Opened 2 years ago

Closed 2 years ago

#9329 closed defect (can't reproduce)

Crash in event loop

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.13.6-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 [39835]
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 [39835]
User ID:               581685

Date/Time:             2023-07-07 09:54:14.182 +0200
OS Version:            Mac OS X 10.13.6 (17G14042)
Report Version:        12
Anonymous UUID:        9D557B09-8913-C4DD-7DC2-2E1A87166C5B


Time Awake Since Boot: 4800000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  CrBrowserMain  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000048
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0x48:
--> 
    __TEXT                 00000001081cd000-00000001081ce000 [    4K] r-x/r-x SM=COW  /Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX

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             	0x000000010825206d cfunction_call + 125
6   org.python.python             	0x00000001082136cc _PyObject_Call + 140
7   QtCore.abi3.so                	0x00000001103d0957 PyQtSlot::call(_object*, _object*) const + 39
8   QtCore.abi3.so                	0x00000001103d0866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
9   QtCore.abi3.so                	0x00000001103d1455 PyQtSlotProxy::unislot(void**) + 85
10  QtCore.abi3.so                	0x00000001103d13ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
11  QtCore                        	0x0000000116c9ab9f QObject::event(QEvent*) + 943
12  QtWidgets                     	0x00000001176d09ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
13  QtWidgets                     	0x00000001176d1e11 QApplication::notify(QObject*, QEvent*) + 497
14  QtWidgets.abi3.so             	0x0000000117283db9 sipQApplication::notify(QObject*, QEvent*) + 233
15  QtCore                        	0x0000000116c6fa34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
16  QtCore                        	0x0000000116c70d79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809
17  libqcocoa.dylib               	0x000000012745d259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313
18  libqcocoa.dylib               	0x000000012745d9c8 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               	0x000000012745c62f QCocoaEventDispatcher::processEvents(QFlags) + 2495
31  QtCore                        	0x0000000116c6bacf QEventLoop::exec(QFlags) + 431
32  QtCore                        	0x0000000116c70042 QCoreApplication::exec() + 130
33  QtWidgets.abi3.so             	0x0000000117375702 meth_QApplication_exec_(_object*, _object*) + 82
34  org.python.python             	0x000000010825206d cfunction_call + 125
35  org.python.python             	0x000000010821317d _PyObject_MakeTpCall + 365
36  org.python.python             	0x00000001082eb61c call_function + 876
37  org.python.python             	0x00000001082e8ab3 _PyEval_EvalFrameDefault + 25219
38  org.python.python             	0x0000000108213948 function_code_fastcall + 104
39  org.python.python             	0x000000010821598a method_vectorcall + 202
40  org.python.python             	0x00000001082eb58c call_function + 732
41  org.python.python             	0x00000001082e8ab3 _PyEval_EvalFrameDefault + 25219
42  org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
43  org.python.python             	0x00000001082138d1 _PyFunction_Vectorcall + 289
44  org.python.python             	0x00000001082eb58c call_function + 732
45  org.python.python             	0x00000001082e8b4b _PyEval_EvalFrameDefault + 25371
46  org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
47  org.python.python             	0x00000001082e270b PyEval_EvalCode + 139
48  org.python.python             	0x00000001082df592 builtin_exec + 626
49  org.python.python             	0x000000010825186a cfunction_vectorcall_FASTCALL + 218
50  org.python.python             	0x00000001082eb58c call_function + 732
51  org.python.python             	0x00000001082e8b4b _PyEval_EvalFrameDefault + 25371
52  org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
53  org.python.python             	0x00000001082138d1 _PyFunction_Vectorcall + 289
54  org.python.python             	0x00000001082eb58c call_function + 732
55  org.python.python             	0x00000001082e8b4b _PyEval_EvalFrameDefault + 25371
56  org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
57  org.python.python             	0x00000001082138d1 _PyFunction_Vectorcall + 289
58  org.python.python             	0x0000000108351e20 pymain_run_module + 208
59  org.python.python             	0x0000000108351537 Py_RunMain + 1431
60  org.python.python             	0x0000000108351b3f pymain_main + 223
61  org.python.python             	0x0000000108351a4b Py_Main + 43
62  edu.ucsf.cgl.ChimeraX         	0x00000001081cddc8 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           	0x0000000109502a9f 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           	0x0000000109502a9f 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           	0x0000000109502a9f 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               	0x000000011b079e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2   QtWebEngineCore               	0x000000011b079cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
5   QtWebEngineCore               	0x000000011b00da94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
7   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b017778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4   QtWebEngineCore               	0x000000011b018150 base::internal::WorkerThread::RunWorker() + 1024
5   QtWebEngineCore               	0x000000011b017c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b079e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2   QtWebEngineCore               	0x000000011b079cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
5   QtWebEngineCore               	0x000000011ef46f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
7   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b066e18 base::ConditionVariable::Wait() + 104
3   QtWebEngineCore               	0x000000011c31e5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011af9720f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
6   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
7   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b079e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2   QtWebEngineCore               	0x000000011b079cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
5   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
6   QtWebEngineCore               	0x000000011b06ae07 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:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff5d9571fa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff5d956714 mach_msg + 60
2   QtWebEngineCore               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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 12:: VizCompositorThread
0   libsystem_kernel.dylib        	0x00007fff5d9571fa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff5d956714 mach_msg + 60
2   QtWebEngineCore               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011b01776a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5   QtWebEngineCore               	0x000000011b018150 base::internal::WorkerThread::RunWorker() + 1024
6   QtWebEngineCore               	0x000000011b017d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011af971db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5   QtWebEngineCore               	0x000000011b00262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6   QtWebEngineCore               	0x000000011afc67cb base::RunLoop::Run() + 395
7   QtWebEngineCore               	0x000000011b021a7d base::Thread::ThreadMain() + 413
8   QtWebEngineCore               	0x000000011b06ae07 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b06f2cf base::WaitableEvent::Wait() + 31
4   QtWebEngineCore               	0x000000011b01776a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5   QtWebEngineCore               	0x000000011b017e3d base::internal::WorkerThread::RunWorker() + 237
6   QtWebEngineCore               	0x000000011b017c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7   QtWebEngineCore               	0x000000011b06ae07 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           	0x00000001626552eb 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           	0x00000001626552eb 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           	0x00000001626552eb 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               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b017778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4   QtWebEngineCore               	0x000000011b018150 base::internal::WorkerThread::RunWorker() + 1024
5   QtWebEngineCore               	0x000000011b017cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6   QtWebEngineCore               	0x000000011b06ae07 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:
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 24:
0   libsystem_pthread.dylib       	0x00007fff5db27bdc start_wqthread + 0
1   ???                           	0x000000000002790f 0 + 162063

