![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5775 closed defect (duplicate)
Crash during or after saving session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch, pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110191144 (2021-10-19 11:44:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700010f72000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010f482dc0 (most recent call first):
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [72753]
Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [72753]
User ID: 1673611984
Date/Time: 2021-12-13 15:59:14.221 -0500
OS Version: Mac OS X 10.15.7 (19H1323)
Report Version: 12
Anonymous UUID: 0F18A509-2CB7-99E1-BF68-E73E1E554599
Time Awake Since Boot: 9000000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff70eca33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff70f86e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff70de193e raise + 26
3 libsystem_platform.dylib 0x00007fff70f7b5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010833706d cfunction_call + 125
6 org.python.python 0x00000001082f86cc _PyObject_Call + 140
7 QtCore.abi3.so 0x00000001157ad957 PyQtSlot::call(_object*, _object*) const + 39
8 QtCore.abi3.so 0x00000001157ad866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9 QtCore.abi3.so 0x00000001157ae455 PyQtSlotProxy::unislot(void**) + 85
10 QtCore.abi3.so 0x00000001157ae3ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11 QtCore 0x0000000115b89b9f QObject::event(QEvent*) + 943
12 QtWidgets 0x000000011817d9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13 QtWidgets 0x000000011817ee11 QApplication::notify(QObject*, QEvent*) + 497
14 QtWidgets.abi3.so 0x0000000117d30db9 sipQApplication::notify(QObject*, QEvent*) + 233
15 QtCore 0x0000000115b5ea34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16 QtCore 0x0000000115b5fd79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17 libqcocoa.dylib 0x0000000126548259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18 libqcocoa.dylib 0x00000001265489c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
19 com.apple.CoreFoundation 0x00007fff36cc27e2 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
20 com.apple.CoreFoundation 0x00007fff36cc2781 __CFRunLoopDoSource0 + 103
21 com.apple.CoreFoundation 0x00007fff36cc259b __CFRunLoopDoSources0 + 209
22 com.apple.CoreFoundation 0x00007fff36cc12ca __CFRunLoopRun + 927
23 com.apple.CoreFoundation 0x00007fff36cc08ce CFRunLoopRunSpecific + 462
24 com.apple.HIToolbox 0x00007fff358ecabd RunCurrentEventLoopInMode + 292
25 com.apple.HIToolbox 0x00007fff358ec7d5 ReceiveNextEventCommon + 584
26 com.apple.HIToolbox 0x00007fff358ec579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
27 com.apple.AppKit 0x00007fff33f33739 _DPSNextEvent + 883
28 com.apple.AppKit 0x00007fff33f31f80 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
29 com.apple.AppKit 0x00007fff33f23c8e -[NSApplication run] + 658
30 libqcocoa.dylib 0x000000012654762f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31 QtCore 0x0000000115b5aacf QEventLoop::exec(QFlags) + 431
32 QtCore 0x0000000115b5f042 QCoreApplication::exec() + 130
33 QtWidgets.abi3.so 0x0000000117e22702 meth_QApplication_exec_(_object*, _object*) + 82
34 org.python.python 0x000000010833706d cfunction_call + 125
35 org.python.python 0x00000001082f817d _PyObject_MakeTpCall + 365
36 org.python.python 0x00000001083d061c call_function + 876
37 org.python.python 0x00000001083cdab3 _PyEval_EvalFrameDefault + 25219
38 org.python.python 0x00000001082f8948 function_code_fastcall + 104
39 org.python.python 0x00000001082fa98a method_vectorcall + 202
40 org.python.python 0x00000001083d058c call_function + 732
41 org.python.python 0x00000001083cdab3 _PyEval_EvalFrameDefault + 25219
42 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
43 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
44 org.python.python 0x00000001083d058c call_function + 732
45 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
46 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
47 org.python.python 0x00000001083c770b PyEval_EvalCode + 139
48 org.python.python 0x00000001083c4592 builtin_exec + 626
49 org.python.python 0x000000010833686a cfunction_vectorcall_FASTCALL + 218
50 org.python.python 0x00000001083d058c call_function + 732
51 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
52 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
53 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
54 org.python.python 0x00000001083d058c call_function + 732
55 org.python.python 0x00000001083cdb4b _PyEval_EvalFrameDefault + 25371
56 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
57 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
58 org.python.python 0x0000000108436e20 pymain_run_module + 208
59 org.python.python 0x0000000108436537 Py_RunMain + 1431
60 org.python.python 0x0000000108436b3f pymain_main + 223
61 org.python.python 0x0000000108436a4b Py_Main + 43
62 edu.ucsf.cgl.ChimeraX 0x00000001082aedc8 main + 120
63 libdyld.dylib 0x00007fff70d82cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000108f7ea9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011bcd0a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011bcdac44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011fc09f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 8:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011bcdacd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 9:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011bd29e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x000000011cfe15f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 10:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bc5a20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 11:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff70eccb96 kevent64 + 10
