![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6748 closed defect (nonchimerax)
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-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x000000011bc2fdc0 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 496 in swap_buffers
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 179 in draw
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [39039]
Path: /Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [39039]
User ID: 447249914
Date/Time: 2022-04-29 16:29:24.349 -0700
OS Version: Mac OS X 10.15.7 (19H1824)
Report Version: 12
Bridge OS Version: 6.4 (19P4242)
Anonymous UUID: D556620D-B394-F785-66D2-A34AB72EE930
Sleep/Wake UUID: 6EC5D4FC-11C9-4CC4-B906-0250CC46D1B0
Time Awake Since Boot: 200000 seconds
Time Since Wake: 23000 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: 0x00000813
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6d62632a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6d6e2e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6d53d93e raise + 26
3 libsystem_platform.dylib 0x00007fff6d6d75fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff6d5ad808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff54b140a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff54b0b18f gpusGenerateCrashLog + 89
8 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2bf7ff18 gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff54b0c6a1 gpusSubmitDataBuffers + 490
10 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2b1ec096 IntelCommandBuffer::getNew(GLDContextRec*) + 48
11 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2b1ebea4 intelSubmitCommands + 171
12 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2b316d8a gldPresentFramebufferData + 120
13 GLEngine 0x00007fff3e1ba8d1 glSwap_Exec + 97
14 com.apple.opengl 0x00007fff3e19c473 CGLFlushDrawable + 59
15 com.apple.AppKit 0x00007fff30e79faa -[NSOpenGLContext flushBuffer] + 20
16 libqcocoa.dylib 0x000000012c4b9f5d QCocoaGLContext::swapBuffers(QPlatformSurface*) + 541
17 QtGui 0x000000011eac813c QOpenGLContext::swapBuffers(QSurface*) + 412
18 QtGui.abi3.so 0x000000011b8c600f meth_QOpenGLContext_swapBuffers(_object*, _object*) + 95
19 org.python.python 0x000000010e24706d cfunction_call + 125
20 org.python.python 0x000000010e20817d _PyObject_MakeTpCall + 365
21 org.python.python 0x000000010e2e061c call_function + 876
22 org.python.python 0x000000010e2ddab3 _PyEval_EvalFrameDefault + 25219
23 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
24 org.python.python 0x000000010e2088d1 _PyFunction_Vectorcall + 289
25 org.python.python 0x000000010e2e058c call_function + 732
26 org.python.python 0x000000010e2dda92 _PyEval_EvalFrameDefault + 25186
27 org.python.python 0x000000010e208948 function_code_fastcall + 104
28 org.python.python 0x000000010e2e058c call_function + 732
29 org.python.python 0x000000010e2dda92 _PyEval_EvalFrameDefault + 25186
30 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
31 org.python.python 0x000000010e2088d1 _PyFunction_Vectorcall + 289
32 org.python.python 0x000000010e20a98a method_vectorcall + 202
33 org.python.python 0x000000010e2e058c call_function + 732
34 org.python.python 0x000000010e2ddbe1 _PyEval_EvalFrameDefault + 25521
35 org.python.python 0x000000010e208948 function_code_fastcall + 104
36 org.python.python 0x000000010e2e058c call_function + 732
37 org.python.python 0x000000010e2dda92 _PyEval_EvalFrameDefault + 25186
38 org.python.python 0x000000010e208948 function_code_fastcall + 104
39 org.python.python 0x000000010e20a9d2 method_vectorcall + 274
40 QtCore.abi3.so 0x000000011b5aa957 PyQtSlot::call(_object*, _object*) const + 39
41 QtCore.abi3.so 0x000000011b5aa866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
42 QtCore.abi3.so 0x000000011b5ab455 PyQtSlotProxy::unislot(void**) + 85
43 QtCore.abi3.so 0x000000011b5ab3ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
44 QtCore 0x000000011be95f6e void doActivate(QObject*, int, void**) + 1118
45 QtCore 0x000000011be9f4c2 QTimer::timerEvent(QTimerEvent*) + 98
46 QtCore.abi3.so 0x000000011b493bf9 sipQTimer::timerEvent(QTimerEvent*) + 121
47 QtCore 0x000000011be8d85f QObject::event(QEvent*) + 111
48 QtCore.abi3.so 0x000000011b493a7a sipQTimer::event(QEvent*) + 186
49 QtWidgets 0x000000011e40f9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
50 QtWidgets 0x000000011e410e11 QApplication::notify(QObject*, QEvent*) + 497
51 QtWidgets.abi3.so 0x000000011dfc2db9 sipQApplication::notify(QObject*, QEvent*) + 233
52 QtCore 0x000000011be62a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
53 QtCore 0x000000011bec835f QTimerInfoList::activateTimers() + 991
54 libqcocoa.dylib 0x000000012c4988f2 QCocoaEventDispatcherPrivate::activateTimersSourceCallback(void*) + 18
55 com.apple.CoreFoundation 0x00007fff3385d682 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
56 com.apple.CoreFoundation 0x00007fff3385d621 __CFRunLoopDoSource0 + 103
57 com.apple.CoreFoundation 0x00007fff3385d497 __CFRunLoopDoSources0 + 301
58 com.apple.CoreFoundation 0x00007fff3385c16a __CFRunLoopRun + 927
59 com.apple.CoreFoundation 0x00007fff3385b76e CFRunLoopRunSpecific + 462
60 com.apple.HIToolbox 0x00007fff32487aad RunCurrentEventLoopInMode + 292
61 com.apple.HIToolbox 0x00007fff324876e4 ReceiveNextEventCommon + 359
62 com.apple.HIToolbox 0x00007fff32487569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
63 com.apple.AppKit 0x00007fff30ad0659 _DPSNextEvent + 883
64 com.apple.AppKit 0x00007fff30aceea0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
65 com.apple.AppKit 0x00007fff30ac0bae -[NSApplication run] + 658
66 libqcocoa.dylib 0x000000012c49962f QCocoaEventDispatcher::processEvents(QFlags) + 2495
67 QtCore 0x000000011be5eacf QEventLoop::exec(QFlags) + 431
68 QtCore 0x000000011be63042 QCoreApplication::exec() + 130
69 QtWidgets.abi3.so 0x000000011e0b4702 meth_QApplication_exec_(_object*, _object*) + 82
70 org.python.python 0x000000010e24706d cfunction_call + 125
71 org.python.python 0x000000010e20817d _PyObject_MakeTpCall + 365
72 org.python.python 0x000000010e2e061c call_function + 876
73 org.python.python 0x000000010e2ddab3 _PyEval_EvalFrameDefault + 25219
74 org.python.python 0x000000010e208948 function_code_fastcall + 104
75 org.python.python 0x000000010e20a98a method_vectorcall + 202
76 org.python.python 0x000000010e2e058c call_function + 732
77 org.python.python 0x000000010e2ddab3 _PyEval_EvalFrameDefault + 25219
