![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9280 closed defect (can't reproduce)
Crash handling event
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.13.6-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.
Process: ChimeraX [54267]
Path: /Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [54267]
User ID: 581685
Date/Time: 2023-06-22 20:43:45.870 +0200
OS Version: Mac OS X 10.13.6 (17G14042)
Report Version: 12
Anonymous UUID: 9D557B09-8913-C4DD-7DC2-2E1A87166C5B
Time Awake Since Boot: 3600000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff5d960b66 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff5db2b080 pthread_kill + 333
2 libsystem_c.dylib 0x00007fff5d86e6fe raise + 26
3 libsystem_platform.dylib 0x00007fff5db1ef5a _sigtramp + 26
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010844006d cfunction_call + 125
6 org.python.python 0x00000001084016cc _PyObject_Call + 140
7 QtCore.abi3.so 0x000000011665b957 PyQtSlot::call(_object*, _object*) const + 39
8 QtCore.abi3.so 0x000000011665b866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9 QtCore.abi3.so 0x000000011665c455 PyQtSlotProxy::unislot(void**) + 85
10 QtCore.abi3.so 0x000000011665c3ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11 QtCore 0x0000000116a37b9f QObject::event(QEvent*) + 943
12 QtWidgets 0x00000001175299ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13 QtWidgets 0x000000011752ae11 QApplication::notify(QObject*, QEvent*) + 497
14 QtWidgets.abi3.so 0x00000001170dcdb9 sipQApplication::notify(QObject*, QEvent*) + 233
15 QtCore 0x0000000116a0ca34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16 QtCore 0x0000000116a0dd79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17 libqcocoa.dylib 0x0000000127645259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18 libqcocoa.dylib 0x00000001276459c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40
19 com.apple.CoreFoundation 0x00007fff358d4691 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
20 com.apple.CoreFoundation 0x00007fff3598ec8c __CFRunLoopDoSource0 + 108
21 com.apple.CoreFoundation 0x00007fff358b714c __CFRunLoopDoSources0 + 300
22 com.apple.CoreFoundation 0x00007fff358b656d __CFRunLoopRun + 1293
23 com.apple.CoreFoundation 0x00007fff358b5dd3 CFRunLoopRunSpecific + 483
24 com.apple.HIToolbox 0x00007fff34ba0d96 RunCurrentEventLoopInMode + 286
25 com.apple.HIToolbox 0x00007fff34ba0a0f ReceiveNextEventCommon + 366
26 com.apple.HIToolbox 0x00007fff34ba0884 _BlockUntilNextEventMatchingListInModeWithFilter + 64
27 com.apple.AppKit 0x00007fff32e4da3b _DPSNextEvent + 2085
28 com.apple.AppKit 0x00007fff335e3e34 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 3044
29 com.apple.AppKit 0x00007fff32e4284d -[NSApplication run] + 764
30 libqcocoa.dylib 0x000000012764462f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31 QtCore 0x0000000116a08acf QEventLoop::exec(QFlags) + 431
32 QtCore 0x0000000116a0d042 QCoreApplication::exec() + 130
33 QtWidgets.abi3.so 0x00000001171ce702 meth_QApplication_exec_(_object*, _object*) + 82
34 org.python.python 0x000000010844006d cfunction_call + 125
35 org.python.python 0x000000010840117d _PyObject_MakeTpCall + 365
36 org.python.python 0x00000001084d961c call_function + 876
37 org.python.python 0x00000001084d6ab3 _PyEval_EvalFrameDefault + 25219
38 org.python.python 0x0000000108401948 function_code_fastcall + 104
39 org.python.python 0x000000010840398a method_vectorcall + 202
40 org.python.python 0x00000001084d958c call_function + 732
41 org.python.python 0x00000001084d6ab3 _PyEval_EvalFrameDefault + 25219
42 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
43 org.python.python 0x00000001084018d1 _PyFunction_Vectorcall + 289
44 org.python.python 0x00000001084d958c call_function + 732
45 org.python.python 0x00000001084d6b4b _PyEval_EvalFrameDefault + 25371
46 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
47 org.python.python 0x00000001084d070b PyEval_EvalCode + 139
48 org.python.python 0x00000001084cd592 builtin_exec + 626
49 org.python.python 0x000000010843f86a cfunction_vectorcall_FASTCALL + 218
50 org.python.python 0x00000001084d958c call_function + 732
51 org.python.python 0x00000001084d6b4b _PyEval_EvalFrameDefault + 25371
52 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
53 org.python.python 0x00000001084018d1 _PyFunction_Vectorcall + 289
54 org.python.python 0x00000001084d958c call_function + 732
55 org.python.python 0x00000001084d6b4b _PyEval_EvalFrameDefault + 25371
56 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
57 org.python.python 0x00000001084018d1 _PyFunction_Vectorcall + 289
58 org.python.python 0x000000010853fe20 pymain_run_module + 208
59 org.python.python 0x000000010853f537 Py_RunMain + 1431
60 org.python.python 0x000000010853fb3f pymain_main + 223
61 org.python.python 0x000000010853fa4b Py_Main + 43
62 edu.ucsf.cgl.ChimeraX 0x00000001083badc8 main + 120
63 libdyld.dylib 0x00007fff5d810015 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x000000010a26ca9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x000000010a26ca9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x000000010a26ca9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff5d961c02 kevent64 + 10
1 QtWebEngineCore 0x000000011b228e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011b228cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011b1bca94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b1c6778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011b1c7150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011b1c6c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff5d961c02 kevent64 + 10
1 QtWebEngineCore 0x000000011b228e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011b228cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011f0f5f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1461db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
10 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
11 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 8:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 QtWebEngineCore 0x000000011b215e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x000000011c4cd5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
6 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
7 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 9:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b14620f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 10:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff5d961c02 kevent64 + 10
1 QtWebEngineCore 0x000000011b228e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011b228cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 11:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b14620f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1461db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
10 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
11 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 13:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1c676a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011b1c7150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x000000011b1c6d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1461db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
10 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
11 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1461db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
10 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
11 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1461db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000011b1b162b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011b1757cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000011b1d0a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
10 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
11 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 17:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff358b7405 __CFRunLoopServiceMachPort + 341
3 com.apple.CoreFoundation 0x00007fff358b6757 __CFRunLoopRun + 1783
4 com.apple.CoreFoundation 0x00007fff358b5dd3 CFRunLoopRunSpecific + 483
