![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#4481 closed defect (can't reproduce)
Crash during garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [3750]
Path: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.1.1 (1.1.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [3750]
User ID: 501
Date/Time: 2021-04-02 13:19:18.702 -0600
OS Version: macOS 11.2.3 (20D91)
Report Version: 12
Anonymous UUID: 90270F8A-A9B7-9910-0147-E467CF8397D0
Sleep/Wake UUID: 5D36F908-AA8A-4C48-B32E-32822E06A721
Time Awake Since Boot: 72000 seconds
Time Since Wake: 2300 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000000a9
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0xa9:
-->
__TEXT 106169000-10616a000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff2042e462 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff2045c610 pthread_kill + 263
2 libsystem_c.dylib 0x00007fff2033eba3 raise + 26
3 libsystem_platform.dylib 0x00007fff204a0d7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x00000001061e4980 tupletraverse + 64
6 org.python.python 0x00000001062ca9a3 collect + 2083
7 org.python.python 0x00000001062cb14e _PyObject_GC_Alloc + 286
8 org.python.python 0x00000001061e60a1 PyType_GenericAlloc + 225
9 _ctypes.cpython-37m-darwin.so 0x000000010d8687bf GenericPyCData_new + 47
10 org.python.python 0x00000001061e943c type_call + 44
11 org.python.python 0x00000001061996df _PyObject_FastCallKeywords + 575
12 org.python.python 0x000000010626ebcd call_function + 765
13 org.python.python 0x000000010626b817 _PyEval_EvalFrameDefault + 26567
14 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
15 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
16 org.python.python 0x000000010619a873 _PyObject_Call_Prepend + 131
17 org.python.python 0x00000001061ede3f slot_tp_init + 175
18 org.python.python 0x00000001061e9534 type_call + 292
19 org.python.python 0x0000000106199112 _PyObject_FastCallDict + 354
20 org.python.python 0x000000010619aa90 _PyObject_CallFunctionVa + 272
21 org.python.python 0x000000010619b15a _PyObject_CallMethod_SizeT + 202
22 _multiarray_umath.cpython-37m-darwin.so 0x000000010737f325 array_ctypes_get + 69
23 org.python.python 0x00000001061d6ebb _PyObject_GenericGetAttrWithDict + 171
24 org.python.python 0x0000000106269bee _PyEval_EvalFrameDefault + 19358
25 org.python.python 0x0000000106199d61 function_code_fastcall + 177
26 org.python.python 0x000000010626ebd4 call_function + 772
27 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
28 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
29 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
30 org.python.python 0x00000001061a1ca0 property_descr_get + 160
31 org.python.python 0x00000001061d6ebb _PyObject_GenericGetAttrWithDict + 171
32 org.python.python 0x0000000106269bee _PyEval_EvalFrameDefault + 19358
33 org.python.python 0x0000000106199d61 function_code_fastcall + 177
34 org.python.python 0x000000010626ebd4 call_function + 772
35 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
36 org.python.python 0x0000000106199d61 function_code_fastcall + 177
37 org.python.python 0x000000010626ebd4 call_function + 772
38 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
39 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
40 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
41 org.python.python 0x000000010626ebd4 call_function + 772
42 org.python.python 0x00000001062655c4 _PyEval_EvalFrameDefault + 1396
43 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
44 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
45 org.python.python 0x000000010626ba3a _PyEval_EvalFrameDefault + 27114
46 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
47 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
48 org.python.python 0x000000010626ebd4 call_function + 772
49 org.python.python 0x00000001062655c4 _PyEval_EvalFrameDefault + 1396
50 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
51 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
52 org.python.python 0x000000010626ba3a _PyEval_EvalFrameDefault + 27114
53 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
54 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
55 org.python.python 0x000000010626ebd4 call_function + 772
56 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
57 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
58 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
59 org.python.python 0x000000010626ebd4 call_function + 772
60 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
61 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
62 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
63 org.python.python 0x000000010626ebd4 call_function + 772
64 org.python.python 0x00000001062655c4 _PyEval_EvalFrameDefault + 1396
65 org.python.python 0x0000000106199d61 function_code_fastcall + 177
66 org.python.python 0x000000010626ebd4 call_function + 772
67 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
68 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
69 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
70 org.python.python 0x000000010626ebd4 call_function + 772
71 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
72 org.python.python 0x0000000106199d61 function_code_fastcall + 177
73 org.python.python 0x000000010626ebd4 call_function + 772
74 org.python.python 0x000000010626b817 _PyEval_EvalFrameDefault + 26567
75 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