78 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
79 org.python.python 0x000000010e2088d1 _PyFunction_Vectorcall + 289
80 org.python.python 0x000000010e2e058c call_function + 732
81 org.python.python 0x000000010e2ddb4b _PyEval_EvalFrameDefault + 25371
82 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
83 org.python.python 0x000000010e2d770b PyEval_EvalCode + 139
84 org.python.python 0x000000010e2d4592 builtin_exec + 626
85 org.python.python 0x000000010e24686a cfunction_vectorcall_FASTCALL + 218
86 org.python.python 0x000000010e2e058c call_function + 732
87 org.python.python 0x000000010e2ddb4b _PyEval_EvalFrameDefault + 25371
88 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
89 org.python.python 0x000000010e2088d1 _PyFunction_Vectorcall + 289
90 org.python.python 0x000000010e2e058c call_function + 732
91 org.python.python 0x000000010e2ddb4b _PyEval_EvalFrameDefault + 25371
92 org.python.python 0x000000010e2e1283 _PyEval_EvalCode + 2611
93 org.python.python 0x000000010e2088d1 _PyFunction_Vectorcall + 289
94 org.python.python 0x000000010e346e20 pymain_run_module + 208
95 org.python.python 0x000000010e346537 Py_RunMain + 1431
96 org.python.python 0x000000010e346b3f pymain_main + 223
97 org.python.python 0x000000010e346a4b Py_Main + 43
98 edu.ucsf.cgl.ChimeraX 0x000000010e1c2dc8 main + 120
99 libdyld.dylib 0x00007fff6d4decc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010ee8fa9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010ee8fa9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010ee8fa9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6d628b86 kevent64 + 10
1 QtWebEngineCore 0x0000000121c65e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000121c65cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000121bf9a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c03778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000121c04150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000121c03c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6d628b86 kevent64 + 10
1 QtWebEngineCore 0x0000000121c65e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000121c65cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000125b32f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121b831db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 8:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000121c52e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x0000000122f0a5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 9:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121b8320f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 10:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6d628b86 kevent64 + 10
1 QtWebEngineCore 0x0000000121c65e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x0000000121c65cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121b831db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 12:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121b8320f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121b831db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121c0376a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000121c04150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x0000000121c03d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121b831db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121b831db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x0000000121bee62b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x0000000121bb27cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x0000000121c0da7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 17:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3385d825 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff3385c2f2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff3385b76e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff30c71ea4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 18:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c5b2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x0000000121c0376a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000121c03e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x0000000121c03c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000018c41a2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000018c41a2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000018c41a2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMM.7.6.dylib 0x000000012e69f8d3 OpenMM::threadBody(void*) + 195
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 libOpenMMOpenCL.dylib 0x000000012eb60353 threadBody(void*) + 115
3 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 31:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6d61fdea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6d620160 mach_msg + 60
2 QtWebEngineCore 0x0000000121c5b492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000121c03778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000121c04150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000121c03cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000121c56e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 32:
0 libsystem_pthread.dylib 0x00007fff6d6deb68 start_wqthread + 0
Thread 33:
0 libsystem_pthread.dylib 0x00007fff6d6deb68 start_wqthread + 0
Thread 34:: Thread (pooled)
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 QtCore 0x000000011bc94aaf QWaitConditionPrivate::wait_relative(QDeadlineTimer) + 303
3 QtCore 0x000000011bc9477e QWaitConditionPrivate::wait(QDeadlineTimer) + 94
4 QtCore 0x000000011bc9469d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93
5 QtCore 0x000000011bc90ccd QThreadPoolThread::run() + 605
6 QtCore 0x000000011bc8c619 QThreadPrivate::start(void*) + 329
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 35:: Thread (pooled)
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 QtCore 0x000000011bc94aaf QWaitConditionPrivate::wait_relative(QDeadlineTimer) + 303
3 QtCore 0x000000011bc9477e QWaitConditionPrivate::wait(QDeadlineTimer) + 94
4 QtCore 0x000000011bc9469d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93
5 QtCore 0x000000011bc90ccd QThreadPoolThread::run() + 605
6 QtCore 0x000000011bc8c619 QThreadPrivate::start(void*) + 329
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 36:: Thread (pooled)
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 QtCore 0x000000011bc94aaf QWaitConditionPrivate::wait_relative(QDeadlineTimer) + 303
