![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8239 closed defect (nonchimerax)
Graphics crash, macOS 10.14.6, NVIDIA GeForce GTX 775M
| 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-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x000000010afa95c0 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1178 in draw_background
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/camera.py", line 184 in draw_background
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 227 in _draw_scene
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [1095]
Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [1095]
User ID: 501
Date/Time: 2022-12-28 00:19:35.756 -0500
OS Version: Mac OS X 10.14.6 (18G103)
Report Version: 12
Anonymous UUID: 7AA5A8FD-86CB-5B4F-C532-80185CFB19B1
Time Awake Since Boot: 360000 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: 0x0000002b
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff5d2912c6 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff5d34cbf1 pthread_kill + 284
2 libsystem_c.dylib 0x00007fff5d1aed8a raise + 26
3 libsystem_platform.dylib 0x00007fff5d341b5d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff5d1fb6a6 abort + 127
6 libGPUSupportMercury.dylib 0x00007fff4c268240 gpusGenerateCrashLog + 166
7 com.apple.GeForceGLDriver 0x00007fff2c361f3f 0x7fff2c05a000 + 3178303
8 libGPUSupportMercury.dylib 0x00007fff4c269730 gpusSubmitDataBuffers + 490
9 com.apple.GeForceGLDriver 0x00007fff2c35d415 0x7fff2c05a000 + 3159061
10 com.apple.GeForceGLDriver 0x00007fff2c341188 0x7fff2c05a000 + 3043720
11 libGPUSupportMercury.dylib 0x00007fff4c26b0a9 gldUpdateDrawFramebuffer + 163
12 GLEngine 0x00007fff3af662da gleUpdateDrawFramebufferState + 602
13 GLEngine 0x00007fff3ae84dd4 glClear_Exec + 205
14 libffi.dylib 0x00007fff5acfff6c ffi_call_unix64 + 76
15 libffi.dylib 0x00007fff5ad00775 ffi_call + 785
16 _ctypes.cpython-39-darwin.so 0x000000010a16cd0d _ctypes_callproc + 1037
17 _ctypes.cpython-39-darwin.so 0x000000010a166a96 PyCFuncPtr_call + 1206
18 org.python.python 0x00000001093ffadc _PyObject_Call + 140
19 org.python.python 0x0000000109458526 slot_tp_call + 230
20 org.python.python 0x00000001093ff5b7 _PyObject_MakeTpCall + 359
21 org.python.python 0x00000001094d7e9c call_function + 876
22 org.python.python 0x00000001094d52a2 _PyEval_EvalFrameDefault + 25554
23 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
24 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
25 org.python.python 0x00000001094d7e0c call_function + 732
26 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
27 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
28 org.python.python 0x00000001094d7e0c call_function + 732
29 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
30 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
31 org.python.python 0x00000001094d7e0c call_function + 732
32 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
33 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
34 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
35 org.python.python 0x00000001094d7e0c call_function + 732
36 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
37 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
38 org.python.python 0x0000000109401d6a method_vectorcall + 202
39 org.python.python 0x00000001094d7e0c call_function + 732
40 org.python.python 0x00000001094d52a2 _PyEval_EvalFrameDefault + 25554
41 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
42 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
43 org.python.python 0x0000000109401d6a method_vectorcall + 202
44 org.python.python 0x00000001094d7e0c call_function + 732
45 org.python.python 0x00000001094d52a2 _PyEval_EvalFrameDefault + 25554
46 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
47 org.python.python 0x00000001094d7e0c call_function + 732
48 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
49 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
50 org.python.python 0x00000001094d7e0c call_function + 732
51 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
52 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
53 org.python.python 0x00000001094d7e0c call_function + 732
54 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
55 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
56 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
57 org.python.python 0x00000001094d7e0c call_function + 732
58 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
59 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
60 org.python.python 0x00000001094d7e0c call_function + 732
61 org.python.python 0x00000001094d527e _PyEval_EvalFrameDefault + 25518
62 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
63 org.python.python 0x0000000109401db2 method_vectorcall + 274
64 QtCore.abi3.so 0x000000010aa23f98 PyQtSlot::call(_object*, _object*) const + 40
65 QtCore.abi3.so 0x000000010aa23e9a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362
66 QtCore.abi3.so 0x000000010aa24de5 PyQtSlotProxy::unislot(void**) + 85
67 QtCore.abi3.so 0x000000010aa24d5a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
68 QtCore 0x000000011705fd67 0x116fa2000 + 777575
69 QtCore 0x0000000117074b57 QTimer::timerEvent(QTimerEvent*) + 199
70 QtCore.abi3.so 0x000000010a914b69 sipQTimer::timerEvent(QTimerEvent*) + 121
71 QtCore 0x00000001170584cd QObject::event(QEvent*) + 109
72 QtCore.abi3.so 0x000000010a9149ea sipQTimer::event(QEvent*) + 186
73 QtWidgets 0x0000000119563a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
74 QtWidgets 0x0000000119564a43 QApplication::notify(QObject*, QEvent*) + 499
75 QtWidgets.abi3.so 0x00000001190831e6 sipQApplication::notify(QObject*, QEvent*) + 230
76 QtCore 0x000000011700fc3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
77 QtCore 0x0000000117199521 QTimerInfoList::activateTimers() + 961
78 libqcocoa.dylib 0x000000012605f4a5 0x126047000 + 99493
79 com.apple.CoreFoundation 0x00007fff3121dde3 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
80 com.apple.CoreFoundation 0x00007fff3121dd89 __CFRunLoopDoSource0 + 108
81 com.apple.CoreFoundation 0x00007fff3120174b __CFRunLoopDoSources0 + 195
82 com.apple.CoreFoundation 0x00007fff31200d15 __CFRunLoopRun + 1189
83 com.apple.CoreFoundation 0x00007fff3120061e CFRunLoopRunSpecific + 455
84 com.apple.HIToolbox 0x00007fff3045f1ab RunCurrentEventLoopInMode + 292
85 com.apple.HIToolbox 0x00007fff3045eee5 ReceiveNextEventCommon + 603
86 com.apple.HIToolbox 0x00007fff3045ec76 _BlockUntilNextEventMatchingListInModeWithFilter + 64
87 com.apple.AppKit 0x00007fff2e7f777d _DPSNextEvent + 1135
88 com.apple.AppKit 0x00007fff2e7f646b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1361
89 com.apple.AppKit 0x00007fff2e7f0588 -[NSApplication run] + 699
90 libqcocoa.dylib 0x00000001260600ac 0x126047000 + 102572
91 QtCore 0x0000000117019326 QEventLoop::exec(QFlags) + 486
92 QtCore 0x0000000117010235 QCoreApplication::exec() + 133
93 QtWidgets.abi3.so 0x000000011916fd9a meth_QApplication_exec(_object*, _object*) + 90
94 org.python.python 0x000000010943e71d cfunction_call + 125
95 org.python.python 0x00000001093ff5b7 _PyObject_MakeTpCall + 359
96 org.python.python 0x00000001094d7e9c call_function + 876
97 org.python.python 0x00000001094d52a2 _PyEval_EvalFrameDefault + 25554
98 org.python.python 0x00000001093ffd28 function_code_fastcall + 104
99 org.python.python 0x0000000109401d6a method_vectorcall + 202
100 org.python.python 0x00000001094d7e0c call_function + 732
101 org.python.python 0x00000001094d52a2 _PyEval_EvalFrameDefault + 25554
102 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
103 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
104 org.python.python 0x00000001094d7e0c call_function + 732