76 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
77 org.python.python 0x000000010626ba3a _PyEval_EvalFrameDefault + 27114
78 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
79 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
80 org.python.python 0x000000010619a873 _PyObject_Call_Prepend + 131
81 org.python.python 0x00000001061999d8 PyObject_Call + 136
82 org.python.python 0x000000010626ba3a _PyEval_EvalFrameDefault + 27114
83 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
84 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
85 org.python.python 0x000000010626ebd4 call_function + 772
86 org.python.python 0x00000001062655c4 _PyEval_EvalFrameDefault + 1396
87 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
88 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
89 QtCore.so 0x000000011036cf17 PyQtSlot::call(_object*, _object*) const + 39
90 QtCore.so 0x000000011036ce26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
91 QtCore.so 0x000000011036d925 PyQtSlotProxy::unislot(void**) + 85
92 QtCore.so 0x000000011036d89a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
93 QtCore 0x000000010fdee13d QMetaObject::activate(QObject*, int, int, void**) + 1773
94 QtWidgets 0x000000010f0c8075 QAction::activate(QAction::ActionEvent) + 309
95 QtWidgets.so 0x000000010eb7aeae sipQToolButton::nextCheckState() + 94
96 QtWidgets 0x000000010f1bbc73 0x10f0c1000 + 1027187
97 QtWidgets 0x000000010f1bcdff QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 271
98 QtWidgets 0x000000010f2b42cf QToolButton::mouseReleaseEvent(QMouseEvent*) + 15
99 QtWidgets.so 0x000000010eb79f98 sipQToolButton::mouseReleaseEvent(QMouseEvent*) + 120
100 QtWidgets 0x000000010f10d3bd QWidget::event(QEvent*) + 445
101 QtWidgets 0x000000010f2b485f QToolButton::event(QEvent*) + 319
102 QtWidgets.so 0x000000010eb7a8b0 sipQToolButton::event(QEvent*) + 192
103 QtWidgets 0x000000010f0d167d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
104 QtWidgets 0x000000010f0d44d8 QApplication::notify(QObject*, QEvent*) + 7336
105 QtWidgets.so 0x000000010ec913ca sipQApplication::notify(QObject*, QEvent*) + 234
106 QtCore 0x000000010fdbd324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
107 QtWidgets 0x000000010f0d1fa0 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 896
108 QtWidgets 0x000000010f12c90e 0x10f0c1000 + 440590
109 QtWidgets 0x000000010f12b5c9 0x10f0c1000 + 435657
110 QtWidgets 0x000000010f0d167d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
111 QtWidgets 0x000000010f0d2a82 QApplication::notify(QObject*, QEvent*) + 594
112 QtWidgets.so 0x000000010ec913ca sipQApplication::notify(QObject*, QEvent*) + 234
113 QtCore 0x000000010fdbd324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
114 QtGui 0x000000010f6a6779 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 3961
115 QtGui 0x000000010f68d46b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219
116 libqcocoa.dylib 0x0000000119dbf900 0x119d89000 + 223488
117 libqcocoa.dylib 0x0000000119dc0068 0x119d89000 + 225384
118 com.apple.CoreFoundation 0x00007fff20554a0c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
119 com.apple.CoreFoundation 0x00007fff20554974 __CFRunLoopDoSource0 + 180
120 com.apple.CoreFoundation 0x00007fff205546ef __CFRunLoopDoSources0 + 248
121 com.apple.CoreFoundation 0x00007fff20553121 __CFRunLoopRun + 890
122 com.apple.CoreFoundation 0x00007fff205526ce CFRunLoopRunSpecific + 563
123 com.apple.HIToolbox 0x00007fff287da630 RunCurrentEventLoopInMode + 292
124 com.apple.HIToolbox 0x00007fff287da282 ReceiveNextEventCommon + 283
125 com.apple.HIToolbox 0x00007fff287da14f _BlockUntilNextEventMatchingListInModeWithFilter + 64
126 com.apple.AppKit 0x00007fff22d729b1 _DPSNextEvent + 883
127 com.apple.AppKit 0x00007fff22d71177 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
128 com.apple.AppKit 0x00007fff22d6368a -[NSApplication run] + 586
129 libqcocoa.dylib 0x0000000119dbede3 0x119d89000 + 220643
130 QtCore 0x000000010fdb893f QEventLoop::exec(QFlags) + 431
131 QtCore 0x000000010fdbd932 QCoreApplication::exec() + 130
132 QtWidgets.so 0x000000010ed807d2 meth_QApplication_exec_(_object*, _object*) + 82
133 org.python.python 0x000000010619a382 _PyMethodDef_RawFastCallKeywords + 226
134 org.python.python 0x00000001061998b9 _PyCFunction_FastCallKeywords + 41
135 org.python.python 0x000000010626eb60 call_function + 656
136 org.python.python 0x000000010626b817 _PyEval_EvalFrameDefault + 26567
137 org.python.python 0x0000000106199d61 function_code_fastcall + 177
138 org.python.python 0x000000010626ebd4 call_function + 772
139 org.python.python 0x000000010626b817 _PyEval_EvalFrameDefault + 26567
140 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
141 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
142 org.python.python 0x000000010626ebd4 call_function + 772
143 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
144 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
145 org.python.python 0x0000000106264fb0 PyEval_EvalCode + 48
146 org.python.python 0x0000000106262547 builtin_exec + 583
147 org.python.python 0x000000010619a52d _PyMethodDef_RawFastCallKeywords + 653
148 org.python.python 0x00000001061998b9 _PyCFunction_FastCallKeywords + 41
149 org.python.python 0x000000010626eb60 call_function + 656
150 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
151 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
152 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