1 QtWebEngineCore 0x000000011bd3ce6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011bd3ccc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 12:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bc5a20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 15:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bcda76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011bcdb150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x000000011bcdad34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 16:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 17:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bc5a1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011bcc562b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011bc897cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011bce4a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 18:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff36cc2985 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff36cc1452 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff36cc08ce CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff340d4f74 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 19:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bd322cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011bcda76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011bcdae3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x000000011bcdac74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 20:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 21:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff70ec3dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70ec4170 mach_msg + 60
2 QtWebEngineCore 0x000000011bd32492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011bcda778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011bcdae3d base::internal::WorkerThread::RunWorker() + 237
5 QtWebEngineCore 0x000000011bcdacd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011bd2de07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 24:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 25:
0 libsystem_pthread.dylib 0x00007fff70f82b68 start_wqthread + 0
Thread 26:
0 libsystem_kernel.dylib 0x00007fff70ec6882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70f87425 _pthread_cond_wait + 698
2 org.python.python 0x0000000108426d6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x0000000108475a1f acquire_timed + 111
4 org.python.python 0x0000000108475b30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000108300e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x00000001083d058c call_function + 732
7 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
9 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001083d058c call_function + 732
11 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x00000001083d1283 _PyEval_EvalCode + 2611
13 org.python.python 0x00000001082f88d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x00000001083d058c call_function + 732
15 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x00000001082f8948 function_code_fastcall + 104
17 org.python.python 0x00000001083d058c call_function + 732
18 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x00000001082f8948 function_code_fastcall + 104
20 org.python.python 0x00000001083d058c call_function + 732
21 org.python.python 0x00000001083cda92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x00000001082f8948 function_code_fastcall + 104
23 org.python.python 0x00000001082fa9d2 method_vectorcall + 274
24 org.python.python 0x00000001084753c6 t_bootstrap + 70
25 org.python.python 0x00000001084268c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff70f87109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff70f82b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010f482dc0 rcx: 0x00007fb5e015fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fb5e015fa80 rsp: 0x00007fb5e015fa58
r8: 0x00007fb5e015ff48 r9: 0xc7c2c9a3e05cf30e r10: 0x000000010f482dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000600000de5e30 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff70eca33a rfl: 0x0000000000000246 cr2: 0x000000010d023000
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff6eb40000 - 0x7fff6ec30fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6ec31000 - 0x7fff6ee88fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6eea2000 - 0x7fff6eea3fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6eea4000 - 0x7fff6eebcff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6eed4000 - 0x7fff6ef7bff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6ef7c000 - 0x7fff6f1deff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6f54b000 - 0x7fff6f57afff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6f6aa000 - 0x7fff6fb26ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6fb27000 - 0x7fff6fb3efff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6fbc7000 - 0x7fff6fbfafde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6fc0d000 - 0x7fff6fc11fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6fc14000 - 0x7fff6fc4afff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff6fc8a000 - 0x7fff6fc98ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6fc99000 - 0x7fff6fc9cff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff6fc9d000 - 0x7fff6fc9ffff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff6fcce000 - 0x7fff6fce6fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6fce8000 - 0x7fff6fd2cff7 libsandbox.1.dylib (1217.141.3) /usr/lib/libsandbox.1.dylib
0x7fff6fd40000 - 0x7fff6fd41ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6fd42000 - 0x7fff6ff2cff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff70122000 - 0x7fff7017cff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff7017d000 - 0x7fff70180ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff70181000 - 0x7fff7018eff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff70194000 - 0x7fff70276fff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib
0x7fff7027a000 - 0x7fff702a2fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff702a3000 - 0x7fff702b5ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff70b64000 - 0x7fff70b69ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff70b6a000 - 0x7fff70b75fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff70b76000 - 0x7fff70b7dfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff70b7e000 - 0x7fff70b87ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff70b88000 - 0x7fff70c1afdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff70d27000 - 0x7fff70d67ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff70d68000 - 0x7fff70d9efff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff70d9f000 - 0x7fff70d9fffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff70da0000 - 0x7fff70dacff3 libkxld.dylib (6153.141.35) /usr/lib/system/libkxld.dylib
0x7fff70dad000 - 0x7fff70dadff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff70dae000 - 0x7fff70db3ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff70db4000 - 0x7fff70db6ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff70db7000 - 0x7fff70db8ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff70db9000 - 0x7fff70dd0ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff70dd1000 - 0x7fff70dd1ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff70dd2000 - 0x7fff70e59fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff70e5a000 - 0x7fff70e5dffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff70e5e000 - 0x7fff70e61fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff70e62000 - 0x7fff70e6afff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff70e6b000 - 0x7fff70e72fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff70e73000 - 0x7fff70e74ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff70e75000 - 0x7fff70ec2ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff70ec3000 - 0x7fff70eefff7 libsystem_kernel.dylib (6153.141.35) /usr/lib/system/libsystem_kernel.dylib
0x7fff70ef0000 - 0x7fff70f37fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff70f38000 - 0x7fff70f5ffff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff70f60000 - 0x7fff70f6dffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff70f6e000 - 0x7fff70f77ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff70f78000 - 0x7fff70f80fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff70f81000 - 0x7fff70f8bfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff70f8c000 - 0x7fff70f90ff3 libsystem_sandbox.dylib (1217.141.3) /usr/lib/system/libsystem_sandbox.dylib
0x7fff70f91000 - 0x7fff70f93fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff70f94000 - 0x7fff70f9bffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff70f9c000 - 0x7fff70fb2ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff70fb4000 - 0x7fff70fb9ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff70fba000 - 0x7fff70fefffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 94
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 918098070
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 1760K 2
CG image 2564K 25
CoreAnimation 3224K 68
CoreGraphics 8K 1
CoreImage 24K 2
CoreServices 124K 1
CoreUI image data 3204K 29
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 947.9M 186
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 248.0M 4 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 24K 4
OpenGL GLSL 384K 4
STACK GUARD 104K 26
Stack 156.7M 27
Stack Guard 56.0M 1
VM_ALLOCATE 204.5M 180
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 64.0M 547
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 482.1M 150
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 553.8M 511
__UNICODE 564K 1
mapped file 393.0M 55
shared memory 2836K 22
=========== ======= =======
TOTAL 3.4G 1874
TOTAL, minus reserved VM space 2.8G 1874
===== Log before crash start =====
UCSF ChimeraX version: 1.3.dev202110191144 (2021-10-19)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Deposit/Apo/run_class001.mrc"
Opened run_class001.mrc as #1, grid size 260,260,260, pixel 1.03, shown at
level 0.0131, step 2, values float32
> volume #1 step 1
> volume #1 level 0.00581
> volume #1 level 0.009019
> volume #1 level 0.006394
> open /Users/xiang.feng/Downloads/cryosparc_P3_J29_005_volume_map.mrc
Opened cryosparc_P3_J29_005_volume_map.mrc as #2, grid size 280,280,280, pixel
0.828, shown at level 0.304, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1736
> volume #2 level 0.141
> close #1
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Deposit/FMN/HydABC_mono_72-coot-1.pdb"
Chain information for HydABC_mono_72-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> select #1
14063 atoms, 14306 bonds, 114 pseudobonds, 1801 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-5.0143,0,1,0,-41.82,0,0,1,7.0646
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.88397,-0.1729,-0.4344,77.933,0.19943,0.97978,0.015847,-59.684,0.42288,-0.10064,0.90058,-8.117
> view matrix models
> #1,0.83931,-0.25209,-0.48167,97.605,0.27875,0.96022,-0.016815,-60.825,0.46675,-0.12015,0.87619,-6.9142
> view matrix models
> #1,-0.68417,-0.57263,-0.45167,276.86,0.53619,0.024883,-0.84373,129.36,0.49439,-0.81943,0.29001,146.94
> view matrix models
> #1,0.79279,-0.58945,0.15503,71.157,-0.52197,-0.78794,-0.32665,271.38,0.3147,0.17805,-0.93234,178.43
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.79279,-0.58945,0.15503,75.621,-0.52197,-0.78794,-0.32665,307.36,0.3147,0.17805,-0.93234,168.46
> view matrix models
> #1,0.79279,-0.58945,0.15503,75.67,-0.52197,-0.78794,-0.32665,310.56,0.3147,0.17805,-0.93234,176.65
> ui tool show "Fit in Map"
Fit molecule HydABC_mono_72-coot-1.pdb (#1) to map