3 QtCore 0x000000011bc9477e QWaitConditionPrivate::wait(QDeadlineTimer) + 94
4 QtCore 0x000000011bc9469d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93
5 QtCore 0x000000011bc90ccd QThreadPoolThread::run() + 605
6 QtCore 0x000000011bc8c619 QThreadPrivate::start(void*) + 329
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 37:: Thread (pooled)
0 libsystem_kernel.dylib 0x00007fff6d622872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6d6e3425 _pthread_cond_wait + 698
2 QtCore 0x000000011bc94aaf QWaitConditionPrivate::wait_relative(QDeadlineTimer) + 303
3 QtCore 0x000000011bc9477e QWaitConditionPrivate::wait(QDeadlineTimer) + 94
4 QtCore 0x000000011bc9469d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93
5 QtCore 0x000000011bc90ccd QThreadPoolThread::run() + 605
6 QtCore 0x000000011bc8c619 QThreadPrivate::start(void*) + 329
7 libsystem_pthread.dylib 0x00007fff6d6e3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6d6deb8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011bc2fdc0 rcx: 0x00007f86e4955a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007f86e4955a80 rsp: 0x00007f86e4955a58
r8: 0x00007f86e4955f48 r9: 0x590a64feb41858ab r10: 0x000000011bc2fdc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007f86e979d518 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff6d62632a rfl: 0x0000000000000246 cr2: 0x000000010e4317b8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff6d64c000 - 0x7fff6d693fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6d694000 - 0x7fff6d6bbfff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6d6bc000 - 0x7fff6d6c9ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6d6ca000 - 0x7fff6d6d3ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6d6d4000 - 0x7fff6d6dcfef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6d6dd000 - 0x7fff6d6e7fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6d6e8000 - 0x7fff6d6ecff3 libsystem_sandbox.dylib (1217.141.8) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6d6ed000 - 0x7fff6d6effff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6d6f0000 - 0x7fff6d6f7ffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6d6f8000 - 0x7fff6d70eff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6d710000 - 0x7fff6d715ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6d716000 - 0x7fff6d74bffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 121
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: 425220
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=10.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=10.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 1920K 15
Activity Tracing 256K 1
CG backing stores 992K 2
CG image 1276K 104
CoreAnimation 3264K 127
CoreGraphics 8K 1
CoreImage 60K 11
CoreUI image data 5048K 55
Foundation 24K 2
Kernel Alloc Once 8K 1
MALLOC 9.5G 47165
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 544K 2 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenCL 6416K 62
OpenCL (reserved) 32K 3 reserved VM address space (unallocated)
OpenGL GLSL 384K 5
STACK GUARD 148K 37
Stack 139.3M 38
Stack Guard 56.0M 1
VM_ALLOCATE 188.1M 251
VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)
__DATA 57.7M 685
__DATA_CONST 44K 4
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 501.0M 270
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 698.0M 629
__UNICODE 564K 1
mapped file 473.7M 111
shared memory 2864K 30
=========== ======= =======
TOTAL 11.8G 49632
TOTAL, minus reserved VM space 11.6G 49632
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_2.8A_map.mrc
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.256, step 1, values float32
> volume #2 color #b2b2b283
> ui tool show "Side View"
> volume #2 level 0.07817
> volume #2 level 0.1637
> select /A:168-196
415 atoms, 422 bonds, 29 residues, 1 model selected
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for PaGS_chainA_isolde.pdb
---
Chain | Description
1.2/A | No description available
Done loading forcefield
Opened PaGS_2.8A_map.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.36, shown
at step 1, values float32
> select /A:96
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:196
17 atoms, 17 bonds, 1 residue, 1 model selected
> cview /A:196
> volume #1.1.1.1 level 0.2747
> volume #1.1.1.1 level 0.128
> volume #1.1.1.1 level 0.1729
> volume #1.1.1.1 level 0.1566
> volume #1.1.1.1 level 0.181
> volume #1.1.1.1 level 0.1213
> cview /A:194
> cview /A:195
> select /A:195
12 atoms, 11 bonds, 1 residue, 1 model selected
Populating font family aliases took 242 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
ISOLDE: started sim
> volume #1.1.1.1 level 0.1346
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /A:190-168
Nothing selected
> select /A:168-190
326 atoms, 330 bonds, 23 residues, 1 model selected
> volume #1.1.1.1 level 0.1933
> cview /A:168-190
> volume #1.1.1.1 level 0.07321
> delete /A:168-190
> cview /A:167
> select /A:167
24 atoms, 25 bonds, 1 residue, 1 model selected
> volume #1.1.1.1 level 0.05549
> select /A:191-194
60 atoms, 61 bonds, 4 residues, 1 model selected
> cview /A:191-194
> volume #1.1.1.1 level 0.1184
ISOLDE: started sim
ISOLDE: paused sim
> clipper spotlight radius 13.00
> volume #1.1.1.1 level 0.1916
> select /A:191-194
60 atoms, 61 bonds, 4 residues, 1 model selected
> volume #1.1.1.1 level 0.1658
> close session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_2.8A_map.mrc
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.256, step 1, values float32
> volume #2 color #ffffb26e
> volume #2 color #e1fff56e
> volume #2 level 0.3491
> select /A:191-194
60 atoms, 61 bonds, 4 residues, 1 model selected
> cview /A:167-190
> select /A:167-190
350 atoms, 356 bonds, 24 residues, 1 model selected
> volume #2 level 0.1899
> ui tool show "Side View"
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #3
---
Chain | Description
A | No description available
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> select #1
7344 atoms, 7440 bonds, 477 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-3.1538,0,1,0,-47.599,0,0,1,1.389
> ui tool show "Fit in Map"
Fit molecule PaGS_chainA.pdb (#3) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.2758, steps = 44
shifted from previous position = 1.37
rotated from previous position = 0.607 degrees
atoms outside contour = 1421, contour level = 0.18989
