![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8783 closed defect (fixed)
Crash emitting color_pause signal
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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: Segmentation fault
Thread 0x00007000160ad000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010f170e00 (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/widgets/color_button.py", line 147 in
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 [2004]
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 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [2004]
User ID: 501
Date/Time: 2023-04-04 12:02:46.754 -0400
OS Version: macOS 11.5.2 (20G95)
Report Version: 12
Bridge OS Version: 5.5 (18P4759a)
Anonymous UUID: 9B1C8494-F3C1-3858-797E-056E9F4C35D8
Time Awake Since Boot: 770 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff203ce92e __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff203fd5bd pthread_kill + 263
2 libsystem_c.dylib 0x00007fff202e1bd5 raise + 26
3 libsystem_platform.dylib 0x00007fff20442d7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x000000010d915f4f method_vectorcall_VARARGS + 303
6 org.python.python 0x000000010d9e5e0c call_function + 732
7 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
10 QtCore.abi3.so 0x000000011b2aff98 PyQtSlot::call(_object*, _object*) const + 40
11 QtCore.abi3.so 0x000000011b2afe9a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362
12 QtCore.abi3.so 0x000000011b2b0de5 PyQtSlotProxy::unislot(void**) + 85
13 QtCore.abi3.so 0x000000011b2b0d5a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
14 QtCore 0x000000011b5c6d67 0x11b509000 + 777575
15 QtCore 0x000000011b5dbb57 QTimer::timerEvent(QTimerEvent*) + 199
16 QtCore.abi3.so 0x000000011b1a0b69 sipQTimer::timerEvent(QTimerEvent*) + 121
17 QtCore 0x000000011b5bf4cd QObject::event(QEvent*) + 109
18 QtCore.abi3.so 0x000000011b1a09ea sipQTimer::event(QEvent*) + 186
19 QtWidgets 0x000000011dfd9a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
20 QtWidgets 0x000000011dfdaa43 QApplication::notify(QObject*, QEvent*) + 499
21 QtWidgets.abi3.so 0x000000011daf61e6 sipQApplication::notify(QObject*, QEvent*) + 230
22 QtCore 0x000000011b576c3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
23 QtCore 0x000000011b700521 QTimerInfoList::activateTimers() + 961
24 libqcocoa.dylib 0x000000012ab054a5 0x12aaed000 + 99493
25 com.apple.CoreFoundation 0x00007fff204f694c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
26 com.apple.CoreFoundation 0x00007fff204f68b4 __CFRunLoopDoSource0 + 180
27 com.apple.CoreFoundation 0x00007fff204f6634 __CFRunLoopDoSources0 + 242
28 com.apple.CoreFoundation 0x00007fff204f505c __CFRunLoopRun + 893
29 com.apple.CoreFoundation 0x00007fff204f461c CFRunLoopRunSpecific + 563
30 com.apple.HIToolbox 0x00007fff2873aa83 RunCurrentEventLoopInMode + 292
31 com.apple.HIToolbox 0x00007fff2873a7e5 ReceiveNextEventCommon + 587
32 com.apple.HIToolbox 0x00007fff2873a583 _BlockUntilNextEventMatchingListInModeWithFilter + 70
33 com.apple.AppKit 0x00007fff22cfc172 _DPSNextEvent + 864
34 com.apple.AppKit 0x00007fff22cfa945 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364
35 com.apple.AppKit 0x00007fff22cecc69 -[NSApplication run] + 586
36 libqcocoa.dylib 0x000000012ab060ac 0x12aaed000 + 102572
37 QtCore 0x000000011b580326 QEventLoop::exec(QFlags) + 486
38 QtCore 0x000000011b577235 QCoreApplication::exec() + 133
39 QtWidgets.abi3.so 0x000000011dbe2d9a meth_QApplication_exec(_object*, _object*) + 90
40 org.python.python 0x000000010d94c71d cfunction_call + 125
41 org.python.python 0x000000010d90d5b7 _PyObject_MakeTpCall + 359
42 org.python.python 0x000000010d9e5e9c call_function + 876
43 org.python.python 0x000000010d9e32a2 _PyEval_EvalFrameDefault + 25554
44 org.python.python 0x000000010d90dd28 function_code_fastcall + 104
45 org.python.python 0x000000010d90fd6a method_vectorcall + 202
46 org.python.python 0x000000010d9e5e0c call_function + 732
47 org.python.python 0x000000010d9e32a2 _PyEval_EvalFrameDefault + 25554
48 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
49 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
50 org.python.python 0x000000010d9e5e0c call_function + 732
51 org.python.python 0x000000010d9e334b _PyEval_EvalFrameDefault + 25723
52 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
53 org.python.python 0x000000010d9dcdab PyEval_EvalCode + 139
54 org.python.python 0x000000010d9d9c12 builtin_exec + 626