cryosparc_P3_J29_005_volume_map.mrc (#2) using 14063 atoms
average map value = 0.33, steps = 172
shifted from previous position = 3.69
rotated from previous position = 21.6 degrees
atoms outside contour = 1287, contour level = 0.14095
Position of HydABC_mono_72-coot-1.pdb (#1) relative to
cryosparc_P3_J29_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.77192958 -0.63568721 -0.00514748 100.80870746
-0.63570533 -0.77192466 -0.00332560 279.70934805
-0.00185943 0.00583941 -0.99998123 234.41108003
Axis 0.94125662 -0.33768702 -0.00186104
Axis point 0.00000000 157.63472067 117.66688729
Rotation angle (degrees) 179.72105440
Shift along axis -0.00360009
> volume #2 color #ffffb281
> volume #2 level 0.1775
> volume #2 level 0.1443
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Extenal_modeling/Fd_domain_2a96b.result/Fd_domain_2a96b_unrelaxed_model_1.pdb"
Chain information for Fd_domain_2a96b_unrelaxed_model_1.pdb #3
---
Chain | Description
A | No description available
> select #3
431 atoms, 437 bonds, 57 residues, 1 model selected
> view matrix models #3,1,0,0,107.94,0,1,0,131.47,0,0,1,169.26
> view matrix models #3,1,0,0,89.938,0,1,0,148.32,0,0,1,172.1
> view matrix models #3,1,0,0,104.2,0,1,0,156.2,0,0,1,151.29
Fit molecule Fd_domain_2a96b_unrelaxed_model_1.pdb (#3) to map
cryosparc_P3_J29_005_volume_map.mrc (#2) using 431 atoms
average map value = 0.1178, steps = 188
shifted from previous position = 9.4
rotated from previous position = 29 degrees
atoms outside contour = 304, contour level = 0.14428
Position of Fd_domain_2a96b_unrelaxed_model_1.pdb (#3) relative to
cryosparc_P3_J29_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.87699118 -0.13558103 0.46098184 95.44287726
0.16852055 0.98521572 -0.03083522 158.44568321
-0.44998589 0.10472713 0.88687368 149.34178089
Axis 0.13976858 0.93923327 0.31353725
Axis point 208.40889628 0.00000000 -88.06785903
Rotation angle (degrees) 29.00938436
Shift along axis 208.98158428
> view matrix models
> #3,0.87699,-0.13558,0.46098,94.304,0.16852,0.98522,-0.030835,158.8,-0.44999,0.10473,0.88687,150.51
Fit molecule Fd_domain_2a96b_unrelaxed_model_1.pdb (#3) to map
cryosparc_P3_J29_005_volume_map.mrc (#2) using 431 atoms
average map value = 0.1188, steps = 68
shifted from previous position = 1.1
rotated from previous position = 12.5 degrees
atoms outside contour = 307, contour level = 0.14428
Position of Fd_domain_2a96b_unrelaxed_model_1.pdb (#3) relative to
cryosparc_P3_J29_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.76554704 -0.14538678 0.62673791 95.00632599
0.24842852 0.96538175 -0.07950687 158.99061691
-0.59348209 0.21656582 0.77516337 150.44781413
Axis 0.22499027 0.92726426 0.29926640
Axis point 152.42408494 0.00000000 -17.80860237
Rotation angle (degrees) 41.14506763
Shift along axis 213.82579089
> hide #!1 models
> show #!1 models
> hide #!2 models
> select clear
> select #1/B:537
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:57
14 atoms, 13 bonds, 2 residues, 2 models selected
> select clear
> show #!2 models
> volume #2 level 0.168
> volume #2 level 0.1413
> volume #2 level 0.1976
> volume #2 level 0.1532
> volume #2 level 0.1591
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/revised_supplementary_fig9_new.cxs"
Opened TightTargetVol.mrc as #2, grid size 260,260,260, pixel 1.03, shown at
level 0.194, step 1, values float32
opened ChimeraX session
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3.dev202110191144 (2021-10-19)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/revised_supplementary_fig9_new.cxs"
Opened TightTargetVol.mrc as #2, grid size 260,260,260, pixel 1.03, shown at
level 0.194, step 1, values float32
Log from Tue Nov 23 17:36:16 2021UCSF ChimeraX version: 1.3.dev202110191144
(2021-10-19)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb"
Summary of feedback from opening /Users/xiang.feng/OneDrive - Van Andel
Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.131 14910
Ignored bad PDB record found on line 23
ANGLE : 1.274 16.764 20213
Ignored bad PDB record found on line 24
CHIRALITY : 0.073 0.354 2267
16 messages similar to the above omitted
Chain information for mono_Apo-coot-20.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> select ::name="3NI"::name="FCO"::name="FES"::name="SF4"
68 atoms, 15 bonds, 114 pseudobonds, 11 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 68 atom styles
> style sel ball
Changed 68 atom styles
> style sel stick
Changed 68 atom styles
> color sel byhetero
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Apo_state/TightTargetVol.mrc"
Opened TightTargetVol.mrc as #2, grid size 260,260,260, pixel 1.03, shown at
level 0.048, step 2, values float32
> volume #2 step 1
> color #2 #b2b2b281 models
> color #2 #b2b2b282 models
> volume #2 style mesh sdLevel 1.5 surfaceSmoothing true smoothingIterations 3
> smoothLines true subdivideSurface true
> select #1/B:601
8 atoms, 18 pseudobonds, 1 residue, 2 models selected
> view sel
> select ::name="CYS"
324 atoms, 271 bonds, 54 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 324 atom styles
> color sel byhetero
> volume #2 style mesh sdLevel 2 surfaceSmoothing true smoothingIterations 3
> smoothLines true subdivideSurface true
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> ui tool show "Volume Viewer"
> volume #2 style mesh sdLevel 3 surfaceSmoothing true smoothingIterations 3
> smoothLines true subdivideSurface true
> volume #2 level 0.22
> volume #2 style mesh sdLevel 3 surfaceSmoothing true smoothingIterations 3
> smoothLines true subdivideSurface true
> lighting soft
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> graphics silhouettes false
> select clear
> ui tool show Distances
> select /B:601@FE4
1 atom, 1 residue, 1 model selected
> select add /B:455@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE4 /B:455@SG
Distance between /B SF4 601 FE4 and CYS 455 SG: 1.717Å
