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#8145 closed defect (can't reproduce)
Crash in QMainWindow::removeDockWidget
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203230115 (2022-03-23 01:15:14 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700021942000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070002093f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001f93c000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001e939000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001d936000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001c933000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001b930000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001a92d000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001992a000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700018927000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001080f9dc0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2309 in destroy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2177 in _destroy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 807 in remove_tool
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 370 in remove_tool
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [96729]
Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.4.0 (1.4.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [96729]
User ID: 501
Date/Time: 2022-12-07 18:30:15.498 +0000
OS Version: Mac OS X 10.15.7 (19H2026)
Report Version: 12
Anonymous UUID: 0E709B12-8DF7-25BC-87B8-66F9158E646D
Sleep/Wake UUID: 70FEF9FF-1BDF-4C43-A59D-E647E4F4667D
Time Awake Since Boot: 400000 seconds
Time Since Wake: 27000 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 0x000053f72422f4c8
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x53f72422f4c8:
mapped file 000000015a2cc000-000000015a5da000 [ 3128K] r--/rwx SM=COW
-->
MALLOC_NANO 0000600000000000-0000600008000000 [128.0M] rw-/rwx SM=PRV
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6b04932a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6b105e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6af6093e raise + 26
3 libsystem_platform.dylib 0x00007fff6b0fa5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtWidgets 0x0000000118b15fee QMainWindow::removeDockWidget(QDockWidget*) + 30
6 QtWidgets.abi3.so 0x000000011851d80f meth_QMainWindow_removeDockWidget(_object*, _object*) + 95
7 org.python.python 0x000000010469906d cfunction_call + 125
8 org.python.python 0x000000010465a17d _PyObject_MakeTpCall + 365
9 org.python.python 0x000000010473261c call_function + 876
10 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c98a method_vectorcall + 202
19 org.python.python 0x000000010473258c call_function + 732
20 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
21 org.python.python 0x000000010465a948 function_code_fastcall + 104
22 org.python.python 0x000000010465c98a method_vectorcall + 202
23 org.python.python 0x000000010473258c call_function + 732
24 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
25 org.python.python 0x000000010465a948 function_code_fastcall + 104
26 org.python.python 0x000000010465c9d2 method_vectorcall + 274
27 QtCore.abi3.so 0x0000000107bbdd57 PyQtSlot::call(_object*, _object*) const + 39
28 QtCore.abi3.so 0x0000000107bbdc66 PyQtSlot::invoke(void**, _object*, void*, bool) const + 358
29 QtCore.abi3.so 0x0000000107bbeb95 PyQtSlotProxy::unislot(void**) + 85
30 QtCore.abi3.so 0x0000000107bbeb0a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
31 QtCore 0x00000001161621b7 0x116079000 + 954807
32 QtWidgets 0x0000000118b615f1 0x118971000 + 2033137
33 QtCore 0x0000000116162472 0x116079000 + 955506
34 QtWidgets 0x0000000118aa7a1f 0x118971000 + 1272351
35 QtWidgets 0x0000000118aa78bc 0x118971000 + 1271996
36 QtWidgets 0x0000000118aa8979 QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 185
37 QtWidgets 0x00000001189d24e7 QWidget::event(QEvent*) + 391
38 QtWidgets 0x000000011897db97 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
39 QtWidgets 0x000000011898030f QApplication::notify(QObject*, QEvent*) + 6159
40 QtWidgets.abi3.so 0x00000001184a30b9 sipQApplication::notify(QObject*, QEvent*) + 233
41 QtCore 0x000000011611116a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
42 QtWidgets 0x000000011897e347 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 935
43 QtWidgets 0x00000001189e932f 0x118971000 + 492335
44 QtWidgets 0x00000001189e806b 0x118971000 + 487531
45 QtWidgets 0x000000011897db97 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
46 QtWidgets 0x000000011897ecf7 QApplication::notify(QObject*, QEvent*) + 503
47 QtWidgets.abi3.so 0x00000001184a30b9 sipQApplication::notify(QObject*, QEvent*) + 233
48 QtCore 0x000000011611116a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
49 QtGui 0x000000011901d8d0 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 2352
50 QtGui 0x000000011906b14c QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 444
51 libqcocoa.dylib 0x0000000124a9bfdb 0x124a84000 + 98267
52 com.apple.CoreFoundation 0x00007fff3127cf92 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
53 com.apple.CoreFoundation 0x00007fff3127cf31 __CFRunLoopDoSource0 + 103
54 com.apple.CoreFoundation 0x00007fff3127cd4b __CFRunLoopDoSources0 + 209
55 com.apple.CoreFoundation 0x00007fff3127ba7a __CFRunLoopRun + 927
56 com.apple.CoreFoundation 0x00007fff3127b07e CFRunLoopRunSpecific + 462
57 com.apple.HIToolbox 0x00007fff2fea7aad RunCurrentEventLoopInMode + 292
58 com.apple.HIToolbox 0x00007fff2fea76e4 ReceiveNextEventCommon + 359
59 com.apple.HIToolbox 0x00007fff2fea7569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
60 com.apple.AppKit 0x00007fff2e4f03c9 _DPSNextEvent + 883
61 com.apple.AppKit 0x00007fff2e4eec10 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
62 com.apple.AppKit 0x00007fff2e4e091e -[NSApplication run] + 658
63 libqcocoa.dylib 0x0000000124a9adcd 0x124a84000 + 93645
64 QtCore 0x000000011611a356 QEventLoop::exec(QFlags) + 454
65 QtCore 0x0000000116111782 QCoreApplication::exec() + 130
66 QtWidgets.abi3.so 0x000000011859078a meth_QApplication_exec(_object*, _object*) + 90
67 org.python.python 0x000000010469906d cfunction_call + 125
68 org.python.python 0x000000010465a17d _PyObject_MakeTpCall + 365
69 org.python.python 0x000000010473261c call_function + 876
70 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
71 org.python.python 0x000000010465a948 function_code_fastcall + 104
72 org.python.python 0x000000010465c98a method_vectorcall + 202
73 org.python.python 0x000000010473258c call_function + 732
74 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
75 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
76 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
77 org.python.python 0x000000010473258c call_function + 732
78 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
79 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
80 org.python.python 0x000000010472970b PyEval_EvalCode + 139
81 org.python.python 0x0000000104726592 builtin_exec + 626
82 org.python.python 0x000000010469886a cfunction_vectorcall_FASTCALL + 218
83 org.python.python 0x000000010473258c call_function + 732
84 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
85 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
86 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
87 org.python.python 0x000000010473258c call_function + 732
88 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
89 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
90 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
91 org.python.python 0x0000000104798e20 pymain_run_module + 208
92 org.python.python 0x0000000104798537 Py_RunMain + 1431
93 org.python.python 0x0000000104798b3f pymain_main + 223
94 org.python.python 0x0000000104798a4b Py_Main + 43
95 edu.ucsf.cgl.ChimeraX 0x0000000104617dc8 main + 120
96 libdyld.dylib 0x00007fff6af01cc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6b04bb86 kevent64 + 10
1 QtWebEngineCore 0x000000011cd55d87 0x119a66000 + 53411207
2 QtWebEngineCore 0x000000011cd55c81 0x119a66000 + 53410945
3 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
4 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
5 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
6 QtWebEngineCore 0x000000011cceac5d 0x119a66000 + 52972637
7 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
8 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
9 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011ccf7a28 0x119a66000 + 53025320
4 QtWebEngineCore 0x000000011ccf84a0 0x119a66000 + 53028000
5 QtWebEngineCore 0x000000011ccf803d 0x119a66000 + 53026877
6 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
7 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6b04bb86 kevent64 + 10
1 QtWebEngineCore 0x000000011cd55d87 0x119a66000 + 53411207
2 QtWebEngineCore 0x000000011cd55c81 0x119a66000 + 53410945
3 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
4 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
5 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
6 QtWebEngineCore 0x0000000121546e32 0x119a66000 + 128847410
7 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
8 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
9 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 5:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011cd2b0d4 0x119a66000 + 53235924
3 QtWebEngineCore 0x000000011ea8d3dd 0x119a66000 + 84046813
4 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
5 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 6:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 7:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6b04bb86 kevent64 + 10
1 QtWebEngineCore 0x000000011cd55d87 0x119a66000 + 53411207
2 QtWebEngineCore 0x000000011cd55c81 0x119a66000 + 53410945
3 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
4 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
5 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
6 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
7 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
8 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 9:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 10:: NetworkService
0 libsystem_kernel.dylib 0x00007fff6b04bb86 kevent64 + 10
1 QtWebEngineCore 0x000000011cd55d87 0x119a66000 + 53411207
2 QtWebEngineCore 0x000000011cd55c81 0x119a66000 + 53410945
3 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
4 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
5 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
6 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
7 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
8 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011ccf7a1a 0x119a66000 + 53025306
5 QtWebEngineCore 0x000000011ccf84a0 0x119a66000 + 53028000
6 QtWebEngineCore 0x000000011ccf812d 0x119a66000 + 53027117
7 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
8 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 14:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3127d135 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff3127bc02 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff3127b07e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2e691bf4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011cc6d457 0x119a66000 + 52458583
5 QtWebEngineCore 0x000000011ccddf5d 0x119a66000 + 52920157
6 QtWebEngineCore 0x000000011cc9d718 0x119a66000 + 52655896
7 QtWebEngineCore 0x000000011cd04398 0x119a66000 + 53076888
8 QtWebEngineCore 0x000000011cd0454b 0x119a66000 + 53077323
9 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
10 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 16:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011cd333cf 0x119a66000 + 53269455
4 QtWebEngineCore 0x000000011ccf7a1a 0x119a66000 + 53025306
5 QtWebEngineCore 0x000000011ccf81ff 0x119a66000 + 53027327
6 QtWebEngineCore 0x000000011ccf806d 0x119a66000 + 53026925
7 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
8 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
11 org.python.python 0x000000010465a948 function_code_fastcall + 104
12 org.python.python 0x000000010473258c call_function + 732
13 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
14 org.python.python 0x000000010465a948 function_code_fastcall + 104
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465c9d2 method_vectorcall + 274
19 org.python.python 0x00000001047d73c6 t_bootstrap + 70
20 org.python.python 0x00000001047888c9 pythread_wrapper + 25
21 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
22 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff6b0493c6 poll + 10
1 select.cpython-39-darwin.so 0x0000000107238802 select_poll_poll + 482
2 org.python.python 0x000000010466306f method_vectorcall_FASTCALL + 335
3 org.python.python 0x000000010473258c call_function + 732
4 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
5 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
6 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
7 org.python.python 0x000000010473258c call_function + 732
8 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
9 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
10 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
11 org.python.python 0x000000010473258c call_function + 732
12 org.python.python 0x000000010472fbe1 _PyEval_EvalFrameDefault + 25521
13 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
14 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
15 org.python.python 0x000000010473258c call_function + 732
16 org.python.python 0x000000010472fab3 _PyEval_EvalFrameDefault + 25219
17 org.python.python 0x000000010465a948 function_code_fastcall + 104
18 org.python.python 0x000000010465ca79 method_vectorcall + 441
19 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
20 org.python.python 0x000000010465a948 function_code_fastcall + 104
21 org.python.python 0x000000010473258c call_function + 732
22 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
23 org.python.python 0x000000010465a948 function_code_fastcall + 104
