The following bug report has been submitted:
Platform: Darwin-19.6.0-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 [3264]
Path: /Users/USER/Desktop/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 [3264]
User ID: 501
Date/Time: 2021-02-18 12:18:08.083 -0800
OS Version: Mac OS X 10.15.7 (19H2)
Report Version: 12
Anonymous UUID: 56853D17-9C97-4C1A-51C8-3D7A60777C64
Sleep/Wake UUID: A047CBBB-E577-4818-B68A-02AEA2DCC98A
Time Awake Since Boot: 95000 seconds
Time Since Wake: 63000 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 kernel error: 0xfffffff9
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff71c0d33a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff71cc9e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff71b2493e raise + 26
3 libsystem_platform.dylib 0x00007fff71cbe5fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff71b94808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff58ebf0a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff58eb618f gpusGenerateCrashLog + 89
8 com.apple.AMDRadeonX4000GLDriver 0x000000011e913cd1 gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff58eb755b gpusSubmitDataBuffers + 164
10 com.apple.AMDRadeonX4000GLDriver 0x000000011e8ee857 glrATI_Hwl_SubmitPacketsWithToken + 91
11 com.apple.AMDRadeonX4000GLDriver 0x000000011e946512 gldPresentFramebufferData + 83
12 GLEngine 0x00007fff4271c8d1 glSwap_Exec + 97
13 com.apple.opengl 0x00007fff426fe473 CGLFlushDrawable + 59
14 com.apple.AppKit 0x00007fff3520b75a -[NSOpenGLContext flushBuffer] + 20
15 libqcocoa.dylib 0x000000011ceabd3d 0x11ce55000 + 355645
16 QtGui 0x0000000112966a6c QOpenGLContext::swapBuffers(QSurface*) + 412
17 QtGui.so 0x000000011542c59f meth_QOpenGLContext_swapBuffers(_object*, _object*) + 95
18 org.python.python 0x0000000101312382 _PyMethodDef_RawFastCallKeywords + 226
19 org.python.python 0x00000001013118b9 _PyCFunction_FastCallKeywords + 41
20 org.python.python 0x00000001013e6b60 call_function + 656
21 org.python.python 0x00000001013e3817 _PyEval_EvalFrameDefault + 26567
22 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
23 org.python.python 0x0000000101311879 _PyFunction_FastCallKeywords + 217
24 org.python.python 0x00000001013e6bd4 call_function + 772
25 org.python.python 0x00000001013e37fa _PyEval_EvalFrameDefault + 26538
26 org.python.python 0x0000000101311d61 function_code_fastcall + 177
27 org.python.python 0x00000001013e6bd4 call_function + 772
28 org.python.python 0x00000001013e37fa _PyEval_EvalFrameDefault + 26538
29 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
30 org.python.python 0x0000000101311879 _PyFunction_FastCallKeywords + 217
31 org.python.python 0x00000001013e6bd4 call_function + 772
32 org.python.python 0x00000001013dd5c4 _PyEval_EvalFrameDefault + 1396
33 org.python.python 0x0000000101311d61 function_code_fastcall + 177
34 org.python.python 0x00000001013e6bd4 call_function + 772
35 org.python.python 0x00000001013e37fa _PyEval_EvalFrameDefault + 26538
36 org.python.python 0x0000000101311d61 function_code_fastcall + 177
37 org.python.python 0x00000001013e6bd4 call_function + 772
38 org.python.python 0x00000001013e37fa _PyEval_EvalFrameDefault + 26538
39 org.python.python 0x0000000101311d61 function_code_fastcall + 177
40 org.python.python 0x00000001013e6bd4 call_function + 772
41 org.python.python 0x00000001013e38ae _PyEval_EvalFrameDefault + 26718
42 org.python.python 0x0000000101311d61 function_code_fastcall + 177
43 org.python.python 0x00000001013e6bd4 call_function + 772
44 org.python.python 0x00000001013e38ae _PyEval_EvalFrameDefault + 26718
45 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
46 org.python.python 0x0000000101311879 _PyFunction_FastCallKeywords + 217
47 org.python.python 0x00000001013e6bd4 call_function + 772
48 org.python.python 0x00000001013e3817 _PyEval_EvalFrameDefault + 26567
49 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
50 org.python.python 0x0000000101311377 _PyFunction_FastCallDict + 455
51 org.python.python 0x0000000101312873 _PyObject_Call_Prepend + 131
52 org.python.python 0x00000001013119d8 PyObject_Call + 136
53 sip.so 0x0000000114ff0f7a call_method + 76
54 sip.so 0x0000000114fecd07 sip_api_call_procedure_method + 152
55 QtWidgets.so 0x0000000111e889d7 sipQGraphicsView::mouseMoveEvent(QMouseEvent*) + 103
56 QtWidgets 0x00000001123863e7 QWidget::event(QEvent*) + 487
57 QtWidgets 0x000000011242e21d QFrame::event(QEvent*) + 45
58 QtWidgets 0x00000001126a3ef7 QGraphicsView::viewportEvent(QEvent*) + 1191
59 QtWidgets.so 0x0000000111e89e50 sipQGraphicsView::viewportEvent(QEvent*) + 192
60 QtCore 0x00000001130365d4 QCoreApplicationPrivate::sendThroughObjectEventFilters(QObject*, QEvent*) + 148
61 QtWidgets 0x000000011234a668 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 248
62 QtWidgets 0x000000011234d4d8 QApplication::notify(QObject*, QEvent*) + 7336
63 QtWidgets.so 0x0000000111f0a3ca sipQApplication::notify(QObject*, QEvent*) + 234
64 QtCore 0x0000000113036324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
65 QtWidgets 0x000000011234afa0 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 896
66 QtWidgets 0x00000001123a590e 0x11233a000 + 440590
67 QtWidgets 0x00000001123a45c9 0x11233a000 + 435657
68 QtWidgets 0x000000011234a67d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
69 QtWidgets 0x000000011234ba82 QApplication::notify(QObject*, QEvent*) + 594
70 QtWidgets.so 0x0000000111f0a3ca sipQApplication::notify(QObject*, QEvent*) + 234
71 QtCore 0x0000000113036324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
72 QtGui 0x000000011291f779 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 3961
73 QtGui 0x000000011290646b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219
74 libqcocoa.dylib 0x000000011ce8b900 0x11ce55000 + 223488
75 libqcocoa.dylib 0x000000011ce8c068 0x11ce55000 + 225384
76 com.apple.CoreFoundation 0x00007fff37bf0d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
77 com.apple.CoreFoundation 0x00007fff37bf0cf1 __CFRunLoopDoSource0 + 103
78 com.apple.CoreFoundation 0x00007fff37bf0b0b __CFRunLoopDoSources0 + 209
79 com.apple.CoreFoundation 0x00007fff37bef83a __CFRunLoopRun + 927
80 com.apple.CoreFoundation 0x00007fff37beee3e CFRunLoopRunSpecific + 462
81 com.apple.HIToolbox 0x00007fff3681babd RunCurrentEventLoopInMode + 292
82 com.apple.HIToolbox 0x00007fff3681b6f4 ReceiveNextEventCommon + 359
83 com.apple.HIToolbox 0x00007fff3681b579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
84 com.apple.AppKit 0x00007fff34e61039 _DPSNextEvent + 883
85 com.apple.AppKit 0x00007fff34e5f880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
86 com.apple.AppKit 0x00007fff34e5158e -[NSApplication run] + 658
87 libqcocoa.dylib 0x000000011ce8ade3 0x11ce55000 + 220643
88 QtCore 0x000000011303193f QEventLoop::exec(QFlags) + 431
89 QtCore 0x0000000113036932 QCoreApplication::exec() + 130
90 QtWidgets.so 0x0000000111ff97d2 meth_QApplication_exec_(_object*, _object*) + 82
91 org.python.python 0x0000000101312382 _PyMethodDef_RawFastCallKeywords + 226
92 org.python.python 0x00000001013118b9 _PyCFunction_FastCallKeywords + 41
93 org.python.python 0x00000001013e6b60 call_function + 656
94 org.python.python 0x00000001013e3817 _PyEval_EvalFrameDefault + 26567
95 org.python.python 0x0000000101311d61 function_code_fastcall + 177
96 org.python.python 0x00000001013e6bd4 call_function + 772
97 org.python.python 0x00000001013e3817 _PyEval_EvalFrameDefault + 26567
98 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
99 org.python.python 0x0000000101311879 _PyFunction_FastCallKeywords + 217
100 org.python.python 0x00000001013e6bd4 call_function + 772
101 org.python.python 0x00000001013e38ae _PyEval_EvalFrameDefault + 26718
102 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
103 org.python.python 0x00000001013dcfb0 PyEval_EvalCode + 48
104 org.python.python 0x00000001013da547 builtin_exec + 583
105 org.python.python 0x000000010131252d _PyMethodDef_RawFastCallKeywords + 653
106 org.python.python 0x00000001013118b9 _PyCFunction_FastCallKeywords + 41
107 org.python.python 0x00000001013e6b60 call_function + 656
108 org.python.python 0x00000001013e38ae _PyEval_EvalFrameDefault + 26718
109 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
110 org.python.python 0x0000000101311879 _PyFunction_FastCallKeywords + 217