5 com.apple.AppKit 0x00007fff32f8afc4 _NSEventThread + 184
6 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
7 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
8 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 18:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b21e2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011b1c676a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x000000011b1c6e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x000000011b1c6c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 19:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x0000000158bfe2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 20:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x0000000158bfe2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 21:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 libopenblas.0.dylib 0x0000000158bfe2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 22:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b1c6778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011b1c7150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011b1c6cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 23:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff5d9571fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d956714 mach_msg + 60
2 QtWebEngineCore 0x000000011b21e492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011b1c6778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x000000011b1c7150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x000000011b1c6cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011b219e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 24:
0 libsystem_kernel.dylib 0x00007fff5d96128a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff5db2820e _pthread_wqthread + 1552
2 libsystem_pthread.dylib 0x00007fff5db27be9 start_wqthread + 13
Thread 25:
0 libsystem_pthread.dylib 0x00007fff5db27bdc start_wqthread + 0
1 ??? 0x4058504320000000 0 + 4636544065607827456
Thread 26:
0 libsystem_kernel.dylib 0x00007fff5d96128a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff5db28009 _pthread_wqthread + 1035
2 libsystem_pthread.dylib 0x00007fff5db27be9 start_wqthread + 13
Thread 27:
0 libsystem_kernel.dylib 0x00007fff5d96128a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff5db28009 _pthread_wqthread + 1035
2 libsystem_pthread.dylib 0x00007fff5db27be9 start_wqthread + 13
Thread 28:
0 libsystem_pthread.dylib 0x00007fff5db27bdc start_wqthread + 0
1 ??? 0x000000000004b55f 0 + 308575
Thread 29:
0 libsystem_kernel.dylib 0x00007fff5d960a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5db29589 _pthread_cond_wait + 732
2 org.python.python 0x000000010852fd6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010857ea1f acquire_timed + 111
4 org.python.python 0x000000010857eb30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000108409e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x00000001084d958c call_function + 732
7 org.python.python 0x00000001084d6a92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
9 org.python.python 0x00000001084018d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001084d958c call_function + 732
11 org.python.python 0x00000001084d6a92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x00000001084da283 _PyEval_EvalCode + 2611
13 org.python.python 0x00000001084018d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x00000001084d958c call_function + 732
15 org.python.python 0x00000001084d6a92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x0000000108401948 function_code_fastcall + 104
17 org.python.python 0x00000001084d958c call_function + 732
18 org.python.python 0x00000001084d6a92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x0000000108401948 function_code_fastcall + 104
20 org.python.python 0x00000001084d958c call_function + 732
21 org.python.python 0x00000001084d6a92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x0000000108401948 function_code_fastcall + 104
23 org.python.python 0x00000001084039d2 method_vectorcall + 274
24 org.python.python 0x000000010857e3c6 t_bootstrap + 70
25 org.python.python 0x000000010852f8c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff5db28661 _pthread_body + 340
27 libsystem_pthread.dylib 0x00007fff5db2850d _pthread_start + 377
28 libsystem_pthread.dylib 0x00007fff5db27bf9 thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007fff96246380 rcx: 0x00000001088a3a48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00000001088a3a80 rsp: 0x00000001088a3a48
r8: 0x00000001088a3f48 r9: 0xffffffff00000000 r10: 0x00007fff962463c8 r11: 0x0000000000000287
r12: 0x0000000000000307 r13: 0x000060c000046c30 r14: 0x000000000000000b r15: 0x000000000000002d
rip: 0x00007fff5d960b66 rfl: 0x0000000000000286 cr2: 0x0000000108531920
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x1083c5000 - 0x108629fff +org.python.python (3.9.6, [c] 2001-2019 Python Software Foundation. - 3.9.6) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
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0x108cdd000 - 0x108cdefff +_random.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_random.cpython-39-darwin.so
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0x1093b7000 - 0x1094ceff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x10953c000 - 0x109572fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x109586000 - 0x10959bff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x1095eb000 - 0x1095fafff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x10964b000 - 0x109662fff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x109773000 - 0x109775fff +fcntl.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/fcntl.cpython-39-darwin.so
0x10977d000 - 0x10978afff +_socket.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_socket.cpython-39-darwin.so
0x1097de000 - 0x1097edff3 +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x109806000 - 0x109808fff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x109811000 - 0x109815ff7 +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
0x1098f0000 - 0x109901ff7 +_ctypes.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so
0x109958000 - 0x10995bffb +lapack_lite.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/lapack_lite.cpython-39-darwin.so
0x109968000 - 0x109983ff3 +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
0x109a5c000 - 0x109a6ffff +_pocketfft_internal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/fft/_pocketfft_internal.cpython-39-darwin.so
0x109abb000 - 0x109b2effb +mtrand.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/mtrand.cpython-39-darwin.so
0x109b91000 - 0x109bb0fff +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
0x109bd3000 - 0x109c06fff +_common.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_common.cpython-39-darwin.so
0x109c64000 - 0x109c6aff7 +_hashlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_hashlib.cpython-39-darwin.so
0x109c78000 - 0x109cd0fff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.1.1.dylib
0x109cff000 - 0x109d05ff7 +_blake2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_blake2.cpython-39-darwin.so
0x109d0f000 - 0x109d62fff +_bounded_integers.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_bounded_integers.cpython-39-darwin.so
0x109d92000 - 0x109da1ff3 +_mt19937.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_mt19937.cpython-39-darwin.so
0x109db4000 - 0x109dc3ff7 +_philox.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_philox.cpython-39-darwin.so
0x109dd5000 - 0x109de4ffb +_pcg64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_pcg64.cpython-39-darwin.so
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0x109e38000 - 0x109e38fff +_load_libs.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic_lib/_load_libs.cpython-39-darwin.so
0x109e87000 - 0x109e87fff +_opcode.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_opcode.cpython-39-darwin.so
0x109e8f000 - 0x109e8ffff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x109e96000 - 0x109ee0adf dyld (551.5) /usr/lib/dyld
0x109f34000 - 0x10dae66ef +libopenblas.0.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libopenblas.0.dylib