Thread 25:
0   libsystem_pthread.dylib       	0x00007fff5db27bdc start_wqthread + 0
1   ???                           	0x4058504320000000 0 + 4636544065607827456

Thread 26:
0   libsystem_pthread.dylib       	0x00007fff5db27bdc start_wqthread + 0
1   ???                           	0x0000000800009000 0 + 34359775232

Thread 27:: ThreadPoolForegroundWorker
0   libsystem_kernel.dylib        	0x00007fff5d9571fa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff5d956714 mach_msg + 60
2   QtWebEngineCore               	0x000000011b06f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3   QtWebEngineCore               	0x000000011b017778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4   QtWebEngineCore               	0x000000011b017e3d base::internal::WorkerThread::RunWorker() + 237
5   QtWebEngineCore               	0x000000011b017cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6   QtWebEngineCore               	0x000000011b06ae07 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 28:
0   libsystem_kernel.dylib        	0x00007fff5d960a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff5db29589 _pthread_cond_wait + 732
2   org.python.python             	0x0000000108341d6c PyThread_acquire_lock_timed + 700
3   org.python.python             	0x0000000108390a1f acquire_timed + 111
4   org.python.python             	0x0000000108390b30 lock_PyThread_acquire_lock + 48
5   org.python.python             	0x000000010821be54 method_vectorcall_VARARGS_KEYWORDS + 388
6   org.python.python             	0x00000001082eb58c call_function + 732
7   org.python.python             	0x00000001082e8a92 _PyEval_EvalFrameDefault + 25186
8   org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
9   org.python.python             	0x00000001082138d1 _PyFunction_Vectorcall + 289
10  org.python.python             	0x00000001082eb58c call_function + 732
11  org.python.python             	0x00000001082e8a92 _PyEval_EvalFrameDefault + 25186
12  org.python.python             	0x00000001082ec283 _PyEval_EvalCode + 2611
13  org.python.python             	0x00000001082138d1 _PyFunction_Vectorcall + 289
14  org.python.python             	0x00000001082eb58c call_function + 732
15  org.python.python             	0x00000001082e8a92 _PyEval_EvalFrameDefault + 25186
16  org.python.python             	0x0000000108213948 function_code_fastcall + 104
17  org.python.python             	0x00000001082eb58c call_function + 732
18  org.python.python             	0x00000001082e8a92 _PyEval_EvalFrameDefault + 25186
19  org.python.python             	0x0000000108213948 function_code_fastcall + 104
20  org.python.python             	0x00000001082eb58c call_function + 732
21  org.python.python             	0x00000001082e8a92 _PyEval_EvalFrameDefault + 25186
22  org.python.python             	0x0000000108213948 function_code_fastcall + 104
23  org.python.python             	0x00000001082159d2 method_vectorcall + 274
24  org.python.python             	0x00000001083903c6 t_bootstrap + 70
25  org.python.python             	0x00000001083418c9 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: 0x00000001086b6a48  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x000000000000000b  rbp: 0x00000001086b6a80  rsp: 0x00000001086b6a48
   r8: 0x00000001086b6f48   r9: 0xffffffff00000000  r10: 0x00007fff962463c8  r11: 0x0000000000000287
  r12: 0x0000000000000307  r13: 0x0000000108251ff0  r14: 0x000000000000000b  r15: 0x000000000000002d
  rip: 0x00007fff5d960b66  rfl: 0x0000000000000286  cr2: 0x00000001083ca13f
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