111 org.python.python 0x00000001013e6bd4 call_function + 772
112 org.python.python 0x00000001013e38ae _PyEval_EvalFrameDefault + 26718
113 org.python.python 0x00000001013e7a2c _PyEval_EvalCodeWithName + 3276
114 org.python.python 0x0000000101311377 _PyFunction_FastCallDict + 455
115 org.python.python 0x0000000101441af3 pymain_run_module + 147
116 org.python.python 0x0000000101440bdc pymain_main + 5900
117 org.python.python 0x000000010143f4c3 Py_Main + 51
118 edu.ucsf.cgl.ChimeraX 0x00000001012e1dc8 main + 120
119 libdyld.dylib 0x00007fff71ac5cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102c00c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102c00c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102c00c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102c00c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102c00c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 6:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff37bf0ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff37bef9c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff37beee3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff35002954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x00000001179b105d 0x11585b000 + 34955357
5 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 8:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff71c0b766 kevent + 10
1 QtWebEngineCore 0x0000000117cbe9a9 0x11585b000 + 38156713
2 QtWebEngineCore 0x0000000117cbbcbd 0x11585b000 + 38145213
3 QtWebEngineCore 0x0000000117a72cdc 0x11585b000 + 35749084
4 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
5 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
6 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
7 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 9:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff71c0b766 kevent + 10
1 QtWebEngineCore 0x0000000117cbe9a9 0x11585b000 + 38156713
2 QtWebEngineCore 0x0000000117cbbcbd 0x11585b000 + 38145213
3 QtWebEngineCore 0x0000000117a72cc4 0x11585b000 + 35749060
4 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
5 QtWebEngineCore 0x0000000117a1ba74 0x11585b000 + 35392116
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 10:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd421 0x11585b000 + 35267617
4 QtWebEngineCore 0x0000000117a14d28 0x11585b000 + 35364136
5 QtWebEngineCore 0x0000000117a1565b 0x11585b000 + 35366491
6 QtWebEngineCore 0x0000000117a152c4 0x11585b000 + 35365572
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 11:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd421 0x11585b000 + 35267617
4 QtWebEngineCore 0x0000000117a14d28 0x11585b000 + 35364136
5 QtWebEngineCore 0x0000000117a1565b 0x11585b000 + 35366491
6 QtWebEngineCore 0x0000000117a152c4 0x11585b000 + 35365572
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 12:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd421 0x11585b000 + 35267617
4 QtWebEngineCore 0x0000000117a14d28 0x11585b000 + 35364136
5 QtWebEngineCore 0x0000000117a1565b 0x11585b000 + 35366491
6 QtWebEngineCore 0x0000000117a15234 0x11585b000 + 35365428
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 13:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd421 0x11585b000 + 35267617
4 QtWebEngineCore 0x0000000117a14d28 0x11585b000 + 35364136
5 QtWebEngineCore 0x0000000117a1565b 0x11585b000 + 35366491
6 QtWebEngineCore 0x0000000117a15234 0x11585b000 + 35365428
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 14:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff71c0b766 kevent + 10
1 QtWebEngineCore 0x0000000117cbe9a9 0x11585b000 + 38156713
2 QtWebEngineCore 0x0000000117cbbcbd 0x11585b000 + 38145213
3 QtWebEngineCore 0x0000000117a72cc4 0x11585b000 + 35749060
4 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
5 QtWebEngineCore 0x0000000117348fe4 0x11585b000 + 28237796
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 15:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x0000000117a14d1a 0x11585b000 + 35364122
5 QtWebEngineCore 0x0000000117a153bf 0x11585b000 + 35365823
6 QtWebEngineCore 0x0000000117a15264 0x11585b000 + 35365476
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 16:: CompositorTileWorker1/58883
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000117a6afa8 0x11585b000 + 35717032
3 QtWebEngineCore 0x00000001189f14c8 0x11585b000 + 51995848
4 QtWebEngineCore 0x0000000117a2b694 0x11585b000 + 35456660
5 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
6 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 17:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179b1052 0x11585b000 + 34955346
4 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
5 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
6 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
7 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 18:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff71c0b766 kevent + 10
1 QtWebEngineCore 0x0000000117cbe9a9 0x11585b000 + 38156713
2 QtWebEngineCore 0x0000000117cbbcbd 0x11585b000 + 38145213
3 QtWebEngineCore 0x0000000117a72cdc 0x11585b000 + 35749084
4 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
5 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
6 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
7 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 19:: AudioThread
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x00000001179b105d 0x11585b000 + 34955357
5 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x00000001179b105d 0x11585b000 + 34955357
5 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 21:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x0000000117a14d1a 0x11585b000 + 35364122
5 QtWebEngineCore 0x0000000117a1565b 0x11585b000 + 35366491
6 QtWebEngineCore 0x0000000117a15324 0x11585b000 + 35365668
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 22:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd22f 0x11585b000 + 35267119
4 QtWebEngineCore 0x00000001179b105d 0x11585b000 + 34955357
5 QtWebEngineCore 0x00000001179da085 0x11585b000 + 35123333
6 QtWebEngineCore 0x0000000117a2c9bc 0x11585b000 + 35461564
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 23:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff71c09882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff71cca425 _pthread_cond_wait + 698
2 QtCore 0x0000000112e768ab 0x112e4c000 + 174251
3 QtCore 0x0000000112e7680c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x0000000112575762 0x11233a000 + 2340706
5 QtCore 0x0000000112e6e0b3 0x112e4c000 + 139443
6 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 24:
0 libsystem_pthread.dylib 0x00007fff71cc5b68 start_wqthread + 0
Thread 25:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff71c06dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff71c07170 mach_msg + 60
2 QtWebEngineCore 0x00000001179fd32d 0x11585b000 + 35267373
3 QtWebEngineCore 0x00000001179fd421 0x11585b000 + 35267617
4 QtWebEngineCore 0x0000000117a14d28 0x11585b000 + 35364136
5 QtWebEngineCore 0x0000000117a153bf 0x11585b000 + 35365823
6 QtWebEngineCore 0x0000000117a152c4 0x11585b000 + 35365572
7 QtWebEngineCore 0x0000000117a6c717 0x11585b000 + 35723031
8 libsystem_pthread.dylib 0x00007fff71cca109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff71cc5b8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010d400dc0 rcx: 0x00007ffa9de77a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007ffa9de77a80 rsp: 0x00007ffa9de77a58
r8: 0x00007ffa9de77f48 r9: 0x5ca67a8f63b44084 r10: 0x000000010d400dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007ffaa2df5f50 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff71c0d33a rfl: 0x0000000000000246 cr2: 0x00000001014ea7c8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff6f5b8000 - 0x7fff6f6bcfef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib
0x7fff6f6bf000 - 0x7fff6f6cafff libcsfde.dylib (551) /usr/lib/libcsfde.dylib
0x7fff6f6d2000 - 0x7fff6f731ff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib
0x7fff6f733000 - 0x7fff6f798ff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib
0x7fff6f83b000 - 0x7fff6f83bfff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6f83c000 - 0x7fff6f854fff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib
0x7fff6f862000 - 0x7fff6f864fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6f873000 - 0x7fff6f878fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6f879000 - 0x7fff6f882ff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6f883000 - 0x7fff6f973fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6f974000 - 0x7fff6fbcbfff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6fbe5000 - 0x7fff6fbe6fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6fbe7000 - 0x7fff6fbffff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6fc17000 - 0x7fff6fcbeff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6fcbf000 - 0x7fff6ff21ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff7028e000 - 0x7fff702bdfff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff703ed000 - 0x7fff70869ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff7086a000 - 0x7fff70881fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff7090a000 - 0x7fff7093dfde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff7093e000 - 0x7fff7093fff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff70950000 - 0x7fff70954fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff70957000 - 0x7fff7098dff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff709cd000 - 0x7fff709dbff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff70a11000 - 0x7fff70a29fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff70a2b000 - 0x7fff70a6fff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff70a70000 - 0x7fff70a82ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff70a83000 - 0x7fff70a84ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff70a85000 - 0x7fff70c6fff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff70d63000 - 0x7fff70d90ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff70e65000 - 0x7fff70ebfff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff70ec0000 - 0x7fff70ec3ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff70ec4000 - 0x7fff70ed1ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff70ed7000 - 0x7fff70fb9fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff70fbd000 - 0x7fff70fe5fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff70fe6000 - 0x7fff70ff8ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff718a7000 - 0x7fff718acff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff718ad000 - 0x7fff718b8fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff718b9000 - 0x7fff718c0fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff718c1000 - 0x7fff718caff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff718cb000 - 0x7fff7195dfdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff71a6a000 - 0x7fff71aaaff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff71aab000 - 0x7fff71ae1fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff71ae2000 - 0x7fff71ae2ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff71ae3000 - 0x7fff71aefff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib
0x7fff71af0000 - 0x7fff71af0ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff71af1000 - 0x7fff71af6ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff71af7000 - 0x7fff71af9ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff71afa000 - 0x7fff71afbff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff71afc000 - 0x7fff71b13ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff71b14000 - 0x7fff71b14ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff71b15000 - 0x7fff71b9cfff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff71b9d000 - 0x7fff71ba0ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff71ba1000 - 0x7fff71ba4fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff71ba5000 - 0x7fff71badfff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff71bae000 - 0x7fff71bb5fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff71bb6000 - 0x7fff71bb7ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff71bb8000 - 0x7fff71c05ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff71c06000 - 0x7fff71c32ff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff71c33000 - 0x7fff71c7afff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff71c7b000 - 0x7fff71ca2fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff71ca3000 - 0x7fff71cb0ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff71cb1000 - 0x7fff71cbaff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff71cbb000 - 0x7fff71cc3fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff71cc4000 - 0x7fff71ccefff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff71ccf000 - 0x7fff71cd3ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff71cd4000 - 0x7fff71cd6fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff71cd7000 - 0x7fff71cdeffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff71cdf000 - 0x7fff71cf5ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff71cf7000 - 0x7fff71cfcff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff71cfd000 - 0x7fff71d32ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 15
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: 59146
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=930.9M resident=0K(0%) swapped_out_or_unallocated=930.9M(100%)
Writable regions: Total=7.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.7G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 1744K 4
CG image 232K 16
CoreAnimation 148K 14
CoreGraphics 8K 1
CoreImage 32K 4
CoreServices 236K 1
CoreUI image data 2196K 18
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 5.1G 461
MALLOC guard page 32K 6
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 100K 25
Stack 148.2M 26
Stack Guard 56.0M 1
VM_ALLOCATE 2.2G 326
VM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)
__DATA 61.6M 550
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 413.3M 139
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 517.7M 510
__UNICODE 564K 1
mapped file 82.8M 53
shared memory 652K 18
=========== ======= =======
TOTAL 8.8G 2204
TOTAL, minus reserved VM space 8.6G 2204
System Profile:
Network Service: Wi-Fi, AirPort, en1
Thunderbolt Bus: iMac, Apple Inc., 47.4
Boot Volume File System Type: apfs
Memory Module: BANK 0/ChannelA-DIMM0, 4 GB, DDR4, 2667 MHz, Micron, 4ATF51264HZ-2G6E3
Memory Module: BANK 2/ChannelB-DIMM0, 4 GB, DDR4, 2667 MHz, Micron, 4ATF51264HZ-2G6E3
USB Device: USB 3.1 Bus
USB Device: Magic Keyboard
USB Device: FaceTime HD Camera (Built-in)
USB Device: USB Optical Mouse
USB Device: USB Mass Storage Device
USB Device: 6ft USB-C to HDMI Cable
Serial ATA Device: APPLE HDD HTS541010A9E632, 1 TB
Model: iMac19,2, BootROM 1037.140.50.0.0, 6 processors, 6-Core Intel Core i5, 3 GHz, 8 GB, SMC 2.47f3
Graphics: kHW_AMDRadeonPro560XItem, Radeon Pro 560X, spdisplays_pcie_device, 4 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Feb 28 2020 15:24:56 version 9.30.357.35.32.5.47 FWID 01-9ce4adf3
Bluetooth: Version 7.0.6f7, 3 services, 27 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/e.olmedillas/Documents/SARS2_S /Structures solved/VFLIP D614G
> COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Sat Jan 9 11:59:55 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
Log from Wed Jan 6 18:02:54 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs" format
> session
Log from Wed Jan 6 17:24:49 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
Log from Wed Jan 6 17:17:03 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
Log from Mon Jan 4 13:49:25 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
Log from Mon Dec 7 16:30:09 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs" format
> session
Log from Thu Dec 3 14:29:14 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs" format
> session
Log from Thu Dec 3 12:05:50 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
Log from Wed Nov 18 14:29:20 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G complex COVIC69.mrc"
Opened VFLIP D614G complex COVIC69.mrc, grid size 512,512,512, pixel 0.66,
shown at level 0.0315, step 2, values float32
> volume #1 step 1
> volume #1 level 0.02613
> volume #1 level 0.02379
> volume #1 level 0.01811
> set bgColor white
> lighting soft
> transparency 50
> transparency 70
> transparency 40
> open 7a95
Summary of feedback from opening 7a95 fetched from pdb
---
note | Fetching compressed mmCIF 7a95 from
http://files.rcsb.org/download/7a95.cif
7a95 title:
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Clockwise
Direction [more info...]
