![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 years ago
Closed 6 years ago
#1781 closed defect (fixed)
Crash finding 6-member planar NR2 ring in 5vrj
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-12)
Description
This happened during protonation of the attached structure.
Please describe steps that led to the crash here.
Process: ChimeraX [34701]
Path: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 0.9.0 (0.9.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [34701]
User ID: 1574452387
Date/Time: 2019-03-15 14:16:19.659 +0000
OS Version: Mac OS X 10.14.3 (18D109)
Report Version: 12
Bridge OS Version: 3.0 (14Y674)
Anonymous UUID: B8F22D49-9671-CB90-FDDE-D01E7D515AFA
Time Awake Since Boot: 20000 seconds
System Integrity Protection: enabled
Crashed Thread: 29
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000058
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x58:
-->
__TEXT 0000000104963000-0000000104964000 [ 4K] r-x/rwx SM=COW /Applications/ChimeraX.app/Contents/MacOS/ChimeraX
Thread 0:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff658a694e __ulock_wait + 10
1 libsystem_pthread.dylib 0x00007fff6596270a _pthread_join + 356
2 libc++.1.dylib 0x00007fff62e80978 std::__1::thread::join() + 24
3 _chem_group.cpython-37m-darwin.so 0x00000001218dffb8 find_6ring_planar_NR2(_object*, _object*) + 792
4 org.python.python 0x0000000104988c79 PyCFunction_Call + 345
5 org.python.python 0x0000000104a4ad49 _PyEval_EvalFrameDefault + 6697
6 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
7 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
8 org.python.python 0x0000000104a52271 call_function + 721
9 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
10 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
11 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
12 org.python.python 0x0000000104a52271 call_function + 721
13 org.python.python 0x0000000104a4aa09 _PyEval_EvalFrameDefault + 5865
14 org.python.python 0x0000000104988df3 function_code_fastcall + 195
15 org.python.python 0x0000000104a52271 call_function + 721
16 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
17 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
18 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
19 org.python.python 0x0000000104a52271 call_function + 721
20 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
21 org.python.python 0x0000000104988df3 function_code_fastcall + 195
22 org.python.python 0x0000000104a52271 call_function + 721
23 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
24 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
25 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
26 org.python.python 0x0000000104a52271 call_function + 721
27 org.python.python 0x0000000104a4aa09 _PyEval_EvalFrameDefault + 5865
28 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
29 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
30 org.python.python 0x0000000104a52271 call_function + 721
31 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
32 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
33 org.python.python 0x00000001049883d2 _PyFunction_FastCallDict + 450
34 org.python.python 0x0000000104a4ac45 _PyEval_EvalFrameDefault + 6437
35 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
36 org.python.python 0x00000001049883d2 _PyFunction_FastCallDict + 450
37 org.python.python 0x0000000104a4ac45 _PyEval_EvalFrameDefault + 6437
38 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
39 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
40 org.python.python 0x0000000104a52271 call_function + 721
41 org.python.python 0x0000000104a4a8c0 _PyEval_EvalFrameDefault + 5536
42 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
43 org.python.python 0x00000001049883d2 _PyFunction_FastCallDict + 450
44 org.python.python 0x0000000104989886 _PyObject_Call_Prepend + 150
45 org.python.python 0x0000000104988a58 PyObject_Call + 136
46 QtCore.so 0x0000000112313828 PyQtSlot::call(_object*, _object*) const + 40
47 QtCore.so 0x0000000112313727 PyQtSlot::invoke(void**, _object*, void*, bool) const + 391
48 QtCore.so 0x0000000112314268 PyQtSlotProxy::unislot(void**) + 88
49 QtCore.so 0x00000001123141da PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
50 QtCore 0x0000000111e7b3d6 QMetaObject::activate(QObject*, int, int, void**) + 2230
