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Opened 21 months ago
Closed 21 months ago
#14389 closed defect (can't reproduce)
Crash going to full screen
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000002023e8e00 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [79766]
Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: X86-64 (Translated)
Parent Process: ??? [1]
Responsible: ChimeraX [79766]
User ID: 501
Date/Time: 2024-01-16 16:25:18.577 -0800
OS Version: macOS 11.0.1 (20B29)
Report Version: 12
Anonymous UUID: 2F13B4AB-0A14-8C3C-6EB3-E6ACA0EEC5F5
Sleep/Wake UUID: 4ACB3D24-A686-4DA2-B280-EA7541699147
Time Awake Since Boot: 370000 seconds
Time Since Wake: 15000 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:
*** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'Invalid parameter not satisfying: !isnan(newOrigin.y)'
terminating with uncaught exception of type NSException
abort() called
Application Specific Backtrace 1:
0 CoreFoundation 0x00007fff2051c083 __exceptionPreprocess + 242
1 libobjc.A.dylib 0x00007fff2025417c objc_exception_throw + 48
2 CoreFoundation 0x00007fff2054507e +[NSException raise:format:arguments:] + 88
3 Foundation 0x00007fff212336c9 -[NSAssertionHandler handleFailureInMethod:object:file:lineNumber:description:] + 191
4 AppKit 0x00007fff22c2a8b0 -[NSView setFrameOrigin:] + 1395
5 AppKit 0x00007fff22c34c40 -[NSView setFrame:] + 394
6 AppKit 0x00007fff23183dc6 -[_NSFullScreenDetachedToolbarMenuBarCompanionController updateContentViewForMenuBarReveal] + 311
7 AppKit 0x00007fff23183c73 -[_NSFullScreenDetachedToolbarMenuBarCompanionController setMenuBarReveal:] + 198
8 AppKit 0x00007fff236be7dc __32+[_NSFullScreenSpace initialize]_block_invoke + 326
9 AppKit 0x00007fff232279c6 __57+[NSCGSSpace addMenuBarRevealChangedNotificationHandler:]_block_invoke + 238
10 Foundation 0x00007fff21135d6b -[__NSObserver _doit:] + 287
11 CoreFoundation 0x00007fff20497885 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
12 CoreFoundation 0x00007fff20533224 ___CFXRegistrationPost_block_invoke + 49
13 CoreFoundation 0x00007fff205331a7 _CFXRegistrationPost + 454
14 CoreFoundation 0x00007fff20468536 _CFXNotificationPost + 787
15 Foundation 0x00007fff21109abe -[NSNotificationCenter postNotificationName:object:userInfo:] + 59
16 SkyLight 0x00007fff24d33ebd _ZL41post_coordinated_distributed_notification19CGSNotificationTypePvjS0_ + 471
17 SkyLight 0x00007fff24b54824 CGSPostLocalNotification + 274
18 SkyLight 0x00007fff24b542b8 _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ + 98
19 SkyLight 0x00007fff24df039c _ZN21CGSDatagramReadStream26dispatchMainQueueDatagramsEv + 202
20 SkyLight 0x00007fff24df02c3 ___ZN21CGSDatagramReadStream15mainQueueWakeupEv_block_invoke + 18
21 libdispatch.dylib 0x00007fff201fd5dd _dispatch_call_block_and_release + 12
22 libdispatch.dylib 0x00007fff201fe7c7 _dispatch_client_callout + 8
23 libdispatch.dylib 0x00007fff2020ab86 _dispatch_main_queue_callback_4CF + 940
24 CoreFoundation 0x00007fff204df346 __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
25 CoreFoundation 0x00007fff204a1178 __CFRunLoopRun + 2745
26 CoreFoundation 0x00007fff2049ffd2 CFRunLoopRunSpecific + 567
27 HIToolbox 0x00007fff28954fd0 RunCurrentEventLoopInMode + 292
28 HIToolbox 0x00007fff28954dcc ReceiveNextEventCommon + 709
29 HIToolbox 0x00007fff28954aef _BlockUntilNextEventMatchingListInModeWithFilter + 64
30 AppKit 0x00007fff22beef85 _DPSNextEvent + 883
31 AppKit 0x00007fff22bed74b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
32 AppKit 0x00007fff22bdfbda -[NSApplication run] + 586
33 libqcocoa.dylib 0x000000014821f0ac qt_plugin_instance + 57692
34 QtCore 0x0000000123b6a326 _ZN10QEventLoop4execE6QFlagsINS_17ProcessEventsFlagEE + 486
