![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5147 closed defect (duplicate)
Graphics hardware encountered an error and was reset
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000111c3a5c0 (most recent call first):
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/opengl.py", line 2692 in draw_elements
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 1695 in draw
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 823 in _draw_geometry
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 758 in draw_self
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 751 in draw
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/sideview/tool.py", line 483 in draw
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 1511 in _draw_multiple
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py", line 1549 in draw_overlays
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/view.py", line 172 in draw
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/sideview/tool.py", line 276 in render
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/sideview/tool.py", line 112 in _redraw
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130 in invoke
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 213 in _activate
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 182 in activate
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 350 in activate_trigger
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/updateloop.py", line 88 in draw_new_frame
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/updateloop.py", line 138 in _redraw_timer_callback
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 87 in _run_code
File "/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 194 in _run_module_as_main
Process: ChimeraX [11597]
Path: /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.2.3 (1.2.3.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [11597]
User ID: 479104604
Date/Time: 2021-09-01 17:29:59.326 -0700
OS Version: Mac OS X 10.14.6 (18G87)
Report Version: 12
Anonymous UUID: 122A6F6A-D537-C9DF-0F9A-C6FAB78E30CD
Time Awake Since Boot: 1300000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics hardware encountered an error and was reset: 0x0000002b
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff703a62c6 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff70461bf1 pthread_kill + 284
2 libsystem_c.dylib 0x00007fff702c3d8a raise + 26
3 libsystem_platform.dylib 0x00007fff70456b5d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff703106a6 abort + 127
6 libGPUSupportMercury.dylib 0x00007fff5f37f240 gpusGenerateCrashLog + 166
7 com.apple.GeForceGLDriver 0x00007fff3f477f3f 0x7fff3f170000 + 3178303
8 libGPUSupportMercury.dylib 0x00007fff5f380730 gpusSubmitDataBuffers + 490
9 com.apple.GeForceGLDriver 0x00007fff3f473415 0x7fff3f170000 + 3159061
10 com.apple.GeForceGLDriver 0x00007fff3f472881 gldUpdateDispatch + 241
11 GLEngine 0x00007fff4e07cbe7 gleDoDrawDispatchCoreGL3 + 630
12 GLEngine 0x00007fff4e032f27 glDrawElementsInstanced_ACC_GL3Exec + 225
13 _ctypes.cpython-38-darwin.so 0x0000000119b5cf97 ffi_call_unix64 + 79
14 _ctypes.cpython-38-darwin.so 0x0000000119b5d7f8 ffi_call + 872
15 _ctypes.cpython-38-darwin.so 0x0000000119b57df2 _ctypes_callproc + 962
16 _ctypes.cpython-38-darwin.so 0x0000000119b51b90 PyCFuncPtr_call + 1152
17 org.python.python 0x000000010e152ef2 PyObject_Call + 162
18 org.python.python 0x000000010e1a8c19 slot_tp_call + 201
19 wrapper.cpython-38-darwin.so 0x00000001301a0971 __Pyx_PyObject_Call + 97
20 wrapper.cpython-38-darwin.so 0x00000001301ad7fd __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 765
21 latebind.cpython-38-darwin.so 0x0000000130209041 __Pyx_PyObject_Call + 97
22 latebind.cpython-38-darwin.so 0x00000001302085ce __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 302
23 org.python.python 0x000000010e152a85 _PyObject_MakeTpCall + 373
24 org.python.python 0x000000010e221665 call_function + 533
25 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
26 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
27 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
28 org.python.python 0x000000010e22160c call_function + 444
29 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
30 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
31 org.python.python 0x000000010e22160c call_function + 444
32 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
33 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
34 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
35 org.python.python 0x000000010e155a9a method_vectorcall + 170
36 org.python.python 0x000000010e22160c call_function + 444
37 org.python.python 0x000000010e21e598 _PyEval_EvalFrameDefault + 25976
