The following bug report has been submitted:
Platform: macOS-10.16-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.
I had just used the visualization button to edit the cut-off color and was moving around to model to get a view of it.
Fatal Python error: Segmentation fault
Thread 0x0000700013dec000 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010e1cbe00 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2776 in set_matrix
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 767 in set_projection_matrix
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 675 in _use_shader
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 751 in _opengl_shader
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 648 in shader
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 790 in _draw_geometry
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 759 in draw_self
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 752 in draw
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1539 in _draw_multiple
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1526 in draw_opaque
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1550 in draw_depth
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 231 in _draw_scene
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165 in draw
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/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 [1716]
Path: /Applications/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 [1716]
User ID: 501
Date/Time: 2022-08-02 16:08:31.910 -0500
OS Version: macOS 11.1 (20C69)
Report Version: 12
Anonymous UUID: C23B016C-A05B-49F4-7A04-7F2E7B85AC6E
Sleep/Wake UUID: 9481B9B3-6BDF-4459-B8B3-744CC759C18C
Time Awake Since Boot: 10000 seconds
Time Since Wake: 1700 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 0x00007fff2033f462 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff2036d610 pthread_kill + 263
2 libsystem_c.dylib 0x00007fff2024fba3 raise + 26
3 libsystem_platform.dylib 0x00007fff203b1d7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtWidgets 0x000000010d4f9dc7 QGridLayout::~QGridLayout() + 39
6 QtWidgets.abi3.so 0x000000010cf6a438 non-virtual thunk to sipQGridLayout::~sipQGridLayout() + 56
7 QtWidgets 0x000000010d4d5960 QBoxLayout::~QBoxLayout() + 176
8 QtWidgets.abi3.so 0x000000010cfdf307 sipQVBoxLayout::~sipQVBoxLayout() + 55
9 QtWidgets 0x000000010d50a98a QWidget::~QWidget() + 634
10 QtWidgets.abi3.so 0x000000010cffcf17 sipQWidget::~sipQWidget() + 55
11 QtCore 0x000000010c93029f QObjectPrivate::deleteChildren() + 159
12 QtWidgets 0x000000010d50ac10 QWidget::~QWidget() + 1280
13 QtWidgets.abi3.so 0x000000010cffcf17 sipQWidget::~sipQWidget() + 55
14 QtCore 0x000000010c93029f QObjectPrivate::deleteChildren() + 159
15 QtWidgets 0x000000010d50ac10 QWidget::~QWidget() + 1280
16 QtWidgets.abi3.so 0x000000010cfb0407 sipQDockWidget::~sipQDockWidget() + 55
17 sip.cpython-39-darwin.so 0x000000010ce882e7 forgetObject + 183
18 sip.cpython-39-darwin.so 0x000000010ce87fd5 sipWrapper_dealloc + 37
19 org.python.python 0x00000001031acb3b subtype_dealloc + 1019
20 org.python.python 0x000000010318b8c2 dict_dealloc + 162
21 org.python.python 0x00000001031be97f subtype_clear + 239
22 org.python.python 0x0000000103299c29 collect + 3193
23 org.python.python 0x000000010329a3c2 _PyObject_GC_Alloc + 338
24 org.python.python 0x00000001031abc3c PyType_GenericAlloc + 60
25 _ctypes.cpython-39-darwin.so 0x0000000109d71870 GenericPyCData_new + 48
26 org.python.python 0x00000001031aeeb6 type_call + 86
27 org.python.python 0x00000001031595b7 _PyObject_MakeTpCall + 359
28 org.python.python 0x0000000103231e9c call_function + 876
29 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
30 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
31 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
32 org.python.python 0x000000010315bd6a method_vectorcall + 202
33 org.python.python 0x0000000103231e0c call_function + 732
34 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554
35 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
36 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
37 org.python.python 0x0000000103231e0c call_function + 732
38 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
39 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
40 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
41 org.python.python 0x000000010315bd6a method_vectorcall + 202
42 org.python.python 0x0000000103231e0c call_function + 732
43 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554
44 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
45 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