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    0x7fff5c016000 -     0x7fff5c06afff  libcurl.4.dylib (105.40.2)  /usr/lib/libcurl.4.dylib
    0x7fff5c12b000 -     0x7fff5c12bfff  libenergytrace.dylib (16)  /usr/lib/libenergytrace.dylib
    0x7fff5c12c000 -     0x7fff5c145ff3  libexpat.1.dylib (16.1.1.1)  /usr/lib/libexpat.1.dylib
    0x7fff5c146000 -     0x7fff5c152ffb  libexslt.0.dylib (15.16)  /usr/lib/libexslt.0.dylib
    0x7fff5c153000 -     0x7fff5c154fff  libffi.dylib (18.1)  /usr/lib/libffi.dylib
    0x7fff5c15d000 -     0x7fff5c161ff7  libgermantok.dylib (17)  /usr/lib/libgermantok.dylib
    0x7fff5c162000 -     0x7fff5c167ff3  libheimdal-asn1.dylib (520.50.9)  /usr/lib/libheimdal-asn1.dylib
    0x7fff5c193000 -     0x7fff5c284ff7  libiconv.2.dylib (51.50.1)  /usr/lib/libiconv.2.dylib
    0x7fff5c285000 -     0x7fff5c4acffb  libicucore.A.dylib (59181.0.1)  /usr/lib/libicucore.A.dylib
    0x7fff5c4f9000 -     0x7fff5c4fafff  liblangid.dylib (128)  /usr/lib/liblangid.dylib
    0x7fff5c4fb000 -     0x7fff5c514ffb  liblzma.5.dylib (10)  /usr/lib/liblzma.5.dylib
    0x7fff5c515000 -     0x7fff5c52bff7  libmarisa.dylib (9)  /usr/lib/libmarisa.dylib
    0x7fff5c52c000 -     0x7fff5c5dbfff  libmecab.1.0.0.dylib (779.7.6)  /usr/lib/libmecab.1.0.0.dylib
    0x7fff5c5dc000 -     0x7fff5c804ff7  libmecabra.dylib (779.7.6)  /usr/lib/libmecabra.dylib
    0x7fff5c9dc000 -     0x7fff5cb57fff  libnetwork.dylib (1229.70.2)  /usr/lib/libnetwork.dylib
    0x7fff5cbde000 -     0x7fff5cfcc7e7  libobjc.A.dylib (723)  /usr/lib/libobjc.A.dylib
    0x7fff5cfcd000 -     0x7fff5cfcefff  libodfde.dylib (24.50.1)  /usr/lib/libodfde.dylib
    0x7fff5cfdf000 -     0x7fff5cfe3fff  libpam.2.dylib (22)  /usr/lib/libpam.2.dylib
    0x7fff5cfe6000 -     0x7fff5d01eff7  libpcap.A.dylib (79.20.3)  /usr/lib/libpcap.A.dylib
    0x7fff5d069000 -     0x7fff5d06cff7  libpmenergy.dylib (187.70.3)  /usr/lib/libpmenergy.dylib
    0x7fff5d06d000 -     0x7fff5d06ffff  libpmsample.dylib (187.70.3)  /usr/lib/libpmsample.dylib
    0x7fff5d09d000 -     0x7fff5d0b9ffb  libresolv.9.dylib (65.1)  /usr/lib/libresolv.9.dylib
    0x7fff5d0bb000 -     0x7fff5d0f4ff3  libsandbox.1.dylib (765.70.2)  /usr/lib/libsandbox.1.dylib
    0x7fff5d0f5000 -     0x7fff5d107fff  libsasl2.2.dylib (211.0.2)  /usr/lib/libsasl2.2.dylib
    0x7fff5d108000 -     0x7fff5d109ff3  libspindump.dylib (252)  /usr/lib/libspindump.dylib
    0x7fff5d10a000 -     0x7fff5d29dff7  libsqlite3.dylib (274.8.1)  /usr/lib/libsqlite3.dylib
    0x7fff5d2f9000 -     0x7fff5d34cffb  libssl.35.dylib (22.50.3)  /usr/lib/libssl.35.dylib
    0x7fff5d3f5000 -     0x7fff5d406fff  libsystemstats.dylib (403.50.9)  /usr/lib/libsystemstats.dylib
    0x7fff5d424000 -     0x7fff5d459fff  libtidy.A.dylib (15.18.4)  /usr/lib/libtidy.A.dylib
    0x7fff5d471000 -     0x7fff5d4d1ff3  libusrtcp.dylib (1229.70.2)  /usr/lib/libusrtcp.dylib
    0x7fff5d4d2000 -     0x7fff5d4d5ffb  libutil.dylib (51.20.1)  /usr/lib/libutil.dylib
    0x7fff5d4d6000 -     0x7fff5d4e3ff3  libxar.1.dylib (417.1)  /usr/lib/libxar.1.dylib
    0x7fff5d4e7000 -     0x7fff5d5ceffb  libxml2.2.dylib (31.20)  /usr/lib/libxml2.2.dylib
    0x7fff5d5cf000 -     0x7fff5d5f7fff  libxslt.1.dylib (15.16)  /usr/lib/libxslt.1.dylib
    0x7fff5d5f8000 -     0x7fff5d60affb  libz.1.dylib (70)  /usr/lib/libz.1.dylib
    0x7fff5d6a6000 -     0x7fff5d6aaff7  libcache.dylib (80)  /usr/lib/system/libcache.dylib
    0x7fff5d6ab000 -     0x7fff5d6b5ff3  libcommonCrypto.dylib (60118.50.1)  /usr/lib/system/libcommonCrypto.dylib
    0x7fff5d6b6000 -     0x7fff5d6bdfff  libcompiler_rt.dylib (62)  /usr/lib/system/libcompiler_rt.dylib
    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: 83
    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: 3629511
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=917.4M resident=0K(0%) swapped_out_or_unallocated=917.4M(100%)
Writable regions: Total=4.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.3G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               256K        3 
Activity Tracing                   256K        2 
CG backing stores                 2668K        7 
CG image                          2148K       48 
CoreAnimation                     41.4M      103 
CoreGraphics                         8K        2 
CoreImage                          264K       34 
CoreUI image data                 5688K       35 
CoreUI image file                  216K        6 
Foundation                          24K        3 
Image IO                            64K        2 
Kernel Alloc Once                    8K        2 
MALLOC                             3.8G      768 
MALLOC guard page                   48K       13 
MALLOC_LARGE (reserved)            384K        2         reserved VM address space (unallocated)
Mach message                        24K        5 
Memory Tag 242                      12K        2 
Memory Tag 251                      48K        4 
OpenGL GLSL                        384K        6 
STACK GUARD                        112K       29 
Stack                            157.7M       30 
Stack Guard                       56.0M        2 
VM_ALLOCATE                      165.8M      168 
VM_ALLOCATE (reserved)           128.0M        3         reserved VM address space (unallocated)
__DATA                            56.8M      601 
__FONT_DATA                          4K        2 
__GLSLBUILTINS                    2588K        2 
__LINKEDIT                       297.0M      207 
__TEXT                           620.4M      557 
__UNICODE                          560K        2 
mapped file                      128.6M      257 
shared memory                     6004K       22 
===========                     =======  ======= 
TOTAL                              5.4G     2897 
TOTAL, minus reserved VM space     5.3G     2897 