> select /B:601@FE2
1 atom, 1 residue, 1 model selected
> select add /B:501@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE2 /B:501@SG
Distance between /B SF4 601 FE2 and CYS 501 SG: 1.929Å
> select /B:601@FE1
1 atom, 1 residue, 1 model selected
> select add /B:458@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE1 /B:458@SG
Distance between /B SF4 601 FE1 and CYS 458 SG: 1.269Å
> select /B:601@FE3
1 atom, 1 residue, 1 model selected
> select add /B:461@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE3 /B:461@SG
Distance between /B SF4 601 FE3 and CYS 461 SG: 2.866Å
> hide #3.1 models
> graphics silhouettes true
> graphics silhouettes false
> volume #2 color #13131382
[Repeated 1 time(s)]
> volume step 2
> volume step 1
[Repeated 3 time(s)]
> volume style mesh
> volume #2 style mesh sdLevel 3 surfaceSmoothing true smoothingIterations 4
> smoothLines true subdivideSurface true
> volume #2 style mesh sdLevel 3 surfaceSmoothing true smoothingIterations 4
> smoothLines true subdivideSurface true squareMesh false
> view sel
> select #2
2 models selected
> select clear
> ui tool show "Side View"
> color #1/B salmon
> color byhetero
> select clear
> style ball
Changed 14600 atom styles
> style stick
Changed 14600 atom styles
> select /B:601@S3
1 atom, 1 residue, 1 model selected
> select add /B:601@FE4
2 atoms, 1 residue, 1 model selected
> select add /B:601@S2
3 atoms, 1 residue, 1 model selected
> select clear
Drag select of 8 atoms, 1 residues, 21 pseudobonds, 2 TightTargetVol.mrc
> hide #!2 models
Drag select of 5 atoms, 20 pseudobonds
> select clear
> select add /B:601@S1
1 atom, 1 residue, 1 model selected
> select add /B:601@FE3
2 atoms, 1 residue, 1 model selected
> select add /B:601@FE2
3 atoms, 1 residue, 1 model selected
> select add /B:601@S4
4 atoms, 1 residue, 1 model selected
> select add /B:601@FE1
5 atoms, 1 residue, 1 model selected
> select add /B:601@S2
6 atoms, 1 residue, 1 model selected
> select add /B:601@FE4
7 atoms, 1 residue, 1 model selected
> select add /B:601@S3
8 atoms, 1 residue, 1 model selected
Drag select of 1 pseudobonds
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #1.1 models
> show #1.1 models
> color #1.1 #a18adc models
> select #1.1
114 pseudobonds, 1 model selected
> style stick
Changed 14600 atom styles
> style sphere
Changed 14600 atom styles
> style stick
Changed 14600 atom styles
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> ~select #1.1
Nothing selected
> show #2.1 models
> style ball
Changed 14600 atom styles
> style ball
Changed 14600 atom styles
> style stick
Changed 14600 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style sphere
Changed 14600 atom styles
> style stick
Changed 14600 atom styles
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/4hea_mono.pdb"
Summary of feedback from opening /Users/xiang.feng/OneDrive - Van Andel
Institute/NiFeABCSL/Revision/4hea_mono.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU 1 17
VAL 1 21 1 5
Start residue of secondary structure not found: HELIX 2 2 THR 1 28 HIS 1 35 1
8
Start residue of secondary structure not found: HELIX 3 3 TYR 1 38 GLU 1 47 1
10
Start residue of secondary structure not found: HELIX 4 4 THR 1 49 GLY 1 61 1
13
Start residue of secondary structure not found: HELIX 5 5 PRO 1 71 SER 1 77 1
7
292 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (144 )
Cannot find LINK/SSBOND residue CYS (353 )
Cannot find LINK/SSBOND residue CYS (359 )
Cannot find LINK/SSBOND residue CYS (88 )
Cannot find LINK/SSBOND residue CYS (124 )
32 messages similar to the above omitted
4hea_mono.pdb title:
Crystal structure of the entire respiratory complex I from thermus
thermophilus [more info...]
Chain information for 4hea_mono.pdb #4
---
Chain | Description | UniProt
B | nadh-quinone oxidoreductase subunit 1 | NQO1_THET8
C | nadh-quinone oxidoreductase subunit 2 | NQO2_THET8
D | nadh-quinone oxidoreductase subunit 3 | NQO3_THET8
E | nadh-quinone oxidoreductase subunit 4 | NQO4_THET8
F | nadh-quinone oxidoreductase subunit 5 | NQO5_THET8
G | nadh-quinone oxidoreductase subunit 6 | NQO6_THET8
I | nadh-quinone oxidoreductase subunit 15 | NQO15_THET8
O | nadh-quinone oxidoreductase subunit 9 | NQO9_THET8
P | nadh-quinone oxidoreductase subunit 7 | NQO7_THET8
Q | nadh-quinone oxidoreductase subunit 8 | NQO8_THET8
R | nadh-quinone oxidoreductase subunit 10 | NQO10_THET8
S | nadh-quinone oxidoreductase subunit 11 | NQO11_THET8
T | nadh-quinone oxidoreductase subunit 12 | NQO12_THET8
U | nadh-quinone oxidoreductase subunit 13 | NQO13_THET8
V | nadh-quinone oxidoreductase subunit 14 | NQO14_THET8
X | putative uncharacterized protein TTHA1528 | Q5SI52_THET8
Non-standard residues in 4hea_mono.pdb #4
---
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
SF4 — iron/sulfur cluster
> select #4
36999 atoms, 38013 bonds, 39 pseudobonds, 4780 residues, 3 models selected
> view sel
> hide sel atoms
> show sel cartoons
> select ::name="3NI"::name="FCO"::name="FES"::name="FMN"::name="SF4"
163 atoms, 140 bonds, 114 pseudobonds, 21 residues, 3 models selected
> show sel atoms
> open /Users/xiang.feng/Research/peptide.pdb
Chain information for peptide.pdb #5
---
Chain | Description
F | No description available
> close #5
> open
> /Users/xiang.feng/Research/HyDABC_Amobi/Apo_state/hydABC_apply_ncs_8-coot-7_real_space_refined.pdb
Chain information for hydABC_apply_ncs_8-coot-7_real_space_refined.pdb #5
---
Chain | Description
A | No description available
B | No description available
C H | No description available
F | No description available
G | No description available
I L | No description available
M S | No description available
> hide #!4 models
> select #5
29130 atoms, 29631 bonds, 227 pseudobonds, 3755 residues, 3 models selected
> view sel
> style sel stick
Changed 29130 atom styles
> hide sel atoms
> show sel cartoons
> hide #!3 models
