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Opened 2 years ago
Closed 2 years ago
#9783 closed defect (nonchimerax)
Graphics crash, macOS 10.15.7, Intel HD Graphics 6000
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000112984dc0 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2730 in draw_elements
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1740 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 840 in _draw_geometry
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 775 in draw_self
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 768 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1555 in _draw_multiple
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1542 in draw_opaque
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame
File "/Applications/ChimeraX-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [5772]
Path: /Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.6.1 (1.6.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [5772]
User ID: 501
Date/Time: 2023-09-14 14:02:21.149 -0400
OS Version: Mac OS X 10.15.7 (19H1824)
Report Version: 12
Anonymous UUID: C990FE9C-CA33-F0FB-E7E8-A8F33C381FB7
Sleep/Wake UUID: 7055915E-D378-434D-AC46-D8B042A9BE38
Time Awake Since Boot: 18000 seconds
Time Since Wake: 7400 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics hardware encountered an error and was reset: 0x00000813
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff67ff032a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff680ace60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff67f0793e raise + 26
3 libsystem_platform.dylib 0x00007fff680a15fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff67f77808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff4f4de0a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff4f4d518f gpusGenerateCrashLog + 89
8 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff238d9640 gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff4f4d66a1 gpusSubmitDataBuffers + 490
10 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff234b1412 IntelCommandBuffer::getNew(GLDContextRec*) + 48
11 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff234b126c intelSubmitCommands + 171
12 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff234ace2f updateDispatch + 6858
13 GLEngine 0x00007fff38c4d74c gleDoDrawDispatchCoreGL3 + 693
14 GLEngine 0x00007fff38c21fb6 glDrawElementsInstanced_ACC_GL3Exec + 290
15 libffi.dylib 0x00007fff65c4a905 ffi_call_unix64 + 85
16 libffi.dylib 0x00007fff65c4a244 ffi_call_int + 694
17 _ctypes.cpython-39-darwin.so 0x000000010b77ad0d _ctypes_callproc + 1037
18 _ctypes.cpython-39-darwin.so 0x000000010b774a96 PyCFuncPtr_call + 1206
19 org.python.python 0x0000000104a38adc _PyObject_Call + 140
20 org.python.python 0x0000000104a91526 slot_tp_call + 230
21 wrapper.cpython-39-darwin.so 0x00000001208c12ae __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 830
22 latebind.cpython-39-darwin.so 0x000000012092149e __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 158
23 org.python.python 0x0000000104a385b7 _PyObject_MakeTpCall + 359
24 org.python.python 0x0000000104b10e9c call_function + 876
25 org.python.python 0x0000000104b0e2a2 _PyEval_EvalFrameDefault + 25554
26 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
27 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
28 org.python.python 0x0000000104b10e0c call_function + 732
29 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
30 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
31 org.python.python 0x0000000104b10e0c call_function + 732
32 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
33 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
34 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
35 org.python.python 0x0000000104a3ad6a method_vectorcall + 202
36 org.python.python 0x0000000104b10e0c call_function + 732
37 org.python.python 0x0000000104b0e3e8 _PyEval_EvalFrameDefault + 25880
38 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
39 org.python.python 0x0000000104b10e0c call_function + 732
40 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
41 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
42 org.python.python 0x0000000104b10e0c call_function + 732
43 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
44 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
45 org.python.python 0x0000000104b10e0c call_function + 732
46 org.python.python 0x0000000104b0e34b _PyEval_EvalFrameDefault + 25723
47 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
48 org.python.python 0x0000000104b10e0c call_function + 732
49 org.python.python 0x0000000104b0e34b _PyEval_EvalFrameDefault + 25723
50 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
51 org.python.python 0x0000000104b10e0c call_function + 732
52 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
53 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
54 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
55 org.python.python 0x0000000104b10e0c call_function + 732
56 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
57 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
58 org.python.python 0x0000000104a3ad6a method_vectorcall + 202
59 org.python.python 0x0000000104b10e0c call_function + 732
60 org.python.python 0x0000000104b0e2a2 _PyEval_EvalFrameDefault + 25554
61 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
62 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
63 org.python.python 0x0000000104a3ad6a method_vectorcall + 202
64 org.python.python 0x0000000104b10e0c call_function + 732
65 org.python.python 0x0000000104b0e2a2 _PyEval_EvalFrameDefault + 25554
66 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
67 org.python.python 0x0000000104b10e0c call_function + 732
68 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
69 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
70 org.python.python 0x0000000104b10e0c call_function + 732
71 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
72 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
73 org.python.python 0x0000000104b10e0c call_function + 732
74 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
75 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
76 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
77 org.python.python 0x0000000104b10e0c call_function + 732
78 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
79 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
80 org.python.python 0x0000000104b10e0c call_function + 732
81 org.python.python 0x0000000104b0e27e _PyEval_EvalFrameDefault + 25518
82 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
83 org.python.python 0x0000000104a3adb2 method_vectorcall + 274
84 QtCore.abi3.so 0x000000010e048298 PyQtSlot::call(_object*, _object*) const + 40
85 QtCore.abi3.so 0x000000010e04819a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362
86 QtCore.abi3.so 0x000000010e0491a5 PyQtSlotProxy::unislot(void**) + 85
87 QtCore.abi3.so 0x000000010e04911a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
88 QtCore 0x000000010e3322be 0x10e275000 + 774846
89 QtCore 0x000000010e34680a QTimer::timerEvent(QTimerEvent*) + 202
90 QtCore.abi3.so 0x000000010df3a9a9 sipQTimer::timerEvent(QTimerEvent*) + 121
91 QtCore 0x000000010e32a52d QObject::event(QEvent*) + 109
92 QtCore.abi3.so 0x000000010df3a82a sipQTimer::event(QEvent*) + 186
93 QtWidgets 0x00000001109e79c7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
94 QtWidgets 0x00000001109e890c QApplication::notify(QObject*, QEvent*) + 508
95 QtWidgets.abi3.so 0x0000000110536186 sipQApplication::notify(QObject*, QEvent*) + 230
96 QtCore 0x000000010e2e312a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