38 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
39 org.python.python 0x000000010e22160c call_function + 444
40 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
41 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
42 org.python.python 0x000000010e22160c call_function + 444
43 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
44 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
45 org.python.python 0x000000010e22160c call_function + 444
46 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
47 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
48 org.python.python 0x000000010e22160c call_function + 444
49 org.python.python 0x000000010e21e505 _PyEval_EvalFrameDefault + 25829
50 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
51 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
52 org.python.python 0x000000010e22160c call_function + 444
53 org.python.python 0x000000010e21e505 _PyEval_EvalFrameDefault + 25829
54 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
55 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
56 org.python.python 0x000000010e22160c call_function + 444
57 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
58 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
59 org.python.python 0x000000010e155a9a method_vectorcall + 170
60 org.python.python 0x000000010e22160c call_function + 444
61 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
62 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
63 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
64 org.python.python 0x000000010e155a9a method_vectorcall + 170
65 org.python.python 0x000000010e22160c call_function + 444
66 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
67 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
68 org.python.python 0x000000010e22160c call_function + 444
69 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
70 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
71 org.python.python 0x000000010e22160c call_function + 444
72 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
73 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
74 org.python.python 0x000000010e22160c call_function + 444
75 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
76 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
77 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
78 org.python.python 0x000000010e22160c call_function + 444
79 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
80 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
81 org.python.python 0x000000010e22160c call_function + 444
82 org.python.python 0x000000010e21e44a _PyEval_EvalFrameDefault + 25642
83 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
84 org.python.python 0x000000010e155adb method_vectorcall + 235
85 org.python.python 0x000000010e152dad PyVectorcall_Call + 109
86 QtCore.abi3.so 0x000000011c5c1957 PyQtSlot::call(_object*, _object*) const + 39
87 QtCore.abi3.so 0x000000011c5c1866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
88 QtCore.abi3.so 0x000000011c5c2455 PyQtSlotProxy::unislot(void**) + 85
89 QtCore.abi3.so 0x000000011c5c23ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
90 QtCore 0x000000011c9a5f6e void doActivate(QObject*, int, void**) + 1118
91 QtCore 0x000000011c9af4c2 QTimer::timerEvent(QTimerEvent*) + 98
92 QtCore.abi3.so 0x000000011c4aabf9 sipQTimer::timerEvent(QTimerEvent*) + 121
93 QtCore 0x000000011c99d85f QObject::event(QEvent*) + 111
94 QtCore.abi3.so 0x000000011c4aaa7a sipQTimer::event(QEvent*) + 186
95 QtWidgets 0x000000011d5c29ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
96 QtWidgets 0x000000011d5c3e11 QApplication::notify(QObject*, QEvent*) + 497
97 QtWidgets.abi3.so 0x000000011d175db9 sipQApplication::notify(QObject*, QEvent*) + 233
98 QtCore 0x000000011c972a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
99 QtCore 0x000000011c9d835f QTimerInfoList::activateTimers() + 991
100 libqcocoa.dylib 0x000000012d53f8f2 QCocoaEventDispatcherPrivate::activateTimersSourceCallback(void*) + 18
101 com.apple.CoreFoundation 0x00007fff44333683 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
102 com.apple.CoreFoundation 0x00007fff44333629 __CFRunLoopDoSource0 + 108
103 com.apple.CoreFoundation 0x00007fff44316feb __CFRunLoopDoSources0 + 195
104 com.apple.CoreFoundation 0x00007fff443165b5 __CFRunLoopRun + 1189
105 com.apple.CoreFoundation 0x00007fff44315ebe CFRunLoopRunSpecific + 455
106 com.apple.HIToolbox 0x00007fff435751ab RunCurrentEventLoopInMode + 292
107 com.apple.HIToolbox 0x00007fff43574ee5 ReceiveNextEventCommon + 603
108 com.apple.HIToolbox 0x00007fff43574c76 _BlockUntilNextEventMatchingListInModeWithFilter + 64
109 com.apple.AppKit 0x00007fff4190d79d _DPSNextEvent + 1135