51 QtCore 0x0000000111e7b6aa QMetaObject::activate(QObject*, int, int, void**) + 2954
52 QtWidgets 0x000000011131e12e QWidgetLineControl::processKeyEvent(QKeyEvent*) + 334
53 QtWidgets 0x0000000111314d72 QLineEdit::keyPressEvent(QKeyEvent*) + 34
54 QtWidgets 0x0000000111201cfb QWidget::event(QEvent*) + 587
55 QtWidgets 0x0000000111314187 QLineEdit::event(QEvent*) + 599
56 QtWidgets 0x00000001112dc1f6 QComboBox::keyPressEvent(QKeyEvent*) + 838
57 QtWidgets.so 0x0000000110e7a8f9 meth_QComboBox_keyPressEvent(_object*, _object*) + 137
58 org.python.python 0x00000001049893ab _PyMethodDef_RawFastCallKeywords + 251
59 org.python.python 0x000000010498893c _PyCFunction_FastCallKeywords + 44
60 org.python.python 0x0000000104a52209 call_function + 617
61 org.python.python 0x0000000104a4a8da _PyEval_EvalFrameDefault + 5562
62 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
63 org.python.python 0x00000001049883d2 _PyFunction_FastCallDict + 450
64 org.python.python 0x0000000104989886 _PyObject_Call_Prepend + 150
65 org.python.python 0x0000000104988a58 PyObject_Call + 136
66 sip.so 0x00000001121e334a call_method + 76
67 sip.so 0x00000001121df284 sip_api_call_procedure_method + 152
68 QtWidgets.so 0x0000000110d7f6d7 sipQComboBox::keyPressEvent(QKeyEvent*) + 103
69 QtWidgets 0x0000000111201cfb QWidget::event(QEvent*) + 587
70 QtWidgets 0x00000001112dbb25 QComboBox::event(QEvent*) + 373
71 QtWidgets.so 0x0000000110d7ebe0 sipQComboBox::event(QEvent*) + 192
72 QtWidgets 0x00000001111c7b82 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 306
73 QtWidgets 0x00000001111c8feb QApplication::notify(QObject*, QEvent*) + 715
74 QtWidgets.so 0x0000000110d99f8a sipQApplication::notify(QObject*, QEvent*) + 234
75 QtCore 0x0000000111e4aa7f QCoreApplication::notifyInternal2(QObject*, QEvent*) + 159
76 QtWidgets 0x0000000111220c96 0x1111b6000 + 437398
77 QtWidgets 0x00000001111c7b82 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 306
78 QtWidgets 0x00000001111c8e9f QApplication::notify(QObject*, QEvent*) + 383
79 QtWidgets.so 0x0000000110d99f8a sipQApplication::notify(QObject*, QEvent*) + 234
80 QtCore 0x0000000111e4aa7f QCoreApplication::notifyInternal2(QObject*, QEvent*) + 159
81 QtGui 0x0000000111793c35 QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 165
82 QtGui 0x000000011177928b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 155
83 QtGui 0x0000000111775060 QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 576
84 libqcocoa.dylib 0x000000011a4447db 0x11a423000 + 137179
85 libqcocoa.dylib 0x000000011a4449a8 0x11a423000 + 137640
86 com.apple.AppKit 0x00007fff35bda436 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6946
87 com.apple.AppKit 0x00007fff35bd86c9 -[NSWindow(NSEventRouting) sendEvent:] + 481
88 libqcocoa.dylib 0x000000011a432377 0x11a423000 + 62327
89 libqcocoa.dylib 0x000000011a431c34 0x11a423000 + 60468
90 com.apple.AppKit 0x00007fff35a7630b -[NSApplication(NSEvent) sendEvent:] + 2823
91 libqcocoa.dylib 0x000000011a44dd5a 0x11a423000 + 175450
92 com.apple.AppKit 0x00007fff35a6319d -[NSApplication run] + 755
93 libqcocoa.dylib 0x000000011a44a53d 0x11a423000 + 161085
94 QtCore 0x0000000111e46742 QEventLoop::exec(QFlags) + 418
95 QtCore 0x0000000111e4b172 QCoreApplication::exec() + 402
96 QtWidgets.so 0x0000000110e87dc2 meth_QApplication_exec_(_object*, _object*) + 82
97 org.python.python 0x00000001049893ab _PyMethodDef_RawFastCallKeywords + 251
98 org.python.python 0x000000010498893c _PyCFunction_FastCallKeywords + 44
99 org.python.python 0x0000000104a52209 call_function + 617
100 org.python.python 0x0000000104a4a8da _PyEval_EvalFrameDefault + 5562
101 org.python.python 0x0000000104988df3 function_code_fastcall + 195
102 org.python.python 0x0000000104a52271 call_function + 721
103 org.python.python 0x0000000104a4a8da _PyEval_EvalFrameDefault + 5562
104 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
105 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
106 org.python.python 0x0000000104a52271 call_function + 721
107 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
108 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
109 org.python.python 0x0000000104a49280 PyEval_EvalCode + 48
110 org.python.python 0x0000000104a469c3 builtin_exec + 563