0x113d84000 - 0x113f9af4f +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
0x114038000 - 0x1140c3fff +_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_generator.cpython-39-darwin.so
0x11622e000 - 0x1162cfff7 +libarrays.dylib (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x1163f3000 - 0x116411ff3 +_geometry.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/geometry/_geometry.cpython-39-darwin.so
0x116526000 - 0x116685ff7 +QtCore.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtCore.abi3.so
0x116814000 - 0x116d847df +QtCore (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore
0x116ee4000 - 0x116efbff7 +sip.cpython-39-darwin.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/sip.cpython-39-darwin.so
0x116f92000 - 0x117222ff7 +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtWidgets.abi3.so
0x117519000 - 0x11795ffff +QtWidgets (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWidgets.framework/Versions/5/QtWidgets
0x117b5c000 - 0x118045fff +QtGui (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtGui.framework/Versions/5/QtGui
0x1181f8000 - 0x118361ff3 +QtGui.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtGui.abi3.so
0x11864e000 - 0x11866ffff +QtWebEngineWidgets.abi3.so (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/QtWebEngineWidgets.abi3.so
0x1186a1000 - 0x1186c4ff7 +QtWebEngineWidgets (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWebEngineWidgets.framework/Versions/5/QtWebEngineWidgets
0x1186fc000 - 0x1203eaf4f +QtWebEngineCore (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWebEngineCore.framework/Versions/5/QtWebEngineCore
0x124a64000 - 0x124da8ff7 +QtQuick (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQuick.framework/Versions/5/QtQuick
0x124fcc000 - 0x124ff7ff7 +QtPrintSupport (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtPrintSupport.framework/Versions/5/QtPrintSupport
0x125025000 - 0x12507dff3 +QtQmlModels (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQmlModels.framework/Versions/5/QtQmlModels
0x1250be000 - 0x1250d7ff3 +QtWebChannel (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtWebChannel.framework/Versions/5/QtWebChannel
0x1250ee000 - 0x125446ffb +QtQml (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtQml.framework/Versions/5/QtQml
0x1255ba000 - 0x1256cafff +QtNetwork (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtNetwork.framework/Versions/5/QtNetwork
0x125758000 - 0x1257befff +QtPositioning (0) /Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt5/Qt/lib/QtPositioning.framework/Versions/5/QtPositioning
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0x7fff5d6be000 - 0x7fff5d6c7ffb libcopyfile.dylib (146.50.5) /usr/lib/system/libcopyfile.dylib
0x7fff5d6c8000 - 0x7fff5d74dffb libcorecrypto.dylib (562.70.3) /usr/lib/system/libcorecrypto.dylib
0x7fff5d7d5000 - 0x7fff5d80eff7 libdispatch.dylib (913.60.3) /usr/lib/system/libdispatch.dylib
0x7fff5d80f000 - 0x7fff5d82cff7 libdyld.dylib (551.5) /usr/lib/system/libdyld.dylib
0x7fff5d82d000 - 0x7fff5d82dffb libkeymgr.dylib (28) /usr/lib/system/libkeymgr.dylib
0x7fff5d82e000 - 0x7fff5d83aff3 libkxld.dylib (4570.71.82.8) /usr/lib/system/libkxld.dylib
0x7fff5d83b000 - 0x7fff5d83bff7 liblaunch.dylib (1205.70.16) /usr/lib/system/liblaunch.dylib
0x7fff5d83c000 - 0x7fff5d840ffb libmacho.dylib (906) /usr/lib/system/libmacho.dylib
0x7fff5d841000 - 0x7fff5d843fff libquarantine.dylib (86.70.1) /usr/lib/system/libquarantine.dylib
0x7fff5d844000 - 0x7fff5d845ff3 libremovefile.dylib (45) /usr/lib/system/libremovefile.dylib
0x7fff5d846000 - 0x7fff5d85dfff libsystem_asl.dylib (356.70.1) /usr/lib/system/libsystem_asl.dylib
0x7fff5d85e000 - 0x7fff5d85efff libsystem_blocks.dylib (67) /usr/lib/system/libsystem_blocks.dylib
0x7fff5d85f000 - 0x7fff5d8e8ff7 libsystem_c.dylib (1244.50.9) /usr/lib/system/libsystem_c.dylib
0x7fff5d8e9000 - 0x7fff5d8ecffb libsystem_configuration.dylib (963.50.9) /usr/lib/system/libsystem_configuration.dylib
0x7fff5d8ed000 - 0x7fff5d8f0ffb libsystem_coreservices.dylib (51) /usr/lib/system/libsystem_coreservices.dylib
0x7fff5d8f1000 - 0x7fff5d8f2fff libsystem_darwin.dylib (1244.50.9) /usr/lib/system/libsystem_darwin.dylib
0x7fff5d8f3000 - 0x7fff5d8f9ffb libsystem_dnssd.dylib (878.70.4) /usr/lib/system/libsystem_dnssd.dylib
0x7fff5d8fa000 - 0x7fff5d943ff7 libsystem_info.dylib (517.30.1) /usr/lib/system/libsystem_info.dylib
0x7fff5d944000 - 0x7fff5d96aff7 libsystem_kernel.dylib (4570.71.82.8) /usr/lib/system/libsystem_kernel.dylib
0x7fff5d96b000 - 0x7fff5d9b6fcb libsystem_m.dylib (3147.50.1) /usr/lib/system/libsystem_m.dylib
0x7fff5d9b7000 - 0x7fff5d9d6ff7 libsystem_malloc.dylib (140.50.7) /usr/lib/system/libsystem_malloc.dylib
0x7fff5d9d7000 - 0x7fff5db07ff7 libsystem_network.dylib (1229.70.2) /usr/lib/system/libsystem_network.dylib
0x7fff5db08000 - 0x7fff5db12ffb libsystem_networkextension.dylib (767.70.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff5db13000 - 0x7fff5db1cff3 libsystem_notify.dylib (172) /usr/lib/system/libsystem_notify.dylib
0x7fff5db1d000 - 0x7fff5db24ff7 libsystem_platform.dylib (161.50.1) /usr/lib/system/libsystem_platform.dylib
0x7fff5db25000 - 0x7fff5db30fff libsystem_pthread.dylib (301.50.1) /usr/lib/system/libsystem_pthread.dylib
0x7fff5db31000 - 0x7fff5db34fff libsystem_sandbox.dylib (765.70.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff5db35000 - 0x7fff5db36ff3 libsystem_secinit.dylib (30) /usr/lib/system/libsystem_secinit.dylib
0x7fff5db37000 - 0x7fff5db3eff7 libsystem_symptoms.dylib (820.60.3) /usr/lib/system/libsystem_symptoms.dylib
0x7fff5db3f000 - 0x7fff5db53ff7 libsystem_trace.dylib (829.70.2) /usr/lib/system/libsystem_trace.dylib
0x7fff5db55000 - 0x7fff5db5aff7 libunwind.dylib (35.3) /usr/lib/system/libunwind.dylib
0x7fff5db5b000 - 0x7fff5db88fff libxpc.dylib (1205.70.16) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 1152
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: 2659481
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=919.9M resident=0K(0%) swapped_out_or_unallocated=919.9M(100%)
Writable regions: Total=6.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 3
Activity Tracing 256K 2
CG backing stores 3256K 8
CG image 1684K 57
CoreAnimation 13.2M 95
CoreGraphics 8K 2
CoreImage 280K 35
CoreServices 164K 2
CoreUI image data 5696K 41
CoreUI image file 216K 6
Foundation 24K 3
Image IO 64K 2
Kernel Alloc Once 8K 2
MALLOC 5.5G 1178
MALLOC guard page 48K 12
MALLOC_LARGE (reserved) 384K 2 reserved VM address space (unallocated)
Mach message 24K 3
Memory Tag 242 12K 2
Memory Tag 251 36K 3
OpenGL GLSL 384K 6
STACK GUARD 116K 30
Stack 158.2M 31
Stack Guard 56.0M 2
VM_ALLOCATE 172.8M 124
VM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)
__DATA 57.1M 611
__FONT_DATA 4K 2
__GLSLBUILTINS 2588K 2
__LINKEDIT 298.2M 216
__TEXT 621.7M 566
__UNICODE 560K 2
mapped file 467.7M 245
shared memory 5512K 28
=========== ======= =======
TOTAL 7.5G 3293
TOTAL, minus reserved VM space 7.3G 3293
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v5.cxs
Updating list of available bundles failed: Internal Server Error
Log from Tue Jun 27 13:51:33 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v2.cxs
Log from Tue May 16 19:06:24 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure.cxs
Log from Fri Apr 28 18:17:25 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure.cxs
Log from Thu Apr 20 13:54:59 2023UCSF 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/srengac/Documents/Phenix/Sen1/RealSpaceRefine_43/Pol2-EC_Sen1_noATP-
> RSR43-noH.pdb
Chain information for Pol2-EC_Sen1_noATP-RSR43-noH.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
T | No description available
Y | No description available
Z | No description available
> show cartoons
> style sphere
Changed 40290 atom styles
> hide target a
> lighting soft
> lighting flat
> color dark gray
> select /O:1102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
123 atoms, 123 bonds, 14 residues, 1 model selected
> select up
5523 atoms, 5625 bonds, 690 residues, 1 model selected
> color sel yellow
> select clear
> select /Q:12
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
278 atoms, 310 bonds, 13 residues, 1 model selected