110 com.apple.AppKit 0x00007fff4190c48b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1361
111 com.apple.AppKit 0x00007fff419065a8 -[NSApplication run] + 699
112 libqcocoa.dylib 0x000000012d54062f QCocoaEventDispatcher::processEvents(QFlags) + 2495
113 QtCore 0x000000011c96eacf QEventLoop::exec(QFlags) + 431
114 QtCore 0x000000011c973042 QCoreApplication::exec() + 130
115 QtWidgets.abi3.so 0x000000011d267702 meth_QApplication_exec_(_object*, _object*) + 82
116 org.python.python 0x000000010e1530c2 cfunction_call_varargs + 290
117 org.python.python 0x000000010e152a85 _PyObject_MakeTpCall + 373
118 org.python.python 0x000000010e221665 call_function + 533
119 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
120 org.python.python 0x000000010e1533d0 function_code_fastcall + 128
121 org.python.python 0x000000010e155a9a method_vectorcall + 170
122 org.python.python 0x000000010e22160c call_function + 444
123 org.python.python 0x000000010e21e46e _PyEval_EvalFrameDefault + 25678
124 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
125 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
126 org.python.python 0x000000010e22160c call_function + 444
127 org.python.python 0x000000010e21e505 _PyEval_EvalFrameDefault + 25829
128 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
129 org.python.python 0x000000010e217f44 PyEval_EvalCode + 100
130 org.python.python 0x000000010e215332 builtin_exec + 626
131 org.python.python 0x000000010e18f5ff cfunction_vectorcall_FASTCALL + 175
132 org.python.python 0x000000010e22160c call_function + 444
133 org.python.python 0x000000010e21e505 _PyEval_EvalFrameDefault + 25829
134 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
135 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
136 org.python.python 0x000000010e22160c call_function + 444
137 org.python.python 0x000000010e21e505 _PyEval_EvalFrameDefault + 25829
138 org.python.python 0x000000010e222454 _PyEval_EvalCodeWithName + 2804
139 org.python.python 0x000000010e15356e _PyFunction_Vectorcall + 270
140 org.python.python 0x000000010e152dad PyVectorcall_Call + 109
141 org.python.python 0x000000010e284eb3 pymain_run_module + 195
142 org.python.python 0x000000010e284585 Py_RunMain + 1413
143 org.python.python 0x000000010e284bdf pymain_main + 223
144 org.python.python 0x000000010e284aeb Py_Main + 43
145 edu.ucsf.cgl.ChimeraX 0x000000010e124dc8 main + 120
146 libdyld.dylib 0x00007fff7026b3d5 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x0000000111f9c27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x0000000111f9c27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x0000000111f9c27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff703a80a6 kevent64 + 10
1 QtWebEngineCore 0x00000001212c1e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001212c1cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000121255a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000012125f778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000121260150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000012125fc44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff703a80a6 kevent64 + 10
1 QtWebEngineCore 0x00000001212c1e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001212c1cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012518ef06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 8:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 QtWebEngineCore 0x00000001212aee18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x00000001225665f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
6 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
7 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 9:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001211df20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 10:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff703a80a6 kevent64 + 10
1 QtWebEngineCore 0x00000001212c1e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001212c1cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 12:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000012125f76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000121260150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x000000012125fd34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001211df1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012124a62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000012120e7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121269a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 17:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 com.apple.GeForceMTLDriver 0x00007fff402cf04e 0x7fff4016b000 + 1458254
