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Opened 2 years ago
Closed 2 years ago
#9829 closed defect (duplicate)
XMAS: crash in ~QGridLayout()
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700016775000 (most recent call first):
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700015772000 (most recent call first):
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700013d60000 (most recent call first):
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000011a124dc0 (most recent call first):
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [19878]
Path: /Volumes/*/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [19878]
User ID: 505
Date/Time: 2023-09-22 15:13:21.039 +0200
OS Version: Mac OS X 10.15.7 (19H15)
Report Version: 12
Bridge OS Version: 5.0.1 (18P2561)
Anonymous UUID: 1C80D7C0-D9D6-B7E4-ABEB-8C57BCD37ACF
Sleep/Wake UUID: CF6441C9-2BAA-437D-ABA0-8B42B28E9D0D
Time Awake Since Boot: 16000 seconds
Time Since Wake: 6800 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6dca833a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6dd64e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6dbbf93e raise + 26
3 libsystem_platform.dylib 0x00007fff6dd595fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtWidgets 0x00000001242f56d7 QGridLayout::~QGridLayout() + 39
6 QtWidgets.abi3.so 0x0000000123d65f18 non-virtual thunk to sipQGridLayout::~sipQGridLayout() + 56
7 QtWidgets 0x00000001242d28c0 QBoxLayout::~QBoxLayout() + 176
8 QtWidgets.abi3.so 0x0000000123dd9d57 sipQVBoxLayout::~sipQVBoxLayout() + 55
9 QtWidgets 0x000000012430629a QWidget::~QWidget() + 634
10 QtWidgets.abi3.so 0x0000000123df7537 sipQWidget::~sipQWidget() + 55
11 QtCore 0x00000001196e889f QObjectPrivate::deleteChildren() + 159
12 QtWidgets 0x0000000124306520 QWidget::~QWidget() + 1280
13 QtWidgets.abi3.so 0x0000000123df7537 sipQWidget::~sipQWidget() + 55
14 QtCore 0x00000001196e889f QObjectPrivate::deleteChildren() + 159
15 QtWidgets 0x0000000124306520 QWidget::~QWidget() + 1280
16 QtWidgets.abi3.so 0x0000000123dab9e7 sipQDockWidget::~sipQDockWidget() + 55
17 QtCore 0x00000001196e9770 QObject::event(QEvent*) + 784
18 QtWidgets 0x0000000124317f3a QWidget::event(QEvent*) + 4330
19 QtWidgets 0x0000000124430df7 QDockWidget::event(QEvent*) + 775
20 QtWidgets.abi3.so 0x0000000123dac0df sipQDockWidget::event(QEvent*) + 191
21 QtWidgets 0x00000001242c4a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
22 QtWidgets 0x00000001242c5a43 QApplication::notify(QObject*, QEvent*) + 499
23 QtWidgets.abi3.so 0x0000000123de41e6 sipQApplication::notify(QObject*, QEvent*) + 230
24 QtCore 0x00000001196a0c3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
25 QtCore 0x00000001196a1d52 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 802
26 libqcocoa.dylib 0x0000000130beeb8b 0x130bd5000 + 105355
27 libqcocoa.dylib 0x0000000130bef29b 0x130bd5000 + 107163
28 com.apple.CoreFoundation 0x00007fff33c88d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
29 com.apple.CoreFoundation 0x00007fff33c88cf1 __CFRunLoopDoSource0 + 103
30 com.apple.CoreFoundation 0x00007fff33c88b0b __CFRunLoopDoSources0 + 209
31 com.apple.CoreFoundation 0x00007fff33c8783a __CFRunLoopRun + 927
32 com.apple.CoreFoundation 0x00007fff33c86e3e CFRunLoopRunSpecific + 462
33 com.apple.HIToolbox 0x00007fff328b3abd RunCurrentEventLoopInMode + 292
34 com.apple.HIToolbox 0x00007fff328b37d5 ReceiveNextEventCommon + 584
35 com.apple.HIToolbox 0x00007fff328b3579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
36 com.apple.AppKit 0x00007fff30ef9039 _DPSNextEvent + 883
37 com.apple.AppKit 0x00007fff30ef7880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
38 com.apple.AppKit 0x00007fff30ee958e -[NSApplication run] + 658
39 libqcocoa.dylib 0x0000000130bee0ac 0x130bd5000 + 102572
40 QtCore 0x00000001196aa326 QEventLoop::exec(QFlags) + 486
41 QtCore 0x00000001196a1235 QCoreApplication::exec() + 133
42 QtWidgets.abi3.so 0x0000000123ed0d9a meth_QApplication_exec(_object*, _object*) + 90
43 org.python.python 0x000000010be1171d cfunction_call + 125
44 org.python.python 0x000000010bdd25b7 _PyObject_MakeTpCall + 359
45 org.python.python 0x000000010beaae9c call_function + 876
46 org.python.python 0x000000010bea82a2 _PyEval_EvalFrameDefault + 25554
47 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
48 org.python.python 0x000000010bdd4d6a method_vectorcall + 202
49 org.python.python 0x000000010beaae0c call_function + 732
50 org.python.python 0x000000010bea82a2 _PyEval_EvalFrameDefault + 25554
51 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
52 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
53 org.python.python 0x000000010beaae0c call_function + 732
54 org.python.python 0x000000010bea834b _PyEval_EvalFrameDefault + 25723
55 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
56 org.python.python 0x000000010bea1dab PyEval_EvalCode + 139
57 org.python.python 0x000000010be9ec12 builtin_exec + 626
58 org.python.python 0x000000010be11023 cfunction_vectorcall_FASTCALL + 195
59 org.python.python 0x000000010beaae0c call_function + 732
60 org.python.python 0x000000010bea834b _PyEval_EvalFrameDefault + 25723
61 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
62 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
63 org.python.python 0x000000010beaae0c call_function + 732
64 org.python.python 0x000000010bea834b _PyEval_EvalFrameDefault + 25723
65 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
66 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
67 org.python.python 0x000000010bf11870 pymain_run_module + 208
68 org.python.python 0x000000010bf10f87 Py_RunMain + 1431
69 org.python.python 0x000000010bf1158f pymain_main + 223
70 org.python.python 0x000000010bf1149b Py_Main + 43
71 edu.ucsf.cgl.ChimeraX 0x000000010bd8bdc8 main + 120
72 libdyld.dylib 0x00007fff6db60cc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6dcaab96 kevent64 + 10
1 QtWebEngineCore 0x0000000129340a2a 0x1253e0000 + 66456106
2 QtWebEngineCore 0x0000000129340927 0x1253e0000 + 66455847