Position of PaGS_chainA.pdb (#3) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99994706 -0.01028868 -0.00011788 3.18240870
0.01028835 0.99994389 -0.00252435 -1.63731312
0.00014385 0.00252300 0.99999681 -1.12707935
Axis 0.23821047 -0.01235242 0.97113500
Axis point 161.24456492 315.80387586 0.00000000
Rotation angle (degrees) 0.60702102
Shift along axis -0.31623836
> undo
> color #1 #dbb2cd transparency 0
> color #3 #8be588 transparency 0
> color #3 #3ae5d8 transparency 0
> color #1 #e39fd9 transparency 0
> color #1 #e2bee3 transparency 0
> color #1 #e099e3 transparency 0
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> select #1
7344 atoms, 7440 bonds, 477 residues, 1 model selected
> ~select #1
Nothing selected
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> close session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1020, in
_sim_end_cb
self._pr_sim_end_cb()
File "/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File "/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2375, in get_restraints
return self._get_restraints(atoms)
File "/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File "/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_2.8A_map.mrc
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.256, step 1, values float32
> volume #2 color #b2ffff7f
> volume #2 color #b2ffff80
> ui tool show "Side View"
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #3
---
Chain | Description
A | No description available
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #1 to #3
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 PaGS_chainA.pdb, chain A (#3) with PaGS_chainA_isolde.pdb, chain A
(#1), sequence alignment score = 2314.9
RMSD between 411 pruned atom pairs is 0.934 angstroms; (across all 477 pairs:
1.507)
> hide #!2 models
> ~select #3
Nothing selected
> show #!2 models
> hide #1 models
> ui mousemode right "translate selected models"
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> view matrix models #3,1,0,0,-13.748,0,1,0,-39.35,0,0,1,-7.4672
> view matrix models #3,1,0,0,-13.761,0,1,0,-39.386,0,0,1,-7.4677
> view matrix models #3,1,0,0,-12.404,0,1,0,-45.028,0,0,1,-6.9245
> view matrix models #3,1,0,0,-13.202,0,1,0,-47.566,0,0,1,-6.8679
> ui tool show "Side View"
> cofr sel
> view sel
> ui tool show "Fit in Map"
Fit molecule PaGS_chainA.pdb (#3) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.09421, steps = 56
shifted from previous position = 1.67
rotated from previous position = 5.95 degrees
atoms outside contour = 3098, contour level = 0.25644
Position of PaGS_chainA.pdb (#3) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99821433 -0.04397693 -0.04042495 3.80653919
0.04725046 0.99534904 0.08395048 -73.33223240
0.03654505 -0.08571067 0.99564961 2.35181383
Axis -0.81787708 -0.37104544 0.43977536
Axis point 0.00000000 -139.81030774 754.69959787
Rotation angle (degrees) 5.95345096
Shift along axis 25.13057883
> show #1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.86619,0.42427,-0.26402,-15.136,-0.28752,0.85527,0.4311,-36.039,0.40871,-0.29751,0.86281,-15.483
> view matrix models
> #3,0.90661,0.36972,0.20337,-98.555,-0.42129,0.76588,0.48575,0.44702,0.023831,-0.52606,0.85011,114.92
> view matrix models
> #3,0.93468,0.34554,-0.08347,-48.102,-0.28246,0.86449,0.41577,-36.118,0.21583,-0.36504,0.90563,32.043
> view matrix models
> #3,0.94197,0.31988,-0.10185,-41.514,-0.2492,0.86957,0.42632,-46.326,0.22494,-0.3762,0.89882,33.383
> view matrix models
> #3,0.62645,0.6932,-0.35642,3.5807,-0.70215,0.70041,0.12811,139.66,0.33845,0.17001,0.9255,-99.861
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62645,0.6932,-0.35642,6.3205,-0.70215,0.70041,0.12811,146.28,0.33845,0.17001,0.9255,-98.687
Fit molecule PaGS_chainA.pdb (#3) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.2766, steps = 112
shifted from previous position = 5.49
rotated from previous position = 22.6 degrees
atoms outside contour = 1809, contour level = 0.25644
Position of PaGS_chainA.pdb (#3) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.63143998 0.77542042 -0.00259204 -69.75286345
-0.77542470 0.63143761 -0.00175387 198.20992594
0.00027673 0.00311740 0.99999510 -1.26912643
Axis 0.00314102 -0.00184980 -0.99999336
Axis point 173.63300869 172.48603588 0.00000000
Rotation angle (degrees) 50.84382666
Shift along axis 0.68337463
> ~select #3
Nothing selected
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #4
---
Chain | Description
A | No description available
> hide #4 models
> show #4 models
> ui mousemode right "rotate selected models"
> select #4
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> ui mousemode right select
> select #2
4 models selected
> ~select #2
Nothing selected
> select #4
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.5985,0.47216,0.64719,145.51,0.76332,0.58131,0.2818,-140.16,-0.24316,0.66267,-0.70833,238.25
> view matrix models
> #4,-0.64772,0.76039,-0.047544,227.9,0.7519,0.64806,0.12108,-121.1,0.12288,0.042677,-0.9915,326.31
> view matrix models
> #4,-0.58474,0.74357,-0.32432,267.44,0.77615,0.62908,0.042908,-108.66,0.23593,-0.22664,-0.94497,343.92
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.58474,0.74357,-0.32432,265.7,0.77615,0.62908,0.042908,-94.851,0.23593,-0.22664,-0.94497,386.73
> view matrix models
> #4,-0.58474,0.74357,-0.32432,266.22,0.77615,0.62908,0.042908,-97.473,0.23593,-0.22664,-0.94497,386.78
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.90317,0.38289,0.19411,-87.576,0.41415,-0.89616,-0.15928,307.7,0.11296,0.22424,-0.96796,332.71
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.90317,0.38289,0.19411,-84.721,0.41415,-0.89616,-0.15928,297.98,0.11296,0.22424,-0.96796,331.84
Fit molecule PaGS_chainA.pdb (#4) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.2801, steps = 88
shifted from previous position = 2.9
rotated from previous position = 17.7 degrees
atoms outside contour = 1778, contour level = 0.25644
Position of PaGS_chainA.pdb (#4) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.83151718 0.55549650 -0.00167405 -66.12881578
0.55549869 -0.83151623 0.00139813 222.89400760
-0.00061534 -0.00209250 -0.99999762 404.95708371
Axis -0.95695268 -0.29024337 0.00059830
Axis point 0.00000000 121.66837509 202.35182947
Rotation angle (degrees) 179.89550237
Shift along axis -1.16907617
> ~select #4
Nothing selected
> color #1 #db75d7 transparency 0
> color #1 #d844db transparency 0
> color #1 #d9a5db transparency 0
> color #1 #db30d4 transparency 0
