![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8293 closed defect (nonchimerax)
Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics
| 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: macOS-10.15.4-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [48925]
Path: /Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.4.0 (1.4.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [48925]
User ID: 501
Date/Time: 2023-01-12 14:50:39.322 +0800
OS Version: Mac OS X 10.15.4 (19E2269)
Report Version: 12
Bridge OS Version: 4.4 (17P4538)
Anonymous UUID: 7ED00352-FA9F-E401-886C-DD8264CB522A
Sleep/Wake UUID: A265A7EF-58E8-401E-BB4A-1B6FA6AC7EBB
Time Awake Since Boot: 120000 seconds
Time Since Wake: 6400 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: 0x00000813
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff69b0633a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff69bc2e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff69a1d93e raise + 26
3 libsystem_platform.dylib 0x00007fff69bb75fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff69a8d808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff50e0a0a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff50e0118f gpusGenerateCrashLog + 89
8 com.apple.driver.AppleIntelICLGraphicsGLDriver 0x00007fff25a20ac8 gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff50e026a1 gpusSubmitDataBuffers + 490
10 com.apple.driver.AppleIntelICLGraphicsGLDriver 0x00007fff24c8ee50 IntelCommandBuffer::getNew(GLDContextRec*) + 48
11 com.apple.driver.AppleIntelICLGraphicsGLDriver 0x00007fff24c8ec3c intelSubmitCommands + 171
12 com.apple.driver.AppleIntelICLGraphicsGLDriver 0x00007fff24db8d2e gldPresentFramebufferData + 120
13 GLEngine 0x00007fff3a72a8d1 glSwap_Exec + 97
14 com.apple.opengl 0x00007fff3a70c473 CGLFlushDrawable + 59
15 com.apple.AppKit 0x00007fff2d2382fa -[NSOpenGLContext flushBuffer] + 20
16 libqcocoa.dylib 0x000000012a80d313 0x12a78f000 + 516883
17 QtGui 0x000000011e0245c4 QOpenGLContext::swapBuffers(QSurface*) + 212
18 QtGui.abi3.so 0x000000011e5f744f meth_QOpenGLContext_swapBuffers(_object*, _object*) + 95
19 org.python.python 0x000000010c86a71d cfunction_call + 125
20 org.python.python 0x000000010c82b5b7 _PyObject_MakeTpCall + 359
21 org.python.python 0x000000010c903e9c call_function + 876
22 org.python.python 0x000000010c9012a2 _PyEval_EvalFrameDefault + 25554
23 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
24 org.python.python 0x000000010c82bcb1 _PyFunction_Vectorcall + 289
25 org.python.python 0x000000010c903e0c call_function + 732
26 org.python.python 0x000000010c90127e _PyEval_EvalFrameDefault + 25518
27 org.python.python 0x000000010c82bd28 function_code_fastcall + 104
28 org.python.python 0x000000010c903e0c call_function + 732
29 org.python.python 0x000000010c90127e _PyEval_EvalFrameDefault + 25518
30 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
31 org.python.python 0x000000010c82bcb1 _PyFunction_Vectorcall + 289
32 org.python.python 0x000000010c82dd6a method_vectorcall + 202
33 org.python.python 0x000000010c903e0c call_function + 732
34 org.python.python 0x000000010c9013e8 _PyEval_EvalFrameDefault + 25880
35 org.python.python 0x000000010c82bd28 function_code_fastcall + 104
36 org.python.python 0x000000010c903e0c call_function + 732
37 org.python.python 0x000000010c90127e _PyEval_EvalFrameDefault + 25518
38 org.python.python 0x000000010c82bd28 function_code_fastcall + 104
39 org.python.python 0x000000010c82ddb2 method_vectorcall + 274
40 QtCore.abi3.so 0x000000011aca5607 PyQtSlot::call(_object*, _object*) const + 39
41 QtCore.abi3.so 0x000000011aca5516 PyQtSlot::invoke(void**, _object*, void*, bool) const + 358
42 QtCore.abi3.so 0x000000011aca6445 PyQtSlotProxy::unislot(void**) + 85
43 QtCore.abi3.so 0x000000011aca63ba PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
44 QtCore 0x000000011afb79e7 0x11aefb000 + 772583
45 QtCore 0x000000011afcc4d7 QTimer::timerEvent(QTimerEvent*) + 199
46 QtCore.abi3.so 0x000000011ab94bf9 sipQTimer::timerEvent(QTimerEvent*) + 121
47 QtCore 0x000000011afafbad QObject::event(QEvent*) + 109
48 QtCore.abi3.so 0x000000011ab94a7a sipQTimer::event(QEvent*) + 186
49 QtWidgets 0x000000011d6b1067 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
50 QtWidgets 0x000000011d6b2023 QApplication::notify(QObject*, QEvent*) + 499
51 QtWidgets.abi3.so 0x000000011d1d3829 sipQApplication::notify(QObject*, QEvent*) + 233
52 QtCore 0x000000011af66dca QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
53 QtCore 0x000000011b0f2a01 QTimerInfoList::activateTimers() + 961
54 libqcocoa.dylib 0x000000012a7a7885 0x12a78f000 + 100485
55 com.apple.CoreFoundation 0x00007fff2fc10f12 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
56 com.apple.CoreFoundation 0x00007fff2fc10eb1 __CFRunLoopDoSource0 + 103
57 com.apple.CoreFoundation 0x00007fff2fc10d27 __CFRunLoopDoSources0 + 301
58 com.apple.CoreFoundation 0x00007fff2fc0f9fa __CFRunLoopRun + 927
59 com.apple.CoreFoundation 0x00007fff2fc0effe CFRunLoopRunSpecific + 462
60 com.apple.HIToolbox 0x00007fff2e842abd RunCurrentEventLoopInMode + 292
61 com.apple.HIToolbox 0x00007fff2e8427d5 ReceiveNextEventCommon + 584
62 com.apple.HIToolbox 0x00007fff2e842579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
63 com.apple.AppKit 0x00007fff2ce8dc99 _DPSNextEvent + 883
64 com.apple.AppKit 0x00007fff2ce8c4e0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
65 com.apple.AppKit 0x00007fff2ce7e1ee -[NSApplication run] + 658
66 libqcocoa.dylib 0x000000012a7a848c 0x12a78f000 + 103564
67 QtCore 0x000000011af70516 QEventLoop::exec(QFlags) + 486
68 QtCore 0x000000011af673e5 QCoreApplication::exec() + 133
69 QtWidgets.abi3.so 0x000000011d2c090a meth_QApplication_exec(_object*, _object*) + 90
70 org.python.python 0x000000010c86a71d cfunction_call + 125
71 org.python.python 0x000000010c82b5b7 _PyObject_MakeTpCall + 359
72 org.python.python 0x000000010c903e9c call_function + 876
73 org.python.python 0x000000010c9012a2 _PyEval_EvalFrameDefault + 25554
74 org.python.python 0x000000010c82bd28 function_code_fastcall + 104
75 org.python.python 0x000000010c82dd6a method_vectorcall + 202
76 org.python.python 0x000000010c903e0c call_function + 732
77 org.python.python 0x000000010c9012a2 _PyEval_EvalFrameDefault + 25554
78 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
79 org.python.python 0x000000010c82bcb1 _PyFunction_Vectorcall + 289
80 org.python.python 0x000000010c903e0c call_function + 732
81 org.python.python 0x000000010c90134b _PyEval_EvalFrameDefault + 25723
82 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
83 org.python.python 0x000000010c8fadab PyEval_EvalCode + 139
84 org.python.python 0x000000010c8f7c12 builtin_exec + 626
85 org.python.python 0x000000010c86a023 cfunction_vectorcall_FASTCALL + 195
86 org.python.python 0x000000010c903e0c call_function + 732
87 org.python.python 0x000000010c90134b _PyEval_EvalFrameDefault + 25723
88 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
89 org.python.python 0x000000010c82bcb1 _PyFunction_Vectorcall + 289
90 org.python.python 0x000000010c903e0c call_function + 732
91 org.python.python 0x000000010c90134b _PyEval_EvalFrameDefault + 25723
92 org.python.python 0x000000010c904b03 _PyEval_EvalCode + 2611
93 org.python.python 0x000000010c82bcb1 _PyFunction_Vectorcall + 289
94 org.python.python 0x000000010c96a870 pymain_run_module + 208
95 org.python.python 0x000000010c969f87 Py_RunMain + 1431
96 org.python.python 0x000000010c96a58f pymain_main + 223
97 org.python.python 0x000000010c96a49b Py_Main + 43
98 edu.ucsf.cgl.ChimeraX 0x000000010c7e4dc8 main + 120
99 libdyld.dylib 0x00007fff699becc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff69b08b96 kevent64 + 10
1 QtWebEngineCore 0x0000000122c445ca 0x11ece2000 + 66463178
2 QtWebEngineCore 0x0000000122c444c7 0x11ece2000 + 66462919
3 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
4 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
5 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
6 QtWebEngineCore 0x0000000122bca84d 0x11ece2000 + 65964109
7 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
8 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
9 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122bd6d5f 0x11ece2000 + 66014559
4 QtWebEngineCore 0x0000000122bd780c 0x11ece2000 + 66017292
5 QtWebEngineCore 0x0000000122bd737d 0x11ece2000 + 66016125
6 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff69b08b96 kevent64 + 10
1 QtWebEngineCore 0x0000000122c445ca 0x11ece2000 + 66463178
2 QtWebEngineCore 0x0000000122c444c7 0x11ece2000 + 66462919
3 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
4 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
5 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
6 QtWebEngineCore 0x0000000121b09e32 0x11ece2000 + 48397874
7 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
8 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
9 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 5:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff69b02882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69bc3425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000122c0a8bb 0x11ece2000 + 66226363
3 QtWebEngineCore 0x0000000124cdb55d 0x11ece2000 + 100635997
4 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
5 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 6:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 7:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff69b08b96 kevent64 + 10
1 QtWebEngineCore 0x0000000122c445ca 0x11ece2000 + 66463178
2 QtWebEngineCore 0x0000000122c444c7 0x11ece2000 + 66462919
3 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
4 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
5 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
6 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
7 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
8 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 9:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122b48028 0x11ece2000 + 65429544
4 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
5 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
6 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
7 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
8 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
9 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 10:: NetworkService
0 libsystem_kernel.dylib 0x00007fff69b08b96 kevent64 + 10
1 QtWebEngineCore 0x0000000122c445ca 0x11ece2000 + 66463178
2 QtWebEngineCore 0x0000000122c444c7 0x11ece2000 + 66462919
3 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
4 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
5 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
6 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
7 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
8 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122bd6d5f 0x11ece2000 + 66014559
4 QtWebEngineCore 0x0000000122bd780c 0x11ece2000 + 66017292
5 QtWebEngineCore 0x0000000122bd746d 0x11ece2000 + 66016365
6 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 14:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2fc110b5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2fc0fb82 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2fc0effe CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2d02f5b4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122c1278f 0x11ece2000 + 66258831
4 QtWebEngineCore 0x0000000122b48089 0x11ece2000 + 65429641
5 QtWebEngineCore 0x0000000122bc119c 0x11ece2000 + 65925532
6 QtWebEngineCore 0x0000000122b78ff8 0x11ece2000 + 65630200
7 QtWebEngineCore 0x0000000122be3458 0x11ece2000 + 66065496
8 QtWebEngineCore 0x0000000122be35ea 0x11ece2000 + 66065898
9 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 16:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122bd6d5f 0x11ece2000 + 66014559
4 QtWebEngineCore 0x0000000122bd753a 0x11ece2000 + 66016570
5 QtWebEngineCore 0x0000000122bd73ad 0x11ece2000 + 66016173
6 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 17:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122bd6d5f 0x11ece2000 + 66014559