111 org.python.python 0x000000010498955e _PyMethodDef_RawFastCallKeywords + 686
112 org.python.python 0x000000010498893c _PyCFunction_FastCallKeywords + 44
113 org.python.python 0x0000000104a52209 call_function + 617
114 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
115 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
116 org.python.python 0x00000001049888f6 _PyFunction_FastCallKeywords + 230
117 org.python.python 0x0000000104a52271 call_function + 721
118 org.python.python 0x0000000104a4a96b _PyEval_EvalFrameDefault + 5707
119 org.python.python 0x0000000104a52e81 _PyEval_EvalCodeWithName + 2721
120 org.python.python 0x00000001049883d2 _PyFunction_FastCallDict + 450
121 org.python.python 0x0000000104aa74c3 pymain_run_module + 147
122 org.python.python 0x0000000104aa62d6 pymain_main + 4262
123 org.python.python 0x0000000104aa5223 Py_Main + 51
124 edu.ucsf.cgl.ChimeraX 0x0000000104963e16 main + 278
125 libdyld.dylib 0x00007fff6576aed9 start + 1
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 com.apple.AppKit 0x00007fff35a72f89 _NSEventThread + 160
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 2:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff658ac2ee poll + 10
1 QtCore 0x0000000111e9db40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x0000000111e9f1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x0000000111e46742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001129a0c4a 0x11297f000 + 138314
5 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
6 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
7 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
8 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 3:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff658aa716 kevent + 10
1 QtWebEngineCore 0x0000000113aad469 0x11297f000 + 18015337
2 QtWebEngineCore 0x0000000113aaa75d 0x11297f000 + 18003805
3 QtWebEngineCore 0x000000011359e99f 0x11297f000 + 12712351
4 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
5 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
6 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
7 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
8 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
10 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 4:: WorkerPool/78339
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff659615c6 _pthread_cond_wait + 775
2 QtWebEngineCore 0x00000001135d82bb 0x11297f000 + 12948155
3 QtWebEngineCore 0x00000001135f66e9 0x11297f000 + 13072105
4 QtWebEngineCore 0x00000001135f6c57 0x11297f000 + 13073495
5 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 5:: WorkerPool/51203
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff659615c6 _pthread_cond_wait + 775
2 QtWebEngineCore 0x00000001135d82bb 0x11297f000 + 12948155
3 QtWebEngineCore 0x00000001135f66e9 0x11297f000 + 13072105
4 QtWebEngineCore 0x00000001135f6c57 0x11297f000 + 13073495
5 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 6:: Chrome_DBThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x0000000112c6c958 0x11297f000 + 3070296
10 QtWebEngineCore 0x0000000112c6cd1f 0x11297f000 + 3071263
11 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
12 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 7:: Chrome_FileThread
0 libsystem_kernel.dylib 0x00007fff658aa716 kevent + 10
1 QtWebEngineCore 0x0000000113aad469 0x11297f000 + 18015337
2 QtWebEngineCore 0x0000000113aaa75d 0x11297f000 + 18003805
3 QtWebEngineCore 0x000000011359e99f 0x11297f000 + 12712351
4 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
5 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
6 QtWebEngineCore 0x0000000112c6c9d8 0x11297f000 + 3070424
7 QtWebEngineCore 0x0000000112c6cd2f 0x11297f000 + 3071279
8 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
9 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
10 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
12 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 8:: Chrome_FileUserBlockingThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x0000000112c6ca58 0x11297f000 + 3070552
10 QtWebEngineCore 0x0000000112c6cd3f 0x11297f000 + 3071295
11 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
12 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 9:: Chrome_ProcessLauncherThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x0000000112c6cad8 0x11297f000 + 3070680