> color #3 #3adee5 transparency 0
> color #3 #89e5d2 transparency 0
> color #3 #8ae5d7 transparency 0
> color #3 #89e5d6 transparency 0
> color #3 #8ae5e4 transparency 0
> color #2 #f2fff580 models
> volume #2 level 0.234
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #5
---
Chain | Description
A | No description available
> color #5 #cae0fd transparency 0
> color #5 #bbc9fd transparency 0
> select #5
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> view matrix models #5,1,0,0,-19.8,0,1,0,-32.253,0,0,1,39.911
> view matrix models #5,1,0,0,-20.732,0,1,0,-33.706,0,0,1,42.209
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.3931,0.39054,0.83244,-111.97,0.48395,0.6819,-0.54845,19.376,-0.78183,0.61846,0.079057,264.64
> view matrix models
> #5,-0.53906,0.5884,0.60266,97.756,0.63616,0.75338,-0.16651,-97.026,-0.55201,0.29363,-0.78043,431.47
> view matrix models
> #5,-0.64294,0.59725,0.47951,141.33,0.61586,0.77533,-0.13993,-101.53,-0.45535,0.20535,-0.86631,442.46
> ui tool show Matchmaker
> matchmaker #4 to #5
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 PaGS_chainA.pdb, chain A (#5) with PaGS_chainA.pdb, chain A (#4),
sequence alignment score = 2493.7
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> undo
> select #4
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> view matrix models
> #4,-0.79705,0.33034,0.50555,221.09,0.29482,0.94344,-0.15165,-60.46,-0.52706,0.028171,-0.84936,488.72
> view matrix models
> #4,-0.79588,-0.60206,-0.064017,500.69,-0.604,0.79684,0.01508,135.14,0.041933,0.050669,-0.99783,386
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.79588,-0.60206,-0.064017,516.89,-0.604,0.79684,0.01508,175.39,0.041933,0.050669,-0.99783,386.51
> view matrix models
> #4,-0.79588,-0.60206,-0.064017,519.08,-0.604,0.79684,0.01508,172.74,0.041933,0.050669,-0.99783,391.1
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.66283,0.61411,-0.4284,33.498,0.45376,-0.78455,-0.42258,318.34,-0.59561,0.085703,-0.79869,488.85
> view matrix models
> #4,-0.17998,0.97064,0.15956,45.069,0.97634,0.15651,0.14923,-78.752,0.11987,0.18265,-0.97584,344.95
> view matrix models
> #4,0.39129,0.91859,0.055569,-52.123,0.917,-0.39427,0.060556,54.671,0.077536,0.027262,-0.99662,387.46
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.39129,0.91859,0.055569,-25.093,0.917,-0.39427,0.060556,-69.817,0.077536,0.027262,-0.99662,364.38
> view matrix models
> #4,0.39129,0.91859,0.055569,-26.976,0.917,-0.39427,0.060556,-67.192,0.077536,0.027262,-0.99662,367.8
> ~select #4
Nothing selected
> select #4
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> view matrix models
> #4,0.39129,0.91859,0.055569,-27.67,0.917,-0.39427,0.060556,-66.446,0.077536,0.027262,-0.99662,362.11
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.56276,0.82543,0.044378,-45.802,0.61161,-0.45189,0.64941,-95.106,0.55609,-0.33832,-0.75914,282.72
> view matrix models
> #4,0.3783,-0.0067064,-0.92566,328.43,0.8808,-0.305,0.36217,-130.11,-0.28475,-0.95233,-0.10947,466.35
> view matrix models
> #4,0.3774,-0.0086192,-0.92601,329.05,0.88088,-0.30515,0.36185,-130.04,-0.28569,-0.95227,-0.10757,466.2
> view matrix models
> #4,-0.16396,-0.72103,-0.67323,537.33,-0.73391,-0.36686,0.57165,199.49,-0.65916,0.58782,-0.46902,322.64
> view matrix models
> #4,-0.19386,-0.43025,-0.88165,526.72,-0.7955,-0.45698,0.39793,261.66,-0.5741,0.77849,-0.25368,228.71
> view matrix models
> #4,-0.82207,0.54513,0.16444,290.7,0.0096585,-0.27541,0.96128,-52.435,0.56931,0.79182,0.22114,-112.03
> view matrix models
> #4,-0.56435,0.80951,0.16186,184.32,-0.34046,-0.40684,0.84768,70.234,0.75206,0.42328,0.50521,-134.11
> view matrix models
> #4,-0.60202,0.7425,-0.2937,288,-0.6113,-0.19194,0.76777,103.76,0.5137,0.64176,0.56944,-134.58
> view matrix models
> #4,-0.50753,0.8408,-0.1883,229.44,-0.14671,0.13102,0.98046,-98.376,0.84905,0.52524,0.056856,-93.412
> view matrix models
> #4,-0.40942,0.8971,-0.16606,193.12,0.22756,0.27668,0.93363,-199.94,0.88351,0.34446,-0.31742,1.1435
> view matrix models
> #4,-0.36277,0.91623,-0.17005,179.94,0.38748,0.31427,0.86666,-230.15,0.8475,0.24851,-0.46903,54.76
> view matrix models
> #4,-0.37475,0.91173,-0.16824,183.1,0.34739,0.30633,0.88628,-223.37,0.85958,0.27369,-0.43152,40.523
> view matrix models
> #4,-0.73226,0.67062,0.11857,255.48,0.45205,0.34842,0.82113,-242.58,0.50936,0.65488,-0.55828,68.578
> view matrix models
> #4,-0.73071,0.67219,0.11929,254.71,0.45621,0.35079,0.81781,-243.35,0.50788,0.652,-0.56298,70.303
> view matrix models
> #4,-0.77121,0.62946,0.094988,276.14,0.33849,0.27911,0.89862,-218.5,0.53913,0.72518,-0.42832,25.121
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.77121,0.62946,0.094988,277.69,0.33849,0.27911,0.89862,-93.441,0.53913,0.72518,-0.42832,44.688
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.78082,0.62019,0.075474,285.1,0.44495,0.46722,0.76402,-128.08,0.43857,0.63014,-0.64076,123.4
> view matrix models
> #4,-0.6167,0.77483,-0.13901,258.59,0.43018,0.47959,0.76481,-127.31,0.65926,0.41186,-0.62908,113.95
> view matrix models
> #4,0.27798,0.95596,0.094122,-15.215,0.85032,-0.29047,0.43885,-15,0.44686,-0.04196,-0.89362,294.68
> view matrix models
> #4,0.24741,0.96114,-0.12243,29.848,0.88016,-0.17012,0.44314,-45.137,0.40509,-0.2174,-0.88805,336.08
> view matrix models
> #4,0.22727,0.89627,-0.38085,93.471,0.90289,-0.0474,0.42725,-70.49,0.36488,-0.44097,-0.82,374.91
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.22727,0.89627,-0.38085,93.726,0.90289,-0.0474,0.42725,-78.414,0.36488,-0.44097,-0.82,379.57
> view matrix models
> #4,0.22727,0.89627,-0.38085,93.989,0.90289,-0.0474,0.42725,-84.767,0.36488,-0.44097,-0.82,381.1
> view matrix models
> #4,0.22727,0.89627,-0.38085,95.155,0.90289,-0.0474,0.42725,-92.843,0.36488,-0.44097,-0.82,385.71
> ui tool show Matchmaker
> matchmaker #1 to #4
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 PaGS_chainA.pdb, chain A (#4) with PaGS_chainA_isolde.pdb, chain A
(#1), sequence alignment score = 2314.9
RMSD between 411 pruned atom pairs is 0.934 angstroms; (across all 477 pairs:
1.507)
> close session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_2.8A_map.mrc
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.256, step 1, values float32
> volume #2 color #f0ffed
> volume #2 color #f0ffed81
> volume #2 color #f0ffed82
> color #2 #f0fff6 models transparency 0
> color #2 #f0fff67c models
> color #2 #f0fff67d models
> color #2 #fefff87d models
> color #2 #8f8f8c7d models