> select up
40290 atoms, 41221 bonds, 4918 residues, 1 model selected
> select clear
> select /Q:5
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
278 atoms, 310 bonds, 13 residues, 1 model selected
> color sel red
> select clear
> select /P:21
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
348 atoms, 390 bonds, 16 residues, 1 model selected
> close #1
> open
> /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_43/Pol2-EC_Sen1_noATP-
> RSR43-noH.pdb format pdb
Chain information for Pol2-EC_Sen1_noATP-RSR43-noH.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
T | No description available
Y | No description available
Z | No description available
> show cartoons
> hide target a
> lighting flat
> color dark gray
> select /O:1421
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 13 residues, 1 model selected
> select up
5523 atoms, 5625 bonds, 690 residues, 1 model selected
> color sel yellow
> select clear
> select /P:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
626 atoms, 700 bonds, 29 residues, 1 model selected
> color sel red
> select clear
> select /N:15
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
629 atoms, 703 bonds, 31 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #9fffffff
[Repeated 2 time(s)]
> color sel #88ffffff
> color sel #88ceffff
[Repeated 3 time(s)]
> select clear
> select /T:45
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
849 atoms, 952 bonds, 41 residues, 1 model selected
> color sel #30ceffff
> color sel #3030ffff
> color sel #3030c6ff
> select clear
[Repeated 1 time(s)]
> select /Y:38
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
739 atoms, 755 bonds, 98 residues, 1 model selected
> select up
40290 atoms, 41221 bonds, 4918 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /M:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 101 bonds, 12 residues, 1 model selected
> select up
508 atoms, 515 bonds, 65 residues, 1 model selected
> select up
40290 atoms, 41221 bonds, 4918 residues, 1 model selected
> select clear
> select /Y:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
739 atoms, 755 bonds, 98 residues, 1 model selected
> color sel cyan
> color sel forest green
> select clear
[Repeated 1 time(s)]
> select /M:18
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select up
508 atoms, 515 bonds, 65 residues, 1 model selected
> color sel magenta
> select clear
> select /Z:858
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
193 atoms, 195 bonds, 24 residues, 1 model selected
> select up
593 atoms, 600 bonds, 75 residues, 1 model selected
> color sel forest green
> select clear
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> select clear
> cartoon style xsection oval modeHelix default
> cartoon style modeHelix tube sides 20
> select clear
> set silhouetteDepthJump 0.19
> set silhouetteDepthJump 0.5
> set silhouetteDepthJump 2
> set silhouetteDepthJump 0.05
> set silhouetteDepthJump 0.01
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> turn z 90
> turn x, -90
Expected an axis vector or a keyword
> turn x -90
> ui tool show "Side View"
> turn x 90
> turn Z -90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview.png width 3000 height 2001 supersample 3 transparentBackground true
> turn Z 90
> turn x -90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> Sen1_sideview.png width 3000 height 2001 supersample 3
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
[Repeated 5 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> turn x 90
> turn z -90
> view orient
[Repeated 3 time(s)]
> view
> ui tool show "Side View"
[Repeated 1 time(s)]
> view
[Repeated 2 time(s)]
> view orient
> undo
[Repeated 8 time(s)]
> view matrix
camera position:
-0.5363,0.14021,-0.8323,-333.85,0.021991,0.98809,0.15228,266.48,0.84374,0.063364,-0.533,-132.16
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0
> view orient
> undo
> view orient
> select ions
10 atoms, 10 residues, 1 model selected
> show sel target ab
> color sel byelement
> select clear
> select /A:1803@MG
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> select /M:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
98 atoms, 101 bonds, 12 residues, 1 model selected
> select up
508 atoms, 515 bonds, 65 residues, 1 model selected
> color sel #d783ffff
> color sel #ff2f92ff
> color sel #942193ff
> select clear
> select /M:201@ZN
1 atom, 1 residue, 1 model selected
> color sel byelement
> select clear
> select /T:44
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
849 atoms, 952 bonds, 41 residues, 1 model selected
> select add /N:16
870 atoms, 975 bonds, 42 residues, 1 model selected
> select up
1478 atoms, 1655 bonds, 72 residues, 1 model selected
> select add /P:22
1500 atoms, 1679 bonds, 73 residues, 1 model selected
> select up
2104 atoms, 2355 bonds, 101 residues, 1 model selected
> nucleotides sel fill
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 2104 atom styles
> select clear
[Repeated 2 time(s)]
> select ::name="DA"
399 atoms, 442 bonds, 19 residues, 1 model selected
> style sel ringFill thin
Changed 19 residue ring styles
> select clear
> select nucleic-acid
2104 atoms, 2355 bonds, 1 pseudobond, 101 residues, 2 models selected
> style (#!1 & sel) sphere
Changed 2104 atom styles
> style (#!1 & sel) ringFill off
Changed 101 residue ring styles
> style (#!1 & sel) ball
Changed 2104 atom styles
> style (#!1 & sel) stick
Changed 2104 atom styles
> style (#!1 & sel) ringFill thick
Changed 101 residue ring styles
> select clear
> nucleotides atoms
> select nucleic-acid
2104 atoms, 2355 bonds, 1 pseudobond, 101 residues, 2 models selected
> hide (#!1 & sel) target a
> select clear
> select ions
10 atoms, 10 residues, 1 model selected
> style sel sphere
Changed 10 atom styles
> size ligand atomRadius +.5
Changed 0 atom radii
> size ligand atomRadius +.5
Changed 0 atom radii
> size ligand atomRadius +.5
Changed 0 atom radii
> size ligand atomRadius +.5
Changed 0 atom radii
> size ligand atomRadius +.5
Changed 0 atom radii
> size ligand atomRadius +.5
Changed 0 atom radii
> style sel sphere
Changed 10 atom styles
> select clear
> select /A:1803@MG
1 atom, 1 residue, 1 model selected
> select clear
> select /M:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
43 atoms, 42 bonds, 6 residues, 1 model selected
> select up
508 atoms, 515 bonds, 65 residues, 1 model selected
> color sel #945200ff
> color sel #941751ff
> color sel #942193ff
> select clear
> select /M:201@ZN
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview.png width 3000 height 2001 supersample 3
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview.png width 3000 height 2001 supersample 3 transparentBackground true
> select down
Nothing selected
> view matrix
camera position:
0.33446,-0.65246,-0.68002,-118.46,0.91892,0.38588,0.08172,214.79,0.20909,-0.65222,0.72862,514.57
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0
> view spec
Expected an objects specifier or a view name or a keyword
> view matrix camera
> -0.5363,0.14021,-0.8323,-333.85,0.021991,0.98809,0.15228,266.48,0.84374,0.063364,-0.533,-132.16
> select clear
[Repeated 1 time(s)]
> select /A
11023 atoms, 11217 bonds, 5 pseudobonds, 1403 residues, 2 models selected
> select add /D:136
11027 atoms, 11220 bonds, 5 pseudobonds, 1404 residues, 2 models selected
> select up
11070 atoms, 11263 bonds, 5 pseudobonds, 1410 residues, 2 models selected
> select up
12293 atoms, 12496 bonds, 5 pseudobonds, 1562 residues, 2 models selected
> select add /G:153
12302 atoms, 12504 bonds, 5 pseudobonds, 1563 residues, 2 models selected
> select up
12321 atoms, 12523 bonds, 5 pseudobonds, 1566 residues, 2 models selected
> select up
13633 atoms, 13864 bonds, 5 pseudobonds, 1733 residues, 2 models selected
> select add /H:109
13642 atoms, 13872 bonds, 5 pseudobonds, 1734 residues, 2 models selected
> select up
13656 atoms, 13886 bonds, 5 pseudobonds, 1736 residues, 2 models selected
> select
40290 atoms, 41221 bonds, 16 pseudobonds, 4918 residues, 2 models selected
> select subtract /O:1095
40285 atoms, 41217 bonds, 16 pseudobonds, 4917 residues, 2 models selected
> select subtract /O:1556
40280 atoms, 41213 bonds, 16 pseudobonds, 4916 residues, 2 models selected
