![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7092 closed defect (can't reproduce)
Crash in event loop after session opened
| 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 0x0000700017c32000 (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 0x00000001193a1dc0 (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 [578]
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 [578]
User ID: 573055
Date/Time: 2022-06-14 18:12:38.871 +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: 1800000 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 0x000020708e4bb5d0
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x20708e4bb5d0:
VM_ALLOCATE 00000001a75d7000-00000001a79d8000 [ 4100K] rw-/rw- SM=PRV
-->
MALLOC_NANO 0000600000000000-0000600008000000 [128.0M] rw-/rwx SM=PRV
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6c53a33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6c5f6e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6c45193e raise + 26
3 libsystem_platform.dylib 0x00007fff6c5eb5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010d03606d cfunction_call + 125
6 org.python.python 0x000000010cff76cc _PyObject_Call + 140
7 QtCore.abi3.so 0x00000001183b1957 PyQtSlot::call(_object*, _object*) const + 39
8 QtCore.abi3.so 0x00000001183b1866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9 QtCore.abi3.so 0x00000001183b2455 PyQtSlotProxy::unislot(void**) + 85
10 QtCore.abi3.so 0x00000001183b23ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11 QtCore 0x000000011878db9f QObject::event(QEvent*) + 943
12 QtWidgets 0x0000000124f389ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13 QtWidgets 0x0000000124f39e11 QApplication::notify(QObject*, QEvent*) + 497
14 QtWidgets.abi3.so 0x0000000118df3db9 sipQApplication::notify(QObject*, QEvent*) + 233
15 QtCore 0x0000000118762a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16 QtCore 0x0000000118763d79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17 libqcocoa.dylib 0x0000000133262259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18 libqcocoa.dylib 0x00000001332629c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
19 com.apple.CoreFoundation 0x00007fff32655682 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
20 com.apple.CoreFoundation 0x00007fff32655621 __CFRunLoopDoSource0 + 103
21 com.apple.CoreFoundation 0x00007fff3265543b __CFRunLoopDoSources0 + 209
22 com.apple.CoreFoundation 0x00007fff3265416a __CFRunLoopRun + 927
23 com.apple.CoreFoundation 0x00007fff3265376e CFRunLoopRunSpecific + 462
24 com.apple.HIToolbox 0x00007fff3127faad RunCurrentEventLoopInMode + 292
25 com.apple.HIToolbox 0x00007fff3127f7c5 ReceiveNextEventCommon + 584
26 com.apple.HIToolbox 0x00007fff3127f569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
27 com.apple.AppKit 0x00007fff2f8c8659 _DPSNextEvent + 883
28 com.apple.AppKit 0x00007fff2f8c6ea0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
29 com.apple.AppKit 0x00007fff2f8b8bae -[NSApplication run] + 658
30 libqcocoa.dylib 0x000000013326162f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31 QtCore 0x000000011875eacf QEventLoop::exec(QFlags) + 431
32 QtCore 0x0000000118763042 QCoreApplication::exec() + 130
33 QtWidgets.abi3.so 0x0000000118ee5702 meth_QApplication_exec_(_object*, _object*) + 82
34 org.python.python 0x000000010d03606d cfunction_call + 125
35 org.python.python 0x000000010cff717d _PyObject_MakeTpCall + 365
36 org.python.python 0x000000010d0cf61c call_function + 876
37 org.python.python 0x000000010d0ccab3 _PyEval_EvalFrameDefault + 25219
38 org.python.python 0x000000010cff7948 function_code_fastcall + 104
39 org.python.python 0x000000010cff998a method_vectorcall + 202
40 org.python.python 0x000000010d0cf58c call_function + 732
41 org.python.python 0x000000010d0ccab3 _PyEval_EvalFrameDefault + 25219
42 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
43 org.python.python 0x000000010cff78d1 _PyFunction_Vectorcall + 289
44 org.python.python 0x000000010d0cf58c call_function + 732
45 org.python.python 0x000000010d0ccb4b _PyEval_EvalFrameDefault + 25371
46 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
47 org.python.python 0x000000010d0c670b PyEval_EvalCode + 139
48 org.python.python 0x000000010d0c3592 builtin_exec + 626
49 org.python.python 0x000000010d03586a cfunction_vectorcall_FASTCALL + 218
50 org.python.python 0x000000010d0cf58c call_function + 732
51 org.python.python 0x000000010d0ccb4b _PyEval_EvalFrameDefault + 25371
52 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
53 org.python.python 0x000000010cff78d1 _PyFunction_Vectorcall + 289
54 org.python.python 0x000000010d0cf58c call_function + 732
55 org.python.python 0x000000010d0ccb4b _PyEval_EvalFrameDefault + 25371
56 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
57 org.python.python 0x000000010cff78d1 _PyFunction_Vectorcall + 289
58 org.python.python 0x000000010d135e20 pymain_run_module + 208
59 org.python.python 0x000000010d135537 Py_RunMain + 1431
60 org.python.python 0x000000010d135b3f pymain_main + 223
61 org.python.python 0x000000010d135a4b Py_Main + 43
62 edu.ucsf.cgl.ChimeraX 0x000000010cfb2dc8 main + 120
63 libdyld.dylib 0x00007fff6c3f2cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 6:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 7:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010dc96a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 8:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6c53cb96 kevent64 + 10
