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#7666 closed defect (can't reproduce)

Crash disposing of Qt widgets during garbage collection

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Window Toolkit	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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x0000000115f71dc0 (most recent call first):
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_internal.py", line 283 in data_as
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 322 in pointer
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 240 in set_cvec_pointer
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 123 in __init__
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 1431 in __init__
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2119 in process_changes
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2121 in changes
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/changes.py", line 25 in check_for_changes
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 58 in draw_new_frame
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


Process:               ChimeraX [14977]
Path:                  /Volumes/VOLUME/ChimeraX-1.4.app/Contents/MacOS/ChimeraX
Identifier:            edu.ucsf.cgl.ChimeraX
Version:               1.4.0 (1.4.0.0)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           ChimeraX [14977]
User ID:               505

Date/Time:             2022-09-24 18:50:37.429 +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:       578D9218-BA6D-4F98-80C9-33BD8DC26789

Time Awake Since Boot: 130000 seconds
Time Since Wake:       17000 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        	0x00007fff6e06733a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6e123e60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff6df7e93e raise + 26
3   libsystem_platform.dylib      	0x00007fff6e1185fd _sigtramp + 29
4   ???                           	000000000000000000 0 + 0
5   QtWidgets                     	0x0000000115779dc7 QGridLayout::~QGridLayout() + 39
6   QtWidgets.abi3.so             	0x00000001151ea438 non-virtual thunk to sipQGridLayout::~sipQGridLayout() + 56
7   QtWidgets                     	0x0000000115755960 QBoxLayout::~QBoxLayout() + 176
8   QtWidgets.abi3.so             	0x000000011525f307 sipQVBoxLayout::~sipQVBoxLayout() + 55
9   QtWidgets                     	0x000000011578a98a QWidget::~QWidget() + 634
10  QtWidgets.abi3.so             	0x000000011527cf17 sipQWidget::~sipQWidget() + 55
11  QtCore                        	0x0000000114bb129f QObjectPrivate::deleteChildren() + 159
12  QtWidgets                     	0x000000011578ac10 QWidget::~QWidget() + 1280
13  QtWidgets.abi3.so             	0x000000011527cf17 sipQWidget::~sipQWidget() + 55
14  QtCore                        	0x0000000114bb129f QObjectPrivate::deleteChildren() + 159
15  QtWidgets                     	0x000000011578ac10 QWidget::~QWidget() + 1280
16  QtWidgets.abi3.so             	0x0000000115230407 sipQDockWidget::~sipQDockWidget() + 55
17  sip.cpython-39-darwin.so      	0x00000001151082e7 forgetObject + 183
18  sip.cpython-39-darwin.so      	0x0000000115107fd5 sipWrapper_dealloc + 37
19  org.python.python             	0x000000010d419b3b subtype_dealloc + 1019
20  org.python.python             	0x000000010d3f88c2 dict_dealloc + 162
21  org.python.python             	0x000000010d42b97f subtype_clear + 239
22  org.python.python             	0x000000010d506c29 collect + 3193
23  org.python.python             	0x000000010d5073c2 _PyObject_GC_Alloc + 338
24  org.python.python             	0x000000010d507435 _PyObject_GC_New + 21
25  org.python.python             	0x000000010d3fb032 new_dict_with_shared_keys + 370
26  org.python.python             	0x000000010d3fb19e _PyObjectDict_SetItem + 78
27  org.python.python             	0x000000010d409c4f _PyObject_GenericSetAttrWithDict + 303
28  org.python.python             	0x000000010d409059 PyObject_SetAttr + 73
29  org.python.python             	0x000000010d4991da _PyEval_EvalFrameDefault + 13066
30  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
31  org.python.python             	0x000000010d49ee0c call_function + 732
32  org.python.python             	0x000000010d49c27e _PyEval_EvalFrameDefault + 25518
33  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
34  org.python.python             	0x000000010d49ee0c call_function + 732
35  org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
36  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
37  org.python.python             	0x000000010d49ee0c call_function + 732
38  org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
39  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
40  org.python.python             	0x000000010d49ee0c call_function + 732
41  org.python.python             	0x000000010d49c2a2 _PyEval_EvalFrameDefault + 25554
42  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
43  org.python.python             	0x000000010d3c6415 _PyObject_FastCallDictTstate + 293
44  org.python.python             	0x000000010d3c6f98 _PyObject_Call_Prepend + 152
45  org.python.python             	0x000000010d420b05 slot_tp_init + 165
46  org.python.python             	0x000000010d41bfb9 type_call + 345
47  org.python.python             	0x000000010d3c65b7 _PyObject_MakeTpCall + 359
48  org.python.python             	0x000000010d49ee9c call_function + 876
49  org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
50  org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
51  org.python.python             	0x000000010d3c6cb1 _PyFunction_Vectorcall + 289
52  org.python.python             	0x000000010d49ee0c call_function + 732
53  org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
54  org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
55  org.python.python             	0x000000010d3c6cb1 _PyFunction_Vectorcall + 289
56  org.python.python             	0x000000010d3d0323 property_descr_get + 115
57  org.python.python             	0x000000010d4095e3 _PyObject_GenericGetAttrWithDict + 163
58  org.python.python             	0x000000010d49a842 _PyEval_EvalFrameDefault + 18802
59  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
60  org.python.python             	0x000000010d49ee0c call_function + 732
61  org.python.python             	0x000000010d49c2a2 _PyEval_EvalFrameDefault + 25554
62  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
63  org.python.python             	0x000000010d49ee0c call_function + 732
64  org.python.python             	0x000000010d49c27e _PyEval_EvalFrameDefault + 25518
65  org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
66  org.python.python             	0x000000010d3c8db2 method_vectorcall + 274
67  QtCore.abi3.so                	0x00000001148a7607 PyQtSlot::call(_object*, _object*) const + 39
68  QtCore.abi3.so                	0x00000001148a7516 PyQtSlot::invoke(void**, _object*, void*, bool) const + 358
69  QtCore.abi3.so                	0x00000001148a8445 PyQtSlotProxy::unislot(void**) + 85
70  QtCore.abi3.so                	0x00000001148a83ba PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
71  QtCore                        	0x0000000114bb99e7 0x114afd000 + 772583
72  QtCore                        	0x0000000114bce4d7 QTimer::timerEvent(QTimerEvent*) + 199
73  QtCore.abi3.so                	0x0000000114796bf9 sipQTimer::timerEvent(QTimerEvent*) + 121
74  QtCore                        	0x0000000114bb1bad QObject::event(QEvent*) + 109
75  QtCore.abi3.so                	0x0000000114796a7a sipQTimer::event(QEvent*) + 186
76  QtWidgets                     	0x0000000115747067 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
77  QtWidgets                     	0x0000000115748023 QApplication::notify(QObject*, QEvent*) + 499
78  QtWidgets.abi3.so             	0x0000000115269829 sipQApplication::notify(QObject*, QEvent*) + 233
79  QtCore                        	0x0000000114b68dca QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
80  QtCore                        	0x0000000114cf4a01 QTimerInfoList::activateTimers() + 961
81  libqcocoa.dylib               	0x000000013208f885 0x132077000 + 100485
82  com.apple.CoreFoundation      	0x00007fff3404ad52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
83  com.apple.CoreFoundation      	0x00007fff3404acf1 __CFRunLoopDoSource0 + 103
84  com.apple.CoreFoundation      	0x00007fff3404ab0b __CFRunLoopDoSources0 + 209
85  com.apple.CoreFoundation      	0x00007fff3404983a __CFRunLoopRun + 927
86  com.apple.CoreFoundation      	0x00007fff34048e3e CFRunLoopRunSpecific + 462
87  com.apple.HIToolbox           	0x00007fff32c75abd RunCurrentEventLoopInMode + 292
88  com.apple.HIToolbox           	0x00007fff32c757d5 ReceiveNextEventCommon + 584
89  com.apple.HIToolbox           	0x00007fff32c75579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
90  com.apple.AppKit              	0x00007fff312bb039 _DPSNextEvent + 883
91  com.apple.AppKit              	0x00007fff312b9880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
92  com.apple.AppKit              	0x00007fff312ab58e -[NSApplication run] + 658
93  libqcocoa.dylib               	0x000000013209048c 0x132077000 + 103564
94  QtCore                        	0x0000000114b72516 QEventLoop::exec(QFlags) + 486
95  QtCore                        	0x0000000114b693e5 QCoreApplication::exec() + 133
96  QtWidgets.abi3.so             	0x000000011535690a meth_QApplication_exec(_object*, _object*) + 90
97  org.python.python             	0x000000010d40571d cfunction_call + 125
98  org.python.python             	0x000000010d3c65b7 _PyObject_MakeTpCall + 359
99  org.python.python             	0x000000010d49ee9c call_function + 876
100 org.python.python             	0x000000010d49c2a2 _PyEval_EvalFrameDefault + 25554
101 org.python.python             	0x000000010d3c6d28 function_code_fastcall + 104
102 org.python.python             	0x000000010d3c8d6a method_vectorcall + 202
103 org.python.python             	0x000000010d49ee0c call_function + 732
104 org.python.python             	0x000000010d49c2a2 _PyEval_EvalFrameDefault + 25554
105 org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
106 org.python.python             	0x000000010d3c6cb1 _PyFunction_Vectorcall + 289
107 org.python.python             	0x000000010d49ee0c call_function + 732
108 org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
109 org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
110 org.python.python             	0x000000010d495dab PyEval_EvalCode + 139
111 org.python.python             	0x000000010d492c12 builtin_exec + 626
112 org.python.python             	0x000000010d405023 cfunction_vectorcall_FASTCALL + 195
113 org.python.python             	0x000000010d49ee0c call_function + 732
114 org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
115 org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
116 org.python.python             	0x000000010d3c6cb1 _PyFunction_Vectorcall + 289
117 org.python.python             	0x000000010d49ee0c call_function + 732
118 org.python.python             	0x000000010d49c34b _PyEval_EvalFrameDefault + 25723
119 org.python.python             	0x000000010d49fb03 _PyEval_EvalCode + 2611
120 org.python.python             	0x000000010d3c6cb1 _PyFunction_Vectorcall + 289
121 org.python.python             	0x000000010d505870 pymain_run_module + 208
122 org.python.python             	0x000000010d504f87 Py_RunMain + 1431
123 org.python.python             	0x000000010d50558f pymain_main + 223
124 org.python.python             	0x000000010d50549b Py_Main + 43
125 edu.ucsf.cgl.ChimeraX         	0x000000010d37bdc8 main + 120
126 libdyld.dylib                 	0x00007fff6df1fcc9 start + 1