System Profile:
Network Service: Ethernet, Ethernet, en0
Boot Volume File System Type: apfs
Memory Module: BANK 0/DIMM0, 8 GB, DDR4, 2400 MHz, 0x802C, 0x3841544631473634485A2D324733423220202020
Memory Module: BANK 1/DIMM0, 8 GB, DDR4, 2400 MHz, 0x802C, 0x3841544631473634485A2D324733423220202020
USB Device: USB 3.0 Bus
USB Device: Bluetooth USB Host Controller
USB Device: FaceTime HD Camera (Built-in)
Thunderbolt Bus: iMac, Apple Inc., 33.1
Model: iMac18,3, BootROM 428.0.0.0.0, 4 processors, Intel Core i5, 3,5 GHz, 16 GB, SMC 2.41f1
Graphics: Radeon Pro 575, Radeon Pro 575, PCIe
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x16F), Broadcom BCM43xx 1.0 (7.77.37.33.1a1)
Bluetooth: Version 6.0.7f22, 3 services, 27 devices, 1 incoming serial ports


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/RNAalone_Sen1-movement.cxs

Log from Wed Jul 5 18:20:04 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/RNAalone_Sen1-movement.cxs

Log from Tue Jul 4 15:54:35 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/Sen1-movement.cxs
> format session

Log from Tue Jun 27 18:31:53 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/Sen1-movement.cxs

Log from Tue Jun 27 18:29:08 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/Sen1-movement.cxs

Log from Tue Jun 27 14:31:08 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/test-
> movement.cxs format session

Opened qlgzuizmyn.pqr.dx as #6, grid size 161,225,225, pixel 0.543,0.495,0.48,
shown at level 39.1,45.3, step 1, values float32  
Opened 1qll0kpcmk.pqr.dx as #8, grid size 193,193,193, pixel
0.505,0.479,0.488, shown at level -47.6,47.6, step 1, values float32  
Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  
Map values for surface "2xzo-edit.pdb_A SES surface": minimum -371.2, mean
2.415, maximum 249  
Log from Tue May 2 15:00:54 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/test-
> movement.cxs

Opened qlgzuizmyn.pqr.dx as #6, grid size 161,225,225, pixel 0.543,0.495,0.48,
shown at level 39.1,45.3, step 1, values float32  
Opened 1qll0kpcmk.pqr.dx as #8, grid size 193,193,193, pixel
0.505,0.479,0.488, shown at level -47.6,47.6, step 1, values float32  
Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  
Map values for surface "2xzo-edit.pdb_A SES surface": minimum -371.2, mean
2.415, maximum 249  
Log from Sun Apr 30 14:20:24 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 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

> hide #!1 models

> open
> /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_70/Sen1-RNA_ADPBeF3-RSR68-coot-0.updated_real_space_refined.pdb

Chain information for
Sen1-RNA_ADPBeF3-RSR68-coot-0.updated_real_space_refined.pdb #2  
---  
Chain | Description  
O | No description available  
P | No description available  
  

> select #2/O:1536

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select up

11144 atoms, 11246 bonds, 694 residues, 1 model selected  

> select clear

> select #2/O:1422@HH12

1 atom, 1 residue, 1 model selected  

> select clear

> select H

5739 atoms, 708 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open
> /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_62/Sen1-alone_noATP-
> RSR59-coot-0.updated_real_space_refined.pdb

Chain information for Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb #3  
---  
Chain | Description  
O | No description available  
P | No description available  
  

> select #3/O:1677

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select H

5696 atoms, 703 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #!2 to #3/O pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sen1-alone_noATP-RSR59-coot-0.updated_real_space_refined.pdb, chain
O (#3) with Sen1-RNA_ADPBeF3-RSR68-coot-0.updated_real_space_refined.pdb,
chain O (#2), sequence alignment score = 3471.6  
RMSD between 452 pruned atom pairs is 0.557 angstroms; (across all 690 pairs:
4.886)  
  

> hide #!2 models

> select #3/O:1536

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

228 atoms, 229 bonds, 27 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> color sel dark gray

> select clear

[Repeated 2 time(s)]

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> select #3/O:1098

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> select #3/O

5523 atoms, 5625 bonds, 2 pseudobonds, 690 residues, 2 models selected  

> select clear

> select #3/P

278 atoms, 310 bonds, 13 residues, 1 model selected  

> color sel red

> color sel dark gray

> select clear

> hide #!3 models

> show #!3 models

> show #!2 models

> select clear

> select #2/O:1532

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> color sel #fbec5dff

> select clear

> select #3/O:1869

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

86 atoms, 86 bonds, 10 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> color sel #fbec5dff

> select clear

> select #3/P:12

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

278 atoms, 310 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark salmon

> color sel light coral

> color sel #ff7e79ff

> select clear

> select #2/P:13

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> color sel red

> select clear

> hide #!3 models

> select #2/O:1533

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> color sel #929000ff

> select clear

> color #2 #666633ff

> select clear

> select #2/P:12

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> select up

5865 atoms, 5995 bonds, 710 residues, 1 model selected  

> select down

276 atoms, 307 bonds, 13 residues, 1 model selected  

> color sel red

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> color sel byelement

> select clear

> select #2/O:1532

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> color sel byelement

> select clear

> cartoon style #2 xsection oval modeHelix default

> cartoon style #2 modeHelix tube sides 20

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

4 atoms, 2 bonds, 2 residues, 1 model selected  

> select up

6 atoms, 3 bonds, 3 residues, 1 model selected  

> select up

8 atoms, 4 bonds, 4 residues, 1 model selected  

> select clear

> select #2/7:902@MG

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> select #2/7:903@F3

1 atom, 1 residue, 1 model selected  

> select #2/7:903@BE

1 atom, 1 residue, 1 model selected  

> select #2/7:903@F3

1 atom, 1 residue, 1 model selected  

> select add #2/7:903@BE

2 atoms, 1 residue, 1 model selected  

> select add #2/7:903@F2

3 atoms, 1 residue, 1 model selected  

> select add #2/7:903@F1

4 atoms, 1 residue, 1 model selected  

> color sel byelement

> select clear

> select #2/O:1464

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

69 atoms, 68 bonds, 8 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> select clear