97 QtCore 0x000000010e46cc21 QTimerInfoList::activateTimers() + 993
98 libqcocoa.dylib 0x000000011e1c4aa5 0x11e1af000 + 88741
99 com.apple.CoreFoundation 0x00007fff2e227682 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
100 com.apple.CoreFoundation 0x00007fff2e227621 __CFRunLoopDoSource0 + 103
101 com.apple.CoreFoundation 0x00007fff2e22743b __CFRunLoopDoSources0 + 209
102 com.apple.CoreFoundation 0x00007fff2e22616a __CFRunLoopRun + 927
103 com.apple.CoreFoundation 0x00007fff2e22576e CFRunLoopRunSpecific + 462
104 com.apple.HIToolbox 0x00007fff2ce51aad RunCurrentEventLoopInMode + 292
105 com.apple.HIToolbox 0x00007fff2ce517c5 ReceiveNextEventCommon + 584
106 com.apple.HIToolbox 0x00007fff2ce51569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
107 com.apple.AppKit 0x00007fff2b49a659 _DPSNextEvent + 883
108 com.apple.AppKit 0x00007fff2b498ea0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
109 com.apple.AppKit 0x00007fff2b48abae -[NSApplication run] + 658
110 libqcocoa.dylib 0x000000011e1c5753 0x11e1af000 + 91987
111 QtCore 0x000000010e2ec4b6 QEventLoop::exec(QFlags) + 486
112 QtCore 0x000000010e2e3725 QCoreApplication::exec() + 133
113 QtWidgets.abi3.so 0x000000011062254a meth_QApplication_exec(_object*, _object*) + 90
114 org.python.python 0x0000000104a7771d cfunction_call + 125
115 org.python.python 0x0000000104a385b7 _PyObject_MakeTpCall + 359
116 org.python.python 0x0000000104b10e9c call_function + 876
117 org.python.python 0x0000000104b0e2a2 _PyEval_EvalFrameDefault + 25554
118 org.python.python 0x0000000104a38d28 function_code_fastcall + 104
119 org.python.python 0x0000000104a3ad6a method_vectorcall + 202
120 org.python.python 0x0000000104b10e0c call_function + 732
121 org.python.python 0x0000000104b0e2a2 _PyEval_EvalFrameDefault + 25554
122 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
123 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
124 org.python.python 0x0000000104b10e0c call_function + 732
125 org.python.python 0x0000000104b0e34b _PyEval_EvalFrameDefault + 25723
126 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
127 org.python.python 0x0000000104b07dab PyEval_EvalCode + 139
128 org.python.python 0x0000000104b04c12 builtin_exec + 626
129 org.python.python 0x0000000104a77023 cfunction_vectorcall_FASTCALL + 195
130 org.python.python 0x0000000104b10e0c call_function + 732
131 org.python.python 0x0000000104b0e34b _PyEval_EvalFrameDefault + 25723
132 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
133 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
134 org.python.python 0x0000000104b10e0c call_function + 732
135 org.python.python 0x0000000104b0e34b _PyEval_EvalFrameDefault + 25723
136 org.python.python 0x0000000104b11b03 _PyEval_EvalCode + 2611
137 org.python.python 0x0000000104a38cb1 _PyFunction_Vectorcall + 289
138 org.python.python 0x0000000104b77870 pymain_run_module + 208
139 org.python.python 0x0000000104b76f87 Py_RunMain + 1431
140 org.python.python 0x0000000104b7758f pymain_main + 223
141 org.python.python 0x0000000104b7749b Py_Main + 43
142 edu.ucsf.cgl.ChimeraX 0x00000001049eedc8 main + 120
143 libdyld.dylib 0x00007fff67ea8cc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff67ff2b86 kevent64 + 10
1 QtWebEngineCore 0x0000000116e943ca 0x1129bf000 + 72176586
2 QtWebEngineCore 0x0000000116e9426f 0x1129bf000 + 72176239
3 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
4 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
5 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
6 QtWebEngineCore 0x0000000116e41aad 0x1129bf000 + 71838381
7 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
8 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
9 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4eafd 0x1129bf000 + 71891709
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff67ff2b86 kevent64 + 10
1 QtWebEngineCore 0x0000000116e943ca 0x1129bf000 + 72176586
2 QtWebEngineCore 0x0000000116e9426f 0x1129bf000 + 72176239
3 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
4 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
5 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
6 QtWebEngineCore 0x0000000114678572 0x1129bf000 + 30119282
7 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
8 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
9 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 5:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116db8e08 0x1129bf000 + 71278088
4 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
5 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
6 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
7 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
8 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
9 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 6:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff67ff2b86 kevent64 + 10
1 QtWebEngineCore 0x0000000116e943ca 0x1129bf000 + 72176586
2 QtWebEngineCore 0x0000000116e9426f 0x1129bf000 + 72176239
3 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
4 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
5 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
6 QtWebEngineCore 0x0000000119aba882 0x1129bf000 + 118470786
7 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
8 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
9 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 7:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff67fec872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff680ad425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000116e85e22 0x1129bf000 + 72117794
3 QtWebEngineCore 0x00000001190c8505 0x1129bf000 + 108041477
4 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
5 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 8:: ThreadPoolSingleThreadSharedForeground0
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4ebbd 0x1129bf000 + 71891901
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 10:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 11:: NetworkService
0 libsystem_kernel.dylib 0x00007fff67ff2b86 kevent64 + 10
1 QtWebEngineCore 0x0000000116e943ca 0x1129bf000 + 72176586
2 QtWebEngineCore 0x0000000116e9426f 0x1129bf000 + 72176239
3 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
4 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
5 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
6 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
7 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
8 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 13:: ThreadPoolSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4ebed 0x1129bf000 + 71891949
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 15:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2e227825 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2e2262f2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2e22576e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2b63bea4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 16:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e8d71f 0x1129bf000 + 72148767
4 QtWebEngineCore 0x0000000116db8e69 0x1129bf000 + 71278185
5 QtWebEngineCore 0x0000000116e34ff3 0x1129bf000 + 71786483
6 QtWebEngineCore 0x0000000116deca32 0x1129bf000 + 71490098
7 QtWebEngineCore 0x0000000116e5ba58 0x1129bf000 + 71944792
8 QtWebEngineCore 0x0000000116e5bbea 0x1129bf000 + 71945194
9 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
10 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking2
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4ed0c 0x1129bf000 + 71892236
5 QtWebEngineCore 0x0000000116e4eb2d 0x1129bf000 + 71891757