Thread 1:: ThreadPoolServiceThread
0   libsystem_kernel.dylib        	0x00007fff6e069b96 kevent64 + 10
1   QtWebEngineCore               	0x000000012a5bb5ca 0x126659000 + 66463178
2   QtWebEngineCore               	0x000000012a5bb4c7 0x126659000 + 66462919
3   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
4   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
5   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
6   QtWebEngineCore               	0x000000012a54184d 0x126659000 + 65964109
7   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
8   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
9   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
10  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 2:: Chrome_IOThread
0   libsystem_kernel.dylib        	0x00007fff6e069b96 kevent64 + 10
1   QtWebEngineCore               	0x000000012a5bb5ca 0x126659000 + 66463178
2   QtWebEngineCore               	0x000000012a5bb4c7 0x126659000 + 66462919
3   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
4   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
5   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
6   QtWebEngineCore               	0x0000000129480e32 0x126659000 + 48397874
7   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
8   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
9   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
10  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 3:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 4:: CompositorTileWorker1
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   QtWebEngineCore               	0x000000012a5818bb 0x126659000 + 66226363
3   QtWebEngineCore               	0x000000012c65255d 0x126659000 + 100635997
4   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
5   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
6   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 5:: Chrome_InProcGpuThread
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 6:: Chrome_ChildIOThread
0   libsystem_kernel.dylib        	0x00007fff6e069b96 kevent64 + 10
1   QtWebEngineCore               	0x000000012a5bb5ca 0x126659000 + 66463178
2   QtWebEngineCore               	0x000000012a5bb4c7 0x126659000 + 66462919
3   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
4   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
5   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
6   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
7   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
8   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
9   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 7:: VizCompositorThread
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 8:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 9:: NetworkService
0   libsystem_kernel.dylib        	0x00007fff6e069b96 kevent64 + 10
1   QtWebEngineCore               	0x000000012a5bb5ca 0x126659000 + 66463178
2   QtWebEngineCore               	0x000000012a5bb4c7 0x126659000 + 66462919
3   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
4   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
5   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
6   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
7   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
8   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
9   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 10:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 11:: ThreadPoolSingleThreadForegroundBlocking0
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a54dd5f 0x126659000 + 66014559
4   QtWebEngineCore               	0x000000012a54e80c 0x126659000 + 66017292
5   QtWebEngineCore               	0x000000012a54e46d 0x126659000 + 66016365
6   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
7   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 12:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 13:: com.apple.NSEventThread
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   com.apple.CoreFoundation      	0x00007fff3404aef5 __CFRunLoopServiceMachPort + 247
3   com.apple.CoreFoundation      	0x00007fff340499c2 __CFRunLoopRun + 1319
4   com.apple.CoreFoundation      	0x00007fff34048e3e CFRunLoopRunSpecific + 462
5   com.apple.AppKit              	0x00007fff3145c954 _NSEventThread + 132
6   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
7   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 14:: MemoryInfra
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 15:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a54dd5f 0x126659000 + 66014559
4   QtWebEngineCore               	0x000000012a54e53a 0x126659000 + 66016570
5   QtWebEngineCore               	0x000000012a54e3ad 0x126659000 + 66016173
6   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
7   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 16:: ThreadPoolBackgroundWorker
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a54dd5f 0x126659000 + 66014559
4   QtWebEngineCore               	0x000000012a54e80c 0x126659000 + 66017292
5   QtWebEngineCore               	0x000000012a54e37d 0x126659000 + 66016125
6   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
7   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 17:: NetworkConfigWatcher
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a58978f 0x126659000 + 66258831
4   QtWebEngineCore               	0x000000012a4bf089 0x126659000 + 65429641
5   QtWebEngineCore               	0x000000012a53819c 0x126659000 + 65925532
6   QtWebEngineCore               	0x000000012a4efff8 0x126659000 + 65630200
7   QtWebEngineCore               	0x000000012a55a458 0x126659000 + 66065496
8   QtWebEngineCore               	0x000000012a55a5ea 0x126659000 + 66065898
9   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
10  libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
11  libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 18:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 19:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 20:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 21:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 22:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 23:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 24:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 25:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   interpreter.cpython-39-darwin.so	0x0000000149904fe3 th_worker(void*) + 115
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 26:: ThreadPoolForegroundWorker
0   libsystem_kernel.dylib        	0x00007fff6e060dfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff6e061170 mach_msg + 60
2   QtWebEngineCore               	0x000000012a5899c6 0x126659000 + 66259398
3   QtWebEngineCore               	0x000000012a54dd5f 0x126659000 + 66014559
4   QtWebEngineCore               	0x000000012a54e80c 0x126659000 + 66017292
5   QtWebEngineCore               	0x000000012a54e40d 0x126659000 + 66016269
6   QtWebEngineCore               	0x000000012a5824a8 0x126659000 + 66229416
7   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
8   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 27:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 28:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 29:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 30:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 31:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 32:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 33:
0   libsystem_kernel.dylib        	0x00007fff6e063882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff6e124425 _pthread_cond_wait + 698
2   libopenblas64_.0.dylib        	0x000000010e15249f blas_thread_server + 207
3   libsystem_pthread.dylib       	0x00007fff6e124109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff6e11fb8b thread_start + 15