Chain information for 7a95 #2
---
Chain | Description
A B C | Spike glycoprotein
D | Angiotensin-converting enzyme 2
> vop zflip #1
> volume zflip #1
Expected a density maps specifier or a keyword
> vop zflip #1
> volume zflip #1
Expected a density maps specifier or a keyword
> select ~sel
29887 atoms, 30648 bonds, 16 pseudobonds, 3794 residues, 4 models selected
> vop zFlip #2
> volume zFlip #2
Expected a density maps specifier or a keyword
> vop zFlip #1
> volume zFlip #1
Expected a density maps specifier or a keyword
> vop zFlip in #1
> volume zFlip in #1
Expected a density maps specifier or a keyword
> ~select #2
2 models selected
> vop zFlip inMap #1
> volume zFlip inMap #1
Expected a density maps specifier or a keyword
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume sel region all imageMode "full region"
> mousemode rightMode "crop volume"
> volume sel style surface
> ui mousemode right pivot
> vop zFlip #1
> volume zFlip #1
Expected a density maps specifier or a keyword
> vop zflip #1
> volume zflip #1
Expected a density maps specifier or a keyword
> vop zflip #1
> volume zflip #1
Expected a density maps specifier or a keyword
> ui mousemode right "rotate selected models"
> vop zflip #1
> volume zflip #1
Expected a density maps specifier or a keyword
> ui mousemode right "move planes"
> ui mousemode right select
> toolshed show
> vop zFlip #0
> volume zFlip #0
Expected a density maps specifier or a keyword
> vop zFlip #1
> volume zFlip #1
Expected a density maps specifier or a keyword
> vop zFlip inMap #1
> volume zFlip inMap #1
Expected a density maps specifier or a keyword
> vop zFlip onMap #1
> volume zFlip onMap #1
Expected a density maps specifier or a keyword
> vop zFlip #2
> volume zFlip #2
Expected a density maps specifier or a keyword
> view orient
> view orient
> ui mousemode right "move planes"
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> vop zFlip #2
> volume zFlip #2
Expected a density maps specifier or a keyword
> vop zFlip model-spec
> volume zFlip model-spec
Expected a density maps specifier or a keyword
> vop zFlip #1
> volume zFlip #1
Expected a density maps specifier or a keyword
> vop zFlip #0
> volume zFlip #0
Expected a density maps specifier or a keyword
> vop zFlip #1
> volume zFlip #1
Expected a density maps specifier or a keyword
> vop zFlip #2
> volume zFlip #2
Expected a density maps specifier or a keyword
> vop flip #1
> volume #3 level 0.01578
> select #1
3 models selected
> select #2
29887 atoms, 30648 bonds, 16 pseudobonds, 3794 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #2 inMap #3 search 100 radius 5
Found 63 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02435 (3), 0.02422 (8), 0.02417 (4), 0.02403 (3), 0.02311 (2), 0.02195 (1),
0.02185 (2), 0.02173 (1), 0.02168 (3), 0.02141 (1), 0.02115 (1), 0.0211 (1),
0.02094 (2), 0.02017 (2), 0.02016 (1), 0.02012 (1), 0.01982 (1), 0.01982 (3),
0.01981 (1), 0.01977 (1), 0.01968 (3), 0.01956 (1), 0.01953 (2), 0.01951 (2),
0.01946 (1), 0.01939 (1), 0.0193 (1), 0.01912 (1), 0.01905 (3), 0.01903 (1),
0.01903 (1), 0.01903 (1), 0.01903 (1), 0.01903 (1), 0.01854 (1), 0.01846 (1),
0.01846 (1), 0.01846 (1), 0.01836 (1), 0.01835 (1), 0.01832 (2), 0.01824 (4),
0.0182 (1), 0.01817 (2), 0.01807 (1), 0.01797 (1), 0.01779 (1), 0.01768 (1),
0.01763 (1), 0.01745 (1), 0.0174 (4), 0.01736 (1), 0.01736 (1), 0.01731 (1),
0.01728 (1), 0.01718 (1), 0.01713 (1), 0.01701 (1), 0.01686 (1), 0.01648 (1),
0.01582 (2), 0.0154 (1), 0.01433 (1)
Best fit found:
Fit molecule 7a95 (#2) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 29887 atoms
average map value = 0.02435, steps = 592
shifted from previous position = 23.3
rotated from previous position = 45.4 degrees
atoms outside contour = 13177, contour level = 0.015776
Position of 7a95 (#2) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.97846382 -0.14353041 -0.14834950 -21.39864433
0.11772041 0.97836358 -0.17013692 -91.18655752
0.16955961 0.14900902 0.97418984 -173.54260121
Axis 0.61286757 -0.61049244 0.50168947
Axis point 0.00000000 875.01235281 -806.94951152
Rotation angle (degrees) 15.09207989
Shift along axis -44.51032564
Found 63 fits. List window not yet implemented.
