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Opened 4 years ago
Closed 4 years ago
#5368 closed defect (can't reproduce)
Crash removing destroyed tool/dock widget
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | 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.dev202110050748 (2021-10-05 07:48:25 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001073dedc0 (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 2285 in destroy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2156 in _destroy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 787 in remove_tool
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 353 in remove_tool
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
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 1016 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 [1077]
Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [1077]
User ID: 501
Date/Time: 2021-10-08 09:53:42.264 -0400
OS Version: Mac OS X 10.15.7 (19H2)
Report Version: 12
Anonymous UUID: 7514A429-EA01-7F5A-AA39-25127A0E7BE5
Sleep/Wake UUID: 006115E3-29B8-47A7-9532-225EEB0E4CAF
Time Awake Since Boot: 2300 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 0x000002ab6c1e5608
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x2ab6c1e5608:
VM_ALLOCATE 0000000145f71000-0000000146514000 [ 5772K] rw-/rwx 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 0x00007fff6c72e33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6c7eae60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6c64593e raise + 26
3 libsystem_platform.dylib 0x00007fff6c7df5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtWidgets 0x000000011149a741 QMainWindow::removeDockWidget(QDockWidget*) + 33
6 QtWidgets.abi3.so 0x0000000110f7429f meth_QMainWindow_removeDockWidget(_object*, _object*) + 95
7 org.python.python 0x000000010500706d cfunction_call + 125
8 org.python.python 0x0000000104fc817d _PyObject_MakeTpCall + 365
9 org.python.python 0x00000001050a061c call_function + 876
10 org.python.python 0x000000010509dab3 _PyEval_EvalFrameDefault + 25219
11 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
12 org.python.python 0x00000001050a058c call_function + 732
13 org.python.python 0x000000010509da92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
15 org.python.python 0x00000001050a058c call_function + 732
16 org.python.python 0x000000010509da92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
18 org.python.python 0x0000000104fca98a method_vectorcall + 202
19 org.python.python 0x00000001050a058c call_function + 732
20 org.python.python 0x000000010509dab3 _PyEval_EvalFrameDefault + 25219
21 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
22 org.python.python 0x0000000104fca98a method_vectorcall + 202
23 org.python.python 0x00000001050a058c call_function + 732
24 org.python.python 0x000000010509dab3 _PyEval_EvalFrameDefault + 25219
25 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
26 org.python.python 0x0000000104fca9d2 method_vectorcall + 274
27 QtCore.abi3.so 0x0000000106513957 PyQtSlot::call(_object*, _object*) const + 39
28 QtCore.abi3.so 0x0000000106513866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
29 QtCore.abi3.so 0x0000000106514455 PyQtSlotProxy::unislot(void**) + 85
30 QtCore.abi3.so 0x00000001065143ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
31 QtCore 0x00000001068f7f6e void doActivate(QObject*, int, void**) + 1118
32 QtWidgets 0x00000001114e1acc QDialogButtonBoxPrivate::_q_handleButtonClicked() + 780
33 QtCore 0x00000001068f80d5 void doActivate(QObject*, int, void**) + 1477
34 QtWidgets 0x00000001114361df QAbstractButtonPrivate::emitClicked() + 111
35 QtWidgets 0x0000000111436059 QAbstractButtonPrivate::click() + 233
36 QtWidgets 0x000000011143720f QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 271
37 QtWidgets 0x0000000111386dfd QWidget::event(QEvent*) + 445
38 QtWidgets 0x000000011134c9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
39 QtWidgets 0x000000011134f755 QApplication::notify(QObject*, QEvent*) + 6965
40 QtWidgets.abi3.so 0x0000000110effdb9 sipQApplication::notify(QObject*, QEvent*) + 233
41 QtCore 0x00000001068c4a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
42 QtWidgets 0x000000011134d310 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 896
43 QtWidgets 0x00000001113a6022 QWidgetWindow::handleMouseEvent(QMouseEvent*) + 3266
44 QtWidgets 0x00000001113a46e9 QWidgetWindow::event(QEvent*) + 233
45 QtWidgets 0x000000011134c9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
46 QtWidgets 0x000000011134de11 QApplication::notify(QObject*, QEvent*) + 497
47 QtWidgets.abi3.so 0x0000000110effdb9 sipQApplication::notify(QObject*, QEvent*) + 233
48 QtCore 0x00000001068c4a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
