![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8152 closed defect (can't reproduce)
Crash in QMainWindow::removeDockWidget
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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.
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:
0x104617000 - 0x104617ff3 +edu.ucsf.cgl.ChimeraX (1.4.0 - 1.4.0.0) /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
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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
System Profile:
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Boot Volume File System Type: apfs
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E3
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E3
USB Device: USB 3.1 Bus
USB Device: Basic
USB Device: USB Optical Mouse
USB Device: FaceTime HD Camera (Built-in)
USB Device: Keyboard Hub
USB Device: Apple Keyboard
Thunderbolt Bus: iMac, Apple Inc., 47.4
Model: iMac19,1, BootROM 1731.140.1.0.0, 6 processors, 6-Core Intel Core i5, 3 GHz, 16 GB, SMC 2.46f13
Graphics: kHW_AMDRadeonPro570XItem, Radeon Pro 570X, spdisplays_pcie_device, 4 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Oct 28 2020 13:06:41 version 9.30.357.42.32.5.48 FWID 01-4f9e2d7c
Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.4.dev202203230115 (2022-03-23)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/ig/Documents/Danyang/GluA1/Figs/Fig3C_splay_Composite_side.cxs
Opened run_class001.mrc as #1, grid size 128,128,128, pixel 2.89, shown at
level 0.0928, step 1, values float32
Opened run_it025_class009.mrc as #10, grid size 128,128,128, pixel 2.89, shown
at level 0.0413, step 1, values float32
Log from Sat Dec 3 20:11:09 2022UCSF 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 /Users/ig/Downloads/6qkz.pdb
6qkz.pdb title:
Full length GLUA1/2-Γ8 complex [more info...]
Chain information for 6qkz.pdb #1
---
Chain | Description | UniProt
A C | GLUA1 | GRIA1_RAT
B D | glutamate receptor 2 | GRIA2_RAT
I J | voltage-dependent calcium channel γ-8 subunit | CCG8_RAT
Non-standard residues in 6qkz.pdb #1
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
E2Q —
6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[F]quinoxaline-7-sulfonamide
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> show cartoons
> hide atoms
> ui tool show "Color Actions"
> set bgColor white
> select /A/C
6178 atoms, 6174 bonds, 8 pseudobonds, 1522 residues, 2 models selected
> set bgColor cornflower blue
> set bgColor white
> color sel sky blue target c
> color sel tomato target c
> select /B/D
6229 atoms, 6225 bonds, 6 pseudobonds, 1546 residues, 2 models selected
> color sel salmon target c
> select /A/C
6178 atoms, 6174 bonds, 8 pseudobonds, 1522 residues, 2 models selected
> color sel royal blue target c
> color sel sky blue target c
> select /I/J
1296 atoms, 1288 bonds, 6 pseudobonds, 324 residues, 2 models selected
> color sel silver target c
> lighting shadows false
> select /A:415
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B/D
6229 atoms, 6225 bonds, 6 pseudobonds, 1546 residues, 2 models selected
> color sel light coral target c
> select clear
> style sphere
Changed 13949 atom styles
> show surfaces
[Repeated 1 time(s)]
> style stick
Changed 13949 atom styles
> style sphere
Changed 13949 atom styles
> style ball
Changed 13949 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 13949 atom styles
> show surfaces
> hide surfaces
> show surfaces
> select /A/C
6178 atoms, 6174 bonds, 8 pseudobonds, 1522 residues, 2 models selected
> color sel sky blue target c
[Repeated 1 time(s)]
> select clear
> select /I/J
1296 atoms, 1288 bonds, 6 pseudobonds, 324 residues, 2 models selected
> color sel silver target c
> select /A/C
6178 atoms, 6174 bonds, 8 pseudobonds, 1522 residues, 2 models selected
> color sel sky blue target cs
> select /B/D
6229 atoms, 6225 bonds, 6 pseudobonds, 1546 residues, 2 models selected