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #2 inMap #3 search 100 radius 5
Found 60 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02435 (7), 0.02422 (4), 0.02417 (1), 0.02403 (5), 0.02212 (1), 0.02195 (4),
0.02185 (1), 0.02178 (1), 0.02174 (1), 0.02173 (1), 0.02169 (2), 0.02168 (2),
0.02168 (4), 0.02141 (1), 0.02115 (2), 0.02109 (2), 0.02107 (1), 0.02094 (1),
0.02088 (1), 0.02038 (1), 0.02017 (5), 0.02016 (1), 0.02012 (3), 0.01977 (1),
0.01977 (2), 0.01968 (1), 0.01953 (4), 0.01951 (1), 0.01948 (1), 0.01946 (1),
0.01945 (1), 0.01934 (1), 0.0193 (3), 0.01911 (1), 0.01905 (3), 0.01903 (1),
0.01902 (1), 0.01896 (1), 0.01854 (2), 0.01846 (1), 0.01846 (1), 0.01835 (1),
0.01834 (2), 0.01832 (1), 0.01824 (1), 0.01816 (1), 0.01811 (1), 0.01811 (2),
0.01805 (1), 0.01797 (1), 0.0179 (1), 0.01755 (1), 0.01745 (1), 0.01742 (1),
0.0174 (1), 0.0174 (1), 0.01736 (1), 0.01648 (1), 0.01621 (1), 0.01582 (1)
Best fit found:
Fit molecule 7a95 (#2) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 29887 atoms
average map value = 0.02435, steps = 640
shifted from previous position = 13.6
rotated from previous position = 42.2 degrees
atoms outside contour = 13177, contour level = 0.015776
Position of 7a95 (#2) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.97847188 -0.14352429 -0.14830244 -21.41243924
0.11774671 0.97838562 -0.16999188 -91.22830525
0.16949497 0.14887011 0.97422231 -173.49706998
Axis 0.61259528 -0.61055001 0.50195190
Axis point 0.00000000 875.48710659 -807.82606594
Rotation angle (degrees) 15.08519468
Shift along axis -44.50489992
Found 60 fits. List window not yet implemented.
> ui mousemode right select
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #2 inMap #3 search 100 radius 5
Found 58 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02435 (6), 0.02417 (7), 0.02403 (1), 0.02311 (3), 0.0225 (1), 0.02198 (1),
0.02195 (4), 0.02168 (1), 0.02168 (1), 0.02147 (1), 0.02141 (4), 0.02107 (1),
0.02088 (2), 0.02066 (1), 0.02017 (2), 0.02016 (2), 0.02012 (5), 0.01982 (3),
0.01977 (1), 0.01977 (1), 0.01969 (2), 0.01968 (5), 0.01953 (1), 0.01946 (4),
0.0193 (1), 0.01908 (1), 0.01903 (1), 0.01903 (1), 0.01903 (1), 0.01866 (3),
0.0185 (1), 0.01849 (3), 0.01846 (1), 0.01836 (1), 0.01834 (1), 0.01834 (3),
0.01811 (1), 0.0181 (1), 0.01799 (1), 0.01795 (1), 0.01779 (1), 0.01764 (1),
0.01762 (1), 0.01733 (1), 0.01731 (1), 0.01713 (1), 0.01705 (1), 0.01703 (1),
0.01684 (1), 0.01624 (1), 0.01603 (1), 0.01603 (1), 0.01556 (1), 0.01554 (1),
0.01543 (1), 0.0154 (1), 0.01535 (1), 0.01437 (1)
Best fit found:
Fit molecule 7a95 (#2) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 29887 atoms
average map value = 0.02435, steps = 1148
shifted from previous position = 18.6
rotated from previous position = 77.2 degrees
atoms outside contour = 13174, contour level = 0.015776
Position of 7a95 (#2) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.97847938 -0.14352237 -0.14825493 -21.42305203
0.11773812 0.97837272 -0.17007203 -91.20524716
0.16945777 0.14895667 0.97421554 -173.50825440
Axis 0.61286239 -0.61033431 0.50188815
Axis point 0.00000000 874.97304154 -807.39978818
Rotation angle (degrees) 15.08653476
Shift along axis -44.54542792
Found 58 fits. List window not yet implemented.
> volume #3 level 0.006088
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #2 inMap #3 search 100 radius 5
Found 65 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02435 (3), 0.02422 (2), 0.02417 (4), 0.02403 (2), 0.02311 (2), 0.0225 (1),
0.02198 (1), 0.02195 (3), 0.02191 (4), 0.02185 (4), 0.02173 (1), 0.02168 (1),
0.02147 (1), 0.02141 (1), 0.02141 (2), 0.02115 (1), 0.02107 (1), 0.02088 (1),
0.02036 (1), 0.02012 (5), 0.01982 (1), 0.01982 (2), 0.01981 (1), 0.01977 (3),
0.01977 (4), 0.01974 (1), 0.01969 (2), 0.01968 (2), 0.01948 (1), 0.01946 (4),
0.01938 (1), 0.0193 (1), 0.01912 (1), 0.01908 (1), 0.01903 (1), 0.01903 (1),
0.01903 (1), 0.01903 (1), 0.01896 (1), 0.01893 (1), 0.01866 (2), 0.01834 (1),
0.01833 (2), 0.01828 (1), 0.01824 (1), 0.01822 (1), 0.0181 (1), 0.01799 (1),
0.01785 (1), 0.01772 (1), 0.01768 (1), 0.01756 (1), 0.01746 (1), 0.0174 (2),
0.01733 (1), 0.01713 (1), 0.01713 (1), 0.01712 (1), 0.01709 (1), 0.01689 (1),
0.01689 (1), 0.01658 (1), 0.01617 (1), 0.01611 (1), 0.01439 (1)
Best fit found:
Fit molecule 7a95 (#2) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 29887 atoms
average map value = 0.02435, steps = 832
shifted from previous position = 15.5
rotated from previous position = 61.7 degrees
atoms outside contour = 9058, contour level = 0.0060881
Position of 7a95 (#2) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.97847857 -0.14353163 -0.14825119 -21.42117584
0.11773805 0.97836281 -0.17012914 -91.19243954
0.16946241 0.14901289 0.97420614 -173.52179725
Axis 0.61299222 -0.61024856 0.50183387
Axis point 0.00000000 874.70172667 -807.10003028
Rotation angle (degrees) 15.08874872
Shift along axis -44.56007411
Found 65 fits. List window not yet implemented.
> open 7A97
Summary of feedback from opening 7A97 fetched from pdb
---
note | Fetching compressed mmCIF 7a97 from
http://files.rcsb.org/download/7a97.cif
7a97 title:
SARS-CoV-2 Spike Glycoprotein with 2 ACE2 Bound [more info...]