35 QtCore 0x0000000123b61235 _ZN16QCoreApplication4execEv + 133
36 QtWidgets.abi3.so 0x0000000126734d9a _ZL22meth_QApplication_execP7_objectS0_ + 90
37 Python 0x000000010a4e971d cfunction_call + 125
38 Python 0x000000010a4aa5b7 _PyObject_MakeTpCall + 359
39 Python 0x000000010a582e9c call_function + 876
40 Python 0x000000010a5802a2 _PyEval_EvalFrameDefault + 25554
41 Python 0x000000010a4aad28 function_code_fastcall + 104
42 Python 0x000000010a4acd6a method_vectorcall + 202
43 Python 0x000000010a582e0c call_function + 732
44 Python 0x000000010a5802a2 _PyEval_EvalFrameDefault + 25554
45 Python 0x000000010a583b03 _PyEval_EvalCode + 2611
46 Python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
47 Python 0x000000010a582e0c call_function + 732
48 Python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
49 Python 0x000000010a583b03 _PyEval_EvalCode + 2611
50 Python 0x000000010a579dab PyEval_EvalCode + 139
51 Python 0x000000010a576c12 builtin_exec + 626
52 Python 0x000000010a4e9023 cfunction_vectorcall_FASTCALL + 195
53 Python 0x000000010a582e0c call_function + 732
54 Python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
55 Python 0x000000010a583b03 _PyEval_EvalCode + 2611
56 Python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
57 Python 0x000000010a582e0c call_function + 732
58 Python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
59 Python 0x000000010a583b03 _PyEval_EvalCode + 2611
60 Python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
61 Python 0x000000010a5e9870 pymain_run_module + 208
62 Python 0x000000010a5e8f87 Py_RunMain + 1431
63 Python 0x000000010a5e958f pymain_main + 223
64 Python 0x000000010a5e949b Py_Main + 43
65 ChimeraX 0x00000001021a4dc8 main + 120
66 libdyld.dylib 0x00007fff203c5631 start + 1
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff2037c462 __pthread_kill + 10
2 libsystem_c.dylib 0x00007fff2028cba3 raise + 26
3 libsystem_platform.dylib 0x00007fff203eed7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff202fd720 abort + 120
6 libc++abi.dylib 0x00007fff2036f418 abort_message + 231
7 libc++abi.dylib 0x00007fff20360a7d demangling_terminate_handler() + 266
8 libobjc.A.dylib 0x00007fff2025677b _objc_terminate() + 96
9 libc++abi.dylib 0x00007fff2036e847 std::__terminate(void (*)()) + 8
10 libc++abi.dylib 0x00007fff2036e7e9 std::terminate() + 41
11 libdispatch.dylib 0x00007fff201fe7db _dispatch_client_callout + 28
12 libdispatch.dylib 0x00007fff2020ab86 _dispatch_main_queue_callback_4CF + 940
13 com.apple.CoreFoundation 0x00007fff204df346 __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
14 com.apple.CoreFoundation 0x00007fff204a1178 __CFRunLoopRun + 2745
15 com.apple.CoreFoundation 0x00007fff2049ffd2 CFRunLoopRunSpecific + 567
16 com.apple.HIToolbox 0x00007fff28954fd0 RunCurrentEventLoopInMode + 292
17 com.apple.HIToolbox 0x00007fff28954dcc ReceiveNextEventCommon + 709
18 com.apple.HIToolbox 0x00007fff28954aef _BlockUntilNextEventMatchingListInModeWithFilter + 64
19 com.apple.AppKit 0x00007fff22beef85 _DPSNextEvent + 883
20 com.apple.AppKit 0x00007fff22bed74b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
21 com.apple.AppKit 0x00007fff22bdfbda -[NSApplication run] + 586
22 libqcocoa.dylib 0x000000014821f0ac 0x148206000 + 102572
23 QtCore 0x0000000123b6a326 QEventLoop::exec(QFlags) + 486
24 QtCore 0x0000000123b61235 QCoreApplication::exec() + 133
25 QtWidgets.abi3.so 0x0000000126734d9a meth_QApplication_exec(_object*, _object*) + 90
26 org.python.python 0x000000010a4e971d cfunction_call + 125
27 org.python.python 0x000000010a4aa5b7 _PyObject_MakeTpCall + 359
28 org.python.python 0x000000010a582e9c call_function + 876
29 org.python.python 0x000000010a5802a2 _PyEval_EvalFrameDefault + 25554