24 org.python.python 0x000000010473258c call_function + 732
25 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
26 org.python.python 0x000000010465a948 function_code_fastcall + 104
27 org.python.python 0x000000010465c9d2 method_vectorcall + 274
28 org.python.python 0x00000001047d73c6 t_bootstrap + 70
29 org.python.python 0x00000001047888c9 pythread_wrapper + 25
30 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
31 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x0000000104676bba calliter_iternext + 74
7 org.python.python 0x000000010472f3fb _PyEval_EvalFrameDefault + 23499
8 org.python.python 0x000000010465a948 function_code_fastcall + 104
9 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
10 org.python.python 0x000000010465a948 function_code_fastcall + 104
11 org.python.python 0x000000010473258c call_function + 732
12 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
13 org.python.python 0x000000010465a948 function_code_fastcall + 104
14 org.python.python 0x000000010473258c call_function + 732
15 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010465a948 function_code_fastcall + 104
17 org.python.python 0x000000010465c9d2 method_vectorcall + 274
18 org.python.python 0x00000001047d73c6 t_bootstrap + 70
19 org.python.python 0x00000001047888c9 pythread_wrapper + 25
20 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
21 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788c76 PyThread_acquire_lock_timed + 454
3 _queue.cpython-39-darwin.so 0x000000012544857e _queue_SimpleQueue_get_impl + 526
4 _queue.cpython-39-darwin.so 0x0000000125448126 _queue_SimpleQueue_get + 198
5 org.python.python 0x0000000104698934 cfunction_vectorcall_FASTCALL_KEYWORDS + 132
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fb4b _PyEval_EvalFrameDefault + 25371
8 org.python.python 0x000000010465a948 function_code_fastcall + 104
9 org.python.python 0x00000001047301c3 _PyEval_EvalFrameDefault + 27027
10 org.python.python 0x000000010465a948 function_code_fastcall + 104
11 org.python.python 0x000000010473258c call_function + 732
12 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
13 org.python.python 0x000000010465a948 function_code_fastcall + 104
14 org.python.python 0x000000010473258c call_function + 732
15 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010465a948 function_code_fastcall + 104
17 org.python.python 0x000000010465c9d2 method_vectorcall + 274
18 org.python.python 0x00000001047d73c6 t_bootstrap + 70
19 org.python.python 0x00000001047888c9 pythread_wrapper + 25
20 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
21 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010846549f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010846549f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010846549f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010846549f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010846549f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 31:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011ccf7a28 0x119a66000 + 53025320
4 QtWebEngineCore 0x000000011ccf84a0 0x119a66000 + 53028000
5 QtWebEngineCore 0x000000011ccf80cd 0x119a66000 + 53027021
6 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
7 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 32:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 QtWebEngineCore 0x000000011cd335c3 0x119a66000 + 53269955
3 QtWebEngineCore 0x000000011ccf7a28 0x119a66000 + 53025320
4 QtWebEngineCore 0x000000011ccf84a0 0x119a66000 + 53028000
5 QtWebEngineCore 0x000000011ccf80cd 0x119a66000 + 53027021
6 QtWebEngineCore 0x000000011cd2c6e8 0x119a66000 + 53241576
7 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 33:
0 libsystem_pthread.dylib 0x00007fff6b101b68 start_wqthread + 0
Thread 34:: Dispatch queue: com.apple.root.user-interactive-qos
0 libsystem_kernel.dylib 0x00007fff6b042dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6b043160 mach_msg + 60
2 com.apple.QuartzCore 0x00007fff3cba16d9 CA::CA_BLOCKED_WAITING_FOR_CLIENT_FENCES(unsigned int, unsigned long) + 170
3 com.apple.QuartzCore 0x00007fff3cb835ee CA::Context::commit_transaction(CA::Transaction*, double) + 1906
4 com.apple.QuartzCore 0x00007fff3cb81bb4 CA::Transaction::commit() + 644
5 com.apple.AppKit 0x00007fff2e548704 NSPerformVisuallyAtomicChange + 154
6 com.apple.AppKit 0x00007fff2e79635c __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 80
7 libdispatch.dylib 0x00007fff6aea76c4 _dispatch_call_block_and_release + 12
8 libdispatch.dylib 0x00007fff6aea8658 _dispatch_client_callout + 8
9 libdispatch.dylib 0x00007fff6aeb6aa8 _dispatch_root_queue_drain + 663
10 libdispatch.dylib 0x00007fff6aeb7097 _dispatch_worker_thread2 + 92
11 libsystem_pthread.dylib 0x00007fff6b1029f7 _pthread_wqthread + 220
12 libsystem_pthread.dylib 0x00007fff6b101b77 start_wqthread + 15
Thread 35:
0 libsystem_kernel.dylib 0x00007fff6b045872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6b106425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104788d6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x00000001047d7a1f acquire_timed + 111
4 org.python.python 0x00000001047d7b30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000104662e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x000000010473258c call_function + 732
7 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010473258c call_function + 732
11 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x0000000104733283 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010465a8d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010473258c call_function + 732
15 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010465a948 function_code_fastcall + 104
17 org.python.python 0x000000010473258c call_function + 732
18 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x000000010465a948 function_code_fastcall + 104
20 org.python.python 0x000000010473258c call_function + 732
21 org.python.python 0x000000010472fa92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x000000010465a948 function_code_fastcall + 104
23 org.python.python 0x000000010465c9d2 method_vectorcall + 274
24 org.python.python 0x00000001047d73c6 t_bootstrap + 70
25 org.python.python 0x00000001047888c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff6b106109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6b101b8b thread_start + 15
Thread 36:
0 libsystem_pthread.dylib 0x00007fff6b101b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001080f9dc0 rcx: 0x00007fd9a1755a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fd9a1755a80 rsp: 0x00007fd9a1755a58
r8: 0x00007fd9a1755f48 r9: 0xf444fa32e4b48ca1 r10: 0x00000001080f9dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fd9a1605950 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6b04932a rfl: 0x0000000000000246 cr2: 0x00000001048837b8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff58e53000 - 0x7fff58e55ffe com.apple.OAuth (25 - 25) /System/Library/PrivateFrameworks/OAuth.framework/Versions/A/OAuth
0x7fff590fe000 - 0x7fff59149ffb com.apple.OTSVG (1.0 - 643.1.5.8) /System/Library/PrivateFrameworks/OTSVG.framework/Versions/A/OTSVG
0x7fff5a366000 - 0x7fff5a371ff2 com.apple.PerformanceAnalysis (1.243.3 - 243.3) /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
0x7fff5a372000 - 0x7fff5a39affb com.apple.persistentconnection (1.0 - 1.0) /System/Library/PrivateFrameworks/PersistentConnection.framework/Versions/A/PersistentConnection
0x7fff5a39b000 - 0x7fff5a3a9ffe com.apple.PersonaKit (1.0 - 1) /System/Library/PrivateFrameworks/PersonaKit.framework/Versions/A/PersonaKit
0x7fff5a553000 - 0x7fff5a553ffa com.apple.PhoneNumbers (1.0 - 1) /System/Library/PrivateFrameworks/PhoneNumbers.framework/Versions/A/PhoneNumbers
0x7fff5be15000 - 0x7fff5be45ff7 com.apple.pluginkit.framework (1.0 - 1) /System/Library/PrivateFrameworks/PlugInKit.framework/Versions/A/PlugInKit
0x7fff5be70000 - 0x7fff5be83ffc com.apple.PowerLog (1.0 - 1) /System/Library/PrivateFrameworks/PowerLog.framework/Versions/A/PowerLog
0x7fff5cb09000 - 0x7fff5cb29ff1 com.apple.proactive.support.ProactiveEventTracker (1.0 - 258.5) /System/Library/PrivateFrameworks/ProactiveEventTracker.framework/Versions/A/ProactiveEventTracker
0x7fff5cbb0000 - 0x7fff5cc19ff2 com.apple.proactive.support.ProactiveSupport (1.0 - 258.5) /System/Library/PrivateFrameworks/ProactiveSupport.framework/Versions/A/ProactiveSupport
0x7fff5ccff000 - 0x7fff5cd59ff6 com.apple.ProtectedCloudStorage (1.0 - 1) /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
0x7fff5cd5a000 - 0x7fff5cd73ffb com.apple.ProtocolBuffer (1 - 274.24.9.16.3) /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
0x7fff5cdad000 - 0x7fff5ce2afff com.apple.Quagga (1.0 - 1) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga
0x7fff5ce85000 - 0x7fff5ce88ff4 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff5ce89000 - 0x7fff5ceacff0 com.apple.quicklook.QuickLookSupport (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x7fff5cef3000 - 0x7fff5cf6cff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff5d1d3000 - 0x7fff5d1fcff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x7fff5d280000 - 0x7fff5d2caffa com.apple.ResponseKit (1.0 - 148.2) /System/Library/PrivateFrameworks/ResponseKit.framework/Versions/A/ResponseKit
0x7fff5d361000 - 0x7fff5d39cff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff5d7e9000 - 0x7fff5d80aff7 com.apple.SMBClient (3.4.1 - 3.4.1) /System/Library/PrivateFrameworks/SMBClient.framework/Versions/A/SMBClient
0x7fff5ec7d000 - 0x7fff5ec80ff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff5edf3000 - 0x7fff5ef1afff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff5ef73000 - 0x7fff5ef91ff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff5ef92000 - 0x7fff5efb2ff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff5efb3000 - 0x7fff5efc5ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff6032f000 - 0x7fff60625fff com.apple.SkyLight (1.600.0 - 451.6) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff60e72000 - 0x7fff60e80ffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff60f42000 - 0x7fff611ceff6 com.apple.spotlight.index (10.7.0 - 2076.7.2) /System/Library/PrivateFrameworks/SpotlightIndex.framework/Versions/A/SpotlightIndex
0x7fff6155c000 - 0x7fff6159dff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff616b4000 - 0x7fff616bdff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.2) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff6172e000 - 0x7fff61758ffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff61974000 - 0x7fff61984ff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff61d2b000 - 0x7fff61e86ff5 com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff61ea9000 - 0x7fff61f6fff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff62106000 - 0x7fff62107fff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff6213f000 - 0x7fff62397ff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff6242e000 - 0x7fff62434ffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff62dc6000 - 0x7fff62de6ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff63b92000 - 0x7fff63c7dff2 com.apple.ViewBridge (468 - 468) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff63e23000 - 0x7fff63e24fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff641b3000 - 0x7fff641eefff libAWDSupport.dylib (949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupport.dylib
0x7fff641ef000 - 0x7fff644cfff7 libAWDSupportFramework.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupportFramework.dylib
0x7fff644d0000 - 0x7fff644e1fff libprotobuf-lite.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf-lite.dylib
0x7fff644e2000 - 0x7fff6453bffb libprotobuf.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf.dylib
0x7fff6453c000 - 0x7fff64580ff6 com.apple.awd (1.0 - 949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/WirelessDiagnostics
0x7fff64a54000 - 0x7fff64a57ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff64ad1000 - 0x7fff64adfff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff64ca7000 - 0x7fff64cdcffe com.apple.iCalendar (7.0 - 810.6.1) /System/Library/PrivateFrameworks/iCalendar.framework/Versions/A/iCalendar
0x7fff64e21000 - 0x7fff64e23ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff64e24000 - 0x7fff64e37ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff64e69000 - 0x7fff64e75ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff64e76000 - 0x7fff64ea7ffd com.apple.contacts.vCard (1.0 - 3455.18) /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
0x7fff678fa000 - 0x7fff67906ff9 libAudioStatistics.dylib (1104.104) /usr/lib/libAudioStatistics.dylib
0x7fff67907000 - 0x7fff6793affa libAudioToolboxUtility.dylib (1104.104) /usr/lib/libAudioToolboxUtility.dylib
0x7fff67941000 - 0x7fff67975fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff67978000 - 0x7fff67982fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff67983000 - 0x7fff67a0bfff libCoreStorage.dylib (551.0.1) /usr/lib/libCoreStorage.dylib
0x7fff67a0e000 - 0x7fff67a10ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff67a56000 - 0x7fff67c0dffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff67c34000 - 0x7fff67c3aff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff67d1c000 - 0x7fff67d23fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff67d52000 - 0x7fff67d72ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff67df2000 - 0x7fff67ecfff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff67ee4000 - 0x7fff67ee5fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff67ee6000 - 0x7fff67f71ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff67f72000 - 0x7fff67f73fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff67f8b000 - 0x7fff67fa1fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff67fd6000 - 0x7fff68048ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib
0x7fff68049000 - 0x7fff680e2fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff680e6000 - 0x7fff680e6ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff680e7000 - 0x7fff681abffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff681ac000 - 0x7fff681bcffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff681bd000 - 0x7fff681c9fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff681ca000 - 0x7fff6821cfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6821d000 - 0x7fff68232ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff68233000 - 0x7fff68233fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff68234000 - 0x7fff68245fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff68246000 - 0x7fff6825dfd7 libcompression.dylib (87.1) /usr/lib/libcompression.dylib
0x7fff68537000 - 0x7fff6854dff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6854e000 - 0x7fff6854ffff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff689f2000 - 0x7fff68af6fcf libcrypto.44.dylib (47.140.3) /usr/lib/libcrypto.44.dylib
0x7fff68af9000 - 0x7fff68b04fff libcsfde.dylib (551.0.1) /usr/lib/libcsfde.dylib
0x7fff68b0c000 - 0x7fff68b6bff7 libcups.2.dylib (483.9) /usr/lib/libcups.2.dylib
0x7fff68b6d000 - 0x7fff68bd2ff7 libcurl.4.dylib (118.120.6) /usr/lib/libcurl.4.dylib
0x7fff68c75000 - 0x7fff68c75fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff68c76000 - 0x7fff68c90ff7 libexpat.1.dylib (19.60.3) /usr/lib/libexpat.1.dylib
0x7fff68c9e000 - 0x7fff68ca0fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff68ca1000 - 0x7fff68ca6f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff68caf000 - 0x7fff68cb4fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff68cb5000 - 0x7fff68cbeff7 libheimdal-asn1.dylib (564.140.8) /usr/lib/libheimdal-asn1.dylib
0x7fff68cbf000 - 0x7fff68daffff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff68db0000 - 0x7fff69007fff libicucore.A.dylib (64261.1.1) /usr/lib/libicucore.A.dylib
0x7fff69021000 - 0x7fff69022fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff69023000 - 0x7fff6903bff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff69053000 - 0x7fff690faff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff690fb000 - 0x7fff6935dff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff696ca000 - 0x7fff696f9fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff69829000 - 0x7fff69ca5ff5 libnetwork.dylib (1880.120.5) /usr/lib/libnetwork.dylib
0x7fff69ca6000 - 0x7fff69cbdfff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff69d46000 - 0x7fff69d79fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff69d7a000 - 0x7fff69d7bff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff69d8c000 - 0x7fff69d90fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff69d93000 - 0x7fff69dc9fff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff69e09000 - 0x7fff69e17ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff69e18000 - 0x7fff69e1bff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff69e1c000 - 0x7fff69e1efff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff69e4d000 - 0x7fff69e65fff libresolv.9.dylib (67.40.3) /usr/lib/libresolv.9.dylib
0x7fff69e67000 - 0x7fff69eabff7 libsandbox.1.dylib (1217.141.9) /usr/lib/libsandbox.1.dylib
0x7fff69eac000 - 0x7fff69ebeff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff69ebf000 - 0x7fff69ec0ff7 libspindump.dylib (281.4) /usr/lib/libspindump.dylib
0x7fff69ec1000 - 0x7fff6a0abff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff6a19f000 - 0x7fff6a1ccffb libssl.46.dylib (47.140.3) /usr/lib/libssl.46.dylib
0x7fff6a24e000 - 0x7fff6a27fff7 libtidy.A.dylib (17.3) /usr/lib/libtidy.A.dylib
0x7fff6a2a1000 - 0x7fff6a2fbff8 libusrtcp.dylib (1880.120.5) /usr/lib/libusrtcp.dylib
0x7fff6a2fc000 - 0x7fff6a2ffffb libutil.dylib (57.140.1) /usr/lib/libutil.dylib
0x7fff6a300000 - 0x7fff6a30dfff libxar.1.dylib (425.7) /usr/lib/libxar.1.dylib
0x7fff6a313000 - 0x7fff6a3f5ff7 libxml2.2.dylib (33.14) /usr/lib/libxml2.2.dylib
0x7fff6a3f9000 - 0x7fff6a421fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff6a422000 - 0x7fff6a434ff3 libz.1.dylib (76.0.1) /usr/lib/libz.1.dylib
0x7fff6ace3000 - 0x7fff6ace8ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6ace9000 - 0x7fff6acf4fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6acf5000 - 0x7fff6acfcfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6acfd000 - 0x7fff6ad06ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6ad07000 - 0x7fff6ad99fdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff6aea6000 - 0x7fff6aee6ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6aee7000 - 0x7fff6af1dfff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff6af1e000 - 0x7fff6af1effb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6af1f000 - 0x7fff6af2bff3 libkxld.dylib (6153.141.66) /usr/lib/system/libkxld.dylib
0x7fff6af2c000 - 0x7fff6af2cff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff6af2d000 - 0x7fff6af32ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6af33000 - 0x7fff6af35ff3 libquarantine.dylib (110.40.6) /usr/lib/system/libquarantine.dylib
0x7fff6af36000 - 0x7fff6af37ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6af38000 - 0x7fff6af4fff3 libsystem_asl.dylib (377.60.4) /usr/lib/system/libsystem_asl.dylib
0x7fff6af50000 - 0x7fff6af50ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6af51000 - 0x7fff6afd8fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff6afd9000 - 0x7fff6afdcffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff6afdd000 - 0x7fff6afe0fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6afe1000 - 0x7fff6afe9fff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff6afea000 - 0x7fff6aff1fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6aff2000 - 0x7fff6aff3ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6aff4000 - 0x7fff6b041ff7 libsystem_info.dylib (538.1) /usr/lib/system/libsystem_info.dylib
0x7fff6b042000 - 0x7fff6b06eff7 libsystem_kernel.dylib (6153.141.66) /usr/lib/system/libsystem_kernel.dylib
0x7fff6b06f000 - 0x7fff6b0b6fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6b0b7000 - 0x7fff6b0defff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6b0df000 - 0x7fff6b0ecffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6b0ed000 - 0x7fff6b0f6ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6b0f7000 - 0x7fff6b0fffef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6b100000 - 0x7fff6b10afff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6b10b000 - 0x7fff6b10fff3 libsystem_sandbox.dylib (1217.141.9) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6b110000 - 0x7fff6b112fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6b113000 - 0x7fff6b11affb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6b11b000 - 0x7fff6b131ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6b133000 - 0x7fff6b138ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6b139000 - 0x7fff6b16effe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 146
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: 493909
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=5.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.6G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 896K 7
Activity Tracing 256K 1
CG backing stores 8644K 14
CG image 8440K 53
CoreAnimation 1932K 67
CoreGraphics 8K 1
CoreImage 40K 4
CoreUI image data 4020K 35
Foundation 24K 2
Image IO 4K 1
Kernel Alloc Once 8K 1
MALLOC 4.7G 17021
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 144K 36
Stack 308.8M 37
Stack Guard 56.0M 1
VM_ALLOCATE 344.0M 315
VM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)
__DATA 74.6M 598
__DATA_CONST 180K 10
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 418.5M 151
__OBJC_RO 32.3M 1
__OBJC_RW 1904K 1
__TEXT 613.1M 573
__UNICODE 564K 1
mapped file 93.9M 69
shared memory 3368K 34
=========== ======= =======
TOTAL 6.9G 19053
TOTAL, minus reserved VM space 6.7G 19053
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203230115 (2022-03-23)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/cephfs/dzhang/A1GX/211207_A1G3_ZK/Refine3D/job257/run_class001.mrc
Opened run_class001.mrc as #1, grid size 384,384,384, pixel 1.07, shown at
level 0.00322, step 2, values float32
> volume #1 level 0.001945
> open /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/rf068_TMD.mrc
Opened rf068_TMD.mrc as #2, grid size 160,160,160, pixel 2.12, shown at level
0.023, step 1, values float32
> volume #2 level 0.005018
> close #2
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Refine3D/job068/run_class001.mrc
Opened run_class001.mrc as #2, grid size 160,160,160, pixel 2.12, shown at
level 0.0252, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Refine3D/job044/run_class001.mrc
Opened run_class001.mrc as #3, grid size 256,256,256, pixel 1.33, shown at
level 0.00651, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Refine3D/job045/run_class001.mrc
Opened run_class001.mrc as #4, grid size 256,256,256, pixel 1.33, shown at
level 0.0056, step 1, values float32
> ~tile
> tile
3 models tiled
> tile column3
Expected a models specifier or a keyword
> tile columns 3
3 models tiled
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Refine3D/job077/run_class001.mrc
Opened run_class001.mrc as #5, grid size 256,256,256, pixel 1.33, shown at
level 0.00552, step 1, values float32
> color #5 #f7915f models transparency 0
> ~tile
> tile
4 models tiled
> ~tile
> hide #!3 models
> hide #!4 models
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job032/run_it025_class001.mrc
Opened run_it025_class001.mrc as #6, grid size 160,160,160, pixel 2.12, shown
at level 0.0231, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job032/run_it025_class002.mrc
Opened run_it025_class002.mrc as #7, grid size 160,160,160, pixel 2.12, shown
at level 0.025, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job032/run_it025_class003.mrc
Opened run_it025_class003.mrc as #8, grid size 160,160,160, pixel 2.12, shown
at level 0.0255, step 1, values float32
> hide #!5 models
> hide #!2 models
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job033/run_it025_class001.mrc
Opened run_it025_class001.mrc as #9, grid size 160,160,160, pixel 2.12, shown
at level 0.0241, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job033/run_it025_class002.mrc
Opened run_it025_class002.mrc as #10, grid size 160,160,160, pixel 2.12, shown
at level 0.0238, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/221007_A1G3_tandem_quis_2/Class3D/job033/run_it025_class003.mrc
Opened run_it025_class003.mrc as #11, grid size 160,160,160, pixel 2.12, shown
at level 0.0257, step 1, values float32
> tile
6 models tiled
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!3 models
> volume #3 level 0.009035
> volume #3 level 0.008252
> surface dust #3 size 13.3
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> volume #3 level 0.008078
> volume #3 level 0.00773
> show #!4 models
> show #!2 models
> show #!1 models
> hide #!1 models
> ~tile
> tile
3 models tiled
> show #!5 models
> hide #!5 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> ~tile
> show #!10 models
> hide #!10 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> tile
3 models tiled
> volume #3 level 0.006426
> ui tool show "Side View"
> volume #3 level 0.006687
> ui tool show "Color Actions"
> set bgColor white
> open /Users/ig/Documents/Danyang/GluA1/models/A1G3_quis_c2_coot1.pdb
Chain information for A1G3_quis_c2_coot1.pdb #12
---
Chain | Description
A C | No description available
B | No description available
D | No description available
E | No description available
F H | No description available
G | No description available
> select add #12
17258 atoms, 17657 bonds, 2310 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-271.84,0,1,0,282.77,0,0,1,-46.795
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.87478,-0.252,0.41383,-280.6,-0.013662,0.84093,0.54097,216.24,-0.48433,-0.47889,0.73219,166.42
> view matrix models
> #12,0.95171,-0.13283,0.27678,-289.94,0.066966,0.96966,0.2351,234.61,-0.29961,-0.20521,0.93173,52.241
> view matrix models
> #12,0.40909,0.63293,0.6573,-394.58,-0.83621,-0.028295,0.54769,505.93,0.36524,-0.77369,0.51768,107.97
> view matrix models
> #12,0.6007,0.56431,0.56631,-399.83,-0.45908,-0.33646,0.82222,444.62,0.65453,-0.75389,0.056956,136.37
> view matrix models
> #12,0.39156,0.78914,0.47322,-385.56,-0.75719,-0.015875,0.653,471.44,0.52282,-0.614,0.59132,40.329
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.39156,0.78914,0.47322,-306.13,-0.75719,-0.015875,0.653,370.26,0.52282,-0.614,0.59132,67.305
> hide #!2 models
> hide #!4 models
> fitmap #12 inMap #3
Fit molecule A1G3_quis_c2_coot1.pdb (#12) to map run_class001.mrc (#3) using
17258 atoms
average map value = 0.01025, steps = 104
shifted from previous position = 17.3
rotated from previous position = 8.4 degrees
atoms outside contour = 3872, contour level = 0.006687
Position of A1G3_quis_c2_coot1.pdb (#12) relative to run_class001.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999305 -0.00336539 0.00159452 0.23050826
0.00336577 0.99999429 -0.00023591 -0.50065626
-0.00159371 0.00024128 0.99999869 0.24378906
Axis 0.06393749 0.42718750 0.90189957
Axis point 151.49614767 67.78770501 0.00000000
Rotation angle (degrees) 0.21380853
Shift along axis 0.02073727
> hide sel atoms
> show sel cartoons
> select subtract #12
Nothing selected
> fitmap #12 inMap #3
Fit molecule A1G3_quis_c2_coot1.pdb (#12) to map run_class001.mrc (#3) using
17258 atoms
average map value = 0.01025, steps = 144
shifted from previous position = 17
rotated from previous position = 0.00463 degrees
atoms outside contour = 3868, contour level = 0.006687
Position of A1G3_quis_c2_coot1.pdb (#12) relative to run_class001.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999312 -0.00335898 0.00156429 0.23736471
0.00335924 0.99999433 -0.00016123 -0.51352610
-0.00156373 0.00016649 0.99999875 0.23610878
Axis 0.04417891 0.42168127 0.90566723
Axis point 153.96444308 70.24869869 0.00000000
Rotation angle (degrees) 0.21250994
Shift along axis 0.00777816
> volume #3 color #b2b2ff78
> select add #12
17258 atoms, 17657 bonds, 2310 residues, 1 model selected
> view matrix models
> #12,0.42873,0.75537,0.49558,-314.39,-0.86168,0.17707,0.47555,387.96,0.27147,-0.63092,0.7268,85.816
> view matrix models
> #12,0.42873,0.75537,0.49558,-376.53,-0.86168,0.17707,0.47555,452.68,0.27147,-0.63092,0.7268,75.061