1 QtWebEngineCore 0x0000000128aa4e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000128aa4cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000128a38a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 9:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a42778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000128a43150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000128a42c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 10:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6c53cb96 kevent64 + 10
1 QtWebEngineCore 0x0000000128aa4e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000128aa4cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012c971f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001289c21db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 12:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000128a91e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x0000000129d495f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 13:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001289c220f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 14:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6c53cb96 kevent64 + 10
1 QtWebEngineCore 0x0000000128aa4e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000128aa4cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001289c21db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 16:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001289c220f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 17:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001289c21db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 18:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000128a4276a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000128a43150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x0000000128a42d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 19:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001289c21db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001289c21db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000128a2d62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001289f17cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000128a4ca7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000153dfa2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 28:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff32655825 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff326542f2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff3265376e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2fa69ea4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 29:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a9a2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000128a4276a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000128a42e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x0000000128a42c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 30:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a42778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000128a43150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000128a42cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 31:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 32:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 33:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 34:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 35:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 36:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 37:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 38:
0 libsystem_pthread.dylib 0x00007fff6c5f2b68 start_wqthread + 0
Thread 39:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6c533dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c534170 mach_msg + 60
2 QtWebEngineCore 0x0000000128a9a492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000128a42778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000128a42e3d base::internal::WorkerThread::RunWorker() + 237
5 QtWebEngineCore 0x0000000128a42cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000128a95e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 40:
0 libsystem_kernel.dylib 0x00007fff6c536882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c5f7425 _pthread_cond_wait + 698
2 org.python.python 0x000000010d125d6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010d174a1f acquire_timed + 111
4 org.python.python 0x000000010d174b30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010cfffe54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x000000010d0cf58c call_function + 732
7 org.python.python 0x000000010d0cca92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010cff78d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010d0cf58c call_function + 732
11 org.python.python 0x000000010d0cca92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x000000010d0d0283 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010cff78d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010d0cf58c call_function + 732
15 org.python.python 0x000000010d0cca92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010cff7948 function_code_fastcall + 104
17 org.python.python 0x000000010d0cf58c call_function + 732
18 org.python.python 0x000000010d0cca92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x000000010cff7948 function_code_fastcall + 104
20 org.python.python 0x000000010d0cf58c call_function + 732
21 org.python.python 0x000000010d0cca92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x000000010cff7948 function_code_fastcall + 104
23 org.python.python 0x000000010cff99d2 method_vectorcall + 274
24 org.python.python 0x000000010d1743c6 t_bootstrap + 70
25 org.python.python 0x000000010d1258c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff6c5f7109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6c5f2b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001193a1dc0 rcx: 0x00007ffdb013fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007ffdb013fa80 rsp: 0x00007ffdb013fa58