4 QtWebEngineCore 0x0000000122bd780c 0x11ece2000 + 66017292
5 QtWebEngineCore 0x0000000122bd740d 0x11ece2000 + 66016269
6 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff69b02882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69bc3425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010dc5149f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff69b02882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69bc3425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010dc5149f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff69b02882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69bc3425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010dc5149f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 21:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff69affdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69b00170 mach_msg + 60
2 QtWebEngineCore 0x0000000122c129c6 0x11ece2000 + 66259398
3 QtWebEngineCore 0x0000000122bd6d5f 0x11ece2000 + 66014559
4 QtWebEngineCore 0x0000000122bd780c 0x11ece2000 + 66017292
5 QtWebEngineCore 0x0000000122bd740d 0x11ece2000 + 66016269
6 QtWebEngineCore 0x0000000122c0b4a8 0x11ece2000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69bc3109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69bbeb8b thread_start + 15
Thread 22:: Dispatch queue: NSCGSDisableUpdates
0 libsystem_kernel.dylib 0x00007fff69affe4e semaphore_timedwait_trap + 10
1 com.apple.SkyLight 0x00007fff5ec0d65a CGSUpdateManager::enable_updates_common() + 302
2 com.apple.SkyLight 0x00007fff5ec0da1e SLSReenableUpdateToken + 104
3 libdispatch.dylib 0x00007fff699646c4 _dispatch_call_block_and_release + 12
4 libdispatch.dylib 0x00007fff69965658 _dispatch_client_callout + 8
5 libdispatch.dylib 0x00007fff6996ac44 _dispatch_lane_serial_drain + 597
6 libdispatch.dylib 0x00007fff6996b5d6 _dispatch_lane_invoke + 363
7 libdispatch.dylib 0x00007fff69974c09 _dispatch_workloop_worker_thread + 596
8 libsystem_pthread.dylib 0x00007fff69bbfa3d _pthread_wqthread + 290
9 libsystem_pthread.dylib 0x00007fff69bbeb77 start_wqthread + 15
Thread 23:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 24:: Dispatch queue: com.apple.root.user-interactive-qos
0 libsystem_kernel.dylib 0x00007fff69b01516 kevent_id + 10
1 libdispatch.dylib 0x00007fff699808b9 _dispatch_kq_poll + 163
2 libdispatch.dylib 0x00007fff699813aa _dispatch_event_loop_wait_for_ownership + 476
3 libdispatch.dylib 0x00007fff69971930 __DISPATCH_WAIT_FOR_QUEUE__ + 270
4 libdispatch.dylib 0x00007fff69971593 _dispatch_sync_f_slow + 171
5 com.apple.AppKit 0x00007fff2d025c46 NSCGSDisableUpdates + 506
6 com.apple.AppKit 0x00007fff2d025962 NSCGSTransactionRunPreCommitActionsForOrder_ + 123
7 com.apple.AppKit 0x00007fff2d0258bc NSCGSTransactionRunPreCommitActions_ + 21
8 com.apple.AppKit 0x00007fff2d025893 __39+[_NSCGSTransaction currentTransaction]_block_invoke.32 + 34
9 com.apple.QuartzCore 0x00007fff3b6cf454 CA::Transaction::run_commit_handlers(CATransactionPhase) + 106
10 com.apple.QuartzCore 0x00007fff3b6cfda6 CA::Context::commit_transaction(CA::Transaction*, double) + 2014
11 com.apple.QuartzCore 0x00007fff3b6ce304 CA::Transaction::commit() + 644
12 com.apple.AppKit 0x00007fff2cee5fe4 NSPerformVisuallyAtomicChange + 154
13 com.apple.AppKit 0x00007fff2d134e87 -[NSAnimation(NSInternal) _advanceTimeWithDisplayLink:] + 172
14 com.apple.AppKit 0x00007fff2d092a94 -[NSScreenDisplayLink _fire] + 180
15 com.apple.AppKit 0x00007fff2d7dfd62 ___NSRunLoopTimerCreateWithHandler_block_invoke + 34
16 com.apple.CoreFoundation 0x00007fff2fc2b9b9 __CFRUNLOOP_IS_CALLING_OUT_TO_A_TIMER_CALLBACK_FUNCTION__ + 20
17 com.apple.CoreFoundation 0x00007fff2fc2b51f __CFRunLoopDoTimer + 859
18 com.apple.CoreFoundation 0x00007fff2fc2b007 __CFRunLoopDoTimers + 322
19 com.apple.CoreFoundation 0x00007fff2fc0fdaa __CFRunLoopRun + 1871
20 com.apple.CoreFoundation 0x00007fff2fc0effe CFRunLoopRunSpecific + 462
21 com.apple.Foundation 0x00007fff322a32a8 -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212
22 com.apple.AppKit 0x00007fff2d134da0 -[NSAnimation(NSInternal) _runBlocking] + 344
23 com.apple.AppKit 0x00007fff2d134a7d __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 97
24 libdispatch.dylib 0x00007fff699646c4 _dispatch_call_block_and_release + 12
25 libdispatch.dylib 0x00007fff69965658 _dispatch_client_callout + 8
26 libdispatch.dylib 0x00007fff69973aa8 _dispatch_root_queue_drain + 663
27 libdispatch.dylib 0x00007fff69974097 _dispatch_worker_thread2 + 92
28 libsystem_pthread.dylib 0x00007fff69bbf9f7 _pthread_wqthread + 220
29 libsystem_pthread.dylib 0x00007fff69bbeb77 start_wqthread + 15
Thread 25:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 27:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 28:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 29:
0 libsystem_pthread.dylib 0x00007fff69bbeb68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011409ddc0 rcx: 0x000000010cd08418 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x000000010cd08440 rsp: 0x000000010cd08418
r8: 0x000000010cd08f48 r9: 0x95ee2b68ba34e324 r10: 0x000000011409ddc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000130ff43c8 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff69b0633a rfl: 0x0000000000000246 cr2: 0x000000010cd078c0
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x11d096000 - 0x11d345fff +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtWidgets.abi3.so
0x11d6a3000 - 0x11db66fff +QtWidgets (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtWidgets.framework/Versions/A/QtWidgets
0x11dcc1000 - 0x11e340fe7 +QtGui (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/Qt6/lib/QtGui.framework/Versions/A/QtGui
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0x11e51c000 - 0x11e683ff3 +QtGui.abi3.so (0) /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtGui.abi3.so
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0x7fff5706d000 - 0x7fff57089ff0 com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x7fff57718000 - 0x7fff5771affe com.apple.OAuth (25 - 25) /System/Library/PrivateFrameworks/OAuth.framework/Versions/A/OAuth
0x7fff579b6000 - 0x7fff57a01ffb com.apple.OTSVG (1.0 - 643.1.4.4) /System/Library/PrivateFrameworks/OTSVG.framework/Versions/A/OTSVG
0x7fff58c09000 - 0x7fff58c14ff2 com.apple.PerformanceAnalysis (1.243.2 - 243.2) /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
0x7fff58c15000 - 0x7fff58c3dffb com.apple.persistentconnection (1.0 - 1.0) /System/Library/PrivateFrameworks/PersistentConnection.framework/Versions/A/PersistentConnection
0x7fff58c3e000 - 0x7fff58c4cffe com.apple.PersonaKit (1.0 - 1) /System/Library/PrivateFrameworks/PersonaKit.framework/Versions/A/PersonaKit
0x7fff58df6000 - 0x7fff58df6ffa com.apple.PhoneNumbers (1.0 - 1) /System/Library/PrivateFrameworks/PhoneNumbers.framework/Versions/A/PhoneNumbers
0x7fff5a6b6000 - 0x7fff5a6e6ff7 com.apple.pluginkit.framework (1.0 - 1) /System/Library/PrivateFrameworks/PlugInKit.framework/Versions/A/PlugInKit
0x7fff5a711000 - 0x7fff5a724ffc com.apple.PowerLog (1.0 - 1) /System/Library/PrivateFrameworks/PowerLog.framework/Versions/A/PowerLog
0x7fff5b3aa000 - 0x7fff5b3caff1 com.apple.proactive.support.ProactiveEventTracker (1.0 - 258.5) /System/Library/PrivateFrameworks/ProactiveEventTracker.framework/Versions/A/ProactiveEventTracker
0x7fff5b451000 - 0x7fff5b4baff2 com.apple.proactive.support.ProactiveSupport (1.0 - 258.5) /System/Library/PrivateFrameworks/ProactiveSupport.framework/Versions/A/ProactiveSupport
0x7fff5b5a0000 - 0x7fff5b5faff6 com.apple.ProtectedCloudStorage (1.0 - 1) /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
0x7fff5b5fb000 - 0x7fff5b614ffb com.apple.ProtocolBuffer (1 - 274.24.9.16.3) /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
0x7fff5b64e000 - 0x7fff5b6cbfff com.apple.Quagga (1.0 - 1) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga
0x7fff5b726000 - 0x7fff5b729ff4 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff5b72a000 - 0x7fff5b74dff0 com.apple.quicklook.QuickLookSupport (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x7fff5b794000 - 0x7fff5b80dff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff5ba73000 - 0x7fff5ba9cff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x7fff5bb20000 - 0x7fff5bb6affa com.apple.ResponseKit (1.0 - 148.2) /System/Library/PrivateFrameworks/ResponseKit.framework/Versions/A/ResponseKit
0x7fff5bc01000 - 0x7fff5bc3cff0 com.apple.RunningBoardServices (1.0 - 223.100.31) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff5d519000 - 0x7fff5d51cff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff5d68f000 - 0x7fff5d7b6ff1 com.apple.Sharing (1526.14 - 1526.14) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff5d80f000 - 0x7fff5d82dff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff5d82e000 - 0x7fff5d84eff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff5d84f000 - 0x7fff5d861ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff5ebc9000 - 0x7fff5eebffff com.apple.SkyLight (1.600.0 - 450.9) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff5f70c000 - 0x7fff5f71affb com.apple.SpeechRecognitionCore (6.0.91 - 6.0.91) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff5f7dc000 - 0x7fff5fa66ffe com.apple.spotlight.index (10.7.0 - 2076.3) /System/Library/PrivateFrameworks/SpotlightIndex.framework/Versions/A/SpotlightIndex
0x7fff5fdf4000 - 0x7fff5fe35ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff5ff4c000 - 0x7fff5ff55ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.100.26) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff5ffc6000 - 0x7fff5fff0ffc com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff6020b000 - 0x7fff6021bff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff605c1000 - 0x7fff6071cff5 com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff6073e000 - 0x7fff60804ff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff6098c000 - 0x7fff6098dfff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff609c5000 - 0x7fff60c1dff0 com.apple.UIFoundation (1.0 - 661.2) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff60cb4000 - 0x7fff60cbaffe com.apple.URLFormatting (119 - 119.17) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff61890000 - 0x7fff618b0ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff6265c000 - 0x7fff62746ff8 com.apple.ViewBridge (464.1 - 464.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff628ec000 - 0x7fff628edfff com.apple.WatchdogClient.framework (1.0 - 67.101.1) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff62c78000 - 0x7fff62cb3fff libAWDSupport.dylib (949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupport.dylib
0x7fff62cb4000 - 0x7fff62f94ff7 libAWDSupportFramework.dylib (3541) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupportFramework.dylib
0x7fff62f95000 - 0x7fff62fa6fff libprotobuf-lite.dylib (3541) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf-lite.dylib
0x7fff62fa7000 - 0x7fff63000ffb libprotobuf.dylib (3541) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf.dylib
0x7fff63001000 - 0x7fff63045ff6 com.apple.awd (1.0 - 949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/WirelessDiagnostics
0x7fff63519000 - 0x7fff6351cffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff63596000 - 0x7fff635a4ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff6376c000 - 0x7fff637a1ffe com.apple.iCalendar (7.0 - 810.4.1) /System/Library/PrivateFrameworks/iCalendar.framework/Versions/A/iCalendar
0x7fff638e6000 - 0x7fff638e8ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff638e9000 - 0x7fff638fcffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff6392e000 - 0x7fff6393affd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff6393b000 - 0x7fff6396cffd com.apple.contacts.vCard (1.0 - 3455.17) /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
0x7fff663ba000 - 0x7fff663c6ff9 libAudioStatistics.dylib (1104.80) /usr/lib/libAudioStatistics.dylib
0x7fff663c7000 - 0x7fff663faffa libAudioToolboxUtility.dylib (1104.80) /usr/lib/libAudioToolboxUtility.dylib
0x7fff66401000 - 0x7fff66435fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff66438000 - 0x7fff66442fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff66443000 - 0x7fff664cbfff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib
0x7fff664ce000 - 0x7fff664d0ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff66516000 - 0x7fff666cdffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff666f4000 - 0x7fff666faff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff667dc000 - 0x7fff667e3fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff66812000 - 0x7fff66832fff libMobileGestalt.dylib (826.100.27) /usr/lib/libMobileGestalt.dylib
0x7fff668b2000 - 0x7fff6698fff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff669a4000 - 0x7fff669a5fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff669a6000 - 0x7fff66a31ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff66a32000 - 0x7fff66a33fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff66a4b000 - 0x7fff66a61fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff66a96000 - 0x7fff66b08ff7 libarchive.2.dylib (72.100.1) /usr/lib/libarchive.2.dylib
0x7fff66b09000 - 0x7fff66ba2fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff66ba6000 - 0x7fff66ba6ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff66ba7000 - 0x7fff66c6bffe libboringssl.dylib (283.101.1) /usr/lib/libboringssl.dylib
0x7fff66c6c000 - 0x7fff66c7cffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff66c7d000 - 0x7fff66c89fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff66c8a000 - 0x7fff66cdcfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff66cdd000 - 0x7fff66cf2ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff66cf3000 - 0x7fff66cf3fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff66cf4000 - 0x7fff66d05fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff66d06000 - 0x7fff66d1dfd7 libcompression.dylib (87) /usr/lib/libcompression.dylib
0x7fff66ff7000 - 0x7fff6700dff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6700e000 - 0x7fff6700ffff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff674b2000 - 0x7fff675b6fef libcrypto.44.dylib (47.100.4) /usr/lib/libcrypto.44.dylib
0x7fff675b9000 - 0x7fff675c4fff libcsfde.dylib (551) /usr/lib/libcsfde.dylib
0x7fff675cc000 - 0x7fff6762bff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib
0x7fff6762d000 - 0x7fff67694ff7 libcurl.4.dylib (118.100.2) /usr/lib/libcurl.4.dylib
0x7fff67737000 - 0x7fff67737fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff67738000 - 0x7fff67750fff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib
0x7fff67751000 - 0x7fff6775dffb libexslt.0.dylib (16.9) /usr/lib/libexslt.0.dylib
0x7fff6775e000 - 0x7fff67760fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff67761000 - 0x7fff67766f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff6776f000 - 0x7fff67774fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff67775000 - 0x7fff6777eff7 libheimdal-asn1.dylib (564.100.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6777f000 - 0x7fff6786ffff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff67870000 - 0x7fff67ac7fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff67ae1000 - 0x7fff67ae2fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff67ae3000 - 0x7fff67afbff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff67b13000 - 0x7fff67bbaff7 libmecab.dylib (883.10) /usr/lib/libmecab.dylib
0x7fff67bbb000 - 0x7fff67e1dfe1 libmecabra.dylib (883.10) /usr/lib/libmecabra.dylib
0x7fff6818a000 - 0x7fff681b9fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff682e9000 - 0x7fff68764ff5 libnetwork.dylib (1880.100.30) /usr/lib/libnetwork.dylib
0x7fff68765000 - 0x7fff6877cfff libnetworkextension.dylib (1095.100.29) /usr/lib/libnetworkextension.dylib
0x7fff68804000 - 0x7fff68837fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff68838000 - 0x7fff68839ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6884a000 - 0x7fff6884efff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff68851000 - 0x7fff68887ff7 libpcap.A.dylib (89.100.1) /usr/lib/libpcap.A.dylib
0x7fff688c7000 - 0x7fff688d5ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff688d6000 - 0x7fff688d9ff3 libpmenergy.dylib (214.100.2) /usr/lib/libpmenergy.dylib
0x7fff688da000 - 0x7fff688dcfff libpmsample.dylib (214.100.2) /usr/lib/libpmsample.dylib
0x7fff6890b000 - 0x7fff68923fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff68925000 - 0x7fff68969ff7 libsandbox.1.dylib (1217.101.2) /usr/lib/libsandbox.1.dylib
0x7fff6896a000 - 0x7fff6897cff7 libsasl2.2.dylib (213) /usr/lib/libsasl2.2.dylib
0x7fff6897d000 - 0x7fff6897eff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6897f000 - 0x7fff68b69ff7 libsqlite3.dylib (308.4) /usr/lib/libsqlite3.dylib
0x7fff68c5d000 - 0x7fff68c8affb libssl.46.dylib (47.100.4) /usr/lib/libssl.46.dylib
0x7fff68d0c000 - 0x7fff68d3dff7 libtidy.A.dylib (17.1) /usr/lib/libtidy.A.dylib
0x7fff68d5f000 - 0x7fff68db9ff8 libusrtcp.dylib (1880.100.30) /usr/lib/libusrtcp.dylib
0x7fff68dba000 - 0x7fff68dbdffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff68dbe000 - 0x7fff68dcbff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff68dd1000 - 0x7fff68eb3ff7 libxml2.2.dylib (33.3) /usr/lib/libxml2.2.dylib
0x7fff68eb7000 - 0x7fff68edffff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff68ee0000 - 0x7fff68ef2ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff697a0000 - 0x7fff697a5ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff697a6000 - 0x7fff697b1fff libcommonCrypto.dylib (60165) /usr/lib/system/libcommonCrypto.dylib
0x7fff697b2000 - 0x7fff697b9fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff697ba000 - 0x7fff697c3ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff697c4000 - 0x7fff69856fe3 libcorecrypto.dylib (866.100.30) /usr/lib/system/libcorecrypto.dylib
0x7fff69963000 - 0x7fff699a3ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff699a4000 - 0x7fff699dafff libdyld.dylib (750.5) /usr/lib/system/libdyld.dylib
0x7fff699db000 - 0x7fff699dbffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff699dc000 - 0x7fff699e8ff3 libkxld.dylib (6153.101.6) /usr/lib/system/libkxld.dylib
0x7fff699e9000 - 0x7fff699e9ff7 liblaunch.dylib (1738.100.39) /usr/lib/system/liblaunch.dylib
0x7fff699ea000 - 0x7fff699efff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff699f0000 - 0x7fff699f2ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff699f3000 - 0x7fff699f4ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff699f5000 - 0x7fff69a0cff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff69a0d000 - 0x7fff69a0dff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff69a0e000 - 0x7fff69a95fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff69a96000 - 0x7fff69a99ffb libsystem_configuration.dylib (1061.101.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff69a9a000 - 0x7fff69a9dfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff69a9e000 - 0x7fff69aa6fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff69aa7000 - 0x7fff69aaefff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff69aaf000 - 0x7fff69ab0ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff69ab1000 - 0x7fff69afeff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff69aff000 - 0x7fff69b2bff7 libsystem_kernel.dylib (6153.101.6) /usr/lib/system/libsystem_kernel.dylib
0x7fff69b2c000 - 0x7fff69b73fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff69b74000 - 0x7fff69b9bfff libsystem_malloc.dylib (283.100.5) /usr/lib/system/libsystem_malloc.dylib
0x7fff69b9c000 - 0x7fff69ba9ffb libsystem_networkextension.dylib (1095.100.29) /usr/lib/system/libsystem_networkextension.dylib
0x7fff69baa000 - 0x7fff69bb3ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff69bb4000 - 0x7fff69bbcfef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff69bbd000 - 0x7fff69bc7fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff69bc8000 - 0x7fff69bccff3 libsystem_sandbox.dylib (1217.101.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff69bcd000 - 0x7fff69bcffff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff69bd0000 - 0x7fff69bd7ffb libsystem_symptoms.dylib (1238.100.26) /usr/lib/system/libsystem_symptoms.dylib
0x7fff69bd8000 - 0x7fff69beeff2 libsystem_trace.dylib (1147.100.8) /usr/lib/system/libsystem_trace.dylib
0x7fff69bf0000 - 0x7fff69bf5ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff69bf6000 - 0x7fff69c2bffe libxpc.dylib (1738.100.39) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 7
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: 96545
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 4
Activity Tracing 256K 1
CG backing stores 992K 2
CG image 240K 18
CoreAnimation 1400K 15
CoreGraphics 8K 1
CoreImage 28K 3
CoreUI image data 3032K 25
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 1.4G 1024
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
Memory Tag 242 12K 1
OpenGL GLSL 256K 3
STACK GUARD 116K 29
Stack 150.2M 30
Stack Guard 56.0M 1
VM_ALLOCATE 198.7M 185
__DATA 64.0M 605
__DATA_CONST 124K 7
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 419.2M 179
__OBJC_RO 32.2M 1
__OBJC_RW 1892K 2
__TEXT 617.3M 574
__UNICODE 564K 1
mapped file 397.3M 57
shared memory 2840K 23
=========== ======= =======
TOTAL 3.5G 2807
TOTAL, minus reserved VM space 3.3G 2807
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4 Supple
> figure7/D1-Legobody beita1AR 20230112.cxs"
Log from Tue Sep 27 22:27:02 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
Log from Tue Sep 27 18:04:18 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
Log from Mon Sep 26 23:14:01 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/interface beita2AR.cxs"
Log from Mon Sep 26 16:53:06 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/G A NB的副本.cxs"
Log from Mon Sep 26 14:28:39 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
Log from Mon Sep 26 12:32:47 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody LSd.cxs"
Log from Sun Sep 18 21:06:55 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure2/D1-Legobody LSd.cxs"
Log from Sun Sep 18 20:47:23 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alicefan/Desktop/paper/figure/figure2/D1-Legobody LSd.cxs"
Log from Sun Sep 18 20:26:22 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/alicefan/Desktop/20220523/20220627-D1-LSD-coot-1.pdb
Chain information for 20220627-D1-LSD-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> style stick
Changed 8611 atom styles
> show cartoons
> set bgColor white
> hide atoms
> color bychain
> hide #1.1 models
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> cartoon style width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> cartoon style #!1 xsection oval modeHelix default
> cartoon style #!1 xsection rectangle modeHelix default
> cartoon style (#!1 & coil) xsection oval
> cartoon style #!1 xsection barbell modeHelix default
> cartoon style #!1 modeHelix tube sides 20
> cartoon style #!1 xsection oval modeHelix default
> cartoon style strand xsection rectangle width 1.5
> cartoon style width 1.2 thickness 0.2
> cartoon style width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.6
> cartoon style helix width 1.5 thickness 0.6
> cartoon style strand xsection rectangle width 1.5
> cartoon style helix width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.6
> cartoon style helix width 1.3 thickness 0.6
> cartoon style width 1.2 thickness 0.4
> cartoon style width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.6
> cartoon style helix width 1.3 thickness 0.6
> cartoon style strand xsection rectangle width 1.3
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> show atoms
> hide atoms
> show atoms
> select /A:401@C6
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 24 atom styles
> undo
> style sel ball
Changed 24 atom styles
> hide sel atoms
> undo
> select clear
> hide atoms
> show atoms
> hide atoms
> show ligand
> select /A:401@C14
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> color sel byhetero
> style sel sphere
Changed 24 atom styles
> undo
> select clear
> save "/Users/alicefan/Desktop/paper/figure/D1-Legobody LSd.cxs"
——— End of log from Sun Sep 18 20:26:22 2022 ———
opened ChimeraX session
> show color
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color name
Missing or invalid "name" argument: Expected a text string