105 org.python.python 0x00000001094d534b _PyEval_EvalFrameDefault + 25723
106 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
107 org.python.python 0x00000001094cedab PyEval_EvalCode + 139
108 org.python.python 0x00000001094cbc12 builtin_exec + 626
109 org.python.python 0x000000010943e023 cfunction_vectorcall_FASTCALL + 195
110 org.python.python 0x00000001094d7e0c call_function + 732
111 org.python.python 0x00000001094d534b _PyEval_EvalFrameDefault + 25723
112 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
113 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
114 org.python.python 0x00000001094d7e0c call_function + 732
115 org.python.python 0x00000001094d534b _PyEval_EvalFrameDefault + 25723
116 org.python.python 0x00000001094d8b03 _PyEval_EvalCode + 2611
117 org.python.python 0x00000001093ffcb1 _PyFunction_Vectorcall + 289
118 org.python.python 0x000000010953e870 pymain_run_module + 208
119 org.python.python 0x000000010953df87 Py_RunMain + 1431
120 org.python.python 0x000000010953e58f pymain_main + 223
121 org.python.python 0x000000010953e49b Py_Main + 43
122 edu.ucsf.cgl.ChimeraX 0x00000001093b4dc8 main + 120
123 libdyld.dylib 0x00007fff5d1563d5 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 libopenblas64_.0.dylib 0x000000010b31b23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 libopenblas64_.0.dylib 0x000000010b31b23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 libopenblas64_.0.dylib 0x000000010b31b23f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff5d2930a6 kevent64 + 10
1 QtWebEngineCore 0x000000011e5dfa2a 0x11a67f000 + 66456106
2 QtWebEngineCore 0x000000011e5df927 0x11a67f000 + 66455847
3 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
4 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
5 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
6 QtWebEngineCore 0x000000011e5662ad 0x11a67f000 + 65958573
7 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
8 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
9 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 5:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5727bf 0x11a67f000 + 66009023
4 QtWebEngineCore 0x000000011e57326c 0x11a67f000 + 66011756
5 QtWebEngineCore 0x000000011e572ddd 0x11a67f000 + 66010589
6 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
7 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 6:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff5d2930a6 kevent64 + 10
1 QtWebEngineCore 0x000000011e5dfa2a 0x11a67f000 + 66456106
2 QtWebEngineCore 0x000000011e5df927 0x11a67f000 + 66455847
3 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
4 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
5 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
6 QtWebEngineCore 0x000000011d4a43a2 0x11a67f000 + 48386978
7 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
8 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
9 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 8:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 QtWebEngineCore 0x000000011e5a5d1b 0x11a67f000 + 66219291
3 QtWebEngineCore 0x000000012067392d 0x11a67f000 + 100616493
4 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
5 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
6 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
7 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 9:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 10:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff5d2930a6 kevent64 + 10
1 QtWebEngineCore 0x000000011e5dfa2a 0x11a67f000 + 66456106
2 QtWebEngineCore 0x000000011e5df927 0x11a67f000 + 66455847
3 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
4 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
5 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
6 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
7 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
8 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 12:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 13:: NetworkService
0 libsystem_kernel.dylib 0x00007fff5d2930a6 kevent64 + 10
1 QtWebEngineCore 0x000000011e5dfa2a 0x11a67f000 + 66456106
2 QtWebEngineCore 0x000000011e5df927 0x11a67f000 + 66455847
3 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
4 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
5 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
6 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
7 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
8 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 15:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5727bf 0x11a67f000 + 66009023
4 QtWebEngineCore 0x000000011e57326c 0x11a67f000 + 66011756
5 QtWebEngineCore 0x000000011e572ecd 0x11a67f000 + 66010829
6 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
7 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 17:
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 com.apple.GeForceMTLDriver 0x00007fff2d1b904e 0x7fff2d055000 + 1458254
3 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 18:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 19:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5727bf 0x11a67f000 + 66009023
4 QtWebEngineCore 0x000000011e572f9a 0x11a67f000 + 66011034
5 QtWebEngineCore 0x000000011e572e0d 0x11a67f000 + 66010637
6 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
7 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 20:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3120194e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff31200ebc __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff3120061e CFRunLoopRunSpecific + 455
5 com.apple.AppKit 0x00007fff2e7ff4a2 _NSEventThread + 175
6 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 21:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5adbef 0x11a67f000 + 66251759
4 QtWebEngineCore 0x000000011e4e31c9 0x11a67f000 + 65421769
5 QtWebEngineCore 0x000000011e55ca5c 0x11a67f000 + 65919580
6 QtWebEngineCore 0x000000011e514998 0x11a67f000 + 65624472
7 QtWebEngineCore 0x000000011e57eeb8 0x11a67f000 + 66059960
8 QtWebEngineCore 0x000000011e57f04a 0x11a67f000 + 66060362
9 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
10 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 22:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff5d28b22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5d28b76c mach_msg + 60
2 QtWebEngineCore 0x000000011e5ade26 0x11a67f000 + 66252326
3 QtWebEngineCore 0x000000011e5727bf 0x11a67f000 + 66009023
4 QtWebEngineCore 0x000000011e57326c 0x11a67f000 + 66011756
5 QtWebEngineCore 0x000000011e572e6d 0x11a67f000 + 66010733
6 QtWebEngineCore 0x000000011e5a6908 0x11a67f000 + 66222344
7 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 23:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff5d28e86a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5d34d56e _pthread_cond_wait + 722
2 QtCore 0x00000001171a48eb 0x116fa2000 + 2107627
3 QtCore 0x00000001171a485e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94
4 QtGui 0x0000000119fbfe0d QFileInfoGatherer::run() + 125
5 QtCore 0x000000011719a663 0x116fa2000 + 2066019
6 libsystem_pthread.dylib 0x00007fff5d34a2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff5d34d249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5d34940d thread_start + 13
Thread 24:
0 libsystem_pthread.dylib 0x00007fff5d3493f0 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010afa95c0 rcx: 0x00007fc07809fa48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fc07809fa80 rsp: 0x00007fc07809fa48
r8: 0x00007fc07809ff48 r9: 0xea42012b19c1a06a r10: 0x000000010afa966c r11: 0x0000000000000206