r8: 0x00007ffdb013ff48 r9: 0x4fb1a5b1f875455b r10: 0x00000001193a1dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000600002732af0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6c53a33a rfl: 0x0000000000000246 cr2: 0x00007ffdb013ef00
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x1117ae000 - 0x1118c5ff7 +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
0x111933000 - 0x111969fff +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
0x11197d000 - 0x111992ff7 +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
0x1179a2000 - 0x1179b1fff +_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
0x1179c2000 - 0x1179d9fff +_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
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0x117a12000 - 0x117a14fff +_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
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0x117cba000 - 0x117ed0f4f +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
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0x11807f000 - 0x11810afff +_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
0x118175000 - 0x118175fff +_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
0x11817d000 - 0x11817dfff +_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
0x118184000 - 0x118225ff7 +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
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0x11827c000 - 0x1183dbff7 +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
0x11856a000 - 0x118ada7df +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
0x118c7b000 - 0x118c92ff7 +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
0x118ca9000 - 0x118f39ff7 +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
0x119230000 - 0x119251fff +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
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0x7fff5e854000 - 0x7fff5e88fff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff5ecdc000 - 0x7fff5ecfdff7 com.apple.SMBClient (3.4.1 - 3.4.1) /System/Library/PrivateFrameworks/SMBClient.framework/Versions/A/SMBClient
0x7fff5f5b8000 - 0x7fff5f604ff9 com.apple.Safari.SafeBrowsing (15609 - 15609.4.1) /System/Library/PrivateFrameworks/SafariSafeBrowsing.framework/Versions/A/SafariSafeBrowsing
0x7fff60170000 - 0x7fff60173ff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff6020c000 - 0x7fff60299ff6 com.apple.ShareKit (641.6 - 641.6) /System/Library/PrivateFrameworks/ShareKit.framework/Versions/A/ShareKit
0x7fff602e6000 - 0x7fff6040dfff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff60466000 - 0x7fff60484ff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff60485000 - 0x7fff604a5ff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff604a6000 - 0x7fff604b8ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff61822000 - 0x7fff61b18fff com.apple.SkyLight (1.600.0 - 451.6) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff62365000 - 0x7fff62373ffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff62435000 - 0x7fff626c1ffe com.apple.spotlight.index (10.7.0 - 2076.7.1) /System/Library/PrivateFrameworks/SpotlightIndex.framework/Versions/A/SpotlightIndex
0x7fff62a4f000 - 0x7fff62a90ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff62ba7000 - 0x7fff62bb0ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.2) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff62c21000 - 0x7fff62c4bffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff62e67000 - 0x7fff62e77ff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff6339c000 - 0x7fff63462ff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff635f9000 - 0x7fff635fafff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff63632000 - 0x7fff6388aff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff63921000 - 0x7fff63927ffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff64255000 - 0x7fff642b6ff9 com.apple.UserActivity (358 - 358) /System/Library/PrivateFrameworks/UserActivity.framework/Versions/A/UserActivity
0x7fff642b7000 - 0x7fff642d7ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff65083000 - 0x7fff6516eff2 com.apple.ViewBridge (468 - 468) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff65314000 - 0x7fff65315fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff654e8000 - 0x7fff654e8fff com.apple.WebInspectorUI (15609 - 15609.4.1) /System/Library/PrivateFrameworks/WebInspectorUI.framework/Versions/A/WebInspectorUI
0x7fff656a4000 - 0x7fff656dffff libAWDSupport.dylib (949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupport.dylib
0x7fff656e0000 - 0x7fff659c0ff7 libAWDSupportFramework.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupportFramework.dylib
0x7fff659c1000 - 0x7fff659d2fff libprotobuf-lite.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf-lite.dylib
0x7fff659d3000 - 0x7fff65a2cffb libprotobuf.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf.dylib
0x7fff65a2d000 - 0x7fff65a71ff6 com.apple.awd (1.0 - 949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/WirelessDiagnostics
0x7fff65f45000 - 0x7fff65f48ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff65fc2000 - 0x7fff65fd0ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff66198000 - 0x7fff661cdffe com.apple.iCalendar (7.0 - 810.6.1) /System/Library/PrivateFrameworks/iCalendar.framework/Versions/A/iCalendar
0x7fff66312000 - 0x7fff66314ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff66315000 - 0x7fff66328ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff6635a000 - 0x7fff66366ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff66367000 - 0x7fff66398ffd com.apple.contacts.vCard (1.0 - 3455.18) /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