> color sel light coral target cs
> select /I/J
1296 atoms, 1288 bonds, 6 pseudobonds, 324 residues, 2 models selected
> color sel silver target cs
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes true
> select clear
> select /I/J
1296 atoms, 1288 bonds, 6 pseudobonds, 324 residues, 2 models selected
> color sel light gray target cs
> select clear
> ui tool show "Side View"
> save /Users/ig/Documents/Danyang/GluA1/Figs/Fig3A_6QKZ_side.pdb
> save /Users/ig/Documents/Danyang/GluA1/Figs/Fig3A_6QKZ_side.cxs
> close session
> open
> /Volumes/cephfs/dzhang/A1GX/220930_A2ir_G2_F231A_des/Refine3D/job086/run_class001.mrc
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.45, shown at
level 0.00751, step 1, values float32
> ui tool show "Side View"
> volume #1 level 0.003438
> close session
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Refine3D/job061/run_class001.mrc
Opened run_class001.mrc as #1, grid size 128,128,128, pixel 2.89, shown at
level 0.0641, step 1, values float32
> volume #1 level 0.02212
> volume #1 level 0.02014
> volume #1 level 0.02212
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class001.mrc
Opened run_it025_class001.mrc as #2, grid size 128,128,128, pixel 2.89, shown
at level 0.0241, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class002.mrc
Opened run_it025_class002.mrc as #3, grid size 128,128,128, pixel 2.89, shown
at level 0.0002, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class003.mrc
Opened run_it025_class003.mrc as #4, grid size 128,128,128, pixel 2.89, shown
at level 0.026, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class004.mrc
Opened run_it025_class004.mrc as #5, grid size 128,128,128, pixel 2.89, shown
at level 0.0263, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class005.mrc
Opened run_it025_class005.mrc as #6, grid size 128,128,128, pixel 2.89, shown
at level 0.0164, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class006.mrc
Opened run_it025_class006.mrc as #7, grid size 128,128,128, pixel 2.89, shown
at level 0.0226, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class007.mrc
Opened run_it025_class007.mrc as #8, grid size 128,128,128, pixel 2.89, shown
at level 0.0002, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class008.mrc
Opened run_it025_class008.mrc as #9, grid size 128,128,128, pixel 2.89, shown
at level 0.026, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class009.mrc
Opened run_it025_class009.mrc as #10, grid size 128,128,128, pixel 2.89, shown
at level 0.0251, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class010.mrc
Opened run_it025_class010.mrc as #11, grid size 128,128,128, pixel 2.89, shown
at level 0.0215, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class011.mrc
Opened run_it025_class011.mrc as #12, grid size 128,128,128, pixel 2.89, shown
at level 0.0194, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class012.mrc
Opened run_it025_class012.mrc as #13, grid size 128,128,128, pixel 2.89, shown
at level 0.0251, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class013.mrc
Opened run_it025_class013.mrc as #14, grid size 128,128,128, pixel 2.89, shown
at level 0.0189, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class014.mrc
Opened run_it025_class014.mrc as #15, grid size 128,128,128, pixel 2.89, shown
at level 0.0262, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class015.mrc
Opened run_it025_class015.mrc as #16, grid size 128,128,128, pixel 2.89, shown
at level 0.0212, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class016.mrc
Opened run_it025_class016.mrc as #17, grid size 128,128,128, pixel 2.89, shown
at level 0.0192, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class017.mrc
Opened run_it025_class017.mrc as #18, grid size 128,128,128, pixel 2.89, shown
at level 0.0192, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class018.mrc