3 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
4 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
5 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
6 QtWebEngineCore 0x00000001292c72ad 0x1253e0000 + 65958573
7 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
8 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 2:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d426c 0x1253e0000 + 66011756
5 QtWebEngineCore 0x00000001292d3e6d 0x1253e0000 + 66010733
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 3:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d426c 0x1253e0000 + 66011756
5 QtWebEngineCore 0x00000001292d3ddd 0x1253e0000 + 66010589
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 4:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6dcaab96 kevent64 + 10
1 QtWebEngineCore 0x0000000129340a2a 0x1253e0000 + 66456106
2 QtWebEngineCore 0x0000000129340927 0x1253e0000 + 66455847
3 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
4 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
5 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
6 QtWebEngineCore 0x00000001282053a2 0x1253e0000 + 48386978
7 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
8 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x000000012930ebef 0x1253e0000 + 66251759
4 QtWebEngineCore 0x00000001292441c9 0x1253e0000 + 65421769
5 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
6 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
7 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
8 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
9 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 6:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d426c 0x1253e0000 + 66011756
5 QtWebEngineCore 0x00000001292d3e6d 0x1253e0000 + 66010733
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 7:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000129306d1b 0x1253e0000 + 66219291
3 QtWebEngineCore 0x000000012b3d492d 0x1253e0000 + 100616493
4 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
5 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 8:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x0000000129244168 0x1253e0000 + 65421672
4 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
5 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
6 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
7 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
8 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 9:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6dcaab96 kevent64 + 10
1 QtWebEngineCore 0x0000000129340a2a 0x1253e0000 + 66456106
2 QtWebEngineCore 0x0000000129340927 0x1253e0000 + 66455847
3 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
4 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
5 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
6 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
7 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
8 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x000000012930ebef 0x1253e0000 + 66251759
4 QtWebEngineCore 0x00000001292441c9 0x1253e0000 + 65421769
5 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
6 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
7 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
8 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
9 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 11:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x0000000129244168 0x1253e0000 + 65421672
4 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
5 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
6 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
7 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
8 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 12:: NetworkService
0 libsystem_kernel.dylib 0x00007fff6dcaab96 kevent64 + 10
1 QtWebEngineCore 0x0000000129340a2a 0x1253e0000 + 66456106
2 QtWebEngineCore 0x0000000129340927 0x1253e0000 + 66455847
3 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
4 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
5 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
6 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
7 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
8 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x000000012930ebef 0x1253e0000 + 66251759
4 QtWebEngineCore 0x00000001292441c9 0x1253e0000 + 65421769
5 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
6 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
7 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
8 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
9 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d426c 0x1253e0000 + 66011756
5 QtWebEngineCore 0x00000001292d3ecd 0x1253e0000 + 66010829
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x000000012930ebef 0x1253e0000 + 66251759
4 QtWebEngineCore 0x00000001292441c9 0x1253e0000 + 65421769
5 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
6 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
7 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
8 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
9 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 16:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000140a09e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 24:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff33c88ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff33c879c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff33c86e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff3109a954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 25:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d426c 0x1253e0000 + 66011756
5 QtWebEngineCore 0x00000001292d3ddd 0x1253e0000 + 66010589
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 26:
0 libsystem_pthread.dylib 0x00007fff6dd60b68 start_wqthread + 0
Thread 27:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x000000012930ebef 0x1253e0000 + 66251759
4 QtWebEngineCore 0x00000001292441c9 0x1253e0000 + 65421769