r12: 0x0000000000000307 r13: 0x00007fc048c88000 r14: 0x0000000000000006 r15: 0x000000000000002d
rip: 0x00007fff5d2912c6 rfl: 0x0000000000000206 cr2: 0x00007fc07809ff48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
0x1093b4000 - 0x1093b4ff3 +edu.ucsf.cgl.ChimeraX (1.5.0 - 1.5.0.0) /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
0x1093c0000 - 0x109628fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
0x109793000 - 0x109795fff +_heapq.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_heapq.cpython-39-darwin.so
0x10979f000 - 0x1097a3ff7 +binascii.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/binascii.cpython-39-darwin.so
0x1097ad000 - 0x1097b2fff +zlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/zlib.cpython-39-darwin.so
0x1097bc000 - 0x1097befff +_bz2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bz2.cpython-39-darwin.so
0x1097c8000 - 0x1097f9fff +_lzma.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_lzma.cpython-39-darwin.so
0x10980b000 - 0x10980cfff +grp.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/grp.cpython-39-darwin.so
0x109816000 - 0x10981bff7 +_struct.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_struct.cpython-39-darwin.so
0x10982a000 - 0x109832fff +math.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/math.cpython-39-darwin.so
0x109840000 - 0x109841ff7 +_bisect.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bisect.cpython-39-darwin.so
0x10984b000 - 0x10984cfff +_random.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_random.cpython-39-darwin.so
0x109856000 - 0x10985afff +_sha512.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_sha512.cpython-39-darwin.so
0x109864000 - 0x109864fff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x10986b000 - 0x10990cff7 +libarrays.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x109930000 - 0x109935fff +_json.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_json.cpython-39-darwin.so
0x10993f000 - 0x109d82ffb +_multiarray_umath.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so
0x109edb000 - 0x109ff2ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x10a060000 - 0x10a096fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x10a0aa000 - 0x10a0bfff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x10a0cf000 - 0x10a0defff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x10a0f2000 - 0x10a109fff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x10a11c000 - 0x10a12fffb +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x10a149000 - 0x10a14bfff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x10a155000 - 0x10a159ff7 +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
0x10a163000 - 0x10a174ff7 +_ctypes.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so
0x10a18d000 - 0x10a1a8fff +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
0x10a1c5000 - 0x10a1d8fff +_pocketfft_internal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/fft/_pocketfft_internal.cpython-39-darwin.so
0x10a1e4000 - 0x10a257ff3 +mtrand.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/mtrand.cpython-39-darwin.so
0x10a2ba000 - 0x10a2d9ff3 +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
0x10a2fc000 - 0x10a32ffff +_common.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_common.cpython-39-darwin.so
0x10a34d000 - 0x10a353fff +_hashlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_hashlib.cpython-39-darwin.so
0x10a362000 - 0x10a3bbff7 +libssl.1.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.1.1.dylib
0x10a3ed000 - 0x10a60497f +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.1.1.dylib
0x10a6a4000 - 0x10a6aafff +_blake2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_blake2.cpython-39-darwin.so
0x10a6b4000 - 0x10a707ff7 +_bounded_integers.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_bounded_integers.cpython-39-darwin.so
0x10a737000 - 0x10a746fff +_mt19937.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_mt19937.cpython-39-darwin.so
0x10a759000 - 0x10a768ff3 +_philox.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_philox.cpython-39-darwin.so
0x10a77a000 - 0x10a789fff +_pcg64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_pcg64.cpython-39-darwin.so
0x10a79d000 - 0x10a7a4ff3 +_sfc64.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_sfc64.cpython-39-darwin.so
0x10a7b5000 - 0x10a844ffb +_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_generator.cpython-39-darwin.so
0x10a8b4000 - 0x10a8b4fff +_opcode.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_opcode.cpython-39-darwin.so
0x10a8be000 - 0x10a8dcff3 +_geometry.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/geometry/_geometry.cpython-39-darwin.so
0x10a8f1000 - 0x10aa74ffb +QtCore.abi3.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/PyQt6/QtCore.abi3.so
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0x7fff57e7a000 - 0x7fff58031ffb com.apple.UIFoundation (1.0 - 551.2) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff58cad000 - 0x7fff58d86fff com.apple.ViewBridge (401.1 - 401.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff5955e000 - 0x7fff59561fff com.apple.dt.XCTTargetBootstrap (1.0 - 14490.66) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff59962000 - 0x7fff59964ffb com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff59965000 - 0x7fff5997afff com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff59c2e000 - 0x7fff59c62fff libCRFSuite.dylib (41.15.4) /usr/lib/libCRFSuite.dylib
0x7fff59c65000 - 0x7fff59c6fff7 libChineseTokenizer.dylib (28.15.3) /usr/lib/libChineseTokenizer.dylib
0x7fff59c70000 - 0x7fff59cf9fff libCoreStorage.dylib (546.50.1) /usr/lib/libCoreStorage.dylib
0x7fff59cfd000 - 0x7fff59cfeffb libDiagnosticMessagesClient.dylib (107) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff59d35000 - 0x7fff59f8cff3 libFosl_dynamic.dylib (18.3.4) /usr/lib/libFosl_dynamic.dylib
0x7fff59fac000 - 0x7fff59fb3fff libMatch.1.dylib (31.200.1) /usr/lib/libMatch.1.dylib
0x7fff59fdd000 - 0x7fff59ffcfff libMobileGestalt.dylib (645.270.1) /usr/lib/libMobileGestalt.dylib
0x7fff59ffd000 - 0x7fff59ffdfff libOpenScriptingUtil.dylib (179.1) /usr/lib/libOpenScriptingUtil.dylib
0x7fff5a13d000 - 0x7fff5a13effb libSystem.B.dylib (1252.250.1) /usr/lib/libSystem.B.dylib
0x7fff5a1ba000 - 0x7fff5a1bbfff libThaiTokenizer.dylib (2.15.1) /usr/lib/libThaiTokenizer.dylib
0x7fff5a1cd000 - 0x7fff5a1e3ffb libapple_nghttp2.dylib (1.24.1) /usr/lib/libapple_nghttp2.dylib
0x7fff5a1e4000 - 0x7fff5a20dffb libarchive.2.dylib (54.250.1) /usr/lib/libarchive.2.dylib
0x7fff5a20e000 - 0x7fff5a28dfff libate.dylib (1.13.8) /usr/lib/libate.dylib
0x7fff5a291000 - 0x7fff5a291ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff5a361000 - 0x7fff5a371ffb libbsm.0.dylib (39.200.18) /usr/lib/libbsm.0.dylib
0x7fff5a372000 - 0x7fff5a37ffff libbz2.1.0.dylib (38.200.3) /usr/lib/libbz2.1.0.dylib
0x7fff5a380000 - 0x7fff5a3d3ff7 libc++.1.dylib (400.9.4) /usr/lib/libc++.1.dylib
0x7fff5a3d4000 - 0x7fff5a3e9ff7 libc++abi.dylib (400.17) /usr/lib/libc++abi.dylib
0x7fff5a3ea000 - 0x7fff5a3eaff3 libcharset.1.dylib (51.200.6) /usr/lib/libcharset.1.dylib
0x7fff5a3eb000 - 0x7fff5a3fbffb libcmph.dylib (6.15.1) /usr/lib/libcmph.dylib
0x7fff5a3fc000 - 0x7fff5a414ffb libcompression.dylib (52.250.2) /usr/lib/libcompression.dylib
0x7fff5a689000 - 0x7fff5a69ffff libcoretls.dylib (155.220.1) /usr/lib/libcoretls.dylib
0x7fff5a6a0000 - 0x7fff5a6a1ff3 libcoretls_cfhelpers.dylib (155.220.1) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff5a83f000 - 0x7fff5a937ff7 libcrypto.35.dylib (22.260.1) /usr/lib/libcrypto.35.dylib
0x7fff5ab3a000 - 0x7fff5ab45ff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib
0x7fff5ab4d000 - 0x7fff5aba3ff3 libcups.2.dylib (462.12) /usr/lib/libcups.2.dylib