153 org.python.python 0x000000010626ebd4 call_function + 772
154 org.python.python 0x000000010626b8ae _PyEval_EvalFrameDefault + 26718
155 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
156 org.python.python 0x0000000106199377 _PyFunction_FastCallDict + 455
157 org.python.python 0x00000001062c9af3 pymain_run_module + 147
158 org.python.python 0x00000001062c8bdc pymain_main + 5900
159 org.python.python 0x00000001062c74c3 Py_Main + 51
160 edu.ucsf.cgl.ChimeraX 0x0000000106169dc8 main + 120
161 libdyld.dylib 0x00007fff20477621 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 libopenblasp-r0.3.7.dylib 0x0000000107a8ec3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 2:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff20554bf7 __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff205532ca __CFRunLoopRun + 1315
4 com.apple.CoreFoundation 0x00007fff205526ce CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff22ef87c6 _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 3:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114f7d05d 0x112e27000 + 34955357
5 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 4:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff2042c7e2 kevent + 10
1 QtWebEngineCore 0x000000011528a9a9 0x112e27000 + 38156713
2 QtWebEngineCore 0x0000000115287cbd 0x112e27000 + 38145213
3 QtWebEngineCore 0x000000011503ecdc 0x112e27000 + 35749084
4 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
5 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
6 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 5:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff2042c7e2 kevent + 10
1 QtWebEngineCore 0x000000011528a9a9 0x112e27000 + 38156713
2 QtWebEngineCore 0x0000000115287cbd 0x112e27000 + 38145213
3 QtWebEngineCore 0x000000011503ecc4 0x112e27000 + 35749060
4 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
5 QtWebEngineCore 0x0000000114fe7a74 0x112e27000 + 35392116
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 6:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc9421 0x112e27000 + 35267617
4 QtWebEngineCore 0x0000000114fe0d28 0x112e27000 + 35364136
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe12c4 0x112e27000 + 35365572
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 7:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc9421 0x112e27000 + 35267617
4 QtWebEngineCore 0x0000000114fe0d28 0x112e27000 + 35364136
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe1234 0x112e27000 + 35365428
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 8:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff2042c7e2 kevent + 10
1 QtWebEngineCore 0x000000011528a9a9 0x112e27000 + 38156713
2 QtWebEngineCore 0x0000000115287cbd 0x112e27000 + 38145213
3 QtWebEngineCore 0x000000011503ecc4 0x112e27000 + 35749060
4 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
5 QtWebEngineCore 0x0000000114914fe4 0x112e27000 + 28237796
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 9:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114fe0d1a 0x112e27000 + 35364122
5 QtWebEngineCore 0x0000000114fe13bf 0x112e27000 + 35365823
6 QtWebEngineCore 0x0000000114fe1264 0x112e27000 + 35365476
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 10:: CompositorTileWorker1/76035
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 QtWebEngineCore 0x0000000115036fa8 0x112e27000 + 35717032
3 QtWebEngineCore 0x0000000115fbd4c8 0x112e27000 + 51995848
4 QtWebEngineCore 0x0000000114ff7694 0x112e27000 + 35456660
5 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
6 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 11:: AudioThread
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114f7d05d 0x112e27000 + 34955357
5 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114f7d05d 0x112e27000 + 34955357
5 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 13:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114f7d052 0x112e27000 + 34955346
4 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
5 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
6 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 14:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff2042c7e2 kevent + 10
1 QtWebEngineCore 0x000000011528a9a9 0x112e27000 + 38156713
2 QtWebEngineCore 0x0000000115287cbd 0x112e27000 + 38145213
3 QtWebEngineCore 0x000000011503ecdc 0x112e27000 + 35749084
4 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
5 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
6 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 15:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114fe0d1a 0x112e27000 + 35364122
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe1324 0x112e27000 + 35365668
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc922f 0x112e27000 + 35267119
4 QtWebEngineCore 0x0000000114f7d05d 0x112e27000 + 34955357
5 QtWebEngineCore 0x0000000114fa6085 0x112e27000 + 35123333
6 QtWebEngineCore 0x0000000114ff89bc 0x112e27000 + 35461564
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 17:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 QtCore 0x000000010fbfd8ab 0x10fbd3000 + 174251
3 QtCore 0x000000010fbfd80c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x000000010f2fc762 0x10f0c1000 + 2340706
5 QtCore 0x000000010fbf50b3 0x10fbd3000 + 139443
6 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 libopenblasp-r0.3.7.dylib 0x0000000158a5fc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 19:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc9421 0x112e27000 + 35267617