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff67fec872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff680ad425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010585e23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 19:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4eafd 0x1129bf000 + 71891709
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 20:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4eb8d 0x1129bf000 + 71891853
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 21:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff67fe9dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67fea160 mach_msg + 60
2 QtWebEngineCore 0x0000000116e8d933 0x1129bf000 + 72149299
3 QtWebEngineCore 0x0000000116e4e4af 0x1129bf000 + 71890095
4 QtWebEngineCore 0x0000000116e4f057 0x1129bf000 + 71893079
5 QtWebEngineCore 0x0000000116e4eb8d 0x1129bf000 + 71891853
6 QtWebEngineCore 0x0000000116e87458 0x1129bf000 + 72123480
7 libsystem_pthread.dylib 0x00007fff680ad109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff680a8b8b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff680a8b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000112984dc0 rcx: 0x00007fe2cc055a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fe2cc055a80 rsp: 0x00007fe2cc055a58
r8: 0x00007fe2cc055f48 r9: 0x4fc0a50a9ccef1ca r10: 0x0000000112984dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fe2cc90c3f8 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff67ff032a rfl: 0x0000000000000246 cr2: 0x00007fe2cc39bbe0
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x1049f9000 - 0x104c61fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
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0x104e7c000 - 0x104e7dfff +_random.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_random.cpython-39-darwin.so
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0x104e95000 - 0x104e95fff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x104e9f000 - 0x104f40ff7 +libarrays.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x104f66000 - 0x104f6bfff +_json.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_json.cpython-39-darwin.so
0x104f75000 - 0x1053bcfcb +_multiarray_umath.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so
0x105515000 - 0x109221e47 +libopenblas64_.0.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libopenblas64_.0.dylib
0x1094e1000 - 0x1095f8ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x109667000 - 0x10969dfff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x1096b3000 - 0x1096c8ff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x10b6da000 - 0x10b6e9fff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x10b6fd000 - 0x10b714fff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x10b727000 - 0x10b73affb +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x10b757000 - 0x10b759fff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x10b763000 - 0x10b767ff7 +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
0x10b771000 - 0x10b782ff7 +_ctypes.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so
0x10b79b000 - 0x10b7b6fff +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
0x10b7d3000 - 0x10b7e6fff +_pocketfft_internal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/fft/_pocketfft_internal.cpython-39-darwin.so
0x10b7f3000 - 0x10b866ff3 +mtrand.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/mtrand.cpython-39-darwin.so
0x10b8cb000 - 0x10b8eaff3 +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
0x10b90f000 - 0x10b946fff +_common.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_common.cpython-39-darwin.so
0x10b967000 - 0x10b96dfff +_hashlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_hashlib.cpython-39-darwin.so
0x10b97c000 - 0x10b9d5ff7 +libssl.1.1.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.1.1.dylib
0x10ba07000 - 0x10bc1e97f +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
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0x10bcce000 - 0x10bd21ff7 +_bounded_integers.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_bounded_integers.cpython-39-darwin.so
0x10bd52000 - 0x10bd61fff +_mt19937.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_mt19937.cpython-39-darwin.so
0x10bd76000 - 0x10bd85ff3 +_philox.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_philox.cpython-39-darwin.so
0x10bd9a000 - 0x10bda9fff +_pcg64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_pcg64.cpython-39-darwin.so
0x10bdbe000 - 0x10bdc5ff3 +_sfc64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_sfc64.cpython-39-darwin.so
0x10bdd6000 - 0x10be65ffb +_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_generator.cpython-39-darwin.so
0x10bed6000 - 0x10bed6fff +_opcode.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_opcode.cpython-39-darwin.so
0x10dee0000 - 0x10defeff3 +_geometry.cpython-39-darwin.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/geometry/_geometry.cpython-39-darwin.so
0x10df15000 - 0x10e09cffb +QtCore.abi3.so (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtCore.abi3.so
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0x7fff66db0000 - 0x7fff66dbeff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff66dbf000 - 0x7fff66dc2ff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff66dc3000 - 0x7fff66dc5fff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff66df4000 - 0x7fff66e0cfff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff66e0e000 - 0x7fff66e52ff7 libsandbox.1.dylib (1217.141.8) /usr/lib/libsandbox.1.dylib
0x7fff66e53000 - 0x7fff66e65ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff66e66000 - 0x7fff66e67ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff66e68000 - 0x7fff67052ff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff67146000 - 0x7fff67173ffb libssl.46.dylib (47.140.2) /usr/lib/libssl.46.dylib
0x7fff671f5000 - 0x7fff67226ff7 libtidy.A.dylib (17.3) /usr/lib/libtidy.A.dylib
0x7fff67248000 - 0x7fff672a2ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff672a3000 - 0x7fff672a6ffb libutil.dylib (57.140.1) /usr/lib/libutil.dylib
0x7fff672a7000 - 0x7fff672b4fff libxar.1.dylib (425.7) /usr/lib/libxar.1.dylib
0x7fff672ba000 - 0x7fff6739cfff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib
0x7fff673a0000 - 0x7fff673c8fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff673c9000 - 0x7fff673dbff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff67c8a000 - 0x7fff67c8fff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff67c90000 - 0x7fff67c9bfff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff67c9c000 - 0x7fff67ca3fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff67ca4000 - 0x7fff67cadff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff67cae000 - 0x7fff67d40fdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff67e4d000 - 0x7fff67e8dff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff67e8e000 - 0x7fff67ec4fff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff67ec5000 - 0x7fff67ec5ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff67ec6000 - 0x7fff67ed2ff3 libkxld.dylib (6153.141.59) /usr/lib/system/libkxld.dylib
0x7fff67ed3000 - 0x7fff67ed3ff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff67ed4000 - 0x7fff67ed9ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff67eda000 - 0x7fff67edcff3 libquarantine.dylib (110.40.6) /usr/lib/system/libquarantine.dylib
0x7fff67edd000 - 0x7fff67edeff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff67edf000 - 0x7fff67ef6ff3 libsystem_asl.dylib (377.60.4) /usr/lib/system/libsystem_asl.dylib