55 org.python.python 0x000000010d94c023 cfunction_vectorcall_FASTCALL + 195
56 org.python.python 0x000000010d9e5e0c call_function + 732
57 org.python.python 0x000000010d9e334b _PyEval_EvalFrameDefault + 25723
58 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
59 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
60 org.python.python 0x000000010d9e5e0c call_function + 732
61 org.python.python 0x000000010d9e334b _PyEval_EvalFrameDefault + 25723
62 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
63 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
64 org.python.python 0x000000010da4c870 pymain_run_module + 208
65 org.python.python 0x000000010da4bf87 Py_RunMain + 1431
66 org.python.python 0x000000010da4c58f pymain_main + 223
67 org.python.python 0x000000010da4c49b Py_Main + 43
68 edu.ucsf.cgl.ChimeraX 0x000000010d8bfdc8 main + 120
69 libdyld.dylib 0x00007fff20418f3d start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff203d11d2 kevent64 + 10
1 QtWebEngineCore 0x0000000123059a2a 0x11f0f9000 + 66456106
2 QtWebEngineCore 0x0000000123059927 0x11f0f9000 + 66455847
3 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
4 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
5 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
6 QtWebEngineCore 0x0000000122fe02ad 0x11f0f9000 + 65958573
7 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
8 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 2:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fed26c 0x11f0f9000 + 66011756
5 QtWebEngineCore 0x0000000122fece6d 0x11f0f9000 + 66010733
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 3:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fed26c 0x11f0f9000 + 66011756
5 QtWebEngineCore 0x0000000122fecddd 0x11f0f9000 + 66010589
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 4:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff203d11d2 kevent64 + 10
1 QtWebEngineCore 0x0000000123059a2a 0x11f0f9000 + 66456106
2 QtWebEngineCore 0x0000000123059927 0x11f0f9000 + 66455847
3 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
4 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
5 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
6 QtWebEngineCore 0x0000000121f1e3a2 0x11f0f9000 + 48386978
7 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
8 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 6:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fed26c 0x11f0f9000 + 66011756
5 QtWebEngineCore 0x0000000122fece6d 0x11f0f9000 + 66010733
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 7:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff203cacde __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff203fde49 _pthread_cond_wait + 1298
2 QtWebEngineCore 0x000000012301fd1b 0x11f0f9000 + 66219291
3 QtWebEngineCore 0x00000001250ed92d 0x11f0f9000 + 100616493
4 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
5 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 8:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 9:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff203d11d2 kevent64 + 10
1 QtWebEngineCore 0x0000000123059a2a 0x11f0f9000 + 66456106
2 QtWebEngineCore 0x0000000123059927 0x11f0f9000 + 66455847
3 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
4 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
5 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
6 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
7 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 11:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 12:: NetworkService
0 libsystem_kernel.dylib 0x00007fff203d11d2 kevent64 + 10
1 QtWebEngineCore 0x0000000123059a2a 0x11f0f9000 + 66456106
2 QtWebEngineCore 0x0000000123059927 0x11f0f9000 + 66455847
3 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
4 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
5 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
6 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
7 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fed26c 0x11f0f9000 + 66011756
5 QtWebEngineCore 0x0000000122fececd 0x11f0f9000 + 66010829
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 16:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fed26c 0x11f0f9000 + 66011756
5 QtWebEngineCore 0x0000000122fecddd 0x11f0f9000 + 66010589
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 17:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff204f6b2f __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff204f520f __CFRunLoopRun + 1328