0x7fff68d06000 - 0x7fff68d1bffe libAccessibility.dylib (2790.70.1) /usr/lib/libAccessibility.dylib
0x7fff68deb000 - 0x7fff68df7ff9 libAudioStatistics.dylib (1104.102) /usr/lib/libAudioStatistics.dylib
0x7fff68df8000 - 0x7fff68e2bffa libAudioToolboxUtility.dylib (1104.102) /usr/lib/libAudioToolboxUtility.dylib
0x7fff68e32000 - 0x7fff68e66fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff68e69000 - 0x7fff68e73fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff68e74000 - 0x7fff68efcfff libCoreStorage.dylib (551.0.1) /usr/lib/libCoreStorage.dylib
0x7fff68eff000 - 0x7fff68f01ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff68f47000 - 0x7fff690feffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff69125000 - 0x7fff6912bff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff6920d000 - 0x7fff69214fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff69243000 - 0x7fff69263ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff692e3000 - 0x7fff693c0ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff693d5000 - 0x7fff693d6fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff693d7000 - 0x7fff69462ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff69463000 - 0x7fff69464fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff6947c000 - 0x7fff69492fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff694c7000 - 0x7fff69539ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib
0x7fff6953a000 - 0x7fff695d3fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff695d7000 - 0x7fff695d7ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff695d8000 - 0x7fff6969cffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff6969d000 - 0x7fff696adffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff696ae000 - 0x7fff696bafff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff696bb000 - 0x7fff6970dfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6970e000 - 0x7fff69723ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff69724000 - 0x7fff69724fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff69725000 - 0x7fff69736fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff69737000 - 0x7fff6974efd7 libcompression.dylib (87.1) /usr/lib/libcompression.dylib
0x7fff69a28000 - 0x7fff69a3eff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff69a3f000 - 0x7fff69a40fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff69ee3000 - 0x7fff69fe7fcf libcrypto.44.dylib (47.140.2) /usr/lib/libcrypto.44.dylib
0x7fff69fea000 - 0x7fff69ff5fff libcsfde.dylib (551.0.1) /usr/lib/libcsfde.dylib
0x7fff69ffd000 - 0x7fff6a05cff7 libcups.2.dylib (483.8) /usr/lib/libcups.2.dylib
0x7fff6a05e000 - 0x7fff6a0c3ff7 libcurl.4.dylib (118.120.6) /usr/lib/libcurl.4.dylib
0x7fff6a166000 - 0x7fff6a166fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6a167000 - 0x7fff6a181ff7 libexpat.1.dylib (19.60.3) /usr/lib/libexpat.1.dylib
0x7fff6a182000 - 0x7fff6a18effb libexslt.0.dylib (16.12) /usr/lib/libexslt.0.dylib
0x7fff6a18f000 - 0x7fff6a191fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6a192000 - 0x7fff6a197f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff6a1a0000 - 0x7fff6a1a5fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6a1a6000 - 0x7fff6a1afff7 libheimdal-asn1.dylib (564.140.7) /usr/lib/libheimdal-asn1.dylib
0x7fff6a1b0000 - 0x7fff6a2a0fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6a2a1000 - 0x7fff6a4f8fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6a512000 - 0x7fff6a513fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6a514000 - 0x7fff6a52cff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6a544000 - 0x7fff6a5ebff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6a5ec000 - 0x7fff6a84eff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6abbb000 - 0x7fff6abeafff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6ad1a000 - 0x7fff6b196ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6b197000 - 0x7fff6b1aefff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6b237000 - 0x7fff6b26afde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6b26b000 - 0x7fff6b26cff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6b27d000 - 0x7fff6b281fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6b284000 - 0x7fff6b2bafff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff6b2fa000 - 0x7fff6b308ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6b309000 - 0x7fff6b30cff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff6b30d000 - 0x7fff6b30ffff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff6b33e000 - 0x7fff6b356fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6b358000 - 0x7fff6b39cff7 libsandbox.1.dylib (1217.141.7) /usr/lib/libsandbox.1.dylib
0x7fff6b39d000 - 0x7fff6b3afff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6b3b0000 - 0x7fff6b3b1ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6b3b2000 - 0x7fff6b59cff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff6b690000 - 0x7fff6b6bdffb libssl.46.dylib (47.140.2) /usr/lib/libssl.46.dylib
0x7fff6b73f000 - 0x7fff6b770ff7 libtidy.A.dylib (17.3) /usr/lib/libtidy.A.dylib
0x7fff6b792000 - 0x7fff6b7ecff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff6b7ed000 - 0x7fff6b7f0ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6b7f1000 - 0x7fff6b7feff7 libxar.1.dylib (425.5) /usr/lib/libxar.1.dylib
0x7fff6b804000 - 0x7fff6b8e6fff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib
0x7fff6b8ea000 - 0x7fff6b912fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff6b913000 - 0x7fff6b925ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6c1d4000 - 0x7fff6c1d9ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6c1da000 - 0x7fff6c1e5fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6c1e6000 - 0x7fff6c1edfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6c1ee000 - 0x7fff6c1f7ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6c1f8000 - 0x7fff6c28afdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff6c397000 - 0x7fff6c3d7ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6c3d8000 - 0x7fff6c40efff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff6c40f000 - 0x7fff6c40fffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6c410000 - 0x7fff6c41cff3 libkxld.dylib (6153.141.50) /usr/lib/system/libkxld.dylib
0x7fff6c41d000 - 0x7fff6c41dff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff6c41e000 - 0x7fff6c423ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6c424000 - 0x7fff6c426ff3 libquarantine.dylib (110.40.5) /usr/lib/system/libquarantine.dylib
0x7fff6c427000 - 0x7fff6c428ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6c429000 - 0x7fff6c440ff3 libsystem_asl.dylib (377.60.3) /usr/lib/system/libsystem_asl.dylib
0x7fff6c441000 - 0x7fff6c441ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6c442000 - 0x7fff6c4c9fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff6c4ca000 - 0x7fff6c4cdffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff6c4ce000 - 0x7fff6c4d1fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6c4d2000 - 0x7fff6c4dafff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff6c4db000 - 0x7fff6c4e2fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6c4e3000 - 0x7fff6c4e4ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6c4e5000 - 0x7fff6c532ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff6c533000 - 0x7fff6c55fff7 libsystem_kernel.dylib (6153.141.50) /usr/lib/system/libsystem_kernel.dylib
0x7fff6c560000 - 0x7fff6c5a7fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6c5a8000 - 0x7fff6c5cffff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6c5d0000 - 0x7fff6c5ddffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6c5de000 - 0x7fff6c5e7ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6c5e8000 - 0x7fff6c5f0fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6c5f1000 - 0x7fff6c5fbfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6c5fc000 - 0x7fff6c600ff3 libsystem_sandbox.dylib (1217.141.7) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6c601000 - 0x7fff6c603fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6c604000 - 0x7fff6c60bffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6c60c000 - 0x7fff6c622ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6c624000 - 0x7fff6c629ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6c62a000 - 0x7fff6c65fffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 365957
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: 207758510
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=11.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=11.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 1024K 8
Activity Tracing 256K 1
CG backing stores 2096K 4
CG image 476K 34
CoreAnimation 4076K 75
CoreGraphics 8K 1
CoreImage 48K 6
CoreUI image data 3804K 33
Foundation 28K 2
Kernel Alloc Once 8K 1
MALLOC 9.0G 735
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 1.5G 15 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 24K 2
OpenGL GLSL 384K 5
STACK GUARD 160K 40
Stack 163.8M 41
Stack Guard 56.0M 1
VM_ALLOCATE 189.2M 173
VM_ALLOCATE (reserved) 384.0M 3 reserved VM address space (unallocated)
__DATA 77.4M 708
__DATA_CONST 157K 9
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 494.6M 212
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 724.0M 652
__UNICODE 564K 1
mapped file 442.3M 69
shared memory 3960K 40
=========== ======= =======
TOTAL 13.1G 2887
TOTAL, minus reserved VM space 11.1G 2887
===== 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/PIC-NCP_final.pdb
Chain information for PIC-NCP_final.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
a | No description available
b | No description available
c g | No description available
d h | No description available
e | No description available
f | No description available
> show cartoons
> hide atoms
> close
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/Refine3D/job851/run_class001.mrc
Opened run_class001.mrc as #1, grid size 400,400,400, pixel 1.05, shown at
level 0.0027, step 2, values float32
> volume #1 step 1
> volume #1 level 0.00551
> volume #1 level 0.00345
> volume #1 level 0.00239
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job177/run_class001.mrc
Opened run_class001.mrc as #2, grid size 400,400,400, pixel 1.05, shown at
level 0.00417, step 2, values float32
> volume #2 step 1
> volume #2 level 0.006941
> volume #2 level 0.003439
> volume #2 level 0.009568
> volume #2 level 0.008374
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job175/mask.mrc
Opened mask.mrc as #3, grid size 400,400,400, pixel 1.05, shown at level
0.241, step 2, values float32
> volume #2 level 0.004792
> volume #2 level 0.007101
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job165/run_class001.mrc
Opened run_class001.mrc as #4, grid size 400,400,400, pixel 1.05, shown at
level 0.00489, step 2, values float32
> volume #4 step 1
> volume #4 level 0.008787
> volume #4 level 0.004612
> volume #4 level 0.006003
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job173/run_class001.mrc
Opened run_class001.mrc as #5, grid size 400,400,400, pixel 1.05, shown at
level 0.00344, step 2, values float32
> volume #5 step 1
> volume #5 level 0.001766
> volume #5 level 0.002301
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job189/postprocess.mrc
Opened postprocess.mrc as #6, grid size 400,400,400, pixel 1.05, shown at