> select #2/O:1097

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

123 atoms, 123 bonds, 14 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> hide sel target a

> select clear

> select add #2/O:1552

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> color sel #999966ff

> select clear

> show #!3 models

> select #3/O:1280

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

75 atoms, 75 bonds, 9 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> cartoon style sel modeHelix tube sides 20

> select clear

> toolshed show

Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl  
[Repeated 1 time(s)]

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/srengac/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/srengac/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/tzdata  
sysconfig: /Users/srengac/Library/Python/3.9/include/tzdata  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/srengac/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application Support/ChimeraX  
sysconfig: /Users/srengac/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/pandas  
sysconfig: /Users/srengac/Library/Python/3.9/include/pandas  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/et-xmlfile  
sysconfig: /Users/srengac/Library/Python/3.9/include/et-xmlfile  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/seaborn  
sysconfig: /Users/srengac/Library/Python/3.9/include/seaborn  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/qtrangeslider  
sysconfig: /Users/srengac/Library/Python/3.9/include/qtrangeslider  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/openpyxl  
sysconfig: /Users/srengac/Library/Python/3.9/include/openpyxl  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-XMAS  
sysconfig: /Users/srengac/Library/Python/3.9/include/ChimeraX-XMAS  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/srengac/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/srengac/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 23.1.2 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/srengac/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core~=1.3 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.3)  
Collecting openpyxl  
Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)  
Collecting pandas  
Downloading pandas-2.0.1-cp39-cp39-macosx_10_9_x86_64.whl (11.8 MB)  
Collecting qtrangeslider  
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)  
Collecting seaborn  
Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)  
Requirement already satisfied: ChimeraX-UI~=1.3 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.13.7)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0)  
Collecting et-xmlfile  
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)  
Collecting tzdata>=2022.1  
Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB)  
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2021.3)  
Requirement already satisfied: numpy>=1.20.3 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (1.21.2)  
Requirement already satisfied: python-dateutil>=2.8.2 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2)  
Requirement already satisfied: six>=1.5 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.2->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)  
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.4.3)  
Requirement already satisfied: pillow>=6.2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (8.3.2)  
Requirement already satisfied: kiwisolver>=1.0.1 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.3.2)  
Requirement already satisfied: cycler>=0.10 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(0.11.0)  
Requirement already satisfied: pyparsing>=2.2.1 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.6)  
Installing collected packages: tzdata, pandas, et-xmlfile, seaborn,
qtrangeslider, openpyxl, ChimeraX-XMAS  
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-2.0.1 qtrangeslider-0.1.5 seaborn-0.12.2 tzdata-2023.3  
\---  

Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-2.0.1 qtrangeslider-0.1.5 seaborn-0.12.2 tzdata-2023.3  
Installed ChimeraX-XMAS (1.1.2)  

> select #3/O:1653

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide #!2 models

> select add #3/O:1652

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel byelement

> color sel byhetero

> undo

[Repeated 1 time(s)]

> color sel byhetero

> select clear

> show #!2 models

> hide #!3 models

> select #2/O:1653

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #2/O:1652

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add #2/7:903@F3

28 atoms, 29 bonds, 2 residues, 1 model selected  

> select add #2/7:903@BE

29 atoms, 29 bonds, 2 residues, 1 model selected  

> select add #2/7:903@F2

30 atoms, 29 bonds, 2 residues, 1 model selected  

> color sel #666633ff

> color sel byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> color sel #999966ff

> color sel byhetero

> select clear

> show #!3 models

> select #2/P:13

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> select add #3/P:13

298 atoms, 331 bonds, 14 residues, 2 models selected  

> select up

554 atoms, 617 bonds, 26 residues, 2 models selected  

> nucleotides sel fill

> select clear

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

278 atoms, 310 bonds, 13 residues, 1 model selected  

> color sel #ff7e79ff

> color sel #ffcc99ff

> select clear

[Repeated 1 time(s)]

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show Contacts

> hide #!2 models

> select #3/O:1206

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> select up

5801 atoms, 5935 bonds, 703 residues, 1 model selected  

> ui tool show Contacts

> contacts distanceOnly 4.0 color #000000

285840 distances  

> contacts distanceOnly 4.0 intraModel false intraMol false color #000000

212105 distances  

> contacts distanceOnly 4.0 interModel false intraMol false color #000000

11750 distances  

> close #4

> hide #!3 models

> open /Users/srengac/Documents/Phenix/Sen1/Maps/19Jan2023_noATP/final-
> pdb/Final-final/Sen1-RNA_noATP.pdb

Chain information for Sen1-RNA_noATP.pdb #4  
---  
Chain | Description  
C | No description available  
O | No description available  
P | No description available  
  

> select #4/P:13

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

278 atoms, 310 bonds, 13 residues, 1 model selected  

> nucleotides sel fill

> color sel red

> select clear

> select #4/C:157

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

89 atoms, 88 bonds, 12 residues, 1 model selected  

> select up

2078 atoms, 2116 bonds, 264 residues, 1 model selected  

> cartoon hide sel

> select clear

> cartoon style #4 modeHelix tube sides 20

> select #4/O:1534

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/O:1201

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

62 atoms, 63 bonds, 8 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> undo