4 QtWebEngineCore 0x0000000114fe0d28 0x112e27000 + 35364136
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe1234 0x112e27000 + 35365428
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 20:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc9421 0x112e27000 + 35267617
4 QtWebEngineCore 0x0000000114fe0d28 0x112e27000 + 35364136
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe12c4 0x112e27000 + 35365572
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 21:: JavaScriptCore bmalloc scavenger
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 libc++.1.dylib 0x00007fff203c3cf2 std::__1::condition_variable::wait(std::__1::unique_lock&) + 18
3 com.apple.JavaScriptCore 0x00007fff37584cb4 void std::__1::condition_variable_any::wait >(std::__1::unique_lock&) + 84
4 com.apple.JavaScriptCore 0x00007fff375895cb bmalloc::Scavenger::threadRunLoop() + 331
5 com.apple.JavaScriptCore 0x00007fff37589159 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6 com.apple.JavaScriptCore 0x00007fff3758bb07 void* std::__1::__thread_proxy >, void (*)(bmalloc::Scavenger*), bmalloc::Scavenger*> >(void*) + 39
7 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 22:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff20427e7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff204281f0 mach_msg + 60
2 QtWebEngineCore 0x0000000114fc932d 0x112e27000 + 35267373
3 QtWebEngineCore 0x0000000114fc9421 0x112e27000 + 35267617
4 QtWebEngineCore 0x0000000114fe0d28 0x112e27000 + 35364136
5 QtWebEngineCore 0x0000000114fe165b 0x112e27000 + 35366491
6 QtWebEngineCore 0x0000000114fe12c4 0x112e27000 + 35365572
7 QtWebEngineCore 0x0000000115038717 0x112e27000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 23:
0 libsystem_pthread.dylib 0x00007fff20458458 start_wqthread + 0
Thread 24:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 QtCore 0x000000010fbfd8ab 0x10fbd3000 + 174251
3 QtCore 0x000000010fbfd80c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x000000010f2fc762 0x10f0c1000 + 2340706
5 QtCore 0x000000010fbf50b3 0x10fbd3000 + 139443
6 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 25:
0 libsystem_pthread.dylib 0x00007fff20458458 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff20458458 start_wqthread + 0
Thread 27:
0 libsystem_pthread.dylib 0x00007fff20458458 start_wqthread + 0
Thread 28:
0 libsystem_pthread.dylib 0x00007fff20458458 start_wqthread + 0
Thread 29:
0 libsystem_kernel.dylib 0x00007fff2042a8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2045ce6f _pthread_cond_wait + 1254
2 org.python.python 0x00000001062b30af PyThread_acquire_lock_timed + 351
3 org.python.python 0x00000001062fe9df acquire_timed + 111
4 org.python.python 0x00000001062fe75c lock_PyThread_acquire_lock + 44
5 org.python.python 0x000000010619a56a _PyMethodDef_RawFastCallKeywords + 714
6 org.python.python 0x00000001061a0571 _PyMethodDescr_FastCallKeywords + 81
7 org.python.python 0x000000010626ebfe call_function + 814
8 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
9 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
10 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
11 org.python.python 0x000000010626ebd4 call_function + 772
12 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
13 org.python.python 0x000000010626fa2c _PyEval_EvalCodeWithName + 3276
14 org.python.python 0x0000000106199879 _PyFunction_FastCallKeywords + 217
15 org.python.python 0x000000010626ebd4 call_function + 772
16 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
17 org.python.python 0x0000000106199d61 function_code_fastcall + 177
18 org.python.python 0x000000010626ebd4 call_function + 772
19 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
20 org.python.python 0x0000000106199d61 function_code_fastcall + 177
21 org.python.python 0x000000010626ebd4 call_function + 772
22 org.python.python 0x000000010626b7fa _PyEval_EvalFrameDefault + 26538
23 org.python.python 0x0000000106199d61 function_code_fastcall + 177
24 org.python.python 0x000000010619a873 _PyObject_Call_Prepend + 131
25 org.python.python 0x00000001061999d8 PyObject_Call + 136
26 org.python.python 0x00000001062ff287 t_bootstrap + 71
27 org.python.python 0x00000001062b2d19 pythread_wrapper + 25
28 libsystem_pthread.dylib 0x00007fff2045c950 _pthread_start + 224
29 libsystem_pthread.dylib 0x00007fff2045847b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000111209e00 rcx: 0x00007f844d677a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007f844d677a80 rsp: 0x00007f844d677a58
r8: 0x00007f844d677f48 r9: 0x7e8c59b0f944c871 r10: 0x0000000111209e00 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000133f5ded0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff2042e462 rfl: 0x0000000000000246 cr2: 0x00000001063727c8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
48 8b 40 18 4a 8b 1c e8-48 ff 03 48 89 df 4c 89 H.@.J...H..H..L.
fe 4c 89 f2 4c 89 e1 31-c0 e8 72 e9 ec ff 48 85 .L..L..1..r...H.
c0 74 9d 48 ff 08 74 b8-48 ff 0b 74 a0 49 ff c5 .t.H..t.H..t.I..
48 8d 05 39 a0 12 00 48-8b 80 88 02 00 00 4c 3b H..9...H......L;
68 10 7c bc 49 ff 0c 24-74 24 48 83 c4 08 5b 41 h.|.I..$t$H...[A
5c 41 5d 41 5e 41 5f 5d-c3 31 ff 48 83 c4 08 5b \A]A^A_].1.H...[
41 5c 41 5d 41 5e 41 5f-5d e9 f2 8e fb ff 49 8b A\A]A^A_].....I.
44 24 08 4c 89 e7 48 83-c4 08 5b 41 5c 41 5d 41 D$.L..H...[A\A]A
5e 41 5f 5d ff 60 30 66-0f 1f 84 00 00 00 00 00 ^A_].`0f........