5 QtWebEngineCore 0x00000001292bda5c 0x1253e0000 + 65919580
6 QtWebEngineCore 0x0000000129275998 0x1253e0000 + 65624472
7 QtWebEngineCore 0x00000001292dfeb8 0x1253e0000 + 66059960
8 QtWebEngineCore 0x00000001292e004a 0x1253e0000 + 66060362
9 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 28:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6dca1dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6dca2170 mach_msg + 60
2 QtWebEngineCore 0x000000012930ee26 0x1253e0000 + 66252326
3 QtWebEngineCore 0x00000001292d37bf 0x1253e0000 + 66009023
4 QtWebEngineCore 0x00000001292d3f9a 0x1253e0000 + 66011034
5 QtWebEngineCore 0x00000001292d3e0d 0x1253e0000 + 66010637
6 QtWebEngineCore 0x0000000129307908 0x1253e0000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 29:
0 libsystem_pthread.dylib 0x00007fff6dd60b68 start_wqthread + 0
Thread 30:
0 libsystem_pthread.dylib 0x00007fff6dd60b68 start_wqthread + 0
Thread 31:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 org.python.python 0x000000010bf0179c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010bf5069f acquire_timed + 111
4 org.python.python 0x000000010bf507b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010bddb14e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x000000010beaae0c call_function + 732
7 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010beaae0c call_function + 732
11 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010beaae0c call_function + 732
15 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
17 org.python.python 0x000000010beaae0c call_function + 732
18 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
20 org.python.python 0x000000010beaae0c call_function + 732
21 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
23 org.python.python 0x000000010bdd4db2 method_vectorcall + 274
24 org.python.python 0x000000010bf50046 t_bootstrap + 70
25 org.python.python 0x000000010bf012f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 32:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 org.python.python 0x000000010bf0179c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010bf5069f acquire_timed + 111
4 org.python.python 0x000000010bf507b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010bddb14e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x000000010beaae0c call_function + 732
7 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010beaae0c call_function + 732
11 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010beaae0c call_function + 732
15 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
17 org.python.python 0x000000010beaae0c call_function + 732
18 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
20 org.python.python 0x000000010beaae0c call_function + 732
21 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
23 org.python.python 0x000000010bdd4db2 method_vectorcall + 274
24 org.python.python 0x000000010bf50046 t_bootstrap + 70
25 org.python.python 0x000000010bf012f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 33:
0 libsystem_kernel.dylib 0x00007fff6dca4882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6dd65425 _pthread_cond_wait + 698
2 org.python.python 0x000000010bf0179c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010bf5069f acquire_timed + 111
4 org.python.python 0x000000010bf507b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010bddb14e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x000000010beaae0c call_function + 732
7 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010beaae0c call_function + 732
11 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x000000010beabb03 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010bdd2cb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010beaae0c call_function + 732
15 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
17 org.python.python 0x000000010beaae0c call_function + 732
18 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
20 org.python.python 0x000000010beaae0c call_function + 732
21 org.python.python 0x000000010bea827e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x000000010bdd2d28 function_code_fastcall + 104
23 org.python.python 0x000000010bdd4db2 method_vectorcall + 274
24 org.python.python 0x000000010bf50046 t_bootstrap + 70
25 org.python.python 0x000000010bf012f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff6dd65109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6dd60b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011a124dc0 rcx: 0x00007f896014fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007f896014fa80 rsp: 0x00007f896014fa58
r8: 0x00007f896014ff48 r9: 0xc77898e2648e8702 r10: 0x000000011a124dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6dca833a rfl: 0x0000000000000246 cr2: 0x000000010bffc7b8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff5f7c8000 - 0x7fff5f845fff com.apple.Quagga (1.0 - 1) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga
0x7fff5f8a0000 - 0x7fff5f8a3ff4 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff5f8a4000 - 0x7fff5f8c7ff0 com.apple.quicklook.QuickLookSupport (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x7fff5f90e000 - 0x7fff5f987ff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff5fbee000 - 0x7fff5fc17ff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x7fff5fc9b000 - 0x7fff5fce5ffa com.apple.ResponseKit (1.0 - 148.2) /System/Library/PrivateFrameworks/ResponseKit.framework/Versions/A/ResponseKit
0x7fff5fd7c000 - 0x7fff5fdb7ff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff61698000 - 0x7fff6169bff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff6180e000 - 0x7fff61935fff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff619ad000 - 0x7fff619cdff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff619ce000 - 0x7fff619e0ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff62d4a000 - 0x7fff63040ff7 com.apple.SkyLight (1.600.0 - 451.4) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff6388d000 - 0x7fff6389bffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff6395d000 - 0x7fff63be9ffe com.apple.spotlight.index (10.7.0 - 2076.7) /System/Library/PrivateFrameworks/SpotlightIndex.framework/Versions/A/SpotlightIndex