> color name chainA
Missing or invalid "color" argument: Missing color name or specifier
> color name chain A
Missing or invalid "color" argument: Invalid color name or specifier
> color name chain #1
Missing or invalid "color" argument: Color constant should have 3 (4), 6 (8),
or 12 (16) hexadecimal digits
> select /A
2165 atoms, 2224 bonds, 3 pseudobonds, 271 residues, 2 models selected
> color name
Missing or invalid "name" argument: Expected a text string
> color name
Missing or invalid "name" argument: Expected a text string
> color show cname
Unknown color 'cname'
> color (#!1 & sel) #83ffffff
> color (#!1 & sel) #8338ffff
> color (#!1 & sel) #8338ecff
> select clear
> undo
[Repeated 4 time(s)]
> color show
Illegal color name: ""
> color show
Illegal color name: ""
> color show
Illegal color name: ""
> color show #1
Illegal color name: "#1"
> color show target cartoon
Unknown color 'target cartoon'
> color show target c
Unknown color 'target c'
> color show target #1
Unknown color 'target #1'
> color (#!1 & sel) #8338ecff
> select clear
> select /B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color sel #e738ecff
> color sel #e7c6ecff
> color sel #e7c6ffff
[Repeated 1 time(s)]
> select clear
> select /B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color sel #ffc6ffff
> color sel #ffd6ffff
[Repeated 2 time(s)]
> select clear
[Repeated 1 time(s)]
> select /A
2165 atoms, 2224 bonds, 3 pseudobonds, 271 residues, 2 models selected
> color (#!1 & sel) #86d6ffff
> color (#!1 & sel) #8671ffff
> color (#!1 & sel) #8671e1ff
> select clear
> select /B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color sel #ff71e1ff
> color sel #ffc8e1ff
[Repeated 1 time(s)]
> select clear
> select /C
2672 atoms, 2735 bonds, 7 pseudobonds, 343 residues, 2 models selected
> color (#!1 & sel) #84c8e1ff
> color (#!1 & sel) #848ce1ff
> color (#!1 & sel) #848ca9ff
> color (#!1 & sel) #84a9a9ff
> color (#!1 & sel) #84a98cff
> select clear
> select /C
2672 atoms, 2735 bonds, 7 pseudobonds, 343 residues, 2 models selected
> select clear
> select /H
1536 atoms, 1576 bonds, 2 pseudobonds, 202 residues, 2 models selected
> select clear
> select /H
1536 atoms, 1576 bonds, 2 pseudobonds, 202 residues, 2 models selected
> color (#!1 & sel) #6ca98cff
> color (#!1 & sel) #6c758cff
> color (#!1 & sel) #6c757dff
[Repeated 1 time(s)]
> select clear
> select /L
1309 atoms, 1338 bonds, 1 pseudobond, 171 residues, 2 models selected
> color (#!1 & sel) #f7757dff
> color (#!1 & sel) #f7257dff
> color (#!1 & sel) #f72585ff
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> select /A:401@N3
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> color sel #3a2585ff
> color sel #3a0c85ff
> color sel #3a0ca3ff
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> save "/Users/alicefan/Desktop/paper/figure/figure2/D1-Legobody LSd.cxs"
——— End of log from Sun Sep 18 20:47:23 2022 ———
opened ChimeraX session
> select /A:401@N3
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> color sel #e5ffffff
> color sel #e500ffff
> color sel #e500a4ff
> select clear
> select /A:401@C19
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> select /A:401@N3
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 27 bonds, 1 residue, 1 model selected
> style sel ball
Changed 24 atom styles
> style sel ball
Changed 24 atom styles
> style sel sphere
Changed 24 atom styles
> size ligand atomRadius 0.5
Changed 47 atom radii
> size ligand atomRadius 0.1
Changed 47 atom radii
> size ligand atomRadius 1
Changed 47 atom radii
> size ligand atomRadius 1.5
Changed 47 atom radii
> select clear
> size ligand atomRadius 1.2
Changed 47 atom radii
> save "/Users/alicefan/Desktop/paper/figure/figure2/D1 legobody LSD
> transparent.png" width 621 height 599 supersample 3 transparentBackground
> true
> save "/Users/alicefan/Desktop/paper/figure/figure2/D1 legobody LSD.png"
> width 621 height 599 supersample 3
> cartoon style width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> select /B:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:53
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:336
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:121
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add /A:121
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add /B:106@CA
20 atoms, 17 bonds, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add /A:57@CA
28 atoms, 25 bonds, 4 residues, 1 model selected
> select up
36 atoms, 33 bonds, 4 residues, 1 model selected
> select add /A:336
44 atoms, 40 bonds, 5 residues, 1 model selected
> select add /A:53
54 atoms, 50 bonds, 6 residues, 1 model selected
> color sel byhetero
> select clear
Drag select of 2 residues
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> cartoon suppressBackboneDisplay false
> select /A:120@OD2
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select /A:121@NH1
1 atom, 1 residue, 1 model selected
> select add /A:120@OD2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance /A:121@NH1 /A:120@OD2
Distance between /A ARG 121 NH1 and ASP 120 OD2: 4.892Å
> select clear
> hide distance
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide distance
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show Distances
> distance style symbol false
[Repeated 2 time(s)]
> ui tool show Distances
> distance style symbol true
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style color gold
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]Must select one or more distances in the table
> distance style color gold
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> save "/Users/alicefan/Desktop/paper/figure/figure2/D1-Legobody LSd.cxs"
——— End of log from Sun Sep 18 21:06:55 2022 ———
opened ChimeraX session
> hide #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> open 6TKO
6tko title:
Phosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled
to arrestin-2 in lipid nanodisc. [more info...]
Chain information for 6tko #3
---
Chain | Description | UniProt
A | Beta-1 adrenergic receptor | ADRB1_MELGA
B | Beta-arrestin-1 | ARRB1_HUMAN
H | Fab30 heavy chain |
L | Fab30 light chain |
Non-standard residues in 6tko #3
---
H98 —
~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-
ethyl]-2-oxidanyl-phenyl]methanamide
> hide #!3 models
> hide #!1 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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 20220627-D1-LSD-coot-1.pdb, chain A (#1) with 6tko, chain A (#3),
sequence alignment score = 818
RMSD between 221 pruned atom pairs is 0.876 angstroms; (across all 256 pairs:
1.928)
> show #!1 models
> hide #!1 models
> show #!1 models
> rename #3 "beita1A ARRB1"
> open 7JJO
7jjo title:
Structural Basis of the Activation of Heterotrimeric Gs-protein by
Isoproterenol-bound Beta1-Adrenergic Receptor [more info...]
Chain information for 7jjo #4
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short |
GNAS2_BOVIN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_BOVIN
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_BOVIN
N | Nanobody 35 |
R | Beta1-Adrenergic Receptor |
Non-standard residues in 7jjo #4
---
5FW — isoprenaline
> ui tool show Matchmaker
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!3-4 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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 20220627-D1-LSD-coot-1.pdb, chain A (#1) with beita1A ARRB1, chain
A (#3), sequence alignment score = 818
RMSD between 221 pruned atom pairs is 0.876 angstroms; (across all 256 pairs:
1.928)
Matchmaker 20220627-D1-LSD-coot-1.pdb, chain A (#1) with 7jjo, chain R (#4),
sequence alignment score = 826.4
RMSD between 240 pruned atom pairs is 0.817 angstroms; (across all 262 pairs:
1.580)
> hide #!4 models
> hide #!1 models
> show #!4 models
> style #!4 stick
Changed 15658 atom styles
> show #!4 cartoons
> hide #!4 atoms
> rename #4 "beita1A Gs"
> show #!3 models
> show #!1 models
> hide atoms
> cartoon style width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> hide #3.1 models
> hide #4.1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!3 models
> color #!3 bychain
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
beita1A ARRB1 #3/B LYS 17
beita1A ARRB1 #3/B LYS 49
beita1A ARRB1 #3/B GLU 92
beita1A ARRB1 #3/B GLU 134
beita1A ARRB1 #3/B HIS 159
beita1A ARRB1 #3/B LEU 191
beita1A ARRB1 #3/B MET 192
beita1A ARRB1 #3/B SER 193
beita1A ARRB1 #3/B ASP 194
beita1A ARRB1 #3/B ASN 311
beita1A ARRB1 #3/B SER 341
beita1A ARRB1 #3/B LYS 357
beita1A ARRB1 #3/B GLU 358
beita1A ARRB1 #3/B GLU 359
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp8w0fykey/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp8w0fykey/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp8w0fykey/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HIS) ``
Charges for residue HIS determined
Coulombic values for beita1A ARRB1_B SES surface #3.2: minimum, -21.16, mean
-0.57, maximum 21.74
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
> select clear
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> transparency #3 50 target c
> select clear
> transparency #3 80 target c
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> show #!4 models
> hide #!3 models
> select #4/A
3310 atoms, 3340 bonds, 5 pseudobonds, 200 residues, 2 models selected
> color sel bychain
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
beita1A Gs #4/A GLU 15
beita1A Gs #4/A GLU 16
beita1A Gs #4/A LYS 17
beita1A Gs #4/A ARG 20
beita1A Gs #4/A GLU 21
beita1A Gs #4/A LYS 24
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for beita1A Gs_A SES surface #4.2: minimum, -10.54, mean
1.98, maximum 16.88
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!1 models
> hide sel surfaces
> color (#!4 & sel) lime
> select clear
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> select ~sel
27903 atoms, 28409 bonds, 25 pseudobonds, 2887 residues, 8 models selected
> color (#!4 & sel) lime
> select clear
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!4 models
> hide #!3 surfaces
> hide #!3 models
> show #!3 models
> show #!1 models
> show #!4 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel rosy brown
> color sel burly wood
> color sel tan
[Repeated 1 time(s)]
> color sel rosy brown
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel light coral
> color sel rosy brown
> color sel peru
> color sel rosy brown
> color sel olive
> color sel rosy brown
> color sel tan
> color sel rosy brown
> color (#!4 & sel) #bcffffff
> color (#!4 & sel) #bc8fffff
> color (#!4 & sel) #bc8f8fff
> select clear
> hide #!4 models
> show #!4 models
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> select ~sel
27903 atoms, 28409 bonds, 25 pseudobonds, 2887 residues, 8 models selected
> color (#!4 & sel) #7a8f8fff
> color (#!4 & sel) #7ab28fff
> color (#!4 & sel) #7ab226ff
> select clear
> hide #!4 models
> show #!4 models
> show #!3 models
> transparency #4 80 target c
> select clear
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!3 models
> show #!1 models
> transparency #1 80 target c
> hide #!3 models
> show #!4 models
> transparency #1 50 target c
> transparency #4 50 target c
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!3 & sel) #f3b226ff
> color (#!3 & sel) #f3a426ff
> color (#!3 & sel) #f3a459ff
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> select ~sel
30088 atoms, 30594 bonds, 24 pseudobonds, 2873 residues, 8 models selected
> show #!4 models
> show #!1 models
> select subtract #2
30088 atoms, 30594 bonds, 23 pseudobonds, 2873 residues, 8 models selected
> select add #2.1
30088 atoms, 30594 bonds, 23 pseudobonds, 2873 residues, 9 models selected
> select subtract #2.1
30088 atoms, 30594 bonds, 23 pseudobonds, 2873 residues, 8 models selected
> hide #!1 models
> hide #!3 models
> select subtract #1
21477 atoms, 21775 bonds, 10 pseudobonds, 1762 residues, 6 models selected
> select add #3
23743 atoms, 24098 bonds, 12 pseudobonds, 2056 residues, 6 models selected
> select subtract #3
15658 atoms, 15820 bonds, 6 pseudobonds, 1003 residues, 4 models selected
> select clear
> hide #!4 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select ~sel