> view matrix models
> #12,0.42873,0.75537,0.49558,-376.77,-0.86168,0.17707,0.47555,452.68,0.27147,-0.63092,0.7268,75.192
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.45316,-0.28563,-0.84443,192.4,0.89132,-0.13069,-0.43412,362.22,0.013637,-0.94939,0.31382,247.78
> view matrix models
> #12,-0.63059,-0.41983,-0.65276,212.1,0.74399,-0.087535,-0.66243,421.02,0.22097,-0.90337,0.36755,194.34
> view matrix models
> #12,-0.57809,-0.3738,-0.72532,208,0.80223,-0.097912,-0.58893,399.61,0.14913,-0.92233,0.35648,212.03
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.57809,-0.3738,-0.72532,197.07,0.80223,-0.097912,-0.58893,393.73,0.14913,-0.92233,0.35648,222.51
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.33697,-0.82408,0.45535,22.3,0.81094,-0.0083137,0.58507,168.32,-0.47836,0.56642,0.67108,21.375
> view matrix models
> #12,-0.32623,-0.93223,0.15659,91.989,0.9001,-0.25573,0.35275,236.37,-0.2888,0.25602,0.92252,-3.2279
> view matrix models
> #12,-0.56311,-0.79079,0.23991,94.195,0.82077,-0.50144,0.27368,306.17,-0.096119,0.35102,0.93142,-54.522
> view matrix models
> #12,-0.56384,-0.68001,0.46869,34.75,0.80889,-0.34018,0.47955,244.11,-0.16666,0.64951,0.74186,-59.566
> view matrix models
> #12,-0.22085,-0.86626,0.44813,10.609,0.8822,0.018478,0.4705,171.72,-0.41586,0.49925,0.76014,6.1621
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.5569,-0.61854,0.55432,10.058,0.78909,-0.1857,0.58554,204.15,-0.25924,0.76349,0.5915,-38.803
> view matrix models
> #12,-0.55344,-0.62425,0.55137,19.76,0.79343,-0.19382,0.57697,209.45,-0.25331,0.7568,0.60257,-47.965
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.59044,-0.75602,0.28252,96.465,0.71509,-0.32773,0.61745,238.75,-0.37421,0.56659,0.73413,-17.839
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.59044,-0.75602,0.28252,149.3,0.71509,-0.32773,0.61745,183.44,-0.37421,0.56659,0.73413,-8.4876
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.55557,-0.78076,0.28593,146.86,0.76867,-0.35118,0.53462,192.84,-0.317,0.51681,0.79525,-20.789
> view matrix models
> #12,-0.64132,-0.73009,0.23597,161.98,0.62438,-0.31785,0.71353,180.44,-0.44593,0.60493,0.6597,10.653
> view matrix models
> #12,-0.51612,-0.84171,0.15856,173.04,0.84564,-0.47136,0.25042,250.49,-0.13604,0.26334,0.95506,-37.339
> view matrix models
> #12,-0.73745,-0.58094,0.3445,133.93,0.66827,-0.55364,0.4969,251.58,-0.097936,0.59665,0.7965,-72.72
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.73745,-0.58094,0.3445,136.69,0.66827,-0.55364,0.4969,240.49,-0.097936,0.59665,0.7965,-66.355
> select subtract #12
Nothing selected
> fitmap #12 inMap #3
Fit molecule A1G3_quis_c2_coot1.pdb (#12) to map run_class001.mrc (#3) using
17258 atoms
average map value = 0.009783, steps = 148
shifted from previous position = 16.8
rotated from previous position = 16 degrees
atoms outside contour = 4860, contour level = 0.006687
Position of A1G3_quis_c2_coot1.pdb (#12) relative to run_class001.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99912111 0.00429130 -0.04169598 346.66167665
-0.00145968 -0.99770424 -0.06770574 350.60129320
-0.04189080 -0.06758537 0.99683366 19.13138742
Axis 0.02091400 0.03384935 -0.99920810
Axis point 173.78349133 175.37509478 0.00000000
Rotation angle (degrees) 179.83511591
Shift along axis 0.00147202
> hide #12 models
> volume #3 level 0.007817
> show #12 models
> hide #!3 models
> show #!3 models
> select add #12
17258 atoms, 17657 bonds, 2310 residues, 1 model selected
> view matrix models
> #12,0.28967,0.7087,-0.6433,-134.32,-0.84664,-0.12376,-0.51757,647.11,-0.44642,0.69457,0.56416,1.6081
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.44588,0.64741,0.61811,-375.13,-0.86276,0.12692,0.48942,428.17,0.23841,-0.7515,0.61515,120.53
> view matrix models
> #12,0.41092,0.66884,0.61951,-372.96,-0.87223,0.090721,0.4806,437.57,0.26524,-0.73785,0.62067,112.55
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.41092,0.66884,0.61951,-311.65,-0.87223,0.090721,0.4806,392.59,0.26524,-0.73785,0.62067,109.63
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.37955,0.61289,0.69304,-309.71,-0.89334,0.047998,0.4468,409.57,0.24058,-0.78871,0.56574,132.37
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.37955,0.61289,0.69304,-306.12,-0.89334,0.047998,0.4468,401.82,0.24058,-0.78871,0.56574,135.87
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.38963,0.6524,0.65005,-306.71,-0.88871,0.081138,0.45124,397.59,0.24164,-0.75352,0.6114,119.23
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.21506,0.83544,0.50575,-282,-0.91161,-0.01403,0.41082,425.01,0.35031,-0.5494,0.75858,39.328
> select subtract #12
Nothing selected
> fitmap #12 inMap #3
Fit molecule A1G3_quis_c2_coot1.pdb (#12) to map run_class001.mrc (#3) using
17258 atoms
average map value = 0.0096, steps = 176
shifted from previous position = 8.8
rotated from previous position = 7.34 degrees
atoms outside contour = 6453, contour level = 0.0078174
Position of A1G3_quis_c2_coot1.pdb (#12) relative to run_class001.mrc (#3)
coordinates:
Matrix rotation and translation
-0.00253556 -0.99851229 -0.05446781 349.27941597
0.99996729 -0.00211348 -0.00780544 0.88846750
0.00767871 -0.05448582 0.99848500 8.22149688
Axis -0.02334030 -0.03107341 0.99924455
Axis point 174.29197650 174.80639334 0.00000000
Rotation angle (degrees) 90.17658721
Shift along axis 0.03539175
> select /C
2946 atoms, 3014 bonds, 403 residues, 1 model selected
> select add /C
2946 atoms, 3014 bonds, 403 residues, 1 model selected
> select add /C
2946 atoms, 3014 bonds, 403 residues, 1 model selected
> select add /A
5903 atoms, 6039 bonds, 806 residues, 1 model selected
> ui tool show "Color Actions"
> show #!6 models
> show #!5 models
> show #!7 models
> hide #!5 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #!3 models
> hide #12 models
> select add #12
17258 atoms, 17657 bonds, 2310 residues, 1 model selected
> select up
17258 atoms, 17657 bonds, 2310 residues, 23 models selected
> select subtract #1
17258 atoms, 17657 bonds, 2310 residues, 21 models selected
> select subtract #2
17258 atoms, 17657 bonds, 2310 residues, 19 models selected
> select subtract #3
17258 atoms, 17657 bonds, 2310 residues, 17 models selected
> select subtract #4
17258 atoms, 17657 bonds, 2310 residues, 15 models selected
> select subtract #5
17258 atoms, 17657 bonds, 2310 residues, 13 models selected
> select add #6
17258 atoms, 17657 bonds, 2310 residues, 14 models selected
> select add #7
17258 atoms, 17657 bonds, 2310 residues, 15 models selected
> select add #8
17258 atoms, 17657 bonds, 2310 residues, 16 models selected
> select subtract #7
17258 atoms, 17657 bonds, 2310 residues, 13 models selected
> select subtract #6
17258 atoms, 17657 bonds, 2310 residues, 10 models selected
> select subtract #12
9 models selected
> select add #11
10 models selected
> select add #10
11 models selected
> select subtract #11
8 models selected
> select subtract #8
5 models selected
> select add #9
6 models selected
> select subtract #10
3 models selected
> select subtract #9
Nothing selected
> ~tile
> tile
6 models tiled
> ~tile
> hide #!6 models
> hide #!7 models
> hide #!9 models
> hide #!10 models
> volume #8 level 0.02381
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> tile
2 models tiled
> show #!7 models
> show #!9 models
> show #!10 models
> show #12 models
> hide #12 models
> tile
5 models tiled
> ~tile
> show #12 models
> ~tile
> tile
6 models tiled
> hide #12 models
> show #!6 models
> ~tile
> tile
6 models tiled
> show #!1 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> volume #1 level 0.003107
> volume #1 level 0.0016
> show #!2 models
> show #!3 models
> show #12 models
> volume #3 level 0.01112
> volume #3 level 0.009122
> close session
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220930_A2ir_G2_F231A_des/c3_job072_deepEMhancer.mrc
Opened c3_job072_deepEMhancer.mrc as #1, grid size 256,256,256, pixel 1.45,
shown at level 0.000264, step 1, values float32
> volume #1 level 0.1084
> surface dust #1 size 14.5
> volume #1 level 0.08476
> volume #1 level 0.08138
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220930_A2ir_G2_F231A_des/c1_job079_deepEMhancer.mrc
Opened c1_job079_deepEMhancer.mrc as #2, grid size 256,256,256, pixel 1.45,
shown at level 0.000124, step 1, values float32
> volume #2 level 0.08199
> tile
2 models tiled
> ~tile
> surface dust #1 size 14.5
> surface dust #2 size 14.5
> hide #!1 models
> volume #2 level 0.0694
> volume #1 level 0.05096
> volume #2 level 0.07569
> ui tool show "Side View"
> tile
2 models tiled
> volume #1 level 0.05445
> volume #1 level 0.07185
> ui tool show "Map Eraser"
> ~tile
Can only have one displayed volume when erasing
> hide #!2 models
> volume erase #1 center 193.49,157.16,280.59 radius 8.5111
Opened c3_job072_deepEMhancer.mrc copy as #4, grid size 256,256,256, pixel
1.45, shown at step 1, values float32
> surface dust #4 size 14.5
> volume erase #4 center 185.25,157.05,271.02 radius 8.5111
> hide #!4 models
> show #!4 models
> hide #3 models
> show #!2 models
> tile
2 models tiled
> hide #!4 models
> ~tile
> tile
2 models tiled
> volume #2 level 0.06273
> color green
> show #3 models
Can only have one displayed volume when erasing
> volume erase #1 center 170.04,128.77,253.32 radius 8.5111
Opened c3_job072_deepEMhancer.mrc copy as #5, grid size 256,256,256, pixel
1.45, shown at step 1, values float32
> volume erase #5 center 176.87,121,250.87 radius 8.5111
> surface dust #5 size 14.5
> volume erase #5 center 166.04,134.37,255.28 radius 8.5111
> volume erase #5 center 228.93,136.47,270.14 radius 8.5111
> volume erase #5 center 236.03,140.34,273.67 radius 8.5111
> volume erase #5 center 228.51,133.71,268.66 radius 8.5111
> volume erase #5 center 232.93,139.99,272.83 radius 8.5111
> volume erase #5 center 234.72,142.47,274.48 radius 8.5111
> hide #!5 models
> show #!5 models
> volume erase #5 center 240.97,145.4,277.34 radius 8.5111
> volume erase #5 center 235.11,141.74,274.19 radius 8.5111
> volume erase #5 center 233.46,136.81,271.33 radius 8.5111
> volume erase #5 center 241.02,148.3,278.82 radius 8.5111
> volume erase #5 center 236.74,141.3,274.33 radius 8.5111
> volume erase #5 center 208.33,205.26,300.56 radius 8.5111
> volume erase #5 center 225.71,196.89,300.13 radius 8.5111
> volume erase #5 center 243.73,179.79,295.39 radius 8.5111
> volume erase #5 center 240.88,183.63,296.71 radius 8.5111
> volume erase #5 center 232.94,190.91,298.67 radius 8.5111
> volume erase #5 center 243.09,173.97,292.31 radius 8.5111
> volume erase #5 center 241.29,182.72,296.36 radius 8.5111
> ~tile
> volume erase #5 center 433.19,-8.3009,198.81 radius 8.5111
> volume erase #5 center 431.01,-18.652,187.69 radius 8.5111
> close #4
> close #1
> open /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_A_to_B.pdb
> /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_A_to_C.pdb
> /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_A_to_D.pdb
> /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_A.pdb
Chain information for 1mm7_A_to_B.pdb #1
---
Chain | Description
B | No description available
Chain information for 1mm7_A_to_C.pdb #3
---
Chain | Description
C | No description available
Chain information for 1mm7_A_to_D.pdb #4
---
Chain | Description
D | No description available
Chain information for 1mm7_A.pdb #6
---
Chain | Description
A | No description available
> ~tile
> close #2
> select add #5
2 models selected
> select subtract #5
Nothing selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #3
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select add #4
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select add #6
7852 atoms, 7996 bonds, 1036 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.22963,0.74852,0.62208,249.02,-0.68558,0.32927,-0.64927,172.26,-0.69083,-0.57558,0.43756,272.38,#3,-0.22963,0.74852,0.62208,249.02,-0.68558,0.32927,-0.64927,172.26,-0.69083,-0.57558,0.43756,272.38,#4,-0.22963,0.74852,0.62208,249.02,-0.68558,0.32927,-0.64927,172.26,-0.69083,-0.57558,0.43756,272.38,#6,-0.22963,0.74852,0.62208,249.02,-0.68558,0.32927,-0.64927,172.26,-0.69083,-0.57558,0.43756,272.38
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.099355,0.81407,0.5722,225.24,-0.43681,0.48099,-0.76016,122.54,-0.89405,-0.32547,0.30781,280.18,#3,-0.099355,0.81407,0.5722,225.24,-0.43681,0.48099,-0.76016,122.54,-0.89405,-0.32547,0.30781,280.18,#4,-0.099355,0.81407,0.5722,225.24,-0.43681,0.48099,-0.76016,122.54,-0.89405,-0.32547,0.30781,280.18,#6,-0.099355,0.81407,0.5722,225.24,-0.43681,0.48099,-0.76016,122.54,-0.89405,-0.32547,0.30781,280.18
> select subtract #4
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select subtract #3
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select subtract #6
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> view matrix models
> #1,-0.13792,0.76951,0.62356,231.1,-0.53721,0.4708,-0.69982,129.74,-0.8321,-0.4315,0.34845,284.31
> select subtract #1
Nothing selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #4
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select add #3
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select add #6
7852 atoms, 7996 bonds, 1036 residues, 4 models selected
> view matrix models
> #1,0.030365,0.85817,0.51247,203.07,-0.60076,0.42544,-0.67682,145.12,-0.79885,-0.28732,0.52847,227.59,#3,0.08436,0.87893,0.46943,198.03,-0.50614,0.4436,-0.73962,137.68,-0.85832,-0.1752,0.48228,222.84,#4,0.08436,0.87893,0.46943,198.03,-0.50614,0.4436,-0.73962,137.68,-0.85832,-0.1752,0.48228,222.84,#6,0.08436,0.87893,0.46943,198.03,-0.50614,0.4436,-0.73962,137.68,-0.85832,-0.1752,0.48228,222.84
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.030365,0.85817,0.51247,214.98,-0.60076,0.42544,-0.67682,143,-0.79885,-0.28732,0.52847,237.38,#3,0.08436,0.87893,0.46943,209.94,-0.50614,0.4436,-0.73962,135.56,-0.85832,-0.1752,0.48228,232.63,#4,0.08436,0.87893,0.46943,209.94,-0.50614,0.4436,-0.73962,135.56,-0.85832,-0.1752,0.48228,232.63,#6,0.08436,0.87893,0.46943,209.94,-0.50614,0.4436,-0.73962,135.56,-0.85832,-0.1752,0.48228,232.63
> select subtract #6