46 org.python.python 0x0000000103231e0c call_function + 732
47 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
48 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
49 org.python.python 0x0000000103228e5a PyEval_EvalCodeEx + 154
50 arraydatatype.cpython-39-darwin.so 0x000000011f180ada __Pyx_PyFunction_FastCallDict + 314
51 arraydatatype.cpython-39-darwin.so 0x000000011f185c9c __pyx_pw_17OpenGL_accelerate_13arraydatatype_13ArrayDatatype_17asArray + 924
52 org.python.python 0x00000001031986db cfunction_call + 59
53 wrapper.cpython-39-darwin.so 0x000000011f1cff7c __Pyx_PyObject_CallOneArg + 268
54 wrapper.cpython-39-darwin.so 0x000000011f1cdb1c __pyx_f_17OpenGL_accelerate_7wrapper_19CallFuncPyConverter_c_call + 252
55 wrapper.cpython-39-darwin.so 0x000000011f1cadc0 __pyx_f_17OpenGL_accelerate_7wrapper_22PyArgCalculatorElement_c_call + 272
56 wrapper.cpython-39-darwin.so 0x000000011f1cbd77 __pyx_f_17OpenGL_accelerate_7wrapper_15PyArgCalculator_c_call + 183
57 wrapper.cpython-39-darwin.so 0x000000011f1dcfe7 __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 119
58 latebind.cpython-39-darwin.so 0x000000011f23949e __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 158
59 org.python.python 0x00000001031595b7 _PyObject_MakeTpCall + 359
60 org.python.python 0x0000000103231e9c call_function + 876
61 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554
62 org.python.python 0x0000000103159d28 function_code_fastcall + 104
63 org.python.python 0x0000000103231e0c call_function + 732
64 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
65 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
66 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
67 org.python.python 0x0000000103231e0c call_function + 732
68 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
69 org.python.python 0x0000000103159d28 function_code_fastcall + 104
70 org.python.python 0x0000000103231e0c call_function + 732
71 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
72 org.python.python 0x0000000103159d28 function_code_fastcall + 104
73 org.python.python 0x0000000103231e0c call_function + 732
74 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
75 org.python.python 0x0000000103159d28 function_code_fastcall + 104
76 org.python.python 0x0000000103231e0c call_function + 732
77 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
78 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
79 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
80 org.python.python 0x000000010315bd6a method_vectorcall + 202
81 org.python.python 0x0000000103231e0c call_function + 732
82 org.python.python 0x000000010322f3e8 _PyEval_EvalFrameDefault + 25880
83 org.python.python 0x0000000103159d28 function_code_fastcall + 104
84 org.python.python 0x0000000103231e0c call_function + 732
85 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
86 org.python.python 0x0000000103159d28 function_code_fastcall + 104
87 org.python.python 0x0000000103231e0c call_function + 732
88 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
89 org.python.python 0x0000000103159d28 function_code_fastcall + 104
90 org.python.python 0x0000000103231e0c call_function + 732
91 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
92 org.python.python 0x0000000103159d28 function_code_fastcall + 104
93 org.python.python 0x0000000103231e0c call_function + 732
94 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
95 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
96 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
97 org.python.python 0x0000000103231e0c call_function + 732
98 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
99 org.python.python 0x0000000103159d28 function_code_fastcall + 104
100 org.python.python 0x0000000103231e0c call_function + 732
101 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
102 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
103 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
104 org.python.python 0x000000010315bd6a method_vectorcall + 202
105 org.python.python 0x0000000103231e0c call_function + 732
106 org.python.python 0x000000010322f3e8 _PyEval_EvalFrameDefault + 25880
107 org.python.python 0x0000000103159d28 function_code_fastcall + 104
108 org.python.python 0x0000000103231e0c call_function + 732
109 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
110 org.python.python 0x0000000103159d28 function_code_fastcall + 104
111 org.python.python 0x000000010315bdb2 method_vectorcall + 274
112 QtCore.abi3.so 0x000000010c626607 PyQtSlot::call(_object*, _object*) const + 39
113 QtCore.abi3.so 0x000000010c626516 PyQtSlot::invoke(void**, _object*, void*, bool) const + 358
114 QtCore.abi3.so 0x000000010c627445 PyQtSlotProxy::unislot(void**) + 85
