![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3209 closed defect (nonchimerax)
Graphics hardware error
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I plugged in the second display
Process: ChimeraX [60568]
Path: /Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.0.0 (1.0.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [60568]
User ID: 501
Date/Time: 2020-05-13 18:58:07.955 -0700
OS Version: Mac OS X 10.15.4 (19E287)
Report Version: 12
Anonymous UUID: BD2C74B7-6492-4378-685C-E4DE89870557
Sleep/Wake UUID: 88E1D71B-633E-4BA6-A9E4-318D8B4F697D
Time Awake Since Boot: 290000 seconds
Time Since Wake: 12000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics hardware encountered an error and was reset: 0x00008813
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff676fb33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff677b7e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6761293e raise + 26
3 libsystem_platform.dylib 0x00007fff677ac5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff67682808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff4e9ff0a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff4e9f618f gpusGenerateCrashLog + 89
8 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff239e139b gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff4e9f76a1 gpusSubmitDataBuffers + 490
10 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff235ab5fa IntelCommandBuffer::getNew(GLDContextRec*) + 48
11 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff235ab40f intelSubmitCommands + 178
12 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff2359f8a2 updateDispatch + 7136
13 GLEngine 0x00007fff3824f74c gleDoDrawDispatchCoreGL3 + 693
14 GLEngine 0x00007fff38223fb6 glDrawElementsInstanced_ACC_GL3Exec + 290
15 _ctypes.cpython-37m-darwin.so 0x000000010bfe7e47 ffi_call_unix64 + 79
16 _ctypes.cpython-37m-darwin.so 0x000000010bfe86d5 ffi_call + 901
17 _ctypes.cpython-37m-darwin.so 0x000000010bfe2f84 _ctypes_callproc + 804
18 _ctypes.cpython-37m-darwin.so 0x000000010bfdc74c PyCFuncPtr_call + 1196
19 org.python.python 0x00000001066e29c8 PyObject_Call + 136
20 org.python.python 0x0000000106735906 slot_tp_call + 198
21 wrapper.cpython-37m-darwin.so 0x000000010cb86181 __Pyx_PyObject_Call + 97
22 wrapper.cpython-37m-darwin.so 0x000000010cb9328d __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 765
23 latebind.cpython-37m-darwin.so 0x000000010cbeffa1 __Pyx_PyObject_Call + 97
24 latebind.cpython-37m-darwin.so 0x000000010cbef522 __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 306
25 org.python.python 0x00000001066e26cf _PyObject_FastCallKeywords + 575
26 org.python.python 0x00000001067b7b5d call_function + 765
27 org.python.python 0x00000001067b47a7 _PyEval_EvalFrameDefault + 26567
28 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
29 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
30 org.python.python 0x00000001067b7b64 call_function + 772
31 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
32 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
33 org.python.python 0x00000001067b7b64 call_function + 772
34 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
35 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
36 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
37 org.python.python 0x00000001067b7b64 call_function + 772
38 org.python.python 0x00000001067ae554 _PyEval_EvalFrameDefault + 1396
39 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
40 org.python.python 0x00000001067b7b64 call_function + 772
41 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
42 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
43 org.python.python 0x00000001067b7b64 call_function + 772
44 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
45 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
46 org.python.python 0x00000001067b7b64 call_function + 772
47 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
48 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
49 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
50 org.python.python 0x00000001067b7b64 call_function + 772
51 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
52 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
53 org.python.python 0x00000001067b7b64 call_function + 772
54 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
55 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