4 com.apple.CoreFoundation 0x00007fff204f461c CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff22e8223a _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 18:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000123027bef 0x11f0f9000 + 66251759
4 QtWebEngineCore 0x0000000122f5d1c9 0x11f0f9000 + 65421769
5 QtWebEngineCore 0x0000000122fd6a5c 0x11f0f9000 + 65919580
6 QtWebEngineCore 0x0000000122f8e998 0x11f0f9000 + 65624472
7 QtWebEngineCore 0x0000000122ff8eb8 0x11f0f9000 + 66059960
8 QtWebEngineCore 0x0000000122ff904a 0x11f0f9000 + 66060362
9 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 19:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff203c82ba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff203c862c mach_msg + 60
2 QtWebEngineCore 0x0000000123027e26 0x11f0f9000 + 66252326
3 QtWebEngineCore 0x0000000122fec7bf 0x11f0f9000 + 66009023
4 QtWebEngineCore 0x0000000122fecf9a 0x11f0f9000 + 66011034
5 QtWebEngineCore 0x0000000122fece0d 0x11f0f9000 + 66010637
6 QtWebEngineCore 0x0000000123020908 0x11f0f9000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff203cacde __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff203fde49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x000000010f4fa23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff203cacde __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff203fde49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x000000010f4fa23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff203cacde __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff203fde49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x000000010f4fa23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 23:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 24:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 25:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 27:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 28:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 29:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 30:
0 libsystem_pthread.dylib 0x00007fff203f9420 start_wqthread + 0
Thread 31:
0 libsystem_kernel.dylib 0x00007fff203cacde __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff203fde49 _pthread_cond_wait + 1298
2 org.python.python 0x000000010da3c79c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010da8b69f acquire_timed + 111
4 org.python.python 0x000000010da8b7b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010d91614e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x000000010d9e5e0c call_function + 732
7 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010d9e5e0c call_function + 732
11 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x000000010d9e6b03 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010d90dcb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010d9e5e0c call_function + 732
15 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x000000010d90dd28 function_code_fastcall + 104
17 org.python.python 0x000000010d9e5e0c call_function + 732
18 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x000000010d90dd28 function_code_fastcall + 104
20 org.python.python 0x000000010d9e5e0c call_function + 732
21 org.python.python 0x000000010d9e327e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x000000010d90dd28 function_code_fastcall + 104
23 org.python.python 0x000000010d90fdb2 method_vectorcall + 274
24 org.python.python 0x000000010da8b046 t_bootstrap + 70
25 org.python.python 0x000000010da3c2f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff203fd8fc _pthread_start + 224
27 libsystem_pthread.dylib 0x00007fff203f9443 thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010f170e00 rcx: 0x00007fa65933f418 rdx: 0x0000000000000000
rdi: 0x0000000000000103 rsi: 0x000000000000000b rbp: 0x00007fa65933f440 rsp: 0x00007fa65933f418
r8: 0x00007fa65933ff48 r9: 0x29303a823cb80ab4 r10: 0x000000010f170e00 r11: 0x0000000000000246
r12: 0x0000000000000103 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff203ce92e rfl: 0x0000000000000246 cr2: 0x00007fa65933e8c0
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
e5 41 57 41 56 41 55 41-54 53 48 83 ec 48 48 89 .AWAVAUATSH..HH.
fb 48 8b 7f 20 48 8b 47-08 f6 40 30 02 75 1d 49 .H.. H.G..@0.u.I
89 f6 48 8b 4b 10 48 8b-41 40 48 85 c0 74 2a 4c ..H.K.H.A@H..t*L
89 f6 ff d0 85 c0 0f 88-53 03 00 00 48 8b 1d 22 ........S...H.."
50 05 00 48 83 03 01 48-89 d8 48 83 c4 48 5b 41 P..H...H..H..H[A
5c 41 5d 41 5e 41 5f 5d-c3 4c 8b 61 38 48 8b 07 \A]A^A_].L.a8H..