0x7fff67ef7000 - 0x7fff67ef7ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff67ef8000 - 0x7fff67f7ffff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff67f80000 - 0x7fff67f83ffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff67f84000 - 0x7fff67f87fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff67f88000 - 0x7fff67f90fff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff67f91000 - 0x7fff67f98fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff67f99000 - 0x7fff67f9affb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff67f9b000 - 0x7fff67fe8ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff67fe9000 - 0x7fff68015ff7 libsystem_kernel.dylib (6153.141.59) /usr/lib/system/libsystem_kernel.dylib
0x7fff68016000 - 0x7fff6805dfff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6805e000 - 0x7fff68085fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff68086000 - 0x7fff68093ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff68094000 - 0x7fff6809dff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6809e000 - 0x7fff680a6fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff680a7000 - 0x7fff680b1fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff680b2000 - 0x7fff680b6ff3 libsystem_sandbox.dylib (1217.141.8) /usr/lib/system/libsystem_sandbox.dylib
0x7fff680b7000 - 0x7fff680b9fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff680ba000 - 0x7fff680c1ffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff680c2000 - 0x7fff680d8ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff680da000 - 0x7fff680dfff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff680e0000 - 0x7fff68115ffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 5
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: 12513
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=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 640K 5
Activity Tracing 256K 1
CG backing stores 248K 2
CG image 256K 34
CoreAnimation 764K 75
CoreGraphics 8K 1
CoreImage 20K 4
CoreServices 12K 1
CoreUI image data 1560K 26
Foundation 20K 2
IOKit 7940K 1
Kernel Alloc Once 8K 1
MALLOC 720.6M 862
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 88K 22
Stack 161.7M 23
Stack Guard 56.0M 1
VM_ALLOCATE 83.0M 187
__DATA 62.6M 615
__DATA_CONST 56K 5
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 420.6M 273
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 616.3M 583
__UNICODE 564K 1
mapped file 114.5M 52
shared memory 2844K 26
=========== ======= =======
TOTAL 2.4G 2823
TOTAL, minus reserved VM space 2.2G 2823
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kelly/Desktop/Alphafold Figures /RMSD of Solved vs
> Predicted/ADGRF1/ADGRF1 Solved.cxs"
opened ChimeraX session
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/R
Alignment identifier is 3/R
> select #3/R:567
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:567-575
67 atoms, 68 bonds, 9 residues, 1 model selected
> color #3 white
> color sel yellow
> ui tool show Contacts
> contacts sel distanceOnly 3.0 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
0 distances
atom1 atom2 distance
No distances
> contacts sel distanceOnly 3.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
No atoms match given atom specifier
> select #3/R:567-568
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/R:567-575
67 atoms, 68 bonds, 9 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 3.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
9 distances
atom1 atom2 distance
GPR110_Gs complex_7wxw.pdb #3/R THR 567 OG1 GPR110_Gs complex_7wxw.pdb #3/R TYR 590 CE2 3.052
GPR110_Gs complex_7wxw.pdb #3/R PRO 575 CB GPR110_Gs complex_7wxw.pdb #3/R TRP 737 NE1 3.177
GPR110_Gs complex_7wxw.pdb #3/R PRO 575 CG GPR110_Gs complex_7wxw.pdb #3/R TRP 737 NE1 3.181
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R THR 810 CG2 3.182
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R HIS 820 CD2 3.236
GPR110_Gs complex_7wxw.pdb #3/R PRO 575 O GPR110_Gs complex_7wxw.pdb #3/R ARG 729 NH2 3.370
GPR110_Gs complex_7wxw.pdb #3/R PHE 569 N GPR110_Gs complex_7wxw.pdb #3/R THR 589 OG1 3.417
GPR110_Gs complex_7wxw.pdb #3/R SER 574 CB GPR110_Gs complex_7wxw.pdb #3/R THR 810 CG2 3.430
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R HIS 820 NE2 3.486
9 distances
> contacts sel distanceOnly 3.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
9 distances
atom1 atom2 distance
GPR110_Gs complex_7wxw.pdb #3/R THR 567 OG1 GPR110_Gs complex_7wxw.pdb #3/R TYR 590 CE2 3.052
GPR110_Gs complex_7wxw.pdb #3/R PRO 575 CB GPR110_Gs complex_7wxw.pdb #3/R TRP 737 NE1 3.177
GPR110_Gs complex_7wxw.pdb #3/R TRP 737 NE1 GPR110_Gs complex_7wxw.pdb #3/R PRO 575 CG 3.181
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R THR 810 CG2 3.182
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R HIS 820 CD2 3.236
GPR110_Gs complex_7wxw.pdb #3/R PRO 575 O GPR110_Gs complex_7wxw.pdb #3/R ARG 729 NH2 3.370
GPR110_Gs complex_7wxw.pdb #3/R PHE 569 N GPR110_Gs complex_7wxw.pdb #3/R THR 589 OG1 3.417
GPR110_Gs complex_7wxw.pdb #3/R THR 810 CG2 GPR110_Gs complex_7wxw.pdb #3/R SER 574 CB 3.430
GPR110_Gs complex_7wxw.pdb #3/R SER 570 OG GPR110_Gs complex_7wxw.pdb #3/R HIS 820 NE2 3.486
9 distances
> label sel attribute name
> select up
98 atoms, 96 bonds, 11 residues, 1 model selected
> show sel cartoons
> style sel stick
Changed 98 atom styles
> select ~sel
20468 atoms, 20866 bonds, 2 pseudobonds, 2263 residues, 7 models selected
> hide sel & #!3 cartoons
> undo
> select #3/R:567-568
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/R:567-575
67 atoms, 68 bonds, 9 residues, 1 model selected
> undo
> select #3/R:816
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:816
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #5.1 models
> ui tool show "Side View"
> select #3/R:575-576
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/R:575-576
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/R:733
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/R:733-734
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #3/R:649
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:649-650
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/R:647-648
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/R:647-648
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/R:647-648
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/R:647-648
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/R:567
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:567
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:577
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:577
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:840
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:840
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:836-837
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/R:836-837
17 atoms, 17 bonds, 2 residues, 1 model selected
> save /Users/kelly/Desktop/image5.png supersample 3
> hide #!3 models
> show #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:1-9
138 atoms, 139 bonds, 9 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 3.0 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
155 distances
atom1 atom2 distance
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A HIS 254 HD1 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A SER 8 HG best_model (3).pdb #2/A THR 244 O 2.018
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 HG 2.070
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 HH12 2.087
best_model (3).pdb #2/A PRO 9 HA best_model (3).pdb #2/A ARG 163 HH21 2.110
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A ALA 262 HA 2.130
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 HH21 2.154
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG13 2.164
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HE3 2.179