49 QtGui 0x00000001119b9e2e QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 3534
50 QtGui 0x000000011199ed7b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219
51 libqcocoa.dylib 0x000000011f213260 QCocoaEventDispatcherPrivate::processPostedEvents() + 320
52 libqcocoa.dylib 0x000000011f2139c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
53 com.apple.CoreFoundation 0x00007fff32548d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
54 com.apple.CoreFoundation 0x00007fff32548cf1 __CFRunLoopDoSource0 + 103
55 com.apple.CoreFoundation 0x00007fff32548b0b __CFRunLoopDoSources0 + 209
56 com.apple.CoreFoundation 0x00007fff3254783a __CFRunLoopRun + 927
57 com.apple.CoreFoundation 0x00007fff32546e3e CFRunLoopRunSpecific + 462
58 com.apple.HIToolbox 0x00007fff31173abd RunCurrentEventLoopInMode + 292
59 com.apple.HIToolbox 0x00007fff311736f4 ReceiveNextEventCommon + 359
60 com.apple.HIToolbox 0x00007fff31173579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
61 com.apple.AppKit 0x00007fff2f7b9039 _DPSNextEvent + 883
62 com.apple.AppKit 0x00007fff2f7b7880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
63 com.apple.AppKit 0x00007fff2f7a958e -[NSApplication run] + 658
64 libqcocoa.dylib 0x000000011f21262f QCocoaEventDispatcher::processEvents(QFlags) + 2495
65 QtCore 0x00000001068c0acf QEventLoop::exec(QFlags) + 431
66 QtCore 0x00000001068c5042 QCoreApplication::exec() + 130
67 QtWidgets.abi3.so 0x0000000110ff1702 meth_QApplication_exec_(_object*, _object*) + 82
68 org.python.python 0x000000010500706d cfunction_call + 125
69 org.python.python 0x0000000104fc817d _PyObject_MakeTpCall + 365
70 org.python.python 0x00000001050a061c call_function + 876
71 org.python.python 0x000000010509dab3 _PyEval_EvalFrameDefault + 25219
72 org.python.python 0x0000000104fc8948 function_code_fastcall + 104
73 org.python.python 0x0000000104fca98a method_vectorcall + 202
74 org.python.python 0x00000001050a058c call_function + 732
75 org.python.python 0x000000010509dab3 _PyEval_EvalFrameDefault + 25219
76 org.python.python 0x00000001050a1283 _PyEval_EvalCode + 2611
77 org.python.python 0x0000000104fc88d1 _PyFunction_Vectorcall + 289
78 org.python.python 0x00000001050a058c call_function + 732
79 org.python.python 0x000000010509db4b _PyEval_EvalFrameDefault + 25371
80 org.python.python 0x00000001050a1283 _PyEval_EvalCode + 2611
81 org.python.python 0x000000010509770b PyEval_EvalCode + 139
82 org.python.python 0x0000000105094592 builtin_exec + 626
83 org.python.python 0x000000010500686a cfunction_vectorcall_FASTCALL + 218
84 org.python.python 0x00000001050a058c call_function + 732
85 org.python.python 0x000000010509db4b _PyEval_EvalFrameDefault + 25371
86 org.python.python 0x00000001050a1283 _PyEval_EvalCode + 2611
87 org.python.python 0x0000000104fc88d1 _PyFunction_Vectorcall + 289
88 org.python.python 0x00000001050a058c call_function + 732
89 org.python.python 0x000000010509db4b _PyEval_EvalFrameDefault + 25371
90 org.python.python 0x00000001050a1283 _PyEval_EvalCode + 2611
91 org.python.python 0x0000000104fc88d1 _PyFunction_Vectorcall + 289
92 org.python.python 0x0000000105106e20 pymain_run_module + 208
93 org.python.python 0x0000000105106537 Py_RunMain + 1431
94 org.python.python 0x0000000105106b3f pymain_main + 223
95 org.python.python 0x0000000105106a4b Py_Main + 43
96 edu.ucsf.cgl.ChimeraX 0x0000000104f7edc8 main + 120
97 libdyld.dylib 0x00007fff6c5e6cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff6c72a882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c7eb425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000107751a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 2:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6c730b96 kevent64 + 10
1 QtWebEngineCore 0x0000000114b47e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000114b47cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000114adba94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 3:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114ae5778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000114ae6150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000114ae5c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 4:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6c730b96 kevent64 + 10
1 QtWebEngineCore 0x0000000114b47e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000114b47cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000118a14f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 6:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114ae5778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000114ae6150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000114ae5cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 7:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6c72a882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6c7eb425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000114b34e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x0000000115dec5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 8:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114a6520f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 9:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6c730b96 kevent64 + 10