10 QtWebEngineCore 0x0000000112c6cd4c 0x11297f000 + 3071308
11 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
12 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 10:: Chrome_CacheThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x0000000112c6cb58 0x11297f000 + 3070808
10 QtWebEngineCore 0x0000000112c6cd59 0x11297f000 + 3071321
11 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
12 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 11:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff658aa716 kevent + 10
1 QtWebEngineCore 0x0000000113aad469 0x11297f000 + 18015337
2 QtWebEngineCore 0x0000000113aaa75d 0x11297f000 + 18003805
3 QtWebEngineCore 0x000000011359e986 0x11297f000 + 12712326
4 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
5 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
6 QtWebEngineCore 0x0000000112c6cbd8 0x11297f000 + 3070936
7 QtWebEngineCore 0x0000000112c6cd66 0x11297f000 + 3071334
8 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
9 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
10 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
12 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 12:: BrowserBlockingWorker1/71171
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff65961593 _pthread_cond_wait + 724
2 QtWebEngineCore 0x00000001135eec1f 0x11297f000 + 13040671
3 QtWebEngineCore 0x00000001135ee2e6 0x11297f000 + 13038310
4 QtWebEngineCore 0x00000001135f218d 0x11297f000 + 13054349
5 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 13:: IndexedDB
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
10 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 14:: CompositorTileWorker1/56323
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff65961593 _pthread_cond_wait + 724
2 QtWebEngineCore 0x000000011418dcf8 0x11297f000 + 25226488
3 QtWebEngineCore 0x00000001135f218d 0x11297f000 + 13054349
4 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
5 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
6 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
7 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 15:: AudioThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
10 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 16:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff658a417a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff658a46d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff38519fde __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff3851952d __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff38518c64 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x000000011359f90f 0x11297f000 + 12716303
6 QtWebEngineCore 0x000000011359f2a4 0x11297f000 + 12714660
7 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
8 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
9 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
10 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 17:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff658aa716 kevent + 10
1 QtWebEngineCore 0x0000000113aad469 0x11297f000 + 18015337
2 QtWebEngineCore 0x0000000113aaa75d 0x11297f000 + 18003805
3 QtWebEngineCore 0x000000011359e99f 0x11297f000 + 12712351
4 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
5 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
6 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
7 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
8 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
10 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff658ac2ee poll + 10
1 QtCore 0x0000000111e9db40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x0000000111e9f1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x0000000111e46742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001129a0c4a 0x11297f000 + 138314
5 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
6 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
7 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
8 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 19:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff65961593 _pthread_cond_wait + 724
2 QtCore 0x0000000111c8c58b 0x111c5f000 + 185739
3 QtCore 0x0000000111c8c522 QWaitCondition::wait(QMutex*, unsigned long) + 162
4 QtWidgets 0x00000001113ed862 0x1111b6000 + 2324578