56 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
57 org.python.python 0x00000001067b7b64 call_function + 772
58 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
59 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
60 org.python.python 0x00000001067b7b64 call_function + 772
61 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
62 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
63 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
64 org.python.python 0x00000001067b7b64 call_function + 772
65 org.python.python 0x00000001067ae554 _PyEval_EvalFrameDefault + 1396
66 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
67 org.python.python 0x00000001067b7b64 call_function + 772
68 org.python.python 0x00000001067b478a _PyEval_EvalFrameDefault + 26538
69 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
70 org.python.python 0x00000001066e3873 _PyObject_Call_Prepend + 131
71 org.python.python 0x00000001066e29c8 PyObject_Call + 136
72 QtCore.so 0x0000000116a18f17 PyQtSlot::call(_object*, _object*) const + 39
73 QtCore.so 0x0000000116a18e26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
74 QtCore.so 0x0000000116a19925 PyQtSlotProxy::unislot(void**) + 85
75 QtCore.so 0x0000000116a1989a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
76 QtCore 0x00000001149e32dd QMetaObject::activate(QObject*, int, int, void**) + 1773
77 QtCore 0x00000001149eb392 QTimer::timerEvent(QTimerEvent*) + 98
78 QtCore.so 0x000000011690f028 sipQTimer::timerEvent(QTimerEvent*) + 120
79 QtCore 0x00000001149dbc56 QObject::event(QEvent*) + 102
80 QtCore.so 0x000000011690ee9b sipQTimer::event(QEvent*) + 187
81 QtWidgets 0x0000000113cc670d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
82 QtWidgets 0x0000000113cc7b12 QApplication::notify(QObject*, QEvent*) + 594
83 QtWidgets.so 0x000000010d5df3ca sipQApplication::notify(QObject*, QEvent*) + 234
84 QtCore 0x00000001149b24c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
85 QtCore 0x0000000114a0badf QTimerInfoList::activateTimers() + 991
86 libqcocoa.dylib 0x000000011e655032 0x11e620000 + 217138
87 com.apple.CoreFoundation 0x00007fff2d66cf12 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
88 com.apple.CoreFoundation 0x00007fff2d66ceb1 __CFRunLoopDoSource0 + 103
89 com.apple.CoreFoundation 0x00007fff2d66cccb __CFRunLoopDoSources0 + 209
90 com.apple.CoreFoundation 0x00007fff2d66b9fa __CFRunLoopRun + 927
91 com.apple.CoreFoundation 0x00007fff2d66affe CFRunLoopRunSpecific + 462
92 com.apple.HIToolbox 0x00007fff2c29eabd RunCurrentEventLoopInMode + 292
93 com.apple.HIToolbox 0x00007fff2c29e7d5 ReceiveNextEventCommon + 584
94 com.apple.HIToolbox 0x00007fff2c29e579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
95 com.apple.AppKit 0x00007fff2a8e9c99 _DPSNextEvent + 883
96 com.apple.AppKit 0x00007fff2a8e84e0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
97 com.apple.AppKit 0x00007fff2a8da1ee -[NSApplication run] + 658
98 libqcocoa.dylib 0x000000011e655de3 0x11e620000 + 220643
99 QtCore 0x00000001149adadf QEventLoop::exec(QFlags) + 431
100 QtCore 0x00000001149b2ad2 QCoreApplication::exec() + 130
101 QtWidgets.so 0x000000010d6ce7d2 meth_QApplication_exec_(_object*, _object*) + 82
102 org.python.python 0x00000001066e3382 _PyMethodDef_RawFastCallKeywords + 226
103 org.python.python 0x00000001066e28a9 _PyCFunction_FastCallKeywords + 41
104 org.python.python 0x00000001067b7af0 call_function + 656
105 org.python.python 0x00000001067b47a7 _PyEval_EvalFrameDefault + 26567
106 org.python.python 0x00000001066e2d51 function_code_fastcall + 177
107 org.python.python 0x00000001067b7b64 call_function + 772
108 org.python.python 0x00000001067b47a7 _PyEval_EvalFrameDefault + 26567
109 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
110 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
111 org.python.python 0x00000001067b7b64 call_function + 772
112 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
113 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
114 org.python.python 0x00000001067adf40 PyEval_EvalCode + 48
115 org.python.python 0x00000001067ab4d7 builtin_exec + 583
116 org.python.python 0x00000001066e3535 _PyMethodDef_RawFastCallKeywords + 661
117 org.python.python 0x00000001066e28a9 _PyCFunction_FastCallKeywords + 41
118 org.python.python 0x00000001067b7af0 call_function + 656
119 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