55 48 89 e5 53 50 48 8b-47 08[f6]80 a9 00 00 00 UH..SPH.G....... /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
0x106176000 - 0x106371fff +org.python.python (3.7.8, [c] 2001-2019 Python Software Foundation. - 3.7.8) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/Python
0x1066ec000 - 0x1066edfff +_heapq.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_heapq.cpython-37m-darwin.so
0x1067b6000 - 0x1067b9fff +zlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/zlib.cpython-37m-darwin.so
0x1067c3000 - 0x1067d7fff +libz.1.2.11.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libz.1.2.11.dylib
0x106820000 - 0x106821fff +_bz2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bz2.cpython-37m-darwin.so
0x10682a000 - 0x10682dfff +_lzma.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_lzma.cpython-37m-darwin.so
0x106838000 - 0x106838fff +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so
0x106880000 - 0x106885fff +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so
0x106891000 - 0x106893fff +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so
0x10689d000 - 0x1068fafff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libssl.1.1.dylib
0x106929000 - 0x106af0fff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libcrypto.1.1.dylib
0x106b89000 - 0x106b8efff +_blake2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_blake2.cpython-37m-darwin.so
0x106b98000 - 0x106ba8fff +_sha3.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_sha3.cpython-37m-darwin.so
0x106bb3000 - 0x106bb3fff +_bisect.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bisect.cpython-37m-darwin.so
0x106bbb000 - 0x106bbcfff +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so
0x106c84000 - 0x106c8afff +_json.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_json.cpython-37m-darwin.so
0x106cd3000 - 0x106ce0fff +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
0x106cf6000 - 0x106cfffff +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so
0x106d51000 - 0x106d54fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so
0x106d5f000 - 0x106d63fff +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so
0x106d71000 - 0x106d75fff +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so
0x106e7e000 - 0x106e8cfff +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so
0x106edc000 - 0x106edcfff +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so
0x106ee4000 - 0x106f22fff +_decimal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_decimal.cpython-37m-darwin.so
0x106f86000 - 0x106fb3fff +pyexpat.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so
0x106fcb000 - 0x106fccfff +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
0x107095000 - 0x107096fff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so
0x1070de000 - 0x1070f0fff +_pickle.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_pickle.cpython-37m-darwin.so
0x107141000 - 0x107144fff +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so
0x1072cf000 - 0x107632fff +_multiarray_umath.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
0x107758000 - 0x10b1c3fff +libopenblasp-r0.3.7.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libopenblasp-r0.3.7.dylib
0x10b4cd000 - 0x10b5e4fff +libgfortran.3.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x10b652000 - 0x10b688fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x10b69c000 - 0x10b6b1fff +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x10d841000 - 0x10d84efff +_multiarray_tests.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_tests.cpython-37m-darwin.so
0x10d864000 - 0x10d876fff +_ctypes.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so
0x10d90c000 - 0x10d90dfff +lapack_lite.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/lapack_lite.cpython-37m-darwin.so
0x10d915000 - 0x10d92efff +_umath_linalg.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/_umath_linalg.cpython-37m-darwin.so
0x10da02000 - 0x10da13fff +_pocketfft_internal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/fft/_pocketfft_internal.cpython-37m-darwin.so
0x10da9c000 - 0x10db07fff +mtrand.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/mtrand.cpython-37m-darwin.so
0x10db62000 - 0x10db7ffff +_bit_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bit_generator.cpython-37m-darwin.so
0x10dba0000 - 0x10dbcffff +_common.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_common.cpython-37m-darwin.so
0x10dbea000 - 0x10dc3efff +_bounded_integers.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bounded_integers.cpython-37m-darwin.so
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0x7fff44065000 - 0x7fff442defff com.apple.RawCamera.bundle (9.10.0 - 1430) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff46d66000 - 0x7fff46d71fff libGPUSupportMercury.dylib (18.1.1) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
0x7fff483d4000 - 0x7fff48423fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x7fff52362000 - 0x7fff52390fff com.apple.HelpData (2.3 - 200) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x7fff52391000 - 0x7fff523abfff com.apple.shortcut (2.16 - 117) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff523ac000 - 0x7fff5243efff com.apple.Symbolication (12.2 - 64541.7.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff54f27000 - 0x7fff54f5efff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x7fff56582000 - 0x7fff56585fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff62abc000 - 0x7fff62b9ffff com.apple.driver.AppleIntelBDWGraphicsMTLDriver (16.1.12 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsMTLDriver
0x7fff645b5000 - 0x7fff64abcfff com.apple.driver.AppleIntelBDWGraphicsGLDriver (16.1.12 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsGLDriver
0x7fff6a53d000 - 0x7fff6a541fff libmetal_timestamp.dylib (31001.161) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x7fff6c9ab000 - 0x7fff6c9b1fff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6c9b2000 - 0x7fff6c9b6fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6c9b7000 - 0x7fff6c9c6fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6c9c7000 - 0x7fff6c9c9fff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6c9ca000 - 0x7fff6c9d2fff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6c9d3000 - 0x7fff6ca06fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6ca07000 - 0x7fff6ca43fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6ca44000 - 0x7fff6cbd8fff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6cbd9000 - 0x7fff6cbe3fff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6cbe4000 - 0x7fff6cd5ffff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6cd60000 - 0x7fff6cd89fff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6e01a000 - 0x7fff6e072fff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6f0f1000 - 0x7fff6f0f8fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff74487000 - 0x7fff74492fff com.apple.SymptomAnalytics (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff746b0000 - 0x7fff746c8fff com.apple.SymptomPresentationFeed (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff781df000 - 0x7fff781e6fff libRosetta.dylib (203.30) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 75
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: 56293
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=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 816K 6
CG image 324K 41
CoreAnimation 216K 43
CoreGraphics 12K 2
CoreServices 624K 2
CoreUI image data 1984K 30
Foundation 32K 2
JS JIT generated code 1.0G 3
Kernel Alloc Once 336K 3
MALLOC 454.5M 427
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 116K 29
Stack 154.7M 30
Stack Guard 56.0M 1
VM_ALLOCATE 214.2M 483
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
WebKit Malloc 1128K 6
__CTF 759 1
__DATA 32.2M 730
__DATA_CONST 28.7M 320
__DATA_DIRTY 1770K 215
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 523.9M 201
__OBJC_RO 60.5M 1
__OBJC_RW 2449K 2
__TEXT 695.0M 685
__UNICODE 588K 1
mapped file 698.6M 96
shared memory 52K 7
=========== ======= =======
TOTAL 4.1G 3391
TOTAL, minus reserved VM space 3.9G 3391
System Profile:
Thunderbolt Bus: MacBook Air, Apple Inc., 27.2
Boot Volume File System Type: apfs
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1600 MHz, 0x80AD, 0x483943434E4E4E424C54424C41522D4E5444
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x80AD, 0x483943434E4E4E424C54424C41522D4E5444
USB Device: USB 3.0 Bus
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Serial ATA Device: APPLE SSD SM0128G, 121.33 GB
Model: MacBookAir7,2, BootROM 426.0.0.0.0, 2 processors, Dual-Core Intel Core i5, 1.8 GHz, 8 GB, SMC 2.27f2
Graphics: kHW_IntelHDGraphics6000Item, Intel HD Graphics 6000, spdisplays_builtin
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x117), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1675.1)
Bluetooth: Version 8.0.3d9, 3 services, 25 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/juliaenterria/Desktop/ATP1A3 & PRDM16/ATP1A3/ATP1A3 cardiac
> mutations (aa changed).cxs"
Log from Fri Apr 2 19:22:16 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations.cxs"
Log from Fri Apr 2 13:17:49 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 chimera.cxs" format session
Log from Wed Mar 31 11:44:37 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:user
> view # clip false
Expected an objects specifier or a view name or a keyword
> help help:user
> open "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/4xe5.pdb"
4xe5.pdb title:
Crystal structure of the Na,K-atpase from bovine [more info...]
Chain information for 4xe5.pdb #1
---
Chain | Description
A | sodium/potassium-transporting atpase subunit α-1
B | sodium/potassium-transporting atpase subunit β
G | sodium/potassium-transporting atpase subunit γ
Non-standard residues in 4xe5.pdb #1
---
CLR — cholesterol
MG — magnesium ion
OBN — ouabain
Empty filename passed to function
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 chimera.cxs"
opened ChimeraX session
> open /Users/juliaenterria/Desktop/coords.pdb format pdb
No such file/path: /Users/juliaenterria/Desktop/coords.pdb
> open "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3.pdb"
ATP1A3.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for ATP1A3.pdb #2
---
Chain | Description
A | No description available
Non-standard residues in ATP1A3.pdb #2
---
MG — (MG)
> hide #!1 models
> hide #2 models
> show #2 models
> view
> close #1
> help help:user/findseq.html
> select sequence 231-233
Nothing selected
> select sequence I274
Nothing selected
> select sequence E815
Nothing selected
> ui mousemode right "mark maximum"
> ui mousemode right "move markers"
> ui mousemode right select
> select /A:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:426
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select clear
> select /A:747
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "mark maximum"
> ui mousemode right "mark point"
> toolshed show
> ui mousemode right "mark surface"
> ui mousemode right "map eraser"
> ui mousemode right "map eraser"
> ui mousemode right "map eraser"
> ui mousemode right "map eraser"
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> close #1
> ui mousemode right select
> ui mousemode right clip
> undo
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> select clear
> ui mousemode right select
> select /A:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select sequence E:815
Nothing selected
> select /A:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:382
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> open "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 4ret.pdb"
ATP1A3 4ret.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for ATP1A3 4ret.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in ATP1A3 4ret.pdb #1