best_model (3).pdb #2/A THR 1 H best_model (3).pdb #2/A ALA 79 HB3 2.180
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 HG21 2.206
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A TRP 238 HE3 2.262
best_model (3).pdb #2/A LEU 6 HD11 best_model (3).pdb #2/A TRP 238 HH2 2.263
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD21 2.264
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CG1 2.310
best_model (3).pdb #2/A PHE 3 HD2 best_model (3).pdb #2/A THR 23 HG22 2.318
best_model (3).pdb #2/A THR 1 HB best_model (3).pdb #2/A ALA 79 HB1 2.342
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A GLY 241 HA2 2.352
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 HE1 2.354
best_model (3).pdb #2/A SER 2 HA best_model (3).pdb #2/A THR 23 HG21 2.380
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A PHE 257 HD1 2.381
best_model (3).pdb #2/A LEU 6 HA best_model (3).pdb #2/A TRP 168 HE1 2.389
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HB3 2.393
best_model (3).pdb #2/A PHE 3 O best_model (3).pdb #2/A PHE 257 HE1 2.401
best_model (3).pdb #2/A PHE 3 H best_model (3).pdb #2/A THR 23 HG21 2.423
best_model (3).pdb #2/A THR 1 HG23 best_model (3).pdb #2/A PHE 75 HZ 2.424
best_model (3).pdb #2/A THR 1 HG1 best_model (3).pdb #2/A ALA 79 HA 2.428
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD22 2.431
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 HD1 2.431
best_model (3).pdb #2/A SER 4 CB best_model (3).pdb #2/A HIS 254 HD1 2.434
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB1 2.443
best_model (3).pdb #2/A ILE 5 HD13 best_model (3).pdb #2/A VAL 166 HG22 2.475
best_model (3).pdb #2/A PHE 3 HE1 best_model (3).pdb #2/A TYR 102 OH 2.481
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A LEU 178 HD11 2.482
best_model (3).pdb #2/A SER 8 HB2 best_model (3).pdb #2/A HIS 254 HE1 2.486
best_model (3).pdb #2/A SER 8 HB3 best_model (3).pdb #2/A THR 244 HB 2.487
best_model (3).pdb #2/A PHE 3 H best_model (3).pdb #2/A THR 23 OG1 2.488
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB3 2.489
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A VAL 11 HG23 2.492
best_model (3).pdb #2/A PHE 3 HB3 best_model (3).pdb #2/A ALA 258 HA 2.507
best_model (3).pdb #2/A LEU 6 HD23 best_model (3).pdb #2/A PHE 75 HE2 2.509
best_model (3).pdb #2/A LEU 6 HD12 best_model (3).pdb #2/A TRP 238 HH2 2.515
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A VAL 11 HG22 2.518
best_model (3).pdb #2/A SER 2 OG best_model (3).pdb #2/A VAL 19 HG13 2.519
best_model (3).pdb #2/A MET 7 HG2 best_model (3).pdb #2/A PHE 257 HZ 2.522
best_model (3).pdb #2/A THR 1 H2 best_model (3).pdb #2/A ALA 79 HB3 2.528
best_model (3).pdb #2/A LEU 6 HD21 best_model (3).pdb #2/A TRP 168 CH2 2.536
best_model (3).pdb #2/A LEU 6 HD23 best_model (3).pdb #2/A PHE 75 HD2 2.537
best_model (3).pdb #2/A PHE 3 HD2 best_model (3).pdb #2/A ALA 262 HB1 2.538
best_model (3).pdb #2/A SER 4 OG best_model (3).pdb #2/A HIS 254 HD1 2.554
best_model (3).pdb #2/A LEU 6 HA best_model (3).pdb #2/A TRP 168 NE1 2.573
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HB 2.576
best_model (3).pdb #2/A PRO 9 HB2 best_model (3).pdb #2/A TRP 171 HB3 2.582
best_model (3).pdb #2/A MET 7 O best_model (3).pdb #2/A ILE 245 HG13 2.605
best_model (3).pdb #2/A LEU 6 HB3 best_model (3).pdb #2/A PHE 181 HE1 2.615
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 HD22 2.615
best_model (3).pdb #2/A MET 7 CE best_model (3).pdb #2/A TRP 238 HE3 2.628
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A PHE 257 HZ 2.629
best_model (3).pdb #2/A SER 2 OG best_model (3).pdb #2/A VAL 19 HG12 2.645
best_model (3).pdb #2/A SER 8 HB3 best_model (3).pdb #2/A THR 244 OG1 2.652
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A HIS 254 ND1 2.654
best_model (3).pdb #2/A PHE 3 CZ best_model (3).pdb #2/A LEU 27 HD21 2.655
best_model (3).pdb #2/A THR 1 OG1 best_model (3).pdb #2/A ALA 79 HA 2.668
best_model (3).pdb #2/A LEU 6 HD21 best_model (3).pdb #2/A TRP 168 CZ2 2.669
best_model (3).pdb #2/A PRO 9 HB2 best_model (3).pdb #2/A TRP 171 CG 2.673
best_model (3).pdb #2/A ILE 5 HG21 best_model (3).pdb #2/A PHE 75 HE2 2.689
best_model (3).pdb #2/A MET 7 HA best_model (3).pdb #2/A VAL 182 HG22 2.691
best_model (3).pdb #2/A PHE 3 CE2 best_model (3).pdb #2/A ALA 262 HA 2.692
best_model (3).pdb #2/A MET 7 HB3 best_model (3).pdb #2/A ILE 245 HD13 2.710
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A PHE 181 HE1 2.710
best_model (3).pdb #2/A LEU 6 HD21 best_model (3).pdb #2/A TRP 168 HH2 2.723
best_model (3).pdb #2/A SER 2 C best_model (3).pdb #2/A PHE 75 HZ 2.727
best_model (3).pdb #2/A PHE 3 CD2 best_model (3).pdb #2/A THR 23 HG22 2.728
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A TRP 238 CE3 2.729
best_model (3).pdb #2/A SER 2 HA best_model (3).pdb #2/A THR 23 OG1 2.732
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A HIS 254 HA 2.735
best_model (3).pdb #2/A SER 2 O best_model (3).pdb #2/A PHE 75 HZ 2.745
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A PHE 106 HZ 2.748
best_model (3).pdb #2/A THR 1 H3 best_model (3).pdb #2/A LYS 20 HE3 2.754
best_model (3).pdb #2/A PRO 9 HA best_model (3).pdb #2/A ARG 163 NH2 2.768
best_model (3).pdb #2/A LEU 6 HB2 best_model (3).pdb #2/A TRP 238 HZ3 2.772
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A PHE 181 HE1 2.772
best_model (3).pdb #2/A PRO 9 HB2 best_model (3).pdb #2/A TRP 171 HB2 2.774
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A HIS 254 HD1 2.777
best_model (3).pdb #2/A LEU 6 HB3 best_model (3).pdb #2/A TRP 238 HZ3 2.779
best_model (3).pdb #2/A MET 7 HG2 best_model (3).pdb #2/A TRP 238 HZ3 2.780
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A VAL 11 HG23 2.786
best_model (3).pdb #2/A THR 1 N best_model (3).pdb #2/A ALA 79 HB3 2.791
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A HIS 254 HD1 2.797
best_model (3).pdb #2/A PRO 9 C best_model (3).pdb #2/A ARG 163 HH21 2.797
best_model (3).pdb #2/A LEU 6 HD22 best_model (3).pdb #2/A TRP 168 CE2 2.800
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 HD21 2.803
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 CD2 2.806
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 HG13 2.816
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A ASP 72 OD1 2.819
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A TRP 238 HZ3 2.820
best_model (3).pdb #2/A LEU 6 CD1 best_model (3).pdb #2/A TRP 238 HH2 2.832
best_model (3).pdb #2/A LEU 6 HA best_model (3).pdb #2/A TRP 168 CE2 2.835
best_model (3).pdb #2/A THR 1 H best_model (3).pdb #2/A ALA 79 HB1 2.837
best_model (3).pdb #2/A SER 8 HG best_model (3).pdb #2/A HIS 254 HE1 2.843
best_model (3).pdb #2/A PRO 9 HB2 best_model (3).pdb #2/A TRP 171 CB 2.847
best_model (3).pdb #2/A SER 8 HA best_model (3).pdb #2/A ILE 245 HG13 2.856
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 CG 2.860
best_model (3).pdb #2/A PHE 3 HE1 best_model (3).pdb #2/A TYR 102 HE1 2.865
best_model (3).pdb #2/A PHE 3 C best_model (3).pdb #2/A PHE 257 HE1 2.865
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A PHE 181 HD1 2.866
best_model (3).pdb #2/A PRO 9 CA best_model (3).pdb #2/A ARG 163 HH21 2.874
best_model (3).pdb #2/A ILE 5 HD13 best_model (3).pdb #2/A VAL 166 HG21 2.876
best_model (3).pdb #2/A LEU 6 HD12 best_model (3).pdb #2/A TRP 238 HZ3 2.879
best_model (3).pdb #2/A SER 2 HB2 best_model (3).pdb #2/A VAL 19 HB 2.880
best_model (3).pdb #2/A PRO 9 HA best_model (3).pdb #2/A ARG 163 HH22 2.880
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 CD2 2.881
best_model (3).pdb #2/A MET 7 SD best_model (3).pdb #2/A VAL 182 HG22 2.885
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A TRP 238 HE3 2.886