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 18:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001212b72cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000012125f76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000012125fe3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x000000012125fc74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 19:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff443171ee __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff4431675c __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff44315ebe CFRunLoopRunSpecific + 455
5 com.apple.AppKit 0x00007fff419154c2 _NSEventThread + 175
6 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 20:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60
2 QtWebEngineCore 0x00000001212b7492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000012125f778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000121260150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000012125fcd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x00000001212b2e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 21:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x000000019f3f72eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 22:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x000000019f3f72eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 23:
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 libopenblas.0.dylib 0x000000019f3f72eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 24:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722
2 QtCore 0x000000011c7a475b QWaitConditionPrivate::wait(QDeadlineTimer) + 59
3 QtCore 0x000000011c7a469d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93
4 QtWidgets 0x000000011d7f2c68 QFileInfoGatherer::run() + 136
5 QtCore 0x000000011c79c619 QThreadPrivate::start(void*) + 329
6 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13
Thread 25:
0 libsystem_pthread.dylib 0x00007fff7045e3f0 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000111c3a5c0 rcx: 0x000000010e60ba48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x000000010e60ba80 rsp: 0x000000010e60ba48
r8: 0x000000010e60bf48 r9: 0x5b1e9d13fa92f9a6 r10: 0x0000000111c3a66c r11: 0x0000000000000206
r12: 0x0000000000000307 r13: 0x0000000132983000 r14: 0x0000000000000006 r15: 0x000000000000002d
rip: 0x00007fff703a62c6 rfl: 0x0000000000000206 cr2: 0x000000010e60bf48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x10ea8c000 - 0x10ea91fff +_json.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_json.cpython-38-darwin.so
0x10eadb000 - 0x10eaefff7 +_ssl.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_ssl.cpython-38-darwin.so
0x10eb08000 - 0x10eb60fff +libssl.1.1.dylib (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libssl.1.1.dylib
0x10eb8f000 - 0x10eda5da7 +libcrypto.1.1.dylib (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libcrypto.1.1.dylib
0x10ee43000 - 0x10ee50fff +_socket.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_socket.cpython-38-darwin.so
0x10eedd000 - 0x10eee0ff7 +select.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/select.cpython-38-darwin.so
0x10eeea000 - 0x10eeeffff +_struct.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_struct.cpython-38-darwin.so
0x10eefc000 - 0x10ef00fff +binascii.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/binascii.cpython-38-darwin.so
0x10ef49000 - 0x10ef4cff7 +_hashlib.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_hashlib.cpython-38-darwin.so
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0x10f0a0000 - 0x10f0a0ff7 +_scproxy.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_scproxy.cpython-38-darwin.so
0x10f0a8000 - 0x10f0f1fff +_decimal.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_decimal.cpython-38-darwin.so
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0x10f192000 - 0x10f193fff +_queue.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_queue.cpython-38-darwin.so
0x10f2ad000 - 0x10f2c3ff7 +_pickle.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_pickle.cpython-38-darwin.so
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0x10f332000 - 0x10f333fff +_posixsubprocess.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_posixsubprocess.cpython-38-darwin.so
0x10f4bd000 - 0x10f832feb +_multiarray_umath.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-darwin.so
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0x7fff6cd7a000 - 0x7fff6cd84ff7 libChineseTokenizer.dylib (28.15.3) /usr/lib/libChineseTokenizer.dylib
0x7fff6cd85000 - 0x7fff6ce0efff libCoreStorage.dylib (546.50.1) /usr/lib/libCoreStorage.dylib
0x7fff6ce12000 - 0x7fff6ce13ffb libDiagnosticMessagesClient.dylib (107) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff6ce4a000 - 0x7fff6d0a1ff3 libFosl_dynamic.dylib (18.3.4) /usr/lib/libFosl_dynamic.dylib