0x7fff63f77000 - 0x7fff63fb8ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff640cf000 - 0x7fff640d8ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.1) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff64149000 - 0x7fff64173ffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff6438f000 - 0x7fff6439fff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff64746000 - 0x7fff648a1ff5 com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff648c4000 - 0x7fff6498aff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff64b21000 - 0x7fff64b22fff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff64b5a000 - 0x7fff64db2ff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff64e49000 - 0x7fff64e4fffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff65a28000 - 0x7fff65a48ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff667f4000 - 0x7fff668deff8 com.apple.ViewBridge (464.1 - 464.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff66a84000 - 0x7fff66a85fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff66e14000 - 0x7fff66e4ffff libAWDSupport.dylib (949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupport.dylib
0x7fff66e50000 - 0x7fff67130ff7 libAWDSupportFramework.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupportFramework.dylib
0x7fff67131000 - 0x7fff67142fff libprotobuf-lite.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf-lite.dylib
0x7fff67143000 - 0x7fff6719cffb libprotobuf.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf.dylib
0x7fff6719d000 - 0x7fff671e1ff6 com.apple.awd (1.0 - 949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/WirelessDiagnostics
0x7fff676b5000 - 0x7fff676b8ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff67732000 - 0x7fff67740ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff67908000 - 0x7fff6793dffe com.apple.iCalendar (7.0 - 810.6.1) /System/Library/PrivateFrameworks/iCalendar.framework/Versions/A/iCalendar
0x7fff67a82000 - 0x7fff67a84ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff67a85000 - 0x7fff67a98ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff67aca000 - 0x7fff67ad6ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff67ad7000 - 0x7fff67b08ffd com.apple.contacts.vCard (1.0 - 3455.18) /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
0x7fff6a55b000 - 0x7fff6a567ff9 libAudioStatistics.dylib (1104.93) /usr/lib/libAudioStatistics.dylib
0x7fff6a568000 - 0x7fff6a59bffa libAudioToolboxUtility.dylib (1104.93) /usr/lib/libAudioToolboxUtility.dylib
0x7fff6a5a2000 - 0x7fff6a5d6fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff6a5d9000 - 0x7fff6a5e3fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff6a5e4000 - 0x7fff6a66cfff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib
0x7fff6a66f000 - 0x7fff6a671ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff6a6b7000 - 0x7fff6a86effb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff6a895000 - 0x7fff6a89bff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff6a97d000 - 0x7fff6a984fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff6a9b3000 - 0x7fff6a9d3ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff6aa53000 - 0x7fff6ab30ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff6ab45000 - 0x7fff6ab46fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff6ab47000 - 0x7fff6abd2ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff6abd3000 - 0x7fff6abd4fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff6abec000 - 0x7fff6ac02fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff6ac37000 - 0x7fff6aca9ff7 libarchive.2.dylib (72.140.1) /usr/lib/libarchive.2.dylib
0x7fff6acaa000 - 0x7fff6ad43fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff6ad47000 - 0x7fff6ad47ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff6ad48000 - 0x7fff6ae0cffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff6ae0d000 - 0x7fff6ae1dffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff6ae1e000 - 0x7fff6ae2afff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff6ae2b000 - 0x7fff6ae7dfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6ae7e000 - 0x7fff6ae93ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff6ae94000 - 0x7fff6ae94fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff6ae95000 - 0x7fff6aea6fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff6aea7000 - 0x7fff6aebefd7 libcompression.dylib (87) /usr/lib/libcompression.dylib
0x7fff6b198000 - 0x7fff6b1aeff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6b1af000 - 0x7fff6b1b0fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff6b653000 - 0x7fff6b757fef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib
0x7fff6b75a000 - 0x7fff6b765fff libcsfde.dylib (551) /usr/lib/libcsfde.dylib
0x7fff6b76d000 - 0x7fff6b7ccff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib
0x7fff6b7ce000 - 0x7fff6b833ff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib
0x7fff6b8d6000 - 0x7fff6b8d6fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6b8d7000 - 0x7fff6b8effff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib
0x7fff6b8f0000 - 0x7fff6b8fcffb libexslt.0.dylib (16.9) /usr/lib/libexslt.0.dylib