Chain information for 7a97 #4
---
Chain | Description
A B C | Spike glycoprotein
D E | Angiotensin-converting enzyme 2
> ~select #2
Nothing selected
> select #4
34626 atoms, 35524 bonds, 17 pseudobonds, 4373 residues, 2 models selected
> volume #!3 hide
> show #!3 models
> hide #!2 models
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> ui mousemode right "translate selected models"
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ~select #3
Nothing selected
> select #4
34626 atoms, 35524 bonds, 17 pseudobonds, 4373 residues, 2 models selected
> ui mousemode right "rotate selected models"
> fitmap #4 inMap #3 search 100 radius 5
Found 59 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02145 (2), 0.02143 (2), 0.02126 (3), 0.02118 (4), 0.02111 (1), 0.02049 (4),
0.02008 (1), 0.01906 (2), 0.0189 (1), 0.01885 (1), 0.01877 (3), 0.01854 (1),
0.01852 (2), 0.0185 (1), 0.01843 (1), 0.01831 (1), 0.0182 (1), 0.01804 (2),
0.01791 (1), 0.01749 (4), 0.01746 (2), 0.01744 (2), 0.01698 (2), 0.01683 (2),
0.01672 (1), 0.01666 (4), 0.01662 (5), 0.01661 (1), 0.01652 (1), 0.0164 (2),
0.01639 (3), 0.01636 (3), 0.01632 (1), 0.01632 (1), 0.01622 (1), 0.01622 (1),
0.01618 (1), 0.01616 (1), 0.01585 (1), 0.01575 (1), 0.01563 (2), 0.01548 (2),
0.01537 (1), 0.01536 (1), 0.01525 (1), 0.0152 (2), 0.01517 (2), 0.015 (3),
0.01491 (1), 0.0148 (1), 0.01465 (1), 0.01444 (1), 0.01429 (1), 0.01409 (2),
0.01384 (1), 0.0135 (1), 0.01341 (1), 0.01297 (1), 0.01265 (1)
Best fit found:
Fit molecule 7a97 (#4) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 34626 atoms
average map value = 0.02145, steps = 1304
shifted from previous position = 10.9
rotated from previous position = 80.7 degrees
atoms outside contour = 11151, contour level = 0.0060881
Position of 7a97 (#4) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
-0.95605115 0.28577338 0.06557281 336.51931661
-0.26118230 -0.93170164 0.25242020 429.68878503
0.13322923 0.22420018 0.96539337 -185.23190811
Axis -0.05113746 -0.12260012 -0.99113782
Axis point 204.52478426 202.00343955 0.00000000
Rotation angle (degrees) 163.98296635
Shift along axis 113.70170953
Found 59 fits. List window not yet implemented.
> open 7a98
Summary of feedback from opening 7a98 fetched from pdb
---
note | Fetching compressed mmCIF 7a98 from
http://files.rcsb.org/download/7a98.cif
7a98 title:
SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound [more info...]
Chain information for 7a98 #5
---
Chain | Description
A B C | Spike glycoprotein
D E F | Angiotensin-converting enzyme 2
> ~select #4
Nothing selected
> select #5
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> show sel atoms
> ~select #5
Nothing selected
> select #5
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> show sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide #!4 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #5 inMap #3 search 100 radius 5
Found 60 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.01917 (2), 0.01915 (1), 0.01914 (1), 0.01906 (6), 0.01905 (4), 0.01905 (3),
0.01765 (1), 0.01763 (1), 0.0176 (2), 0.01747 (1), 0.01746 (2), 0.01627 (1),
0.01625 (1), 0.01624 (1), 0.01613 (2), 0.01572 (2), 0.0157 (3), 0.01569 (4),
0.0156 (2), 0.0154 (1), 0.01538 (3), 0.01537 (2), 0.01536 (1), 0.01531 (1),
0.01523 (5), 0.01523 (3), 0.01522 (3), 0.01518 (2), 0.01514 (3), 0.01514 (2),
0.01479 (1), 0.01468 (1), 0.01465 (1), 0.01464 (1), 0.01464 (2), 0.01458 (1),
0.01444 (1), 0.01431 (1), 0.01429 (1), 0.01425 (2), 0.01409 (1), 0.01398 (2),
0.01397 (1), 0.01394 (1), 0.01394 (1), 0.01386 (1), 0.01386 (1), 0.01363 (1),
0.01363 (1), 0.01354 (1), 0.01353 (1), 0.01331 (1), 0.01313 (1), 0.013 (1),
0.01281 (1), 0.01281 (2), 0.01279 (1), 0.01237 (1), 0.01232 (1), 0.01115 (1)
Best fit found:
Fit molecule 7a98 (#5) to map VFLIP D614G complex COVIC69.mrc z flip (#3)
using 39435 atoms
average map value = 0.01917, steps = 472
shifted from previous position = 10.6
rotated from previous position = 30.3 degrees
atoms outside contour = 13543, contour level = 0.0060881
Position of 7a98 (#5) relative to VFLIP D614G complex COVIC69.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.43253413 0.90015318 -0.05136702 -183.26863399
0.90158787 -0.43228001 0.01653420 33.99067722
-0.00732161 -0.05346349 -0.99854295 463.79060428
Axis -0.84625384 -0.53249750 0.01734507
Axis point 0.00000000 80.29356531 228.65766832
Rotation angle (degrees) 177.62972019
Shift along axis 145.03631434
Found 60 fits. List window not yet implemented.
> ~select #5
Nothing selected
> select #3
2 models selected
> transparency #3.1 50
> transparency #3.1 40
> transparency #3.1 70
> transparency #3.1 60
> ~select #3
Nothing selected
> ui mousemode right "rotate selected models"
> save /Users/e.olmedillas/Desktop/image14.png supersample 3
> save /Users/e.olmedillas/Desktop/image15.png supersample 3
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> set bgColor black
> ui mousemode right "rotate selected models"
> select #1
3 models selected
> ui mousemode right "translate selected models"
> ~select #1
Nothing selected
> select #5
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> show #!3 models
> hide #!3 models
Must specify one map, got 0
> fitmap #5 inMap #1 search 100 radius 5
Found 55 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Average map values and times found:
0.02684 (14), 0.02683 (7), 0.02683 (4), 0.01634 (1), 0.01622 (3), 0.0162 (3),
0.01617 (1), 0.01589 (2), 0.01579 (2), 0.01576 (1), 0.01574 (3), 0.01573 (1),
0.01567 (1), 0.01567 (1), 0.01567 (1), 0.01566 (1), 0.01565 (2), 0.01551 (2),
0.01549 (1), 0.01548 (1), 0.01546 (1), 0.01519 (3), 0.01518 (5), 0.01505 (3),
0.01501 (1), 0.01496 (1), 0.01493 (1), 0.01493 (1), 0.01492 (1), 0.01434 (1),
0.01431 (1), 0.0143 (2), 0.01421 (1), 0.01414 (1), 0.01411 (2), 0.01403 (1),
0.01399 (2), 0.01395 (1), 0.01394 (1), 0.01386 (1), 0.01358 (2), 0.01356 (1),
0.01355 (1), 0.01355 (1), 0.01353 (1), 0.01353 (1), 0.0135 (1), 0.01326 (1),
0.01324 (1), 0.01322 (1), 0.01322 (1), 0.01305 (2), 0.01299 (1), 0.01248 (1),
0.01243 (1)
Best fit found:
Fit molecule 7a98 (#5) to map VFLIP D614G complex COVIC69.mrc (#1) using 39435
atoms
average map value = 0.02684, steps = 728
shifted from previous position = 18.8
rotated from previous position = 48 degrees
atoms outside contour = 18209, contour level = 0.018114
Position of 7a98 (#5) relative to VFLIP D614G complex COVIC69.mrc (#1)
coordinates:
Matrix rotation and translation
-0.76311499 0.64605196 -0.01650679 206.84298880
-0.64625282 -0.76299590 0.01394756 553.02707106
-0.00358376 0.02131117 0.99976644 -127.04762362
Axis 0.00569767 -0.00999933 -0.99993377
Axis point 204.63211033 239.37082687 0.00000000
Rotation angle (degrees) 139.74465591
Shift along axis 122.68783314
Found 55 fits. List window not yet implemented.