1 QtWebEngineCore 0x0000000114b47e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000114b47cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 11:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114ae576a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000114ae6150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x0000000114ae5d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 14:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114a651db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000114ad062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000114a947cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000114aefa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 16:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff32548ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff325479c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff32546e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2f95a954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 QtWebEngineCore 0x0000000114b3d492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000114b3d2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000114ae576a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000114ae5e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x0000000114ae5c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x0000000114b38e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6c7eb109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6c7e6b8b thread_start + 15
Thread 18:
0 libsystem_pthread.dylib 0x00007fff6c7e6b68 start_wqthread + 0
Thread 19:: Dispatch queue: com.apple.root.user-interactive-qos
0 libsystem_kernel.dylib 0x00007fff6c727dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6c728170 mach_msg + 60
2 com.apple.QuartzCore 0x00007fff3e038825 CA::CA_BLOCKED_WAITING_FOR_CLIENT_FENCES(unsigned int, unsigned long) + 170
3 com.apple.QuartzCore 0x00007fff3e01a72a CA::Context::commit_transaction(CA::Transaction*, double) + 1906
4 com.apple.QuartzCore 0x00007fff3e018cf0 CA::Transaction::commit() + 644
5 com.apple.AppKit 0x00007fff2f811384 NSPerformVisuallyAtomicChange + 154
6 com.apple.AppKit 0x00007fff2fa5fe1c __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 80
7 libdispatch.dylib 0x00007fff6c58c6c4 _dispatch_call_block_and_release + 12
8 libdispatch.dylib 0x00007fff6c58d658 _dispatch_client_callout + 8
9 libdispatch.dylib 0x00007fff6c59baa8 _dispatch_root_queue_drain + 663
10 libdispatch.dylib 0x00007fff6c59c097 _dispatch_worker_thread2 + 92
11 libsystem_pthread.dylib 0x00007fff6c7e79f7 _pthread_wqthread + 220
12 libsystem_pthread.dylib 0x00007fff6c7e6b77 start_wqthread + 15
Thread 20:
0 libsystem_pthread.dylib 0x00007fff6c7e6b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001073dedc0 rcx: 0x00007fb8ea955a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fb8ea955a80 rsp: 0x00007fb8ea955a58
r8: 0x00007fb8ea955f48 r9: 0xffc8211a58315125 r10: 0x00000001073dedc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fb8e8c047f0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6c72e33a rfl: 0x0000000000000246 cr2: 0x00007fb8ea955f48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff6a708000 - 0x7fff6a720ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6a738000 - 0x7fff6a7dfff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6a7e0000 - 0x7fff6aa42ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6adaf000 - 0x7fff6addefff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6af0e000 - 0x7fff6b38aff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6b38b000 - 0x7fff6b3a2fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6b42b000 - 0x7fff6b45efde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6b45f000 - 0x7fff6b460ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6b471000 - 0x7fff6b475fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6b478000 - 0x7fff6b4aeff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff6b4ee000 - 0x7fff6b4fcff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6b4fd000 - 0x7fff6b500ff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib
0x7fff6b501000 - 0x7fff6b503fff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib
0x7fff6b532000 - 0x7fff6b54afff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6b54c000 - 0x7fff6b590ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff6b591000 - 0x7fff6b5a3ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6b5a4000 - 0x7fff6b5a5ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6b5a6000 - 0x7fff6b790ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff6b884000 - 0x7fff6b8b1ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff6b986000 - 0x7fff6b9e0ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff6b9e1000 - 0x7fff6b9e4ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6b9e5000 - 0x7fff6b9f2ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff6b9f8000 - 0x7fff6badafff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff6bade000 - 0x7fff6bb06fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff6bb07000 - 0x7fff6bb19ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6c3c8000 - 0x7fff6c3cdff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6c3ce000 - 0x7fff6c3d9fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6c3da000 - 0x7fff6c3e1fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6c3e2000 - 0x7fff6c3ebff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6c3ec000 - 0x7fff6c47efdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff6c58b000 - 0x7fff6c5cbff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6c5cc000 - 0x7fff6c602fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff6c603000 - 0x7fff6c603ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6c604000 - 0x7fff6c610ff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib
0x7fff6c611000 - 0x7fff6c611ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff6c612000 - 0x7fff6c617ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6c618000 - 0x7fff6c61aff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff6c61b000 - 0x7fff6c61cff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6c61d000 - 0x7fff6c634ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff6c635000 - 0x7fff6c635ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6c636000 - 0x7fff6c6bdfff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff6c6be000 - 0x7fff6c6c1ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff6c6c2000 - 0x7fff6c6c5fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6c6c6000 - 0x7fff6c6cefff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff6c6cf000 - 0x7fff6c6d6fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6c6d7000 - 0x7fff6c6d8ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6c6d9000 - 0x7fff6c726ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff6c727000 - 0x7fff6c753ff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff6c754000 - 0x7fff6c79bfff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6c79c000 - 0x7fff6c7c3fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6c7c4000 - 0x7fff6c7d1ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6c7d2000 - 0x7fff6c7dbff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6c7dc000 - 0x7fff6c7e4fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6c7e5000 - 0x7fff6c7effff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6c7f0000 - 0x7fff6c7f4ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6c7f5000 - 0x7fff6c7f7fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6c7f8000 - 0x7fff6c7ffffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6c800000 - 0x7fff6c816ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff6c818000 - 0x7fff6c81dff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6c81e000 - 0x7fff6c853ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 2
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: 1369
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=967.5M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=967.5M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 880K 2
CG image 172K 18
CoreAnimation 132K 15
CoreGraphics 8K 1
CoreImage 28K 3
CoreServices 12K 1
CoreUI image data 3376K 28
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 610.7M 602
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 384K 1 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 80K 20
Stack 130.7M 21
Stack Guard 56.0M 1
VM_ALLOCATE 92.9M 82
__DATA 51.8M 548
__DATA_CONST 40K 4
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 480.2M 145
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 525.4M 513
__UNICODE 564K 1
mapped file 392.4M 54
shared memory 2844K 23
=========== ======= =======
TOTAL 2.5G 2108
TOTAL, minus reserved VM space 2.3G 2108
===== Log before crash start =====
> lighting shadows false
> lighting depthCue false
> set bgColor alice blue
> ui mousemode right zoom
> windowsize 570 570
> camera ortho
> color name bluishwhite rgb(201, 218, 222)
Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade
UCSF ChimeraX version: 1.3.dev202110050748 (2021-10-05)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/AphAB/3szp_WT.pdb1"
3szp_WT.pdb1 title:
Full-length structure of the vibrio cholerae virulence activator, APHB, A
member of the LTTR protein family [more info...]