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select subtract #4
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select subtract #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #3
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select add #4
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select add #6
7852 atoms, 7996 bonds, 1036 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.87902,0.26297,-0.3977,599.45,-0.15187,0.63626,0.75638,-173.36,0.45195,0.72527,-0.51935,-6.9711,#3,-0.81802,0.32608,-0.47382,590.73,-0.13601,0.69076,0.71018,-178.53,0.55887,0.64539,-0.52071,-7.7139,#4,-0.81802,0.32608,-0.47382,590.73,-0.13601,0.69076,0.71018,-178.53,0.55887,0.64539,-0.52071,-7.7139,#6,-0.81802,0.32608,-0.47382,590.73,-0.13601,0.69076,0.71018,-178.53,0.55887,0.64539,-0.52071,-7.7139
> hide #!5 models
> show #!5 models
> select subtract #6
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select subtract #4
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select subtract #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #6
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #4
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select add #3
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select add #1
7852 atoms, 7996 bonds, 1036 residues, 4 models selected
> view matrix models
> #1,0.24844,0.56183,0.78907,186.62,-0.78675,0.59225,-0.17398,74.607,-0.56508,-0.57757,0.58915,236.58,#3,0.25128,0.57873,0.77584,185.15,-0.70749,0.65684,-0.26082,64.608,-0.66055,-0.48336,0.57449,235.5,#4,0.25128,0.57873,0.77584,185.15,-0.70749,0.65684,-0.26082,64.608,-0.66055,-0.48336,0.57449,235.5,#6,0.25128,0.57873,0.77584,185.15,-0.70749,0.65684,-0.26082,64.608,-0.66055,-0.48336,0.57449,235.5
> view matrix models
> #1,0.26952,0.49093,0.82846,189.62,-0.7739,0.6224,-0.11705,58.927,-0.5731,-0.60959,0.54768,249.52,#3,0.26218,0.50847,0.82019,188.75,-0.69547,0.68878,-0.20469,48.844,-0.66901,-0.51676,0.53421,248.57,#4,0.26218,0.50847,0.82019,188.75,-0.69547,0.68878,-0.20469,48.844,-0.66901,-0.51676,0.53421,248.57,#6,0.26218,0.50847,0.82019,188.75,-0.69547,0.68878,-0.20469,48.844,-0.66901,-0.51676,0.53421,248.57
> view matrix models
> #1,0.20574,-0.68803,0.69591,427.56,0.74613,-0.34985,-0.56648,34.051,0.63321,0.63579,0.44138,-155.52,#3,0.085645,-0.6639,0.7429,433.4,0.74252,-0.45465,-0.4919,42.281,0.66433,0.59375,0.45402,-154.3,#4,0.085645,-0.6639,0.7429,433.4,0.74252,-0.45465,-0.4919,42.281,0.66433,0.59375,0.45402,-154.3,#6,0.085645,-0.6639,0.7429,433.4,0.74252,-0.45465,-0.4919,42.281,0.66433,0.59375,0.45402,-154.3
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.20574,-0.68803,0.69591,430.29,0.74613,-0.34985,-0.56648,30.18,0.63321,0.63579,0.44138,-150.19,#3,0.085645,-0.6639,0.7429,436.13,0.74252,-0.45465,-0.4919,38.41,0.66433,0.59375,0.45402,-148.97,#4,0.085645,-0.6639,0.7429,436.13,0.74252,-0.45465,-0.4919,38.41,0.66433,0.59375,0.45402,-148.97,#6,0.085645,-0.6639,0.7429,436.13,0.74252,-0.45465,-0.4919,38.41,0.66433,0.59375,0.45402,-148.97
> select subtract #6
5889 atoms, 5997 bonds, 777 residues, 3 models selected
> select subtract #4
3926 atoms, 3998 bonds, 518 residues, 2 models selected
> select subtract #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #6
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 3 models selected
> fitmap #6 inMap #5
Fit molecule 1mm7_A.pdb (#6) to map c3_job072_deepEMhancer.mrc copy (#5) using
1963 atoms
average map value = 0.1934, steps = 140
shifted from previous position = 9.19
rotated from previous position = 23.2 degrees
atoms outside contour = 672, contour level = 0.071847
Position of 1mm7_A.pdb (#6) relative to c3_job072_deepEMhancer.mrc copy (#5)
coordinates:
Matrix rotation and translation
-0.91328050 -0.25523977 -0.31744511 425.05455707
0.25899130 -0.96537895 0.03109637 306.36268903
-0.31439186 -0.05381581 0.94776665 82.83681689
Axis -0.16291563 -0.00585806 0.98662261
Axis point 198.77632172 182.10565688 0.00000000
Rotation angle (degrees) 164.89423194
Shift along axis 10.68595268
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 3 models selected
> select subtract #6
2 models selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 3 models selected
> select subtract #1
2 models selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 3 models selected
> fitmap #1 inMap #5
Fit molecule 1mm7_A_to_B.pdb (#1) to map c3_job072_deepEMhancer.mrc copy (#5)
using 1963 atoms
average map value = 0.2909, steps = 76
shifted from previous position = 8.36
rotated from previous position = 19 degrees
atoms outside contour = 463, contour level = 0.071847
Position of 1mm7_A_to_B.pdb (#1) relative to c3_job072_deepEMhancer.mrc copy
(#5) coordinates:
Matrix rotation and translation
-0.98791654 -0.09621159 0.12150824 352.02119724
0.07354069 -0.98110875 -0.17893405 372.18362140
0.13642831 -0.16783610 0.97632902 29.71700360
Axis 0.06498856 -0.08737060 0.99405375
Axis point 166.99502544 194.94295881 0.00000000
Rotation angle (degrees) 175.10190179
Shift along axis 19.89974110
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #!5 models
> show #!5 models
> color #5 #0080006b models
> color #5 #00800050 models
> color #5 #0080004a models
> select add #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 3 models selected
> fitmap #3 inMap #5
Fit molecule 1mm7_A_to_C.pdb (#3) to map c3_job072_deepEMhancer.mrc copy (#5)
using 1963 atoms
average map value = 0.0982, steps = 144
shifted from previous position = 15.6
rotated from previous position = 42.7 degrees
atoms outside contour = 1102, contour level = 0.071847
Position of 1mm7_A_to_C.pdb (#3) relative to c3_job072_deepEMhancer.mrc copy
(#5) coordinates:
Matrix rotation and translation
-0.67060320 0.13145418 -0.73007612 386.28940379
-0.01455141 -0.98631550 -0.16422545 381.12710684
-0.74167352 -0.09950648 0.66333918 216.75108592
Axis 0.40417257 0.07242625 -0.91181082
Axis point 249.58565554 190.55501148 0.00000000
Rotation angle (degrees) 175.40778231
Shift along axis -13.90479449
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #3
Nothing selected
> volume #5 color #8d404333
> volume #5 color #8d848933
> select add #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 5 models selected
> view matrix models
> #5,-0.22963,0.74852,0.62208,243.63,-0.68558,0.32927,-0.64927,183.32,-0.69083,-0.57558,0.43756,296.04,#3,-0.31828,-0.83037,0.45737,575.04,0.93651,-0.35028,0.015766,-96.749,0.14712,0.43335,0.88914,-95.349
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 5 models selected
> fitmap #1 inMap #5
Fit molecule 1mm7_A_to_B.pdb (#1) to map c3_job072_deepEMhancer.mrc copy (#5)
using 1963 atoms
average map value = 0.2909, steps = 68
shifted from previous position = 2.41
rotated from previous position = 0.0423 degrees
atoms outside contour = 461, contour level = 0.071847
Position of 1mm7_A_to_B.pdb (#1) relative to c3_job072_deepEMhancer.mrc copy
(#5) coordinates:
Matrix rotation and translation
-0.98786561 -0.09612266 0.12199167 351.93163560
0.07344789 -0.98121708 -0.17837728 372.11044417
0.13684640 -0.16725275 0.97637062 29.57159668
Axis 0.06521475 -0.08708208 0.99406426
Axis point 166.96207135 194.88532648 0.00000000
Rotation angle (degrees) 175.10720984
Shift along axis 19.94305036
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #6
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 5 models selected
> fitmap #6 inMap #5
Fit molecule 1mm7_A.pdb (#6) to map c3_job072_deepEMhancer.mrc copy (#5) using
1963 atoms
average map value = 0.1934, steps = 84
shifted from previous position = 2.42
rotated from previous position = 0.0236 degrees
atoms outside contour = 674, contour level = 0.071847
Position of 1mm7_A.pdb (#6) relative to c3_job072_deepEMhancer.mrc copy (#5)
coordinates:
Matrix rotation and translation
-0.91334164 -0.25540548 -0.31713577 425.04943287
0.25919694 -0.96532852 0.03094834 306.34146122
-0.31404458 -0.05393421 0.94787505 82.78480456
Axis -0.16274582 -0.00592674 0.98665023
Axis point 198.74929894 182.11714674 0.00000000
Rotation angle (degrees) 164.88349632
Shift along axis 10.68902161
> select subtract #5
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.17264,-0.2618,0.94956,295.91,-0.32407,0.89526,0.30575,-168.11,-0.93015,-0.36051,0.069719,384.97
> view matrix models
> #3,-0.32767,-0.93666,0.12367,648.26,0.90577,-0.34866,-0.24087,-53.342,0.26873,0.033088,0.96265,-45.899
> view matrix models
> #3,0.086538,0.33761,0.9373,189.93,-0.28859,0.90899,-0.30076,-87.136,-0.95353,-0.24447,0.17609,349.5
> view matrix models
> #3,0.49076,-0.55842,0.66882,341.15,0.46205,0.81759,0.34359,-300.05,-0.73869,0.1404,0.65926,159.5
> view matrix models
> #3,0.4248,-0.32341,0.84555,278.42,0.4709,0.87664,0.098725,-277.39,-0.77317,0.35623,0.52469,141.33
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.4248,-0.32341,0.84555,279.36,0.4709,0.87664,0.098725,-275.7,-0.77317,0.35623,0.52469,139.63
> select subtract #3
Nothing selected
> select add #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> view matrix models
> #3,0.4248,-0.32341,0.84555,276.94,0.4709,0.87664,0.098725,-278.37,-0.77317,0.35623,0.52469,139.33
> view matrix models
> #3,0.4248,-0.32341,0.84555,277.52,0.4709,0.87664,0.098725,-277.49,-0.77317,0.35623,0.52469,139.32
> select subtract #3
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
> select add #3
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 5 models selected
> fitmap #3 inMap #5
Fit molecule 1mm7_A_to_C.pdb (#3) to map c3_job072_deepEMhancer.mrc copy (#5)
using 1963 atoms
average map value = 0.1192, steps = 104
shifted from previous position = 0.921
rotated from previous position = 31.2 degrees
atoms outside contour = 943, contour level = 0.071847
Position of 1mm7_A_to_C.pdb (#3) relative to c3_job072_deepEMhancer.mrc copy
(#5) coordinates:
Matrix rotation and translation
-0.40008802 -0.72465636 -0.56107285 489.73995103
0.78898696 -0.58382563 0.19143456 99.98329389
-0.46629299 -0.36608849 0.80532607 199.09141931
Axis -0.34503655 -0.05865679 0.93675459
Axis point 254.22121761 190.20040463 0.00000000
Rotation angle (degrees) 126.10690978
Shift along axis 11.65691655
> select subtract #3
4 models selected
> select subtract #5
Nothing selected
> select add #4
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> view matrix models
> #4,0.085645,-0.6639,0.7429,430.15,0.74252,-0.45465,-0.4919,34.717,0.66433,0.59375,0.45402,-142.28
> view matrix models
> #4,0.085645,-0.6639,0.7429,429.93,0.74252,-0.45465,-0.4919,35.595,0.66433,0.59375,0.45402,-143.33
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.54016,-0.09206,0.83651,231.18,0.81131,0.32107,-0.48856,-106.33,-0.2236,0.94257,0.24812,7.0291
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.54016,-0.09206,0.83651,233.91,0.81131,0.32107,-0.48856,-106.06,-0.2236,0.94257,0.24812,2.6046
> select subtract #4
Nothing selected
> select add #4
1963 atoms, 1999 bonds, 259 residues, 1 model selected
> select add #5
1963 atoms, 1999 bonds, 259 residues, 5 models selected
> fitmap #4 inMap #5
Fit molecule 1mm7_A_to_D.pdb (#4) to map c3_job072_deepEMhancer.mrc copy (#5)
using 1963 atoms
average map value = 0.168, steps = 84
shifted from previous position = 4.9
rotated from previous position = 14.1 degrees
atoms outside contour = 755, contour level = 0.071847
Position of 1mm7_A_to_D.pdb (#4) relative to c3_job072_deepEMhancer.mrc copy
(#5) coordinates:
Matrix rotation and translation
-0.33947966 -0.94012207 0.03039857 372.68252669
0.85180946 -0.29356077 0.43386946 0.71051330
-0.39896643 0.17318365 0.90046278 79.59616417
Axis -0.14007817 0.23071706 0.96288511
Axis point 193.88699106 123.83598277 0.00000000
Rotation angle (degrees) 111.48692055
Shift along axis 24.60120210
> select subtract #4
4 models selected
> select subtract #5
Nothing selected
> volume #5 level 0.1259
> volume #5 level 0.2138
> volume #5 level 0.09889
> open /Users/ig/Documents/Danyang/GluA1/models/A1G3_quis_c3_coot1.pdb
Chain information for A1G3_quis_c3_coot1.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F H | No description available
G | No description available
> close #2
> open
> /Users/ig/Documents/Danyang/GluA1/analysis/A2irG2_F231A_des_merge_c3_align.pdb
Chain information for A2irG2_F231A_des_merge_c3_align.pdb #2
---
Chain | Description
A B C D | No description available
E | No description available
F | No description available
G H | No description available
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> view matrix models #2,1,0,0,179.91,0,1,0,-182.57,0,0,1,22.104
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.42323,-0.62566,0.6553,269.39,0.89973,0.37535,-0.22272,-190.68,-0.10662,0.68386,0.72178,-27.029
> ui mousemode right "translate selected models"
> style sel sphere
Changed 27977 atom styles
> style sel ball
Changed 27977 atom styles
> style sel stick
Changed 27977 atom styles
> hide sel atoms
> show sel cartoons
> view matrix models
> #2,0.42323,-0.62566,0.6553,381.25,0.89973,0.37535,-0.22272,-160.88,-0.10662,0.68386,0.72178,-35.363
> view matrix models
> #2,0.42323,-0.62566,0.6553,395.36,0.89973,0.37535,-0.22272,-179.05,-0.10662,0.68386,0.72178,-60.249
> select subtract #2
Nothing selected
> hide #1 models
> hide #3 models
> hide #4 models
> hide #6 models
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> view matrix models
> #2,0.42323,-0.62566,0.6553,375.96,0.89973,0.37535,-0.22272,-182.77,-0.10662,0.68386,0.72178,-82.4
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.55169,0.51403,0.65681,159.61,-0.3816,0.85581,-0.34925,-21.946,-0.74163,-0.057957,0.6683,162.48
> select subtract #2
Nothing selected
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> hide #!2 models
> select subtract #2
Nothing selected
> show #!2 models
> hide #!5 models
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> view matrix models
> #2,-0.42772,-0.3063,-0.85043,734.37,0.90157,-0.07686,-0.42575,-70.175,0.065045,-0.94883,0.30903,239.07
> view matrix models
> #2,0.77553,-0.56507,0.28152,371.26,0.63059,0.67212,-0.38808,-157.76,0.030078,0.47849,0.87758,-98.512
> show #!5 models
> view matrix models
> #2,-0.024078,-0.68122,0.73168,448.77,0.71051,-0.52654,-0.46684,46.479,0.70328,0.50863,0.49669,-151.92