30 org.python.python 0x000000010a4aad28 function_code_fastcall + 104
31 org.python.python 0x000000010a4acd6a method_vectorcall + 202
32 org.python.python 0x000000010a582e0c call_function + 732
33 org.python.python 0x000000010a5802a2 _PyEval_EvalFrameDefault + 25554
34 org.python.python 0x000000010a583b03 _PyEval_EvalCode + 2611
35 org.python.python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
36 org.python.python 0x000000010a582e0c call_function + 732
37 org.python.python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
38 org.python.python 0x000000010a583b03 _PyEval_EvalCode + 2611
39 org.python.python 0x000000010a579dab PyEval_EvalCode + 139
40 org.python.python 0x000000010a576c12 builtin_exec + 626
41 org.python.python 0x000000010a4e9023 cfunction_vectorcall_FASTCALL + 195
42 org.python.python 0x000000010a582e0c call_function + 732
43 org.python.python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
44 org.python.python 0x000000010a583b03 _PyEval_EvalCode + 2611
45 org.python.python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
46 org.python.python 0x000000010a582e0c call_function + 732
47 org.python.python 0x000000010a58034b _PyEval_EvalFrameDefault + 25723
48 org.python.python 0x000000010a583b03 _PyEval_EvalCode + 2611
49 org.python.python 0x000000010a4aacb1 _PyFunction_Vectorcall + 289
50 org.python.python 0x000000010a5e9870 pymain_run_module + 208
51 org.python.python 0x000000010a5e8f87 Py_RunMain + 1431
52 org.python.python 0x000000010a5e958f pymain_main + 223
53 org.python.python 0x000000010a5e949b Py_Main + 43
54 edu.ucsf.cgl.ChimeraX 0x00000001021a4dc8 main + 120
55 libdyld.dylib 0x00007fff203c5631 start + 1
Thread 1:: com.apple.rosetta.exceptionserver
0 runtime 0x00007ffdffc7ccb8 0x7ffdffc7a000 + 11448
1 runtime 0x00007ffdffc86018 0x7ffdffc7a000 + 49176
2 runtime 0x00007ffdffc87c3c 0x7ffdffc7a000 + 56380
Thread 2:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 3:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 4:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 5:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 6:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 7:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 8:
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010bf8823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 9:: ThreadPoolServiceThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff2037edde kevent64 + 10
2 QtWebEngineCore 0x000000012dd2a927 0x129dca000 + 66455847
3 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
4 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
5 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
6 QtWebEngineCore 0x000000012dcb12ad 0x129dca000 + 65958573
7 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
8 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 10:: ThreadPoolBackgroundWorker
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbe26c 0x129dca000 + 66011756
5 QtWebEngineCore 0x000000012dcbdddd 0x129dca000 + 66010589
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 11:: Chrome_IOThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff2037edde kevent64 + 10
2 QtWebEngineCore 0x000000012dd2a927 0x129dca000 + 66455847
3 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
4 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
5 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
6 QtWebEngineCore 0x000000012cbef3a2 0x129dca000 + 48386978
7 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
8 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 13:: CompositorTileWorker1
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff203788e2 __psynch_cvwait + 10
2 QtWebEngineCore 0x000000012dcf0d1b 0x129dca000 + 66219291
3 QtWebEngineCore 0x000000012fdbe92d 0x129dca000 + 100616493