30088 atoms, 30594 bonds, 24 pseudobonds, 2873 residues, 8 models selected
> color (#!3 & sel) #0ba459ff
> color (#!3 & sel) #0bbb59ff
> color (#!3 & sel) #0bbb57ff
> select clear
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select ~sel
30088 atoms, 30594 bonds, 24 pseudobonds, 2873 residues, 8 models selected
> color (#!3 & sel) #0bbbbbff
> select clear
> transparency #3 50 target c
> transparency #3 80 target c
> show #!4 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> select ~sel
29670 atoms, 30176 bonds, 25 pseudobonds, 2823 residues, 8 models selected
> select subtract #1
21059 atoms, 21357 bonds, 11 pseudobonds, 1712 residues, 6 models selected
> select add #2
21059 atoms, 21357 bonds, 12 pseudobonds, 1712 residues, 7 models selected
> select subtract #2.1
21059 atoms, 21357 bonds, 12 pseudobonds, 1712 residues, 6 models selected
> select add #2
21059 atoms, 21357 bonds, 12 pseudobonds, 1712 residues, 7 models selected
> select subtract #2
21059 atoms, 21357 bonds, 11 pseudobonds, 1712 residues, 5 models selected
> select add #2.1
21059 atoms, 21357 bonds, 11 pseudobonds, 1712 residues, 6 models selected
> select subtract #2.1
21059 atoms, 21357 bonds, 11 pseudobonds, 1712 residues, 5 models selected
> select subtract #4
5401 atoms, 5537 bonds, 5 pseudobonds, 709 residues, 3 models selected
> select clear
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> select clear
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select ~sel
30088 atoms, 30594 bonds, 24 pseudobonds, 2873 residues, 8 models selected
> color (#!3 & sel) #4ebbbbff
> color (#!3 & sel) #4e80bbff
> color (#!3 & sel) #4e807aff
> color (#!3 & sel) #0b807aff
> color (#!3 & sel) #0bbb7aff
> color (#!3 & sel) #0bbbbbff
> select clear
> hide #!3 models
> show #!1 models
> show #!3 models
> show #!4 models
> transparency #1 80 target c
> transparency #4 80 target c
> transparency #3 80 target c
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!1 models
> show #!1 models
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting simple
> graphics silhouettes false
> lighting full
[Repeated 3 time(s)]
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> save "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody beita1AR.cxs"
——— End of log from Mon Sep 26 12:32:47 2022 ———
opened ChimeraX session
> ui tool show Registration
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> select #1/B
929 atoms, 946 bonds, 124 residues, 1 model selected
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> select #1/C
2672 atoms, 2735 bonds, 7 pseudobonds, 343 residues, 2 models selected
> hide sel cartoons
> select #1/L
1309 atoms, 1338 bonds, 1 pseudobond, 171 residues, 2 models selected
> hide sel cartoons
> select #1/H
1536 atoms, 1576 bonds, 2 pseudobonds, 202 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> show #!3 models
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> select #3/H
1529 atoms, 1572 bonds, 2 pseudobonds, 204 residues, 2 models selected
> hide sel cartoons
> select #3/L
1606 atoms, 1642 bonds, 1 pseudobond, 211 residues, 2 models selected
> hide sel cartoons
> hide #!3 models
> show #!4 models
> select #4/B
5106 atoms, 5153 bonds, 338 residues, 1 model selected
> hide sel cartoons
> select #4/A
3310 atoms, 3340 bonds, 5 pseudobonds, 200 residues, 2 models selected
> select #4/G
882 atoms, 888 bonds, 57 residues, 1 model selected
> hide sel cartoons
> select #4/G
882 atoms, 888 bonds, 57 residues, 1 model selected
> select #4/N
1909 atoms, 1931 bonds, 128 residues, 1 model selected
> hide sel cartoons
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
20220627-D1-LSD-coot-1.pdb #1/A ARG 23
20220627-D1-LSD-coot-1.pdb #1/A PHE 29
20220627-D1-LSD-coot-1.pdb #1/A ARG 50
20220627-D1-LSD-coot-1.pdb #1/A LYS 138
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 20220627-D1-LSD-coot-1.pdb_A SES surface #1.2: minimum,
-11.78, mean 1.62, maximum 15.23
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide #!1 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpz2d7nqa4/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpz2d7nqa4/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpz2d7nqa4/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp9l32c7j4/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp9l32c7j4/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp9l32c7j4/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> hide #!3 models
> show #!3 models
> select add #3
8085 atoms, 8278 bonds, 6 pseudobonds, 1053 residues, 2 models selected
> select subtract #3
1 model selected
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
beita1A Gs #4/R TRP 40
beita1A Gs #4/R GLU 41
beita1A Gs #4/R MET 44
beita1A Gs #4/R LEU 46
beita1A Gs #4/R LEU 47
beita1A Gs #4/R LEU 50
beita1A Gs #4/R LEU 53
beita1A Gs #4/R ARG 247
beita1A Gs #4/R ARG 350
beita1A Gs #4/R LYS 354
beita1A Gs #4/R LEU 357
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for beita1A Gs_R SES surface #4.3: minimum, -17.36, mean
0.80, maximum 35.03
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!1 models
> select clear
> hide #!1 models
> hide #!4 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpm6avog6r/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpm6avog6r/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpm6avog6r/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> mlp sel
Map values for surface "beita1A ARRB1_A SES surface": minimum -25.47, mean
4.782, maximum 170.5
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpijko0cwb/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpijko0cwb/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpijko0cwb/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> select add #3
8085 atoms, 8278 bonds, 6 pseudobonds, 1053 residues, 3 models selected
> color (#!3 & sel) byhetero
> undo
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue SEP (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpzoz0ij_r/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpzoz0ij_r/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(SEP) ``
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`
(SEP) ``
(SEP) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpzoz0ij_r/ante.in.mol2);
atoms read (26), bonds read (25).`
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(SEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(SEP) ``
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(SEP) `Info: Total number of electrons: 126; net charge: -2`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(SEP) ``
Charges for residue SEP determined
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpmhf9tjdp/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpmhf9tjdp/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpmhf9tjdp/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> hide #!3 models
> show #!3 models
> hide sel surfaces
> select clear
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpxqe_n3na/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpxqe_n3na/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpxqe_n3na/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> color (#!3 & sel) byelement
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!4 models
> select add #3
8085 atoms, 8278 bonds, 6 pseudobonds, 1053 residues, 3 models selected
> select subtract #3
2 models selected
> hide #!1 models
> hide #!4 models
> show #!1 models
> transparency #1.2#!1 50
> hide #!1 models
> show #!3 models
> mlp #!3
Map values for surface "beita1A ARRB1_A SES surface": minimum -25.47, mean
-0.2234, maximum 22.91
Map values for surface "beita1A ARRB1_B SES surface": minimum -24.34, mean
-4.627, maximum 23.3
Map values for surface "beita1A ARRB1_H SES surface": minimum -32.93, mean
-4.218, maximum 24.28
Map values for surface "beita1A ARRB1_L SES surface": minimum -26.71, mean
-5.736, maximum 22.64
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide #!3 surfaces
> select #3/B:281
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #3/A:1356
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 2 models selected
> select up
103 atoms, 102 bonds, 13 residues, 2 models selected
> hide sel cartoons
> select clear
> select #3/A:358
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
109 atoms, 111 bonds, 13 residues, 2 models selected
> select up
580 atoms, 599 bonds, 79 residues, 2 models selected
> select up
2266 atoms, 2323 bonds, 294 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpr8rvnoun/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpr8rvnoun/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmpr8rvnoun/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> color sel byhetero
> mlp sel
Map values for surface "beita1A ARRB1_A SES surface": minimum -25.47, mean
0.4104, maximum 23.21
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp7416x_xv/ante.in.mol2 -fi
mol2 -o
/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp7416x_xv/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/yp/014zm8_d4_76vjy4vsws1xkw0000gn/T/tmp7416x_xv/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> color bfactor sel
2266 atoms, 294 residues, 1 surfaces, atom bfactor range 49.5 to 132
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> mlp #!1
Map values for surface "20220627-D1-LSD-coot-1.pdb_A SES surface": minimum
-26.84, mean 0.949, maximum 24.15
Map values for surface "20220627-D1-LSD-coot-1.pdb_B SES surface": minimum
-25.46, mean -6.342, maximum 21.37
Map values for surface "20220627-D1-LSD-coot-1.pdb_C SES surface": minimum
-28.34, mean -3.752, maximum 22.93
Map values for surface "20220627-D1-LSD-coot-1.pdb_H SES surface": minimum
-27.93, mean -4.897, maximum 23.28
Map values for surface "20220627-D1-LSD-coot-1.pdb_L SES surface": minimum
-27.92, mean -5.398, maximum 22.49
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide #!1 surfaces
> hide #!1 models
> show #!4 models
> select add #3
8085 atoms, 8278 bonds, 6 pseudobonds, 1053 residues, 3 models selected
> hide #!4 models
> select subtract #3
4 models selected
> show #!3 models
> hide #!3 models
> show #!1 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> mlp sel
Map values for surface "20220627-D1-LSD-coot-1.pdb_A SES surface": minimum
-26.84, mean 0.949, maximum 24.15
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> color bfactor sel
2165 atoms, 271 residues, 1 surfaces, atom bfactor range 27.9 to 106
> select clear
> hide #!1 models
> show #!3 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> hide #!3 models
> show #!1 models
> mlp sel
Map values for surface "20220627-D1-LSD-coot-1.pdb_A SES surface": minimum
-26.84, mean 0.949, maximum 24.15
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> hide #!1 models
> show #!3 models
> mlp sel
Map values for surface "beita1A ARRB1_A SES surface": minimum -25.47, mean
-0.2234, maximum 22.91
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select #3/A:1356@N
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
42 atoms, 41 bonds, 5 residues, 2 models selected
> hide sel surfaces
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> mlp sel
Map values for surface "beita1A Gs_R SES surface": minimum -26.38, mean 1.162,
maximum 25.13
To also show corresponding color key, enter the above mlp command and add key
true
> show #!2 models
> show #!1 models
> select clear
> transparency #1.2-6#4.2-3#!1-2,4 50
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> transparency #3 0 target c
> transparency #1 0 target c
> transparency #4 0 target c
> show #!3 models
> show #!4 models
> transparency #1.2-6#3.2-5#4.2-3#!1,3-4 80
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> hide sel cartoons
> select clear
> hide #!1 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> hide sel cartoons
> select clear
> hide #!3 models
> show #!4 models
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> hide sel cartoons
> select clear
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> transparency #1.2-6#3.2-5#4.2-3#!1,3-4 80
> transparency #1.2-6#3.2-5#4.2-3#!1,3-4 90
> hide #!1 models
> hide #!3 models
> select #4/A:380
20 atoms, 19 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 3 residues, 2 models selected