level 0.00413, step 2, values float32
> volume #6 step 1
> volume #6 level 0.00485
> volume #6 level 0.01362
> volume #6 level 0.0159
> volume #6 level 0.01427
> volume #6 level 0.01092
> volume #6 level 0.01482
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j165/postprocess.mrc
Opened postprocess.mrc as #7, grid size 400,400,400, pixel 1.05, shown at
level 0.00573, step 2, values float32
> volume #7 level 0.01425
> volume #7 step 1
> volume #7 level 0.0183
> volume #7 level 0.01722
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j165/run_class001.mrc
Opened run_class001.mrc as #8, grid size 400,400,400, pixel 1.05, shown at
level 0.00489, step 2, values float32
> volume #8 step 1
> volume #8 level 0.01166
> volume #8 level 0.01268
> volume #8 level 0.009344
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job859/postprocess.mrc
Opened postprocess.mrc as #9, grid size 400,400,400, pixel 1.05, shown at
level 0.00267, step 2, values float32
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job861/postprocess.mrc
Opened postprocess.mrc as #10, grid size 400,400,400, pixel 1.05, shown at
level 0.00262, step 2, values float32
> volume #9 step 1
> volume #10 step 1
> volume #9 level 0.004808
> volume #9 level 0.003843
> volume #9 level 0.003016
> volume #10 level 0.00645
> volume #10 level 0.004453
> volume #8 level 0.007303
> select #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.56056,-0.342,-0.7542,320.13,0.10532,0.93278,-0.3447,61.923,0.82139,0.1138,0.5589,-110.03
> view matrix models
> #10,0.53865,-0.2786,-0.79513,323.59,-0.098653,0.9164,-0.38792,120.47,0.83673,0.2874,0.46613,-121.92
> view matrix models
> #10,0.50504,-0.16413,-0.84735,323.76,-0.40091,0.8248,-0.39872,206.73,0.76433,0.54108,0.35076,-122.09
> view matrix models
> #10,-0.49135,0.66516,-0.56226,352.46,0.19465,0.7131,0.6735,-143.43,0.84893,0.22148,-0.47985,91.582
> view matrix models
> #10,-0.15357,0.88097,-0.44756,215.11,0.35439,0.4719,0.80729,-169.21,0.9224,-0.034629,-0.38467,96.289
> view matrix models
> #10,0.068079,0.65903,0.74903,-58.749,0.87463,-0.40062,0.273,-28.212,0.47999,0.63653,-0.60368,134.27
> view matrix models
> #10,0.18337,-0.65058,0.73697,132.96,-0.021997,-0.7522,-0.65856,436.16,0.9828,0.10455,-0.15224,9.1668
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.18337,-0.65058,0.73697,-32.874,-0.021997,-0.7522,-0.65856,567.09,0.9828,0.10455,-0.15224,9.6392
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.2861,-0.5301,0.79821,-89.389,-0.066202,-0.84198,-0.53543,565.18,0.95591,0.10035,-0.27598,43.329
> view matrix models
> #10,0.80017,-0.17959,0.57226,-215.06,0.54631,-0.17557,-0.81898,377.65,0.24755,0.96795,-0.042374,11.293
> volume #10 level 0.007328
> view matrix models
> #10,-0.84256,-0.41003,0.34924,244.24,0.33479,0.10923,0.93594,-0.6391,-0.42191,0.90551,0.045243,154.69
> view matrix models
> #10,-0.40364,-0.51839,0.75389,74.88,0.48103,0.58067,0.65683,-51.106,-0.77826,0.62776,0.014983,287.9
> view matrix models
> #10,-0.13575,-0.44358,0.8859,-26.829,0.42825,0.78005,0.4562,-28.553,-0.8934,0.44132,0.08407,329.8
> view matrix models
> #10,-0.57157,-0.52034,0.63447,139.17,0.46882,0.4275,0.77295,-48.228,-0.67344,0.73925,-0.00040315,249.06
> view matrix models
> #10,-0.35097,0.47943,0.80434,-112.23,0.84027,0.54033,0.044584,6.318,-0.41324,0.69151,-0.59249,325.84
> view matrix models
> #10,-0.23531,0.48304,0.84338,-147.54,0.84396,0.53192,-0.069183,31.463,-0.48203,0.6955,-0.53284,327.91
> volume #10 level 0.004932
> view matrix models
> #10,0.084687,0.48696,0.86931,-226.68,0.78056,0.50985,-0.36164,112.96,-0.61932,0.70917,-0.33693,314.44
> view matrix models
> #10,-0.10127,0.48572,0.86823,-183.9,0.82995,0.52247,-0.19549,63.602,-0.54858,0.70078,-0.45603,325.54
> view matrix models
> #10,-0.0073764,0.5377,0.8431,-208.38,0.94375,0.28247,-0.17189,72.052,-0.33057,0.79441,-0.50954,272.1
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.0073764,0.5377,0.8431,-104.88,0.94375,0.28247,-0.17189,-9.6197,-0.33057,0.79441,-0.50954,271.76
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.20484,0.90683,0.36837,-110.98,0.97382,-0.15091,-0.17001,54.422,-0.098582,0.39355,-0.914,372.6
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.20484,0.90683,0.36837,-100.01,0.97382,-0.15091,-0.17001,80.143,-0.098582,0.39355,-0.914,360.47
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.43127,0.50133,0.75011,-167.65,0.90182,-0.21486,-0.3749,151.5,-0.02678,0.83815,-0.54478,190.9
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.43127,0.50133,0.75011,-179.13,0.90182,-0.21486,-0.3749,142.07,-0.02678,0.83815,-0.54478,214.67
> fitmap #10 inMap #8
Fit map postprocess.mrc in map run_class001.mrc using 372887 points
correlation = 0.6991, correlation about mean = 0.1787, overlap = 17.39
steps = 244, shift = 18.4, angle = 16.3 degrees
Position of postprocess.mrc (#10) relative to run_class001.mrc (#8)
coordinates:
Matrix rotation and translation
0.18558828 0.63779898 0.74750883 -140.31814415
0.98205816 -0.09449621 -0.16319392 51.70490479
-0.03344816 0.76438402 -0.64389308 233.98716020
Axis 0.73589281 0.61957127 0.27311759
Axis point 0.00000000 28.03543885 156.58910133
Rotation angle (degrees) 140.93218020
Shift along axis -7.31823116
> volume #10 level 0.007488
> volume #8 level 0.004797
> view matrix models
> #10,0.18559,0.6378,0.74751,-127.13,0.98206,-0.094496,-0.16319,58.647,-0.033448,0.76438,-0.64389,215.19
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.43899,0.72566,0.52982,-152.07,0.88207,-0.46029,-0.10043,127.99,0.17099,0.51142,-0.84215,253.26
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.43899,0.72566,0.52982,-153.59,0.88207,-0.46029,-0.10043,129.77,0.17099,0.51142,-0.84215,260.51