0x7fff6b8fd000 - 0x7fff6b8fffff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6b900000 - 0x7fff6b905f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff6b90e000 - 0x7fff6b913fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6b914000 - 0x7fff6b91dff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6b91e000 - 0x7fff6ba0efff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6ba0f000 - 0x7fff6bc66fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6bc80000 - 0x7fff6bc81fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6bc82000 - 0x7fff6bc9aff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6bcb2000 - 0x7fff6bd59ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6bd5a000 - 0x7fff6bfbcff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6c329000 - 0x7fff6c358fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6c488000 - 0x7fff6c904ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6c905000 - 0x7fff6c91cfff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6c9a5000 - 0x7fff6c9d8fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6c9d9000 - 0x7fff6c9daff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6c9eb000 - 0x7fff6c9effff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6c9f2000 - 0x7fff6ca28ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff6ca68000 - 0x7fff6ca76ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6ca77000 - 0x7fff6ca7aff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib
0x7fff6ca7b000 - 0x7fff6ca7dfff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib
0x7fff6caac000 - 0x7fff6cac4fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6cac6000 - 0x7fff6cb0aff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff6cb0b000 - 0x7fff6cb1dff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6cb1e000 - 0x7fff6cb1fff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6cb20000 - 0x7fff6cd0aff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff6cdfe000 - 0x7fff6ce2bffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff6cead000 - 0x7fff6cedeff7 libtidy.A.dylib (17.2) /usr/lib/libtidy.A.dylib
0x7fff6cf00000 - 0x7fff6cf5aff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff6cf5b000 - 0x7fff6cf5effb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6cf5f000 - 0x7fff6cf6cff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff6cf72000 - 0x7fff6d054fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff6d058000 - 0x7fff6d080fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff6d081000 - 0x7fff6d093ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6d942000 - 0x7fff6d947ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6d948000 - 0x7fff6d953fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6d954000 - 0x7fff6d95bfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6d95c000 - 0x7fff6d965ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6d966000 - 0x7fff6d9f8fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff6db05000 - 0x7fff6db45ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6db46000 - 0x7fff6db7cfff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff6db7d000 - 0x7fff6db7dffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6db7e000 - 0x7fff6db8aff3 libkxld.dylib (6153.141.2.2) /usr/lib/system/libkxld.dylib
0x7fff6db8b000 - 0x7fff6db8bff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff6db8c000 - 0x7fff6db91ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6db92000 - 0x7fff6db94ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff6db95000 - 0x7fff6db96ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6db97000 - 0x7fff6dbaeff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff6dbaf000 - 0x7fff6dbafff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6dbb0000 - 0x7fff6dc37fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff6dc38000 - 0x7fff6dc3bffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff6dc3c000 - 0x7fff6dc3ffff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6dc40000 - 0x7fff6dc48fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff6dc49000 - 0x7fff6dc50fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6dc51000 - 0x7fff6dc52ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6dc53000 - 0x7fff6dca0ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff6dca1000 - 0x7fff6dccdff7 libsystem_kernel.dylib (6153.141.2.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff6dcce000 - 0x7fff6dd15fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6dd16000 - 0x7fff6dd3dfff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6dd3e000 - 0x7fff6dd4bffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6dd4c000 - 0x7fff6dd55ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6dd56000 - 0x7fff6dd5efef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6dd5f000 - 0x7fff6dd69fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6dd6a000 - 0x7fff6dd6eff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6dd6f000 - 0x7fff6dd71fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6dd72000 - 0x7fff6dd79ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6dd7a000 - 0x7fff6dd90ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff6dd92000 - 0x7fff6dd97ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6dd98000 - 0x7fff6ddcdffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 2
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: 17989
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=6.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 1160K 2
CG image 288K 19
CoreAnimation 216K 20
CoreGraphics 8K 1
CoreImage 24K 2
CoreUI image data 2264K 23
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 3.5G 203
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 1.5G 15 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 132K 33
Stack 206.3M 34
Stack Guard 56.0M 1
VM_ALLOCATE 179.5M 700
VM_ALLOCATE (reserved) 384.0M 4 reserved VM address space (unallocated)
__DATA 82.2M 769
__DATA_CONST 160K 8
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 439.3M 410
__OBJC_RO 32.3M 1
__OBJC_RW 1904K 1
__TEXT 755.0M 717
__UNICODE 564K 1
mapped file 96.5M 57
shared memory 2840K 23
=========== ======= =======
TOTAL 7.5G 3068
TOTAL, minus reserved VM space 5.3G 3068
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
Log from Thu May 25 15:31:21 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
Log from Wed May 24 18:16:07 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/pool-mueller-
> group/Elena/Alphafold/230404-PRC1-scml2/output/Scml2-PRC1/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open /Volumes/pool-mueller-
> group/Elena/Alphafold/230404-PRC1-scml2/output/Scml2-PRC1/ranked_1.pdb
Chain information for ranked_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open /Volumes/pool-mueller-