120 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
121 org.python.python 0x00000001066e2869 _PyFunction_FastCallKeywords + 217
122 org.python.python 0x00000001067b7b64 call_function + 772
123 org.python.python 0x00000001067b483e _PyEval_EvalFrameDefault + 26718
124 org.python.python 0x00000001067b89bc _PyEval_EvalCodeWithName + 3276
125 org.python.python 0x00000001066e2367 _PyFunction_FastCallDict + 455
126 org.python.python 0x0000000106812a83 pymain_run_module + 147
127 org.python.python 0x0000000106811b6c pymain_main + 5900
128 org.python.python 0x0000000106810453 Py_Main + 51
129 edu.ucsf.cgl.ChimeraX 0x00000001066b2dc8 main + 120
130 libdyld.dylib 0x00007fff675b3cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff676f7882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff677b8425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001081f2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff676f7882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff677b8425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001081f2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff676f7882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff677b8425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001081f2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 4:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2d66d0b5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2d66bb82 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2d66affe CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2aa8b5b4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x0000000119162fdd 0x117004000 + 34992093
5 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 6:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff676f9766 kevent + 10
1 QtWebEngineCore 0x0000000119470929 0x117004000 + 38193449
2 QtWebEngineCore 0x000000011946dc3d 0x117004000 + 38181949
3 QtWebEngineCore 0x0000000119224c5c 0x117004000 + 35785820
4 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
5 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
6 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
7 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 7:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff676f9766 kevent + 10
1 QtWebEngineCore 0x0000000119470929 0x117004000 + 38193449
2 QtWebEngineCore 0x000000011946dc3d 0x117004000 + 38181949
3 QtWebEngineCore 0x0000000119224c44 0x117004000 + 35785796
4 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
5 QtWebEngineCore 0x00000001191cd9f4 0x117004000 + 35428852
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 8:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af3a1 0x117004000 + 35304353
4 QtWebEngineCore 0x00000001191c6ca8 0x117004000 + 35400872
5 QtWebEngineCore 0x00000001191c75db 0x117004000 + 35403227
6 QtWebEngineCore 0x00000001191c7244 0x117004000 + 35402308
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 9:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af3a1 0x117004000 + 35304353
4 QtWebEngineCore 0x00000001191c6ca8 0x117004000 + 35400872
5 QtWebEngineCore 0x00000001191c75db 0x117004000 + 35403227
6 QtWebEngineCore 0x00000001191c7244 0x117004000 + 35402308
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 10:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af3a1 0x117004000 + 35304353
4 QtWebEngineCore 0x00000001191c6ca8 0x117004000 + 35400872
5 QtWebEngineCore 0x00000001191c75db 0x117004000 + 35403227
6 QtWebEngineCore 0x00000001191c71b4 0x117004000 + 35402164
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 11:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af3a1 0x117004000 + 35304353
4 QtWebEngineCore 0x00000001191c6ca8 0x117004000 + 35400872
5 QtWebEngineCore 0x00000001191c75db 0x117004000 + 35403227
6 QtWebEngineCore 0x00000001191c71b4 0x117004000 + 35402164
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 12:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff676f9766 kevent + 10
1 QtWebEngineCore 0x0000000119470929 0x117004000 + 38193449
2 QtWebEngineCore 0x000000011946dc3d 0x117004000 + 38181949
3 QtWebEngineCore 0x0000000119224c44 0x117004000 + 35785796
4 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
5 QtWebEngineCore 0x0000000118af1fa4 0x117004000 + 28237732
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 13:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x00000001191c6c9a 0x117004000 + 35400858