> hide #2.1 models
> hide #!2 models
> hide #1.2 models
> hide #1.1 models
> hide #!1 models
> select
> ::name="3NI"::name="FCO"::name="FES"::name="FMN"::name="NI"::name="SF4"
292 atoms, 167 bonds, 339 pseudobonds, 42 residues, 5 models selected
> show sel & #!5 atoms
> select clear
> select #5/B:601@S4
1 atom, 1 residue, 1 model selected
> hide #!5 models
> show #!4 models
> select #4
36999 atoms, 38013 bonds, 39 pseudobonds, 4780 residues, 3 models selected
> view sel
> select clear
> select #4/O:202@FE1
1 atom, 1 residue, 1 model selected
> select add #4/O:202@S3
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> hide #!4 cartoons
Drag select of 8 atoms, 12 bonds
> label sel atoms
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> hide #4.3 models
> show #4.3 models
> close #4.3
> label sel atoms attribute idatm_type
> close #4.3
> label sel atoms
> hide #4.3 models
> hide #4.2 models
> hide #4.1 models
> hide #!4 models
> select #4
36999 atoms, 38013 bonds, 39 pseudobonds, 4780 residues, 4 models selected
> show #!4 models
> show #!1 models
> hide #!4 models
> ~select #4
Nothing selected
> select #4.1
36 pseudobonds, 1 model selected
> ~select #4.1
Nothing selected
> select #4
36999 atoms, 38013 bonds, 39 pseudobonds, 4780 residues, 4 models selected
> select #1
14600 atoms, 14846 bonds, 119 pseudobonds, 1881 residues, 4 models selected
> show #1.1 models
> show #1.2 models
> view sel
> select clear
> select #1/B:601
8 atoms, 18 pseudobonds, 1 residue, 2 models selected
> select #1/B:455@SG
1 atom, 1 residue, 1 model selected
> select #1/B:601
8 atoms, 18 pseudobonds, 1 residue, 2 models selected
> select add #1/B:458@SG
9 atoms, 18 pseudobonds, 2 residues, 2 models selected
> select add #1/B:461@SG
10 atoms, 18 pseudobonds, 3 residues, 2 models selected
> select add #1/B:501@SG
11 atoms, 1 bond, 18 pseudobonds, 4 residues, 2 models selected
> select add #1/B:455@SG
12 atoms, 1 bond, 18 pseudobonds, 5 residues, 2 models selected
> label (#!1 & sel) atoms
> select #1/E:201
8 atoms, 18 pseudobonds, 1 residue, 2 models selected
> view sel
> label (#!1 & sel) atoms
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb"
Summary of feedback from opening /Users/xiang.feng/OneDrive - Van Andel
Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.131 14910
Ignored bad PDB record found on line 23
ANGLE : 1.274 16.764 20213
Ignored bad PDB record found on line 24
CHIRALITY : 0.073 0.354 2267
16 messages similar to the above omitted
Chain information for mono_Apo-coot-20.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select #6
14600 atoms, 14859 bonds, 97 pseudobonds, 1881 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel stick
Changed 14600 atom styles
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> close #1
> open "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb"
Summary of feedback from opening /Users/xiang.feng/OneDrive - Van Andel
Institute/NiFeABCSL/Revision/mono_Apo-coot-20.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.131 14910
Ignored bad PDB record found on line 23
ANGLE : 1.274 16.764 20213
Ignored bad PDB record found on line 24
CHIRALITY : 0.073 0.354 2267
16 messages similar to the above omitted
Chain information for mono_Apo-coot-20.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!1 atoms
> show #!1 cartoons
> close #4
> close #5
> select ::name="3NI"::name="FCO"::name="FES"::name="SF4"
68 atoms, 87 bonds, 6 pseudobonds, 11 residues, 2 models selected
> show sel atoms
> select ::name="CYS"
324 atoms, 271 bonds, 54 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 324 atom styles
> color sel byhetero
> color #1/B salmon
> color #1/B salmon
> color #1/C light green
> color #1/A slateblue
> color #1/D orange
> color #1/E grey
> color sel byhetero
> select #1
14600 atoms, 14918 bonds, 7 pseudobonds, 1881 residues, 3 models selected
> color sel byhetero
> show #!2 models
> select #2
2 models selected
> select clear
> volume #2 level 0.1522
> volume #2 level 0.1613
> select /E:201@FE4
1 atom, 1 residue, 1 model selected
> select add /E:85@SG
2 atoms, 2 residues, 1 model selected
> distance /E:201@FE4 /E:85@SG
Distance between /E SF4 201 FE4 and CYS 85 SG: 2.056Å
> show #!3 models
> hide #3.1 models
> select /E:201@FE2
1 atom, 1 residue, 1 model selected
> select add /E:14@SG
2 atoms, 2 residues, 1 model selected
> distance /E:201@FE2 /E:14@SG
Distance between /E SF4 201 FE2 and CYS 14 SG: 1.949Å
> select add /E:149@SG
3 atoms, 3 residues, 1 model selected
> select add /E:201@FE3
4 atoms, 3 residues, 1 model selected
Exactly two atoms must be selected!
> select #2
2 models selected
> select clear
[Repeated 2 time(s)]
> select /E:201@FE3
1 atom, 1 residue, 1 model selected
> select add /E:149@SG
2 atoms, 2 residues, 1 model selected
> distance /E:201@FE3 /E:149@SG
Distance between /E SF4 201 FE3 and CYS 149 SG: 1.511Å
> select /E:201@FE1
1 atom, 1 residue, 1 model selected
> select add /E:17@SG
2 atoms, 2 residues, 1 model selected
> distance /E:201@FE1 /E:17@SG
Distance between /E SF4 201 FE1 and CYS 17 SG: 1.864Å
> select clear
> lighting shadows false
> select clear
> save /Users/xiang.feng/Desktop/SF4_E.png supersample 4 width 800 height 800
> transparentBackground true
> view
> select #1/A:1101
8 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> select #1/A:98
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select /A:1101@FE2
1 atom, 1 residue, 1 model selected
> select add /A:98@ND1
2 atoms, 2 residues, 1 model selected
> distance /A:1101@FE2 /A:98@ND1
Distance between /A SF4 1101 FE2 and HIS 98 ND1: 1.871Å
> select /A:1101@FE3
1 atom, 1 residue, 1 model selected
> select add /A:109@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1101@FE3 /A:109@SG
Distance between /A SF4 1101 FE3 and CYS 109 SG: 2.037Å
> select add /A:103@SG
3 atoms, 3 residues, 1 model selected
Exactly two atoms must be selected!