4 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
5 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 14:: Chrome_InProcGpuThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 15:: Chrome_ChildIOThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff2037edde kevent64 + 10
2 QtWebEngineCore 0x000000012dd2a927 0x129dca000 + 66455847
3 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
4 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
5 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
6 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
7 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 17:: VizCompositorThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 18:: NetworkService
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff2037edde kevent64 + 10
2 QtWebEngineCore 0x000000012dd2a927 0x129dca000 + 66455847
3 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
4 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
5 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
6 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
7 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 19:: NetworkConfigWatcher
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 20:: ThreadPoolSingleThreadForegroundBlocking0
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbe26c 0x129dca000 + 66011756
5 QtWebEngineCore 0x000000012dcbdecd 0x129dca000 + 66010829
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 21:: NetworkConfigWatcher
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 22:: com.apple.NSEventThread
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 com.apple.CoreFoundation 0x00007fff204a24fd __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff204a0be6 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2049ffd2 CFRunLoopRunSpecific + 567
5 com.apple.AppKit 0x00007fff22d7536d _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 23:: MemoryInfra
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcf8bef 0x129dca000 + 66251759
4 QtWebEngineCore 0x000000012dc2e1c9 0x129dca000 + 65421769
5 QtWebEngineCore 0x000000012dca7a5c 0x129dca000 + 65919580
6 QtWebEngineCore 0x000000012dc5f998 0x129dca000 + 65624472
7 QtWebEngineCore 0x000000012dcc9eb8 0x129dca000 + 66059960
8 QtWebEngineCore 0x000000012dcca04a 0x129dca000 + 66060362
9 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 24:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbdf9a 0x129dca000 + 66011034
5 QtWebEngineCore 0x000000012dcbde0d 0x129dca000 + 66010637
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 25:: ThreadPoolForegroundWorker
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbe26c 0x129dca000 + 66011756
5 QtWebEngineCore 0x000000012dcbde6d 0x129dca000 + 66010733
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 26:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 27:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 28:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 29:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 30:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 31:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 32:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 33:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 34:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 35:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 36:
0 runtime 0x00007ffdffcd48a0 0x7ffdffc7a000 + 370848
Thread 37:: ThreadPoolForegroundWorker
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbe26c 0x129dca000 + 66011756
5 QtWebEngineCore 0x000000012dcbde6d 0x129dca000 + 66010733
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 38:: ThreadPoolBackgroundWorker
0 ??? 0x00007ffe95ca29bc ???