> group/Elena/Alphafold/230404-PRC1-scml2/output/Scml2-PRC1/ranked_2.pdb
Chain information for ranked_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> mmaker #2-3 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 3483.8
RMSD between 215 pruned atom pairs is 0.328 angstroms; (across all 700 pairs:
57.000)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
sequence alignment score = 3521.6
RMSD between 175 pruned atom pairs is 0.188 angstroms; (across all 700 pairs:
70.832)
> hide #2 models
> hide #3 models
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks.txt
Unique peptide pairs: 221 out of 221
Unique peptide pairs with pseudobonds: 207
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_1.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_1.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks.txt
Unique peptide pairs: 206 out of 206
Unique peptide pairs with pseudobonds: 196
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_1.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_1.tsv
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/scml2-only-overlap.pb
> hide #4 models
> hide #5 models
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks.txt
Unique peptide pairs: 221 out of 221
Unique peptide pairs with pseudobonds: 207
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_2.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_2.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks.txt
Unique peptide pairs: 206 out of 206
Unique peptide pairs with pseudobonds: 196
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_2.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_2.tsv
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/scml2-only-overlap_model1.pb
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> show #2 models
> hide #1 models
> show #9 models
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks.txt
Unique peptide pairs: 221 out of 221
Unique peptide pairs with pseudobonds: 207
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_3.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_3.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks.txt
Unique peptide pairs: 206 out of 206
Unique peptide pairs with pseudobonds: 196
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_3.pb
Mapping information is stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_3.tsv
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/scml2-only-overlap_model2.pb
> hide #2 models
> show #3 models
> hide #9 models
> hide #10 models
> hide #11 models
> save /Users/elena/Desktop/thesis/AF-scml2-models-xlms.cxs
/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
> select subtract #9
220 pseudobonds, 2 models selected
> select subtract #12
110 pseudobonds, 1 model selected
Pseudobonds are stored in
/Users/elena/Desktop/thesis/figures/xlms/scml2/model0-under35.pb
> hide #13 models
> hide #12 models
> hide #3 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> show #13 models
> select subtract #12
Nothing selected
> show #1 models
Pseudobonds are stored in
/Users/elena/Desktop/thesis/figures/xlms/scml2/model1-under35.pb
> hide #1 models
> show #2 models
> hide #13 models
> show #1 models
> hide #2 models
> hide #1 models
Pseudobonds are stored in
/Users/elena/Desktop/thesis/figures/xlms/scml2/model2-under35.pb
> show #3 models
> hide #14 models
> show #2 models
> mmaker #2-3 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 3483.8
RMSD between 215 pruned atom pairs is 0.328 angstroms; (across all 700 pairs:
57.000)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
sequence alignment score = 3521.6
RMSD between 175 pruned atom pairs is 0.188 angstroms; (across all 700 pairs:
70.832)
> show #14 models
> save /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:700
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A
10825 atoms, 10955 bonds, 140 pseudobonds, 700 residues, 5 models selected
> mmaker #2-3 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain B (#1) with ranked_1.pdb, chain B (#2),
sequence alignment score = 1652.5
RMSD between 209 pruned atom pairs is 0.643 angstroms; (across all 329 pairs:
35.838)
Matchmaker ranked_0.pdb, chain B (#1) with ranked_2.pdb, chain B (#3),
sequence alignment score = 1668.7
RMSD between 209 pruned atom pairs is 0.621 angstroms; (across all 329 pairs:
37.248)
> ui tool show "Color Actions"
> color sel dark blue
> color sel navy
> set bgColor white
> ui tool show "Color Actions"
> color sel midnight blue
[Repeated 2 time(s)]
> select #1/A:700
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A
10825 atoms, 10955 bonds, 142 pseudobonds, 700 residues, 5 models selected
> ui tool show "Color Actions"
> color sel midnight blue
> select #2/A:700
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A
10825 atoms, 10955 bonds, 142 pseudobonds, 700 residues, 5 models selected
> ui tool show "Color Actions"
> color sel midnight blue
> hide #2 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:329
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #1/B
5197 atoms, 5251 bonds, 13 pseudobonds, 329 residues, 5 models selected
> ui tool show "Color Actions"
> color sel khaki
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:329
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/B
5197 atoms, 5251 bonds, 13 pseudobonds, 329 residues, 5 models selected
> ui tool show "Color Actions"
> color sel khaki
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:329
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #3/B
5197 atoms, 5251 bonds, 13 pseudobonds, 329 residues, 5 models selected
> ui tool show "Color Actions"
> color sel khaki
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #1/C
5277 atoms, 5320 bonds, 32 pseudobonds, 340 residues, 5 models selected
> color (#1 & sel) light sea green
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/C
5277 atoms, 5320 bonds, 32 pseudobonds, 340 residues, 5 models selected
No visible atoms, bonds, or surfaces selected
> select #2/C:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/C