Thread 34:
0   libsystem_pthread.dylib       	0x00007fff6e11fb68 start_wqthread + 0

Thread 35:
0   libsystem_pthread.dylib       	0x00007fff6e11fb68 start_wqthread + 0

Thread 36:
0   libsystem_pthread.dylib       	0x00007fff6e11fb68 start_wqthread + 0

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000115f71dc0  rcx: 0x00007fa2e012fa58  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x000000000000000b  rbp: 0x00007fa2e012fa80  rsp: 0x00007fa2e012fa58
   r8: 0x00007fa2e012ff48   r9: 0xe65ff739cb61f015  r10: 0x0000000115f71dc0  r11: 0x0000000000000246
  r12: 0x0000000000000307  r13: 0x0000000000000000  r14: 0x000000000000000b  r15: 0x0000000000000016
  rip: 0x00007fff6e06733a  rfl: 0x0000000000000246  cr2: 0x000000010d64f247
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


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    0x7fff6bcdd000 -     0x7fff6bdcdfff  libiconv.2.dylib (59)  /usr/lib/libiconv.2.dylib
    0x7fff6bdce000 -     0x7fff6c025fff  libicucore.A.dylib (64260.0.1)  /usr/lib/libicucore.A.dylib
    0x7fff6c03f000 -     0x7fff6c040fff  liblangid.dylib (133)  /usr/lib/liblangid.dylib
    0x7fff6c041000 -     0x7fff6c059ff3  liblzma.5.dylib (16)  /usr/lib/liblzma.5.dylib
    0x7fff6c071000 -     0x7fff6c118ff7  libmecab.dylib (883.11)  /usr/lib/libmecab.dylib
    0x7fff6c119000 -     0x7fff6c37bff1  libmecabra.dylib (883.11)  /usr/lib/libmecabra.dylib
    0x7fff6c6e8000 -     0x7fff6c717fff  libncurses.5.4.dylib (57)  /usr/lib/libncurses.5.4.dylib
    0x7fff6c847000 -     0x7fff6ccc3ff5  libnetwork.dylib (1880.120.4)  /usr/lib/libnetwork.dylib
    0x7fff6ccc4000 -     0x7fff6ccdbfff  libnetworkextension.dylib (1095.140.2)  /usr/lib/libnetworkextension.dylib
    0x7fff6cd64000 -     0x7fff6cd97fde  libobjc.A.dylib (787.1)  /usr/lib/libobjc.A.dylib
    0x7fff6cd98000 -     0x7fff6cd99ff7  libodfde.dylib (26)  /usr/lib/libodfde.dylib
    0x7fff6cdaa000 -     0x7fff6cdaefff  libpam.2.dylib (25.100.1)  /usr/lib/libpam.2.dylib
    0x7fff6cdb1000 -     0x7fff6cde7ff7  libpcap.A.dylib (89.120.1)  /usr/lib/libpcap.A.dylib
    0x7fff6ce27000 -     0x7fff6ce35ff9  libperfcheck.dylib (37.100.2)  /usr/lib/libperfcheck.dylib
    0x7fff6ce36000 -     0x7fff6ce39ff3  libpmenergy.dylib (214.120.1)  /usr/lib/libpmenergy.dylib
    0x7fff6ce3a000 -     0x7fff6ce3cfff  libpmsample.dylib (214.120.1)  /usr/lib/libpmsample.dylib
    0x7fff6ce6b000 -     0x7fff6ce83fff  libresolv.9.dylib (67.40.1)  /usr/lib/libresolv.9.dylib
    0x7fff6ce85000 -     0x7fff6cec9ff7  libsandbox.1.dylib (1217.141.2)  /usr/lib/libsandbox.1.dylib
    0x7fff6ceca000 -     0x7fff6cedcff7  libsasl2.2.dylib (213.120.1)  /usr/lib/libsasl2.2.dylib
    0x7fff6cedd000 -     0x7fff6cedeff7  libspindump.dylib (281.3)  /usr/lib/libspindump.dylib
    0x7fff6cedf000 -     0x7fff6d0c9ff7  libsqlite3.dylib (308.5)  /usr/lib/libsqlite3.dylib
    0x7fff6d1bd000 -     0x7fff6d1eaffb  libssl.46.dylib (47.140.1)  /usr/lib/libssl.46.dylib
    0x7fff6d26c000 -     0x7fff6d29dff7  libtidy.A.dylib (17.2)  /usr/lib/libtidy.A.dylib
    0x7fff6d2bf000 -     0x7fff6d319ff8  libusrtcp.dylib (1880.120.4)  /usr/lib/libusrtcp.dylib
    0x7fff6d31a000 -     0x7fff6d31dffb  libutil.dylib (57)  /usr/lib/libutil.dylib
    0x7fff6d31e000 -     0x7fff6d32bff7  libxar.1.dylib (425.2)  /usr/lib/libxar.1.dylib
    0x7fff6d331000 -     0x7fff6d413fff  libxml2.2.dylib (33.5)  /usr/lib/libxml2.2.dylib
    0x7fff6d417000 -     0x7fff6d43ffff  libxslt.1.dylib (16.9)  /usr/lib/libxslt.1.dylib
    0x7fff6d440000 -     0x7fff6d452ff3  libz.1.dylib (76)  /usr/lib/libz.1.dylib
    0x7fff6dd01000 -     0x7fff6dd06ff3  libcache.dylib (83)  /usr/lib/system/libcache.dylib
    0x7fff6dd07000 -     0x7fff6dd12fff  libcommonCrypto.dylib (60165.120.1)  /usr/lib/system/libcommonCrypto.dylib
    0x7fff6dd13000 -     0x7fff6dd1afff  libcompiler_rt.dylib (101.2)  /usr/lib/system/libcompiler_rt.dylib
    0x7fff6dd1b000 -     0x7fff6dd24ff7  libcopyfile.dylib (166.40.1)  /usr/lib/system/libcopyfile.dylib
    0x7fff6dd25000 -     0x7fff6ddb7fdb  libcorecrypto.dylib (866.140.1)  /usr/lib/system/libcorecrypto.dylib
    0x7fff6dec4000 -     0x7fff6df04ff0  libdispatch.dylib (1173.100.2)  /usr/lib/system/libdispatch.dylib
    0x7fff6df05000 -     0x7fff6df3bfff  libdyld.dylib (750.6)  /usr/lib/system/libdyld.dylib
    0x7fff6df3c000 -     0x7fff6df3cffb  libkeymgr.dylib (30)  /usr/lib/system/libkeymgr.dylib
    0x7fff6df3d000 -     0x7fff6df49ff3  libkxld.dylib (6153.141.2.2)  /usr/lib/system/libkxld.dylib
    0x7fff6df4a000 -     0x7fff6df4aff7  liblaunch.dylib (1738.140.1)  /usr/lib/system/liblaunch.dylib
    0x7fff6df4b000 -     0x7fff6df50ff7  libmacho.dylib (959.0.1)  /usr/lib/system/libmacho.dylib