1 libsystem_kernel.dylib 0x00007fff20375e7e mach_msg_trap + 10
2 QtWebEngineCore 0x000000012dcf8e26 0x129dca000 + 66252326
3 QtWebEngineCore 0x000000012dcbd7bf 0x129dca000 + 66009023
4 QtWebEngineCore 0x000000012dcbe26c 0x129dca000 + 66011756
5 QtWebEngineCore 0x000000012dcbdddd 0x129dca000 + 66010589
6 QtWebEngineCore 0x000000012dcf1908 0x129dca000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203aa950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203a647b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000002023e8e00 rcx: 0x0000000000000000 rdx: 0x0000000000000000
rdi: 0xa0f4a54cec054108 rsi: 0x0000000150ad7088 rbp: 0xa0f4a54cec054108 rsp: 0x0000000150ad7088
r8: 0x0000000000000006 r9: 0xa0f4a54cec054108 r10: 0x00000002023e8e00 r11: 0x00007fff2028cb89
r12: 0x0000000000000203 r13: 0x0000003000000008 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: rfl: 0x0000000000000283
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0x7fff3d441000 - 0x7fff3d458fff com.apple.SafariServices.framework (16610 - 16610.2.11.51.8) /System/Library/Frameworks/SafariServices.framework/Versions/A/SafariServices
0x7fff3d5ee000 - 0x7fff3d5f9fff com.apple.MallocStackLogging (1.0 - 1) /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging
0x7fff3d60f000 - 0x7fff3d621fff libmis.dylib (274.40.12) /usr/lib/libmis.dylib
0x7fff3d63e000 - 0x7fff3d7b0fff com.apple.CoreHandwriting (161 - 1.2) /System/Library/PrivateFrameworks/CoreHandwriting.framework/Versions/A/CoreHandwriting
0x7fff3d7b1000 - 0x7fff3da10fff com.apple.imageKit (3.0 - 1099) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit
0x7fff3da11000 - 0x7fff3db30fff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit
0x7fff3db31000 - 0x7fff3db42fff com.apple.sidecar-ui (1.0 - 228) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff3e0ff000 - 0x7fff3e161fff com.apple.ImageCaptureCore (1707 - 1707) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x7fff3e162000 - 0x7fff3e188fff com.apple.quartzfilters (1.10.0 - 97) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters
0x7fff3e3d1000 - 0x7fff3e528fff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer
0x7fff3e529000 - 0x7fff3e8fefff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud
0x7fff3e92b000 - 0x7fff3ea5cfff com.apple.AnnotationKit (1.0 - 383.3) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit
0x7fff3ea5d000 - 0x7fff3eefefff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x7fff3eeff000 - 0x7fff3efecfff com.apple.PDFKit (1.0 - 950.5.4) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit
0x7fff3fd0c000 - 0x7fff3fd8ffff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput
0x7fff40dec000 - 0x7fff40deffff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x7fff411c3000 - 0x7fff411e0fff libCGInterfaces.dylib (543) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff428f9000 - 0x7fff43622fff libfaceCore.dylib (4.0.90) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib
0x7fff43623000 - 0x7fff4373afff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff4373b000 - 0x7fff43754fff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark
0x7fff437cb000 - 0x7fff43a41fff com.apple.RawCamera.bundle (9.10.0 - 1410.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff4434d000 - 0x7fff44351fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
0x7fff45d44000 - 0x7fff45d47fff libpmenergy.dylib (227.40.6) /usr/lib/libpmenergy.dylib
0x7fff47aa9000 - 0x7fff47af7fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x7fff4835f000 - 0x7fff4837afff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x7fff5152f000 - 0x7fff5155dfff com.apple.HelpData (2.3 - 200) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x7fff5155e000 - 0x7fff51578fff com.apple.shortcut (2.16 - 114) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff51579000 - 0x7fff5160afff com.apple.Symbolication (12.2 - 64541.5.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff51782000 - 0x7fff51785fff libpmsample.dylib (227.40.6) /usr/lib/libpmsample.dylib