5277 atoms, 5320 bonds, 32 pseudobonds, 340 residues, 5 models selected
No visible atoms, bonds, or surfaces selected
> ui tool show "Show Sequence Viewer"
> show #2 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #2/C
5277 atoms, 5320 bonds, 32 pseudobonds, 340 residues, 5 models selected
> color (#2 & sel) light sea green
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> select #3/C:340
23 atoms, 22 bonds, 1 residue, 1 model selected
> select #3/C
5277 atoms, 5320 bonds, 32 pseudobonds, 340 residues, 5 models selected
> color (#3 & sel) light sea green
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #2/D
Alignment identifier is 2/D
> sequence chain #3/D
Alignment identifier is 3/D
> select #1/D:323
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/D
5016 atoms, 5064 bonds, 107 pseudobonds, 323 residues, 5 models selected
> ui tool show "Color Actions"
> color sel violet
> color sel plum
> select #3/D:270-323
852 atoms, 856 bonds, 4 pseudobonds, 54 residues, 5 models selected
> select #3/D
5014 atoms, 5062 bonds, 108 pseudobonds, 323 residues, 5 models selected
> ui tool show "Color Actions"
> color sel plum
> select #2/D:322-323
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #2/D
5014 atoms, 5062 bonds, 113 pseudobonds, 323 residues, 5 models selected
> ui tool show "Color Actions"
> color sel plum
> save /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
——— End of log from Wed May 24 18:16:07 2023 ———
opened ChimeraX session
> hide #3 models
> hide #2 models
> lighting flat
> hide #15 models
> hide #14 models
> save /Users/elena/Desktop/image83.png supersample 3
> select add #1
31329 atoms, 31652 bonds, 534 pseudobonds, 2015 residues, 6 models selected
> select add #2
52628 atoms, 53178 bonds, 1072 pseudobonds, 3384 residues, 10 models selected
> turn y -160
> select clear
> turn y -180
> turn y -90
> turn y -70
> turn y -90
> turn y -80
> turn y 80
> turn y -80
> turn y -900
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> save /Users/elena/Desktop/image84.png supersample 3
> turn y -90
> turn y 90
> turn y -100
> save /Users/elena/Desktop/image79.png supersample 3
> turn y -100
> undo
[Repeated 1 time(s)]
> turn y -90
> turn y -120
> turn y 90
> save /Users/elena/Desktop/image80.png supersample 3
> turn y 90
> save /Users/elena/Desktop/image81.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:700
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A
10825 atoms, 10955 bonds, 142 pseudobonds, 700 residues, 5 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> save /Users/elena/Desktop/image82.png supersample 3
> turn y -90
> save /Users/elena/Desktop/image83.png supersample 3
> save /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select #1/A:361
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:361-435
1151 atoms, 1165 bonds, 75 residues, 1 model selected
> turn y 90
> undo
> select clear
Pseudobonds are stored in
/Users/elena/Desktop/thesis/figures/xlms/scml2/model1 5-25.pb
Pseudobonds are stored in
/Users/elena/Desktop/thesis/figures/xlms/scml2/model1 25-35.pb
> hide #16 models
> hide #17 models
> show #17 models
> select clear
[Repeated 1 time(s)]
> show #16 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B
5197 atoms, 5251 bonds, 15 pseudobonds, 329 residues, 6 models selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select clear
> hide #17 models
> hide #16 models
> hide #17 models
> hide #16 models
> save /Users/elena/Desktop/image84.png supersample 3
> turn y -90
> turn y 90
> save /Users/elena/Desktop/image85.png supersample 3
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> hide #16 models
> save /Users/elena/Desktop/image86.png supersample 3
> turn y 90
> save /Users/elena/Desktop/image87.png supersample 3
> select clear
> save /Users/elena/Desktop/thesis/figures/xlms/scml2/AF-Scml2-XLMS.cxs
——— End of log from Thu May 25 15:31:21 2023 ———
opened ChimeraX session
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/1oi1.cif
1oi1.cif title:
Crystal Structure of the MBT domains of Human SCML2 [more info...]
Chain information for 1oi1.cif #18
---
Chain | Description | UniProt
A | SCML2 PROTEIN | Q9UQR0
Non-standard residues in 1oi1.cif #18
---
PEG — di(hydroxyethyl)ether
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/2ckl.cif
2ckl.cif title:
Ring1b-Bmi1 E3 catalytic domain structure [more info...]
Chain information for 2ckl.cif #19
---
Chain | Description | UniProt
A | POLYCOMB GROUP RING FINGER PROTEIN 4 | PCGF4_MOUSE
B | UBIQUITIN LIGASE PROTEIN RING2 | RING2_MOUSE
Non-standard residues in 2ckl.cif #19
---
IOD — iodide ion
ZN — zinc ion
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/2l8e.pdb
2l8e.pdb title:
Solution NMR structure of FCS domain of human polyhomeotic homolog 1 (HPH1)
[more info...]
Chain information for 2l8e.pdb
---
Chain | Description | UniProt
20.1/A 20.2/A 20.3/A 20.4/A 20.5/A 20.6/A 20.7/A 20.8/A 20.9/A 20.10/A 20.11/A
20.12/A 20.13/A 20.14/A 20.15/A 20.16/A 20.17/A 20.18/A 20.19/A 20.20/A |
polyhomeotic-like protein 1 | PHC1_HUMAN
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/2mem.cif
2mem.cif title:
Solution NMR structure of SLED domain of Scml2 [more info...]
Chain information for 2mem.cif
---
Chain | Description | UniProt
21.1/A 21.2/A 21.3/A 21.4/A 21.5/A 21.6/A 21.7/A 21.8/A 21.9/A 21.10/A 21.11/A
21.12/A 21.13/A 21.14/A 21.15/A 21.16/A 21.17/A 21.18/A 21.19/A 21.20/A | Sex
comb on midleg-like protein 2 | SCML2_HUMAN
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/3gs2-2.cif
3gs2-2.cif title:
Ring1B C-terminal domain/Cbx7 Cbox Complex [more info...]
Chain information for 3gs2-2.cif #22
---
Chain | Description | UniProt
A C | E3 ubiquitin-protein ligase RING2 | RING2_HUMAN
B D | Chromobox protein homolog 7 | CBX7_HUMAN
Non-standard residues in 3gs2-2.cif #22
---
SO4 — sulfate ion
ZN — zinc ion
3gs2-2.cif mmCIF Assemblies
---
1| software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/4edu.cif
4edu.cif title:
The MBT repeats of human SCML2 in a complex with histone H2A peptide [more
info...]