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 4 models selected
> fitmap #2 inMap #5
Fit molecule A2irG2_F231A_des_merge_c3_align.pdb (#2) to map
c3_job072_deepEMhancer.mrc copy (#5) using 27977 atoms
average map value = 0.2218, steps = 124
shifted from previous position = 6.1
rotated from previous position = 16.1 degrees
atoms outside contour = 12338, contour level = 0.098887
Position of A2irG2_F231A_des_merge_c3_align.pdb (#2) relative to
c3_job072_deepEMhancer.mrc copy (#5) coordinates:
Matrix rotation and translation
-0.99780934 -0.01625127 -0.06412842 367.92708496
0.01851328 -0.99922150 -0.03483799 357.77462637
-0.06351233 -0.03594890 0.99733340 33.19625318
Axis -0.03193389 -0.01770984 0.99933307
Axis point 182.93584808 180.78466485 0.00000000
Rotation angle (degrees) 179.00335394
Shift along axis 15.08863892
> select subtract #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select subtract #2
Nothing selected
> show #1 models
> show #3 models
> show #4 models
> show #6 models
> hide #!5 models
> color #2 #f66985 transparency 0
> color #1 #2d2822 transparency 0
> color #3 #332a34 transparency 0
> color #4 #1f2a1e transparency 0
> color #6 #101010 transparency 0
> open /Users/ig/Documents/Danyang/GluA1/A2G2_F231A_ZK_rf19_align.pdb
Chain information for A2G2_F231A_ZK_rf19_align.pdb #7
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
F | No description available
G H | No description available
> hide atoms
> show cartoons
> color #7 #54edec transparency 0
> select add #7
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,50.298,0,1,0,-214.43,0,0,1,-144.44
> view matrix models #7,1,0,0,135.16,0,1,0,-334.37,0,0,1,-97.13
> view matrix models #7,1,0,0,238.01,0,1,0,-253.44,0,0,1,-120.56
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.21505,0.84803,0.48436,121.84,-0.39177,0.52922,-0.75262,83.934,-0.89458,-0.02791,0.44604,186.78
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.21505,0.84803,0.48436,155.69,-0.39177,0.52922,-0.75262,93.188,-0.89458,-0.02791,0.44604,186.29
> view matrix models
> #7,0.21505,0.84803,0.48436,125.62,-0.39177,0.52922,-0.75262,94.811,-0.89458,-0.02791,0.44604,234.07
> view matrix models
> #7,0.21505,0.84803,0.48436,144.77,-0.39177,0.52922,-0.75262,113.64,-0.89458,-0.02791,0.44604,229.47
> view matrix models
> #7,0.21505,0.84803,0.48436,133.84,-0.39177,0.52922,-0.75262,111.86,-0.89458,-0.02791,0.44604,239.73
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.10454,0.54858,0.82954,186.59,-0.59188,0.63599,-0.49518,75.938,-0.79922,-0.54275,0.2582,365.56
> view matrix models
> #7,-0.13252,0.4551,0.88053,200.5,-0.55019,0.70516,-0.44726,43.024,-0.82446,-0.54373,0.15694,392.59
> view matrix models
> #7,-0.21434,0.64907,0.72991,209.85,-0.63942,0.47166,-0.60719,143.2,-0.73838,-0.59686,0.31393,352.24
> view matrix models
> #7,-0.19362,0.63498,0.74787,204.65,-0.66282,0.47735,-0.57689,140.35,-0.72331,-0.60741,0.32845,348.2
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.19362,0.63498,0.74787,218.22,-0.66282,0.47735,-0.57689,148.83,-0.72331,-0.60741,0.32845,347.02
> ui mousemode right "rotate selected models"
> select subtract #7
Nothing selected
> show #!5 models
> hide #4 models
> hide #6 models
> hide #3 models
> hide #!2 models
> hide #1 models
> select add #5
2 models selected
> select add #7
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 4 models selected
> fitmap #7 inMap #5
Fit molecule A2G2_F231A_ZK_rf19_align.pdb (#7) to map
c3_job072_deepEMhancer.mrc copy (#5) using 36444 atoms
average map value = 0.1831, steps = 188
shifted from previous position = 8.37
rotated from previous position = 13 degrees
atoms outside contour = 19533, contour level = 0.098887
Position of A2G2_F231A_ZK_rf19_align.pdb (#7) relative to
c3_job072_deepEMhancer.mrc copy (#5) coordinates:
Matrix rotation and translation
0.99858616 0.05293338 0.00487736 -30.91890696
-0.05283500 0.99843239 -0.01847356 -3.70453940
-0.00584758 0.01818974 0.99981748 -21.80321700
Axis 0.32602584 0.09537075 -0.94053792
Axis point -107.38430870 643.28344478 0.00000000
Rotation angle (degrees) 3.22330403
Shift along axis 10.07308510
> select subtract #5
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 2 models selected
> select subtract #7
Nothing selected
Populating font family aliases took 329 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
> save /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_fit_c3_deepE_A.pdb
> models #6 relModel #5
> save /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_fit_c3_deepE_B.pdb
> models #1 relModel #5
> save /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_fit_c3_deepE_C.pdb
> models #3 relModel #5
> save /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_fit_c3_deepE_D.pdb
> models #4 relModel #5
> hide #!7 models
> hide #!5 models
> save
> /Users/ig/Documents/Danyang/GluA1/analysis/A2G2_F231A_ZK_rf19_fit_c3_deepE.pdb
> models #7
> show #1 models
> show #3 models
> show #4 models
> show #6 models
> show #!5 models
> save /Users/ig/Documents/Danyang/GluA1/analysis/1mm7_fit_c3_deepE_A_try2.pdb
> models #6 relModel #5
> show #!2 models
> volume #5 level 0.01101
> hide #6 models
> hide #!5 models
> hide #4 models
> hide #3 models
> hide #1 models
> show #!5 models
> volume #5 level 0.06509
> select add #2/A
4254 atoms, 4324 bonds, 2 pseudobonds, 406 residues, 2 models selected
> close #1,3-4,6#7
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select subtract #2
Nothing selected
> select add /A
4254 atoms, 4324 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add /C
8485 atoms, 8625 bonds, 4 pseudobonds, 812 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> select clear
> select #5
2 models selected
> select clear
> select add /B
4255 atoms, 4325 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add /D
8500 atoms, 8640 bonds, 4 pseudobonds, 812 residues, 2 models selected
> color sel dark red
> color sel fire brick
> color sel dark red
> color sel maroon
> color sel dark red
> color sel purple
> color sel dark red
> color sel indian red
> color sel maroon
> color sel crimson
> color sel dark red
> color sel brown
> select add /A
12754 atoms, 12964 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> select clear
> select add /A
4254 atoms, 4324 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add /C
8485 atoms, 8625 bonds, 4 pseudobonds, 812 residues, 2 models selected
> color sel light pink
> color sel pale violet red
> color sel orchid
> color sel plum
> select clear
> select add /G
2740 atoms, 2771 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add /H
5480 atoms, 5542 bonds, 6 pseudobonds, 354 residues, 2 models selected
> color sel pale green
> color sel light green
> select clear
> select add /E
2750 atoms, 2781 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add /F
5512 atoms, 5574 bonds, 6 pseudobonds, 355 residues, 2 models selected
> color sel cadet blue
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 4 models selected
> color zone #5 near sel & #2 distance 8.67
> graphics silhouettes true
> select subtract #2
2 models selected
> select subtract #5
Nothing selected
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting shadows false
> color #5 #8d848929 models
> color #5 #8d8489ab models
> color #5 #8d8489 models transparency 0
> color #5 #8d8489e1 models
> color zone #5 near #2 distance 8.67
> transparency 0
> transparency 50
> save /Users/ig/Documents/Danyang/GluA1/Figs/Fig4_LBD_TMD.cxs includeMaps
> true
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220930_A2ir_G2_F231A_des/c2_job071_deepEMhancer.mrc
Opened c2_job071_deepEMhancer.mrc as #1, grid size 256,256,256, pixel 1.45,
shown at level 0.000236, step 1, values float32
> select add #1
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,178.32,0,1,0,-117.13,0,0,1,153.6
> select subtract #1
Nothing selected
> select add #5
3 models selected
> view matrix models
> #5,-0.22963,0.74852,0.62208,243.38,-0.68558,0.32927,-0.64927,176,-0.69083,-0.57558,0.43756,284.27
> undo
> select subtract #5
Nothing selected
> select add #1
3 models selected
> view matrix models #1,1,0,0,155.82,0,1,0,-151.82,0,0,1,3.3611
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.25496,0.90951,0.3283,58.871,-0.834,0.37865,-0.40133,167.33,-0.48932,-0.17148,0.85508,140.24
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.25496,0.90951,0.3283,63.316,-0.834,0.37865,-0.40133,209.99,-0.48932,-0.17148,0.85508,222.21
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.020587,0.96885,0.24679,115.44,-0.74889,0.14859,-0.64582,285.78,-0.66238,-0.19811,0.7225,282.68
> view matrix models
> #1,-0.17691,0.83156,0.52651,102.22,-0.81315,0.1779,-0.5542,271.66,-0.55452,-0.52617,0.64471,334.64
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.17691,0.83156,0.52651,121.36,-0.81315,0.1779,-0.5542,176.3,-0.55452,-0.52617,0.64471,280.12
> select subtract #1
Nothing selected
> surface dust #5 size 14.5
> surface dust #1 size 14.5
> volume #1 level 0.09963
> volume #1 level 0.1427
> open
> /Users/ig/Documents/Danyang/GluA1/analysis/A2irG2_F231A_des_merge_c2_align.pdb
Chain information for A2irG2_F231A_des_merge_c2_align.pdb #3
---
Chain | Description
A B C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> view matrix models #3,1,0,0,103.91,0,1,0,-207.94,0,0,1,203
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.68882,0.56145,0.45859,-20.103,0.26245,0.39654,-0.8797,6.1466,-0.67576,0.72631,0.12579,349.08
> view matrix models
> #3,0.38247,0.57169,0.72587,-16.841,0.37504,0.62192,-0.68743,-85.661,-0.84443,0.53515,0.023463,428.7
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.38247,0.57169,0.72587,31.944,0.37504,0.62192,-0.68743,3.7612,-0.84443,0.53515,0.023463,363.36
> view matrix models
> #3,0.38247,0.57169,0.72587,84.729,0.37504,0.62192,-0.68743,21.705,-0.84443,0.53515,0.023463,272.39
> select subtract #3
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.38247,0.57169,0.72587,33.482,0.37504,0.62192,-0.68743,-69.236,-0.84443,0.53515,0.023463,223.48
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.35512,0.71422,0.60315,35.52,-0.43194,0.69756,-0.5717,35.211,-0.82905,-0.057503,0.55622,227.83
> view matrix models
> #3,0.66469,0.69786,0.26677,44.985,-0.73608,0.67285,0.073865,-22.911,-0.12795,-0.24546,0.96092,68.523
> view matrix models
> #3,0.041988,0.62446,0.77992,73.06,-0.4661,0.70271,-0.53754,34.119,-0.88374,-0.34095,0.32057,327.36
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.041988,0.62446,0.77992,68.745,-0.4661,0.70271,-0.53754,34.083,-0.88374,-0.34095,0.32057,341.9
> view matrix models
> #3,0.041988,0.62446,0.77992,79.279,-0.4661,0.70271,-0.53754,12.401,-0.88374,-0.34095,0.32057,325.31
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.27731,0.91963,-0.27817,175.96,-0.87969,0.12662,-0.45838,167.53,-0.38632,0.37182,0.8441,25.775
> view matrix models
> #3,0.078398,0.97226,0.22037,112.68,-0.87198,0.17403,-0.45757,157.96,-0.48323,-0.15629,0.86143,129.54
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2356, steps = 164
shifted from previous position = 34.2
rotated from previous position = 24.4 degrees
atoms outside contour = 14136, contour level = 0.1427
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
0.99980572 -0.00868982 0.01769196 14.21340477
0.00908514 0.99970807 -0.02238829 16.77341936
-0.01749224 0.02254468 0.99959279 15.10828766
Axis 0.75172292 0.58862724 0.29737285
Axis point 0.00000000 -338.00578790 94.98764015
Rotation angle (degrees) 1.71263437
Shift along axis 25.05062838
> volume #1 color #ffb2ff8f
> select subtract #3
Nothing selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.14377,0.53276,-0.83396,376.02,0.024123,-0.84435,-0.53524,185.51,-0.98932,0.056836,-0.13425,386.61
> view matrix models
> #3,-0.45689,-0.72521,-0.51509,637.23,0.32879,0.40036,-0.85534,-22.65,0.82652,-0.56016,0.055521,148.25
> view matrix models
> #3,-0.3703,-0.77153,-0.51733,630.75,0.24441,0.45637,-0.85556,-17.769,0.89618,-0.44326,0.01958,122.73
> view matrix models
> #3,-0.6315,0.14323,0.76203,292.47,0.63512,-0.4682,0.61434,-186.73,0.44478,0.87193,0.2047,-57.758
> view matrix models
> #3,0.0163,-0.86359,0.50394,399.61,0.56833,-0.40667,-0.71528,49.591,0.82264,0.29806,0.48417,-73.694
> view matrix models
> #3,-0.21328,-0.89116,0.40042,461.88,0.87871,-0.35413,-0.32011,-82.389,0.42707,0.28358,0.8586,-69.935
> view matrix models
> #3,0.040494,-0.74746,0.66307,347.45,0.83239,-0.34185,-0.43619,-56.022,0.5527,0.5696,0.60834,-95.982
> view matrix models
> #3,0.087643,-0.82384,0.56,370.7,0.79141,-0.28382,-0.54141,-40.309,0.60498,0.49064,0.62712,-94.739
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2391, steps = 76
shifted from previous position = 4.2
rotated from previous position = 7.65 degrees
atoms outside contour = 13959, contour level = 0.1427
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
-0.99834394 0.00923485 -0.05678096 362.36413548
-0.00718085 -0.99931614 -0.03627227 362.75004997
-0.05707709 -0.03580447 0.99772754 32.07172158
Axis 0.02848115 0.01802953 -0.99943172
Axis point 182.38481827 180.91900398 0.00000000
Rotation angle (degrees) 179.52945241
Shift along axis -15.19273432
> select subtract #3
Nothing selected
> volume #1 level 0.1294
> select #3/C:439
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> color sel medium blue
> select up
1578 atoms, 1609 bonds, 159 residues, 1 model selected
> color sel blue
> select clear
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> view matrix models
> #3,0.66808,-0.5819,-0.46376,411.15,-0.069076,0.57206,-0.8173,11.844,0.74088,0.57805,0.34198,-80.098
> view matrix models
> #3,-0.53023,0.84564,-0.061281,300.57,-0.074092,-0.11821,-0.99022,161.32,-0.84461,-0.5205,0.12533,416.94
> view matrix models
> #3,-0.12276,0.49293,0.86137,127.89,-0.69873,0.57343,-0.42773,50.205,-0.70478,-0.65437,0.27403,389.61
> view matrix models
> #3,-0.28524,0.6691,0.68626,156.54,-0.58721,0.44389,-0.67686,97.41,-0.75751,-0.59605,0.26628,390.02
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.28524,0.6691,0.68626,158.75,-0.58721,0.44389,-0.67686,89.798,-0.75751,-0.59605,0.26628,376.26