> color sel #fbec5dff

> select clear

> select #4/O:1201

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

62 atoms, 63 bonds, 8 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> color sel #fbec5dff

> select clear

> ui tool show Contacts

> contacts distanceOnly 4.0 interModel false intraMol false color #000000
> dashes 5

12678 distances  

> select #4/O:1804

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/O:1804

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/O:1805

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/O:1804

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 3 residues  

> select clear

> select #4/O:1804

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #4/O:1805

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #4/O:1806

17 atoms, 14 bonds, 3 residues, 1 model selected  

> select add #4/O:1714

25 atoms, 21 bonds, 4 residues, 1 model selected  

> select add #4/O:1713

32 atoms, 27 bonds, 5 residues, 1 model selected  
Drag select of 1 residues  

> select add #4/O:1714

32 atoms, 27 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select add #4/O:1753

43 atoms, 37 bonds, 1 pseudobond, 6 residues, 2 models selected  

> select add #4/O:1751

50 atoms, 44 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> select add #4/O:1752

62 atoms, 56 bonds, 2 pseudobonds, 8 residues, 2 models selected  

> select add #4/O:1781

70 atoms, 63 bonds, 2 pseudobonds, 9 residues, 2 models selected  

> select add #4/O:1782

74 atoms, 66 bonds, 2 pseudobonds, 10 residues, 2 models selected  

> select add #4/O:1624

81 atoms, 72 bonds, 2 pseudobonds, 11 residues, 2 models selected  

> select add #4/O:1623

88 atoms, 78 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> select add #4/O:1411

95 atoms, 85 bonds, 2 pseudobonds, 13 residues, 2 models selected  

> select add #4/O:1412

101 atoms, 90 bonds, 3 pseudobonds, 14 residues, 2 models selected  

> select add #4/O:1287

110 atoms, 98 bonds, 3 pseudobonds, 15 residues, 2 models selected  

> select add #4/O:1253

117 atoms, 104 bonds, 3 pseudobonds, 16 residues, 2 models selected  

> select add #4/O:1254

126 atoms, 112 bonds, 3 pseudobonds, 17 residues, 2 models selected  

> select add #4/O:1538

135 atoms, 120 bonds, 3 pseudobonds, 18 residues, 2 models selected  

> select add #4/O:1541

141 atoms, 125 bonds, 4 pseudobonds, 19 residues, 2 models selected  

> show (#!4 & sel-residues & sidechain) target ab

> color (#!4 & sel) byhetero

> select clear

> select #4/O:1623

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide #5 models

> select clear

> contacts distanceOnly 4.5 interModel false intraMol false color #000000
> dashes 5

28047 distances  

> show #5 models

> select #4/O:1538

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #4/O:1537

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel byhetero

> select clear

> hide #5 models

> select #4/O:1779

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel byhetero

> select clear

> hide #!4 models

> show #!3 models

> open /Users/srengac/Downloads/qlgzuizmyn.pqr.dx

Opened qlgzuizmyn.pqr.dx as #6, grid size 161,225,225, pixel 0.543,0.495,0.48,
shown at level -45.3,45.3, step 1, values float32  

> show #!3 surfaces

> ui tool show "Surface Color"

> color electrostatic #6.1#6.2 map #6 palette
> -10,#ff0000:-3,#ffffff:-5,#0000ff

Map values for surface "surface": minimum -373.2, mean 9.608, maximum 423  
Map values for surface "surface": minimum -361.1, mean -5.943, maximum 331.8  

> color electrostatic #6.1#6.2 map #6 palette
> -10,#ff0000:-3,#ffffff:-5,#0000ff

Map values for surface "surface": minimum -373.2, mean 9.608, maximum 423  
Map values for surface "surface": minimum -361.1, mean -5.943, maximum 331.8  

> hide #!6 models

> show #!6 models

> hide #!3 models

> color electrostatic #6.1#6.2 map #6 palette -10,#ff0000:0,#ffffff:10,#0000ff

Map values for surface "surface": minimum -373.2, mean 9.608, maximum 423  
Map values for surface "surface": minimum -361.1, mean -5.943, maximum 331.8  

> color electrostatic #6.1#6.2 map #6 palette -5,#ff0000:0,#ffffff:5,#0000ff

Map values for surface "surface": minimum -373.2, mean 9.608, maximum 423  
Map values for surface "surface": minimum -361.1, mean -5.943, maximum 331.8  

> color electrostatic #6.1#6.2 map #6 palette -15,#ff0000:0,#ffffff:15,#0000ff

Map values for surface "surface": minimum -373.2, mean 9.608, maximum 423  
Map values for surface "surface": minimum -361.1, mean -5.943, maximum 331.8  

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!4 surfaces

> hide #!4 models

> color electrostatic #3.2 map #6 palette -15,#ff0000:0,#ffffff:15,#0000ff

Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  

> show #!3 models

> color electrostatic #3.2 map #6 palette -10,#ff0000:0,#ffffff:10,#0000ff

Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  

> color electrostatic #3.2 map #6 palette -5,#ff0000:0,#ffffff:5,#0000ff

Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  

> hide #!6 models

> volume #6 level 24.77 level 45.35

> volume #6 level 39.08 level 45.35

> turn x 180

> turn x -180

> turn y, 180

Expected an axis vector or a keyword  

> turn y 180

> turn y -180

> turn x -180

> turn x 180

> turn z 180

> turn z -180

> turn y, 90

Expected an axis vector or a keyword  

> turn y 90

[Repeated 3 time(s)]

> turn x, 90

Expected an axis vector or a keyword  

> turn x 90

[Repeated 3 time(s)]