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.43579,0.72615,0.53178,-153.37,0.89356,-0.41986,-0.15895,133.16,0.10785,0.54445,-0.83183,267.19
> fitmap #10 inMap #8
Fit map postprocess.mrc in map run_class001.mrc using 203579 points
correlation = 0.8739, correlation about mean = 0.4813, overlap = 19.59
steps = 280, shift = 9.01, angle = 19.9 degrees
Position of postprocess.mrc (#10) relative to run_class001.mrc (#8)
coordinates:
Matrix rotation and translation
0.27375907 0.91627213 0.29240615 -96.22888268
0.96177648 -0.25874658 -0.08964502 80.32126967
-0.00648015 0.30577050 -0.95208320 354.52360120
Axis 0.79440260 0.60047227 0.09141970
Axis point 0.00000000 48.34913021 188.98973265
Rotation angle (degrees) 165.58898905
Shift along axis 4.19666114
> volume #10 level 0.002137
> volume #10 level 0.005571
> volume #8 level 0.009901
> volume #10 level 0.002696
> volume #10 level 0.005651
> volume #8 level 0.008323
> volume #8 level 0.007859
> volume #10 level 0.004054
> volume #10 level 0.005571
> volume #10 level 0.004293
> volume #8 level 0.005261
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/Refine3D/job836/run_class001.mrc
Opened run_class001.mrc as #11, grid size 400,400,400, pixel 1.05, shown at
level 0.00535, step 2, values float32
> volume #11 level 0.008166
> volume #11 step 1
> volume #11 level 0.003578
> volume #11 level 0.001356
> volume #11 level 0.001141
> open /Users/jabrilg/Desktop/10W_processing/fRef/j397/run_class001.mrc
Opened run_class001.mrc as #12, grid size 400,400,400, pixel 1.05, shown at
level 0.00662, step 2, values float32
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/Import/job829/CAK_gauss_mask-j29.mrc
Opened CAK_gauss_mask-j29.mrc as #13, grid size 400,400,400, pixel 1.05, shown
at level 1, step 2, values float32
> volume #13 step 1
> volume #13 level 1
> volume #13 color #b2ffff5c
> volume #13 level 1
> volume #12 level 0.01372
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job111/run_ct10_class001.mrc
Opened run_ct10_class001.mrc as #14, grid size 400,400,400, pixel 1.05, shown
at level 0.00592, step 2, values float32
> close #14
> open /Users/jabrilg/Desktop/18W_processing/Ref/j87/run_class001.mrc
Opened run_class001.mrc as #14, grid size 400,400,400, pixel 1.05, shown at
level 0.00686, step 2, values float32
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job087/j87_box200_2p1.mrc
Opened j87_box200_2p1.mrc as #15, grid size 200,200,200, pixel 2.1, shown at
level 0.00689, step 1, values float32
> volume #15 level 0.01401
> close #14
> volume #15 level 0.009407
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job113/mask113_box200_2p1.mrc
Opened mask113_box200_2p1.mrc as #14, grid size 200,200,200, pixel 2.1, shown
at level 1, step 1, values float32
> volume #14 level 1.006
> close #14
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Masks/j111_gauss_IIH-ref_box200_2p1.mrc
Opened j111_gauss_IIH-ref_box200_2p1.mrc as #14, grid size 200,200,200, pixel
2.1, shown at level 0.00468, step 1, values float32
> ui tool show "Map Coordinates"
> volume #14 level 0.0045
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job192/mask.mrc
Opened mask.mrc as #16, grid size 200,200,200, pixel 2.1, shown at level 1,
step 1, values float32
> volume #16 level 1
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job187/run_class001.mrc
Opened run_class001.mrc as #17, grid size 400,400,400, pixel 1.05, shown at
level 0.00422, step 2, values float32
> volume #17 step 1
> volume #17 level 0.007065
> volume #17 level 0.01005
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j146/run_class001.mrc
Opened run_class001.mrc as #18, grid size 400,400,400, pixel 1.05, shown at
level 0.00571, step 2, values float32
> open /Users/jabrilg/Desktop/18W_processing/fRef/sub/j165/run_class001.mrc
Opened run_class001.mrc as #19, grid size 400,400,400, pixel 1.05, shown at
level 0.00489, step 2, values float32
> volume #18 step 1
> volume #19 step 1
> volume #18 level 0.01123
> volume #19 level 0.01027
> volume #19 level 0.01213
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job215/run_class001.mrc
Opened run_class001.mrc as #20, grid size 400,400,400, pixel 1.05, shown at
level 0.0107, step 2, values float32
> volume #20 step 1
> volume #20 level 0.01839
> volume #20 level 0.01815
> volume #20 level 0.01661
> volume #20 level 0.01237
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job226/postprocess.mrc
Opened postprocess.mrc as #21, grid size 400,400,400, pixel 1.05, shown at
level 0.0104, step 2, values float32
> volume #21 step 1
> volume #21 level 0.02003
> volume #21 level 0.02786
> volume #21 level 0.01199
> volume #21 level 0.02565
> volume #21 level 0.02183
> volume #21 level 0.01501
> volume #21 level 0.02364
> volume #21 level 0.01942
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job204/postprocess.mrc
Opened postprocess.mrc as #22, grid size 400,400,400, pixel 1.05, shown at
level 0.00574, step 2, values float32
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job220/postprocess.mrc
Opened postprocess.mrc as #23, grid size 400,400,400, pixel 1.05, shown at
level 0.00586, step 2, values float32
> volume #22 level 0.01725
> volume #23 level 0.01905
> volume #22 step 1
> volume #23 step 1
> fitmap #23 inMap #22
Fit map postprocess.mrc in map postprocess.mrc using 51328 points
correlation = 0.9868, correlation about mean = 0.8012, overlap = 32.16
steps = 48, shift = 0.953, angle = 1.69 degrees
Position of postprocess.mrc (#23) relative to postprocess.mrc (#22)
coordinates:
Matrix rotation and translation
0.99958960 0.00339716 0.02844443 -7.08129988
-0.00359172 0.99997049 0.00679152 -0.77946965
-0.02842052 -0.00689090 0.99957230 6.69758259