0x7fff5acd7000 - 0x7fff5acd7fff libenergytrace.dylib (17.200.1) /usr/lib/libenergytrace.dylib
0x7fff5acd8000 - 0x7fff5acf1ffb libexpat.1.dylib (16.1.1) /usr/lib/libexpat.1.dylib
0x7fff5acff000 - 0x7fff5ad00fff libffi.dylib (18.1) /usr/lib/libffi.dylib
0x7fff5ad09000 - 0x7fff5ad0eff7 libgermantok.dylib (17.15.2) /usr/lib/libgermantok.dylib
0x7fff5ad0f000 - 0x7fff5ad14ff7 libheimdal-asn1.dylib (520.270.1) /usr/lib/libheimdal-asn1.dylib
0x7fff5ad3f000 - 0x7fff5ae2ffff libiconv.2.dylib (51.200.6) /usr/lib/libiconv.2.dylib
0x7fff5ae30000 - 0x7fff5b091ffb libicucore.A.dylib (62141.0.1) /usr/lib/libicucore.A.dylib
0x7fff5b0de000 - 0x7fff5b0dffff liblangid.dylib (128.15.1) /usr/lib/liblangid.dylib
0x7fff5b0e0000 - 0x7fff5b0f8ff3 liblzma.5.dylib (10.200.3) /usr/lib/liblzma.5.dylib
0x7fff5b110000 - 0x7fff5b1b4ff7 libmecab.1.0.0.dylib (779.24.1) /usr/lib/libmecab.1.0.0.dylib
0x7fff5b1b5000 - 0x7fff5b3b9fff libmecabra.dylib (779.24.1) /usr/lib/libmecabra.dylib
0x7fff5b591000 - 0x7fff5b8e2ff7 libnetwork.dylib (1229.250.15) /usr/lib/libnetwork.dylib
0x7fff5b974000 - 0x7fff5c0f9fdf libobjc.A.dylib (756.2) /usr/lib/libobjc.A.dylib
0x7fff5c10b000 - 0x7fff5c10fffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib
0x7fff5c112000 - 0x7fff5c147fff libpcap.A.dylib (79.250.1) /usr/lib/libpcap.A.dylib
0x7fff5c19d000 - 0x7fff5c1a0fff libpmenergy.dylib (194.267.1) /usr/lib/libpmenergy.dylib
0x7fff5c1a1000 - 0x7fff5c1a3fff libpmsample.dylib (194.267.1) /usr/lib/libpmsample.dylib
0x7fff5c260000 - 0x7fff5c278ffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib
0x7fff5c27a000 - 0x7fff5c2b5ff3 libsandbox.1.dylib (851.270.1) /usr/lib/libsandbox.1.dylib
0x7fff5c2c9000 - 0x7fff5c2caff7 libspindump.dylib (267.3) /usr/lib/libspindump.dylib
0x7fff5c2cb000 - 0x7fff5c4a8fff libsqlite3.dylib (274.26) /usr/lib/libsqlite3.dylib
0x7fff5c6c1000 - 0x7fff5c6c4ff7 libutil.dylib (51.200.4) /usr/lib/libutil.dylib
0x7fff5c6c5000 - 0x7fff5c6d2fff libxar.1.dylib (417.1) /usr/lib/libxar.1.dylib
0x7fff5c6d7000 - 0x7fff5c7b9ff3 libxml2.2.dylib (32.10) /usr/lib/libxml2.2.dylib
0x7fff5c7ba000 - 0x7fff5c7e2ff3 libxslt.1.dylib (16.5) /usr/lib/libxslt.1.dylib
0x7fff5c7e3000 - 0x7fff5c7f5ff7 libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib
0x7fff5cfd9000 - 0x7fff5cfddff3 libcache.dylib (81) /usr/lib/system/libcache.dylib
0x7fff5cfde000 - 0x7fff5cfe8ff3 libcommonCrypto.dylib (60118.250.2) /usr/lib/system/libcommonCrypto.dylib
0x7fff5cfe9000 - 0x7fff5cff0ff7 libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib
0x7fff5cff1000 - 0x7fff5cffaff7 libcopyfile.dylib (146.250.1) /usr/lib/system/libcopyfile.dylib
0x7fff5cffb000 - 0x7fff5d07ffc3 libcorecrypto.dylib (602.260.2) /usr/lib/system/libcorecrypto.dylib
0x7fff5d106000 - 0x7fff5d13fff7 libdispatch.dylib (1008.270.1) /usr/lib/system/libdispatch.dylib
0x7fff5d140000 - 0x7fff5d16cff7 libdyld.dylib (655.1.1) /usr/lib/system/libdyld.dylib
0x7fff5d16d000 - 0x7fff5d16dffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff5d16e000 - 0x7fff5d17aff3 libkxld.dylib (4903.271.2) /usr/lib/system/libkxld.dylib
0x7fff5d17b000 - 0x7fff5d17bff7 liblaunch.dylib (1336.261.2) /usr/lib/system/liblaunch.dylib
0x7fff5d17c000 - 0x7fff5d181fff libmacho.dylib (927.0.3) /usr/lib/system/libmacho.dylib
0x7fff5d182000 - 0x7fff5d184ffb libquarantine.dylib (86.220.1) /usr/lib/system/libquarantine.dylib
0x7fff5d185000 - 0x7fff5d186ff7 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib
0x7fff5d187000 - 0x7fff5d19eff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib
0x7fff5d19f000 - 0x7fff5d19fff7 libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff5d1a0000 - 0x7fff5d227fff libsystem_c.dylib (1272.250.1) /usr/lib/system/libsystem_c.dylib
0x7fff5d228000 - 0x7fff5d22bffb libsystem_configuration.dylib (963.270.3) /usr/lib/system/libsystem_configuration.dylib
0x7fff5d22c000 - 0x7fff5d22fff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff5d230000 - 0x7fff5d236fff libsystem_darwin.dylib (1272.250.1) /usr/lib/system/libsystem_darwin.dylib
0x7fff5d237000 - 0x7fff5d23dff7 libsystem_dnssd.dylib (878.270.2) /usr/lib/system/libsystem_dnssd.dylib
0x7fff5d23e000 - 0x7fff5d289ffb libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff5d28a000 - 0x7fff5d2b2ff7 libsystem_kernel.dylib (4903.271.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff5d2b3000 - 0x7fff5d2feff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff5d2ff000 - 0x7fff5d329fff libsystem_malloc.dylib (166.270.1) /usr/lib/system/libsystem_malloc.dylib
0x7fff5d32a000 - 0x7fff5d334ff7 libsystem_networkextension.dylib (767.250.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff5d335000 - 0x7fff5d33cfff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff5d33d000 - 0x7fff5d346fef libsystem_platform.dylib (177.270.1) /usr/lib/system/libsystem_platform.dylib
0x7fff5d347000 - 0x7fff5d351ff7 libsystem_pthread.dylib (330.250.2) /usr/lib/system/libsystem_pthread.dylib
0x7fff5d352000 - 0x7fff5d355ff7 libsystem_sandbox.dylib (851.270.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff5d356000 - 0x7fff5d358ff3 libsystem_secinit.dylib (30.260.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff5d359000 - 0x7fff5d360ff3 libsystem_symptoms.dylib (820.267.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff5d361000 - 0x7fff5d376fff libsystem_trace.dylib (906.260.1) /usr/lib/system/libsystem_trace.dylib
0x7fff5d378000 - 0x7fff5d37dffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff5d37e000 - 0x7fff5d3adfff libxpc.dylib (1336.261.2) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 533
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: 189400
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=788.1M resident=0K(0%) swapped_out_or_unallocated=788.1M(100%)
Writable regions: Total=14.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=14.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 3
Activity Tracing 256K 1
CG backing stores 440K 2
CG image 348K 40
CoreAnimation 428K 42
CoreGraphics 8K 1
CoreImage 32K 8
CoreServices 184K 1
CoreUI image data 1572K 32
CoreUI image file 436K 6
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 11.4G 1413
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 632.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Mach message 24K 4
Memory Tag 242 12K 1
OpenGL GLSL 384K 4
STACK GUARD 96K 24
Stack 147.7M 25
Stack Guard 56.0M 1
VM_ALLOCATE 1.5G 454
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 61.2M 493
__DATA_CONST 32K 2
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 252.2M 186
__TEXT 536.3M 479
__UNICODE 564K 1
mapped file 173.4M 138
shared memory 2960K 21
=========== ======= =======
TOTAL 15.1G 3405
TOTAL, minus reserved VM space 14.1G 3405
System Profile:
Network Service: Wi-Fi, AirPort, en1
Thunderbolt Bus: iMac, Apple Inc., 23.10
Boot Volume File System Type: apfs
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3831554738454655352D474E4C2D46
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3831554738454655352D474E4C2D46
Memory Module: BANK 0/DIMM1, 8 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3831554738454655352D474E4C2D46
Memory Module: BANK 1/DIMM1, 8 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3831554738454655352D474E4C2D46
USB Device: USB 3.0 Bus
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: FaceTime HD Camera (Built-in)
USB Device: Keyboard Hub
USB Device: Logitech USB Optical Mouse
USB Device: Apple Keyboard
Serial ATA Device: APPLE SSD SM1024F, 1 TB
Model: iMac14,2, BootROM 433.140.2.0.0, 4 processors, Intel Core i7, 3.5 GHz, 32 GB, SMC 2.15f7
Graphics: kHW_NVidiaGeForceGTX775MItem, NVIDIA GeForce GTX 775M, spdisplays_pcie_device, 2 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x111), Broadcom BCM43xx 1.0 (7.77.61.2 AirPortDriverBrcmNIC-1305.8)