> select up
494 atoms, 496 bonds, 28 residues, 2 models selected
> select ~sel
31860 atoms, 32421 bonds, 25 pseudobonds, 3139 residues, 8 models selected
> select clear
[Repeated 3 time(s)]
> select #4/A:307
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
74 atoms, 74 bonds, 5 residues, 2 models selected
> select up
813 atoms, 827 bonds, 49 residues, 2 models selected
> select up
828 atoms, 841 bonds, 50 residues, 2 models selected
> select down
813 atoms, 827 bonds, 49 residues, 2 models selected
> hide sel cartoons
> select #4/A:288
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
171 atoms, 170 bonds, 10 residues, 2 models selected
> select up
732 atoms, 737 bonds, 42 residues, 2 models selected
> hide sel cartoons
> select clear
> select #4/A:238
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
77 atoms, 75 bonds, 6 residues, 2 models selected
> select up
1500 atoms, 1513 bonds, 90 residues, 2 models selected
> hide sel cartoons
> select clear
> select #4/A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
43 atoms, 41 bonds, 4 residues, 2 models selected
> select up
1271 atoms, 1280 bonds, 81 residues, 2 models selected
> hide sel cartoons
> hide #!4 models
> show #!1 models
> show #!4 models
> show #!3 models
> hide #!1 models
> hide #!4 models
> select clear
[Repeated 2 time(s)]
> select #3/B:68
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
103 atoms, 104 bonds, 13 residues, 2 models selected
> select up
2546 atoms, 2599 bonds, 325 residues, 2 models selected
> select clear
> select #3/B:359
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
56 atoms, 58 bonds, 8 residues, 2 models selected
> select up
138 atoms, 142 bonds, 19 residues, 2 models selected
> select up
144 atoms, 147 bonds, 20 residues, 2 models selected
> select up
2684 atoms, 2741 bonds, 344 residues, 2 models selected
> select down
144 atoms, 147 bonds, 20 residues, 2 models selected
> hide sel cartoons
> select #3/B:329
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 88 bonds, 11 residues, 2 models selected
> select up
2546 atoms, 2599 bonds, 325 residues, 2 models selected
> select down
88 atoms, 88 bonds, 11 residues, 2 models selected
> hide sel cartoons
> show #!4 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:91-98
66 atoms, 67 bonds, 8 residues, 1 model selected
> select #1/B:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:96-111
129 atoms, 132 bonds, 16 residues, 1 model selected
> select #1/B:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:95-96
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/B:94
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:94-112
156 atoms, 160 bonds, 19 residues, 1 model selected
> select ~sel
32198 atoms, 32755 bonds, 26 pseudobonds, 3148 residues, 8 models selected
> hide sel & #!1 cartoons
> select clear
> hide #!1 models
> show #!3 models
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> select #3/B:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
106 atoms, 105 bonds, 13 residues, 2 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/B:75-88
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #3/B:76-77
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/B:46-77
269 atoms, 273 bonds, 32 residues, 1 model selected
> select #3/B:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B:52-82
254 atoms, 258 bonds, 31 residues, 1 model selected
> select #3/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:52-79
231 atoms, 234 bonds, 28 residues, 1 model selected
> select #3/B:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:56-80
205 atoms, 208 bonds, 25 residues, 1 model selected
> select #3/B:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:50-82
274 atoms, 278 bonds, 33 residues, 1 model selected
> select #3/B:78-79
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/B:50-78
243 atoms, 246 bonds, 29 residues, 1 model selected
> select #3/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/B:50-75
215 atoms, 218 bonds, 26 residues, 1 model selected
> select #3/B:53-54
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/B:54-78
205 atoms, 208 bonds, 25 residues, 1 model selected
> select #3/B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:56-82
217 atoms, 220 bonds, 27 residues, 1 model selected
> select #3/B:56-57
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:57-84
225 atoms, 228 bonds, 28 residues, 1 model selected
> select ~sel
32129 atoms, 32687 bonds, 26 pseudobonds, 3139 residues, 8 models selected
> hide sel & #!3 cartoons
> select clear
> show #!1 models
> show #!4 models
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> color bfactor sel
2165 atoms, 271 residues, 1 surfaces, atom bfactor range 27.9 to 106
> coulombic sel
Coulombic values for 20220627-D1-LSD-coot-1.pdb_A SES surface #1.2: minimum,
-11.78, mean 1.62, maximum 15.23
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> hide #!3 models
> hide #!4 models
> transparency (#!1 & sel) 90
> select clear
> undo
[Repeated 6 time(s)]
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB.png" width 648
> height 599 supersample 3
> select #1/B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color (#!1 & sel) hot pink
> select clear
> cartoon style width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> size stickRadius 0.1
Changed 32917 bond radii
> undo
> cartoon style strand xsection rectangle width 1.2
> cartoon style strand xsection rectangle width 1
> select #1/B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color (#!1 & sel) hot pink
> color (#!1 & sel) #f4ffffff
> color (#!1 & sel) #f419ffff
> color (#!1 & sel) #f419a0ff
> select clear
> select #1/B
929 atoms, 946 bonds, 124 residues, 1 model selected
> color (#!1 & sel) #ff19a0ff
> color (#!1 & sel) #ff69a0ff
> color (#!1 & sel) #ff69b4ff
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB.png" width 648
> height 599 supersample 3
[Repeated 1 time(s)]
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB.cxs"
——— End of log from Mon Sep 26 14:28:39 2022 ———
opened ChimeraX session
> hide #!1 models
> hide #!4 models
> hide #!3 surfaces
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> show sel cartoons
> color (#!3 & sel) #f3ffffff
> color (#!3 & sel) #f3a4ffff
> color (#!3 & sel) #f3a459ff
> select clear
> show #!1 models
> hide #!3 models
> hide #!1 surfaces
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> show sel cartoons
> color (#!1 & sel) #86a459ff
> color (#!1 & sel) #867159ff
> color (#!1 & sel) #8671e1ff
> hide #!1 models
> select add #2
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 5 models selected
> select subtract #2
2165 atoms, 2224 bonds, 3 pseudobonds, 271 residues, 3 models selected
> show #!4 models
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> hide #!4 surfaces
> show #!4 cartoons
> undo
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> show sel cartoons
> color (#!4 & sel) #bc71e1ff
> color (#!4 & sel) #bc8fe1ff
> color (#!4 & sel) #bc8f0eff
> hide #!4 models
> show #!4 models
> show #!3 models
> select clear
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> transparency #1 chainA 80 target c
Missing or invalid "percent" argument: Expected a number
> select clear
> hide #!1 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sandy brown
[Repeated 1 time(s)]
> color sel peru
> color sel light salmon
> color sel dark khaki
> color sel olive
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> select clear
> undo
> color sel dark goldenrod
> color sel dark khaki
> color sel peru
> color sel dark khaki
> color sel olive drab
> color sel dark khaki
> color sel olive
> color sel dark khaki
> color (#!3 & sel) #b78f0eff
> color (#!3 & sel) #b76d0eff
> color (#!3 & sel) #b76d6bff
> color (#!3 & sel) #bd6d6bff
> color (#!3 & sel) #bdb76bff
> select clear
> transparency #1/a 80 target c
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> transparency #2/a 80 target c
> transparency #3/a 80 target c
> transparency #4/a 80 target c
> undo
> transparency #4/a 0 target c
> select clear
> transparency #4/r 0 target c
> hide #!1 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> transparency #4/R 0 target c
> transparency #4/R 80 target c
> show #!3 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> hide #!3 models
> hide #!4 models
> select #1/A:269
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
167 atoms, 169 bonds, 21 residues, 2 models selected
> select up
286 atoms, 294 bonds, 35 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #1/A:266
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
167 atoms, 169 bonds, 21 residues, 2 models selected
> select up
286 atoms, 294 bonds, 35 residues, 2 models selected
> select up
315 atoms, 321 bonds, 39 residues, 2 models selected
> select up
1017 atoms, 1041 bonds, 126 residues, 2 models selected
> select up
1064 atoms, 1090 bonds, 131 residues, 2 models selected
> select up
2141 atoms, 2197 bonds, 270 residues, 2 models selected
> hide sel cartoons
> select clear
> select #1/A:156
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:156-234
489 atoms, 498 bonds, 1 pseudobond, 60 residues, 2 models selected
> select #1/A:156
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:156-264
512 atoms, 521 bonds, 2 pseudobonds, 63 residues, 2 models selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 9 time(s)]
> show sel cartoons
> select clear
> select #1/A:264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 3 residues, 2 models selected
> select up
698 atoms, 711 bonds, 87 residues, 2 models selected
> select down
27 atoms, 26 bonds, 3 residues, 2 models selected
> select clear
> select #1/A:268
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
167 atoms, 169 bonds, 21 residues, 2 models selected
> select up
286 atoms, 294 bonds, 35 residues, 2 models selected
> select up
315 atoms, 321 bonds, 39 residues, 2 models selected
> select up
1017 atoms, 1041 bonds, 126 residues, 2 models selected
> hide sel cartoons
> select up
1064 atoms, 1090 bonds, 131 residues, 2 models selected
> undo
[Repeated 1 time(s)]
> select up
1064 atoms, 1090 bonds, 131 residues, 2 models selected
> select up
2141 atoms, 2197 bonds, 270 residues, 2 models selected
> hide sel cartoons
> select clear
> select #1/A:264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:264-298
286 atoms, 294 bonds, 35 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/A:310
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:310-344
289 atoms, 300 bonds, 35 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!1 models
> show #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:287
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:287-318
226 atoms, 232 bonds, 32 residues, 1 model selected
> select #3/A:287
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:287-321
243 atoms, 250 bonds, 35 residues, 1 model selected
> select #3/A:284
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:284-319
246 atoms, 252 bonds, 36 residues, 1 model selected
> select clear
> select #3/A:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
246 atoms, 252 bonds, 36 residues, 2 models selected
> select up
580 atoms, 599 bonds, 79 residues, 2 models selected
> select up
2266 atoms, 2323 bonds, 294 residues, 2 models selected
> select up
8085 atoms, 8278 bonds, 1053 residues, 2 models selected
> select down
2266 atoms, 2323 bonds, 294 residues, 5 models selected
> hide sel cartoons
> select clear
> select #3/A:312-313
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:312-358
363 atoms, 376 bonds, 47 residues, 1 model selected
> show sel cartoons
> select #3/A:280
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:280-311
217 atoms, 222 bonds, 32 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!3 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select #4/R:286
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
576 atoms, 584 bonds, 34 residues, 2 models selected
> select up
1243 atoms, 1266 bonds, 76 residues, 2 models selected
> select up
4451 atoms, 4508 bonds, 280 residues, 2 models selected
> hide sel cartoons
> select #4/R:247
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:247-357