0x7fff53d43000 - 0x7fff53d7afff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x7fff5538d000 - 0x7fff55390fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff69289000 - 0x7fff6928dfff libmetal_timestamp.dylib (31001.152) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x7fff6b6f7000 - 0x7fff6b6fdfff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6b6fe000 - 0x7fff6b702fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6b703000 - 0x7fff6b712fff com.apple.opengl (18.0.50 - 18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6b713000 - 0x7fff6b715fff libCVMSPluginSupport.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6b716000 - 0x7fff6b71efff libGFXShared.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6b71f000 - 0x7fff6b752fff libGLImage.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6b753000 - 0x7fff6b78ffff libGLU.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6b790000 - 0x7fff6b924fff libGLProgrammability.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6b925000 - 0x7fff6b92ffff libGL.dylib (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6b930000 - 0x7fff6baabfff GLEngine (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6baac000 - 0x7fff6bad5fff GLRendererFloat (18.0.50) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6cd66000 - 0x7fff6cdbefff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6e03e000 - 0x7fff6e045fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff73fce000 - 0x7fff73fd9fff com.apple.SymptomAnalytics (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff741f7000 - 0x7fff7420ffff com.apple.SymptomPresentationFeed (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff78315000 - 0x7fff7831cfff libRosetta.dylib (203.1.3) /usr/lib/libRosetta.dylib
Translated Code Information:
tmp0: 0xffffffffffffffff tmp1: 0x00007ffe95ca2990 tmp2: 0x00007fff2037c458
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: 347227
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 3840K 6
CG image 392K 41
CoreAnimation 112K 15
CoreGraphics 12K 2
CoreUI image data 4168K 33
Foundation 36K 2
Kernel Alloc Once 8K 1
MALLOC 2.2G 194
MALLOC guard page 192K 8
MALLOC_MEDIUM (reserved) 856.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 16K 4
OpenGL GLSL 384K 4
Rosetta Arena 2048K 1
Rosetta Generic 1432K 355
Rosetta IndirectBranch 2048K 1
Rosetta JIT 128.0M 1
Rosetta Return Stack 760K 76
Rosetta Thread Context 760K 76
STACK GUARD 44K 11
Stack 161.6M 38
Stack Guard 56.1M 27
VM_ALLOCATE 145.4M 334
VM_ALLOCATE (reserved) 160.1M 17 reserved VM address space (unallocated)
__CTF 759 1
__DATA 35.7M 647
__DATA_CONST 25.4M 308
__DATA_DIRTY 1711K 210
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 539.1M 200
__OBJC_RO 61.0M 1
__OBJC_RW 2466K 2
__TEXT 657.8M 629
__UNICODE 588K 1
mapped file 4.4G 1100
shared memory 2264K 12
unshared pmap 9.8M 5
=========== ======= =======
TOTAL 9.5G 4378
TOTAL, minus reserved VM space 8.4G 4378
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/klhvorecny/Documents/EMData/23sep19b/23sep19b_P08191_FimHGF_fAb475824_Isolde.pdb
Chain information for 23sep19b_P08191_FimHGF_fAb475824_Isolde.pdb #1
---
Chain | Description
A | No description available
F | No description available
G | No description available
H | No description available
I | No description available
L | No description available
M | No description available
> open
> /Users/klhvorecny/Documents/EMData/23sep19b/cryoSPARC/cryosparc_P722_J57_006_volume_map_sharp.mrc
Opened cryosparc_P722_J57_006_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 1.12, shown at level 0.0495, step 2, values float32
> open
> /Users/klhvorecny/Documents/Collaborators/Klevit&Sokurenko/FimComplexStructures/PDBs/2vco.pdb
2vco.pdb title:
Crystal structure of the fimbrial adhesin fimh In complex with its high-
mannose epitope [more info...]
Chain information for 2vco.pdb #3
---
Chain | Description | UniProt
A B | protein fimh | FIMH_ECOLI
Non-standard residues in 2vco.pdb #3
---
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
NI — nickel (II) ion
SO4 — sulfate ion
> volume #2 step 1
> volume #2 level 0.6
> select #1,3
21460 atoms, 21335 bonds, 10 pseudobonds, 1998 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> align #3/A:1-150 toAtoms #1/A:1-150
Unequal number of atoms to pair, 1132 and 2244
> align #3/A:1-150@ca toAtoms #1/A:1-150@ca
RMSD between 150 atom pairs is 2.492 angstroms
> split #3
Split 2vco.pdb (#3) into 4 models