115 QtCore.abi3.so 0x000000010c6273ba PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
116 QtCore 0x000000010c9389e7 0x10c87c000 + 772583
117 QtCore 0x000000010c94d4d7 QTimer::timerEvent(QTimerEvent*) + 199
118 QtCore.abi3.so 0x000000010c515bf9 sipQTimer::timerEvent(QTimerEvent*) + 121
119 QtCore 0x000000010c930bad QObject::event(QEvent*) + 109
120 QtCore.abi3.so 0x000000010c515a7a sipQTimer::event(QEvent*) + 186
121 QtWidgets 0x000000010d4c7067 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
122 QtWidgets 0x000000010d4c8023 QApplication::notify(QObject*, QEvent*) + 499
123 QtWidgets.abi3.so 0x000000010cfe9829 sipQApplication::notify(QObject*, QEvent*) + 233
124 QtCore 0x000000010c8e7dca QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
125 QtCore 0x000000010ca73a01 QTimerInfoList::activateTimers() + 961
126 libqcocoa.dylib 0x000000011bf96885 0x11bf7e000 + 100485
127 com.apple.CoreFoundation 0x00007fff20465a0c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
128 com.apple.CoreFoundation 0x00007fff20465974 __CFRunLoopDoSource0 + 180
129 com.apple.CoreFoundation 0x00007fff204656ef __CFRunLoopDoSources0 + 248
130 com.apple.CoreFoundation 0x00007fff20464121 __CFRunLoopRun + 890
131 com.apple.CoreFoundation 0x00007fff204636ce CFRunLoopRunSpecific + 563
132 com.apple.HIToolbox 0x00007fff286e86d0 RunCurrentEventLoopInMode + 292
133 com.apple.HIToolbox 0x00007fff286e84cc ReceiveNextEventCommon + 709
134 com.apple.HIToolbox 0x00007fff286e81ef _BlockUntilNextEventMatchingListInModeWithFilter + 64
135 com.apple.AppKit 0x00007fff22c80de9 _DPSNextEvent + 883
136 com.apple.AppKit 0x00007fff22c7f5af -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
137 com.apple.AppKit 0x00007fff22c71b0a -[NSApplication run] + 586
138 libqcocoa.dylib 0x000000011bf9748c 0x11bf7e000 + 103564
139 QtCore 0x000000010c8f1516 QEventLoop::exec(QFlags) + 486
140 QtCore 0x000000010c8e83e5 QCoreApplication::exec() + 133
141 QtWidgets.abi3.so 0x000000010d0d690a meth_QApplication_exec(_object*, _object*) + 90
142 org.python.python 0x000000010319871d cfunction_call + 125
143 org.python.python 0x00000001031595b7 _PyObject_MakeTpCall + 359
144 org.python.python 0x0000000103231e9c call_function + 876
145 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554
146 org.python.python 0x0000000103159d28 function_code_fastcall + 104
147 org.python.python 0x000000010315bd6a method_vectorcall + 202
148 org.python.python 0x0000000103231e0c call_function + 732
149 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554
150 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
151 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
152 org.python.python 0x0000000103231e0c call_function + 732
153 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
154 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
155 org.python.python 0x0000000103228dab PyEval_EvalCode + 139
156 org.python.python 0x0000000103225c12 builtin_exec + 626
157 org.python.python 0x0000000103198023 cfunction_vectorcall_FASTCALL + 195
158 org.python.python 0x0000000103231e0c call_function + 732
159 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
160 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
161 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
162 org.python.python 0x0000000103231e0c call_function + 732
163 org.python.python 0x000000010322f34b _PyEval_EvalFrameDefault + 25723
164 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
165 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
166 org.python.python 0x0000000103298870 pymain_run_module + 208
167 org.python.python 0x0000000103297f87 Py_RunMain + 1431
168 org.python.python 0x000000010329858f pymain_main + 223
169 org.python.python 0x000000010329849b Py_Main + 43
170 edu.ucsf.cgl.ChimeraX 0x000000010310edc8 main + 120
171 libdyld.dylib 0x00007fff20388621 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff20338f86 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff2036b07c cthread_yield + 11
2 libopenblas64_.0.dylib 0x0000000103ed144b blas_thread_server + 123
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 2:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff20341dde kevent64 + 10
1 QtWebEngineCore 0x00000001145da5ca 0x110678000 + 66463178
2 QtWebEngineCore 0x00000001145da4c7 0x110678000 + 66462919
3 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
4 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
5 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
6 QtWebEngineCore 0x000000011456084d 0x110678000 + 65964109
7 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
8 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