0x7fff6d0c1000 - 0x7fff6d0c8fff libMatch.1.dylib (31.200.1) /usr/lib/libMatch.1.dylib
0x7fff6d0f2000 - 0x7fff6d111fff libMobileGestalt.dylib (645.270.1) /usr/lib/libMobileGestalt.dylib
0x7fff6d112000 - 0x7fff6d112fff libOpenScriptingUtil.dylib (179.1) /usr/lib/libOpenScriptingUtil.dylib
0x7fff6d252000 - 0x7fff6d253ffb libSystem.B.dylib (1252.250.1) /usr/lib/libSystem.B.dylib
0x7fff6d2cf000 - 0x7fff6d2d0fff libThaiTokenizer.dylib (2.15.1) /usr/lib/libThaiTokenizer.dylib
0x7fff6d2e2000 - 0x7fff6d2f8ffb libapple_nghttp2.dylib (1.24.1) /usr/lib/libapple_nghttp2.dylib
0x7fff6d2f9000 - 0x7fff6d322ffb libarchive.2.dylib (54.250.1) /usr/lib/libarchive.2.dylib
0x7fff6d323000 - 0x7fff6d3a2fff libate.dylib (1.13.8) /usr/lib/libate.dylib
0x7fff6d3a6000 - 0x7fff6d3a6ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff6d476000 - 0x7fff6d486ffb libbsm.0.dylib (39.200.18) /usr/lib/libbsm.0.dylib
0x7fff6d487000 - 0x7fff6d494fff libbz2.1.0.dylib (38.200.3) /usr/lib/libbz2.1.0.dylib
0x7fff6d495000 - 0x7fff6d4e8ff7 libc++.1.dylib (400.9.4) /usr/lib/libc++.1.dylib
0x7fff6d4e9000 - 0x7fff6d4feff7 libc++abi.dylib (400.17) /usr/lib/libc++abi.dylib
0x7fff6d4ff000 - 0x7fff6d4ffff3 libcharset.1.dylib (51.200.6) /usr/lib/libcharset.1.dylib
0x7fff6d500000 - 0x7fff6d510ffb libcmph.dylib (6.15.1) /usr/lib/libcmph.dylib
0x7fff6d511000 - 0x7fff6d529ffb libcompression.dylib (52.250.2) /usr/lib/libcompression.dylib
0x7fff6d79e000 - 0x7fff6d7b4fff libcoretls.dylib (155.220.1) /usr/lib/libcoretls.dylib
0x7fff6d7b5000 - 0x7fff6d7b6ff3 libcoretls_cfhelpers.dylib (155.220.1) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff6d954000 - 0x7fff6da4cff7 libcrypto.35.dylib (22.260.1) /usr/lib/libcrypto.35.dylib
0x7fff6dc4f000 - 0x7fff6dc5aff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib
0x7fff6dc62000 - 0x7fff6dcb8ff3 libcups.2.dylib (462.12) /usr/lib/libcups.2.dylib
0x7fff6ddec000 - 0x7fff6ddecfff libenergytrace.dylib (17.200.1) /usr/lib/libenergytrace.dylib
0x7fff6dded000 - 0x7fff6de06ffb libexpat.1.dylib (16.1.1) /usr/lib/libexpat.1.dylib
0x7fff6de07000 - 0x7fff6de13fff libexslt.0.dylib (16.5) /usr/lib/libexslt.0.dylib
0x7fff6de1e000 - 0x7fff6de23ff7 libgermantok.dylib (17.15.2) /usr/lib/libgermantok.dylib
0x7fff6de24000 - 0x7fff6de29ff7 libheimdal-asn1.dylib (520.270.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6de54000 - 0x7fff6df44fff libiconv.2.dylib (51.200.6) /usr/lib/libiconv.2.dylib
0x7fff6df45000 - 0x7fff6e1a6ffb libicucore.A.dylib (62141.0.1) /usr/lib/libicucore.A.dylib
0x7fff6e1f3000 - 0x7fff6e1f4fff liblangid.dylib (128.15.1) /usr/lib/liblangid.dylib
0x7fff6e1f5000 - 0x7fff6e20dff3 liblzma.5.dylib (10.200.3) /usr/lib/liblzma.5.dylib
0x7fff6e225000 - 0x7fff6e2c9ff7 libmecab.1.0.0.dylib (779.24.1) /usr/lib/libmecab.1.0.0.dylib
0x7fff6e2ca000 - 0x7fff6e4cefff libmecabra.dylib (779.24.1) /usr/lib/libmecabra.dylib
0x7fff6e6a6000 - 0x7fff6e9f7ff7 libnetwork.dylib (1229.250.15) /usr/lib/libnetwork.dylib
0x7fff6ea89000 - 0x7fff6f20efdf libobjc.A.dylib (756.2) /usr/lib/libobjc.A.dylib
0x7fff6f220000 - 0x7fff6f224ffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib
0x7fff6f227000 - 0x7fff6f25cfff libpcap.A.dylib (79.250.1) /usr/lib/libpcap.A.dylib
0x7fff6f2b2000 - 0x7fff6f2b5fff libpmenergy.dylib (194.267.1) /usr/lib/libpmenergy.dylib
0x7fff6f2b6000 - 0x7fff6f2b8fff libpmsample.dylib (194.267.1) /usr/lib/libpmsample.dylib
0x7fff6f375000 - 0x7fff6f38dffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib
0x7fff6f38f000 - 0x7fff6f3caff3 libsandbox.1.dylib (851.270.1) /usr/lib/libsandbox.1.dylib
0x7fff6f3de000 - 0x7fff6f3dfff7 libspindump.dylib (267.3) /usr/lib/libspindump.dylib
0x7fff6f3e0000 - 0x7fff6f5bdfff libsqlite3.dylib (274.26) /usr/lib/libsqlite3.dylib
0x7fff6f7d6000 - 0x7fff6f7d9ff7 libutil.dylib (51.200.4) /usr/lib/libutil.dylib
0x7fff6f7da000 - 0x7fff6f7e7fff libxar.1.dylib (417.1) /usr/lib/libxar.1.dylib
0x7fff6f7ec000 - 0x7fff6f8ceff3 libxml2.2.dylib (32.10) /usr/lib/libxml2.2.dylib
0x7fff6f8cf000 - 0x7fff6f8f7ff3 libxslt.1.dylib (16.5) /usr/lib/libxslt.1.dylib
0x7fff6f8f8000 - 0x7fff6f90aff7 libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib
0x7fff700ee000 - 0x7fff700f2ff3 libcache.dylib (81) /usr/lib/system/libcache.dylib
0x7fff700f3000 - 0x7fff700fdff3 libcommonCrypto.dylib (60118.250.2) /usr/lib/system/libcommonCrypto.dylib
0x7fff700fe000 - 0x7fff70105ff7 libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib
0x7fff70106000 - 0x7fff7010fff7 libcopyfile.dylib (146.250.1) /usr/lib/system/libcopyfile.dylib
0x7fff70110000 - 0x7fff70194fc3 libcorecrypto.dylib (602.260.2) /usr/lib/system/libcorecrypto.dylib
0x7fff7021b000 - 0x7fff70254ff7 libdispatch.dylib (1008.270.1) /usr/lib/system/libdispatch.dylib
0x7fff70255000 - 0x7fff70281ff7 libdyld.dylib (655.1.1) /usr/lib/system/libdyld.dylib