[ff]10 49 8b 74 24 28 48-85 f6 75 07 48 8b 35 0a ..I.t$(H..u.H.5. /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
0x10d8ce000 - 0x10db36fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
0x10dca0000 - 0x10dca2fff +_heapq.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_heapq.cpython-39-darwin.so
0x10dcac000 - 0x10dcb0fff +binascii.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/binascii.cpython-39-darwin.so
0x10dcba000 - 0x10dcbffff +zlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/zlib.cpython-39-darwin.so
0x10dcc9000 - 0x10dccbfff +_bz2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bz2.cpython-39-darwin.so
0x10dcd5000 - 0x10dd06fff +_lzma.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_lzma.cpython-39-darwin.so
0x10dd18000 - 0x10dd19fff +grp.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/grp.cpython-39-darwin.so
0x10dd23000 - 0x10dd28fff +_struct.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_struct.cpython-39-darwin.so
0x10dd37000 - 0x10dd3ffff +math.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/math.cpython-39-darwin.so
0x10dd4d000 - 0x10dd4efff +_bisect.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bisect.cpython-39-darwin.so
0x10dd58000 - 0x10dd59fff +_random.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_random.cpython-39-darwin.so
0x10dd63000 - 0x10dd67fff +_sha512.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_sha512.cpython-39-darwin.so
0x10dd71000 - 0x10dd71fff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x10dd7b000 - 0x10de1cfff +libarrays.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x10de42000 - 0x10de47fff +_json.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_json.cpython-39-darwin.so
0x10de51000 - 0x10e294fff +_multiarray_umath.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so
0x10e3ed000 - 0x10e504fff +libgfortran.3.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x10e573000 - 0x10e5a9fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x10e5bf000 - 0x10e5d4fff +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x10e5e6000 - 0x10e5f5fff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x10e609000 - 0x10e620fff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x10e633000 - 0x10e646fff +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x10e663000 - 0x10e665fff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x10e66f000 - 0x10e673fff +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
0x10e67d000 - 0x10e68efff +_ctypes.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so
0x10e6a7000 - 0x10e6c2fff +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
0x10e6df000 - 0x10e6f2fff +_pocketfft_internal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/fft/_pocketfft_internal.cpython-39-darwin.so
0x10e6ff000 - 0x10e772fff +mtrand.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/mtrand.cpython-39-darwin.so
0x10e7d7000 - 0x10e7f6fff +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
0x10e81b000 - 0x10e84efff +_common.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_common.cpython-39-darwin.so
0x10e86f000 - 0x10e875fff +_hashlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_hashlib.cpython-39-darwin.so
0x10e884000 - 0x10e8ddfff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.1.1.dylib
0x10e90f000 - 0x10eb26fff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
0x10ebc6000 - 0x10ebccfff +_blake2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_blake2.cpython-39-darwin.so
0x10ebd6000 - 0x10ec29fff +_bounded_integers.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_bounded_integers.cpython-39-darwin.so
0x10ec5a000 - 0x10ec69fff +_mt19937.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_mt19937.cpython-39-darwin.so
0x10ec7e000 - 0x10ec8dfff +_philox.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_philox.cpython-39-darwin.so
0x10eca2000 - 0x10ecb1fff +_pcg64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_pcg64.cpython-39-darwin.so
0x10ecc6000 - 0x10eccdfff +_sfc64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_sfc64.cpython-39-darwin.so
0x10ecde000 - 0x10ed6dfff +_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_generator.cpython-39-darwin.so
0x10edde000 - 0x10eddefff +_opcode.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_opcode.cpython-39-darwin.so
0x10ede8000 - 0x10ee06fff +_geometry.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/geometry/_geometry.cpython-39-darwin.so
0x10ee6e000 - 0x10ee85fff +sip.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/sip.cpython-39-darwin.so
0x10ee9e000 - 0x10ef29fff +QtDBus (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtDBus.framework/Versions/A/QtDBus
0x10ef4e000 - 0x10ef5dfff +QtWebEngineWidgets.abi3.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtWebEngineWidgets.abi3.so
0x10ef72000 - 0x10ef85fff +QtWebEngineWidgets (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtWebEngineWidgets.framework/Versions/A/QtWebEngineWidgets
0x10ef9e000 - 0x10efe9fff +QtPrintSupport (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtPrintSupport.framework/Versions/A/QtPrintSupport
0x10f01a000 - 0x10f04dfff +QtWebChannel (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtWebChannel.framework/Versions/A/QtWebChannel
0x10f066000 - 0x10f079fff +QtQuickWidgets (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtQuickWidgets.framework/Versions/A/QtQuickWidgets
0x10f099000 - 0x10f134fff dyld (852.2) /usr/lib/dyld
0x10f1b1000 - 0x112ec0fff +libopenblas64_.0.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libopenblas64_.0.dylib
0x11b17d000 - 0x11b300fff +QtCore.abi3.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtCore.abi3.so
0x11b509000 - 0x11ba0cfff +QtCore (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtCore.framework/Versions/A/QtCore
0x11d9bd000 - 0x11dc68fff +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtWidgets.abi3.so
0x11dfcd000 - 0x11e488fff +QtWidgets (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtWidgets.framework/Versions/A/QtWidgets
0x11e5e5000 - 0x11ec8cfff +QtGui (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtGui.framework/Versions/A/QtGui
0x11edb9000 - 0x11ef20fff +QtGui.abi3.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtGui.abi3.so
0x11f0f9000 - 0x128e60fff +QtWebEngineCore (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtWebEngineCore.framework/Versions/A/QtWebEngineCore