5 QtWebEngineCore 0x00000001191c733f 0x117004000 + 35402559
6 QtWebEngineCore 0x00000001191c71e4 0x117004000 + 35402212
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 14:: CompositorTileWorker1/56323
0 libsystem_kernel.dylib 0x00007fff676f7882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff677b8425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011921cf28 0x117004000 + 35753768
3 QtWebEngineCore 0x000000011a1a5628 0x117004000 + 52041256
4 QtWebEngineCore 0x00000001191dd614 0x117004000 + 35493396
5 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
6 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 15:: AudioThread
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x0000000119162fdd 0x117004000 + 34992093
5 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x0000000119162fdd 0x117004000 + 34992093
5 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 17:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x0000000119162fd2 0x117004000 + 34992082
4 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
5 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
6 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
7 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 18:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff676f9766 kevent + 10
1 QtWebEngineCore 0x0000000119470929 0x117004000 + 38193449
2 QtWebEngineCore 0x000000011946dc3d 0x117004000 + 38181949
3 QtWebEngineCore 0x0000000119224c5c 0x117004000 + 35785820
4 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
5 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
6 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
7 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 19:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x00000001191c6c9a 0x117004000 + 35400858
5 QtWebEngineCore 0x00000001191c75db 0x117004000 + 35403227
6 QtWebEngineCore 0x00000001191c72a4 0x117004000 + 35402404
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff676f4dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff676f5170 mach_msg + 60
2 QtWebEngineCore 0x00000001191af2ad 0x117004000 + 35304109
3 QtWebEngineCore 0x00000001191af1af 0x117004000 + 35303855
4 QtWebEngineCore 0x0000000119162fdd 0x117004000 + 34992093
5 QtWebEngineCore 0x000000011918c005 0x117004000 + 35160069
6 QtWebEngineCore 0x00000001191de93c 0x117004000 + 35498300
7 QtWebEngineCore 0x000000011921e697 0x117004000 + 35759767
8 libsystem_pthread.dylib 0x00007fff677b8109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff677b3b8b thread_start + 15
Thread 21:
0 libsystem_pthread.dylib 0x00007fff677b3b68 start_wqthread + 0
Thread 22:
0 libsystem_pthread.dylib 0x00007fff677b3b68 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff677b3b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010dc7bdc0 rcx: 0x0000000106b67a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x0000000106b67a80 rsp: 0x0000000106b67a58
r8: 0x0000000106b67f48 r9: 0x351cc3e2dea34869 r10: 0x000000010dc7bdc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000125fff1e0 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff676fb33a rfl: 0x0000000000000246 cr2: 0x00007ff1fc01fc28
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff675d0000 - 0x7fff675d0ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
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0x7fff675e5000 - 0x7fff675e7ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
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0x7fff675ea000 - 0x7fff67601ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 4
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: 2030511
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=900.1M resident=0K(0%) swapped_out_or_unallocated=900.1M(100%)
Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 1280K 10
Activity Tracing 256K 1
CG backing stores 1232K 4
CG image 756K 32
CoreAnimation 2908K 76
CoreGraphics 8K 1
CoreImage 40K 6
CoreUI image data 4484K 42
Foundation 24K 2
Kernel Alloc Once 8K 1
MALLOC 337.4M 480
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Memory Tag 242 12K 1
Memory Tag 251 12K 1
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 92K 23
Stack 139.7M 24
Stack Guard 56.0M 1
VM_ALLOCATE 236.1M 771
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 49.8M 543
__DATA_CONST 40K 4
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 411.6M 136