Bluetooth: Version 6.0.14d3, 3 services, 27 devices, 1 incoming serial ports
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6m0r
Summary of feedback from opening 6m0r fetched from pdb
---
warnings | Atom H42 is not in the residue template for PEE /C:301
Atom H42 is not in the residue template for PEE /C:302
Atom H42 is not in the residue template for PEE /C:303
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:304
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:304
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:304
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /C:304
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /C:304
6 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /C:305
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /C:305
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:305
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:305
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:305
11 messages similar to the above omitted
Atom H1 has no neighbors to form bonds with according to residue template for
PEE /C:306
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /C:306
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /C:306
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:306
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:306
15 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /C:307
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /C:307
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:307
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:307
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:307
11 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /C:308
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /C:308
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:308
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:308
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:308
11 messages similar to the above omitted
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:309
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:309
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:309
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /C:309
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /C:309
4 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /C:310
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /C:310
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /C:310
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /C:310
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /C:310
11 messages similar to the above omitted
Atom H42 is not in the residue template for PEE /M:101
Atom H76 is not in the residue template for PEE /M:102
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /E:201
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /E:201
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /E:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /E:201
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /E:201
11 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /E:202
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /E:202
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /E:202
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /E:202
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /E:202
11 messages similar to the above omitted
Atom H1 has no neighbors to form bonds with according to residue template for
PEE /O:101
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /O:101
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /O:101
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /O:101
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /O:101
13 messages similar to the above omitted
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /F:201
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /F:201
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /F:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /F:201
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /F:201
11 messages similar to the above omitted
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /G:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /G:201
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /G:201
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /G:201
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /G:201
8 messages similar to the above omitted
Atom H1 has no neighbors to form bonds with according to residue template for
PEE /H:201
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /H:201
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /H:201
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /H:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /H:201
15 messages similar to the above omitted
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /I:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /I:201
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /I:201
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /I:201
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /I:201
8 messages similar to the above omitted
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /I:202
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /I:202
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /I:202
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /I:202
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /I:202
8 messages similar to the above omitted
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /J:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /J:201
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /J:201
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /J:201
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /J:201
8 messages similar to the above omitted
Atom H42 is not in the residue template for PEE /J:202
Atom H42 is not in the residue template for PEE /K:201
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /K:202
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /K:202
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /K:202
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /K:202
Atom H67 has no neighbors to form bonds with according to residue template for
PEE /K:202
4 messages similar to the above omitted
Atom H76 is not in the residue template for PEE /B:401
Atom H42 is not in the residue template for PEE /A:901
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /A:902
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /A:902
Atom H6 has no neighbors to form bonds with according to residue template for
PEE /A:902
Atom H7 has no neighbors to form bonds with according to residue template for
PEE /A:902
Atom H8 has no neighbors to form bonds with according to residue template for
PEE /A:902
8 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
Atom H1 has no neighbors to form bonds with according to residue template for
PEE /A:905
Atom H2 has no neighbors to form bonds with according to residue template for
PEE /A:905
Atom H3 has no neighbors to form bonds with according to residue template for
PEE /A:905
Atom H4 has no neighbors to form bonds with according to residue template for
PEE /A:905
Atom H5 has no neighbors to form bonds with according to residue template for
PEE /A:905
13 messages similar to the above omitted
notes | Fetching compressed mmCIF 6m0r from
http://files.rcsb.org/download/6m0r.cif
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif
Fetching CCD PEE from http://ligand-expo.rcsb.org/reports/P/PEE/PEE.cif
Fetching CCD PPV from http://ligand-expo.rcsb.org/reports/P/PPV/PPV.cif
Fetching CCD EYR from http://ligand-expo.rcsb.org/reports/E/EYR/EYR.cif
6m0r title:
2.7A Yeast Vo state3 [more info...]
