.335
> volume erase #16 center 155.37,229.57,54.939 radius 34.335
> volume erase #16 center 163.16,219.99,54.58 radius 34.335
> volume erase #16 center 193.98,167.13,37.098 radius 34.335
> volume erase #16 center 211.29,145.99,21.7 radius 34.335
> volume erase #16 center 146.79,114.07,52.067 radius 34.335
> volume erase #16 center 130.64,128.21,49.507 radius 34.335
> volume erase #16 center 145.82,117.83,56.945 radius 34.335
> volume erase #16 center 144.59,102.88,60.561 radius 34.335
> color sample #16.1 map #14 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 2.773, mean 3.533, maximum 8.772
> key rainbow :2.77 :4.27 :5.77 :7.27 :8.77 showTool true
> ui mousemode right "color key"
> ui mousemode right "map eraser"
> surface dust #16 size 10.5
> volume #16 level 0.01474
> color sample #16.1 map #14 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 2.773, mean 3.521, maximum 8.736
> key rainbow :2.77 :4.26 :5.76 :7.24 :8.74 showTool true
> ui mousemode right "color key"
> ui mousemode right "map eraser"
> view matrix camera
> -0.11555,-0.53815,0.83489,954.04,-0.54025,0.73938,0.40181,562.5,-0.83352,-0.40464,-0.37617,-157.57
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j612_cPIC_lres.png" width 1984 height 1134 supersample 3
> transparentBackground true
> hide #!16 models
> open
> /Users/jabrilg/Desktop/18W_processing/Ref/j364/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #15, grid size 400,400,400, pixel 1.05,
shown at level 0.0142, step 2, values float32
> open /Users/jabrilg/Desktop/18W_processing/Ref/j364/relion_locres.mrc
Opened relion_locres.mrc as #17, grid size 400,400,400, pixel 1.05, shown at
level 28, step 2, values float32
> hide #!17 models
> volume #15 level 0.008587
> volume #15 step 1
> open /Users/jabrilg/Desktop/18W_processing/Ref/j364/j364_PIC-NCP-CAK_lres-
> sharpened_map.ccp4
Opened j364_PIC-NCP-CAK_lres-sharpened_map.ccp4 as #18, grid size 400,400,400,
pixel 1.05, shown at level 4.44, step 2, values float32
> volume #18 step 1
> hide #!15 models
> volume #18 level 3.498
> volume #18 level 3.029
> volume #18 level 2.678
> color sample #15.1 map #17 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 2.858, mean 5.348, maximum 21.2
> key rainbow :2.9 :7.4 :12.0 :16.6 :21.2 showTool true
> ui mousemode right "color key"
> ui mousemode right "map eraser"
> color sample #18.1 map #17 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 2.858, mean 4.996, maximum 21.21
> volume #18 level 2.787
> color sample #18.1 map #17 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 2.858, mean 4.973, maximum 21.1
> key rainbow :2.9 :7.4 :12.0 :16.5 :21.1 showTool true
> ui mousemode right "color key"
> ui mousemode right "map eraser"
> surface dust #18 size 10.5
> save "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig4/j364_PIC-NCP_lres.png" width 1943 height 1134 supersample 3
> open "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig3/PIC-NCP18W_colored.cxs"
opened ChimeraX session
===== Log before crash end =====
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
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 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,2
Processor Name: 8-Core Intel Core i7
Processor Speed: 3,8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1615)
Kernel Version: Darwin 19.6.0
Time since boot: 4 days 6:03
Graphics/Displays:
AMD Radeon Pro 5700:
Chipset Model: AMD Radeon Pro 5700
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x731b
Revision ID: 0x0040
ROM Revision: 113-D1820Q-231
VBIOS Version: 113-D182A2XG-013
Option ROM Version: 113-D182A2XG-013
EFI Driver Version: 01.01.231
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: LCD
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 0FFXD46G3GLS
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
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
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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