1243 atoms, 1266 bonds, 76 residues, 1 model selected
> show sel cartoons
> select clear
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB no surface.cxs"
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB no surface.png"
> width 677 height 610 supersample 3
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!4 models
> select #1/A
2165 atoms, 2224 bonds, 4 pseudobonds, 271 residues, 3 models selected
> show sel cartoons
> select clear
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> show sel cartoons
> select clear
Drag select of 2 residues
> select clear
> select #4/R:76
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select clear
> select #1/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:57@C
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #1/B:106@CA
18 atoms, 15 bonds, 3 residues, 2 models selected
> select up
25 atoms, 22 bonds, 3 residues, 3 models selected
> color (#!1 & sel) byhetero
> select clear
> cartoon suppressBackboneDisplay true
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> cartoon suppressBackboneDisplay true
> cartoon #1/a suppressBackboneDisplay true
> cartoon #1/b suppressBackboneDisplay true
> cartoon #1/b:106 suppressBackboneDisplay true
> select clear
> show #!4 models
> select #1/B:106@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:57@NZ
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance #1/B:106@OD1 #1/A:57@NZ
Distance between 20220627-D1-LSD-coot-1.pdb #1/B ASP 106 OD1 and /A LYS 57 NZ:
3.457Å
> distance #1/B:106@OD1 #1/A:57@NZ
Distance already exists; modify distance properties with 'distance style'
> show #!2 models
> select clear
> hide #!2 models
> show #!2 models
> select #1/A:120@OD2
1 atom, 1 residue, 1 model selected
> select add #1/B:106@OD2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/A:120@OD2 #1/B:106@OD2
Distance between 20220627-D1-LSD-coot-1.pdb #1/A ASP 120 OD2 and /B ASP 106
OD2: 7.375Å
> select clear
> transparency #1 80 target c
> transparency #1 0 target c
> transparency #1 80 target c
> transparency #4 80 target c
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB.png" width 696
> height 610 supersample 3
> transparency #4/a 0 target c
> transparency #1/b 0 target c
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB.png" width 696
> height 610 supersample 3
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> show #!3 models
> show #!2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select clear
[Repeated 1 time(s)]
> select #3/B:68
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/B:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> show sel cartoons
> select clear
> select #3/A:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
16 atoms, 14 bonds, 2 residues, 3 models selected
> select add #3/B:67@CA
17 atoms, 14 bonds, 3 residues, 3 models selected
> select up
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add #3/A:351
33 atoms, 29 bonds, 4 residues, 3 models selected
> color (#!3 & sel) byhetero
> select clear
> select #3/B:69@OD2
1 atom, 1 residue, 1 model selected
> select add #3/A:138@OD2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/B:69@OD2 #3/A:138@OD2
Distance between beita1A ARRB1 #3/B ASP 69 OD2 and /A ASP 138 OD2: 7.459Å
> select clear
[Repeated 1 time(s)]
> select #3/B:67@OD2
1 atom, 1 residue, 1 model selected
> select add #3/A:351@NZ
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/B:67@OD2 #3/A:351@NZ
Distance between beita1A ARRB1 #3/B ASP 67 OD2 and /A LYS 351 NZ: 5.961Å
> select clear
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> select #3/A:139
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
267 atoms, 272 bonds, 35 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> show #!1 models
> hide #!2 models
> hide #!3 models
> select #1/A:121
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:121
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> show #!4 models
> show #!2 models
> select clear
> select #1/A:121@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:106@OD2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #1/A:121@NH1 #1/B:106@OD2
Distance between 20220627-D1-LSD-coot-1.pdb #1/A ARG 121 NH1 and /B ASP 106
OD2: 3.473Å
> select clear
> select #1/A:121@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB.png" width 696
> height 610 supersample 3
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!4 models
> show #!2 models
> transparency #1/b 80 target c
> transparency #4/a 80 target c
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB-2.png" width 696
> height 610 supersample 3
> transparency #4/a 0 target c
> transparency #1/b 0 target c
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!2 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB.png" width 696
> height 610 supersample 3
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> color (#!3 & sel) byhetero
> select clear
> select #3/A:139@NH2
1 atom, 1 residue, 1 model selected
> select add #3/B:69@OD2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/A:139@NH2 #3/B:69@OD2
Distance between beita1A ARRB1 #3/A ARG 139 NH2 and /B ASP 69 OD2: 3.012Å
> select clear
> show #!1 models
> show #!4 models
> hide #!4 models
> transparency #1/b 80 target c
> transparency #1/b 80 target a
> transparency #1/a 80 target a
> select #1/A:57@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:106@OD1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #1/A:57@NZ #1/B:106@OD1
> distance style decimalPlaces 1
[Repeated 2 time(s)]Distance already exists; modify distance properties with
'distance style'
> distance style radius 0
> distance style radius 0.01
[Repeated 3 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> select clear
> transparency #1/b 80 target c
> select #1/A:57@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:106@OD1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance style decimalPlaces 0
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style radius 0.5
[Repeated 2 time(s)]
> distance style radius 0
> distance style radius 0.01
[Repeated 3 time(s)]
> distance style radius 0.1
[Repeated 2 time(s)]
> hide #!1 models
> hide #3.2 models
> show #3.2 models
> hide #3.3 models
> show #3.3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> hide #3.5 models
> show #!1 models
> show #!2 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!3 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/AB NB.png" width 696
> height 610 supersample 3
> hide #!2 models
> hide #!3 models
> show #!4 models
> show #!2 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB-3.png" width 696
> height 610 supersample 3
> transparency #1 80 target b
> transparency #1 80 target p
> save "/Users/alicefan/Desktop/paper/figure/figure4/G NB-3.png" width 696
> height 610 supersample 3
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
> show #!2 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/AB NB.png" width 696
> height 610 supersample 3
> save /Users/alicefan/Desktop/paper/figure/figure4/interface.cxs
——— End of log from Mon Sep 26 16:53:06 2022 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> open 4LDE
Summary of feedback from opening 4LDE fetched from pdb
---
note | Fetching compressed mmCIF 4lde from
http://files.rcsb.org/download/4lde.cif
4lde title:
Structure of beta2 adrenoceptor bound to BI167107 and an engineered nanobody
[more info...]
Chain information for 4lde #5
---
Chain | Description | UniProt
A | Lysozyme, Beta-2 adrenergic receptor | ADRB2_HUMAN
B | Camelid Antibody Fragment |
Non-standard residues in 4lde #5
---
1WV — (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate
NA — sodium ion
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
> rename #5 "beita2AR NB"
> rename #5 "beita2AR NB6B9"
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!5 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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 20220627-D1-LSD-coot-1.pdb, chain A (#1) with beita2AR NB6B9, chain
A (#5), sequence alignment score = 743.3
RMSD between 236 pruned atom pairs is 0.884 angstroms; (across all 260 pairs:
1.820)
> cartoon style width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style helix width 1.2 thickness 0.6
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> cartoon style strand xsection rectangle width 1
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!5 to #4/R pairing bs
Parameters
---
Chain pairing | bs
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 beita1A Gs, chain R (#4) with beita2AR NB6B9, chain A (#5),
sequence alignment score = 1696.8
RMSD between 254 pruned atom pairs is 0.743 angstroms; (across all 276 pairs:
1.203)
> show #!3 models
> transparency #5 50 target a
> transparency #5 50 target c
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> ui tool show "Color Actions"
> color goldenrod
> color dark slate gray
> undo
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color dim gray
> color gray
> undo
[Repeated 1 time(s)]
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> transparency #3 50 target c
> transparency #3 0 target c
> transparency #4 0 target c
> transparency #5 0 target c
> select #5/B
915 atoms, 918 bonds, 135 residues, 1 model selected
> select #5/A
3699 atoms, 3712 bonds, 6 pseudobonds, 526 residues, 3 models selected
> color (#!5 & sel) #ccffffff
> color (#!5 & sel) #ccd5ffff
> color (#!5 & sel) #ccd5aeff
> select clear
> show #!1 models
> hide #!3 models
> hide #!4 models
> transparency #1 0 target c
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!5 models
> select #5/A
3699 atoms, 3712 bonds, 6 pseudobonds, 526 residues, 3 models selected
> color (#!5 & sel) #fcd5aeff
> color (#!5 & sel) #fc81aeff
> color (#!5 & sel) #fc814aff
> color (#!5 & sel) #56814aff
> color (#!5 & sel) #56874aff
> color (#!5 & sel) #56876dff
> select clear
> transparency #1 80 target c
> transparency #3 80 target c
> transparency #4 80 target c
> transparency #5 80 target c
> graphics silhouettes true
> graphics silhouettes false
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #5/A
3699 atoms, 3712 bonds, 6 pseudobonds, 526 residues, 3 models selected
> color (#!5 & sel) #00876dff
> color (#!5 & sel) #006c6dff
> color (#!5 & sel) #006cffff
> select clear
> transparency #5 80 target c
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> transparency #5 0 target c
> transparency #4 0 target c
> transparency #3 0 target c
> transparency #3 80 target c
> transparency #4 80 target c
> transparency #5 80 target c
> select #5/B
915 atoms, 918 bonds, 135 residues, 1 model selected
> color sel yellow
> select clear
> ui tool show "Color Actions"
> select #5/B
915 atoms, 918 bonds, 135 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ff6cffff
> color sel #ffccffff
> color sel #ffcc00ff
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> show #!3 models
> transparency #3/b 0 target c
> transparency #4/a 0 target c
> select clear
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select #5/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> select #5/B:57-97
324 atoms, 329 bonds, 41 residues, 1 model selected
> select #5/B:57-108
417 atoms, 425 bonds, 52 residues, 1 model selected
> select #5/B:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/B:97-114
150 atoms, 155 bonds, 18 residues, 1 model selected
> select #5/B:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:96-111
138 atoms, 143 bonds, 16 residues, 1 model selected
> select up
193 atoms, 200 bonds, 23 residues, 1 model selected
> select up
900 atoms, 918 bonds, 120 residues, 1 model selected
> hide sel cartoons
> select #5/B:96-97
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/B:96-111
138 atoms, 143 bonds, 16 residues, 1 model selected
> show sel cartoons
> select clear
> select #5/B:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/B:92-112
184 atoms, 191 bonds, 21 residues, 1 model selected
> show sel cartoons
> select clear
[Repeated 4 time(s)]
> select #5/B:105
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
Populating font family aliases took 645 ms. Replace uses of missing font
family ".AppleSystemFallback" with one that exists to avoid this cost.