9 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 3:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292
5 QtWebEngineCore 0x000000011456d37d 0x110678000 + 66016125
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 4:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff20341dde kevent64 + 10
1 QtWebEngineCore 0x00000001145da5ca 0x110678000 + 66463178
2 QtWebEngineCore 0x00000001145da4c7 0x110678000 + 66462919
3 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
4 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
5 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
6 QtWebEngineCore 0x000000011349fe32 0x110678000 + 48397874
7 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
8 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
9 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 6:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292
5 QtWebEngineCore 0x000000011456d40d 0x110678000 + 66016269
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 7:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 QtWebEngineCore 0x00000001145a08bb 0x110678000 + 66226363
3 QtWebEngineCore 0x000000011667155d 0x110678000 + 100635997
4 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
5 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 8:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 9:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff20341dde kevent64 + 10
1 QtWebEngineCore 0x00000001145da5ca 0x110678000 + 66463178
2 QtWebEngineCore 0x00000001145da4c7 0x110678000 + 66462919
3 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
4 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
5 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
6 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
7 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
8 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 11:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 12:: NetworkService
0 libsystem_kernel.dylib 0x00007fff20341dde kevent64 + 10
1 QtWebEngineCore 0x00000001145da5ca 0x110678000 + 66463178
2 QtWebEngineCore 0x00000001145da4c7 0x110678000 + 66462919
3 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
4 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
5 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
6 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
7 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
8 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292
5 QtWebEngineCore 0x000000011456d46d 0x110678000 + 66016365
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 16:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff20465bf7 __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff204642ca __CFRunLoopRun + 1315
4 com.apple.CoreFoundation 0x00007fff204636ce CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff22e06c16 _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 17:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x00000001145a878f 0x110678000 + 66258831
4 QtWebEngineCore 0x00000001144de089 0x110678000 + 65429641
5 QtWebEngineCore 0x000000011455719c 0x110678000 + 65925532
6 QtWebEngineCore 0x000000011450eff8 0x110678000 + 65630200
7 QtWebEngineCore 0x0000000114579458 0x110678000 + 66065496
8 QtWebEngineCore 0x00000001145795ea 0x110678000 + 66065898
9 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
10 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 18:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d53a 0x110678000 + 66016570
5 QtWebEngineCore 0x000000011456d3ad 0x110678000 + 66016173
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 19:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292
5 QtWebEngineCore 0x000000011456d37d 0x110678000 + 66016125
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 interpreter.cpython-39-darwin.so 0x000000012c758fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 interpreter.cpython-39-darwin.so 0x000000012c758fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 interpreter.cpython-39-darwin.so 0x000000012c758fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 interpreter.cpython-39-darwin.so 0x000000012c758fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 libopenblas.0.dylib 0x000000013904ca9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 25:
0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0
Thread 26:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60
2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398
3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559
4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292
5 QtWebEngineCore 0x000000011456d40d 0x110678000 + 66016269
6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416