0x129af5000 - 0x129ed8fff +QtQuick (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtQuick.framework/Versions/A/QtQuick
0x12a039000 - 0x12a0a0fff +QtOpenGL (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtOpenGL.framework/Versions/A/QtOpenGL
0x12a0d1000 - 0x12a158fff +QtQmlModels (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtQmlModels.framework/Versions/A/QtQmlModels
0x12a189000 - 0x12a56cfff +QtQml (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtQml.framework/Versions/A/QtQml
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0x7fff41252000 - 0x7fff41270fff libCGInterfaces.dylib (544.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff428f0000 - 0x7fff43650fff libfaceCore.dylib (4.3.1) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib
0x7fff43651000 - 0x7fff43764fff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff43765000 - 0x7fff4377dfff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark
0x7fff437ff000 - 0x7fff43a72fff com.apple.RawCamera.bundle (9.10.0 - 1450.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff442db000 - 0x7fff442dffff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
0x7fff45c56000 - 0x7fff45c59fff libpmenergy.dylib (227.140.1) /usr/lib/libpmenergy.dylib
0x7fff46345000 - 0x7fff46350fff libGPUSupportMercury.dylib (18.5.9) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
0x7fff4797b000 - 0x7fff479bbfff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x7fff48209000 - 0x7fff48224fff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x7fff51638000 - 0x7fff516d7fff com.apple.Symbolication (12.5 - 64544.70.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff518c7000 - 0x7fff518cafff libpmsample.dylib (227.140.1) /usr/lib/libpmsample.dylib
0x7fff53f5f000 - 0x7fff53f95fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x7fff5558c000 - 0x7fff5558ffff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff63e4f000 - 0x7fff64e3efff com.apple.driver.AppleIntelICLGraphicsGLDriver (16.5.2 - 16.0.5) /System/Library/Extensions/AppleIntelICLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelICLGraphicsGLDriver
0x7fff652f7000 - 0x7fff65828fff com.apple.driver.AppleIntelICLGraphicsMTLDriver (16.5.2 - 16.0.5) /System/Library/Extensions/AppleIntelICLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelICLGraphicsMTLDriver
0x7fff69688000 - 0x7fff6968cfff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x7fff6bad3000 - 0x7fff6bad9fff libCoreFSCache.dylib (200.10) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6bada000 - 0x7fff6badefff libCoreVMClient.dylib (200.10) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6badf000 - 0x7fff6baeefff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6baef000 - 0x7fff6baf1fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6baf2000 - 0x7fff6bafafff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6bafb000 - 0x7fff6bb2efff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6bb2f000 - 0x7fff6bb6bfff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6bb6c000 - 0x7fff6bcfffff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6bd00000 - 0x7fff6bd0afff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6bd0b000 - 0x7fff6be88fff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6be89000 - 0x7fff6beb1fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6d14a000 - 0x7fff6d1a2fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6e24c000 - 0x7fff6e253fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff6e254000 - 0x7fff6e33bfff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff6f8b9000 - 0x7fff6f8cbfff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x7fff73bcd000 - 0x7fff73bd8fff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff73dee000 - 0x7fff73e06fff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff7797e000 - 0x7fff77985fff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
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: 0
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=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 3240K 6
CG image 412K 19
CoreAnimation 792K 80
CoreGraphics 12K 2
CoreUI image data 4388K 34
Foundation 16K 1
Kernel Alloc Once 8K 1
MALLOC 1.7G 608
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenGL GLSL 384K 4
STACK GUARD 124K 31
Stack 174.2M 32
Stack Guard 56.0M 1
VM_ALLOCATE 175.1M 146
__DATA 36.1M 634
__DATA_CONST 27.6M 311
__DATA_DIRTY 1706K 211
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 531.3M 256
__OBJC_RO 70.2M 1
__OBJC_RW 2496K 2
__TEXT 660.9M 616
__UNICODE 588K 1
mapped file 267.2M 48
shared memory 3092K 26
=========== ======= =======
TOTAL 3.8G 3090
TOTAL, minus reserved VM space 3.7G 3090
===== 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/alexastrauss/Documents/Grad school 2019/Levitz
> lab/23d_paper/figure_drafts/ly37_binding_site2.cxs" format session
Opened P1_J860_ECD_resampled.mrc as #2, grid size 416,416,416, pixel 0.852,
shown at level 0.604, step 1, values float32
Opened J571_ecd_zflip_resampled.mrc as #5, grid size 416,416,416, pixel 0.825,
shown at level 0.56, step 1, values float32
Opened P1_J860_ECD_resampled.mrc 0 as #6.1, grid size 416,416,416, pixel
0.852, shown at level 0.604, step 1, values float32
Opened P1_J860_ECD_resampled.mrc 1 as #6.2, grid size 416,416,416, pixel
0.852, shown at level 0.604, step 1, values float32
opened ChimeraX session
> hide #!5 models
> hide #!6 models
> show #!6.1 models
> show #!6.2 models
> show #!4 models
> hide #!6.2 models
> hide #!6.1 models
> hide #!1 models
> hide #!3 models
> hide #!6 models
> hide #!4 models
> show #!1 models
> show #!2 models
> transparency #1.2-3#2.1 0
> transparency #1.2-3#2.1 50
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.5.2 (20G95)
Kernel Version: Darwin 20.6.0
Time since boot: 13 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-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 (10)
comment:1 by , 3 years ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash emitting color_pause signal |
comment:2 by , 3 years ago
| Cc: | added |
|---|
comment:3 by , 3 years ago
Eric, do you remember back in the annals of history a case where we had some trouble with color buttons and PyQt slots and premature deletion? I vaguely recall such a problem, and that maybe you worked around it somehow.