> close #3
> ~select #5
Nothing selected
> volume #1 change image level -0.003703,0 level 0.04098,0.8 level 0.0979,1
> volume #1 level 0.02381
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> volume #1 level 0.01711
> color zone #1 near #5 distance 5
> volume #1 level 0.02482
> volume #1 level 0.03052
> hide #!5 models
> color zone #1 near #5 distance 15
> volume #1 level 0.02247
> volume #1 level 0.01677
> lighting full
> lighting soft
> color zone #1 near #5 distance 10
> color zone #1 near #5 distance 12
> color zone #1 near #5 distance 20
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> volume #1 level 0.01945
> show #!5 models
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/7A98 fitted.pdb" models #5 relModel #1
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFlipD615G COVIC69
> building/VFlip_D614G_COVIC69_fitted.mrc" models #1
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFlipD615G COVIC69 building/7A98_fitted.pdb"
> models #5 relModel #1
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> volume #1 level 0.01309
> select #5/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> ui tool show "Color Actions"
> color sel teal
> select #5/B
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> color sel pale violet red
> select #5/C
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> select #5/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> hide #!1 models
> color sel teal
> color sel royal blue
> show #!1 models
> color zone #1 near #5 distance 25
> hide #!5 models
> hide #!1 models
> show #!5 models
> select #5/C
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> color sel teal
> color zone #1 near #5 distance 25
> show #!1 models
> hide #!5 models
> lighting soft
> volume #1 level 0.009733
> volume #1 level 0.01577
> set bgColor white
> save /Users/e.olmedillas/Desktop/image2.png supersample 3
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> hide #!1 models
> show #!5 models
> select #5/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select #5/B
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> color sel pale violet red
> select #5/C
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> color sel teal
> select #5/D
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color sel chocolate
> color sel saddle brown
> color sel dark goldenrod
> color sel goldenrod
> color sel dark goldenrod
> select #5/E
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color sel dark goldenrod
> select #5/F
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color sel dark goldenrod
> show #!1 models
> color zone #1 near #5 distance 20
> ui mousemode right "map eraser"
> color zone #1 near #5 distance 10
> color zone #1 near #5 distance 15
> color zone #1 near #5 distance 20
> color zone #1 near #5 distance 17
> color zone #1 near #5 distance 20
> hide #!5 models
> save /Users/e.olmedillas/Desktop/image5.png supersample 3
> save /Users/e.olmedillas/Desktop/image6.png supersample 3
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> open 6xkl
6xkl title:
SARS-CoV-2 HexaPro S One RBD up [more info...]
Chain information for 6xkl #3
---
Chain | Description
A B C | Spike glycoprotein
Non-standard residues in 6xkl #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> matchmaker #3 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a98, chain A (#5) with 6xkl, chain B (#3), sequence alignment
score = 5424.4
RMSD between 613 pruned atom pairs is 1.131 angstroms; (across all 964 pairs:
12.493)
> hide #!1 models
> show #!5 models
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/USEO5_5P_DS3/Vflip reconstruction/MODEL 6ZGE/6ZGE_RBD_A.pdb"
Chain information for 6ZGE_RBD_A.pdb #6
---
Chain | Description
A | No description available
> matchmaker #6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a98, chain A (#5) with 6ZGE_RBD_A.pdb, chain A (#6), sequence
alignment score = 1066.5
RMSD between 169 pruned atom pairs is 1.126 angstroms; (across all 243 pairs:
8.225)
> hide #!3 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.02918
> volume #1 level 0.03354
> hide #!1 models
> show #!1 models
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!5 models
> hide #6 models
> open "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 68/cryosparc_P12_J19_006_volume_map.mrc"
Opened cryosparc_P12_J19_006_volume_map.mrc, grid size 256,256,256, pixel
1.03, shown at level 0.115, step 1, values float32
> hide #!1 models
> select #7
2 models selected
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> volume flip #7
> show #!1 models
> ui mousemode right select
> select #8
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #8 inMap #1 search 100 radius 5
Found 73 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Correlations and times found:
0.8212 (1), 0.8175 (4), 0.815 (4), 0.8068 (3), 0.7984 (2), 0.796 (3), 0.7903
(2), 0.7899 (1), 0.7853 (2), 0.7836 (1), 0.7822 (1), 0.7757 (2), 0.7752 (1),
0.7744 (2), 0.7743 (3), 0.7741 (3), 0.7739 (1), 0.773 (1), 0.7729 (1), 0.7716
(1), 0.7703 (1), 0.7699 (2), 0.7685 (1), 0.7674 (1), 0.7672 (1), 0.7669 (1),
0.7669 (1), 0.7668 (1), 0.7653 (2), 0.7631 (1), 0.762 (1), 0.7618 (1), 0.7611
(1), 0.7608 (1), 0.7595 (1), 0.7584 (1), 0.7582 (1), 0.758 (1), 0.7574 (1),
0.7572 (1), 0.7547 (2), 0.7542 (1), 0.7539 (2), 0.7535 (1), 0.7525 (3), 0.7517
(1), 0.7506 (1), 0.7503 (1), 0.7485 (1), 0.7482 (1), 0.7481 (1), 0.7464 (1),
0.7462 (1), 0.745 (1), 0.7443 (1), 0.7437 (1), 0.7437 (1), 0.743 (2), 0.7418
(1), 0.7417 (1), 0.7395 (1), 0.7391 (2), 0.7374 (1), 0.7371 (1), 0.7365 (1),
0.7361 (1), 0.7358 (1), 0.7297 (1), 0.7255 (1), 0.7254 (1), 0.7219 (1), 0.7126
(1), 0.712 (1)
Best fit found:
Fit map cryosparc_P12_J19_006_volume_map.mrc z flip in map
VFlip_D614G_COVIC69_fitted.mrc using 167571 points
correlation = 0.8212, correlation about mean = 0.2814, overlap = 979.8
steps = 416, shift = 4.8, angle = 28.3 degrees
Position of cryosparc_P12_J19_006_volume_map.mrc z flip (#8) relative to
VFlip_D614G_COVIC69_fitted.mrc (#1) coordinates:
Matrix rotation and translation
0.48891617 -0.87228787 0.00865167 219.48605794
-0.87231001 -0.48881203 0.01175040 347.29340522
-0.00602068 -0.01329188 -0.99989353 305.19031514
Axis -0.86281207 0.50552424 -0.00076290
Axis point 0.00000000 239.22878436 151.00787435
Rotation angle (degrees) 179.16849393
Shift along axis -14.04281572
Found 73 fits. List window not yet implemented.