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.41491,0.50898,0.75418,196.25,-0.55513,0.51512,-0.65305,67.927,-0.72088,-0.68963,0.068825,420.96
> view matrix models
> #3,-0.084219,0.85184,0.51699,123.14,-0.81707,0.23794,-0.52515,137.41,-0.57036,-0.46664,0.67597,249.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.084219,0.85184,0.51699,120.86,-0.81707,0.23794,-0.52515,144.64,-0.57036,-0.46664,0.67597,262.99
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2356, steps = 96
shifted from previous position = 3.44
rotated from previous position = 5.48 degrees
atoms outside contour = 13615, contour level = 0.12944
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
0.99981050 -0.00872794 0.01740041 14.27128796
0.00911927 0.99970437 -0.02253855 16.79628816
-0.01719855 0.02269296 0.99959453 15.01107627
Axis 0.75792212 0.57975769 0.29905700
Axis point -0.00000000 -329.57070268 105.35599246
Rotation angle (degrees) 1.70991119
Shift along axis 25.04346942
> select subtract #3
Nothing selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.32268,0.38926,-0.86276,485.33,0.67663,-0.54252,-0.49784,15.821,-0.66185,-0.74441,-0.088331,459.5
> view matrix models
> #3,0.27473,-0.94398,0.18281,426.05,0.29148,-0.099417,-0.9514,86.185,0.91628,0.31467,0.24783,-50.699
> view matrix models
> #3,0.16129,-0.9567,0.2423,437.07,0.72259,-0.052745,-0.68926,-41.864,0.6722,0.28625,0.68279,-81.157
> view matrix models
> #3,0.25565,-0.94112,0.22123,422.02,0.58995,-0.02942,-0.8069,-2.3608,0.7659,0.3368,0.54769,-81.884
> view matrix models
> #3,0.36087,-0.87109,0.33313,372.26,0.57615,-0.07266,-0.81411,8.6665,0.73337,0.48572,0.47566,-89.03
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.36087,-0.87109,0.33313,367,0.57615,-0.07266,-0.81411,-0.74404,0.73337,0.48572,0.47566,-96.198
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.40302,-0.83904,0.3655,348.59,0.75713,0.081305,-0.64819,-87.364,0.51414,0.53796,0.66803,-101.74
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.40302,-0.83904,0.3655,348.04,0.75713,0.081305,-0.64819,-82.453,0.51414,0.53796,0.66803,-95.737
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2391, steps = 132
shifted from previous position = 11.7
rotated from previous position = 17.1 degrees
atoms outside contour = 13390, contour level = 0.12944
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
-0.99835201 0.00921820 -0.05664170 362.34496094
-0.00718946 -0.99932891 -0.03591691 362.68587814
-0.05693477 -0.03545049 0.99774831 32.01391622
Axis 0.02841053 0.01785211 -0.99943691
Axis point 182.37276524 180.88396551 0.00000000
Rotation angle (degrees) 179.52968508
Shift along axis -15.22677008
> select subtract #3
Nothing selected
> hide #!3 models
> volume #1 level 0.2951
> volume #1 level 0.1394
> show #!3 models
> show #!3 atoms
> hide #!3 atoms
> select add #3/A
4254 atoms, 4324 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add #3/C
8485 atoms, 8625 bonds, 4 pseudobonds, 812 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> select clear
> select add #3/B
4238 atoms, 4308 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add #3/D
8505 atoms, 8645 bonds, 4 pseudobonds, 814 residues, 2 models selected
> color sel dark red
> undo
> color sel dark red
> select clear
> select add #3/H
2740 atoms, 2771 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add #3/G
5480 atoms, 5542 bonds, 6 pseudobonds, 354 residues, 2 models selected
> color sel light green
> select clear
> select add #3/E
2750 atoms, 2781 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add #3/F
5512 atoms, 5574 bonds, 6 pseudobonds, 355 residues, 2 models selected
> color sel cadet blue
> select clear
> color zone #1 near #3 distance 8.67
> transparency #1.1 0
> transparency #1.1 50
> show #!2 models
> show #!5 models
> select add #1
3 models selected
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 5 models selected
> select subtract #2
3 models selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 5 models selected
> select subtract #3
3 models selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 5 models selected
> view matrix models
> #1,-0.17691,0.83156,0.52651,138.94,-0.81315,0.1779,-0.5542,169.65,-0.55452,-0.52617,0.64471,288.33,#3,0.14066,-0.8513,0.50547,393.29,0.84208,-0.16563,-0.51329,-78.213,0.52068,0.49785,0.69357,-82.79
> view matrix models
> #1,-0.17691,0.83156,0.52651,158.01,-0.81315,0.1779,-0.5542,170.3,-0.55452,-0.52617,0.64471,248.93,#3,0.14066,-0.8513,0.50547,412.36,0.84208,-0.16563,-0.51329,-77.556,0.52068,0.49785,0.69357,-122.19
> view matrix models
> #1,-0.17691,0.83156,0.52651,160.98,-0.81315,0.1779,-0.5542,172.26,-0.55452,-0.52617,0.64471,246.87,#3,0.14066,-0.8513,0.50547,415.33,0.84208,-0.16563,-0.51329,-75.598,0.52068,0.49785,0.69357,-124.25
> view matrix models
> #1,-0.17691,0.83156,0.52651,155.22,-0.81315,0.1779,-0.5542,170.6,-0.55452,-0.52617,0.64471,254.63,#3,0.14066,-0.8513,0.50547,409.57,0.84208,-0.16563,-0.51329,-77.26,0.52068,0.49785,0.69357,-116.49
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.16779,0.8827,0.43896,99.139,-0.5862,0.44734,-0.67547,102.45,-0.7926,-0.14397,0.5925,238.07,#3,-0.19886,-0.89612,0.39676,494.13,0.62047,-0.42849,-0.65682,30.668,0.7586,0.11557,0.64123,-82.372
> view matrix models
> #1,0.046112,0.88435,0.46455,116.28,-0.67961,0.3686,-0.63424,126.21,-0.73212,-0.28647,0.61801,248.32,#3,-0.078843,-0.8998,0.42913,468.6,0.71195,-0.35213,-0.60755,-6.6636,0.69779,0.25762,0.66838,-101.07
> view matrix models
> #1,0.043825,0.89337,0.44719,118.41,-0.68222,0.35376,-0.63987,130.52,-0.72983,-0.27704,0.62497,244.81,#3,-0.075637,-0.90822,0.41161,472.61,0.71498,-0.33713,-0.61249,-8.8567,0.69504,0.24797,0.67486,-100.11
> select add #1
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 6 models selected
> select subtract #1
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 2 models selected
> select add #2
55959 atoms, 56767 bonds, 40 pseudobonds, 4668 residues, 4 models selected
> select subtract #3
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 5 models selected
> view matrix models
> #5,-0.25805,0.63544,0.72775,248.92,-0.64419,0.44821,-0.61978,147.91,-0.72002,-0.62874,0.29369,339.61,#2,0.22302,-0.65692,0.72022,405.48,0.69044,-0.41511,-0.59243,50.676,0.68815,0.6294,0.36098,-140.5
> view matrix models
> #5,0.17813,0.65046,0.73836,163.86,-0.30804,0.7495,-0.58597,23.755,-0.93455,-0.12307,0.33388,277.68,#2,-0.21259,-0.67939,0.7023,486.62,0.35846,-0.72285,-0.59076,159.12,0.90902,0.12616,0.3972,-99.115
> view matrix models
> #5,0.065887,0.5269,0.84737,186.01,-0.2525,0.83038,-0.49671,-18.876,-0.96535,-0.18123,0.18775,322.64,#2,-0.10981,-0.55803,0.82253,426.9,0.29886,-0.80777,-0.50812,168.82,0.94796,0.19003,0.25547,-91.149
> view matrix models
> #5,-0.073043,0.82777,0.5563,212.81,-0.11128,0.54754,-0.82935,72.628,-0.9911,-0.12248,0.052116,343.25,#2,0.052876,-0.84593,0.53066,500.55,0.17384,-0.51549,-0.83907,200.05,0.98335,0.13662,0.1198,-63.496
> view matrix models
> #5,0.091836,0.54571,0.83293,180.79,-0.45613,0.7666,-0.45196,20.956,-0.88516,-0.33842,0.31932,311.59,#2,-0.13443,-0.57672,0.8058,437.47,0.49803,-0.74234,-0.44821,112.4,0.85668,0.34106,0.38702,-124.57
> view matrix models
> #5,0.0050992,0.54791,0.83652,195.58,-0.5271,0.71236,-0.46338,46.198,-0.84979,-0.43856,0.29244,328.82,#2,-0.048074,-0.57764,0.81487,421.26,0.56856,-0.68658,-0.45316,91.746,0.82124,0.44152,0.36143,-131.04
> select add #1
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 9 models selected
> select add #3
55959 atoms, 56767 bonds, 40 pseudobonds, 4668 residues, 11 models selected
> view matrix models
> #5,0.21365,0.51676,0.82904,163.34,-0.41104,0.81741,-0.40358,-0.3943,-0.88623,-0.25455,0.38705,292.64,#2,-0.25627,-0.54963,0.79513,454.35,0.45091,-0.79559,-0.40462,127.42,0.85499,0.25484,0.45172,-111.65,#1,0.25159,0.87389,0.41597,90.955,-0.57506,0.48067,-0.66201,85.084,-0.77847,-0.072648,0.62347,205.59,#3,-0.28114,-0.88573,0.36939,512.38,0.60835,-0.46218,-0.64522,29.854,0.74221,0.043321,0.66877,-82.875
> select up
55959 atoms, 56767 bonds, 40 pseudobonds, 4668 residues, 11 models selected
> ~tile
> tile
4 models tiled
> ~tile
> select subtract #5
55959 atoms, 56767 bonds, 40 pseudobonds, 4668 residues, 6 models selected
> select subtract #3
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 4 models selected
> select subtract #2
2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 4 models selected
> fitmap #2 inMap #5
Fit molecule A2irG2_F231A_des_merge_c3_align.pdb (#2) to map
c3_job072_deepEMhancer.mrc copy (#5) using 27977 atoms
average map value = 0.2064, steps = 176
shifted from previous position = 26.5
rotated from previous position = 2.91 degrees
atoms outside contour = 11786, contour level = 0.065087
Position of A2irG2_F231A_des_merge_c3_align.pdb (#2) relative to
c3_job072_deepEMhancer.mrc copy (#5) coordinates:
Matrix rotation and translation
0.99970242 0.01669160 0.01778919 9.68413835
-0.01588169 0.99887261 -0.04473572 25.45349835
-0.01851585 0.04443988 0.99884046 11.61676853
Axis 0.87733860 0.35718084 -0.32046659
Axis point -0.00000000 -349.20074660 467.07369503
Rotation angle (degrees) 2.91312145
Shift along axis 13.86498403
> select subtract #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> view matrix models
> #2,-0.15484,-0.58335,0.79732,443.53,0.40123,-0.77464,-0.48883,145.24,0.9028,0.24422,0.354,-105.33
> select subtract #2
Nothing selected
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 4 models selected
> fitmap #2 inMap #5
Fit molecule A2irG2_F231A_des_merge_c3_align.pdb (#2) to map
c3_job072_deepEMhancer.mrc copy (#5) using 27977 atoms
average map value = 0.2218, steps = 80
shifted from previous position = 6.28
rotated from previous position = 7.41 degrees
atoms outside contour = 10312, contour level = 0.065087
Position of A2irG2_F231A_des_merge_c3_align.pdb (#2) relative to
c3_job072_deepEMhancer.mrc copy (#5) coordinates:
Matrix rotation and translation
-0.99781693 -0.01613305 -0.06403992 367.89769451
0.01837183 -0.99923494 -0.03452562 357.73275578
-0.06343393 -0.03562678 0.99734993 33.14236258
Axis -0.03189194 -0.01755086 0.99933722
Axis point 182.93143610 180.74849783 0.00000000
Rotation angle (degrees) 179.01080314
Shift along axis 15.10890820
> select subtract #2
2 models selected
> select subtract #5
Nothing selected
> hide #!2 models
> show #!3 models
> hide #!5 models
> show #!1 models
> select add #1
2 models selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 4 models selected
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2356, steps = 144
shifted from previous position = 26.6
rotated from previous position = 1.71 degrees
atoms outside contour = 14011, contour level = 0.13938
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
0.99980793 -0.00868445 0.01756915 14.23245064
0.00907704 0.99970809 -0.02239078 16.77908025
-0.01736957 0.02254596 0.99959491 15.08896046
Axis 0.75361844 0.58594508 0.29787181
Axis point 0.00000000 -336.50803366 98.17413763
Rotation angle (degrees) 1.70846891
Shift along axis 25.05203265
> select subtract #3
2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!5 models
> show #!1 models
> hide #!2 models
> hide #!5 models
> show #!3 models
> save /Users/ig/Documents/Danyang/GluA1/Figs/Fig4_LBD_TMD.cxs includeMaps
> true
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!5 models
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220930_A2ir_G2_F231A_des/c1_job079_deepEMhancer.mrc
Opened c1_job079_deepEMhancer.mrc as #4, grid size 256,256,256, pixel 1.45,
shown at level 0.000124, step 1, values float32
> hide #!4 models
> show #!4 models
> select add #4
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,222.85,0,1,0,-126.05,0,0,1,116.27
> view matrix models #4,1,0,0,144.59,0,1,0,-152.76,0,0,1,204.26
> volume #4 level 0.05524
> surface dust #4 size 14.5
> view matrix models #4,1,0,0,142.7,0,1,0,-182.69,0,0,1,-27.259
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.90505,0.36546,0.21754,378.9,-0.41522,-0.64851,-0.63799,325.73,-0.092079,-0.66774,0.73868,165.38
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.90505,0.36546,0.21754,383.78,-0.41522,-0.64851,-0.63799,308.13,-0.092079,-0.66774,0.73868,218.6
> hide #!2 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> select subtract #4
Nothing selected
> volume #4 level 0.052
> volume #4 level 0.04552
> open
> /Users/ig/Documents/Danyang/GluA1/analysis/A2irG2_F231A_des_merge_align.pdb
Chain information for A2irG2_F231A_des_merge_align.pdb #6
---
Chain | Description
A C | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> select add #6
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 2 models selected
> view matrix models #6,1,0,0,279.62,0,1,0,-137.61,0,0,1,59.962
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.57003,0.81788,0.07833,200.2,-0.6136,0.48717,-0.62142,167.05,-0.54641,0.30617,0.77955,141.47
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.57003,0.81788,0.07833,77.068,-0.6136,0.48717,-0.62142,170.27,-0.54641,0.30617,0.77955,120.95
> view matrix models
> #6,0.57003,0.81788,0.07833,58.148,-0.6136,0.48717,-0.62142,123.05,-0.54641,0.30617,0.77955,136.4
> view matrix models
> #6,0.57003,0.81788,0.07833,58.481,-0.6136,0.48717,-0.62142,123.5,-0.54641,0.30617,0.77955,136.47
> view matrix models
> #6,0.57003,0.81788,0.07833,77.282,-0.6136,0.48717,-0.62142,114.3,-0.54641,0.30617,0.77955,123.21
> view matrix models
> #6,0.57003,0.81788,0.07833,0.95852,-0.6136,0.48717,-0.62142,157.15,-0.54641,0.30617,0.77955,171
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.59507,0.7944,0.12171,-7.0785,-0.61258,0.54638,-0.57115,137.9,-0.52022,0.26532,0.81177,167.73
> view matrix models
> #6,0.30179,0.93992,0.15962,12.107,-0.73481,0.33599,-0.58921,198.31,-0.60743,0.060527,0.79206,221.41
> view matrix models
> #6,0.26223,0.87744,0.40167,-13.389,-0.85347,0.40513,-0.3278,160.56,-0.45035,-0.25685,0.85511,237.3
> view matrix models
> #6,0.38496,0.82446,0.41482,-27.931,-0.62025,0.56393,-0.54523,131.62,-0.68345,-0.047399,0.72846,264.37
> view matrix models
> #6,0.23917,0.89126,0.3853,-8.8465,-0.6395,0.44318,-0.62819,170.38,-0.73064,-0.096155,0.67596,290.23
> view matrix models