> color #2 #9a9a977d models
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #3
---
Chain | Description
A | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for PaGS_chainA_isolde.pdb #3
---
Chain | Description
A | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for PaGS_chainA_isolde.pdb #3
---
Chain | Description
A | No description available
> hide #1 models
> show #1 models
> close #3
> volume #2 level 0.1863
> volume #2 level 0.1386
> volume #2 level 0.09375
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #3
---
Chain | Description
A | No description available
> volume #2 level 0.1919
> select #3
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> view matrix models #3,1,0,0,-7.8955,0,1,0,-49.531,0,0,1,-0.13008
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60301,0.7972,0.029153,-76.57,-0.79738,0.60126,0.051751,192.31,0.023728,-0.054453,0.99823,5.2667
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.60301,0.7972,0.029153,-75.542,-0.79738,0.60126,0.051751,198.08,0.023728,-0.054453,0.99823,7.4938
> ~select #3
Nothing selected
> ui tool show "Fit in Map"
Fit molecule PaGS_chainA.pdb (#3) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.2766, steps = 60
shifted from previous position = 3.82
rotated from previous position = 4.15 degrees
atoms outside contour = 1427, contour level = 0.19193
Position of PaGS_chainA.pdb (#3) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.63176574 0.77515457 -0.00272965 -69.76281344
-0.77515928 0.63176348 -0.00173309 198.06281725
0.00038108 0.00321082 0.99999477 -1.30929643
Axis 0.00318895 -0.00200651 -0.99999290
Axis point 173.58631740 172.46294765 0.00000000
Rotation angle (degrees) 50.81976074
Shift along axis 0.68940290
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
Summary of feedback from opening
/Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 SER B
10 HIS B 20 1 11
Start residue of secondary structure not found: HELIX 21 21 ASP B 49 ALA B 54
1 6
Start residue of secondary structure not found: HELIX 22 22 GLY B 60 SER B 62
1 3
Start residue of secondary structure not found: HELIX 23 23 ASP B 80 THR B 82
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 113 THR B
127 1 15
450 messages similar to the above omitted
Chain information for PaGS_chainA.pdb #4
---
Chain | Description
A | No description available
> ui tool show "Build Structure"
> toolshed show
> ui tool show Matchmaker
> matchmaker #4 to #3
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 PaGS_chainA.pdb, chain A (#3) with PaGS_chainA.pdb, chain A (#4),
sequence alignment score = 2493.7
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> hide #3 models
> show #3 models
> select #4
3732 atoms, 3828 bonds, 477 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.63177,0.77515,-0.0027297,-67.211,-0.77516,0.63176,-0.0017331,194.51,0.00038108,0.0032108,0.99999,50.247
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.63319,0.76979,-0.080556,-52.384,-0.76827,0.63773,0.055254,181.52,0.093907,0.026902,0.99522,26.015
> view matrix models
> #4,0.72414,0.26913,0.63497,-107.54,0.51518,0.40099,-0.75749,90.946,-0.45848,0.87565,0.15173,140.23
> view matrix models
> #4,0.91466,0.15972,-0.37134,53.823,0.18851,-0.98116,0.042297,279.39,-0.35758,-0.10869,-0.92754,500.19
> view matrix models
> #4,0.94289,-0.2987,-0.14743,93.725,-0.31899,-0.93716,-0.14134,416.25,-0.095944,0.18029,-0.97892,397.15
> view matrix models
> #4,0.85923,-0.48197,-0.17157,151.24,-0.50451,-0.85388,-0.12789,438.94,-0.084861,0.19644,-0.97684,391.27
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85923,-0.48197,-0.17157,151.59,-0.50451,-0.85388,-0.12789,440.07,-0.084861,0.19644,-0.97684,386.91
> view matrix models
> #4,0.85923,-0.48197,-0.17157,151.08,-0.50451,-0.85388,-0.12789,440.85,-0.084861,0.19644,-0.97684,385.26
Fit molecule PaGS_chainA.pdb (#4) to map PaGS_2.8A_map.mrc (#2) using 3732
atoms
average map value = 0.2807, steps = 104
shifted from previous position = 4.83
rotated from previous position = 17.5 degrees
atoms outside contour = 1396, contour level = 0.19193
Position of PaGS_chainA.pdb (#4) relative to PaGS_2.8A_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.95271800 -0.30385508 0.00070964 62.39199607
-0.30385584 -0.95271368 0.00287678 392.22826142
-0.00019804 -0.00295639 -0.99999561 405.03205479
Axis -0.98810876 0.15375650 -0.00012944
Axis point 0.00000000 201.27092139 202.21886296
Rotation angle (degrees) 179.83088045
Shift along axis -1.39486097
> ~select #4
Nothing selected
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/build_PaGS.cxs
> includeMaps true
> color #1 #db67c8 transparency 0
> color #3 #bde5d6 transparency 0
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/build_PaGS.cxs
> includeMaps true
> ui tool show "Side View"
> select #1
7344 atoms, 7440 bonds, 477 residues, 1 model selected
> ui mousemode right select
> ~select #1
Nothing selected
> volume #2 level 0.1355
> select /A:167-190
718 atoms, 736 bonds, 72 residues, 3 models selected
> select /A:167-192
776 atoms, 797 bonds, 78 residues, 3 models selected
> select /A:167-193
804 atoms, 828 bonds, 81 residues, 3 models selected
> volume #2 level 0.1047
> volume #2 level 0.07133
> select /A:169-193
722 atoms, 740 bonds, 75 residues, 3 models selected
> volume #2 level 0.1124
> select /A:169-190
636 atoms, 648 bonds, 66 residues, 3 models selected
> volume #2 level 0.09442
> volume #2 level 0.2022
> volume #2 level 0.1149
> volume #2 level 0.07903
> delete /A:169-190
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> volume #2 level 0.1509
> volume #2 level 0.1175
> volume #2 level 0.1073
> volume #2 level 0.07133
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/build_PaGS.cxs
> includeMaps true
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for PaGS_chainA_isolde.pdb
---
Chain | Description
1.2/A | No description available
Done loading forcefield
> select /A:191-195
144 atoms, 147 bonds, 15 residues, 3 models selected
> select /A:193
28 atoms, 28 bonds, 3 residues, 3 models selected
> select /A:192
28 atoms, 28 bonds, 3 residues, 3 models selected
> select /A:191
30 atoms, 27 bonds, 3 residues, 3 models selected
> select /A:195
28 atoms, 25 bonds, 3 residues, 3 models selected
> select #1
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 9 models selected
> close #1.1,3#1#1.2
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for PaGS_chainA_isolde.pdb
---
Chain | Description
1.2/A | No description available