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A THR 23 HG22 2.886
best_model (3).pdb #2/A THR 1 H3 best_model (3).pdb #2/A LYS 20 HG2 2.892
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 CE1 2.896
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A PHE 257 CZ 2.900
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 CB 2.902
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 HG22 2.903
best_model (3).pdb #2/A PHE 3 HD2 best_model (3).pdb #2/A THR 23 HA 2.910
best_model (3).pdb #2/A PHE 3 CE2 best_model (3).pdb #2/A LEU 27 HG 2.915
best_model (3).pdb #2/A SER 8 HB3 best_model (3).pdb #2/A THR 244 O 2.919
best_model (3).pdb #2/A MET 7 HB3 best_model (3).pdb #2/A ILE 245 HG12 2.921
best_model (3).pdb #2/A THR 1 HG23 best_model (3).pdb #2/A PHE 75 HE2 2.931
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 CD1 2.934
best_model (3).pdb #2/A SER 8 OG best_model (3).pdb #2/A THR 244 O 2.936
best_model (3).pdb #2/A PHE 3 CE2 best_model (3).pdb #2/A LEU 27 HD21 2.937
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A HIS 254 O 2.941
best_model (3).pdb #2/A LEU 6 HD21 best_model (3).pdb #2/A TRP 168 HZ2 2.944
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A TRP 168 HE1 2.948
best_model (3).pdb #2/A THR 1 H best_model (3).pdb #2/A ALA 79 CB 2.948
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CB 2.959
best_model (3).pdb #2/A LEU 6 HD22 best_model (3).pdb #2/A TRP 168 CD2 2.960
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 CG2 2.961
best_model (3).pdb #2/A SER 4 OG best_model (3).pdb #2/A VAL 19 HG12 2.963
best_model (3).pdb #2/A THR 1 O best_model (3).pdb #2/A PHE 75 HE1 2.964
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 NH1 2.964
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A VAL 11 CG2 2.964
best_model (3).pdb #2/A SER 8 OG best_model (3).pdb #2/A HIS 254 HE1 2.967
best_model (3).pdb #2/A MET 7 O best_model (3).pdb #2/A ILE 245 HD13 2.967
best_model (3).pdb #2/A SER 8 CB best_model (3).pdb #2/A HIS 254 HE1 2.971
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 NH2 2.971
best_model (3).pdb #2/A PHE 3 HB2 best_model (3).pdb #2/A PHE 257 HE1 2.972
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A PHE 257 HE2 2.973
best_model (3).pdb #2/A LEU 6 HD23 best_model (3).pdb #2/A PHE 75 CE2 2.977
best_model (3).pdb #2/A PRO 9 HB2 best_model (3).pdb #2/A TRP 171 CD1 2.983
best_model (3).pdb #2/A LEU 6 HD23 best_model (3).pdb #2/A PHE 75 CD2 2.984
best_model (3).pdb #2/A PHE 3 N best_model (3).pdb #2/A THR 23 HG21 2.986
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A ALA 258 HB3 2.988
best_model (3).pdb #2/A ILE 5 CD1 best_model (3).pdb #2/A VAL 166 HG21 2.989
best_model (3).pdb #2/A SER 2 OG best_model (3).pdb #2/A VAL 19 CG1 2.991
best_model (3).pdb #2/A THR 1 O best_model (3).pdb #2/A THR 23 HG21 2.992
best_model (3).pdb #2/A LEU 6 HD22 best_model (3).pdb #2/A TRP 168 CZ2 2.995
155 distances
> contacts sel distanceOnly 2.0 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
3 distances
atom1 atom2 distance
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A HIS 254 HD1 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A PHE 257 HE2 best_model (3).pdb #2/A TRP 238 HA 1.956
3 distances
> contacts sel distanceOnly 2.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
6 distances
atom1 atom2 distance
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A HIS 254 HD1 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A TRP 238 HA best_model (3).pdb #2/A PHE 257 HE2 1.956
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG13 2.164
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CG1 2.310
best_model (3).pdb #2/A HIS 254 HD1 best_model (3).pdb #2/A SER 4 CB 2.434
6 distances
> contacts sel distanceOnly 2.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
6 distances
atom1 atom2 distance
best_model (3).pdb #2/A HIS 254 HD1 best_model (3).pdb #2/A SER 4 HB3 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A TRP 238 HA best_model (3).pdb #2/A PHE 257 HE2 1.956
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG13 2.164
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CG1 2.310
best_model (3).pdb #2/A SER 4 CB best_model (3).pdb #2/A HIS 254 HD1 2.434
6 distances
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> undo
> select up
99 atoms, 97 bonds, 6 residues, 1 model selected
> select up
835 atoms, 844 bonds, 52 residues, 1 model selected
> select up
5304 atoms, 5379 bonds, 332 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> color #2 #919191ff
> color #2 white
> select #2/A:1-2
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #2/A:1-3
47 atoms, 47 bonds, 3 residues, 1 model selected
> select #2/A:1-2
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #2/A:1-9
138 atoms, 139 bonds, 9 residues, 1 model selected
> color sel yellow
> ui tool show Contacts
> contacts sel distanceOnly 2.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
40 distances
atom1 atom2 distance
best_model (3).pdb #2/A SER 4 HB3 best_model (3).pdb #2/A HIS 254 HD1 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A SER 8 HG best_model (3).pdb #2/A THR 244 O 2.018
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 HG 2.070
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 HH12 2.087
best_model (3).pdb #2/A PRO 9 HA best_model (3).pdb #2/A ARG 163 HH21 2.110
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A ALA 262 HA 2.130
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 HH21 2.154
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG13 2.164
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HE3 2.179
best_model (3).pdb #2/A THR 1 H best_model (3).pdb #2/A ALA 79 HB3 2.180
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 HG21 2.206
best_model (3).pdb #2/A MET 7 HE2 best_model (3).pdb #2/A TRP 238 HE3 2.262
best_model (3).pdb #2/A LEU 6 HD11 best_model (3).pdb #2/A TRP 238 HH2 2.263
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD21 2.264
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CG1 2.310
best_model (3).pdb #2/A PHE 3 HD2 best_model (3).pdb #2/A THR 23 HG22 2.318
best_model (3).pdb #2/A THR 1 HB best_model (3).pdb #2/A ALA 79 HB1 2.342
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A GLY 241 HA2 2.352
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 HE1 2.354
best_model (3).pdb #2/A SER 2 HA best_model (3).pdb #2/A THR 23 HG21 2.380
best_model (3).pdb #2/A SER 4 HG best_model (3).pdb #2/A PHE 257 HD1 2.381
best_model (3).pdb #2/A LEU 6 HA best_model (3).pdb #2/A TRP 168 HE1 2.389
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HB3 2.393
best_model (3).pdb #2/A PHE 3 O best_model (3).pdb #2/A PHE 257 HE1 2.401
best_model (3).pdb #2/A PHE 3 H best_model (3).pdb #2/A THR 23 HG21 2.423
best_model (3).pdb #2/A THR 1 HG23 best_model (3).pdb #2/A PHE 75 HZ 2.424
best_model (3).pdb #2/A THR 1 HG1 best_model (3).pdb #2/A ALA 79 HA 2.428
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD22 2.431
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 HD1 2.431
best_model (3).pdb #2/A SER 4 CB best_model (3).pdb #2/A HIS 254 HD1 2.434
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB1 2.443
best_model (3).pdb #2/A ILE 5 HD13 best_model (3).pdb #2/A VAL 166 HG22 2.475
best_model (3).pdb #2/A PHE 3 HE1 best_model (3).pdb #2/A TYR 102 OH 2.481
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A LEU 178 HD11 2.482
best_model (3).pdb #2/A SER 8 HB2 best_model (3).pdb #2/A HIS 254 HE1 2.486
best_model (3).pdb #2/A SER 8 HB3 best_model (3).pdb #2/A THR 244 HB 2.487
best_model (3).pdb #2/A PHE 3 H best_model (3).pdb #2/A THR 23 OG1 2.488
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB3 2.489