> #6,0.20764,0.95087,0.22965,14.097,-0.5456,0.30743,-0.77962,204.27,-0.81192,0.036581,0.58263,298.2
> view matrix models
> #6,0.048511,0.94799,0.31458,27.067,-0.65538,0.26788,-0.7062,217.01,-0.75374,-0.17191,0.63429,314.61
> view matrix models
> #6,0.46318,0.84719,0.26028,-17.895,-0.57311,0.51032,-0.64118,149.69,-0.67602,0.14781,0.7219,230.83
> view matrix models
> #6,0.23425,0.9118,0.33725,-2.9656,-0.68427,0.40106,-0.60904,181.94,-0.69059,-0.088107,0.71786,274.46
> view matrix models
> #6,0.43375,0.87141,0.22913,-11.402,-0.61647,0.47247,-0.62987,161.67,-0.65714,0.13195,0.74213,226.67
> view matrix models
> #6,0.40579,0.85381,0.3261,-20.788,-0.46919,0.5008,-0.72737,148.63,-0.78435,0.14215,0.60381,271.58
> view matrix models
> #6,0.85868,-0.49591,-0.12939,212.77,0.31371,0.70822,-0.63246,-39.454,0.40528,0.50249,0.76371,-24.746
> view matrix models
> #6,0.83439,-0.43616,0.33699,123.81,0.49992,0.85634,-0.12945,-186.54,-0.23211,0.27648,0.93257,94.394
> view matrix models
> #6,0.99458,0.0631,0.082694,55.801,0.046518,0.44125,-0.89618,99.459,-0.093038,0.89516,0.43593,52.705
> view matrix models
> #6,0.76435,-0.31665,0.56169,75.526,0.59982,0.66882,-0.43919,-116.67,-0.2366,0.67262,0.70115,68.517
> view matrix models
> #6,0.77091,-0.63306,0.07018,215.97,0.50438,0.53947,-0.67422,-36.192,0.38896,0.55516,0.73519,-25.861
> view matrix models
> #6,0.93834,-0.25377,0.23479,92.744,0.34565,0.67468,-0.65217,-35.744,0.0070945,0.69311,0.72079,19.274
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93834,-0.25377,0.23479,166.1,0.34565,0.67468,-0.65217,-74.547,0.0070945,0.69311,0.72079,-29.286
> fitmap #6 inMap #4
Fit molecule A2irG2_F231A_des_merge_align.pdb (#6) to map
c1_job079_deepEMhancer.mrc (#4) using 28006 atoms
average map value = 0.2207, steps = 92
shifted from previous position = 7.21
rotated from previous position = 8.59 degrees
atoms outside contour = 6635, contour level = 0.045515
Position of A2irG2_F231A_des_merge_align.pdb (#6) relative to
c1_job079_deepEMhancer.mrc (#4) coordinates:
Matrix rotation and translation
-0.99822679 0.01122738 -0.05845695 362.22594097
-0.00884138 -0.99912346 -0.04091629 363.71823179
-0.05886510 -0.04032690 0.99745107 33.26180602
Axis 0.02934993 0.02032426 -0.99936255
Axis point 182.51578350 181.28635992 0.00000000
Rotation angle (degrees) 179.42469609
Shift along axis -15.21699314
> show sel atoms
> hide sel atoms
> show sel cartoons
> color #4 #ffb2b298 models
> select subtract #6
Nothing selected
> volume #4 level 0.04227
> show #!3 models
> show #!2 models
> show #!1 models
> show #!5 models
> select add #6
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 2 models selected
> select add #5
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 6 models selected
> select subtract #5
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 2 models selected
> select add #4
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 6 models selected
> view matrix models
> #4,-0.90505,0.36546,0.21754,410.1,-0.41522,-0.64851,-0.63799,292.58,-0.092079,-0.66774,0.73868,212.86,#6,0.88741,-0.38407,0.25494,222.42,0.45777,0.66901,-0.58556,-114.92,0.054338,0.63633,0.7695,-38.79
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.3241,0.11464,0.93905,210.17,-0.9245,0.17214,-0.34009,177.93,-0.20063,-0.97838,0.050193,424,#6,0.26723,-0.15604,0.95091,165.7,0.94136,-0.16865,-0.29222,-105.65,0.20597,0.97325,0.10183,-2.8627
> view matrix models
> #4,-0.65815,-0.14112,0.73954,356.97,-0.73738,-0.077485,-0.67102,254.52,0.152,-0.98696,-0.053062,381.69,#6,0.6147,0.10378,0.7819,91.835,0.77626,0.096199,-0.62303,-63.078,-0.13988,0.98994,-0.02143,76.008
> view matrix models
> #4,-0.4407,0.075791,0.89445,247.16,-0.89374,-0.12996,-0.42934,245.46,0.083701,-0.98862,0.12501,359.4,#6,0.3866,-0.11674,0.91483,144.85,0.91858,0.13712,-0.37069,-139.82,-0.08217,0.98365,0.16025,34.298
> view matrix models
> #4,-0.054979,0.62542,0.77835,97.933,-0.97383,-0.20574,0.096526,171.61,0.22051,-0.75268,0.62036,194.12,#6,0.0035342,-0.65687,0.75399,331.38,0.96825,0.19073,0.16163,-252.76,-0.24998,0.72948,0.63669,20.859
> view matrix models
> #4,0.52984,0.39092,0.75263,40.463,-0.38636,0.90126,-0.19612,-80.696,-0.75498,-0.18687,0.62855,265.38,#6,-0.57666,-0.41498,0.70375,399.6,0.38925,-0.8969,-0.20991,100.63,0.71829,0.15289,0.67873,-55.161
> view matrix models
> #4,0.4047,0.03687,0.9137,97.097,-0.18275,0.98229,0.041304,-178.84,-0.896,-0.18369,0.40427,334.06,#6,-0.4581,-0.069141,0.88621,287.49,0.1713,-0.98515,0.01169,113.62,0.87224,0.15717,0.46314,-43.855
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.4581,-0.069141,0.88621,308.33,0.1713,-0.98515,0.01169,134.44,0.87224,0.15717,0.46314,-59.604
> undo
> view matrix models
> #4,0.4047,0.03687,0.9137,103.11,-0.18275,0.98229,0.041304,-174.02,-0.896,-0.18369,0.40427,327.21
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4047,0.03687,0.9137,191.68,-0.18275,0.98229,0.041304,-130.91,-0.896,-0.18369,0.40427,286.41,#6,-0.4581,-0.069141,0.88621,382.07,0.1713,-0.98515,0.01169,161.55,0.87224,0.15717,0.46314,-91.506
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.506,0.10851,0.85568,171.39,-0.17331,0.98461,-0.02237,-120.64,-0.84494,-0.13698,0.51702,246.56,#6,-0.55643,-0.13724,0.81948,422.6,0.16561,-0.98479,-0.052468,173.96,0.81422,0.10652,0.5707,-92.12
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.506,0.10851,0.85568,174.34,-0.17331,0.98461,-0.02237,-149.21,-0.84494,-0.13698,0.51702,235.12,#6,-0.55643,-0.13724,0.81948,425.55,0.16561,-0.98479,-0.052468,145.39,0.81422,0.10652,0.5707,-103.56
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.15455,0.2094,0.96554,198.17,-0.29398,0.94276,-0.15741,-93.787,-0.94323,-0.25952,0.20726,335.87,#6,-0.21296,-0.24642,0.94548,362.43,0.29439,-0.93889,-0.17839,137.39,0.93166,0.24035,0.27249,-93.298
> select subtract #4
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!3 models
> hide #!2 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #4
4 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.
> select add #1
7 models selected
> fitmap #1 inMap #4
Fit map c2_job071_deepEMhancer.mrc in map c1_job079_deepEMhancer.mrc using
41172 points
correlation = 0.8293, correlation about mean = 0.599, overlap = 5709
steps = 152, shift = 8.45, angle = 19.9 degrees
Position of c2_job071_deepEMhancer.mrc (#1) relative to
c1_job079_deepEMhancer.mrc (#4) coordinates:
Matrix rotation and translation
0.99998666 0.00235904 0.00459027 -1.64708527
-0.00234571 0.99999301 -0.00290481 0.87441966
-0.00459709 0.00289400 0.99998522 0.33343029
Axis 0.48979440 0.77600701 -0.39738465
Axis point 48.93426015 0.00000000 331.14801014
Rotation angle (degrees) 0.33917220
Shift along axis -0.26067743
> select subtract #1
4 models selected
> select add #5
8 models selected
> fitmap #5 inMap #4
Fit map c3_job072_deepEMhancer.mrc copy in map c1_job079_deepEMhancer.mrc
using 54490 points
correlation = 0.846, correlation about mean = 0.6624, overlap = 5133
steps = 180, shift = 7.91, angle = 21 degrees
Position of c3_job072_deepEMhancer.mrc copy (#5) relative to
c1_job079_deepEMhancer.mrc (#4) coordinates:
Matrix rotation and translation
0.99963041 -0.02688500 0.00402496 4.14926445
0.02685264 0.99960823 0.00789125 -6.51114955
-0.00423555 -0.00778025 0.99996074 2.46817721
Axis -0.27696772 0.14599082 0.94972394
Axis point 246.04421912 153.46838417 0.00000000
Rotation angle (degrees) 1.62118229
Shift along axis 0.24430658
> select subtract #4
4 models selected
> select subtract #5
Nothing selected
> show #!2 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> select add #2
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 2 models selected
> select add #5
27977 atoms, 28381 bonds, 20 pseudobonds, 2333 residues, 5 models selected
> fitmap #2 inMap #5
Fit molecule A2irG2_F231A_des_merge_c3_align.pdb (#2) to map
c3_job072_deepEMhancer.mrc copy (#5) using 27977 atoms
average map value = 0.2218, steps = 156
shifted from previous position = 6.69
rotated from previous position = 21 degrees
atoms outside contour = 10319, contour level = 0.065087
Position of A2irG2_F231A_des_merge_c3_align.pdb (#2) relative to
c3_job072_deepEMhancer.mrc copy (#5) coordinates:
Matrix rotation and translation
-0.99782087 -0.01612962 -0.06397931 367.88244097
0.01835986 -0.99923862 -0.03442536 357.71884273
-0.06337533 -0.03552499 0.99735728 33.11021415
Axis -0.03186205 -0.01750028 0.99933906
Axis point 182.92356005 180.73963601 0.00000000
Rotation angle (degrees) 179.01124670
Shift along axis 15.10666113
> select subtract #2
3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!6 models
> hide #!2 models
> show #!4 models
> select add #4
3 models selected
> select add #6
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 5 models selected
> fitmap #6 inMap #4
Fit molecule A2irG2_F231A_des_merge_align.pdb (#6) to map
c1_job079_deepEMhancer.mrc (#4) using 28006 atoms
average map value = 0.2207, steps = 36
shifted from previous position = 0.0103
rotated from previous position = 0.00589 degrees
atoms outside contour = 6320, contour level = 0.042273
Position of A2irG2_F231A_des_merge_align.pdb (#6) relative to
c1_job079_deepEMhancer.mrc (#4) coordinates:
Matrix rotation and translation
-0.99822884 0.01131367 -0.05840528 362.21098871
-0.00892829 -0.99912161 -0.04094249 363.74114571
-0.05881718 -0.04034852 0.99745302 33.26049841
Axis 0.02932502 0.02033622 -0.99936304
Axis point 182.51582281 181.29017961 0.00000000
Rotation angle (degrees) 179.41973123
Shift along axis -15.22034960
> select subtract #6
3 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!1 models
> select add #1
3 models selected
> select add #3
27982 atoms, 28386 bonds, 20 pseudobonds, 2335 residues, 5 models selected
> fitmap #3 inMap #1
Fit molecule A2irG2_F231A_des_merge_c2_align.pdb (#3) to map
c2_job071_deepEMhancer.mrc (#1) using 27982 atoms
average map value = 0.2356, steps = 144
shifted from previous position = 6.89
rotated from previous position = 19.9 degrees
atoms outside contour = 14015, contour level = 0.13938
Position of A2irG2_F231A_des_merge_c2_align.pdb (#3) relative to
c2_job071_deepEMhancer.mrc (#1) coordinates:
Matrix rotation and translation
0.99981053 -0.00867092 0.01742754 14.26040733
0.00906300 0.99970472 -0.02254629 16.81041975
-0.01722689 0.02269997 0.99959389 15.01197477
Axis 0.75804737 0.58059391 0.29711090
Axis point 0.00000000 -331.82428164 105.38112265
Rotation angle (degrees) 1.71018632
Shift along axis 25.03031307
> select subtract #3
3 models selected
> select subtract #1
Nothing selected
> show #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!6 models
> hide #!5 models
> show #!4 models
> show #!6 models
> select add #6/A
4254 atoms, 4324 bonds, 2 pseudobonds, 406 residues, 2 models selected
> select add #6/C
8468 atoms, 8608 bonds, 4 pseudobonds, 812 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> select clear
> select add #6/B
4277 atoms, 4347 bonds, 2 pseudobonds, 408 residues, 2 models selected
> select add #6/D
8546 atoms, 8686 bonds, 4 pseudobonds, 815 residues, 2 models selected
> color sel dark red
> select clear
> select add #6/G
2740 atoms, 2771 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add #6/H
5480 atoms, 5542 bonds, 6 pseudobonds, 354 residues, 2 models selected
> show #!2 models
> hide #!2 models
> select add #6
28006 atoms, 28410 bonds, 20 pseudobonds, 2336 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!6 models
> select add #6/G
2740 atoms, 2771 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add #6/H
5480 atoms, 5542 bonds, 6 pseudobonds, 354 residues, 2 models selected
> color sel light green
> select clear
> select add #6/E
2750 atoms, 2781 bonds, 3 pseudobonds, 177 residues, 2 models selected
> select add #6/F
5512 atoms, 5574 bonds, 6 pseudobonds, 355 residues, 2 models selected
> color sel cadet blue
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202203230115 (2022-03-23)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Populating font family aliases took 330 ms. Replace uses of missing font
family "Lucida Grande" with one that exists to avoid this cost.
OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 16 GB
Boot ROM Version: 1731.140.1.0.0
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2026)
Kernel Version: Darwin 19.6.0
Time since boot: 10 days 3:12
Graphics/Displays:
Radeon Pro 570X:
Chipset Model: Radeon Pro 570X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A14GL-003
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
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
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.36.3
ChimeraX-AtomicLibrary: 6.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
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: 1.5.1
ChimeraX-CommandLine: 1.2.2
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202203230115
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-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: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 2.5
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.31.2
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.4.0
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt6-commercial: 6.2.3
PyQt6-sip: 13.2.0
PyQt6-WebEngine-commercial: 6.2.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (4)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in QMainWindow::removeDockWidget |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 3 years ago
Mysterious. Seems like the current ChimeraX code
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
would need to call the ToolWindows close_request() method if the close button on the title bar is used. But I did not look at what this pre ChimeraX 1.4 build does.
comment:4 by , 3 years ago
According to "git blame" that line containing the lambda was added 1/27/2021, so earlier than the build reporting the bug.
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According to the Python stack trace, ToolInstance.delete() is being called directly from the event loop. I don't know how that can happen. Closing a tool using its [X] button does not do that (there is an intervening lambda function). Kind of a mystery.