Opened run_it025_class018.mrc as #19, grid size 128,128,128, pixel 2.89, shown
at level 0.0176, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class019.mrc
Opened run_it025_class019.mrc as #20, grid size 128,128,128, pixel 2.89, shown
at level 0.0226, step 1, values float32
> open
> /Volumes/cephfs/dzhang/A1GX/220726_A2G2_tandem_F231A_ZK/Class3D/job063/run_it025_class020.mrc
Opened run_it025_class020.mrc as #21, grid size 128,128,128, pixel 2.89, shown
at level 0.0201, step 1, values float32
> hide #!1 models
> tile
18 models tiled
> hide #!6 models
> show #!6 models
> close #6
> hide #!19 models
> show #!19 models
> close #19
> close #14
> hide #!12 models
> show #!12 models
> close #12
> close #21
> hide #!16 models
> show #!16 models
> hide #!18 models
> close #18
> tile
12 models tiled
> close #3
> close #8
> hide #!10 models
> show #!10 models
> hide #!2 models
> show #!2 models
> close #4-5,7
> tile
9 models tiled
> close #9
> close #11
> close #16
> tile
6 models tiled
> volume #10 level 0.02428
> volume #10 level 0.03646
> volume #2 level 0.03616
> volume #2 level 0.04323
> volume #10 level 0.04296
> close #17
> close #13
> tile
4 models tiled
> volume #15 level 0.04539
> volume #20 level 0.03993
> close #20
> tile
3 models tiled
> volume #2 level 0.04558
> close #2
> tile
2 models tiled
> ~tile
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,42.573,0,1,0,92.271,0,0,1,67.433
> view matrix models #1,1,0,0,26.656,0,1,0,84.607,0,0,1,43.198
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.33623,0.47124,0.8154,-84.947,-0.8404,0.5409,0.033941,319.27,-0.42505,-0.69668,0.5779,327.29
> view matrix models
> #1,0.72663,-0.090659,0.68102,-27.521,-0.67032,0.12373,0.73168,241.69,-0.1506,-0.98817,0.029137,429.29
> view matrix models
> #1,0.32354,0.1899,0.92696,-49.784,-0.57209,0.81957,0.031777,218.05,-0.75368,-0.54059,0.3738,394.93
> view matrix models
> #1,0.9039,-0.42154,0.072547,110.4,0.34012,0.81117,0.47573,-27.463,-0.25939,-0.40534,0.87659,188.92
> view matrix models
> #1,0.82034,0.15922,0.54927,-68.096,-0.50363,0.65615,0.56197,141.5,-0.27093,-0.73764,0.61846,299.37
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.82034,0.15922,0.54927,-94.732,-0.50363,0.65615,0.56197,309.78,-0.27093,-0.73764,0.61846,265.41
> select subtract #1
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.82034,0.15922,0.54927,-86.558,-0.50363,0.65615,0.56197,313.66,-0.27093,-0.73764,0.61846,251.97
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.78112,0.15334,0.60526,-88.226,-0.50713,0.72132,0.47173,318.19,-0.36425,-0.67542,0.6412,253.42
> view matrix models
> #1,0.77851,0.14313,0.61109,-86.872,-0.51349,0.70512,0.48902,319.31,-0.3609,-0.6945,0.62244,259.73
> select subtract #1
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.
[Repeated 2 time(s)]
> hide #!15 models
> fitmap #1 inMap #10
Fit map run_class001.mrc in map run_it025_class009.mrc using 59618 points
correlation = 0.4982, correlation about mean = 0.07051, overlap = 66.68
steps = 120, shift = 9.29, angle = 10.6 degrees
Position of run_class001.mrc (#1) relative to run_it025_class009.mrc (#10)
coordinates:
Matrix rotation and translation
0.99942980 -0.02024285 0.02702381 -3.53006133
0.02108413 0.99929018 -0.03121800 -1.53879348
-0.02637268 0.03176997 0.99914720 79.01038675
Axis 0.68213439 0.57826256 0.44755457
Axis point 0.00000000 -2051.27379968 -596.57907697
Rotation angle (degrees) 2.64627330
Shift along axis 32.06365646
> hide #!10 models
> show #!15 models
> fitmap #1 inMap #15
Fit map run_class001.mrc in map run_it025_class014.mrc using 59618 points
correlation = 0.4826, correlation about mean = 0.02115, overlap = 65.67
steps = 128, shift = 2.46, angle = 6.27 degrees
Position of run_class001.mrc (#1) relative to run_it025_class014.mrc (#15)
coordinates:
Matrix rotation and translation
0.99911536 -0.01633028 -0.03875302 6.97551170
0.01848950 0.99825788 0.05602960 -15.03021705
0.03777054 -0.05669656 0.99767673 83.54000666