    0x7fff6df51000 -     0x7fff6df53ff3  libquarantine.dylib (110.40.3)  /usr/lib/system/libquarantine.dylib
    0x7fff6df54000 -     0x7fff6df55ff7  libremovefile.dylib (48)  /usr/lib/system/libremovefile.dylib
    0x7fff6df56000 -     0x7fff6df6dff3  libsystem_asl.dylib (377.60.2)  /usr/lib/system/libsystem_asl.dylib
    0x7fff6df6e000 -     0x7fff6df6eff7  libsystem_blocks.dylib (74)  /usr/lib/system/libsystem_blocks.dylib
    0x7fff6df6f000 -     0x7fff6dff6fff  libsystem_c.dylib (1353.100.2)  /usr/lib/system/libsystem_c.dylib
    0x7fff6dff7000 -     0x7fff6dffaffb  libsystem_configuration.dylib (1061.141.1)  /usr/lib/system/libsystem_configuration.dylib
    0x7fff6dffb000 -     0x7fff6dffefff  libsystem_coreservices.dylib (114)  /usr/lib/system/libsystem_coreservices.dylib
    0x7fff6dfff000 -     0x7fff6e007fff  libsystem_darwin.dylib (1353.100.2)  /usr/lib/system/libsystem_darwin.dylib
    0x7fff6e008000 -     0x7fff6e00ffff  libsystem_dnssd.dylib (1096.100.3)  /usr/lib/system/libsystem_dnssd.dylib
    0x7fff6e010000 -     0x7fff6e011ffb  libsystem_featureflags.dylib (17)  /usr/lib/system/libsystem_featureflags.dylib
    0x7fff6e012000 -     0x7fff6e05fff7  libsystem_info.dylib (538)  /usr/lib/system/libsystem_info.dylib
    0x7fff6e060000 -     0x7fff6e08cff7  libsystem_kernel.dylib (6153.141.2.2)  /usr/lib/system/libsystem_kernel.dylib
    0x7fff6e08d000 -     0x7fff6e0d4fff  libsystem_m.dylib (3178)  /usr/lib/system/libsystem_m.dylib
    0x7fff6e0d5000 -     0x7fff6e0fcfff  libsystem_malloc.dylib (283.100.6)  /usr/lib/system/libsystem_malloc.dylib
    0x7fff6e0fd000 -     0x7fff6e10affb  libsystem_networkextension.dylib (1095.140.2)  /usr/lib/system/libsystem_networkextension.dylib
    0x7fff6e10b000 -     0x7fff6e114ff7  libsystem_notify.dylib (241.100.2)  /usr/lib/system/libsystem_notify.dylib
    0x7fff6e115000 -     0x7fff6e11dfef  libsystem_platform.dylib (220.100.1)  /usr/lib/system/libsystem_platform.dylib
    0x7fff6e11e000 -     0x7fff6e128fff  libsystem_pthread.dylib (416.100.3)  /usr/lib/system/libsystem_pthread.dylib
    0x7fff6e129000 -     0x7fff6e12dff3  libsystem_sandbox.dylib (1217.141.2)  /usr/lib/system/libsystem_sandbox.dylib
    0x7fff6e12e000 -     0x7fff6e130fff  libsystem_secinit.dylib (62.100.2)  /usr/lib/system/libsystem_secinit.dylib
    0x7fff6e131000 -     0x7fff6e138ffb  libsystem_symptoms.dylib (1238.120.1)  /usr/lib/system/libsystem_symptoms.dylib
    0x7fff6e139000 -     0x7fff6e14fff2  libsystem_trace.dylib (1147.120)  /usr/lib/system/libsystem_trace.dylib
    0x7fff6e151000 -     0x7fff6e156ff7  libunwind.dylib (35.4)  /usr/lib/system/libunwind.dylib
    0x7fff6e157000 -     0x7fff6e18cffe  libxpc.dylib (1738.140.1)  /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 42
    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: 119904
    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=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               384K        3 
Activity Tracing                   256K        1 
CG backing stores                 2480K        4 
CG image                           752K       51 
CoreAnimation                     1340K       81 
CoreGraphics                         8K        1 
CoreImage                           32K        4 
CoreServices                       216K        1 
CoreUI image data                 3500K       36 
Foundation                          28K        2 
Kernel Alloc Once                   12K        2 
MALLOC                             1.9G     1341 
MALLOC guard page                   48K        9 
MALLOC_MEDIUM (reserved)           1.4G       15         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)
Mach message                        24K        4 
OpenGL GLSL                        384K        4 
STACK GUARD                        144K       36 
Stack                            153.8M       37 
Stack Guard                       56.0M        1 
VM_ALLOCATE                      299.6M      305 
VM_ALLOCATE (reserved)           320.0M        2         reserved VM address space (unallocated)
__DATA                            83.4M      768 
__DATA_CONST                       180K       10 
__FONT_DATA                          4K        1 
__GLSLBUILTINS                    5176K        1 
__LINKEDIT                       438.2M      373 
__OBJC_RO                         32.3M        1 
__OBJC_RW                         1908K        2 
__TEXT                           747.7M      716 
__UNICODE                          564K        1 
mapped file                      411.1M       72 
shared memory                     2880K       29 
===========                     =======  ======= 
TOTAL                              6.1G     3915 
TOTAL, minus reserved VM space     4.1G     3915 