7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 27:
0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0
Thread 28:
0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0
Thread 29:
0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254
2 org.python.python 0x000000010328879c PyThread_acquire_lock_timed + 700
3 org.python.python 0x00000001032d769f acquire_timed + 111
4 org.python.python 0x00000001032d77b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010316214e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x0000000103231e0c call_function + 732
7 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
9 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x0000000103231e0c call_function + 732
11 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611
13 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x0000000103231e0c call_function + 732
15 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x0000000103159d28 function_code_fastcall + 104
17 org.python.python 0x0000000103231e0c call_function + 732
18 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x0000000103159d28 function_code_fastcall + 104
20 org.python.python 0x0000000103231e0c call_function + 732
21 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x0000000103159d28 function_code_fastcall + 104
23 org.python.python 0x000000010315bdb2 method_vectorcall + 274
24 org.python.python 0x00000001032d7046 t_bootstrap + 70
25 org.python.python 0x00000001032882f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224
27 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15
Thread 30:
0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010e1cbe00 rcx: 0x00007faf44955a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007faf44955a80 rsp: 0x00007faf44955a58
r8: 0x00007faf44955f48 r9: 0x484b8db02a8808c8 r10: 0x000000010e1cbe00 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007faf389a3af0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff2033f462 rfl: 0x0000000000000246 cr2: 0x00007faf44955f48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
49 8b 87 60 01 00 00 48-85 c0 74 59 49 8b 0e 48 I..`...H..tYI..H
85 c9 74 07 8b 09 83 f9-02 7c 15 4c 89 f7 31 f6 ..t......|.L..1.
31 d2 31 c9 e8 ef 5b 00-00 49 8b 87 60 01 00 00 1.1...[..I..`...
49 8b 8f 58 01 00 00 48-8b 19 48 83 c1 08 49 89 I..X...H..H...I.
8f 58 01 00 00 48 83 c0-ff 49 89 87 60 01 00 00 .X...H...I..`...
48 85 db 74 b2 48 8b 3b-48 85 ff 74 9b 48 8b 07 H..t.H.;H..t.H..
[ff]50 08 eb 93 49 8b 9f-e8 00 00 00 48 85 db 74 .P...I......H..t .H...[A^A_].f.
0f 1f 84 00 00 00 00 00-55 48 89 e5 53 50 48 89 ........UH..SPH.
Thread 0 last branch register state not available.
Binary Images:
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0x107ae5000 - 0x107bfcfff +libgfortran.3.dylib (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
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0x107cb4000 - 0x107cc9fff +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
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0x138430000 - 0x1388bbfff +_sparsetools.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/_sparsetools.cpython-39-darwin.so
0x1389fc000 - 0x138a6ffff +_csparsetools.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/_csparsetools.cpython-39-darwin.so
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0x138b68000 - 0x138b83fff +_traversal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/csgraph/_traversal.cpython-39-darwin.so
0x138b9b000 - 0x138bbafff +_min_spanning_tree.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/csgraph/_min_spanning_tree.cpython-39-darwin.so
0x138bd4000 - 0x138bfbfff +_flow.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/csgraph/_flow.cpython-39-darwin.so
0x138c1e000 - 0x138c51fff +_matching.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/csgraph/_matching.cpython-39-darwin.so
0x138c75000 - 0x138ca0fff +_reordering.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/csgraph/_reordering.cpython-39-darwin.so
0x138cc4000 - 0x138cf3fff +_iterative.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/sparse/linalg/isolve/_iterative.cpython-39-darwin.so
0x138d14000 - 0x13c8c7fff +libopenblas.0.dylib (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/.dylibs/libopenblas.0.dylib
0x13eb64000 - 0x13ebbffff +_fblas.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/linalg/_fblas.cpython-39-darwin.so
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0x13ef31000 - 0x13ef9cfff +cython_lapack.cpython-39-darwin.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/linalg/cython_lapack.cpython-39-darwin.so