Axis -0.80160687 -0.54416656 0.24760691
Axis point 0.00000000 1368.34821937 84.77590140
Rotation angle (degrees) 4.03194362
Shift along axis 23.27240654
> show #!10 models
> volume #1 level 0.06164
> hide #!10 models
> show #!10 models
> hide #!15 models
> volume #1 level 0.09276
> surface dust #1 size 28.9
> surface dust #10 size 28.9
> show #!15 models
> hide #!10 models
> show #!10 models
> hide #!15 models
> show #!15 models
> hide #!10 models
> hide #!15 models
> show #!10 models
> show #!15 models
> volume #10 level 0.04864
> volume #15 level 0.04923
> volume #10 level 0.049
> volume #15 level 0.049
> show #!10 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> open /Users/ig/Documents/Danyang/GluA1/A2G2_F231A_ZK_rf19_align.pdb
Chain information for A2G2_F231A_ZK_rf19_align.pdb #2
---
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
> select add #2
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-2.9107,0,1,0,97.609,0,0,1,13.896
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.34957,-0.051723,0.93548,-59.692,-0.82348,0.45925,0.33311,305.26,-0.44685,-0.8868,0.11795,475.59
> view matrix models
> #2,0.68612,-0.015853,0.72732,-91.301,-0.53165,0.6715,0.51618,162.93,-0.49657,-0.74084,0.4523,384.29
> view matrix models
> #2,0.66113,0.14007,0.73708,-120.13,-0.66936,0.55391,0.49512,219.65,-0.33892,-0.82071,0.45996,366.69
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.66113,0.14007,0.73708,-127.06,-0.66936,0.55391,0.49512,367.55,-0.33892,-0.82071,0.45996,341.19
> select subtract #2
Nothing selected
> select add #2
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 2 models selected
> view matrix models
> #2,0.66113,0.14007,0.73708,-111.4,-0.66936,0.55391,0.49512,367.24,-0.33892,-0.82071,0.45996,322.82
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.619,0.29736,0.72692,-132.73,-0.74525,0.51449,0.42415,406.04,-0.24787,-0.80429,0.54007,283.66
> view matrix models
> #2,0.73889,0.33048,0.58721,-134.1,-0.6566,0.54892,0.51728,360.9,-0.15138,-0.76777,0.62258,238.76
> view matrix models
> #2,0.79553,-0.071984,0.60162,-66.56,-0.41893,0.65201,0.63197,266.6,-0.43775,-0.75479,0.48853,323.46
> select subtract #2
Nothing selected
> ui mousemode right "translate selected models"
> select add #2
36444 atoms, 36848 bonds, 20 pseudobonds, 2351 residues, 2 models selected
> view matrix models
> #2,0.79553,-0.071984,0.60162,-63.333,-0.41893,0.65201,0.63197,267.04,-0.43775,-0.75479,0.48853,326.68
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.71389,0.10303,0.69263,-101.88,-0.53001,0.72595,0.43828,316.18,-0.45766,-0.67999,0.57286,297.4
> select subtract #2
Nothing selected
> hide #!10 models
> hide #!15 models
> fitmap #2 inMap #1
Fit molecule A2G2_F231A_ZK_rf19_align.pdb (#2) to map run_class001.mrc (#1)
using 36444 atoms
average map value = 0.08848, steps = 60
shifted from previous position = 3.22
rotated from previous position = 7.94 degrees
atoms outside contour = 19939, contour level = 0.092758
Position of A2G2_F231A_ZK_rf19_align.pdb (#2) relative to run_class001.mrc
(#1) coordinates:
Matrix rotation and translation
0.99993537 -0.00842337 -0.00763533 -15.11733290
0.00839819 0.99995921 -0.00332505 -19.24803222
0.00766303 0.00326071 0.99996532 -21.87396639
Axis 0.27820582 -0.64625621 0.71060146
Axis point 2846.81353187 -1575.08904903 0.00000000
Rotation angle (degrees) 0.67817682
Shift along axis -7.31024205
> show #!10 models
> show #!15 models
> show cartoons
[Repeated 1 time(s)]
> hide surfaces
[Repeated 1 time(s)]
> show cartoons
> hide surfaces
[Repeated 1 time(s)]
> hide atoms
> hide #!1 models
> hide #!15 models
> show #!1 models
> show #!15 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> show #!2 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!1 models
> show #!1 models
> hide #!15 models
> show #!15 models
> hide #!10 models
> volume #15 level 0.06015
> volume #10 level 0.06037