> select down
40280 atoms, 41213 bonds, 16 pseudobonds, 4916 residues, 2 models selected
> select down
40280 atoms, 41213 bonds, 16 pseudobonds, 4916 residues, 2 models selected
> select subtract /O:1097
40272 atoms, 41206 bonds, 16 pseudobonds, 4915 residues, 2 models selected
> select subtract /O:1096
40263 atoms, 41198 bonds, 16 pseudobonds, 4914 residues, 2 models selected
> select down
40263 atoms, 41198 bonds, 16 pseudobonds, 4914 residues, 2 models selected
> select down
40263 atoms, 41198 bonds, 16 pseudobonds, 4914 residues, 2 models selected
> select down
40263 atoms, 41198 bonds, 16 pseudobonds, 4914 residues, 2 models selected
> select subtract /Y:84
40258 atoms, 41194 bonds, 16 pseudobonds, 4913 residues, 2 models selected
> select add /Y:84
40263 atoms, 41198 bonds, 16 pseudobonds, 4914 residues, 2 models selected
> select subtract /Y:34
40258 atoms, 41194 bonds, 16 pseudobonds, 4913 residues, 2 models selected
> select down
40258 atoms, 41194 bonds, 16 pseudobonds, 4913 residues, 2 models selected
> select down
40258 atoms, 41194 bonds, 16 pseudobonds, 4913 residues, 2 models selected
> select down
40258 atoms, 41194 bonds, 16 pseudobonds, 4913 residues, 2 models selected
> select clear
> select /A-L #1
40290 atoms, 41221 bonds, 16 pseudobonds, 4918 residues, 2 models selected
> select #1 /A-L
30823 atoms, 31371 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> surface (#!1 & sel)
> color (#!1 & sel) dark gray
> transparency (#!1 & sel) 50
> cartoon hide (#!1 & sel)
> select clear
> cartoon
> surface hidePatches
> select #1 /A-L
30823 atoms, 31371 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> select clear
> turn x 90
> turn x- 90
Expected an axis vector or a keyword
> turn x -90
[Repeated 1 time(s)]
> turn y 90
> turn y -90
[Repeated 1 time(s)]
> turn y 90
> turn x -90
> turn x 90
[Repeated 1 time(s)]
> turn x -90
> turn y -90
> set silhouetteDepthJump 0.05
> set silhouetteDepthJump 0.1
> set silhouetteDepthJump 0.2
> set silhouetteDepthJump 0.01
> set silhouetteDepthJump 0.005
> set silhouetteDepthJump 0.008
> set silhouetteDepthJump 0.05
> lighting flat
> select /A:1803@MG
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting full
> lighting simple
[Repeated 2 time(s)]
> graphics silhouettes false
> lighting simple
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes true
> select #1 /A-L
30823 atoms, 31371 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color (#!1 & sel) light gray
> color (#!1 & sel) byhetero
> select clear
> select /A:1803@MG
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> select /A:1801@ZN
1 atom, 1 residue, 1 model selected
> select clear
> select ions
10 atoms, 10 residues, 1 model selected
> size ballScale factor +0.3
Invalid "ballScale" argument: Expected a number
> size ballScale 1.8
Changed 1 ball scales
> select clear
> size ballScale 5
Changed 1 ball scales
> size ballScale 5 #1
Expected a keyword
> size ballScale 10
Changed 1 ball scales
> size ballScale 0.3
Changed 1 ball scales
> select clear
> lighting soft
[Repeated 2 time(s)]
> lighting full
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting flat
> lighting soft
> lighting full
> lighting soft
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview.png width 3000 height 2650 supersample 3 transparentBackground true
> view matrix
camera position:
0.13992,-0.83235,-0.53629,-10.69,0.9881,0.15229,0.021434,193.07,0.063828,-0.53291,0.84376,501.01
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0
> turn y 90
> turn x 90
> select /P:21
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
626 atoms, 700 bonds, 29 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> cartoon sel
> hide sel target a
> nucleotides sel tube/slab
[Repeated 1 time(s)]
> cartoon nucrib #1
Expected an atoms specifier or a keyword
> ribbon style x rect
> ribbon style x tube
> cartoon style xsection tube
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> ribbon style x nucrib
> cartoon style xsection nucrib
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview.png width 3000 height 2650 supersample 3 transparentBackground true
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure.cxs
——— End of log from Thu Apr 20 13:54:59 2023 ———
opened ChimeraX session
> select #1 /A-L
30823 atoms, 31371 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #d6d6d6ff
> color (#!1 & sel) #c0c0c0ff
> color (#!1 & sel) #a9a9a9ff
> color (#!1 & sel) #c0c0c0ff
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview.png width 3000 height 2650 supersample 4 transparentBackground true
> turn x -90
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> turn y -90
[Repeated 1 time(s)]
> turn y 90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview.png width 3000 height 2650 supersample 4 transparentBackground true
> select /Y:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 6 residues, 1 model selected
> select up
739 atoms, 755 bonds, 98 residues, 1 model selected
> color sel #d4fb79ff
> color sel #00f900ff
> color sel #8efa00ff
> color sel #929000ff
> color sel #919000ff
> color sel #889000ff
> color sel #729000ff
> color sel #659000ff
> color sel #5e9000ff
> color sel #579000ff
> color sel #519000ff
> color sel #4d9000ff
> color sel #469000ff
> color sel #3f9000ff
[Repeated 1 time(s)]
> color sel #429000ff
> color sel #479000ff
> color sel #6a9000ff
> color sel #6c9000ff
> color sel #4a9000ff
> color sel #399000ff
[Repeated 1 time(s)]
> color sel #3f9000ff
> color sel #469000ff
> color sel #4c9000ff
> color sel #549000ff
> color sel #569000ff
> color sel #5e9000ff
> color sel #669000ff
> color sel #679000ff
> color sel #689000ff
> color sel #6c9000ff
> color sel #6e9000ff
> color sel #6f9000ff
> color sel #709000ff
> color sel #719000ff
[Repeated 1 time(s)]
> color sel #719100ff
> color sel #719200ff
> color sel #719400ff
> color sel #719900ff
> color sel #719b00ff
> color sel #719d00ff
> color sel #71a100ff
> color sel #71a500ff
> color sel #71a900ff
> color sel #71b400ff
> color sel #71be00ff
[Repeated 1 time(s)]
> color sel #71c100ff
> color sel #71bd00ff
> color sel #71b500ff
> color sel #71b400ff
> color sel #71b000ff
> color sel #71ae00ff
[Repeated 1 time(s)]
> color sel #71b600ff
> color sel #71b900ff
> color sel #71ba00ff
> color sel #71bd00ff
> color sel #71be00ff
> color sel #71c100ff
> color sel #71c200ff
[Repeated 1 time(s)]
> color sel #71c000ff
> color sel #71be00ff
[Repeated 2 time(s)]
> color sel #71be01ff
[Repeated 1 time(s)]
> color sel #71be04ff
> color sel #71be0aff
> color sel #71be0cff
> color sel #71be0dff
> color sel #71be11ff
> color sel #71be17ff
> color sel #71be1bff
> color sel #71be1fff
> color sel #71be26ff
> color sel #71be2cff
> color sel #71be2eff
> color sel #71be31ff
> color sel #71be35ff
> color sel #71be38ff
> color sel #71be3bff
> color sel #71be3eff
> color sel #71be41ff
> color sel #71be45ff
> color sel #71be4cff
> color sel #71be4fff
> color sel #71be50ff
> color sel #71be54ff
> color sel #71be57ff
> color sel #71be59ff
> color sel #71be5cff
> color sel #71be5fff
> color sel #71be62ff
[Repeated 1 time(s)]
> color sel #71be64ff
> color sel #71be67ff
> color sel #71be6dff
> color sel #71be6aff
> color sel #71be69ff
> color sel #71be62ff
> color sel #71be5bff
> color sel #71be58ff
> color sel #71be56ff
> color sel #71be55ff
[Repeated 1 time(s)]
> color sel #71be53ff
> color sel #71be52ff
> color sel #71be4eff
[Repeated 2 time(s)]
> color sel #71be49ff
> color sel #71be44ff
> color sel #71be43ff
> color sel #71be42ff
> color sel #71be3cff
> select clear
> color #71be3cff
> color #69be3cff
> color #52be3cff
> color #4ebe3cff
> color #4dbe3cff
> undo
[Repeated 4 time(s)]
> select clear
> select /Y:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 6 residues, 1 model selected
> select up
739 atoms, 755 bonds, 98 residues, 1 model selected
> color sel #4dbe3cff
> color sel #4dbe39ff
> color sel #4dbe29ff
> color sel #4dbe1dff
> color sel #4dbe11ff
> color sel #4dbe10ff
> color sel #4dbe0eff
> color sel #4dbe0dff
> color sel #4dbe04ff
> color sel #4dbe03ff
[Repeated 1 time(s)]
> color sel #4dbe02ff
> color sel #4dbe00ff
[Repeated 2 time(s)]
> color sel #4dbf00ff