Done loading forcefield
> select /A:191-195
144 atoms, 147 bonds, 15 residues, 3 models selected
> select /A:194
30 atoms, 27 bonds, 3 residues, 3 models selected
> delete /A:169-190
Opened PaGS_2.8A_map.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.36, shown
at step 1, values float32
/Users/iphan/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py:446: RuntimeWarning: invalid
value encountered in log
logscores = numpy.log(r.scores)
> select /A:194
30 atoms, 27 bonds, 3 residues, 3 models selected
> cview /A:194
> cview 1/A:194
> view 1/A:194; cofr center showpivot true
Expected an objects specifier or a view name or a keyword
> cview 1/A:194
> view 1/A:194; cofr center showpivot true
Expected an objects specifier or a view name or a keyword
ISOLDE: started sim
ISOLDE: paused sim
> clipper spotlight radius 13.00
> volume #1.1.1.1 level 0.1364
> volume #1.1.1.1 level 0.07835
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #1.1.1.1 level 0.07426
> cview 1/A:194
> view 1/A:194; cofr center showpivot true
Expected an objects specifier or a view name or a keyword
> select /A:194
30 atoms, 27 bonds, 3 residues, 3 models selected
ISOLDE: started sim
> volume #1.1.1.1 level 0.0487
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
ISOLDE: started sim
> clipper spotlight radius 14.00
> volume #1.1.1.1 level 0.09452
ISOLDE: paused sim
> delete /A:191
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close #1.1
> close #1.3
> close #1
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde.pdb
Chain information for PaGS_chainA_isolde.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_2.8A_map.mrc
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.256, step 1, values float32
> color #2 #ffb2ff89 models
> color #2 #ffb2ff8a models
> volume #2 level 0.09965
> volume #2 level 0.1171
> delete /A:169-191
> volume #2 level 0.1942
> volume #2 level 0.09219
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for PaGS_chainA_isolde.pdb
---
Chain | Description
1.2/A | No description available
Done loading forcefield
> select /A:194
30 atoms, 27 bonds, 3 residues, 3 models selected
Opened PaGS_2.8A_map.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.36, shown
at step 1, values float32
ISOLDE: started sim
> volume #1.1.1.1 level 0.07839
> clipper spotlight radius 13.00
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> select /A:197
28 atoms, 25 bonds, 3 residues, 3 models selected
> select /A:200
35 atoms, 32 bonds, 3 residues, 3 models selected
> select /A:210
33 atoms, 30 bonds, 3 residues, 3 models selected
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
> volume #1.1.1.1 level 0.1317
> select /A:210
33 atoms, 30 bonds, 3 residues, 3 models selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /A:214
30 atoms, 27 bonds, 3 residues, 3 models selected
> volume #1.1.1.1 level 0.2512
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
> select clear
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1195
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
ISOLDE: started sim
> select clear
> volume #1.1.1.1 level 0.1892
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /A:221
33 atoms, 30 bonds, 3 residues, 3 models selected
> cview /A:221
ISOLDE: started sim
ISOLDE: paused sim
> cview 1/A:221
> view 1/A:221; cofr center showpivot true
Expected an objects specifier or a view name or a keyword
> cview 1/A:221
> view 1/A:221; cofr center showpivot true
Expected an objects specifier or a view name or a keyword
> select 1/A:221
Expected an objects specifier or a keyword
> select #1/A:221
15 atoms, 14 bonds, 1 residue, 1 model selected
> cview #1/A:221
> cview #1/A:223
> select #1/A:223
10 atoms, 9 bonds, 1 residue, 1 model selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:230
19 atoms, 18 bonds, 1 residue, 1 model selected
> cview #1/A:230
ISOLDE: started sim
ISOLDE: paused sim
> cview #1/A:235
> select #1/A:235
14 atoms, 13 bonds, 1 residue, 1 model selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:238
16 atoms, 15 bonds, 1 residue, 1 model selected
> cview #1/A:238
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.2755
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> cview #1/A:276
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> cview #1/A:280
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> cview #1/A:280
> select #1/A:280
17 atoms, 17 bonds, 1 residue, 1 model selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select #1/A:286
12 atoms, 11 bonds, 1 residue, 1 model selected
> cview #1/A:286
ISOLDE: started sim
> select clear
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
> select clear
Peptide bond must be mobile in the simulation!
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> cview #1/A:290
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> cview #1/A:294
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> cview #1/A:323
ISOLDE: started sim
Unable to flip peptide bond after 50 rounds. Giving up.
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> cview #1/A:331
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> cview #1/A:334
> volume #1.1.1.1 level 0.1517
> volume #1.1.1.1 level 0.08973
> volume #1.1.1.1 level 0.1269
> cview #1/A:335
ISOLDE: started sim
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
No rotamer preview selected! Ignoring command.
> undo
No rotamer preview selected! Ignoring command.
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> cview #1/A:341
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> cview #1/A:346
ISOLDE: started sim
> select clear
> volume #1.1.1.1 level 0.1338
> volume #1.1.1.1 level 0.1083
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> cview #1/A:352
> cview #1/A:357
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> select clear
> cview #1/A:365
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> select clear
> cview #1/A:369
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.2708
> cview #1/A:378
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> cview #1/A:388
> cview #1/A:393
ISOLDE: started sim
> select clear
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1633
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> volume #1.1.1.1 level 0.1499
ISOLDE: started sim
> volume #1.1.1.1 level 0.2868
> volume #1.1.1.1 level 0.2242
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: resumed sim
Unable to flip peptide bond after 50 rounds. Giving up.