---
MG — (MG)
> close #2
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> color bychain
> rainbow
> color sel bychain
> undo
> undo
> undo
> color sel bychain
> select clear
> color sel bychain
> color sel bychain
> select clear
> color sel bychain
> color sel bychain
> rainbow sel
> undo
> color sel bychain
> color sel bychain
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations.cxs"
opened ChimeraX session
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> color sel bychain
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations.cxs"
> ui tool show "Color Actions"
> color sel red
> color sel hot pink
> color sel forest green
> select clear
> color sel forest green
> select clear
> color sel forest green
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations.cxs"
> color sel forest green
> ui tool show "Color Actions"
> color sel red
> color sel red
> color sel bychain
> select clear
> select clear
> color sel red
> color sel red
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations.cxs"
> ui mousemode right select
> select /A:947
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> select clear
> ui tool show Rotamers
> swapaa interactive sel ASN rotLib Dunbrack
/A ILE 274: phi -61.2, psi -44.1 trans
Changed 180 bond radii
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations (aa changed).cxs"
> ui tool show Rotamers
> swapaa interactive sel ASN rotLib Dunbrack
/A ILE 274: phi -61.2, psi -44.1 trans
Changed 180 bond radii
> swapaa #1/A:274 ASN criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ILE 274: phi -61.2, psi -44.1 trans
Applying ASN rotamer (chi angles: -73.2 -20.5) to ATP1A3 4ret.pdb #1/A ASN 274
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
/A VAL 332: phi -60.2, psi -44.1 trans
Changed 90 bond radii
> swapaa #1/A:332 ASP criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A VAL 332: phi -60.2, psi -44.1 trans
Applying ASP rotamer (chi angles: -71.8 -15.3) to ATP1A3 4ret.pdb #1/A ASP 332
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
/A PRO 323: phi -83.5, psi 98.6 trans
Changed 9 bond radii
> swapaa #1/A:323 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A PRO 323: phi -83.5, psi 98.6 trans
Applying SER rotamer (chi angles: 177.4) to ATP1A3 4ret.pdb #1/A SER 323
> swapaa interactive sel GLU rotLib Dunbrack
/A ASP 332: phi -60.2, psi -44.1 trans
Changed 324 bond radii
> swapaa #1/A:332 GLU criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ASP 332: phi -60.2, psi -44.1 trans
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to ATP1A3 4ret.pdb #1/A
GLU 332
> swapaa interactive sel PHE rotLib Dunbrack
/A CYS 333: phi -57.7, psi -46.7 trans
Changed 162 bond radii
> swapaa #1/A:333 PHE criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A CYS 333: phi -57.7, psi -46.7 trans
Applying PHE rotamer (chi angles: 176.9 78.9) to ATP1A3 4ret.pdb #1/A PHE 333
> swapaa interactive sel CYS rotLib Dunbrack
/A GLY 755: phi -65.6, psi -31.0 trans
Changed 9 bond radii
> swapaa #1/A:755 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A GLY 755: phi -65.6, psi -31.0 trans
Applying CYS rotamer (chi angles: -69.3) to ATP1A3 4ret.pdb #1/A CYS 755
> swapaa interactive sel ARG rotLib Dunbrack
/A TYR 768: phi -57.7, psi -50.2 trans
Changed 600 bond radii
> swapaa #1/A:768 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A TYR 768: phi -57.7, psi -50.2 trans
Applying ARG rotamer (chi angles: -178.9 -175.6 63.4 78.5) to ATP1A3 4ret.pdb
#1/A ARG 768
> swapaa interactive sel ARG rotLib Dunbrack
/A ARG 768: phi -57.7, psi -50.2 trans
Changed 600 bond radii
> swapaa #1/A:768 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ARG 768: phi -57.7, psi -50.2 trans
Applying ARG rotamer (chi angles: -178.9 -175.6 63.4 78.5) to ATP1A3 4ret.pdb
#1/A ARG 768
> swapaa interactive sel GLY rotLib Dunbrack
> swapaa sel GLY rotLib Dunbrack
Using Dunbrack library
Swapping /A ASP 801 to GLY
> swapaa interactive sel GLY rotLib Dunbrack
> swapaa sel GLY rotLib Dunbrack
Using Dunbrack library
Swapping /A GLY 801 to GLY
> swapaa interactive sel ILE rotLib Dunbrack
/A THR 804: phi -105.2, psi -56.1 trans
Changed 45 bond radii
> swapaa #1/A:804 ILE criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A THR 804: phi -105.2, psi -56.1 trans
Applying ILE rotamer (chi angles: -62.2 170.7) to ATP1A3 4ret.pdb #1/A ILE 804
> swapaa interactive sel ARG rotLib Dunbrack
/A MET 806: phi -55.3, psi -57.7 trans
Changed 600 bond radii
> swapaa #1/A:806 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A MET 806: phi -55.3, psi -57.7 trans
Applying ARG rotamer (chi angles: -178.7 -176.6 63.4 79.0) to ATP1A3 4ret.pdb
#1/A ARG 806
> swapaa interactive sel PRO rotLib Dunbrack
/A SER 811: phi -58.7, psi -32.1 trans
Changed 10 bond radii
> swapaa #1/A:811 PRO criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A SER 811: phi -58.7, psi -32.1 trans
Applying PRO rotamer (chi angles: -25.3 35.7) to ATP1A3 4ret.pdb #1/A PRO 811
> swapaa interactive sel LYS rotLib Dunbrack
/A GLU 815: phi -58.9, psi 147.4 trans
Changed 438 bond radii
> swapaa #1/A:815 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A GLU 815: phi -58.9, psi 147.4 trans
Applying LYS rotamer (chi angles: -67.1 -178.8 -179.7 179.2) to ATP1A3
4ret.pdb #1/A LYS 815
> swapaa interactive sel PRO rotLib Dunbrack
/A LEU 888: phi -128.5, psi 120.4 trans
Changed 10 bond radii
> swapaa #1/A:888 PRO criteria 2 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A LEU 888: phi -128.5, psi 120.4 trans
Applying PRO rotamer (chi angles: -25.1 36.3) to ATP1A3 4ret.pdb #1/A PRO 888
> swapaa interactive sel PHE rotLib Dunbrack
/A CYS 927: phi -73.3, psi -15.3 trans
Changed 162 bond radii
> swapaa #1/A:927 PHE criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A CYS 927: phi -73.3, psi -15.3 trans
Applying PHE rotamer (chi angles: -72.3 104.3) to ATP1A3 4ret.pdb #1/A PHE 927
> swapaa interactive sel ARG rotLib Dunbrack