__OBJC_RO 32.2M 1
__OBJC_RW 1892K 2
__TEXT 488.5M 507
__UNICODE 564K 1
mapped file 118.2M 44
shared memory 652K 18
=========== ======= =======
TOTAL 2.3G 2751
TOTAL, minus reserved VM space 1.8G 2751
Log:
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/andrewalexander/Desktop/Map_98_00_placed_models.cxs
Log from Wed May 13 19:12:03 2020UCSF ChimeraX version: 1.0rc202005080235
(2020-05-08)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/andrewalexander/Desktop/cryosparc_P7_J98_class_00_00222_volume.mrc
Opened cryosparc_P7_J98_class_00_00222_volume.mrc, grid size 128,128,128,
pixel 1.66, shown at level 0.442, step 1, values float32
> volume #1 level 0.3701
> open
> /Users/andrewalexander/Documents/documents_research/Data/BlaR1_modeling/BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb
Summary of feedback from opening
/Users/andrewalexander/Documents/documents_research/Data/BlaR1_modeling/BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2019-03-23 Time 13:57:15 PDT -0700 (1553374635.60 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/Users/andrewalexander/Documents/documents_research/CLS/2019.02.18_ID/BlaR1_AVI_HR493_05/XDS/XDS_ASCII_scaled1.95A_autobuild_Rfree2.mtz
49 messages similar to the above omitted
Cannot find LINK/SSBOND residue SER (389 )
Cannot find LINK/SSBOND residue SER (389 )
Chain information for BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb #2
---
Chain | Description
B | No description available
> select #2
4054 atoms, 4104 bonds, 2 pseudobonds, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2766, steps = 116
shifted from previous position = 5.49
rotated from previous position = 22.8 degrees
atoms outside contour = 3119, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.43328040 0.78088518 -0.44998493 121.83523567
-0.56235838 -0.15592050 -0.81206025 122.49650685
-0.70428768 0.60490259 0.37158003 100.45325719
Axis 0.71965472 0.12915666 -0.68221378
Axis point 0.00000000 -22.01545095 176.62238351
Rotation angle (degrees) 100.10950412
Shift along axis 34.96994541
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2766, steps = 48
shifted from previous position = 0.0347
rotated from previous position = 0.184 degrees
atoms outside contour = 3116, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.43059927 0.78257597 -0.44962109 121.79632283
-0.56296789 -0.15649152 -0.81152792 122.42187217
-0.70544413 0.60256556 0.37318001 100.32081876
Axis 0.71830515 0.12994828 -0.68348457
Axis point 0.00000000 -22.10319140 176.77546577
Rotation angle (degrees) 100.15758540
Shift along axis 34.82770461
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2766, steps = 48
shifted from previous position = 0.0296
rotated from previous position = 0.158 degrees
atoms outside contour = 3115, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.43293584 0.78116023 -0.44983915 121.83891179
-0.56237103 -0.15594711 -0.81204638 122.48491671
-0.70448945 0.60454049 0.37178679 100.43600814
Axis 0.71947449 0.12933509 -0.68237006
Axis point 0.00000000 -22.04340352 176.64441460
Rotation angle (degrees) 100.11428855
Shift along axis 34.96706149
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2766, steps = 84
shifted from previous position = 0.0647
rotated from previous position = 0.565 degrees
atoms outside contour = 3122, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.42532083 0.78682856 -0.44721696 121.74990418
-0.56263891 -0.15717521 -0.81162394 122.38814787
-0.70890031 0.59682222 0.37585047 100.01716617
Axis 0.71565195 0.13296511 -0.68568402
Axis point 0.00000000 -22.42404057 177.06026510
Rotation angle (degrees) 100.25340084
Shift along axis 34.82373758
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 164
shifted from previous position = 3.27
rotated from previous position = 40.5 degrees
atoms outside contour = 2941, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06136787 0.96178089 -0.26685484 118.66538920
-0.91534059 -0.05237366 -0.39926007 113.08867986
-0.39797687 0.26876481 0.87714303 94.58880976
Axis 0.33455506 0.06566752 -0.94008547
Axis point 134.35850446 -6.79466399 0.00000000
Rotation angle (degrees) 93.26369237
Shift along axis -41.79520635
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 48
shifted from previous position = 0.0465
rotated from previous position = 0.0633 degrees