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A VAL 11 HG23 2.492
40 distances
> contacts sel distanceOnly 2.5 resSeparation 5 ignoreHiddenModels true select
> true dashes 1 showDist true reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: True
44 distances
atom1 atom2 distance
best_model (3).pdb #2/A HIS 254 HD1 best_model (3).pdb #2/A SER 4 HB3 1.750
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG12 1.852
best_model (3).pdb #2/A SER 8 HG best_model (3).pdb #2/A THR 244 O 2.018
best_model (3).pdb #2/A TRP 168 HE1 best_model (3).pdb #2/A LEU 178 HD11 2.054
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A LEU 27 HG 2.070
best_model (3).pdb #2/A PRO 9 O best_model (3).pdb #2/A ARG 163 HH12 2.087
best_model (3).pdb #2/A PRO 9 HA best_model (3).pdb #2/A ARG 163 HH21 2.110
best_model (3).pdb #2/A PHE 3 HE2 best_model (3).pdb #2/A ALA 262 HA 2.130
best_model (3).pdb #2/A ARG 163 HH21 best_model (3).pdb #2/A PRO 9 O 2.154
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 HG13 2.164
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HE3 2.179
best_model (3).pdb #2/A THR 1 H best_model (3).pdb #2/A ALA 79 HB3 2.180
best_model (3).pdb #2/A TRP 168 HE1 best_model (3).pdb #2/A LEU 178 HD13 2.204
best_model (3).pdb #2/A ILE 5 HD12 best_model (3).pdb #2/A VAL 166 HG21 2.206
best_model (3).pdb #2/A TRP 238 HE3 best_model (3).pdb #2/A MET 7 HE2 2.262
best_model (3).pdb #2/A LEU 6 HD11 best_model (3).pdb #2/A TRP 238 HH2 2.263
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD21 2.264
best_model (3).pdb #2/A SER 2 HG best_model (3).pdb #2/A VAL 19 CG1 2.310
best_model (3).pdb #2/A PHE 3 HD2 best_model (3).pdb #2/A THR 23 HG22 2.318
best_model (3).pdb #2/A THR 1 HB best_model (3).pdb #2/A ALA 79 HB1 2.342
best_model (3).pdb #2/A MET 7 HG3 best_model (3).pdb #2/A GLY 241 HA2 2.352
best_model (3).pdb #2/A PHE 257 HE1 best_model (3).pdb #2/A SER 4 HA 2.354
best_model (3).pdb #2/A SER 2 HA best_model (3).pdb #2/A THR 23 HG21 2.380
best_model (3).pdb #2/A PHE 257 HD1 best_model (3).pdb #2/A SER 4 HG 2.381
best_model (3).pdb #2/A LEU 6 HA best_model (3).pdb #2/A TRP 168 HE1 2.389
best_model (3).pdb #2/A MET 7 HE1 best_model (3).pdb #2/A TRP 238 HB3 2.393
best_model (3).pdb #2/A TRP 168 HE1 best_model (3).pdb #2/A LEU 178 CD1 2.395
best_model (3).pdb #2/A PHE 3 O best_model (3).pdb #2/A PHE 257 HE1 2.401
best_model (3).pdb #2/A THR 23 HG21 best_model (3).pdb #2/A PHE 3 H 2.423
best_model (3).pdb #2/A THR 1 HG23 best_model (3).pdb #2/A PHE 75 HZ 2.424
best_model (3).pdb #2/A THR 1 HG1 best_model (3).pdb #2/A ALA 79 HA 2.428
best_model (3).pdb #2/A PHE 3 HZ best_model (3).pdb #2/A LEU 27 HD22 2.431
best_model (3).pdb #2/A SER 4 HA best_model (3).pdb #2/A PHE 257 HD1 2.431
best_model (3).pdb #2/A SER 4 CB best_model (3).pdb #2/A HIS 254 HD1 2.434
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB1 2.443
best_model (3).pdb #2/A TRP 238 HE3 best_model (3).pdb #2/A PHE 257 HZ 2.467
best_model (3).pdb #2/A ILE 5 HD13 best_model (3).pdb #2/A VAL 166 HG22 2.475
best_model (3).pdb #2/A PHE 3 HE1 best_model (3).pdb #2/A TYR 102 OH 2.481
best_model (3).pdb #2/A LEU 6 O best_model (3).pdb #2/A LEU 178 HD11 2.482
best_model (3).pdb #2/A SER 8 HB2 best_model (3).pdb #2/A HIS 254 HE1 2.486
best_model (3).pdb #2/A SER 8 HB3 best_model (3).pdb #2/A THR 244 HB 2.487
best_model (3).pdb #2/A PHE 3 H best_model (3).pdb #2/A THR 23 OG1 2.488
best_model (3).pdb #2/A MET 7 HE3 best_model (3).pdb #2/A ALA 185 HB3 2.489
best_model (3).pdb #2/A SER 4 HB2 best_model (3).pdb #2/A VAL 11 HG23 2.492
44 distances
> label sel attribute name
> select #2/A:319
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:319-322
32 atoms, 31 bonds, 4 residues, 1 model selected
> save /Users/kelly/Desktop/image6.png supersample 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kelly/Desktop/Alphafold Figures /RMSD of Solved vs
> Predicted/ADGRF1/ADGRF1 Solved.cxs"
Log from Thu Aug 17 16:19:38 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kelly/Downloads/ADGRF1_Overlay (3).cxs"
Log from Tue May 16 15:32:50 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Sun Oct 23 22:35:06 2022UCSF ChimeraX version: 1.5.dev202207070159
(2022-07-07)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
Fetching compressed Q96PE1 UniProt info from
https://www.uniprot.org/uniprot/Q96PE1.xml
> alphafold match Q96PE1
Fetching compressed AlphaFold Q96PE1 from
https://alphafold.ebi.ac.uk/files/AF-Q96PE1-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q96PE1 (UniProt Q96PE1)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRA2 Q96PE1 alphafold prediction.cxs"
[Repeated 1 time(s)]
> close session
> ui tool show AlphaFold
Fetching compressed Q8IWK6 UniProt info from
https://www.uniprot.org/uniprot/Q8IWK6.xml
> alphafold match Q8IWK6
Fetching compressed AlphaFold Q8IWK6 from
https://alphafold.ebi.ac.uk/files/AF-Q8IWK6-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q8IWK6 (UniProt Q8IWK6)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRA3 Q8IWK6 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
Fetching compressed O60241 UniProt info from
https://www.uniprot.org/uniprot/O60241.xml
> alphafold match O60241
Fetching compressed AlphaFold O60241 from
https://alphafold.ebi.ac.uk/files/AF-O60241-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: O60241 (UniProt O60241)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRB1 O60241 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
> alphafold predict AGRB3
Missing or invalid "sequences" argument: Sequences argument "AGRB3" is not a
chain specifier, alignment id, UniProt id, or sequence characters
> alphafold match AGRB3
Missing or invalid "sequences" argument: Sequences argument "AGRB3" is not a
chain specifier, alignment id, UniProt id, or sequence characters
> alphafold match AGRB3AGRB3
Missing or invalid "sequences" argument: Sequences argument "AGRB3AGRB3" is
not a chain specifier, alignment id, UniProt id, or sequence characters
Fetching compressed O60242 UniProt info from
https://www.uniprot.org/uniprot/O60242.xml
> alphafold match O60242
Fetching compressed AlphaFold O60242 from
https://alphafold.ebi.ac.uk/files/AF-O60242-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: O60242 (UniProt O60242)
Opened 1 AlphaFold model
> lighting simple
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRB3 O60242 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
Fetching compressed Q6QNK2 UniProt info from
https://www.uniprot.org/uniprot/Q6QNK2.xml
> alphafold match Q6QNK2
Fetching compressed AlphaFold Q6QNK2 from
https://alphafold.ebi.ac.uk/files/AF-Q6QNK2-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q6QNK2 (UniProt Q6QNK2)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRD1 Q6QNK2 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
Fetching compressed Q7Z7M1 UniProt info from
https://www.uniprot.org/uniprot/Q7Z7M1.xml
> alphafold match Q7Z7M1
Fetching compressed AlphaFold Q7Z7M1 from
https://alphafold.ebi.ac.uk/files/AF-Q7Z7M1-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q7Z7M1 (UniProt Q7Z7M1)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRD2 Q7Z7M1 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
Fetching compressed Q14246 UniProt info from
https://www.uniprot.org/uniprot/Q14246.xml
> alphafold match Q14246
Fetching compressed AlphaFold Q14246 from
https://alphafold.ebi.ac.uk/files/AF-Q14246-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q14246 (UniProt Q14246)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRE1 Q14246 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
Populating font family aliases took 342 ms. Replace uses of missing font
family "Calibri" with one that exists to avoid this cost.