> color sel #4dc300ff
> color sel #4dc500ff
> color sel #4dc600ff
> color sel #4dc700ff
> color sel #4dca00ff
> color sel #4dcc00ff
[Repeated 1 time(s)]
> color sel #4dce00ff
> color sel #4dcf00ff
> color sel #4dd000ff
> color sel #4dd100ff
> color sel #4dd300ff
> color sel #4dd600ff
> color sel #4dd900ff
> color sel #4ddc00ff
> color sel #4ddd00ff
> color sel #4de400ff
[Repeated 1 time(s)]
> color sel #4de500ff
> color sel #4de400ff
> color sel #4de100ff
> color sel #4dc600ff
> color sel #4dc300ff
> color sel #4dc100ff
> color sel #4dbd00ff
> color sel #4dbb00ff
> color sel #4db700ff
> color sel #4db300ff
[Repeated 3 time(s)]
> color sel #4eb300ff
> color sel #51b300ff
> color sel #66b300ff
> color sel #6ab300ff
> color sel #70b300ff
> color sel #73b300ff
> color sel #7bb300ff
> color sel #7cb300ff
> color sel #86b300ff
> color sel #8ab300ff
> color sel #8bb300ff
> color sel #8cb300ff
> color sel #8bb300ff
> color sel #86b300ff
> color sel #83b300ff
> color sel #80b300ff
> color sel #76b300ff
> color sel #72b300ff
> color sel #58b300ff
> color sel #55b300ff
> color sel #49b300ff
> color sel #45b300ff
> color sel #41b300ff
> color sel #3eb300ff
> color sel #39b300ff
> color sel #35b300ff
> color sel #32b300ff
[Repeated 1 time(s)]
> color sel #27b300ff
[Repeated 1 time(s)]
> color sel #25b300ff
> color sel #1db300ff
[Repeated 1 time(s)]
> color sel #20b300ff
> color sel #25b300ff
> color sel #29b300ff
> color sel #58f704ff
> color sel #5bf704ff
> color sel #69f704ff
> color sel #83f704ff
> color sel #89f704ff
> color sel #8cf704ff
> color sel #90f704ff
> color sel #94f704ff
> color sel #95f704ff
[Repeated 1 time(s)]
> color sel #92f704ff
> color sel #87f704ff
> color sel #83f704ff
> color sel #81f704ff
> color sel #7ef704ff
> color sel #6ef704ff
> color sel #66f704ff
> color sel #64f704ff
> color sel #59f704ff
> color sel #57f704ff
[Repeated 1 time(s)]
> color sel #56f704ff
> color sel #53f704ff
> color sel #57ad47ff
> color sel #57ac47ff
> color sel #57a947ff
> color sel #57a447ff
> color sel #57a147ff
> color sel #57a047ff
> color sel #579c47ff
> color sel #579b47ff
[Repeated 1 time(s)]
> color sel #579c47ff
[Repeated 1 time(s)]
> color sel #579e47ff
> color sel #57b447ff
> color sel #57ba47ff
> color sel #57be47ff
[Repeated 1 time(s)]
> color sel #57b647ff
> color sel #57a647ff
> color sel #66ff66ff
> color sel #ccff99ff
> color sel #99cc66ff
> color sel #99cc33ff
> color sel #66ff33ff
> color sel #66cc00ff
> select up
40290 atoms, 41221 bonds, 4918 residues, 1 model selected
> select down
739 atoms, 755 bonds, 98 residues, 13 models selected
> color sel #99ff33ff
> color sel #99ff00ff
> color sel #ccff66ff
> color sel #ccff33ff
> color sel #ccff00ff
> color sel #99cc00ff
> color sel #ccff99ff
> color sel #99cc66ff
> select clear
> select /A:1803@MG
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> ui tool show "Side View"
> turn y 90
> turn x 90
> undo
[Repeated 1 time(s)]
> turn x 90
> select down
Nothing selected
> select down
Nothing selected
> turn y 90
> undo
[Repeated 3 time(s)]
> turn x 90
> turn y 90
> turn y -90
> select /O:1095
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /O:1098
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
123 atoms, 123 bonds, 14 residues, 1 model selected
> select up
5523 atoms, 5625 bonds, 690 residues, 1 model selected
> color sel #fbcc66ff
> color sel #fbec66ff
> color sel #fbec5dff
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview.png width 3000 height 2255 supersample 4 transparentBackground true
> turn x -90
> turn y -90
> ui tool show "Side View"
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview.png width 3000 height 2255 supersample 4 transparentBackground true
[Repeated 1 time(s)]
> turn y 90
> turn x 90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure.cxs
——— End of log from Fri Apr 28 18:17:25 2023 ———
opened ChimeraX session
> open /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_82/Pol2ECalone-
> Sen1merged_RSR80-coot0.updated_real_space_refined.pdb
Chain information for Pol2ECalone-
Sen1merged_RSR80-coot0.updated_real_space_refined.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
T | No description available
Y | No description available
Z | No description available
> hide #!1 models
> select #2
85508 atoms, 86479 bonds, 20 pseudobonds, 5276 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> cartoon style (#!2 & sel) modeHelix tube sides 20
> color #2 #d6d6d6 transparency 0
> select clear
> select #2
85508 atoms, 86479 bonds, 20 pseudobonds, 5276 residues, 2 models selected
> color #2 #ebebeb transparency 0
> color #2 white transparency 0
> color #2 #ebebeb transparency 0
> select clear
> select #2
85508 atoms, 86479 bonds, 20 pseudobonds, 5276 residues, 2 models selected
> color #2 #d6d6d6 transparency 0
> select clear
> select #2/P:5
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
942 atoms, 1016 bonds, 29 residues, 1 model selected
> color sel red
> select clear
> select #2/T:45
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
1314 atoms, 1417 bonds, 41 residues, 1 model selected
> color sel blue
> select clear
> select #2/N:21
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
980 atoms, 1054 bonds, 31 residues, 1 model selected
> color sel #88ffffff
> color sel #88ceffff
> color sel #88ceebff
> select clear
> select #2/Y:82
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
91 atoms, 90 bonds, 6 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> select clear
> select #2/Z:606
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
119 atoms, 118 bonds, 8 residues, 1 model selected
> select up
6919 atoms, 6966 bonds, 430 residues, 1 model selected
> color sel forest green
> select clear
> select #2/Y:82
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
91 atoms, 90 bonds, 6 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #8efa00ff
> color sel #00f900ff
> color sel #73fa79ff
> select clear
> select #2/M
985 atoms, 992 bonds, 66 residues, 1 model selected
> color sel #942193ff
> select clear
> select #2/Y:31
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
103 atoms, 103 bonds, 7 residues, 1 model selected
> color sel #73fa79ff
> color sel #33cc00ff
> color sel #66ff33ff
> color sel #99cc00ff
> select clear
> select #2/Y:29
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
103 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> color sel #ccff99ff
> color sel #99cc00ff
> select down
103 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> select down
103 atoms, 103 bonds, 7 residues, 1 model selected
> select down
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
103 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> select down
103 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> color sel #ccff99ff
> color sel #99cc66ff
> color sel #ccff00ff
> color sel #ccff66ff
> color sel #ccff33ff
> color sel #ccff00ff
> color sel #99cc00ff
> color sel #99cc33ff
> color sel #669933ff
> color sel #ccff99ff
> color sel #99cc66ff
> color sel #d4fb79ff
> color sel #73fa79ff
> color sel #8efa00ff
> color sel #00f900ff
[Repeated 1 time(s)]
> color sel #01f900ff
> color sel #03f900ff
> color sel #08f900ff
> color sel #12f900ff
> color sel #2df900ff
> color sel #3df900ff
> color sel #3ef900ff
> color sel #3ff900ff
> color sel #42f900ff
> color sel #44f900ff
> color sel #48f900ff
> color sel #4df900ff
> color sel #50f900ff
> color sel #51f900ff
> color sel #53f900ff
> color sel #58f900ff
> color sel #5df900ff
> color sel #62f900ff
> color sel #66f900ff
> color sel #69f900ff
> color sel #6af900ff
> color sel #72f900ff
> color sel #7cf900ff
> color sel #7ef900ff
> color sel #80f900ff
> color sel #82f900ff
[Repeated 1 time(s)]
> color sel #91f900ff
> color sel #99f900ff
[Repeated 2 time(s)]
> color sel #9af900ff
> color sel #9cf900ff
[Repeated 1 time(s)]
> color sel #9ef900ff
> color sel #a6f900ff
> color sel #a8f900ff
> color sel #a9f900ff
> color sel #abf900ff
> color sel #aef900ff
> color sel #b0f900ff
> color sel #b2f900ff
> color sel #b5f900ff
[Repeated 1 time(s)]
> color sel #b0f900ff
> color sel #a5f900ff
> color sel #9bf900ff
> color sel #99f900ff
> color sel #98f900ff
> color sel #96f900ff