> save "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
——— End of log from Mon Sep 26 23:14:01 2022 ———
opened ChimeraX session
> color sel byhetero
> select clear
> show #!4 models
> show #!3 models
> hide #!3 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita G NB.png" width 661
> height 606 supersample 3
> hide #!4 models
> show #!3 models
> show #!2 models
> transparency #3/b 80 target c
> transparency #3/b 80 target a
> transparency #3/a 80 target a
> transparency #3/a 70 target a
> transparency #3/b 70 target a
> transparency #3/b 70 target c
> transparency #3 70 target p
> hide #!3 models
> show #!4 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita G NB.png" width 661
> height 606 supersample 3
> hide #!2 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> show #!2 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita A NB.png" width 661
> height 606 supersample 3
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> select #1/B:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 3 residues, 2 models selected
> select up
929 atoms, 946 bonds, 124 residues, 2 models selected
> select up
8611 atoms, 8819 bonds, 1111 residues, 2 models selected
> select down
929 atoms, 946 bonds, 124 residues, 6 models selected
> show sel cartoons
> select clear
> select #1/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
74 atoms, 75 bonds, 9 residues, 2 models selected
> select up
929 atoms, 946 bonds, 124 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select #1/B:106@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
48 atoms, 48 bonds, 7 residues, 2 models selected
> select up
929 atoms, 946 bonds, 124 residues, 2 models selected
> show sel surfaces
> undo
> hide sel surfaces
> select clear
> select #1/B:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 3 residues, 2 models selected
> select up
929 atoms, 946 bonds, 124 residues, 2 models selected
> show sel surfaces
> color (#!1 & sel) #ff69ffff
> color (#!1 & sel) #ff69b4ff
> select clear
> hide #!1 models
> show #!3 models
> select #3/B:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 104 bonds, 13 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
103 atoms, 104 bonds, 13 residues, 2 models selected
> hide sel atoms
> select up
2546 atoms, 2599 bonds, 325 residues, 2 models selected
> select up
2551 atoms, 2603 bonds, 326 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> select clear
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> select #4/A:377
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
425 atoms, 427 bonds, 24 residues, 2 models selected
> select up
494 atoms, 496 bonds, 28 residues, 2 models selected
> select up
508 atoms, 509 bonds, 29 residues, 2 models selected
> show sel cartoons
> select up
1053 atoms, 1064 bonds, 62 residues, 2 models selected
> show sel cartoons
> select up
1116 atoms, 1128 bonds, 66 residues, 2 models selected
> show sel cartoons
> select up
1307 atoms, 1323 bonds, 77 residues, 2 models selected
> show sel cartoons
> select up
3310 atoms, 3340 bonds, 200 residues, 2 models selected
> show sel cartoons
> select up
15658 atoms, 15820 bonds, 1003 residues, 2 models selected
> select clear
[Repeated 4 time(s)]
> select #4/A:25
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
358 atoms, 358 bonds, 24 residues, 2 models selected
> select up
503 atoms, 504 bonds, 33 residues, 2 models selected
> select up
539 atoms, 539 bonds, 36 residues, 2 models selected
> select up
1271 atoms, 1280 bonds, 81 residues, 2 models selected
> select up
1315 atoms, 1323 bonds, 84 residues, 2 models selected
> select up
2003 atoms, 2017 bonds, 123 residues, 2 models selected
> select up
3310 atoms, 3340 bonds, 200 residues, 2 models selected
> show sel surfaces
> hide #!4 models
> show #!4 models
> show #!1 models
> show #!3 models
> transparency (#!4 & sel) 0
> select clear
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> transparency #3.2#!3 0
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
Populating font family aliases took 650 ms. Replace uses of missing font
family ".AppleSystemFallback" with one that exists to avoid this cost.
> save "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
——— End of log from Tue Sep 27 18:04:18 2022 ———
opened ChimeraX session
> hide #!4 surfaces
> select #4/A:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
358 atoms, 358 bonds, 24 residues, 2 models selected
> select up
503 atoms, 504 bonds, 33 residues, 2 models selected
> select up
539 atoms, 539 bonds, 36 residues, 2 models selected
> select up
1271 atoms, 1280 bonds, 81 residues, 2 models selected
> select up
1315 atoms, 1323 bonds, 84 residues, 2 models selected
> select up
2003 atoms, 2017 bonds, 123 residues, 2 models selected
> select up
3310 atoms, 3340 bonds, 200 residues, 2 models selected
> select up
15658 atoms, 15820 bonds, 1003 residues, 2 models selected
> select down
3310 atoms, 3340 bonds, 200 residues, 3 models selected
> select clear
> select #4/B
5106 atoms, 5153 bonds, 338 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/G
882 atoms, 888 bonds, 57 residues, 1 model selected
> show sel cartoons
> select #4/N
1909 atoms, 1931 bonds, 128 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> select ~sel
32517 atoms, 33039 bonds, 37 pseudobonds, 3548 residues, 11 models selected
> show sel & #!4 surfaces
> hide sel & #!4 surfaces
> show sel & #!4 surfaces
> hide sel & #!4 surfaces
> hide sel & #!4 cartoons
> select #4/A
3310 atoms, 3340 bonds, 5 pseudobonds, 200 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> select clear
> hide #!4 models
> show #!5 models
> show #!5 cartoons
> select #5/B
915 atoms, 918 bonds, 135 residues, 1 model selected
> show sel surfaces
> color (#!5 & sel) #ffccffff
> color (#!5 & sel) #ffcc00ff
> select clear
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> select #3/B
2684 atoms, 2741 bonds, 1 pseudobond, 344 residues, 2 models selected
> color (#!3 & sel) #0bcc00ff
> color (#!3 & sel) #0bbb00ff
> color (#!3 & sel) #0bbbbbff
> select clear
> hide #!3 models
> show #!1 models
> transparency #1 70 target s
> transparency #1 20 target s
> transparency #1 10 target s
> transparency #1/b 0 target c
> transparency #1 0 target s
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #4/B
5106 atoms, 5153 bonds, 338 residues, 1 model selected
> show sel surfaces
> color (#!4 & sel) #7abbbbff
> color (#!4 & sel) #7ab2bbff
> color (#!4 & sel) #7ab226ff
> select clear
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!4 models
> hide #!1 models
> transparency #1 10 target s
> transparency #4 10 target s
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> transparency #4 20 target s
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> transparency #1 20 target s
> transparency #1 50 target s
> transparency #1 20 target s
> transparency #3 20 target s
> transparency #5 20 target s
> save "/Users/alicefan/Desktop/paper/figure/figure4/D1 NB surface.png" width
> 624 height 606 supersample 3
> hide #!1 models
> show #!3 models
> select #3/A:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita2AR AB surface.png"
> width 624 height 606 supersample 3
> hide #!3 models
> show #!4 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita1AR Gs surface.png"
> width 624 height 606 supersample 3
> hide #!4 models
> show #!5 models
> select #5/A:1281
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
272 atoms, 279 bonds, 34 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select up
272 atoms, 279 bonds, 34 residues, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/alicefan/Desktop/paper/figure/figure4/beita1AR NB6B9
> surface.png" width 624 height 606 supersample 3
> undo
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> hide sel surfaces
[Repeated 1 time(s)]
> hide #!5 models
> show #!4 models
> hide #!4 surfaces
> show #!1 models
> hide #!1,4 surfaces
> hide #!4 models
> show #!5 models
> hide sel surfaces
> show #!3 models
> hide sel surfaces
[Repeated 2 time(s)]
> select clear
> hide #!1,3,5 surfaces
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> hide #!4 models
> hide #!5 models
> select #3/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:80
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/B:80-108
233 atoms, 238 bonds, 29 residues, 1 model selected
> select #3/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:57-80
198 atoms, 201 bonds, 24 residues, 1 model selected
> select #3/B:56-57
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:56-82
217 atoms, 220 bonds, 27 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #3/B:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
106 atoms, 105 bonds, 13 residues, 2 models selected
> select up
2546 atoms, 2599 bonds, 325 residues, 2 models selected
> hide sel cartoons
> select #3/B:56-57
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:56-81
212 atoms, 215 bonds, 26 residues, 1 model selected
> show sel cartoons
> select clear
> select #3/B:341
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> hide #!3 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:380
20 atoms, 19 bonds, 1 residue, 1 model selected
> select #4/A:364-380
307 atoms, 308 bonds, 17 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4/A:380
20 atoms, 19 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 3 residues, 2 models selected
> select up
494 atoms, 496 bonds, 28 residues, 2 models selected
> select up
508 atoms, 509 bonds, 29 residues, 2 models selected
> select up
1053 atoms, 1064 bonds, 62 residues, 2 models selected
> select up
1116 atoms, 1128 bonds, 66 residues, 2 models selected
> select up
1307 atoms, 1323 bonds, 77 residues, 2 models selected
> select up
3310 atoms, 3340 bonds, 200 residues, 2 models selected
> hide sel cartoons
> select #4/A:380
20 atoms, 19 bonds, 1 residue, 1 model selected
> select #4/A:360-380
381 atoms, 383 bonds, 21 residues, 1 model selected
> show sel cartoons
> select #4/A:359
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #4/A:353-359
113 atoms, 112 bonds, 7 residues, 1 model selected
> show sel cartoons
> hide #!4 models
> show #!5 models
> select add #4
15658 atoms, 15820 bonds, 6 pseudobonds, 1003 residues, 3 models selected
> select #5/B:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/N
1909 atoms, 1931 bonds, 128 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> select #5/B:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/B:98-99
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/B:98-111
123 atoms, 128 bonds, 14 residues, 1 model selected
> select #5/B:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/B:95-110
140 atoms, 145 bonds, 16 residues, 1 model selected
> select clear
> select #5/B:105
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
56 atoms, 57 bonds, 7 residues, 2 models selected
> select up
900 atoms, 918 bonds, 120 residues, 2 models selected
> hide sel cartoons
> select #5/B:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/B:95-110
140 atoms, 145 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #5/B:94
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/B:94-113
169 atoms, 175 bonds, 20 residues, 1 model selected
> show sel cartoons
> select clear
> show #!4 models
> show #!3 models
> select #3/A
2266 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "beita1A ARRB1_A SES surface": minimum -25.47, mean
-0.2223, maximum 22.91
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select #5/B:105@CA
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> color bfactor sel
12 atoms, 1 residues, 1 surfaces, atom bfactor range 63.6 to 76.2
> undo
> color (#!5 & sel) byhetero
> select #5/A
3699 atoms, 3712 bonds, 6 pseudobonds, 526 residues, 3 models selected
> show sel surfaces
> mlp sel
Map values for surface "beita2AR NB6B9_A SES surface": minimum -28.23, mean
-1.631, maximum 23.17
To also show corresponding color key, enter the above mlp command and add key
true
> select #4/R
4451 atoms, 4508 bonds, 1 pseudobond, 280 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "beita1A Gs_R SES surface": minimum -26.38, mean 1.162,
maximum 25.13
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> transparency #3 20 target s
> transparency #4 20 target s
> transparency #5 20 target s
> transparency #5 80 target s
> transparency #4 80 target s
> transparency # 80 target s
Missing or invalid "percent" argument: Expected a number
> transparency #3 80 target s
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> hide #5.1 models
> show #5.1 models
> hide #5.2 models
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB beita1AR
> surface.png" width 624 height 606 supersample 3
> transparency #3 90 target s
> transparency #4 90 target s
> transparency #5 90 target s
> save "/Users/alicefan/Desktop/paper/figure/figure4/G A NB beita1AR
> surface.png" width 624 height 606 supersample 3
Populating font family aliases took 626 ms. Replace uses of missing font
family ".AppleSystemFallback" with one that exists to avoid this cost.
> save "/Users/alicefan/Desktop/paper/figure/figure4/D1-Legobody
> beita1AR的副本.cxs"
——— End of log from Tue Sep 27 22:27:02 2022 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1037.107.7.0.0 (iBridge: 17.16.14538.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.4 (19E2269)
Kernel Version: Darwin 19.4.0
Time since boot: 5 days 5:04
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.