Chain information for 2vco.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 2vco.pdb B #3.2
---
Chain | Description
B | No description available
> hide #!3.2 models
> hide #3.4 models
> hide #!3.1 models
> select #3.3
62 atoms, 66 bonds, 5 residues, 1 model selected
> show sel atoms
> fitmap #3.3 inMap #2
Fit molecule 2vco.pdb C (#3.3) to map
cryosparc_P722_J57_006_volume_map_sharp.mrc (#2) using 62 atoms
average map value = 0.6852, steps = 96
shifted from previous position = 1.37
rotated from previous position = 16.2 degrees
atoms outside contour = 23, contour level = 0.6
Position of 2vco.pdb C (#3.3) relative to
cryosparc_P722_J57_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.49846784 0.32828747 0.80234478 277.20420621
-0.77908283 0.23627797 -0.58069155 281.38327988
-0.38021015 -0.91454910 0.13798616 330.25482272
Axis -0.20183198 0.71490791 -0.66945540
Axis point 281.80519338 0.00000000 199.89673416
Rotation angle (degrees) 124.20128016
Shift along axis -75.87641677
> hide #!3 models
> show #!3 models
> select add #3
2939 atoms, 2586 bonds, 10 pseudobonds, 749 residues, 7 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> lighting soft
> set bgColor white
> show #!2 models
> hide #!2 models
> select #1/L:90
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #1,3
21460 atoms, 21335 bonds, 10 pseudobonds, 1998 residues, 8 models selected
> style sel & #1#3.3 stick
Changed 18583 atom styles
> select clear
> set bgColor white
> select #1,3
21460 atoms, 21335 bonds, 10 pseudobonds, 1998 residues, 8 models selected
> style sel & #1#3.3 stick
Changed 18583 atom styles
> color sel & #1#3.3 byhetero
> select clear
> combine #1,3.3 name Fab475_glycan
> hide #1 models
> hide #!3 models
> hide #4 models
> show #4 models
> show #1 models
> hide #1 models
> select #4
62 atoms, 66 bonds, 5 residues, 1 model selected
> show #1 models
> combine #1,4 name Fab475_glycan
> hide #4 models
> hide #1 models
> select subtract #4
Nothing selected
> ui tool show "Build Structure"
> select #5/L:90@CG
1 atom, 1 residue, 1 model selected
> select #5/L:90
14 atoms, 13 bonds, 1 residue, 1 model selected
> save 23sep19b_P08191_FimHGF_fAb475824_glycan.pdb #1
> save 23sep19b_P08191_FimHGF_fAb475824_glycan.pdb #5
> open /Users/klhvorecny/Desktop/23sep19b_P08191_FimHGF_fAb475824_glycan-
> coot-0.pdb
Summary of feedback from opening
/Users/klhvorecny/Desktop/23sep19b_P08191_FimHGF_fAb475824_glycan-coot-0.pdb
---
warnings | Cannot find LINK/SSBOND residue NAG (300 )
Cannot find LINK/SSBOND residue NAG (301 )
Cannot find LINK/SSBOND residue MAN (302 )
Cannot find LINK/SSBOND residue MAN (302 )
Chain information for 23sep19b_P08191_FimHGF_fAb475824_glycan-coot-0.pdb #6
---
Chain | Description
A | No description available
F | No description available
G | No description available
H | No description available
I | No description available
L | No description available
M | No description available
> select #6
18581 atoms, 18812 bonds, 1254 residues, 1 model selected
> style sel stick
Changed 18581 atom styles
> hide #5 models
> hide #3.3 models
> show #5 models
> hide #6 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/klhvorecny/Desktop/23sep19b_P08191_FimHGF_fAb475824_glycan-
> coot-0.pdb
Summary of feedback from opening
/Users/klhvorecny/Desktop/23sep19b_P08191_FimHGF_fAb475824_glycan-coot-0.pdb
---
warnings | Cannot find LINK/SSBOND residue NAG (300 )
Cannot find LINK/SSBOND residue NAG (301 )
Cannot find LINK/SSBOND residue MAN (302 )
Cannot find LINK/SSBOND residue MAN (302 )
Chain information for 23sep19b_P08191_FimHGF_fAb475824_glycan-coot-0.pdb #1
---
Chain | Description
A | No description available
F | No description available
G | No description available
H | No description available
I | No description available
L | No description available
M | No description available
OpenGL version: 4.1 Metal - 70.12.7
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 4 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 11.0.1 (20B29)
Kernel Version: Darwin 20.1.0
Time since boot: 20 days 4:14
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash going to full screen |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Some screen position Y coordinate was NaN