> turn z 90

[Repeated 3 time(s)]

> turn x -180

> turn x 180

> turn y -180

[Repeated 1 time(s)]

> turn x-30

Expected an axis vector or a keyword  

> turn x -30

> turn y 60

> turn y -60

> turn y -180

> turn x -30

> turn x 30

> turn z 30

> turn x -30

[Repeated 21 time(s)]

> turn y -180

> turn x -30

[Repeated 20 time(s)]

> turn y -180

> turn x -30

[Repeated 9 time(s)]

> turn x 300

> turn y 180

> turn y -180

> turn x -300

> hide #!3 models

> open /Users/srengac/Downloads/2xzo-edit.pdb

Chain information for 2xzo-edit.pdb #7  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> view orient

> show #!7 surfaces

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!7 models

> show #!2 models

> hide #!2 models

> show #!3 models

> ui tool show Matchmaker

>

Missing command  

>

Missing command  

>

Missing command  

> show #!7 models

> hide #!3 models

> open /Users/srengac/Downloads/1qll0kpcmk.pqr.dx

Opened 1qll0kpcmk.pqr.dx as #8, grid size 193,193,193, pixel
0.505,0.479,0.488, shown at level -47.6,47.6, step 1, values float32  

> color electrostatic #7.2 map #8 palette -5,#ff0000:0,#ffffff:5,#0000ff

Map values for surface "2xzo-edit.pdb_A SES surface": minimum -371.2, mean
2.415, maximum 249  

> hide #!8 models

> show #!4 models

> hide #!4 models

> color electrostatic #3.2 map #6 palette -5,#ff0000:0,#ffffff:5,#0000ff

Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  
Map values for surface "cap far": minimum -318.6, mean 2.071, maximum 278.4  

> color electrostatic #3.2 map #6 palette -5,#ff0000:0,#ffffff:5,#0000ff

Map values for surface "Sen1-alone_noATP-
RSR59-coot-0.updated_real_space_refined.pdb_O SES surface": minimum -399.8,
mean -0.4522, maximum 434.8  
Map values for surface "cap far": minimum -318.6, mean 2.071, maximum 278.4  

> show #!3 models

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

>

Missing command  

>

Missing command  

>

Missing command  

>

Missing command  

>

Missing command  

>

Missing command  

> hide #!6 models

> hide #!7 models

> hide #!3 models

> show #!2 models

> show #!4 models

> select #4

7879 atoms, 8051 bonds, 2071 pseudobonds, 967 residues, 3 models selected  

> hide sel surfaces

> ~select #4

3 models selected  

> select up

22 atoms, 24 bonds, 1 residue, 2 models selected  

> select up

278 atoms, 310 bonds, 13 residues, 2 models selected  

> color (#!4 & sel) #ffcc99ff

> color (#!4 & sel) #ff9966ff

> select clear

> select up

20 atoms, 21 bonds, 1 residue, 2 models selected  

> select up

278 atoms, 310 bonds, 13 residues, 2 models selected  

> color (#!4 & sel) #ff6600ff

> color (#!4 & sel) #ccccccff

> select clear

[Repeated 1 time(s)]

> select #4/O:1224

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

106 atoms, 109 bonds, 12 residues, 2 models selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 2 models selected  

> color (#!4 & sel) #ccccccff

[Repeated 1 time(s)]

> select clear

> select #2/O:1532

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5557 atoms, 5659 bonds, 694 residues, 1 model selected  

> color sel #fbec5dff

> select clear

> select #4/O:1866

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

86 atoms, 86 bonds, 10 residues, 2 models selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 2 models selected  

> color (#!4 & sel) byhetero

> select clear

> select #2/7:901@C2

1 atom, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> color sel byhetero

> color sel #fbec5dff

> color sel byhetero

> select clear

[Repeated 2 time(s)]

> select #4/P:12

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 45 bonds, 2 residues, 3 models selected  

> select up

554 atoms, 617 bonds, 26 residues, 3 models selected  

> cartoon hide (#!2,4 & sel)

> hide (#!2,4 & sel) target a

> undo

[Repeated 1 time(s)]

> select clear

> save /Users/srengac/Downloads/TEST-MOVEMENT.png width 3000 height 2888
> supersample 4 transparentBackground true

> save /Users/srengac/Downloads/TEST-MOVEMENT.PNG.png width 3000 height 2888
> supersample 4 transparentBackground true

> save /Users/srengac/Downloads/test-movement.png width 3000 height 2888
> supersample 4 transparentBackground true

[Repeated 1 time(s)]

> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/test-
> movement.cxs includeMaps true

——— End of log from Sun Apr 30 14:20:24 2023 ———

opened ChimeraX session  

> select #4/O:1465

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

77 atoms, 76 bonds, 9 residues, 2 models selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 2 models selected  

> hide (#!4 & sel) target a

> select clear

> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/test-
> movement.png width 3000 height 3166 supersample 4 transparentBackground true

> color #2,4 #9fb59dff

> undo

> color #2,4 #ccffccff

> undo

> color #2,4 #ccffffff

> undo

> save /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/test-
> movement.cxs includeMaps true

——— End of log from Tue May 2 15:00:54 2023 ———

opened ChimeraX session  

> close #5#1,3,6-8

> open
> /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_150/Sen1-RNAaloneRSR147.updated_real_space_refined.pdb

Chain information for Sen1-RNAaloneRSR147.updated_real_space_refined.pdb #1  
---  
Chain | Description  
O | No description available  
P | No description available  
  

> hide #!4 models

> cartoon style #1-2 modeHelix tube sides 20

> select #1

11494 atoms, 11627 bonds, 2 pseudobonds, 703 residues, 2 models selected  

> select clear

> select #1/O:1536

17 atoms, 16 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  

> ui tool show "Color Actions"