===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
  
distutils: /Users/elena/Library/Application Support/ChimeraX/1.4/site-packages  
sysconfig: /Users/elena/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
  
distutils: /Users/elena/Library/Application Support/ChimeraX/1.4/site-packages  
sysconfig: /Users/elena/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/pandas  
sysconfig: /Users/elena/Library/Python/3.9/include/pandas  
WARNING: Value for scheme.scripts does not match. Please report this to
  
distutils: /Users/elena/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/elena/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
  
distutils: /Users/elena/Library/Application Support/ChimeraX  
sysconfig: /Users/elena/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/et-xmlfile  
sysconfig: /Users/elena/Library/Python/3.9/include/et-xmlfile  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/seaborn  
sysconfig: /Users/elena/Library/Python/3.9/include/seaborn  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/qtrangeslider  
sysconfig: /Users/elena/Library/Python/3.9/include/qtrangeslider  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/openpyxl  
sysconfig: /Users/elena/Library/Python/3.9/include/openpyxl  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-XMAS  
sysconfig: /Users/elena/Library/Python/3.9/include/ChimeraX-XMAS  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/elena/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/elena/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.  
You should consider upgrading via the
'/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/elena/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl  
Collecting openpyxl  
Downloading openpyxl-3.0.10-py2.py3-none-any.whl (242 kB)  
Collecting pandas  
Downloading pandas-1.5.0-cp39-cp39-macosx_10_9_x86_64.whl (12.1 MB)  
Requirement already satisfied: ChimeraX-UI~=1.3 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.18.3)  
Requirement already satisfied: ChimeraX-Core~=1.3 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.4)  
Collecting qtrangeslider  
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)  
Collecting seaborn  
Downloading seaborn-0.12.0-py3-none-any.whl (285 kB)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)  
Collecting et-xmlfile  
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)  
Requirement already satisfied: pytz>=2020.1 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.1)  
Requirement already satisfied: numpy>=1.20.3 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (1.22.1)  
Requirement already satisfied: python-dateutil>=2.8.1 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2)  
Requirement already satisfied: matplotlib>=3.1 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0)  
Requirement already satisfied: pillow>=6.2.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.0.1)  
Requirement already satisfied: packaging>=20.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.0)  
Requirement already satisfied: pyparsing>=2.2.1 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9)  
Requirement already satisfied: cycler>=0.10 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (0.11.0)  
Requirement already satisfied: fonttools>=4.22.0 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (4.33.3)  
Requirement already satisfied: kiwisolver>=1.0.1 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.2)  
Requirement already satisfied: six>=1.5 in
/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)  
Installing collected packages: pandas, et-xmlfile, seaborn, qtrangeslider,
openpyxl, ChimeraX-XMAS  
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.0.10
pandas-1.5.0 qtrangeslider-0.1.5 seaborn-0.12.0  
\---  

Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.0.10
pandas-1.5.0 qtrangeslider-0.1.5 seaborn-0.12.0  
Installed ChimeraX-XMAS (1.1.2)  
Downloading file 2022.04.21.489026v2.full.pdf  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.4-cp39-cp39-macosx_10_13_x86_64.whl  

> ui tool show XMAS

> open /Volumes/pool-mueller-group/Elena/Alphafold/run_1/run_1/ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /C