> color sel #94f900ff
> color sel #93f900ff
> color sel #91f900ff
> color sel #8bf900ff
> color sel #89f900ff
[Repeated 3 time(s)]
> color sel #89f700ff
> color sel #89f200ff
> color sel #89e700ff
> color sel #89dd00ff
> color sel #89d900ff
> color sel #89d700ff
[Repeated 1 time(s)]
> color sel #89cc00ff
[Repeated 1 time(s)]
> color sel #89cb00ff
> color sel #89cc00ff
> color sel #89cf00ff
[Repeated 1 time(s)]
> color sel #89d400ff
> color sel #89d500ff
> color sel #89d600ff
[Repeated 3 time(s)]
> color sel #89d602ff
> color sel #89d610ff
> color sel #89d62cff
> color sel #89d641ff
> color sel #89d648ff
> color sel #89d64cff
> color sel #89d64fff
> color sel #89d651ff
> color sel #89d654ff
[Repeated 2 time(s)]
> color sel #89d655ff
> color sel #89d656ff
> color sel #99ff00ff
> color sel #99ff66ff
> select clear
> color #2 #b2ff66ff
> undo
> select #2/Y:32
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
103 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> color sel #b2ec66ff
> color sel #b2ec5dff
> select clear
[Repeated 1 time(s)]
> select ::name="MG"
2 atoms, 2 residues, 2 models selected
> show (#!2 & sel) target ab
> select ::name="ZN"
18 atoms, 18 residues, 2 models selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byelement
> select clear
> select ::name="MG"
2 atoms, 2 residues, 2 models selected
> color (#!2 & sel) magenta
> select #2/O:1424
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
202 atoms, 201 bonds, 13 residues, 1 model selected
> select up
11078 atoms, 11180 bonds, 690 residues, 1 model selected
> color sel #fbec5dff
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v2.png width 3000 height 3601 supersample 4 transparentBackground
> true
> ui tool show "Side View"
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v2.png width 3000 height 3601 supersample 4 transparentBackground
> true
[Repeated 1 time(s)]
> select #2/A
22129 atoms, 22323 bonds, 5 pseudobonds, 1403 residues, 2 models selected
> select clear
> select #2/A
22129 atoms, 22323 bonds, 5 pseudobonds, 1403 residues, 2 models selected
> select #2/B
17736 atoms, 17907 bonds, 6 pseudobonds, 1114 residues, 2 models selected
> select clear
> select #2
85508 atoms, 86479 bonds, 20 pseudobonds, 5276 residues, 2 models selected
> select subtract #2/P:5
85474 atoms, 86443 bonds, 20 pseudobonds, 5275 residues, 2 models selected
> select down
85474 atoms, 86443 bonds, 20 pseudobonds, 5275 residues, 2 models selected
> select down
85474 atoms, 86443 bonds, 20 pseudobonds, 5275 residues, 2 models selected
> select clear
> select #2/C:254
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
420 atoms, 419 bonds, 26 residues, 1 model selected
> select up
4120 atoms, 4157 bonds, 265 residues, 1 model selected
> select add #2/K:91
4131 atoms, 4167 bonds, 266 residues, 1 model selected
> select up
4579 atoms, 4619 bonds, 294 residues, 1 model selected
> select up
5969 atoms, 6024 bonds, 380 residues, 1 model selected
> select add #2/H:84
5979 atoms, 6033 bonds, 381 residues, 1 model selected
> select up
6301 atoms, 6359 bonds, 402 residues, 1 model selected
> select up
8077 atoms, 8150 bonds, 513 residues, 1 model selected
> select add #2/D:120
8092 atoms, 8164 bonds, 514 residues, 1 model selected
> select up
8173 atoms, 8244 bonds, 518 residues, 1 model selected
> select up
10634 atoms, 10716 bonds, 672 residues, 1 model selected
> select add #2/G:119
10653 atoms, 10734 bonds, 673 residues, 1 model selected
> select up
10713 atoms, 10795 bonds, 677 residues, 1 model selected
> select up
13331 atoms, 13441 bonds, 843 residues, 1 model selected
> select add #2/F:107
13347 atoms, 13456 bonds, 844 residues, 1 model selected
> select up
13532 atoms, 13643 bonds, 857 residues, 1 model selected
> select up
14726 atoms, 14848 bonds, 928 residues, 1 model selected
> select add #2/A:912
14745 atoms, 14866 bonds, 929 residues, 1 model selected
> select up
14770 atoms, 14892 bonds, 931 residues, 1 model selected
> select up
36855 atoms, 37171 bonds, 2331 residues, 1 model selected
> select add #2/B:667
36872 atoms, 37187 bonds, 2332 residues, 1 model selected
> select up
37065 atoms, 37382 bonds, 2344 residues, 1 model selected
> select up
54591 atoms, 55078 bonds, 3445 residues, 1 model selected
> select subtract #2/B:129
54571 atoms, 55058 bonds, 3444 residues, 1 model selected
> select up
54573 atoms, 55058 bonds, 3445 residues, 1 model selected
> select up
54591 atoms, 55078 bonds, 3445 residues, 1 model selected
> select subtract #2/B:128
54572 atoms, 55060 bonds, 3444 residues, 1 model selected
> select up
54574 atoms, 55060 bonds, 3445 residues, 1 model selected
> select up
54591 atoms, 55078 bonds, 3445 residues, 1 model selected
> select subtract #2/B:1108
54567 atoms, 55055 bonds, 3444 residues, 1 model selected
> select up
54569 atoms, 55055 bonds, 3445 residues, 1 model selected
> select up
54591 atoms, 55078 bonds, 3445 residues, 1 model selected
> select add #2/T:44
54623 atoms, 55111 bonds, 3446 residues, 1 model selected
> select clear
> select add #2/A:968
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
214 atoms, 214 bonds, 12 residues, 1 model selected
> select up
22129 atoms, 22323 bonds, 1403 residues, 1 model selected
> select clear
> select #2/A-L
61789 atoms, 62337 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color (#!2 & sel) #d6d6d6ff
> color (#!2 & sel) #c0c0c0ff
> color (#!2 & sel) #ccccccff
> color (#!2 & sel) #999999ff
> color (#!2 & sel) #ccccccff
> color (#!2 & sel) #c0c0c0ff
> select clear
> select #2/A-L
61789 atoms, 62337 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color (#!2 & sel) #b3b3b3ff
> color (#!2 & sel) #b5b5b5ff
> color (#!2 & sel) #bcbcbcff
> color (#!2 & sel) #c0c0c0ff
> color (#!2 & sel) #c8c8c8ff
[Repeated 1 time(s)]
> color (#!2 & sel) #c2c2c2ff
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v2.png width 3000 height 3601 supersample 4 transparentBackground
> true
> select #2/A-L
61789 atoms, 62337 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> hide #!2 models
> show #!1 models
> color #1 #d7d7d7ff
> undo
> show #!2 models
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #2/A-L
61789 atoms, 62337 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color (#!2 & sel) #cececeff
> color (#!2 & sel) #d2d2d2ff
> color (#!2 & sel) #d8d8d8ff
> color (#!2 & sel) #dcdcdcff
[Repeated 1 time(s)]
> color (#!2 & sel) #dadadaff
[Repeated 1 time(s)]
> select clear
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color #1 #dadadaff
> color #1 #e3e3e3ff
> color #1 #e9e9e9ff
> color #1 #eaeaeaff
> color #1 #e5e5e5ff
> undo
[Repeated 4 time(s)]
> select #2/A-L
61789 atoms, 62337 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> hide #!1 models
> show #!2 models
> show #!1 models
> color (#!2 & sel) #e5e5e5ff
> color (#!2 & sel) #e6e6e6ff
> color (#!2 & sel) #eeeeeeff
[Repeated 1 time(s)]
> color (#!2 & sel) #e5e5e5ff
> color (#!2 & sel) #dededeff
> color (#!2 & sel) #dadadaff
> color (#!2 & sel) #d3d3d3ff
> color (#!2 & sel) #d2d2d2ff
[Repeated 1 time(s)]
> color (#!2 & sel) #c8c8c8ff
> color (#!2 & sel) #bbbbbbff
> color (#!2 & sel) #b2b2b2ff
> color (#!2 & sel) #b1b1b1ff
> color (#!2 & sel) #b6b6b6ff
[Repeated 1 time(s)]
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v2.png width 3000 height 3601 supersample 3 transparentBackground
> true
> turn x, -90
Expected an axis vector or a keyword
> turn x -90
> turn y -90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview_v2.png width 3000 height 3601 supersample 4 transparentBackground
> true
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v2.cxs includeMaps true
——— End of log from Tue May 16 19:06:24 2023 ———
opened ChimeraX session
> hide #!2 models
> open /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_147/Pol2ECalone-
> Sen1merged_RSR144-Rotamerfit-coot.updated_real_space_refined.pdb
Chain information for Pol2ECalone-Sen1merged_RSR144-Rotamerfit-
coot.updated_real_space_refined.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
T | No description available
Y | No description available
Z | No description available
> select #3
85263 atoms, 86214 bonds, 21 pseudobonds, 5268 residues, 2 models selected