/A GLY 947: phi -48.2, psi -54.4 trans
Changed 600 bond radii
> swapaa #1/A:947 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A GLY 947: phi -48.2, psi -54.4 trans
Applying ARG rotamer (chi angles: -177.6 -174.5 63.4 79.8) to ATP1A3 4ret.pdb
#1/A ARG 947
> swapaa interactive sel ASP rotLib Dunbrack
/A ALA 955: phi -62.5, psi -40.7 trans
Changed 90 bond radii
> swapaa #1/A:955 ASP criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ALA 955: phi -62.5, psi -40.7 trans
Applying ASP rotamer (chi angles: -71.8 -15.3) to ATP1A3 4ret.pdb #1/A ASP 955
> swapaa interactive sel GLU rotLib Dunbrack
/A LYS 996: phi -84.4, psi 2.0 trans
Changed 324 bond radii
> swapaa #1/A:996 GLU criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A LYS 996: phi -84.4, psi 2.0 trans
Applying GLU rotamer (chi angles: -65.8 178.9 -4.2) to ATP1A3 4ret.pdb #1/A
GLU 996
> swapaa interactive sel PHE rotLib Dunbrack
/A SER 137: phi -64.0, psi -41.7 trans
Changed 162 bond radii
> swapaa #1/A:137 PHE criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A SER 137: phi -64.0, psi -41.7 trans
Applying PHE rotamer (chi angles: -178.0 77.9) to ATP1A3 4ret.pdb #1/A PHE 137
> swapaa interactive sel ARG rotLib Dunbrack
/A ARG 947: phi -48.2, psi -54.4 trans
Changed 600 bond radii
> swapaa #1/A:947 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ARG 947: phi -48.2, psi -54.4 trans
Applying ARG rotamer (chi angles: -177.6 -174.5 63.4 79.8) to ATP1A3 4ret.pdb
#1/A ARG 947
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations (aa changed).cxs"
No residues selected
> swapaa interactive sel LYS rotLib Dunbrack
/A GLU 818: phi -79.1, psi -14.0 trans
Changed 438 bond radii
> swapaa #1/A:818 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A GLU 818: phi -79.1, psi -14.0 trans
Applying LYS rotamer (chi angles: -67.0 180.0 179.7 178.6) to ATP1A3 4ret.pdb
#1/A LYS 818
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping /A THR 370 to ALA
> swapaa interactive sel MET rotLib Dunbrack
/A THR 613: phi -71.3, psi -40.6 trans
Changed 135 bond radii
> swapaa #1/A:613 MET criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A THR 613: phi -71.3, psi -40.6 trans
Applying MET rotamer (chi angles: -68.8 -59.1 -67.3) to ATP1A3 4ret.pdb #1/A
MET 613
> swapaa interactive sel CYS rotLib Dunbrack
/A ARG 756: phi -80.0, psi -28.6 trans
Changed 9 bond radii
> swapaa #1/A:756 CYS criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ARG 756: phi -80.0, psi -28.6 trans
Applying CYS rotamer (chi angles: -68.1) to ATP1A3 4ret.pdb #1/A CYS 756
> swapaa interactive sel SER rotLib Dunbrack
/A ILE 758: phi -60.2, psi -31.5 trans
Changed 9 bond radii
> swapaa #1/A:758 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ILE 758: phi -60.2, psi -31.5 trans
Applying SER rotamer (chi angles: 66.4) to ATP1A3 4ret.pdb #1/A SER 758
> color sel bychain
> select clear
> swapaa interactive sel TYR rotLib Dunbrack
/A ASP 923: phi -58.0, psi -45.1 trans
Changed 180 bond radii
> swapaa #1/A:923 TYR criteria 1 rotLib Dunbrack
Using Dunbrack library
ATP1A3 4ret.pdb #1/A ASP 923: phi -58.0, psi -45.1 trans
Applying TYR rotamer (chi angles: 177.2 79.4) to ATP1A3 4ret.pdb #1/A TYR 923
> select /A:801
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:955
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show atoms
> hide atoms
> select /A:955
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:888
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:804
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:801
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:323
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:322
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:947
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:919
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:923
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:772
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:927
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:996
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:818
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:815
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:838
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:839
8 atoms, 7 bonds, 1 residue, 1 model selected
> undo
> hide sel atoms
> select /A:137
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:801
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:333
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:332
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:758
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:756
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:755
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:610
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:274
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:947
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:811
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:804
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:919
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:772
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:768
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:801
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> select /A:801
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:806
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:804
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> save "/Users/juliaenterria/Desktop/Dr. Landstrom/ATP1A3 &
> PRDM16/ATP1A3/ATP1A3 cardiac mutations (aa changed).cxs"
opened ChimeraX session
OpenGL version: 4.1 INTEL-16.1.12
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 426.0.0.0.0
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 2 days 7:35
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during garbage collection |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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