Alignment identifier is 1/C  

> select /C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select /C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> color sel yellow

> select clear

> select /C:2

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

> select /C:2-23

353 atoms, 355 bonds, 22 residues, 1 model selected  

> select /C:1-2

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select /C:1-38

613 atoms, 619 bonds, 38 residues, 1 model selected  

> select /B:340

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

> select /B:91-340

3885 atoms, 3917 bonds, 250 residues, 1 model selected  

> color sel light sea green

> select /C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select /C:275-335

866 atoms, 883 bonds, 61 residues, 1 model selected  

> select /C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select /C:330-335

103 atoms, 108 bonds, 6 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /A:162

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

> select /A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel rosy brown

> select clear

> select /C:329

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

> select /C:1-329

5196 atoms, 5250 bonds, 329 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale goldenrod

> color sel medium purple

> select /B:340

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

> select /B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cadet blue

> select /C:329

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

> select /C:1-329

5196 atoms, 5250 bonds, 329 residues, 1 model selected  

> color sel khaki

> color sel pale goldenrod

> select clear

> select /C:1-329

5196 atoms, 5250 bonds, 329 residues, 1 model selected  

> select clear

> select /C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select /C:101-335

3629 atoms, 3672 bonds, 235 residues, 1 model selected  

> select
> /C:9-11,13-15,40-47,65-68,75-77,86-100,106-108,111-114,140-142,144-146,151-154,172-182,211-213,265-267,274-276,286-288,294-297

1358 atoms, 1357 bonds, 80 residues, 1 model selected  

> select /C:101-335

3629 atoms, 3672 bonds, 235 residues, 1 model selected  

> select /C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select /C:100-335

3639 atoms, 3682 bonds, 236 residues, 1 model selected  

> hide sel cartoons

> select /A:1

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

> select /A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select /B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> select clear

> select /B:120

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

> select /B:120-279

2432 atoms, 2446 bonds, 160 residues, 1 model selected  

> select /B:340

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

> select /B:201-340

2176 atoms, 2195 bonds, 140 residues, 1 model selected  

> select clear

> select /B:340

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

> select /B:121-340

3389 atoms, 3415 bonds, 220 residues, 1 model selected  

> hide sel cartoons

> select /B:1

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

> select /B:1-13

169 atoms, 169 bonds, 13 residues, 1 model selected  

> select
> /B:15-17,25-29,47-53,77-80,82-84,108-117,119-140,142-169,195-197,260-278,284-289,315-323

1944 atoms, 1948 bonds, 119 residues, 1 model selected  

> select /B:1

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

> select /B:1-15

200 atoms, 200 bonds, 15 residues, 1 model selected  

> hide sel cartoons

> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-5.pdb

refined-coot-5.pdb title:  
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]  
  
Chain information for refined-coot-5.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> select add #2

13505 atoms, 14334 bonds, 1 pseudobond, 1257 residues, 3 models selected  

> select subtract #2

200 atoms, 200 bonds, 15 residues, 1 model selected  

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide atoms

> show cartoons

> select #1/B:340

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

> select #1/B:121-340

3389 atoms, 3415 bonds, 220 residues, 1 model selected  

> hide sel cartoons

> select #1/B:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/B:1-14

183 atoms, 183 bonds, 14 residues, 1 model selected  

> hide sel cartoons

> select #1/A:1

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

> select #1/A:1-160

2511 atoms, 2547 bonds, 160 residues, 1 model selected  

> select #1/A:162

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> hide sel cartoons

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> select clear

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:99-335

3649 atoms, 3692 bonds, 237 residues, 1 model selected  

> hide sel cartoons

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-4

74 atoms, 74 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker refined-coot-5.pdb, chain L (#2) with ranked_0.pdb, chain B (#1),
sequence alignment score = 474.6  
RMSD between 95 pruned atom pairs is 0.917 angstroms; (across all 101 pairs:
1.217)  
  

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> select clear

> select #1/B:1

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

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> ui tool show "Color Actions"

> hide #!2 models

> select #1/B:340

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

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> show sel cartoons

> select #1/A:1

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show sel cartoons

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:329-335

125 atoms, 130 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select #1/B:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/B:1-16

214 atoms, 215 bonds, 16 residues, 1 model selected  

> select clear

> select #1/B:1

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

> select #1/B:1-4

46 atoms, 46 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select #1/A:1

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

> select #1/A:1-3

35 atoms, 35 bonds, 3 residues, 1 model selected  

> hide sel surfaces

> select clear

> select #1/B:6

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

> select #1/B:6-29

377 atoms, 380 bonds, 24 residues, 1 model selected  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker refined-coot-5.pdb, chain L (#2) with ranked_0.pdb, chain B (#1),
sequence alignment score = 474.6  
RMSD between 95 pruned atom pairs is 0.917 angstroms; (across all 101 pairs:
1.217)  
  

> show #!2 models

> hide #!2 models

> select #1/B:6

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

> select #1/B:6-30

401 atoms, 404 bonds, 25 residues, 1 model selected  

> select #1/B:6-7

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select #1/B:6-30

401 atoms, 404 bonds, 25 residues, 1 model selected  

> select clear

> show #!2 models

> hide #!2 models

> save /Users/elena/Desktop/image10.png supersample 3

> save /Users/elena/Desktop/image11.png supersample 3

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting simple

> select #1/C:1-2

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sandy brown

> color sel light salmon

> color sel crimson

> color sel tomato

> color sel sienna

> color sel indian red

> color sel dark khaki

> select clear

> save /Users/elena/Desktop/image12.png supersample 3

> ui tool show "Color Actions"

> ui tool show "Surface Color"

No surface chosen for coloring  

> ui tool show "Surface Color"

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

Surface Color: no surface chosen  

> color byattribute bfactor /A range 2,30

3343 atoms, 260 residues, atom bfactor range 31.5 to 362  

> color bfactor sel

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> color bfactor sel

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> color bfactor sel

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> undo

> select clear

> save /Users/elena/Desktop/image13.png supersample 3

> color bfactor #1

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> ui tool show "Scale Bar"

> scalebar

> undo

> select clear

> undo

> ui tool show "Scale Bar"

> scalebar off

> ui tool show "Color Key"

> ui mousemode right "color key"

> ui mousemode right translate

> ui tool show "Color Key"

> ui mousemode right "color key"