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1524
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> cview #1/A:399
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
> cview #1/A:405
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/interfaces.cxs
Opened PaGS_3.0A_double-unit_centered_P1_J280_006_volume_map.mrc as #3, grid
size 240,240,240, pixel 1.36, shown at level 0.228, step 1, values float32
Opened PaGS_4.1A_double-unit_extended_centered_P1_J297_003_volume_map.mrc as
#1, grid size 240,240,240, pixel 1.36, shown at level 0.174, step 1, values
float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc as #2, grid size
256,256,256, pixel 1.36, shown at level 0.225, step 1, values float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc z flip as #4, grid
size 256,256,256, pixel 1.36, shown at level 0.189, step 1, values float32
opened ChimeraX session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/interfaces.cxs
Opened PaGS_3.0A_double-unit_centered_P1_J280_006_volume_map.mrc as #3, grid
size 240,240,240, pixel 1.36, shown at level 0.228, step 1, values float32
Opened PaGS_4.1A_double-unit_extended_centered_P1_J297_003_volume_map.mrc as
#1, grid size 240,240,240, pixel 1.36, shown at level 0.174, step 1, values
float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc as #2, grid size
256,256,256, pixel 1.36, shown at level 0.225, step 1, values float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc z flip as #4, grid
size 256,256,256, pixel 1.36, shown at level 0.189, step 1, values float32
opened ChimeraX session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/interfaces.cxs
Opened PaGS_3.0A_double-unit_centered_P1_J280_006_volume_map.mrc as #3, grid
size 240,240,240, pixel 1.36, shown at level 0.228, step 1, values float32
Opened PaGS_4.1A_double-unit_extended_centered_P1_J297_003_volume_map.mrc as
#1, grid size 240,240,240, pixel 1.36, shown at level 0.174, step 1, values
float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc as #2, grid size
256,256,256, pixel 1.36, shown at level 0.225, step 1, values float32
Opened PaGS_3.7A_extended_double_P1_J404_006_volume_map.mrc z flip as #4, grid
size 256,256,256, pixel 1.36, shown at level 0.189, step 1, values float32
opened ChimeraX session
> close session
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/build_PaGS.cxs
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.0713, step 1, values float32
opened ChimeraX session
> cview #1/A:405
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> volume #2 color #9a9a977d
> volume #2 level 0.1087
> ui tool show "Side View"
> volume #2 level 0.08626
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Done loading forcefield
Opened PaGS_2.8A_map.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.36, shown
at step 1, values float32
> cview #1/A:405
> clipper spotlight radius 13.00
> select clear
> cview #1/A:405
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 6 models selected
> select #1.2
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 6 models selected
> select #1
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 13 models selected
> select #1
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 13 models selected
> hide #!1 models
> show #!1 models
> select #1.2
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 6 models selected
> select #1.2/A:405@CA
1 atom, 1 residue, 1 model selected
> select #1.2/A:405@CA
1 atom, 1 residue, 1 model selected
> select #1.2/A:405@CA
1 atom, 1 residue, 1 model selected
> select #1.1.1
4 models selected
> select #1.1
5 models selected
> ui tool show ISOLDE
> set selectionWidth 4
Done loading forcefield
> select #1
7032 atoms, 7122 bonds, 1 pseudobond, 455 residues, 13 models selected
> close session
Window position QRect(-1038,-1730 526x1185) outside any known screen, using
primary screen
> open
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/build_PaGS.cxs
Opened PaGS_2.8A_map.mrc as #2, grid size 256,256,256, pixel 1.36, shown at
level 0.0713, step 1, values float32
opened ChimeraX session
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Done loading forcefield
Opened PaGS_2.8A_map.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.36, shown
at step 1, values float32
> clipper spotlight radius 13.00
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> cview #1/A:405
ISOLDE: started sim
> volume #1.1.1.1 level 0.1396
> volume #1.1.1.1 level 0.07313
> volume #1.1.1.1 level 0.1019
> select clear
ISOLDE: paused sim
ISOLDE: resumed sim
> select clear
> volume #1.1.1.1 level 0.1396
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Side View"
> select clear
> volume #1.1.1.1 level 0.08385
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:405
19 atoms, 18 bonds, 1 residue, 1 model selected
> cview #1/A:405
> volume #1.1.1.1 level 0.1409
> volume #1.1.1.1 level 0.07015
> volume #1.1.1.1 level 0.1272
> volume #1.1.1.1 level 0.08157
> volume #1.1.1.1 level 0.1501
> volume #1.1.1.1 level 0.07472
> volume #1.1.1.1 level 0.1341
> volume #1.1.1.1 level 0.1683
> clipper spotlight radius 14.00
> volume #1.1.1.1 level 0.1262
> volume #1.1.1.1 level 0.08645
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
ISOLDE: started sim
> volume #1.1.1.1 level 0.07282
> volume #1.1.1.1 level 0.09554
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
> volume #1.1.1.1 level 0.107
> volume #1.1.1.1 level 0.08788
> select clear
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1135
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.08322
> select clear
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
ISOLDE: started sim
> volume #1.1.1.1 level 0.1296
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.09694
> volume #1.1.1.1 level 0.1016
ISOLDE: started sim
> volume #1.1.1.1 level 0.08198
> volume #1.1.1.1 level 0.07414
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> cview #1/A:405
> volume #1.1.1.1 level 0.09519
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.09285
> volume #1.1.1.1 level 0.1209
> volume #1.1.1.1 level 0.09051
> volume #1.1.1.1 level 0.1256
> volume #1.1.1.1 level 0.1116
> volume #1.1.1.1 level 0.156
> volume #1.1.1.1 level 0.08349
> volume #1.1.1.1 level 0.1396
> volume #1.1.1.1 level 0.09519
> volume #1.1.1.1 level 0.08583
> volume #1.1.1.1 level 0.09753
> volume #1.1.1.1 level 0.1046
> volume #1.1.1.1 level 0.09285
> save
> /Users/iphan/Documents/ssgcid/CryoEM/gln_synthetase/pnnl_datasets/10_2021/refine_3.1A_double_unit/PaGS_chainA_isolde_chopped.pdb
> models #1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-14.7.23
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.7 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: 1731.100.130.0.0 (iBridge: 19.16.14242.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1824)
Kernel Version: Darwin 19.6.0
Time since boot: 8 days 48 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal: Supported, feature set macOS GPUFamily2 v1
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: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 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: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Crashed in Apple graphics driver. Only Apple can fix this. More details
https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#maccrash
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Reported by Isabelle Phan