Chain information for 6m0r #1
---
Chain | Description | UniProt
A | V-type proton ATPase subunit a, vacuolar isoform | VPH1_YEAST
B | V-type proton ATPase subunit d | VA0D_YEAST
C | V-type proton ATPase subunit c'' | VATO_YEAST
D | V-type proton ATPase subunit c' | VATL2_YEAST
E F G H I J K L | V-type proton ATPase subunit c | VATL1_YEAST
M | V-type proton ATPase subunit e | VA0E_YEAST
N | V0 assembly protein 1 | VOA1_YEAST
O | Uncharacterized protein YPR170W-B | YP17B_YEAST
Non-standard residues in 6m0r #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
EYR —
(6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)
PPV — pyrophosphate
> view ortho
Expected an objects specifier or a view name or a keyword
> ui tool show "Color Actions"
> select /A:3-827
12161 atoms, 12314 bonds, 2 pseudobonds, 750 residues, 2 models selected
> color sel lime
> select /B:1-345
5490 atoms, 5549 bonds, 345 residues, 1 model selected
> color sel cyan
> select /C:16-213
3012 atoms, 3042 bonds, 198 residues, 1 model selected
> color sel yellow
> select /D:7-164
2340 atoms, 2363 bonds, 158 residues, 1 model selected
> color sel orange
> select /E:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> select /G:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> select /E:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> select clear
> select add /E:123@HD2
1 atom, 1 residue, 1 model selected
> select add /F:46@CZ
2 atoms, 2 residues, 1 model selected
> select add /F:122@OE1
3 atoms, 3 residues, 1 model selected
> select add /G:46@NE
4 atoms, 4 residues, 1 model selected
> select add /G:123@CD
5 atoms, 5 residues, 1 model selected
> select add /H:48@OD2
6 atoms, 6 residues, 1 model selected
> select add /H:120@O
7 atoms, 7 residues, 1 model selected
> select add /I:43@O
8 atoms, 8 residues, 1 model selected
> select add /I:46@CD
9 atoms, 9 residues, 1 model selected
> select add /I:127@CG2
10 atoms, 10 residues, 1 model selected
> select up
167 atoms, 159 bonds, 10 residues, 1 model selected
> select up
2064 atoms, 2074 bonds, 137 residues, 1 model selected
> select up
11720 atoms, 11810 bonds, 795 residues, 1 model selected
> color sel hot pink
> select clear
> select /L:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> color sel hot pink
> select /K:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> color sel hot pink
> select /J:1-159
2344 atoms, 2362 bonds, 159 residues, 1 model selected
> color sel hot pink
> select clear
> select
> ::name="BMA"::name="EYR"::name="HOH"::name="MAN"::name="NAG"::name="PEE"::name="PPV"
3372 atoms, 2880 bonds, 221 residues, 1 model selected
> hide sel atoms
> lighting full
> lighting soft
> lighting full
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> view orient
> ui mousemode right zoom
> set bgColor white
> save /Users/wilkenslab/Desktop/image1.png supersample 3
> material
Reflectivity: 0.8
Specular reflectivity 0.3
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> material shiny
> material
Reflectivity: 0.8
Specular reflectivity 1
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> select /B:1-345
5490 atoms, 5549 bonds, 345 residues, 1 model selected
> material shiny
> color sel purple
> color sel cornflower blue
> color sel light sea green
> color sel cyan
> color sel cornflower blue
> color sel dodger blue
> color sel dark turquoise
> color sel dodger blue
> color sel deep sky blue
> select /A:3-827
12161 atoms, 12314 bonds, 2 pseudobonds, 750 residues, 2 models selected
> color sel lawn green
> color sel green
> color sel chartreuse
> color sel spring green
> color sel lime green
> color sel lime
> color sel lime green
> select clear
> save /Users/wilkenslab/Desktop/6m0r_test1.tif width 1162 height 1110
> supersample 3 transparentBackground true
> graphics silhouettes false
> save /Users/wilkenslab/Desktop/6m0r_test2.tif width 1162 height 1110
> supersample 4
> camera ortho
> ui tool show "Side View"
> windowsize 1200 1200
> zoom 1
> zoom 2
> zoom 0.9
> zoom 1
> view
> view orient
> lighting simple
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> view
> select /M:1-71
1159 atoms, 1176 bonds, 71 residues, 1 model selected
> color sel blue
> select /N:212-263
830 atoms, 836 bonds, 52 residues, 1 model selected
> color sel red
> select /O:7-75
1044 atoms, 1060 bonds, 69 residues, 1 model selected
> color sel purple
> select clear
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/test1.tif width 1200
> height 1138 supersample 3
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/test1.tif width 1200
> height 1138 supersample 3
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/test1.tif width 1200
> height 1138 supersample 3 transparentBackground true
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> lighting simple
> savepos top1
Unknown command: savepos top1
> view name top1
> view top1
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> open 7fdc
Summary of feedback from opening 7fdc fetched from pdb
---
note | Fetching compressed mmCIF 7fdc from
http://files.rcsb.org/download/7fdc.cif
7fdc title:
CryoEM Structures of Reconstituted V-ATPase, state3 [more info...]
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show Matchmaker
> matchmaker #2/T to #1/C pairing ss
Parameters
---
Chain pairing | ss
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 6m0r, chain C (#1) with 7fdc, chain T (#2), sequence alignment
score = 902.7
RMSD between 167 pruned atom pairs is 1.148 angstroms; (across all 198 pairs:
1.445)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> sequence chain #2/A#2/C#2/E
Alignment identifier is 1
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> select add #2/W:51@CE2
1141 atoms, 1158 bonds, 160 residues, 1 model selected
> select add #2/W:126@CE1
1142 atoms, 1158 bonds, 161 residues, 1 model selected
> select add #2/X:48@OD2
1143 atoms, 1158 bonds, 162 residues, 1 model selected
> select add #2/X:123@CG
1144 atoms, 1158 bonds, 163 residues, 1 model selected
> select add #2/Y:47@CG
1145 atoms, 1158 bonds, 164 residues, 1 model selected
> select add #2/Y:121@CG
1146 atoms, 1158 bonds, 165 residues, 1 model selected
> select add #2/Z:45@CD1
1147 atoms, 1158 bonds, 166 residues, 1 model selected
> select add #2/a:45@CG
1148 atoms, 1158 bonds, 167 residues, 1 model selected
> select add #2/a:121@CG
1149 atoms, 1158 bonds, 168 residues, 1 model selected
> select add #2/b:45@O
1150 atoms, 1158 bonds, 169 residues, 1 model selected
> select add #2/b:123@CD
1151 atoms, 1158 bonds, 170 residues, 1 model selected
> select add #2/c:47@CD
1152 atoms, 1158 bonds, 171 residues, 1 model selected
> select add #2/c:123@CD
1153 atoms, 1158 bonds, 172 residues, 1 model selected
> select up
1247 atoms, 1259 bonds, 172 residues, 1 model selected
> select up
1715 atoms, 1735 bonds, 228 residues, 1 model selected
> select up
9132 atoms, 9276 bonds, 1274 residues, 1 model selected
> select up
64497 atoms, 65666 bonds, 8295 residues, 1 model selected
> select down
9132 atoms, 9276 bonds, 1274 residues, 1 model selected
> color sel hot pink
> select #2/S:212@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
209 atoms, 210 bonds, 27 residues, 1 model selected
> select up
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #2/e:252@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 6 residues, 1 model selected
> select up
403 atoms, 409 bonds, 52 residues, 1 model selected
> color sel red
> select #2/d:27@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 5 residues, 1 model selected
> select up
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #2/f:72@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
52 atoms, 53 bonds, 6 residues, 1 model selected
> select up
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> select #2/U:52@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
59 atoms, 60 bonds, 7 residues, 1 model selected
> select up
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #2/T:177@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 5 residues, 1 model selected
> select up
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #2/Q:714@CB