Chain information for 3szp_WT.pdb1
---
Chain | Description
1.1/A 1.2/A | No description available
1.1/B 1.2/B | No description available
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/AphAB/1yg2.pdb1"
1yg2.pdb1 title:
Structure of the vibrio cholerae virulence activator APHA [more info...]
Chain information for 1yg2.pdb1
---
Chain | Description
2.1/A 2.2/A | No description available
> delete #@
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #2
> select #2
1 model selected
> ~select #2
Nothing selected
> close #2
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/AphAB/5fhk.cif"
5fhk.cif title:
Regulatory domain of AphB in Vibrio vulnificus [more info...]
Chain information for 5fhk.cif #2
---
Chain | Description | UniProt
A B C D E F | LysR family transcriptional regulator | A0A087IWB4_VIBVL
5fhk.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> close #2
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/AphAB/3t1b_N100E.cif"
3t1b_N100E.cif title:
Crystal structure of the full-length AphB N100E variant [more info...]
Chain information for 3t1b_N100E.cif #2
---
Chain | Description | UniProt
A B C D | Transcriptional regulator, LysR family | Q9KT56_VIBCH
> ui tool show Matchmaker
> matchmaker #!2 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3szp_WT.pdb1, chain A (#1.1) with 3t1b_N100E.cif, chain D (#2),
sequence alignment score = 1448.7
RMSD between 198 pruned atom pairs is 0.539 angstroms; (across all 289 pairs:
26.203)
> matchmaker #!2 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3szp_WT.pdb1, chain A (#1.2) with 3t1b_N100E.cif, chain D (#2),
sequence alignment score = 1448.7
RMSD between 198 pruned atom pairs is 0.539 angstroms; (across all 289 pairs:
26.203)
===== Log before crash end =====
Log:
> lighting shadows false
> lighting depthCue false
> set bgColor alice blue
> ui mousemode right zoom
> windowsize 570 570
> camera ortho
> color name bluishwhite rgb(201, 218, 222)
Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade
UCSF ChimeraX version: 1.3.dev202110050748 (2021-10-05)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/FadR/4p9u.cif"
4p9u.cif title:
FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in
Complex with DNA [more info...]
Chain information for 4p9u.cif #1
---
Chain | Description | UniProt
A B E F | Fatty acid metabolism regulator protein | FADR_VIBCH
C G | DNA (31-mer) |
D H | DNA (31-mer) |
4p9u.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/FadR/4p96.cif"
4p96.cif title:
FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae [more
info...]
Chain information for 4p96.cif #2
---
Chain | Description | UniProt
A B | Fatty acid metabolism regulator protein | G6ZTG9_VIBCL
> open "/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio
> virulence regulator chapter/FadR/4pdk.cif"
Summary of feedback from opening
/Users/charlesmidgett/Charles_stuff/Virulence/writing/2021 vibrio virulence
regulator chapter/FadR/4pdk.cif
---
note | Fetching CCD 3VV from http://ligand-expo.rcsb.org/reports/3/3VV/3VV.cif
4pdk.cif title:
FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in
Complex with oleoyl-CoA [more info...]
Chain information for 4pdk.cif #3
---
Chain | Description | UniProt
A B | Fatty acid metabolism regulator protein | FADR_VIBCH
Non-standard residues in 4pdk.cif #3
---
3VV —
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}
(9Z)-octadec-9-enethioate (non-preferred name) (oleoyl-CoA)
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 192.0.0.0.0
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 42 minutes
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1
charset-normalizer: 2.0.6
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.1
ChimeraX-AtomicLibrary: 4.1.4
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
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
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.dev202110050748
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
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: 2.1.1
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: 2.0.1
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
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: 2.6.3
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: 2.4.4
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-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: 1.13.3
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: 3.2
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 → UI |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash removing destroyed tool/dock widget |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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