> select add /A:1101@FE1
4 atoms, 3 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select /A:1101@FE1
1 atom, 1 residue, 1 model selected
> select add /A:103@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1101@FE1 /A:103@SG
Distance between /A SF4 1101 FE1 and CYS 103 SG: 2.449Å
> select /A:100@SG
1 atom, 1 residue, 1 model selected
> select add /A:1101@S3
2 atoms, 2 residues, 1 model selected
> select /A:1101@FE4
1 atom, 1 residue, 1 model selected
> select add /A:100@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1101@FE4 /A:100@SG
Distance between /A SF4 1101 FE4 and CYS 100 SG: 1.978Å
> select clear
> save /Users/xiang.feng/Desktop/SF4_A3.png supersample 4 width 800 height 800
> transparentBackground true
> view
> select #1/A:801
8 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> select /A:801@FE1
1 atom, 1 residue, 1 model selected
> select add /A:202@SG
2 atoms, 2 residues, 1 model selected
> distance /A:801@FE1 /A:202@SG
Distance between /A SF4 801 FE1 and CYS 202 SG: 2.256Å
> select /A:801@FE3
1 atom, 1 residue, 1 model selected
> select add /A:154@SG
2 atoms, 2 residues, 1 model selected
> distance /A:801@FE3 /A:154@SG
Distance between /A SF4 801 FE3 and CYS 154 SG: 1.971Å
> select /A:801@FE2
1 atom, 1 residue, 1 model selected
> select add /A:148@SG
2 atoms, 2 residues, 1 model selected
> distance /A:801@FE2 /A:148@SG
Distance between /A SF4 801 FE2 and CYS 148 SG: 1.925Å
> select /A:801@FE4
1 atom, 1 residue, 1 model selected
> select add /A:151@SG
2 atoms, 2 residues, 1 model selected
> distance /A:801@FE4 /A:151@SG
Distance between /A SF4 801 FE4 and CYS 151 SG: 1.748Å
Drag select of 2 TightTargetVol.mrc
> select clear
[Repeated 1 time(s)]
> save /Users/xiang.feng/Desktop/SF4_A2.png supersample 4 width 800 height 800
> transparentBackground true
> view
> hide #!2 models
> select /B:601@S3
1 atom, 1 residue, 1 model selected
> select #1/B:601
8 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select /B:601@FE4
1 atom, 1 residue, 1 model selected
> select add /B:455@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE4 /B:455@SG
Distance between /B SF4 601 FE4 and CYS 455 SG: 1.717Å
> select /B:601@FE2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add /B:501@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE2 /B:501@SG
Distance between /B SF4 601 FE2 and CYS 501 SG: 1.929Å
> select /B:601@FE1
1 atom, 1 residue, 1 model selected
> select add /B:458@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE1 /B:458@SG
Distance between /B SF4 601 FE1 and CYS 458 SG: 1.269Å
> select /B:601@FE3
1 atom, 1 residue, 1 model selected
> select add /B:461@SG
2 atoms, 2 residues, 1 model selected
> distance /B:601@FE3 /B:461@SG
Distance between /B SF4 601 FE3 and CYS 461 SG: 2.866Å
> show #!2 models
> select clear
> save /Users/xiang.feng/Desktop/SF4_B1.png supersample 4 width 800 height 800
> transparentBackground true
> view
> hide #!2 models
> select /A:701@FE2
1 atom, 1 residue, 1 model selected
> select add /A:64@SG
2 atoms, 2 residues, 1 model selected
> distance /A:701@FE2 /A:64@SG
Distance between /A FES 701 FE2 and CYS 64 SG: 2.176Å
> select /A:50@SG
1 atom, 1 residue, 1 model selected
> select add /A:701@FE2
2 atoms, 2 residues, 1 model selected
> distance /A:50@SG /A:701@FE2
Distance between /A CYS 50 SG and FES 701 FE2: 2.016Å
> select /A:36@SG
1 atom, 1 residue, 1 model selected
> select add /A:701@FE1
2 atoms, 2 residues, 1 model selected
> distance /A:36@SG /A:701@FE1
Distance between /A CYS 36 SG and FES 701 FE1: 1.389Å
> select /A:47@SG
1 atom, 1 residue, 1 model selected
> select add /A:701@FE1
2 atoms, 2 residues, 1 model selected
> distance /A:47@SG /A:701@FE1
Distance between /A CYS 47 SG and FES 701 FE1: 2.616Å
> hide #!3 models
> show #!3 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> select #1/A:701
4 atoms, 4 bonds, 1 pseudobond, 1 residue, 2 models selected
> view sel
> show #!2 models
> volume #2 style mesh sdLevel 3 surfaceSmoothing true smoothingIterations 4
> smoothLines true subdivideSurface true
> select clear
> save /Users/xiang.feng/Desktop/SF4_A1.png supersample 4 width 800 height 800
> transparentBackground true
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> volume #2 level 0.22
> volume #2 level 0.3
> volume #2 level 0.5
> hide #3.1 models
> volume #2 style mesh sdLevel 4 surfaceSmoothing true smoothingIterations 4
> smoothLines true subdivideSurface true
> save /Users/xiang.feng/Desktop/SF4_A1.png supersample 4 width 800 height 800
> transparentBackground true
> view
> hide #!2 models
> select #1/A:901
8 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select /A:901@FE1
1 atom, 1 residue, 1 model selected
> select add /A:195@SG
2 atoms, 2 residues, 1 model selected
> distance /A:901@FE1 /A:195@SG
Distance between /A SF4 901 FE1 and CYS 195 SG: 1.204Å
> select /A:901@FE2
1 atom, 1 residue, 1 model selected
> select add /A:158@SG
2 atoms, 2 residues, 1 model selected