> color sel #929292ff

> color sel #919191ff

> color sel #797979ff

> color sel #919191ff

> color sel #797979ff

> select clear

> open
> /Users/srengac/Documents/Phenix/Sen1/RealSpaceRefine_114/Sen1-RNA_ADPBeF3-RSR112-coot0.updated_real_space_refined.pdb

Chain information for
Sen1-RNA_ADPBeF3-RSR112-coot0.updated_real_space_refined.pdb #3  
---  
Chain | Description  
O | No description available  
P | No description available  
  

> ui tool show Matchmaker

> matchmaker #!3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sen1-RNA_ADPBeF3-RSR68-coot-0.updated_real_space_refined.pdb, chain
O (#2) with Sen1-RNA_ADPBeF3-RSR112-coot0.updated_real_space_refined.pdb,
chain O (#3), sequence alignment score = 3581.6  
RMSD between 694 pruned atom pairs is 0.195 angstroms; (across all 694 pairs:
0.195)  
  

> hide #!2 models

> select #3/O:1533

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select up

11188 atoms, 11287 bonds, 697 residues, 1 model selected  

> cartoon style sel modeHelix tube sides 20

> select clear

> select #3/O:1532

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select up

11188 atoms, 11287 bonds, 697 residues, 1 model selected  

> select down

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select up

11188 atoms, 11287 bonds, 697 residues, 1 model selected  

> color sel #797979ff

> color sel #fbec5dff

> select clear

> select #3/O:1532

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3

11477 atoms, 11597 bonds, 2 pseudobonds, 706 residues, 2 models selected  

> ~select #3

Nothing selected  

> select #2

5865 atoms, 5995 bonds, 2 pseudobonds, 710 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #3

11477 atoms, 11597 bonds, 2 pseudobonds, 706 residues, 2 models selected  

> select #1

11494 atoms, 11627 bonds, 2 pseudobonds, 703 residues, 2 models selected  

> select H

11391 atoms, 1407 residues, 2 models selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #3/P:9

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

192 atoms, 213 bonds, 9 residues, 1 model selected  

> color sel #919191ff

> select clear

> select #1/P:13

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> color sel red

> select clear

> select #1/P:13

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> nucleotides sel fill

> select clear

> dssp

> select clear

> select #3/O:1531

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

266 atoms, 267 bonds, 31 residues, 1 model selected  

> select up

5589 atoms, 5688 bonds, 697 residues, 1 model selected  

> color sel byhetero

> select clear

> select #3/O:1743

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select #3/O:1365@NZ

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/O:1364@OG1

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select up

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select up

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select up

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select up

29 atoms, 26 bonds, 4 residues, 1 model selected  

> select up

39 atoms, 37 bonds, 4 residues, 1 model selected  

> select add #3/O:1787@CG

40 atoms, 37 bonds, 5 residues, 1 model selected  

> select up

48 atoms, 45 bonds, 5 residues, 1 model selected  

> select up

50 atoms, 46 bonds, 6 residues, 1 model selected  

> select up

56 atoms, 52 bonds, 6 residues, 1 model selected  

> select add #3/O:1334@NZ

57 atoms, 52 bonds, 7 residues, 1 model selected  

> select up

65 atoms, 60 bonds, 7 residues, 1 model selected  

> select up

67 atoms, 61 bonds, 8 residues, 1 model selected  

> select up

76 atoms, 71 bonds, 8 residues, 1 model selected  

> hide sel target a

> select clear

> select #3/O:1820@NE

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

26 atoms, 25 bonds, 3 residues, 1 model selected  

> hide sel target a

> select clear

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/Sen1-movement.cxs

——— End of log from Tue Jun 27 14:31:08 2023 ———

opened ChimeraX session  

> select up

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

276 atoms, 307 bonds, 13 residues, 1 model selected  

> color sel dark gray

> ui tool show "Color Actions"

> color sel #797979ff

> select clear

> select #3/P:9

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

192 atoms, 213 bonds, 9 residues, 1 model selected  

> select up

5781 atoms, 5901 bonds, 706 residues, 1 model selected  

> select down

192 atoms, 213 bonds, 9 residues, 1 model selected  

> color sel red

> select clear

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/Sen1-movement_overall.png
> width 3000 height 3279 supersample 4 transparentBackground true

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/Sen1-movement.cxs

——— End of log from Tue Jun 27 18:29:08 2023 ———

opened ChimeraX session  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

192 atoms, 213 bonds, 9 residues, 1 model selected  

> nucleotides sel fill

> select clear

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/Sen1-movement_overall.png
> width 3000 height 3279 supersample 4 transparentBackground true

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/Sen1-movement.cxs

——— End of log from Tue Jun 27 18:31:53 2023 ———

opened ChimeraX session  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 27 atom styles  

> select clear

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/RNAalone_Sen1-movement.cxs

——— End of log from Tue Jul 4 15:54:35 2023 ———

opened ChimeraX session  

> select #1/O:1868

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

86 atoms, 86 bonds, 10 residues, 1 model selected  

> select up

5523 atoms, 5625 bonds, 690 residues, 1 model selected  

> select up

5799 atoms, 5932 bonds, 703 residues, 1 model selected  

> color sel dark gray

> select clear

> save
> /Users/srengac/Documents/Phenix/Sen1/Figures/20Apr2023/RNAalone_Sen1-movement.cxs

——— End of log from Wed Jul 5 18:20:04 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: 56 days 18:49

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 Eric Pettersen, 2 years ago

Cc: Tom Goddard added
Component: UnassignedCore
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash in event loop

comment:2 by Eric Pettersen, 2 years ago

Resolution: can't reproduce
Status: acceptedclosed
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