0x7fff70282000 - 0x7fff70282ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff70283000 - 0x7fff7028fff3 libkxld.dylib (4903.270.47) /usr/lib/system/libkxld.dylib
0x7fff70290000 - 0x7fff70290ff7 liblaunch.dylib (1336.261.2) /usr/lib/system/liblaunch.dylib
0x7fff70291000 - 0x7fff70296fff libmacho.dylib (927.0.3) /usr/lib/system/libmacho.dylib
0x7fff70297000 - 0x7fff70299ffb libquarantine.dylib (86.220.1) /usr/lib/system/libquarantine.dylib
0x7fff7029a000 - 0x7fff7029bff7 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib
0x7fff7029c000 - 0x7fff702b3ff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib
0x7fff702b4000 - 0x7fff702b4ff7 libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff702b5000 - 0x7fff7033cfff libsystem_c.dylib (1272.250.1) /usr/lib/system/libsystem_c.dylib
0x7fff7033d000 - 0x7fff70340ffb libsystem_configuration.dylib (963.270.3) /usr/lib/system/libsystem_configuration.dylib
0x7fff70341000 - 0x7fff70344ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff70345000 - 0x7fff7034bfff libsystem_darwin.dylib (1272.250.1) /usr/lib/system/libsystem_darwin.dylib
0x7fff7034c000 - 0x7fff70352ff7 libsystem_dnssd.dylib (878.270.2) /usr/lib/system/libsystem_dnssd.dylib
0x7fff70353000 - 0x7fff7039effb libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff7039f000 - 0x7fff703c7ff7 libsystem_kernel.dylib (4903.270.47) /usr/lib/system/libsystem_kernel.dylib
0x7fff703c8000 - 0x7fff70413ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff70414000 - 0x7fff7043efff libsystem_malloc.dylib (166.270.1) /usr/lib/system/libsystem_malloc.dylib
0x7fff7043f000 - 0x7fff70449ff7 libsystem_networkextension.dylib (767.250.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff7044a000 - 0x7fff70451fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff70452000 - 0x7fff7045bfef libsystem_platform.dylib (177.270.1) /usr/lib/system/libsystem_platform.dylib
0x7fff7045c000 - 0x7fff70466ff7 libsystem_pthread.dylib (330.250.2) /usr/lib/system/libsystem_pthread.dylib
0x7fff70467000 - 0x7fff7046aff7 libsystem_sandbox.dylib (851.270.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff7046b000 - 0x7fff7046dff3 libsystem_secinit.dylib (30.260.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff7046e000 - 0x7fff70475ff3 libsystem_symptoms.dylib (820.267.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff70476000 - 0x7fff7048bfff libsystem_trace.dylib (906.260.1) /usr/lib/system/libsystem_trace.dylib
0x7fff7048d000 - 0x7fff70492ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff70493000 - 0x7fff704c2fff libxpc.dylib (1336.261.2) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 20
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: 2968013
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=935.6M resident=0K(0%) swapped_out_or_unallocated=935.6M(100%)
Writable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 768K 5
Activity Tracing 256K 1
CG backing stores 672K 4
CG image 116K 21
CoreAnimation 72K 11
CoreGraphics 8K 1
CoreImage 16K 4
CoreUI image data 992K 22
CoreUI image file 316K 4
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 2.4G 848
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 2048K 12 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 24K 2
Memory Tag 242 12K 1
OpenGL GLSL 384K 5
STACK GUARD 100K 25
Stack 133.2M 26
Stack Guard 56.0M 1
VM_ALLOCATE 315.7M 202
VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)
__DATA 58.2M 582
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 331.3M 214
__TEXT 604.2M 535
__UNICODE 564K 1
mapped file 80.1M 139
shared memory 2840K 20
=========== ======= =======
TOTAL 4.2G 2700
TOTAL, minus reserved VM space 3.9G 2700
Log:
UCSF ChimeraX version: 1.2.3 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/apadavan/Desktop/Review
> Article/Review_Figures/NDUFA8/NDUFA8.cxs"
Log from Wed Aug 25 18:21:17 2021UCSF ChimeraX version: 1.2.3 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/apadavan/Desktop/Review
> Article/Review_Figures/NDUFA2/SOI_A2.cxs"
Log from Wed Aug 18 11:58:00 2021UCSF ChimeraX version: 1.2.3 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/apadavan/Desktop/Review Article/Review_Figures/SOI_A2.cxc"
> open 6ZKC
6zkc title:
Complex I during turnover, closed [more info...]
Chain information for 6zkc #1
---
Chain | Description
1 | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
2 | Mitochondrial complex I, 24 kDa subunit
3 | NADH:ubiquinone oxidoreductase core subunit S1
4 | Mitochondrial complex I, 49 kDa subunit
5 | NADH:ubiquinone oxidoreductase core subunit S3
6 | Mitochondrial complex I, PSST subunit
9 | Mitochondrial complex I, TYKY subunit
A | NADH-ubiquinone oxidoreductase chain 3
H | NADH-ubiquinone oxidoreductase chain 1