5 QtCore 0x0000000111c8afbf 0x111c5f000 + 180159
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff658ac2ee poll + 10
1 QtCore 0x0000000111e9db40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x0000000111e9f1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x0000000111e46742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001129a0c4a 0x11297f000 + 138314
5 QtWebEngineCore 0x000000011359c10e 0x11297f000 + 12701966
6 QtWebEngineCore 0x00000001135c0531 0x11297f000 + 12850481
7 QtWebEngineCore 0x00000001135f436b 0x11297f000 + 13063019
8 QtWebEngineCore 0x00000001135ed667 0x11297f000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 21:
0 libsystem_pthread.dylib 0x00007fff6595d3f8 start_wqthread + 0
1 ??? 0x0000000054485244 0 + 1414025796
Thread 22:
0 libsystem_pthread.dylib 0x00007fff6595d3f8 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff6595d3f8 start_wqthread + 0
1 ??? 0x0000000000001303 0 + 4867
Thread 24:
0 libsystem_pthread.dylib 0x00007fff6595d3f8 start_wqthread + 0
1 ??? 0x0003000400040007 0 + 844442110263303
Thread 25:
0 libsystem_pthread.dylib 0x00007fff6595d3f8 start_wqthread + 0
Thread 26:
0 libopenblasp-r0.3.5.dev.dylib 0x000000010580ca07 blas_thread_server + 567
1 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
2 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
3 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 27:
0 libsystem_kernel.dylib 0x00007fff658a4282 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff65960ebe sched_yield + 11
2 libopenblasp-r0.3.5.dev.dylib 0x000000010580ca05 blas_thread_server + 565
3 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 28:
0 libsystem_kernel.dylib 0x00007fff658a77de __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff65961593 _pthread_cond_wait + 724
2 libopenblasp-r0.3.5.dev.dylib 0x000000010580ca3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 29 Crashed:
0 libsystem_kernel.dylib 0x00007fff658aa23e __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff65960c1c pthread_kill + 285
2 libsystem_c.dylib 0x00007fff657c6096 raise + 26
3 libsystem_platform.dylib 0x00007fff65955b3d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 _chem_group.cpython-37m-darwin.so 0x00000001218e868b void* std::__1::__thread_proxy >, void (*)(std::__1::__wrap_iter, std::__1::__wrap_iter, bool, std::__1::vector >, std::__1::allocator > > >*, std::__1::mutex*), std::__1::__wrap_iter, std::__1::__wrap_iter, bool, std::__1::vector >, std::__1::allocator > > >*, std::__1::mutex*> >(void*) + 59
6 libsystem_pthread.dylib 0x00007fff6595e305 _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6596126f _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff6595d415 thread_start + 13
Thread 29 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000070000e72b000 rcx: 0x000070000e72a898 rdx: 0x0000000000000000
rdi: 0x0000000000008dbb rsi: 0x000000000000000b rbp: 0x000070000e72a8d0 rsp: 0x000070000e72a898
r8: 0x000070000e72ad98 r9: 0x9aa2a37d1ffd1a16 r10: 0x000070000e72b0ac r11: 0x0000000000000287
r12: 0x0000000000008dbb r13: 0x0000600000b03100 r14: 0x000000000000000b r15: 0x000000000000002d
rip: 0x00007fff658aa23e rfl: 0x0000000000000286 cr2: 0x000070000e729ff8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff64fe2000 - 0x7fff651b9fe7 libsqlite3.dylib (274.22) /usr/lib/libsqlite3.dylib
0x7fff652bc000 - 0x7fff65309fff libssl.44.dylib (22.240.1) /usr/lib/libssl.44.dylib
0x7fff65446000 - 0x7fff65449ffb libutil.dylib (51.200.4) /usr/lib/libutil.dylib
0x7fff6544a000 - 0x7fff65457fff libxar.1.dylib (404) /usr/lib/libxar.1.dylib
0x7fff6545c000 - 0x7fff6553ffff libxml2.2.dylib (32.8) /usr/lib/libxml2.2.dylib
0x7fff65540000 - 0x7fff65568ff3 libxslt.1.dylib (16.1) /usr/lib/libxslt.1.dylib
0x7fff65569000 - 0x7fff6557bffb libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib
0x7fff655ec000 - 0x7fff655f0ff3 libcache.dylib (81) /usr/lib/system/libcache.dylib
0x7fff655f1000 - 0x7fff655fbff3 libcommonCrypto.dylib (60118.220.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff655fc000 - 0x7fff65603fff libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib
0x7fff65604000 - 0x7fff6560dff3 libcopyfile.dylib (146.200.3) /usr/lib/system/libcopyfile.dylib
0x7fff6560e000 - 0x7fff65692fdf libcorecrypto.dylib (602.230.1) /usr/lib/system/libcorecrypto.dylib