comment:4 by , 3 years ago
Look at ColorButton's _color_changed_cb(). It is catching the RuntimeError caused by set_color()'s call to setStyleSheet() and in that case it avoids emitting the color_changed signal (which would crash). The color_pause signal does not have the same protection. We probably haven't seem this before because few buttons use the color_pause signal (i.e. they use the default pause_delay of None).
comment:5 by , 3 years ago
I was wondering what that try/except in _color_changed_cb() was about. And I am surprised that self.color_changed.emit() crashes .color_changed.emit() would cause a crash. Why does it cause a crash? Seems like a PyQt bug. Shouldn't it just give a traceback about the QPushButton being deleted?
In any case, I'll protect the similar color_pause signal.
Thanks for the insight.
comment:6 by , 3 years ago
Yeah, signals are weird (https://www.riverbankcomputing.com/static/Docs/PyQt5/signals_slots.html). I mean, they're class variables that become "bound" when an instance references them (sort of like bound methods). So I have the feeling they're never destroyed, so PyQt can figure out that when you call emit() on them it should complain -- it just calls the bound method which goes straight to the dead tool that contained the ColorButton.
comment:8 by , 3 years ago
It doesn't appear to call the dead tool. The QPushButton that the ColorButton derives from is gone and the SIgnal.emit() I'd guess wipes out because it doesn't check that the QPushButton C++ object has been deleted. It seems like it could and should check. We see so many crashes in the Qt event loop and I suspect they are other PyQt lifetime issues.
comment:10 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Maybe fixed in devel branch, not in 1.6.
I wasn't able to reproduce this crash in the current code (which use PyQt 6.4 while ChimeraX 1.5 in this bug report is using PyQt 6.3). Calling the emit method with the QPushButton deleted just gave a traceback saying the C++ object had been deleted and did not crash. That was tested from the shell not from the QTimer callback because the QTimer never calls the callback if the QPushButton is deleted. That is mysterious. I could not find any mechanism which would stop the timer. But maybe the QTimer code actually sees that the callback is a method of a deleted QPushButton and silently does not make the call.
At any rate, I made the QTimer be a child of the QPushButton, so I hope the timer will never be called if the push button has been deleted. But since I had no test case this is just a guess.
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The crash was a QTimer trying to call back into Python. I think we've seen many reports (100?) where PyQt is calling back from Qt into Python and it crashes in Python's C method_vectorcall(). I suspect this is mostly caused by trying to call a deleted Python object which references a bad function pointer. So this would be a PyQt reference counting bug where the Python reference count drops to zero even though some PyQt callback still references the callback and later tries to call it.
In this case the code that registers the QTimer callback looks like this
from Qt.QtCore import QTimer self._pause_timer = t = QTimer() t.setSingleShot(True) t.timeout.connect(lambda *, p=self.color_pause, c=self._color: p.emit(c)) t.start(int(1000*self._pause_delay))So the callback is a lambda function. I'd guess the lambda is only referenced by the PyQt connect() saving a reference to it. I'd guess that either the lambda has been deleted, or the self.color_pause value or the self._color value. But if the lambda has not been delete then its stack frame should keep references to those two values. So it seems like the lambda must have been deleted. It seems like connect() must keep a reference to the lambda, but maybe PyQt released that reference and yet held onto the pointer to the lambda and yet did not clean up the timer and it got invoked.