> distance /A:901@FE2 /A:158@SG
Distance between /A SF4 901 FE2 and CYS 158 SG: 1.634Å
> select /A:901@FE3
1 atom, 1 residue, 1 model selected
> select add /A:198@SG
2 atoms, 2 residues, 1 model selected
> distance /A:901@FE3 /A:198@SG
Distance between /A SF4 901 FE3 and CYS 198 SG: 1.737Å
> select /A:901@FE4
1 atom, 1 residue, 1 model selected
> select add /A:192@SG
2 atoms, 2 residues, 1 model selected
> distance /A:901@FE4 /A:192@SG
Distance between /A SF4 901 FE4 and CYS 192 SG: 1.756Å
> show #!2 models
> select clear
> save /Users/xiang.feng/Desktop/SF4_A5.png supersample 4 width 800 height 800
> transparentBackground true
> hide #!2 models
> view
> select #1/A:1001
8 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> select /A:232@SG
1 atom, 1 residue, 1 model selected
> select add /A:1001@FE2
2 atoms, 2 residues, 1 model selected
> distance /A:232@SG /A:1001@FE2
Distance between /A CYS 232 SG and SF4 1001 FE2: 1.804Å
> select /A:1001@FE3
1 atom, 1 residue, 1 model selected
> select add /A:229@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1001@FE3 /A:229@SG
Distance between /A SF4 1001 FE3 and CYS 229 SG: 1.851Å
> select add /A:264@SG
3 atoms, 3 residues, 1 model selected
Exactly two atoms must be selected!
> select /A:1001@FE1
1 atom, 1 residue, 1 model selected
> select add /A:264@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1001@FE1 /A:264@SG
Distance between /A SF4 1001 FE1 and CYS 264 SG: 1.511Å
> select /A:1001@FE4
1 atom, 1 residue, 1 model selected
> select add /A:236@SG
2 atoms, 2 residues, 1 model selected
> distance /A:1001@FE4 /A:236@SG
Distance between /A SF4 1001 FE4 and CYS 236 SG: 1.926Å
> select clear
> show #!2 models
> save /Users/xiang.feng/Desktop/SF4_A5.png supersample 4 width 800 height 800
> transparentBackground true
> hide #!2 models
> view
> select clear
> select /C:501@FE1
1 atom, 1 residue, 1 model selected
> select #1/C:501
4 atoms, 4 bonds, 1 pseudobond, 1 residue, 2 models selected
> view sel
> show #!2 models
> select clear
> select /C:501@FE2
1 atom, 1 residue, 1 model selected
> select add /C:82@SG
2 atoms, 2 residues, 1 model selected
> distance /C:501@FE2 /C:82@SG
Distance between /C FES 501 FE2 and CYS 82 SG: 1.739Å
> select #2
2 models selected
> select clear
> select /C:501@FE2
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select add /C:87@SG
2 atoms, 2 residues, 1 model selected
> distance /C:501@FE2 /C:87@SG
Distance between /C FES 501 FE2 and CYS 87 SG: 2.148Å
> select /C:501@FE1
1 atom, 1 residue, 1 model selected
> select add /C:123@SG
2 atoms, 2 residues, 1 model selected
> distance /C:501@FE1 /C:123@SG
Distance between /C FES 501 FE1 and CYS 123 SG: 1.605Å
> select /C:127@SG
1 atom, 1 residue, 1 model selected
> select add /C:501@FE1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance /C:127@SG /C:501@FE1
Distance between /C CYS 127 SG and FES 501 FE1: 2.105Å
> show #!2 models
> volume #2 style mesh sdLevel 5 surfaceSmoothing true smoothingIterations 4
> smoothLines true subdivideSurface true
> select #2
2 models selected
> select clear
[Repeated 1 time(s)]
> save /Users/xiang.feng/Desktop/SF4_C1.png supersample 4 width 800 height 800
> transparentBackground true
> hide #!2 models
> view
> save "/Users/xiang.feng/OneDrive - Van Andel
> Institute/NiFeABCSL/Revision/revised_supplementary_fig9_new.cxs"
——— End of log from Tue Nov 23 17:36:16 2021 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-3.10.22
OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
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Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.4 GHz
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L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
Boot ROM Version: 429.140.8.0.0
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 105 days 1:34
Graphics/Displays:
Radeon Pro 570:
Chipset Model: Radeon Pro 570
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D000AA-931
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Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
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Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.2
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
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ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202110191144
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.3
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.2
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.4
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.6
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.8.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash during or after saving session |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Same report as of #5776. Identical crash report (same exact time...). Not sure how it was possible to report the crash twice. This report probably has the correct log, ending with saving a session.