atoms outside contour = 2940, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06062618 0.96201049 -0.26619597 118.66493632
-0.91553552 -0.05264742 -0.39877684 113.10906000
-0.39764203 0.26788818 0.87756295 94.57851933
Axis 0.33387971 0.06583093 -0.94031411
Axis point 134.30291969 -6.73905430 0.00000000
Rotation angle (degrees) 93.28078075
Shift along axis -41.86762686
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 44
shifted from previous position = 0.00968
rotated from previous position = 0.019 degrees
atoms outside contour = 2940, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06094868 0.96197930 -0.26623503 118.66782501
-0.91549432 -0.05239633 -0.39890448 113.11309769
-0.39768759 0.26804936 0.87749309 94.58220323
Axis 0.33401954 0.06583322 -0.94026429
Axis point 134.33216406 -6.75812575 0.00000000
Rotation angle (degrees) 93.26632659
Shift along axis -41.84829547
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 40
shifted from previous position = 0.00949
rotated from previous position = 0.0496 degrees
atoms outside contour = 2943, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06104952 0.96176361 -0.26699012 118.67325697
-0.91536888 -0.05270194 -0.39915201 113.10009020
-0.39796078 0.26876249 0.87715104 94.60576971
Axis 0.33450589 0.06559291 -0.94010817
Axis point 134.34765008 -6.77703396 0.00000000
Rotation angle (degrees) 93.28201745
Shift along axis -41.82418941
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 44
shifted from previous position = 0.0351
rotated from previous position = 0.0222 degrees
atoms outside contour = 2942, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06140930 0.96173194 -0.26702167 118.66601637
-0.91529615 -0.05243503 -0.39935390 113.08934687
-0.39807269 0.26892795 0.87704954 94.59053027
Axis 0.33468483 0.06563217 -0.94004174
Axis point 134.36495717 -6.79585946 0.00000000
Rotation angle (degrees) 93.26694738
Shift along axis -41.78103176
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 48
shifted from previous position = 0.00158
rotated from previous position = 0.00337 degrees
atoms outside contour = 2941, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06138035 0.96172052 -0.26706944 118.66570372
-0.91530471 -0.05247557 -0.39932893 113.08885022
-0.39805745 0.26896087 0.87704636 94.59204015
Axis 0.33468951 0.06560075 -0.94004227
Axis point 134.36238461 -6.79588665 0.00000000
Rotation angle (degrees) 93.26903244
Shift along axis -41.78563620
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 48
shifted from previous position = 0.00159
rotated from previous position = 0.0076 degrees
atoms outside contour = 2942, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06131200 0.96174856 -0.26698419 118.66479149
-0.91533420 -0.05248278 -0.39926039 113.08832073
-0.39800018 0.26885921 0.87710352 94.59040634
Axis 0.33460445 0.06561480 -0.94007157
Axis point 134.35484374 -6.79236301 0.00000000
Rotation angle (degrees) 93.26956043
Shift along axis -41.79571704
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 60
shifted from previous position = 0.00338
rotated from previous position = 0.00233 degrees
atoms outside contour = 2941, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06132690 0.96175750 -0.26694854 118.66640595
-0.91532884 -0.05245798 -0.39927594 113.09239147
-0.39801021 0.26883205 0.87710729 94.59046318
Axis 0.33459822 0.06563759 -0.94007220
Axis point 134.35900661 -6.79084415 0.00000000
Rotation angle (degrees) 93.26831302
Shift along axis -41.79318388
> fitmap #2 inMap #1
Fit molecule BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4054 atoms
average map value = 0.2963, steps = 48
shifted from previous position = 0.0291
rotated from previous position = 0.0117 degrees
atoms outside contour = 2943, contour level = 0.37014
Position of BlaR1_AVI_HR493_05_refine_112_no_water_ChainB.pdb (#2) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.06113042 0.96175480 -0.26700333 118.67418304
-0.91534906 -0.05264681 -0.39920473 113.10320710
-0.39799394 0.26880480 0.87712303 94.60741333
Axis 0.33455245 0.06560270 -0.94009092
Axis point 134.35680989 -6.77992559 0.00000000
Rotation angle (degrees) 93.27891814
Shift along axis -41.81695612
> volume #1 level 0.3383
> open /Users/andrewalexander/Documents/documents_research/Data/BlaR1_in-
> silico/McConkey_BlaR1_model_v1.pdb
McConkey_BlaR1_model_v1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) BlaR1 BJM Model 1 [more
info...]