Axis -0.23228350 0.96538430 -0.11864875
Axis point 232.28322676 0.00000000 251.50547556
Rotation angle (degrees) 1.68771775
Shift along axis 0.09772159
> volume #22 level 0.02248
> volume #22 level 0.025
> volume #23 level 0.025
> volume #23 color #ffb2b2
> volume #22 color #ffb2ff5d
> volume #22 color #8380825d
> volume #22 color #838082
> volume #22 color #838082b1
> volume #22 level 0.023
> volume #23 level 0.023
> volume #21 level 0.02705
> volume #21 level 0.01721
> volume #21 level 0.01701
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job227/run_class001.mrc
Opened run_class001.mrc as #24, grid size 400,400,400, pixel 1.05, shown at
level 0.0138, step 2, values float32
> volume #24 step 1
> volume #24 level 0.01314
> volume #24 level 0.0118
> volume #21 level 0.03348
> lighting shadows false
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job160/mask_box200.mrc
Opened mask_box200.mrc as #25, grid size 200,200,200, pixel 1.05, shown at
level 1, step 1, values float32
> volume #25 level 1
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job160/mask.mrc
Opened mask.mrc as #26, grid size 400,400,400, pixel 1.05, shown at level
0.957, step 2, values float32
> volume #26 step 1
> volume #26 level 1
> volume #25 level 1
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/Refine3D/job229/j229_box200.mrc
Opened j229_box200.mrc as #27, grid size 200,200,200, pixel 1.05, shown at
level 0.0149, step 1, values float32
> reset
Unknown command: reset
> close #26
> close #25
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/MaskCreate/job160/mask_box200.mrc
Opened mask_box200.mrc as #25, grid size 200,200,200, pixel 1.05, shown at
level 1, step 1, values float32
> volume #25 level 1
> volume #27 level 0.01169
> volume #27 level 0.007839
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job265/postprocess.mrc
Opened postprocess.mrc as #26, grid size 400,400,400, pixel 1.05, shown at
level 0.0104, step 2, values float32
> volume #26 step 1
> volume #26 level 0.02797
> open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC-
> AdML18W_1_Fr16/processing/Relion/PostProcess/job263/postprocess.mrc
Opened postprocess.mrc as #28, grid size 400,400,400, pixel 1.05, shown at
level 0.0103, step 2, values float32
> volume #28 step 1
> volume #28 level 0.03185
> volume #28 level 0.02476
> volume #28 level 0.02108
> open /Users/jabrilg/Desktop/10W_processing/Ref/j866/run_class001.mrc
Opened run_class001.mrc as #29, grid size 400,400,400, pixel 1.05, shown at
level 0.0153, step 2, values float32
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job903/postprocess.mrc
Opened postprocess.mrc as #30, grid size 200,200,200, pixel 1.05, shown at
level 0.0197, step 1, values float32
> volume #30 level 0.02157
> volume #30 level 0.02369
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job905/postprocess.mrc
Opened postprocess.mrc as #31, grid size 200,200,200, pixel 1.05, shown at
level 0.0152, step 1, values float32
> volume #31 level 0.01198
> close #31
> close #30
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job903/postprocess_masked.mrc
Opened postprocess_masked.mrc as #30, grid size 200,200,200, pixel 1.05, shown
at level 0.0189, step 1, values float32
> volume #30 level 0.01679
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job901/postprocess.mrc
Opened postprocess.mrc as #31, grid size 200,200,200, pixel 1.05, shown at
level 0.0191, step 1, values float32
> close #30
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job902/postprocess.mrc
Opened postprocess.mrc as #30, grid size 200,200,200, pixel 1.05, shown at
level 0.0198, step 1, values float32
> volume #31 level 0.01857
> close #30
> close #31
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job902/postprocess_masked.mrc
Opened postprocess_masked.mrc as #30, grid size 200,200,200, pixel 1.05, shown
at level 0.0192, step 1, values float32
> volume #30 level 0.01804
> volume #30 level 0.03171
> volume #30 level 0.01949
> close #30
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/PostProcess/job905/postprocess_masked.mrc
Opened postprocess_masked.mrc as #30, grid size 200,200,200, pixel 1.05, shown
at level 0.0151, step 1, values float32
> volume #30 level 0.01358
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/LocalRes/job906/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #31, grid size 200,200,200, pixel 1.05,
shown at level 0.0262, step 1, values float32
> volume #31 level 0.0204
> open
> /private/var/folders/gw/cd2044k913lcl3005y0rjnd400jglz/T/ch.sudo.cyberduck/bc1e946f-fc57-4487-acf6-d771493164f0/media/snfs/P6/Shares/EM11600/DATA/jabrilg/20210727_27_hPIC-
> AdML10W_2/processing/Relion/LocalRes/job906/relion_locres.mrc
Opened relion_locres.mrc as #32, grid size 200,200,200, pixel 1.05, shown at
level 26.3, step 1, values float32
> ui tool show "Surface Color"
> color sample #31.1 map #32 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 3.334, mean 4.155, maximum 7.77
> color sample #31.1 map #32 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.334, mean 4.155, maximum 7.77
> volume #31 level 0.01737
> open "/Users/jabrilg/Desktop/10W_processing/fRef/w:
> sub/j897/j897_CAK_lres_sharp.ccp4"
Opened j897_CAK_lres_sharp.ccp4 as #33, grid size 200,200,200, pixel 1.05,
shown at level 4.56, step 1, values float32
> volume #33 level 3.774
> open "/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for
> figures/Ex.Fig1/Colored_PIC-NCP.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: 21 days 12 minutes
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 after session opened |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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