0x7fff65719000 - 0x7fff65753ff7 libdispatch.dylib (1008.220.2) /usr/lib/system/libdispatch.dylib
0x7fff65754000 - 0x7fff65783ff3 libdyld.dylib (655.1) /usr/lib/system/libdyld.dylib
0x7fff65784000 - 0x7fff65784ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff65785000 - 0x7fff65791ff7 libkxld.dylib (4903.241.1) /usr/lib/system/libkxld.dylib
0x7fff65792000 - 0x7fff65792ff7 liblaunch.dylib (1336.240.2) /usr/lib/system/liblaunch.dylib
0x7fff65793000 - 0x7fff65798fff libmacho.dylib (921) /usr/lib/system/libmacho.dylib
0x7fff65799000 - 0x7fff6579bffb libquarantine.dylib (86.220.1) /usr/lib/system/libquarantine.dylib
0x7fff6579c000 - 0x7fff6579dff3 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib
0x7fff6579e000 - 0x7fff657b5ff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib
0x7fff657b6000 - 0x7fff657b6fff libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff657b7000 - 0x7fff6583ffff libsystem_c.dylib (1272.200.26) /usr/lib/system/libsystem_c.dylib
0x7fff65840000 - 0x7fff65843ff7 libsystem_configuration.dylib (963.200.27) /usr/lib/system/libsystem_configuration.dylib
0x7fff65844000 - 0x7fff65847ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff65848000 - 0x7fff6584effb libsystem_darwin.dylib (1272.200.26) /usr/lib/system/libsystem_darwin.dylib
0x7fff6584f000 - 0x7fff65855ff7 libsystem_dnssd.dylib (878.240.1) /usr/lib/system/libsystem_dnssd.dylib
0x7fff65856000 - 0x7fff658a2ff3 libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff658a3000 - 0x7fff658cbff7 libsystem_kernel.dylib (4903.241.1) /usr/lib/system/libsystem_kernel.dylib
0x7fff658cc000 - 0x7fff65917ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff65918000 - 0x7fff6593cff7 libsystem_malloc.dylib (166.220.1) /usr/lib/system/libsystem_malloc.dylib
0x7fff6593d000 - 0x7fff65948ff3 libsystem_networkextension.dylib (767.240.1) /usr/lib/system/libsystem_networkextension.dylib
0x7fff65949000 - 0x7fff65950fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff65951000 - 0x7fff6595afef libsystem_platform.dylib (177.200.16) /usr/lib/system/libsystem_platform.dylib
0x7fff6595b000 - 0x7fff65965fff libsystem_pthread.dylib (330.230.1) /usr/lib/system/libsystem_pthread.dylib
0x7fff65966000 - 0x7fff65969ff7 libsystem_sandbox.dylib (851.230.3) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6596a000 - 0x7fff6596cff3 libsystem_secinit.dylib (30.220.1) /usr/lib/system/libsystem_secinit.dylib
0x7fff6596d000 - 0x7fff65974ff7 libsystem_symptoms.dylib (820.237.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff65975000 - 0x7fff6598aff7 libsystem_trace.dylib (906.220.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6598c000 - 0x7fff65991ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff65992000 - 0x7fff659c2fff libxpc.dylib (1336.240.2) /usr/lib/system/libxpc.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: 38245
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=719.5M resident=0K(0%) swapped_out_or_unallocated=719.5M(100%)
Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 5
Activity Tracing 256K 2
CG backing stores 9540K 10
CG image 104K 19
CoreAnimation 712K 46
CoreGraphics 8K 2
CoreImage 168K 36
CoreUI image data 2496K 42
CoreUI image file 700K 11
Foundation 4K 2
Kernel Alloc Once 8K 2
MALLOC 298.5M 69
MALLOC guard page 32K 9
MALLOC_LARGE (reserved) 512K 3 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 2 reserved VM address space (unallocated)
Memory Tag 242 12K 2
Memory Tag 251 32K 2
OpenGL GLSL 512K 7
STACK GUARD 56.1M 31
Stack 157.8M 34
VM_ALLOCATE 140.0M 192
VM_ALLOCATE (reserved) 32.0M 2 reserved VM address space (unallocated)
__DATA 59.2M 501
__FONT_DATA 4K 2
__GLSLBUILTINS 5176K 2
__LINKEDIT 234.9M 124
__TEXT 484.6M 476
__UNICODE 564K 2
mapped file 95.7M 73
shared memory 704K 17
=========== ======= =======
TOTAL 1.9G 1697
TOTAL, minus reserved VM space 1.5G 1697
Log:
UCSF ChimeraX version: 0.9 (2019-03-12)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: 5vrj.cif
Attachments (1)
Change History (3)
by , 7 years ago
comment:1 by , 7 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash finding 6-member planar NR2 ring in 5vrj |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Wasn't guaranteeing that the neighbors of the first ring atom were also ring atoms
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