> hide #!15 models
> show #!15 models
> hide #!10 models
> show #!10 models
> hide #!15 models
> close #15
> volume #10 level 0.04616
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220726_A2G2_tandem_F231A_ZK/Class3D/job063/class009.pdb
Chain information for class009.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open
> /Volumes/cephfs/jkrieger/A2G2_F231/220726_A2G2_tandem_F231A_ZK/Class3D/job063/class009.pdb
Chain information for class009.pdb #4
---
Chain | Description
A | No description available
B | No description available
> close #4
> select add #3
13016 atoms, 11988 bonds, 8 pseudobonds, 2750 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,32.759,0,1,0,127.76,0,0,1,3.9545
> view matrix models #3,1,0,0,36.578,0,1,0,109.4,0,0,1,10.477
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.7709,-0.6325,-0.075222,212.37,0.5653,0.62497,0.53837,-21.762,-0.2935,-0.45755,0.83935,180.54
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.7709,-0.6325,-0.075222,145.6,0.5653,0.62497,0.53837,96.011,-0.2935,-0.45755,0.83935,103.57
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.76729,-0.11534,0.63084,-84.118,-0.27977,0.82494,0.49112,219.21,-0.57705,-0.55332,0.60071,217.53
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76729,-0.11534,0.63084,-74.71,-0.27977,0.82494,0.49112,214,-0.57705,-0.55332,0.60071,226.3
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.80857,0.056549,0.58567,-106.44,-0.43074,0.73497,0.52372,252.27,-0.40083,-0.67574,0.61863,214.47
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.
> select add #10
13016 atoms, 11988 bonds, 8 pseudobonds, 2750 residues, 4 models selected
> fitmap #3 inMap #10
Fit molecule class009.pdb (#3) to map run_it025_class009.mrc (#10) using 13016
atoms
average map value = 0.05601, steps = 88
shifted from previous position = 12.4
rotated from previous position = 8 degrees
atoms outside contour = 3221, contour level = 0.046158
Position of class009.pdb (#3) relative to run_it025_class009.mrc (#10)
coordinates:
Matrix rotation and translation
0.99999909 -0.00061820 -0.00118734 0.32863661
0.00061996 0.99999870 0.00147816 -0.39729401
0.00118642 -0.00147889 0.99999819 0.01872346
Axis -0.74130553 -0.59507988 0.31039659
Axis point 0.00000000 12.62417467 269.34575869
Rotation angle (degrees) 0.11427582
Shift along axis -0.00138677
> select subtract #3
2 models selected
> select subtract #10
Nothing selected
> hide #!1 models
> hide #!10 models
> select #2/A
6395 atoms, 6463 bonds, 2 pseudobonds, 410 residues, 2 models selected
> ui tool show "Color Actions"
> hide #!3 models
> select #2/C:443
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 4 residues, 1 model selected
> select up
2376 atoms, 2407 bonds, 158 residues, 1 model selected
> select up
2424 atoms, 2455 bonds, 162 residues, 1 model selected
> color sel thistle target cs
> hide #!2 models
> show #!3 models
> select #3/A:28
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
212 atoms, 214 bonds, 26 residues, 1 model selected
> select up
2526 atoms, 2592 bonds, 320 residues, 1 model selected
> select up
2555 atoms, 2618 bonds, 323 residues, 1 model selected
> select down
2526 atoms, 2592 bonds, 320 residues, 1 model selected
> select down
212 atoms, 214 bonds, 26 residues, 1 model selected
> select clear
> show #!2 models
> hide #!3 models
> select #2/B#3/B
13053 atoms, 12526 bonds, 8 pseudobonds, 1886 residues, 4 models selected
> color sel dark red target cs
> select clear
> select #2/D:745
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
208 atoms, 207 bonds, 15 residues, 1 model selected
> select up
3079 atoms, 3115 bonds, 206 residues, 1 model selected
> color sel dark red target cs
> select clear
[Repeated 1 time(s)]
> select #2/A:397
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 5 residues, 1 model selected
> select up
2401 atoms, 2432 bonds, 158 residues, 1 model selected
> color sel orchid target cs