J | NADH-ubiquinone oxidoreductase chain 6
K | NADH-ubiquinone oxidoreductase chain 4L
L | NADH-ubiquinone oxidoreductase chain 5
M | NADH-ubiquinone oxidoreductase chain 4
N | NADH-ubiquinone oxidoreductase chain 2
V | Mitochondrial complex I, B14.7 subunit
W | NADH:ubiquinone oxidoreductase subunit B5
X j | Acyl carrier protein
Y | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8
Z | Mitochondrial complex I, PDSW subunit
a | Mitochondrial complex I, 10 kDa subunit
b | Mitochondrial complex I, 13 kDa subunit
c | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
d | NADH:ubiquinone oxidoreductase subunit A9
e | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2
f | Mitochondrial complex I, B13 subunit
g | NADH:ubiquinone oxidoreductase subunit A6
h | Mitochondrial complex I, B14.5a subunit
i | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12
k | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial
l | NADH:ubiquinone oxidoreductase subunit S5
m | NADH:ubiquinone oxidoreductase subunit A3
n | NADH:ubiquinone oxidoreductase subunit B3
o | NADH dehydrogenase [ubiquinone] 1 subunit C2
p | NADH:ubiquinone oxidoreductase subunit B4
q | Mitochondrial complex I, B16.6 subunit
r | Mitochondrial complex I, B17 subunit
s | NADH:ubiquinone oxidoreductase subunit B7
t | NADH:ubiquinone oxidoreductase subunit B9
u | NADH:ubiquinone oxidoreductase subunit B2
v | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial
w | Mitochondrial complex I, ESSS subunit
x | Mitochondrial complex I, KFYI subunit
y | Mitochondrial complex I, MNLL subunit
z | Mitochondrial complex I, MWFE subunit
Non-standard residues in 6zkc #1
---
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)
AMP — adenosine monophosphate
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
DCQ — 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
(decylubiquinone)
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
K — potassium ion
MYR — myristic acid
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
SF4 — iron/sulfur cluster
ZMP — S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-
alanyl}amino)ethyl] tetradecanethioate
ZN — zinc ion
> hide atoms
> show cartoons
> set bgColor white
> name core #1/1 /2 /3 /4 /5 /6 /9 /A /H /J /K /N /M /L
> show core surfaces
> rainbow core chains palette
> "#DC050C:#E8601C:#F1932D:#F6C141:#F7F056:#CAE0AB:#90C987:#4EB265:#7BAFDE:#5289C7:#1965B0:#882E72:#AE76A3:#D1BBD7"
> transparency core 325
> name accessory #1/a /b /c /d /e /f /g /h /i /j /k /l /m /n /o /p /q /r /s /t
> /u /v /w /x /y /z /V /W /X /Y /Z
> show accessory surfaces
> rainbow accessory chains palette
> "#E8ECFB:#DDD8EF:#D1C1E1:#C3A8D1:#B58FC2:#A778B4:#9B62A7:#8C4E99:#6F4C9B:#6059A9:#5568B8:#4E79C5:#4D8AC6:#4E96BC:#549EB3:#59A5A9:#60AB9E:#69B190:#77B77D:#8CBC68:#A6BE54:#BEBC48:#D1B541:#DDAA3C:#E49C39:#E78C35:#E67932:#E4632D:#DF4828:#DA2222:#B8221E:#95211B:#721E17:#521A13"
> hide #1 surfaces
> hide #1 cartoons
> show #1/3 surfaces
> transparency #1 0
> show #1/e cartoons
> select #1/e :23 :57
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style (#!1 & sel) ball
Changed 12 atom styles
> color sel byhetero
> select clear
> graphics silhouettes true
> lighting full
> lighting shadows false
> view matrix camera
> 0.95696,-0.28854,0.031465,159.11,-0.28222,-0.95032,-0.13126,61.033,0.067777,0.11673,-0.99085,78.079
> save "/Users/apadavan/Desktop/Review Article/Review_Figures/SOI_A2_1.png"
> width 1233 height 858 supersample 3
> open 1s3a
1s3a title:
NMR Solution Structure of Subunit B8 from Human NADH-Ubiquinone Oxidoreductase
Complex I (CI-B8) [more info...]
Chain information for 1s3a
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A | NADH-ubiquinone
oxidoreductase B8 subunit
> hide #2 cartoons
> show #2.2 cartoons
> mmaker #2.2 to #1/e
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 6zkc, chain e (#1) with 1s3a, chain A (#2.2), sequence alignment
score = 436.1
RMSD between 43 pruned atom pairs is 1.365 angstroms; (across all 85 pairs:
3.321)
> hide #1/e atoms
> select #2.2 :24 :58
20 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> view matrix camera
> 0.95696,-0.28854,0.031465,159.11,-0.28222,-0.95032,-0.13126,61.033,0.067777,0.11673,-0.99085,78.079
> save "/Users/apadavan/Desktop/Review
> Article/Review_Figures/SOI_A2-TRX_1.png" width 1233 height 858 supersample 3
> hide #1/3 surfaces
> save "/Users/apadavan/Desktop/Review
> Article/Review_Figures/SOI_A2-TRX_2.png" width 1233 height 858 supersample 3
executed SOI_A2.cxc
> show #1 surfaces
> hide #1/e surfaces
> select ::name="CYS"
1094 atoms, 963 bonds, 157 residues, 20 models selected
> hide sel H
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select clear
> select H
13091 atoms, 1615 residues, 19 models selected