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
196 atoms, 200 bonds, 25 residues, 1 model selected
> select up
993 atoms, 1023 bonds, 124 residues, 1 model selected
> select up
1045 atoms, 1077 bonds, 130 residues, 1 model selected
> select up
4812 atoms, 4941 bonds, 597 residues, 1 model selected
> color sel lime green
> sequence chain #2/d
Alignment identifier is 2/d
> sequence chain #2/d
Destroying pre-existing alignment with identifier 2/d
Alignment identifier is 2/d
> color sel blue
> color sel lime green
> select clear
> select #2/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select clear
> select
> ::name="BMA"::name="EYR"::name="HOH"::name="MAN"::name="NAG"::name="PEE"::name="PPV"
3372 atoms, 2880 bonds, 221 residues, 1 model selected
> hide #!2 atoms
> show #!2 atoms
> select clear
> select #2/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> hide #2.1 models
> show #2.1 models
> select add #2
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> select subtract #2
Nothing selected
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/B:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light sea green
> select #2/D:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light sea green
> select #2/F:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light sea green
> select #2/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #2/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #2/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel tan
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #2/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> view
> lighting full
> select clear
> view top1
> lighting simple
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> log clear
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> hide sel atoms
> lighting full
> lighting simple
> select #2/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> hide sel atoms
> select #2/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> hide sel atoms
> select #2/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> hide sel cartoons
> select #2/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> turn z 5
> turn z -10
> select #2/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> show sel atoms
> select clear
> select #2/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel #ffffffff
> color sel #fffffffd
> color sel #ffffffec
> color sel #ffffffea
> color sel #ffffffe6
> color sel #ffffffe5
> color sel #ffffffe3
> color sel #ffffffe1
> color sel #ffffffe0
> color sel #ffffffe7
> color sel #fffffff0
> color sel #fffffffa
> color sel #ffffffff
> color sel #fffffffe
> color sel #fffffffa
> color sel #fffffff2
> color sel #ffffffe7
> color sel #ffffffd1
> color sel #ffffffcb
> color sel #ffffffc3
> color sel #ffffffbf
> color sel #ffffffba
> color sel #ffffffb7
> color sel #ffffffb3
> color sel #ffffffb1
> color sel #ffffffb0
> color sel #ffffffaf
> color sel #ffffffae
> color sel #ffffffab
> color sel #ffffffa9
> color sel #ffffffa4
> color sel #ffffffa3
> color sel #ffffffa2
> color sel #ffffff9f
> color sel #ffffff9c
> color sel #ffffff9b
> color sel #ffffff97
> color sel #ffffff92
> color sel #ffffff89
> color sel #ffffff86
> color sel #ffffff83
> color sel #ffffff82
> color sel #ffffff81
> color sel #ffffff80
> color sel #ff4af780
> color sel #33b5ff80
> color sel #20d9ff80
> color sel #1fd8ff80
> color sel #1fd8ff81
> color sel #1fd8ff88
> color sel #1fd8ff94
> color sel #1fd8ffa2
> color sel #1fd8ffad
> color sel #1fd8ffb7
> color sel #1fd8ffc0
> color sel #1fd8ffcd
> color sel #1fd8ffd8
> color sel #1fd8ffe4
> color sel #1fd8ffed
> color sel #1fd8fffb
> color sel #1fd8ffff
> color sel deep sky blue
> select clear
> lighting full
> view name top2
> log clear
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top1.tif width
> 1200 height 1138 supersample 3 transparentBackground true
> windowsize 1200 1200
> windowsize 1000 1000
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> windowsize 1000 1200
> windowsize 1000 1100
> windowsize 1000 1200
> windowsize 1200 1200
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> select #2/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel tan
> color sel burly wood
> color sel coral
> color sel salmon
> color sel rosy brown
> select clear
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice1.tif width
> 1200 height 1200 supersample 3
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> turn x -90
> view
> turn y 30
> turn y -15
> view
> view name side1
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> scalebar
> hide #!3 models
> close #3
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_side1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_side1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> turn x 90
> view
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> lighting simple
> view name top2
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice2.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top2.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> turn x -90
> select #1/O:68@HE1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
454 atoms, 462 bonds, 29 residues, 1 model selected
> select up
1044 atoms, 1060 bonds, 69 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> select #1/J:55@CG2
1 atom, 1 residue, 1 model selected
> select add #1/I:130@CG2
2 atoms, 2 residues, 1 model selected
> select up
35 atoms, 33 bonds, 2 residues, 1 model selected
> select up
718 atoms, 721 bonds, 44 residues, 1 model selected
> select up
4688 atoms, 4724 bonds, 318 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> color sel hot pink
> hide #!1 models
> show #!2 models
> view
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> open 7fda
Summary of feedback from opening 7fda fetched from pdb
---
note | Fetching compressed mmCIF 7fda from
http://files.rcsb.org/download/7fda.cif
7fda title:
CryoEM Structure of Reconstituted V-ATPase, state1 [more info...]
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> matchmaker #4/A#4/C#4/E to #2/A#2/C#2/E pairing ss
Parameters
---
Chain pairing | ss
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 7fdc, chain A (#2) with 7fda, chain A (#4), sequence alignment
score = 2917.4
Matchmaker 7fdc, chain C (#2) with 7fda, chain C (#4), sequence alignment
score = 2870
Matchmaker 7fdc, chain E (#2) with 7fda, chain E (#4), sequence alignment
score = 2894.6
RMSD between 633 pruned atom pairs is 1.255 angstroms; (across all 1782 pairs:
4.969)
> hide #!2 models
> select #4
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> show sel surfaces
> hide sel atoms
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select clear
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> select #4/D:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #4/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #4/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #4/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> color sel burly wood
> color sel rosy brown
> select #4/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #4/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #4/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #4/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #4/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> select #4/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> select #4/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #4/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #4/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #4/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #4/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> hide sel surfaces
> select #4
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel atoms
> show sel surfaces
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel surfaces
> select clear
> open 7fde
Summary of feedback from opening 7fde fetched from pdb
---
note | Fetching compressed mmCIF 7fde from
http://files.rcsb.org/download/7fde.cif
7fde title:
CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 [more info...]