Fetching compressed Q9UHX3 UniProt info from
https://www.uniprot.org/uniprot/Q9UHX3.xml
> alphafold match Q9UHX3
Fetching compressed AlphaFold Q9UHX3 from
https://alphafold.ebi.ac.uk/files/AF-Q9UHX3-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q9UHX3 (UniProt Q9UHX3)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRE2 Q9UHX3 alphafold prediction.cxs"
> close session
> ui tool show AlphaFold
> alphafold match Q14246
1 AlphaFold model found using UniProt identifier: Q14246 (UniProt Q14246)
Opened 1 AlphaFold model
> select add #1
6818 atoms, 6968 bonds, 886 residues, 1 model selected
> close
Fetching compressed Q9BY15 UniProt info from
https://www.uniprot.org/uniprot/Q9BY15.xml
> alphafold match Q9BY15
Fetching compressed AlphaFold Q9BY15 from
https://alphafold.ebi.ac.uk/files/AF-Q9BY15-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q9BY15 (UniProt Q9BY15)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRE3 Q9BY15 alphafold prediction.cxs"
> close
Fetching compressed Q86SQ3 UniProt info from
https://www.uniprot.org/uniprot/Q86SQ3.xml
> alphafold match Q86SQ3
Fetching compressed AlphaFold Q86SQ3 from
https://alphafold.ebi.ac.uk/files/AF-Q86SQ3-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q86SQ3 (UniProt Q86SQ3)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRE4 Q86SQ3 alphafold prediction.cxs"
> close
Fetching compressed Q5T601 UniProt info from
https://www.uniprot.org/uniprot/Q5T601.xml
> alphafold match Q5T601
Fetching compressed AlphaFold Q5T601 from
https://alphafold.ebi.ac.uk/files/AF-Q5T601-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q5T601 (UniProt Q5T601)
Opened 1 AlphaFold model
> save "/Users/rithwik/OneDrive - The University of Western Ontario/PAR-
> Adhesion GPCR Chimera X structures/AGRF1 Q5T601 alphafold prediction.cxs"
——— End of log from Sun Oct 23 22:35:06 2022 ———
opened ChimeraX session
> open "/Users/kelly/Downloads/best_model (3).pdb"
Chain information for best_model (3).pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 to #1
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 AlphaFold Q5T601, chain A (#1) with best_model (3).pdb, chain A
(#2), sequence alignment score = 1531.1
RMSD between 191 pruned atom pairs is 0.854 angstroms; (across all 332 pairs:
11.783)
> save "/Users/kelly/Desktop/ADGRF1_Overlay .cxs"
——— End of log from Tue May 16 15:32:50 2023 ———
opened ChimeraX session
> set bgColor white
> open "/Users/kelly/Downloads/GPR110_Gs complex_7wxw.pdb"
GPR110_Gs complex_7wxw.pdb title:
GPR110/GS complex [more info...]
Chain information for GPR110_Gs complex_7wxw.pdb #3
---
Chain | Description | UniProt
A | engineered mini galpha-S subunit |
B | transducin β chain 1 | GBB1_HUMAN 2-340
C | G γ-I | GBG2_HUMAN 1-71
D | NB35 |
R | adhesion G-protein coupled receptor F1 | AGRF1_HUMAN 1-910
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #3/R
Alignment identifier is 1
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/D
Alignment identifier is 3/D
> select #3/D:92-127
279 atoms, 286 bonds, 36 residues, 1 model selected
> select #3/D
967 atoms, 988 bonds, 127 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #3/D:1-38
285 atoms, 290 bonds, 38 residues, 1 model selected
> select #3/D:93-127
274 atoms, 281 bonds, 35 residues, 1 model selected
> select #3/D
967 atoms, 988 bonds, 127 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select add #3
8121 atoms, 8294 bonds, 2 pseudobonds, 1032 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #3/C
433 atoms, 439 bonds, 56 residues, 1 model selected
> hide sel cartoons
> undo
[Repeated 3 time(s)]
> show sel cartoons
> undo
[Repeated 6 time(s)]
> select add #3
8121 atoms, 8294 bonds, 2 pseudobonds, 1032 residues, 2 models selected
> select subtract #3
Nothing selected
> undo
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel atoms
> select add #3
8121 atoms, 8294 bonds, 2 pseudobonds, 1032 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
8121 atoms, 8294 bonds, 2 pseudobonds, 1032 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> select #3/C
433 atoms, 439 bonds, 56 residues, 1 model selected
> hide sel cartoons
> select #3/B:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B
2600 atoms, 2647 bonds, 338 residues, 1 model selected
> hide sel cartoons
> select #3/A:40-46,210-214,217-222,243-249,286-292,359-363
314 atoms, 319 bonds, 37 residues, 1 model selected
> select #3/A:358-394
322 atoms, 329 bonds, 37 residues, 1 model selected
> select #3/A
1942 atoms, 1981 bonds, 1 pseudobond, 234 residues, 2 models selected
> hide sel cartoons
> select #3/D:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
57 atoms, 58 bonds, 6 residues, 1 model selected
> select up
967 atoms, 988 bonds, 127 residues, 1 model selected
> hide sel cartoons
> matchmaker #3 to #1 showAlignment true
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 AlphaFold Q5T601, chain A (#1) with GPR110_Gs complex_7wxw.pdb,
chain R (#3), sequence alignment score = 3665.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AlphaFold Q5T601 #1/A,
GPR110_Gs complex_7wxw.pdb #3/R
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 186 pruned atom pairs is 1.085 angstroms; (across all 277 pairs:
6.567)
> matchmaker #3 to #2 showAlignment true
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 best_model (3).pdb, chain A (#2) with GPR110_Gs complex_7wxw.pdb,
chain R (#3), sequence alignment score = 1412.3
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: best_model (3).pdb #2/A,
GPR110_Gs complex_7wxw.pdb #3/R
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 227 pruned atom pairs is 1.018 angstroms; (across all 277 pairs:
1.806)
> ui tool show "Show Sequence Viewer"
> ui tool show "Render By Attribute"
> key blue-white-red :0.16 :4.00 :8.00 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #1 target cabs palette
> 0.163806,blue:4,white:8,red noValueColor grey
7141 atoms, 910 residues, atom seq_rmsd range 0.164 to 38.8
> hide #!3 models
> hide #2 models
> save /Users/kelly/Desktop/image2.png supersample 3
> show #2 models
> hide #1 models
> ui tool show "Render By Attribute"
> key blue-white-red :0.11 :4.00 :7.00 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #2 target cabs palette
> 0.108895,blue:4,white:7,red noValueColor grey
5304 atoms, 332 residues, atom seq_rmsd range 0.109 to 7.92
> save /Users/kelly/Desktop/image3.png supersample 3
> show #!3 models
> hide #2 models
> color #3 #00f900ff
> save /Users/kelly/Desktop/image4.png supersample 3
> save "/Users/kelly/Desktop/ADGRF1 Solved.cxs"
——— End of log from Thu Aug 17 16:19:38 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-14.7.23
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
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
Boot ROM Version: 428.60.3.0.0
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1824)
Kernel Version: Darwin 19.6.0
Time since boot: 2 days 21:07
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: Supported, feature set macOS GPUFamily1 v4
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: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 10.15.7, Intel HD Graphics 6000 |
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Apple Intel graphics driver crash.