> color sel thistle target cs
> select clear
> select #2/D:468
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
111 atoms, 111 bonds, 7 residues, 1 model selected
> select up
2406 atoms, 2437 bonds, 158 residues, 1 model selected
> color sel dark red target cs
> select clear
> select #2/H:26
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
322 atoms, 323 bonds, 22 residues, 1 model selected
> select up
1045 atoms, 1058 bonds, 68 residues, 1 model selected
> select up
1057 atoms, 1069 bonds, 69 residues, 1 model selected
> select up
2138 atoms, 2161 bonds, 139 residues, 1 model selected
> select up
2734 atoms, 2767 bonds, 177 residues, 1 model selected
> color sel light green target cs
> select clear
> select #2/G:27
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
322 atoms, 323 bonds, 22 residues, 1 model selected
> select up
1045 atoms, 1058 bonds, 68 residues, 1 model selected
> select up
1057 atoms, 1069 bonds, 69 residues, 1 model selected
> select up
2138 atoms, 2161 bonds, 139 residues, 1 model selected
> color sel light green target cs
> select clear
> select #2/F:100
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
183 atoms, 184 bonds, 11 residues, 1 model selected
> select up
1093 atoms, 1103 bonds, 71 residues, 1 model selected
> select up
1873 atoms, 1895 bonds, 121 residues, 1 model selected
> color sel medium sea green target cs
> select clear
[Repeated 1 time(s)]
> select #2/F:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
346 atoms, 347 bonds, 23 residues, 1 model selected
> select up
1067 atoms, 1080 bonds, 69 residues, 1 model selected
> select up
1079 atoms, 1091 bonds, 70 residues, 1 model selected
> select up
2160 atoms, 2183 bonds, 140 residues, 1 model selected
> color sel cadet blue target cs
> select clear
> select #2/F:179
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
511 atoms, 519 bonds, 31 residues, 1 model selected
> select up
596 atoms, 606 bonds, 38 residues, 1 model selected
> color sel cadet blue target cs
> select clear
> select #2/E:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
322 atoms, 323 bonds, 22 residues, 1 model selected
> select up
1067 atoms, 1080 bonds, 69 residues, 1 model selected
> select up
2744 atoms, 2777 bonds, 177 residues, 1 model selected
> color sel cadet blue target cs
> select clear
> select #2/D:816
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
389 atoms, 392 bonds, 26 residues, 1 model selected
> color sel dark red target cs
> select clear
[Repeated 2 time(s)]
> select #2/G:188
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
603 atoms, 612 bonds, 39 residues, 1 model selected
> select up
1689 atoms, 1709 bonds, 109 residues, 1 model selected
> color sel pale green target cs
> select clear
> show #!1 models
> color #1 #b2b2b266 models
> show #!10 models
> color #10 #cccc996f models
> show #!3 models
> ui tool show "Side View"
> volume #10 level 0.04129
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback
_color_callback(*args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 134, in _color_changed_cb
self.color_changed.emit(self._color)
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
Populating font family aliases took 332 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 134, in _color_changed_cb
self.color_changed.emit(self._color)
See log for complete Python traceback.
> volume #10 color #cccc9941
> volume #10 color #cccc9942
> show surfaces
> hide cartoons
> hide surfaces
> show cartoons
> save /Users/ig/Documents/Danyang/GluA1/Figs/Fig3C_splay_Composite_side.cxs
——— End of log from Sat Dec 3 20:11:09 2022 ———
opened ChimeraX session
Populating font family aliases took 347 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: 11 days 1:00
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 (2)
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 |
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