> color sel light gray
> show sel cartoons
> hide sel atoms
> cartoon style (#!3 & sel) modeHelix tube sides 20
> select clear
> select #3/Y
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> color sel #00f900ff
> color sel #66ff66ff
> color sel #66ff00ff
> color sel #99ff33ff
> select clear
> select #3/Y
1501 atoms, 1517 bonds, 100 residues, 1 model selected
> color sel #ccff99ff
> color sel #99cc66ff
> select clear
> select #3/Z
6903 atoms, 6949 bonds, 5 pseudobonds, 429 residues, 2 models selected
> color sel forest green
> select clear
> select #3/M
985 atoms, 992 bonds, 66 residues, 1 model selected
> color sel #942193ff
> select clear
> select #3/O:1546
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
454 atoms, 455 bonds, 27 residues, 1 model selected
> select up
11078 atoms, 11180 bonds, 690 residues, 1 model selected
> color sel #942193ff
> color sel #fbec5dff
> select clear
> select #3/P:8
31 atoms, 32 bonds, 1 residue, 1 model selected
> select up
938 atoms, 1011 bonds, 29 residues, 1 model selected
> color sel red
> select clear
> select #3/T:8
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
1217 atoms, 1312 bonds, 38 residues, 1 model selected
> color sel blue
> select clear
[Repeated 1 time(s)]
> select #3/N:46
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
853 atoms, 917 bonds, 27 residues, 1 model selected
> color sel #00fdffff
> color sel #66ffffff
> color sel #66ffccff
> color sel #99ffffff
> select clear
> color #3 #ccffffff
> undo
> select #3/N:46
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
853 atoms, 917 bonds, 27 residues, 1 model selected
> select clear
> select #3/N:46
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
853 atoms, 917 bonds, 27 residues, 1 model selected
> color sel #66ffffff
> color sel #99ffffff
> select clear
> dssp
> select clear
> select #3/N:46
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
853 atoms, 917 bonds, 27 residues, 1 model selected
> color sel #99ffffff
> color sel #9affffff
[Repeated 1 time(s)]
> color sel #9bffffff
> color sel #9dffffff
> color sel #9fffffff
> color sel #a0ffffff
> color sel #a1ffffff
> color sel #a5ffffff
> color sel #adffffff
> color sel #b3ffffff
> color sel #bbffffff
> color sel #bcffffff
> color sel #c5ffffff
> color sel #c6ffffff
> color sel #c7ffffff
> color sel #c8ffffff
[Repeated 2 time(s)]
> color sel #c6ffffff
> color sel #c3ffffff
> color sel #c1ffffff
> color sel #c0ffffff
> color sel #bfffffff
> color sel #bcffffff
[Repeated 1 time(s)]
> color sel #bbffffff
> color sel #b9ffffff
> color sel #b6ffffff
> color sel #b5ffffff
> color sel #b2ffffff
> select clear
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color sel dark gray
> color (#!3 & sel) #b2ffffff
> color (#!3 & sel) #c0c0c0ff
> color (#!3 & sel) #a9a9a9ff
> select clear
> ui tool show "Side View"
> select #3
85263 atoms, 86214 bonds, 21 pseudobonds, 5268 residues, 2 models selected
> color (#!3 & sel) byhetero
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v3.cxs
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview_v3.png width 3000 height 3279 supersample 4 transparentBackground
> true
> turn y, 90
Expected an axis vector or a keyword
> turn y 90
> turn x 90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v3.cxs
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v3.png width 3000 height 3279 supersample 4 transparentBackground
> true
> surface #3
> surface hidePatches #3
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> surface (#!3 & sel)
> ui tool show "Color Actions"
> select clear
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color sel dark gray
[Repeated 1 time(s)]
> color sel dim gray
> select clear
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #797979ff
> color (#!3 & sel) #919191ff
> color (#!3 & sel) #797979ff
> color (#!3 & sel) #5e5e5eff
> color (#!3 & sel) #929292ff
> color (#!3 & sel) #919191ff
> color (#!3 & sel) #797979ff
> select clear
> surface hidePatches #3
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> surface (#!3 & sel)
> select clear
> cartoon style nucleic xsection oval width 2 thickness 2
> select clear
> surface hidePatches #3
> select clear
> cartoon style protein modeHelix tube radius 2 sides 24
> cartoon style protein modeHelix tube radius 4 sides 24
> cartoon style protein modeHelix tube radius 2.5 sides 24
> cartoon style protein modeHelix tube radius 2.25 sides 24
> select clear
> turn x -90
> turn y -90
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> surface (#!3 & sel)
> select clear
> select #3/A-L
61788 atoms, 62336 bonds, 13 pseudobonds, 3889 residues, 2 models selected
> color sel dark gray
> color (#!3 & sel) #919191ff
> select clear
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview_v4.png width 3000 height 3279 supersample 4 transparentBackground
> true
> turn y 90
> turn x 90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v4.png width 3000 height 3279 supersample 4 transparentBackground
> true
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v4.cxs
> set silhouetteWidth 3
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_siltest.png width 3000 height 3279 supersample 4
> transparentBackground true
> set silhouetteWidth 1
> set silhouetteWidth 2
> set silhouetteWidth 3
> undo
> turn y 90
> turn x 90
> set silhouetteWidth 2
> set silhouetteWidth 2.2
> set silhouetteWidth 2.5
> set silhouetteWidth 4
> set silhouetteDepthJump 0.19
> set silhouetteWidth 2.5
> set silhouetteWidth 3
> set silhouetteWidth 4
> set silhouetteWidth 3.5
> set silhouetteDepthJump 0.25
> set silhouetteDepthJump 0.15
> set silhouetteDepthJump 0.22
> set silhouetteDepthJump 0.15
> set silhouetteDepthJump 0.19
> set silhouetteDepthJump 0.175
> set silhouetteDepthJump 0.15
> set silhouetteWidth 3
> set silhouetteWidth 2.5
> set silhouetteWidth 3
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_siltest.png width 3000 height 3279 supersample 4
> transparentBackground true
> set silhouetteWidth 5
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_siltestv1.png width 3000 height 3279 supersample 4
> transparentBackground true
> set silhouetteDepthJump 0.15
> set silhouetteWidth 3
> set silhouetteDepthJump 0.14
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> topview_v5.png width 3000 height 3279 supersample 4 transparentBackground
> true
> turn x -90
> turn y -90
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> sideview_v5.png width 3000 height 3279 supersample 4 transparentBackground
> true
> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/overall-
> figure_v5.cxs
——— End of log from Tue Jun 27 13:51:33 2023 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-1.68.25
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Intel Core i5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
Boot ROM Version: 428.0.0.0.0
SMC Version (system): 2.41f1
Software:
System Software Overview:
System Version: macOS 10.13.6 (17G14042)
Kernel Version: Darwin 17.7.0
Time since boot: 49 days 19:56
Graphics/Displays:
Radeon Pro 575:
Chipset Model: Radeon Pro 575
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Dynamic, Max): 4096 MB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c4
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1P-025
EFI Driver Version: 01.00.931
Metal: Supported, feature set macOS GPUFamily1 v3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 4RFMK5681QHL
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-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-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-XMAS: 1.1.2
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
et-xmlfile: 1.1.0
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
openpyxl: 3.1.2
openvr: 1.16.801
packaging: 21.0
pandas: 2.0.1
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
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.12.2
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
tzdata: 2023.3
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 , 2 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash handling event |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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