> volume #8 level 0.0844
> ~select #8
Nothing selected
> hide #!8 models
> hide #!1 models
> show #!8 models
> volume #8 level 0.04161
> show #!1 models
> hide #!8 models
> show #!5 models
> fitmap #7 inMap #1 search 100 radius 5
Found 63 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).
Correlations and times found:
0.8999 (7), 0.8983 (7), 0.8977 (8), 0.7837 (2), 0.7811 (3), 0.7803 (1), 0.7777
(3), 0.7776 (3), 0.777 (1), 0.775 (1), 0.7736 (1), 0.7735 (1), 0.772 (1),
0.7713 (1), 0.7701 (3), 0.7674 (1), 0.7652 (2), 0.7649 (1), 0.7642 (1), 0.7641
(1), 0.7639 (2), 0.7625 (1), 0.7621 (1), 0.7586 (2), 0.7585 (3), 0.7555 (1),
0.7548 (1), 0.7543 (1), 0.7543 (1), 0.7537 (1), 0.7525 (1), 0.7524 (1), 0.7515
(1), 0.7511 (3), 0.7496 (1), 0.7491 (1), 0.7488 (1), 0.7471 (1), 0.7467 (1),
0.7464 (1), 0.7461 (1), 0.7445 (1), 0.7444 (1), 0.7434 (1), 0.7433 (1), 0.7432
(1), 0.7419 (1), 0.7418 (1), 0.7407 (1), 0.7404 (1), 0.7399 (1), 0.7383 (1),
0.7376 (1), 0.736 (1), 0.7356 (1), 0.734 (1), 0.7307 (3), 0.7304 (1), 0.7283
(1), 0.7281 (1), 0.7252 (1), 0.7064 (1), 0.7026 (1)
Best fit found:
Fit map cryosparc_P12_J19_006_volume_map.mrc in map
VFlip_D614G_COVIC69_fitted.mrc using 167571 points
correlation = 0.8999, correlation about mean = 0.4526, overlap = 1314
steps = 760, shift = 58.3, angle = 46.2 degrees
Position of cryosparc_P12_J19_006_volume_map.mrc (#7) relative to
VFlip_D614G_COVIC69_fitted.mrc (#1) coordinates:
Matrix rotation and translation
-0.14471671 -0.98925281 -0.02088027 322.81174437
0.98824039 -0.14555729 0.04684186 50.31650711
-0.04937772 -0.01385590 0.99868408 44.55717343
Axis -0.03067666 0.01440262 0.99942559
Axis point 140.57474639 164.74859930 0.00000000
Rotation angle (degrees) 98.38331576
Shift along axis 35.35348193
Found 63 fits. List window not yet implemented.
> show #!7 models
> volume #7 level 0.02984
> select #7
2 models selected
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!5 models
> hide #!7 models
> volume #1 level 0.02515
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> ~select #7
Nothing selected
> hide #!8 models
> hide #!1 models
> show #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!7 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!1 models
> hide #!7 models
> volume #1 level 0.0218
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
> open 7a98
7a98 title:
SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound [more info...]
Chain information for 7a98 #9
---
Chain | Description
A B C | Spike glycoprotein
D E F | Angiotensin-converting enzyme 2
> open 7a98
7a98 title:
SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound [more info...]
Chain information for 7a98 #10
---
Chain | Description
A B C | Spike glycoprotein
D E F | Angiotensin-converting enzyme 2
> select #9
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> select #10
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #9
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> matchmaker #9 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a97, chain B (#4) with 7a98, chain A (#9), sequence alignment
score = 5916.9
RMSD between 1035 pruned atom pairs is 0.792 angstroms; (across all 1066
pairs: 0.926)
> matchmaker #10 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a97, chain B (#4) with 7a98, chain A (#10), sequence alignment
score = 5916.9
RMSD between 1035 pruned atom pairs is 0.792 angstroms; (across all 1066
pairs: 0.926)
> hide #!5 models
> show #!5 models
> matchmaker #10 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a98, chain A (#5) with 7a98, chain A (#10), sequence alignment
score = 6263.7
RMSD between 1066 pruned atom pairs is 0.000 angstroms; (across all 1066
pairs: 0.000)
> matchmaker #9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7a98, chain A (#5) with 7a98, chain A (#9), sequence alignment
score = 6263.7
RMSD between 1066 pruned atom pairs is 0.000 angstroms; (across all 1066
pairs: 0.000)
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> select #9/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> hide #!5 models
> hide #!1 models
> select #9/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> select #9
39435 atoms, 40470 bonds, 18 pseudobonds, 4962 residues, 2 models selected
> ~select #9
Nothing selected
> hide #!9 models
> hide #!10 models
> show #!9 models
> select #9/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> show #!10 models
> hide #!9 models
> select #10/A
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/B
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/C
8344 atoms, 8552 bonds, 5 pseudobonds, 1066 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> show #!8 models
> hide #!8 models
> show #!1 models
> volume #8 level 0.04054
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!8 models
> volume #1 level 0.01476
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> select #10/D
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color (#!10 & sel) red
> select #10/E
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color (#!10 & sel) red
> select #10/F
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> color (#!10 & sel) red
> volume #1 level 0.009733
> show #!9 models
> hide #!10 models
> select #9/D
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select #9/E
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select #9/F
4801 atoms, 4938 bonds, 1 pseudobond, 588 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> show #!10 models
> color zone #1 near #10 distance 5
> color zone #1 near #10 distance 20
> hide #!10 models
> volume #1 level 0.01476
> ui mousemode right "map eraser"
> volume erase #1 center 148.5,115.53,130.9 radius 14.345
> volume #1 level 0.008548
> color zone #1 near #10 distance 15
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
Drag select of 19 residues
> hide sel target a
> delete atoms sel
> delete bonds sel
> show #!10 models
> show #!1 models
> hide #!10 models
> select clear
> select clear
> volume #1 level 0.006131
> volume #1 level 0.01096
> save /Users/e.olmedillas/Desktop/image11.png supersample 3
> show #!10 models
> color zone #1 near #10 distance 15
> hide #!9 models
> show #!9 models
> hide #!10 models
> save /Users/e.olmedillas/Desktop/image12.png supersample 3
> save "/Users/e.olmedillas/Documents/SARS2_S 13-44-49-003/Structures
> solved/VFLIP D614G COVIC 69/VFLIP D614G WITH 3 ACE2 BOUND.cxs"
opened ChimeraX session
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,2
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 8 GB
Boot ROM Version: 1037.140.50.0.0
SMC Version (system): 2.47f3
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 2 days 1:38
Graphics/Displays:
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C981AA-042
VBIOS Version: 113-C9819A1X-009
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
SE2717H/HX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 93JWK98P0ZDS
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Apple graphics driver crash, 2019 iMac, Radeon Pro 560X graphics. Using 8 Gbytes of memory.