Chain information for 4edu.cif #23
---
Chain | Description | UniProt
A | Sex comb on midleg-like protein 2 | SCML2_HUMAN
T | Histone H2A.J peptide | H2AJ_HUMAN
Non-standard residues in 4edu.cif #23
---
MLZ — N-methyl-lysine
4edu.cif mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/4pzn.pdb
4pzn.pdb title:
Crystal structure of PHC3 sam L971E [more info...]
Chain information for 4pzn.pdb #24
---
Chain | Description | UniProt
A B C D E | polyhomeotic-like protein 3 | PHC3_HUMAN
Non-standard residues in 4pzn.pdb #24
---
EDO — 1,2-ethanediol (ethylene glycol)
> open /Users/elena/Desktop/thesis/figures/xlms/scml2/pdbs/5fr6.cif
5fr6.cif title:
The structure of polycomb ULD complex [more info...]
Chain information for 5fr6.cif #25
---
Chain | Description | UniProt
A | POLYCOMB COMPLEX PROTEIN BMI-1 | BMI1_HUMAN
5fr6.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks.txt
Unique peptide pairs: 221 out of 221
Unique peptide pairs with pseudobonds: 11
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 527, in map_crosslinks
self.align_peptides(peptide_pairs, checked_models)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 681, in align_peptides
self.create_pseudobonds(peptide_pairs)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 745, in create_pseudobonds
self.create_files(pbonds, info_file_path)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 758, in create_files
created_model = self.create_pseudobonds_model(pbonds,
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 838, in create_pseudobonds_model
self.write_file(file_path, group, file_type=".pb")
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 948, in write_file
created_file = open(file_path, "w")
OSError: [Errno 63] File name too long:
'/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_18,19,20.1,20.2,20.3,20.4,20.5,20.6,20.7,20.8,20.9,20.10,20.11,20.12,20.13,20.14,20.15,20.16,20.17,20.18,20.19,20.20,21.1,21.2,21.3,21.4,21.5,21.6,21.7,21.8,21.9,21.10,21.11,21.12,21.13,21.14,21.15,21.16,21.17,21.18,21.19,21.20,22,23,24,25.pb'
OSError: [Errno 63] File name too long:
'/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample06_Crosslinks_18,19,20.1,20.2,20.3,20.4,20.5,20.6,20.7,20.8,20.9,20.10,20.11,20.12,20.13,20.14,20.15,20.16,20.17,20.18,20.19,20.20,21.1,21.2,21.3,21.4,21.5,21.6,21.7,21.8,21.9,21.10,21.11,21.12,21.13,21.14,21.15,21.16,21.17,21.18,21.19,21.20,22,23,24,25.pb'
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 948, in write_file
created_file = open(file_path, "w")
See log for complete Python traceback.
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks.txt
Unique peptide pairs: 206 out of 206
Unique peptide pairs with pseudobonds: 10
Traceback (most recent call last):
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 527, in map_crosslinks
self.align_peptides(peptide_pairs, checked_models)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 681, in align_peptides
self.create_pseudobonds(peptide_pairs)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 745, in create_pseudobonds
self.create_files(pbonds, info_file_path)
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 758, in create_files
created_model = self.create_pseudobonds_model(pbonds,
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 838, in create_pseudobonds_model
self.write_file(file_path, group, file_type=".pb")
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 948, in write_file
created_file = open(file_path, "w")
OSError: [Errno 63] File name too long:
'/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_18,19,20.1,20.2,20.3,20.4,20.5,20.6,20.7,20.8,20.9,20.10,20.11,20.12,20.13,20.14,20.15,20.16,20.17,20.18,20.19,20.20,21.1,21.2,21.3,21.4,21.5,21.6,21.7,21.8,21.9,21.10,21.11,21.12,21.13,21.14,21.15,21.16,21.17,21.18,21.19,21.20,22,23,24,25.pb'
OSError: [Errno 63] File name too long:
'/Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/20230227_EXPL6_BaSt_SA_LC12_16_Orbi4570_sample05_Crosslinks_18,19,20.1,20.2,20.3,20.4,20.5,20.6,20.7,20.8,20.9,20.10,20.11,20.12,20.13,20.14,20.15,20.16,20.17,20.18,20.19,20.20,21.1,21.2,21.3,21.4,21.5,21.6,21.7,21.8,21.9,21.10,21.11,21.12,21.13,21.14,21.15,21.16,21.17,21.18,21.19,21.20,22,23,24,25.pb'
File "/Users/elena/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 948, in write_file
created_file = open(file_path, "w")
See log for complete Python traceback.
Pseudobonds are stored in /Users/elena/Desktop/PRC1_core_project/xl-
ms/Scml2_Scml2-nuc/xtal overlap.pb
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1554.50.3.0.0 (iBridge: 18.16.12561.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 16:56
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
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: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.0.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
seaborn: 0.12.2
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
tzdata: 2023.3
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → XMAS: crash in ~QGridLayout() |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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