Chain information for McConkey_BlaR1_model_v1.pdb #3
---
Chain | Description
A | No description available
Non-standard residues in McConkey_BlaR1_model_v1.pdb #3
---
ZN2 — (ZN2)
> select #3
4846 atoms, 4967 bonds, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #3 inMap #1
Fit molecule McConkey_BlaR1_model_v1.pdb (#3) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4846 atoms
average map value = 0.3035, steps = 148
shifted from previous position = 11.2
rotated from previous position = 3.32 degrees
atoms outside contour = 2819, contour level = 0.33834
Position of McConkey_BlaR1_model_v1.pdb (#3) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.00363098 -0.82727718 -0.56178224 110.70892635
-0.24269742 0.54571849 -0.80205317 124.80506323
0.97009524 0.13343086 -0.20275953 167.69515289
Axis 0.49556113 -0.81149321 0.30967392
Axis point 20.90062115 0.00000000 154.86285288
Rotation angle (degrees) 109.28917104
Shift along axis 5.51539579
> volume #1 level 0.545
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #3 inMap #1
Fit molecule McConkey_BlaR1_model_v1.pdb (#3) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4846 atoms
average map value = 0.3114, steps = 148
shifted from previous position = 13.7
rotated from previous position = 20.7 degrees
atoms outside contour = 4519, contour level = 0.54501
Position of McConkey_BlaR1_model_v1.pdb (#3) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.64883614 -0.68250410 0.33645179 105.15942307
0.33006247 0.65083261 0.68372193 93.39130461
-0.68561682 -0.33257340 0.64755271 92.50935032
Axis -0.57695911 0.58023664 0.57484226
Axis point 193.69019571 0.00000000 -190.46810152
Rotation angle (degrees) 61.73106675
Shift along axis 46.69465423
> volume #1 level 0.393
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #3 inMap #1
Fit molecule McConkey_BlaR1_model_v1.pdb (#3) to map
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) using 4846 atoms
average map value = 0.3119, steps = 84
shifted from previous position = 4.79
rotated from previous position = 9.34 degrees
atoms outside contour = 3421, contour level = 0.39299
Position of McConkey_BlaR1_model_v1.pdb (#3) relative to
cryosparc_P7_J98_class_00_00222_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.66039870 -0.69639781 0.28089790 109.12124953
0.50660230 0.68930868 0.51788767 103.23979047
-0.55428121 -0.19970883 0.80801530 91.80174872
Axis -0.44001327 0.51211215 0.73765132
Axis point -4.77737675 204.87835396 0.00000000
Rotation angle (degrees) 54.62950463
Shift along axis 72.57323434
> volume #1 level 0.6464
> ~select #3
Nothing selected
> volume #1 level 0.4025
> volume #1 level 0.4627
> save /Users/andrewalexander/Desktop/Map_98_00_placed_models.cxs includeMaps
> true
opened ChimeraX session
OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 159.0.0.0.0
SMC Version (system): 2.18f15
Software:
System Software Overview:
System Version: macOS 10.15.4 (19E287)
Kernel Version: Darwin 19.4.0
Time since boot: 4 days 20:13
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG TV:
Resolution: 1366 x 768 (WSGA - Wide eXtended Graphics Array)
UI Looks like: 1366 x 768 @ 60 Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware error |
comment:2 by , 5 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Crashed in Mac OpenGL graphics driver. Apple OpenGL drivers are prone to crashing especially when using lots of graphics memory. Apple switched to their own Metal graphics API some years ago and have no motivation to improve their OpenGL support. Such crashes are also more likely with older hardware (your laptop was released in 2013).