> ui mousemode right translate

> ui mousemode right "color key"

> ui mousemode right translate

> undo

> select clear

> ui tool show "Color Key"

> ui mousemode right "color key"

> key red-white-blue :max : :min

> key blue-white-red :min : :max

> key red-white-blue :max : :min

> key delete

> ui mousemode right translate

> save /Users/elena/Desktop/image14.png supersample 3

> color bfactor #1

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> ui tool show "Color Actions"

> ui tool show "Color Key"

> ui mousemode right "color key"

> key blue-white-red :min : :1

> key blue-white-red :min : :10

> key blue-white-red :min : :100

> key blue-white-red :0 : :100

> ui mousemode right translate

> undo

> ui tool show "Color Key"

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> save /Users/elena/Desktop/image15.png supersample 3

> color bfactor #1

13130 atoms, 837 residues, atom bfactor range 27.5 to 97.3  

> ui tool show "Color Key"

> ui mousemode right "color key"

> key blue-white-red :min : :1

> key blue-white-red :min : :10

> key blue-white-red :min : :100

> key blue-white-red :0 : :100

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0,25000,0,03

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

> key size 0,25000,0,0000

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

> key size 0,25000,0,03

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

> key size 0,,0,03000

Invalid "size" argument: Expected a number  

> key size 0,1,0,03000

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> key labelColor #bfbfbf

> key labelColor default

> key size 0,0,0,03000

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

> key size 0,05,0,03000

Invalid "size" argument: Need exactly 2 ','-separated number >= 0s  

> ui mousemode right translate

> save /Users/elena/Desktop/image16.png supersample 3

> undo

> ui tool show "Color Key"

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> select
> #1/B:41-44,65-68,74-76,104-106,229-236,250-255,295-300,306-308,329-335

761 atoms, 763 bonds, 44 residues, 1 model selected  

> select #1/B:6

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

> select #1/B:6-9

54 atoms, 53 bonds, 4 residues, 1 model selected  

> select #1/B:340

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

> select #1/B:335-340

105 atoms, 106 bonds, 6 residues, 1 model selected  

> select #1/B:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/B:1-20

280 atoms, 281 bonds, 20 residues, 1 model selected  

> select #1/A:1

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

> select #1/A:1-46

772 atoms, 783 bonds, 46 residues, 1 model selected  

> select clear

> select #1/A:162

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

> select #1/A:155-162

141 atoms, 142 bonds, 8 residues, 1 model selected  

> select #1/A:1

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

> select #1/A:1-13

176 atoms, 176 bonds, 13 residues, 1 model selected  

> select #1/C:329

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

> select #1/C:322-329

99 atoms, 98 bonds, 8 residues, 1 model selected  

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-7

131 atoms, 131 bonds, 7 residues, 1 model selected  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker refined-coot-5.pdb, chain L (#2) with ranked_0.pdb, chain B (#1),
sequence alignment score = 474.6  
RMSD between 95 pruned atom pairs is 0.917 angstroms; (across all 101 pairs:
1.217)  
  

> show #!2 models

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

> select subtract #1

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/L

Alignment identifier is 2/L  

> select #1/B:8-9

26 atoms, 25 bonds, 2 residues, 1 model selected  

> select #1/B:8-23

247 atoms, 249 bonds, 16 residues, 1 model selected  

> select #1/B:8

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

> select #1/B:8-120

1797 atoms, 1812 bonds, 113 residues, 1 model selected  

> select clear

> select #1/B:50

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

> select #1/B:50-51

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

> select
> #1/B:15-17,25-29,47-53,77-80,82-84,108-117,119-140,142-169,195-197,260-278,284-289,315-323

1944 atoms, 1948 bonds, 119 residues, 1 model selected  

> select #1/B:52

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/B:52-105

878 atoms, 881 bonds, 54 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/K

Alignment identifier is 2/K  

> select #2/K:5

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

> select #2/K:5-9

37 atoms, 36 bonds, 5 residues, 1 model selected  

> select #2/K:5

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

> select #2/K:5-33

220 atoms, 223 bonds, 29 residues, 1 model selected  

> set bgColor black

> set bgColor transparent

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> sequence chain #2/K

Destroying pre-existing alignment with identifier 2/K  
Alignment identifier is 2/K  

> sequence chain #2/L

Alignment identifier is 2/L  

> select #2/L:15

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

> select #2/L:15-115

787 atoms, 801 bonds, 101 residues, 1 model selected  

> select clear

> select #2/L:115

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

> select #2/L:15-115

787 atoms, 801 bonds, 101 residues, 1 model selected  

> select #2/K:98

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

> select #2/K:5-98

754 atoms, 769 bonds, 94 residues, 1 model selected  

> delete sel

> select #1/A:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> hide sel cartoons

> select #1/B:340

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

> select #1/B:120-340

3400 atoms, 3426 bonds, 221 residues, 1 model selected  

> hide sel cartoons

> hide #!2 models

> show #!2 models

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:99-335

3649 atoms, 3692 bonds, 237 residues, 1 model selected  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #2/L

Alignment identifier is 2/L  

> select #2/L:115

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

> select #2/L:15-115

787 atoms, 801 bonds, 101 residues, 1 model selected  

> delete sel

> select #1/B:1

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

> select #1/B:1-9

117 atoms, 117 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> save /Users/elena/Desktop/image17.png supersample 3

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select #1/B:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> show sel cartoons