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0x7fff56430000 - 0x7fff56433fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff6294d000 - 0x7fff62a30fff com.apple.driver.AppleIntelBDWGraphicsMTLDriver (16.1.7.1 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsMTLDriver
0x7fff64446000 - 0x7fff6494dfff com.apple.driver.AppleIntelBDWGraphicsGLDriver (16.1.7.1 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsGLDriver
0x7fff6c83c000 - 0x7fff6c842fff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6c843000 - 0x7fff6c847fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6c848000 - 0x7fff6c857fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6c858000 - 0x7fff6c85afff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6c85b000 - 0x7fff6c863fff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6c864000 - 0x7fff6c897fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6c898000 - 0x7fff6c8d4fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6c8d5000 - 0x7fff6ca69fff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6ca6a000 - 0x7fff6ca74fff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6ca75000 - 0x7fff6cbf0fff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6cbf1000 - 0x7fff6cc1afff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6deab000 - 0x7fff6df03fff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6ef82000 - 0x7fff6ef89fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff742fb000 - 0x7fff74306fff com.apple.SymptomAnalytics (1.0 - 1431.60.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff74524000 - 0x7fff7453cfff com.apple.SymptomPresentationFeed (1.0 - 1431.60.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff783c3000 - 0x7fff783cafff libRosetta.dylib (203.13.2) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 4
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: 6997
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)
Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 816K 6
CG image 184K 29
CoreAnimation 84K 17
CoreGraphics 12K 2
CoreServices 764K 3
CoreUI image data 1608K 28
Foundation 36K 2
Kernel Alloc Once 8K 1
MALLOC 534.9M 787
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 120K 30
Stack 173.7M 31
Stack Guard 56.0M 1
VM_ALLOCATE 86.8M 116
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__CTF 759 1
__DATA 42.6M 793
__DATA_CONST 25.7M 313
__DATA_DIRTY 1707K 210
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 537.8M 368
__OBJC_RO 60.5M 1
__OBJC_RW 2452K 2
__TEXT 747.7M 750
__UNICODE 588K 1
mapped file 274.8M 59
shared memory 2240K 13
=========== ======= =======
TOTAL 2.8G 3587
TOTAL, minus reserved VM space 2.5G 3587
===== 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
> open 6ysz format mmcif fromDatabase pdb
6ysz title:
Cryo-EM structure of T7 bacteriophage DNA translocation gp15 core protein
intermediate assembly [more info...]
Chain information for 6ysz #1
---
Chain | Description | UniProt
A B C D E F | Internal virion protein gp15 | GP15_BPT7
> save "/Users/simone/Documents/UT/marcotte/chimerax
> sessions/6ysz_crosslinks.cxs"
> select /E:374@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
2532 atoms, 2569 bonds, 316 residues, 1 model selected
> ribbon sel
> clear sel
Unknown command: clear sel
> clear select
Unknown command: clear select
> select clear
> select /F:374@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
2532 atoms, 2569 bonds, 316 residues, 1 model selected
> ribbon sel
> select clear
> select /C:373@C
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
2532 atoms, 2569 bonds, 316 residues, 1 model selected
> ribbon sel
> select clear
> hide
> save "/Users/simone/Documents/UT/marcotte/chimerax
> sessions/6ysz_crosslinks.cxs"
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file:
/Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks.csv
Unique peptide pairs: 280 out of 281
Unique peptide pairs with pseudobonds: 12
Pseudobonds are stored in
/Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks_1.pb
Mapping information is stored in
/Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks_1.tsv
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
> select subtract #2
Nothing selected
===== 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 INTEL-16.1.7
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel 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 Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 425.0.0.0.0
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 11.1 (20C69)
Kernel Version: Darwin 20.2.0
Time since boot: 4:44
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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: 1.4.3
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: 0.11.2
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Simone,
--Eric