> hide sel atoms
> select clear
> select #1/e
691 atoms, 702 bonds, 86 residues, 1 model selected
> select clear
> select #1/e :23 :57
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style (#!1 & sel) stick
Changed 12 atom styles
> select clear
> transparency 80
> transparency 60
> show #1/3 cartoons
> transparency #1/3 60 cartoons
> transparency #1/3 20 cartoons
> save "/Users/apadavan/Desktop/Review Article/Review_Figures/SOI_A2.cxs"
——— End of log from Wed Aug 18 11:58:00 2021 ———
opened ChimeraX session
> view
> close #2
> show #1/e surfaces
> transparency 0
> hide #1 surfaces
> hide #1 cartoons
> hide #1 atoms
> show #1/Y cartoons
> sequence chain #1/Y
Alignment identifier is 1/Y
> select #1/Y :35 :45 :55 :65 :77 :87 :99 :109
48 atoms, 40 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style (#!1 & sel) stick
Changed 48 atom styles
> select clear
> ui tool show Rotamers
No residues selected
> swapaa interactive sel CYS rotLib Dunbrack
/Y CYS 35: phi -101.1, psi 39.9 trans
Changed 9 bond radii
> swapaa #1/Y:35 CYS criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
6zkc #1/Y CYS 35: phi -101.1, psi 39.9 trans
Applying CYS rotamer (chi angles: -177.4) to 6zkc #1/Y CYS 35
> swapaa interactive sel CYS rotLib Dunbrack
/Y CYS 65: phi -71.4, psi -29.6 trans
Changed 9 bond radii
> swapaa #1/Y:65 CYS criteria 2 rotLib Dunbrack retain false
Using Dunbrack library
6zkc #1/Y CYS 65: phi -71.4, psi -29.6 trans
Applying CYS rotamer (chi angles: 66.5) to 6zkc #1/Y CYS 65
> select /Y:65@CB
1 atom, 1 residue, 1 model selected
> swapaa interactive sel CYD rotLib Dunbrack
/Y CYS 35: phi -101.1, psi 39.9 trans
Changed 9 bond radii
> swapaa #1/Y:35 CYD criteria 3 rotLib Dunbrack
Using Dunbrack library
6zkc #1/Y CYS 35: phi -101.1, psi 39.9 trans
Applying CYS rotamer (chi angles: -176.3) to 6zkc #1/Y CYS 35
> ui tool show "Side View"
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping /Y CYS 77 to ALA
> swapaa interactive sel CYS rotLib Dunbrack
/Y ALA 77: phi -124.3, psi 49.0 trans
Changed 9 bond radii
> swapaa #1/Y:77 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
6zkc #1/Y ALA 77: phi -124.3, psi 49.0 trans
Applying CYS rotamer (chi angles: -61.1) to 6zkc #1/Y CYS 77
> select /Y:99@CB
1 atom, 1 residue, 1 model selected
> swapaa interactive sel CYS rotLib Dunbrack
/Y CYS 99: phi -135.1, psi 44.9 trans
Changed 9 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #1/Y:99 CYS criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
6zkc #1/Y CYS 99: phi -135.1, psi 44.9 trans
Applying CYS rotamer (chi angles: -176.3) to 6zkc #1/Y CYS 99
> select /Y:87@CB
1 atom, 1 residue, 1 model selected
> swapaa interactive sel CYS rotLib Dunbrack
/Y CYS 87: phi -64.5, psi -40.5 trans
Changed 9 bond radii
> swapaa #1/Y:87 CYS criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
6zkc #1/Y CYS 87: phi -64.5, psi -40.5 trans
Applying CYS rotamer (chi angles: 62.6) to 6zkc #1/Y CYS 87
> view
> style ball
Changed 67967 atom styles
> save "/Users/apadavan/Desktop/Review
> Article/Review_Figures/NDUFA8/NDUFA8.cxs"
——— End of log from Wed Aug 25 18:21:17 2021 ———
opened ChimeraX session
OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac14,3
Processor Name: Intel Core i7
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: IM143.0118.B12
SMC Version (system): 2.17f7
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G87)
Kernel Version: Darwin 18.7.0
Time since boot: 16 days 3:13
Graphics/Displays:
NVIDIA GeForce GT 750M:
Chipset Model: NVIDIA GeForce GT 750M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 1 GB
Vendor: NVIDIA (0x10de)
Device ID: 0x0fe9
Revision ID: 0x00a2
ROM Revision: 3762
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
HP VH240a:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 6CM1160B4N
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
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: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.3
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
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: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.0
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
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: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Apple graphics driver crash, same as #5146.
You are using very old GeForce GT 750M graphics (circa 2013) with only 1 GB of video RAM which probably contributes to the frequency of these driver crashes. I believe most of the crashes happen when it runs out of video memory. If you are preparing figures you could copy your session (.cxs) files to a computer with more modern graphics.
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Reported by Abhilash Padavannil