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> show sel cartoons

> select #1/A:1

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show sel cartoons

> select clear

> save /Users/elena/Desktop/image18.png supersample 3

> hide #!2 models

> set bgColor white

> set bgColor #ffffff00

> select #1/B:106

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/B:106

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/B:60

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

> select #1/B:60-91

500 atoms, 501 bonds, 32 residues, 1 model selected  

> select #1/B:246

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

> select #1/B:246-340

1517 atoms, 1531 bonds, 95 residues, 1 model selected  

> select clear

> turn y 180

> undo

> turn y 180

> undo

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-210

3454 atoms, 3484 bonds, 210 residues, 1 model selected  

> hide sel cartoons

> select #1/A:1-2

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> hide sel cartoons

> select #1/C:211-212

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select #1/C:211-250

685 atoms, 693 bonds, 40 residues, 1 model selected  

> hide sel cartoons

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-250

4139 atoms, 4178 bonds, 250 residues, 1 model selected  

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:101-335

3629 atoms, 3672 bonds, 235 residues, 1 model selected  

> hide sel cartoons

> save /Users/elena/Desktop/image19.png supersample 3

> select #1/B:101

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

> select #1/B:101-340

3721 atoms, 3752 bonds, 240 residues, 1 model selected  

> hide sel cartoons

> select #1/B:1

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

> select #1/B:1-100

1556 atoms, 1567 bonds, 100 residues, 1 model selected  

> hide sel cartoons

> select #1/C:329-330

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select #1/C:55-330

4335 atoms, 4380 bonds, 276 residues, 1 model selected  

> select #1/C:329

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

> select #1/C:1-329

5196 atoms, 5250 bonds, 329 residues, 1 model selected  

> show sel cartoons

> select clear

> save /Users/elena/Desktop/image20.png supersample 3

> select #1/C:101

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

> select #1/C:101-335

3629 atoms, 3672 bonds, 235 residues, 1 model selected  

> hide sel cartoons

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-100

1670 atoms, 1686 bonds, 100 residues, 1 model selected  

> hide sel cartoons

> select #1/A:162

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show sel cartoons

> select clear

> save /Users/elena/Desktop/image21.png supersample 3

> select #1/A:1

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

> select #1/A:1-5

63 atoms, 63 bonds, 5 residues, 1 model selected  

> select #1/A:162

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> hide sel cartoons

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> show sel cartoons

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> select clear

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:330-335

103 atoms, 108 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select #1/C:1-2

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select #1/C:1-9

172 atoms, 172 bonds, 9 residues, 1 model selected  

> select #1/C:329

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

> select #1/C:325-329

64 atoms, 63 bonds, 5 residues, 1 model selected  

> select #1/C:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-9

172 atoms, 172 bonds, 9 residues, 1 model selected  

> select #1/B:176-177

26 atoms, 25 bonds, 2 residues, 1 model selected  

> select #1/B:176-201

345 atoms, 347 bonds, 26 residues, 1 model selected  

> select #1/B:340

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

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/A:1

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> hide sel cartoons

> select #1/B:340

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

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> hide sel cartoons

> select #1/A:9

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

> select #1/A:9-80

1229 atoms, 1246 bonds, 72 residues, 1 model selected  

> select #1/A:121

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:121-153

477 atoms, 482 bonds, 33 residues, 1 model selected  

> select #1/A:161-162

43 atoms, 43 bonds, 2 residues, 1 model selected  

> select #1/A:121-162

638 atoms, 646 bonds, 42 residues, 1 model selected  

> hide #1 models

> hide #2.1 models

> combine #1 and #2

Expected a keyword  

> combine #1 and #2 name combined refSpec #2

Expected a keyword  

> combine #1 #2 [close falce] [modelID 3] [name combined]

Expected a keyword  

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

13130 atoms, 13270 bonds, 837 residues, 1 model selected  

> select add #2

24894 atoms, 25834 bonds, 1 pseudobond, 1884 residues, 3 models selected  

> select subtract #1

11764 atoms, 12564 bonds, 1 pseudobond, 1047 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2.1

1 pseudobond, 1 model selected  

> select subtract #2.1

Nothing selected  

> select add #2

11764 atoms, 12564 bonds, 1 pseudobond, 1047 residues, 2 models selected  

> select subtract #2

Nothing selected  

> combine #1 #2

Remapping chain ID 'A' in refined-coot-5.pdb #2 to 'K'  
Remapping chain ID 'B' in refined-coot-5.pdb #2 to 'L'  
Remapping chain ID 'C' in refined-coot-5.pdb #2 to 'M'  

> hide #!7 models

> show #!7 models

> select add #7

24894 atoms, 25834 bonds, 1 pseudobond, 1884 residues, 2 models selected  

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!7 models

> undo

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> show #!7 atoms

> select #1/A:162

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show #!7 cartoons

> select #1/B:1

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

> select #1/B:1-220

3377 atoms, 3400 bonds, 220 residues, 1 model selected  

> show #!7 cartoons

> hide #!7 atoms

> select #1/B:1

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

> select #1/B:1-340

5277 atoms, 5320 bonds, 340 residues, 1 model selected  

> show #!7 cartoons

> select #1/A:162

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

> select #1/A:1-162

2554 atoms, 2591 bonds, 162 residues, 1 model selected  

> show #!7 cartoons

> select #1/C:335

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/C:1-335

5299 atoms, 5359 bonds, 335 residues, 1 model selected  

> show #!7 cartoons

> set bgColor black

> set bgColor transparent

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/elena/Desktop/movie10.mp4

Movie saved to /Users/elena/Desktop/movie10.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/elena/Desktop/movie11.mp4

Movie saved to /Users/elena/Desktop/movie11.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/elena/Desktop/movie12.mp4

Movie saved to /Users/elena/Desktop/movie12.mp4  
  

> ui tool show XMAS

> open
> /Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks.txt

Unrecognized file suffix '.txt'  

> open
> /Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks.txt

Unrecognized file suffix '.txt'  
Please select pseudobonds  
Please select pseudobonds  
  
Peptide pair mapping of XlinkX evidence file:
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks.txt  
Unique peptide pairs: 108 out of 108  
Unique peptide pairs with pseudobonds: 60  
Pseudobonds are stored in
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks_7.pb  
Mapping information is stored in
/Users/elena/Downloads/20220909_EXPL6_NiKr_LC12-16_SA_Orbi4324_Sample02_fractionation_Crosslinks_7.tsv  
Please select pseudobonds  
/Users/elena/Library/Application Support/ChimeraX/1.4/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)  
/Users/elena/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/xmas/tool.py:1113: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all axes
decorations.  
plt.tight_layout()  
Venn diagrams can only be plotted for two or three groups  

> select clear


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 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 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
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: 3 days 18:58

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: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR 4K:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    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: 1.2
    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: 1.1.1
    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: 1.9
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    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: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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: 4.10.0
    kiwisolver: 1.4.2
    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: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openpyxl: 3.0.10
    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.5.0
    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: 3.0.29
    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: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    seaborn: 0.12.0
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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 Eric Pettersen, 3 years ago

Component:	Unassigned → Window Toolkit
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash disposing of Qt widgets during garbage collection

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ can't reproduce
Status:	accepted → closed

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