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> ui tool show Matchmaker
> matchmaker #5/A#5/C#5/E to #4/A#4/C#4/E pairing ss
Parameters
---
Chain pairing | ss
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 7fda, chain A (#4) with 7fde, chain A (#5), sequence alignment
score = 2981.6
Matchmaker 7fda, chain C (#4) with 7fde, chain C (#5), sequence alignment
score = 2987.6
Matchmaker 7fda, chain E (#4) with 7fde, chain E (#5), sequence alignment
score = 2921.9
RMSD between 1762 pruned atom pairs is 0.581 angstroms; (across all 1782
pairs: 0.633)
> hide #!4 models
> select #5
39557 atoms, 40247 bonds, 5 pseudobonds, 5045 residues, 2 models selected
> hide sel atoms
> show sel surfaces
> log metadata #5
Metadata for 7fde #5
---
Title | CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 31541 — open map
Experimental method | Electron microscopy
Resolution | 3.8Å
> log chains #5
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> select #5/A:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/C:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> color sel light sea green
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/C:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> select #5/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> select #5/D:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/G:2-232
1833 atoms, 1847 bonds, 231 residues, 1 model selected
> color sel cornflower blue
> select #5/I:7-232
1801 atoms, 1815 bonds, 226 residues, 1 model selected
> color sel cornflower blue
> log metadata #5
Metadata for 7fde #5
---
Title | CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 31541 — open map
Experimental method | Electron microscopy
Resolution | 3.8Å
> log chains #5
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> select #5/K:31-232
1613 atoms, 1626 bonds, 202 residues, 1 model selected
> color sel cornflower blue
> select #5/H:2-113
876 atoms, 881 bonds, 112 residues, 1 model selected
> color sel orange
> select #5/J:2-113
876 atoms, 881 bonds, 112 residues, 1 model selected
> color sel orange
> select #5/L:21-113
731 atoms, 735 bonds, 93 residues, 1 model selected
> color sel orange
> select #5/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #5/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #5/O:5-392
2878 atoms, 2936 bonds, 1 pseudobond, 364 residues, 2 models selected
> color sel rosy brown
> select #5/P:63-272
1418 atoms, 1455 bonds, 1 pseudobond, 181 residues, 2 models selected
> color sel red
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> hide #!5 surfaces
> show #!5 atoms
> show #!5 surfaces
> hide #!5 surfaces
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save name side3
Cannot determine format for 'name'
> view name side3
> lighting simple
> turn x 90
Alignment identifier is 1/D
Alignment identifier is 1/C
Alignment identifier is 1/N
Alignment identifier is 1/M
Alignment identifier is 1
Alignment identifier is 1/O
Alignment identifier is 2
Alignment identifier is 1/A
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 12
Alignment identifier is 13
Alignment identifier is 14
Alignment identifier is 15
Alignment identifier is 16
Alignment identifier is 17
Alignment identifier is 5/P
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
Destroying pre-existing alignment with identifier 1/N
Alignment identifier is 1/N
Destroying pre-existing alignment with identifier 1/M
Alignment identifier is 1/M
Alignment identifier is 18
Destroying pre-existing alignment with identifier 1/O
Alignment identifier is 1/O
Alignment identifier is 19
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 20
Alignment identifier is 21
Alignment identifier is 22
Alignment identifier is 23
Alignment identifier is 24
Alignment identifier is 25
Alignment identifier is 26
Alignment identifier is 27
Alignment identifier is 28
Alignment identifier is 29
Alignment identifier is 30
Alignment identifier is 31
Alignment identifier is 32
Alignment identifier is 33
Alignment identifier is 34
Destroying pre-existing alignment with identifier 5/P
Alignment identifier is 5/P
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/C
Alignment identifier is 4/C
> sequence chain #4/E
Alignment identifier is 4/E
> select #4/A:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/A:256-263
50 atoms, 50 bonds, 8 residues, 1 model selected
> color (#!4 & sel) red
> select clear
> select #4/C:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/C:256-263
50 atoms, 50 bonds, 8 residues, 1 model selected
> color (#!4 & sel) red
> select #4/E:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/E:256-262
43 atoms, 43 bonds, 7 residues, 1 model selected
> color (#!4 & sel) red
> select clear
> view name ploop
> view side3
> view ploop
> view side3
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 atoms
> show #!5 surfaces
> view ploop
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> view side3
> turn y 30
> turn y -60
> view name oxr1
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 target m
> select #2
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> show sel surfaces
> hide sel atoms
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show "Color Actions"
> select #2/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/B:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #2/D:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #2/F:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> select #2/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #2/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #2/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel lime green
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #2/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> select #2/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #2/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #2/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #2/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #2/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #2/e:212-263
403 atoms, 409 bonds, 52 residues, 1 model selected
> color sel red
> select #2/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> select clear
> view ploop
> show #!5 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> open 7fdb
Summary of feedback from opening 7fdb fetched from pdb
---
note | Fetching compressed mmCIF 7fdb from
http://files.rcsb.org/download/7fdb.cif
7fdb title:
CryoEM Structures of Reconstituted V-ATPase,State2 [more info...]
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show Matchmaker
> matchmaker #6/A#6/C#6/E to #4/A#4/C#4/E pairing ss
Parameters
---
Chain pairing | ss
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 7fda, chain A (#4) with 7fdb, chain A (#6), sequence alignment
score = 2879
Matchmaker 7fda, chain C (#4) with 7fdb, chain C (#6), sequence alignment
score = 2978.6
Matchmaker 7fda, chain E (#4) with 7fdb, chain E (#6), sequence alignment
score = 2896.4
RMSD between 689 pruned atom pairs is 1.293 angstroms; (across all 1782 pairs:
4.887)
> hide #!2 models
> hide #!5 models
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show "Color Actions"
> select #6/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #6
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> hide sel atoms
> show sel surfaces
> select #6/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/B:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #6/D:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #6/F:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #6/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #6/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #6/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> select #6/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #6/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #6/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #6/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #6/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #6/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #6/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #6/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #6/e:212-263
403 atoms, 409 bonds, 52 residues, 1 model selected
> color sel red
> select #6/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> select clear
> hide #!6 atoms
> view side3
> view ploop
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf2.cxs
> view side3
> view oxr1
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf2.cxs
Log from Tue Dec 27 23:06:39 2022
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top1.tif width
> 1200 height 1138 supersample 3 transparentBackground true
> windowsize 1200 1200
> windowsize 1000 1000
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> windowsize 1000 1200
> windowsize 1000 1100
> windowsize 1000 1200
[Repeated 1 time(s)]
> windowsize 1200 1200
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> select #2/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel tan
> color sel burly wood
> color sel coral
> color sel salmon
> color sel rosy brown
> select clear
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice1.tif width
> 1200 height 1200 supersample 3
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> turn x -90
> view
> turn y 30
[Repeated 2 time(s)]
> turn y -15
> view
[Repeated 1 time(s)]
> view name side1
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> scalebar
> hide #!3 models
> close #3
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_side1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_side1.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> turn x 90
> view
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> lighting simple
> view name top2
> lighting full
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/7fdc_slice2.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_top2.tif width
> 1200 height 1200 supersample 3 transparentBackground true
> save /Users/wilkenslab/Desktop/2022Dec23_EMBO/Figures/6m0r_7fdc_comp.cxs
> turn x -90
> select #1/O:68@HE1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
454 atoms, 462 bonds, 29 residues, 1 model selected
> select up
1044 atoms, 1060 bonds, 69 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> select #1/J:55@CG2
1 atom, 1 residue, 1 model selected
> select add #1/I:130@CG2
2 atoms, 2 residues, 1 model selected
> select up
35 atoms, 33 bonds, 2 residues, 1 model selected
> select up
718 atoms, 721 bonds, 44 residues, 1 model selected
> select up
4688 atoms, 4724 bonds, 318 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> color sel hot pink
> hide #!1 models
> show #!2 models
> view
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> open 7fda
Summary of feedback from opening 7fda fetched from pdb
---
note | Fetching compressed mmCIF 7fda from
http://files.rcsb.org/download/7fda.cif
7fda title:
CryoEM Structure of Reconstituted V-ATPase, state1 [more info...]
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> matchmaker #4/A#4/C#4/E to #2/A#2/C#2/E pairing ss
Parameters
---
Chain pairing | ss
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 7fdc, chain A (#2) with 7fda, chain A (#4), sequence alignment
score = 2917.4
Matchmaker 7fdc, chain C (#2) with 7fda, chain C (#4), sequence alignment
score = 2870
Matchmaker 7fdc, chain E (#2) with 7fda, chain E (#4), sequence alignment
score = 2894.6
RMSD between 633 pruned atom pairs is 1.255 angstroms; (across all 1782 pairs:
4.969)
> hide #!2 models
> select #4
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> show sel surfaces
> hide sel atoms
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select clear
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #4/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #4/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> select #4/D:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #4/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #4/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #4/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #4/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #4/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> color sel burly wood
> color sel rosy brown
> select #4/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #4/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #4/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #4/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #4/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> log metadata #4
Metadata for 7fda #4
---
Title | CryoEM Structure of Reconstituted V-ATPase, state1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31538 — open map
Experimental method | Electron microscopy
Resolution | 4.2Å
> log chains #4
Chain information for 7fda #4
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #4/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> select #4/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> select #4/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #4/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #4/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #4/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #4/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> hide sel surfaces
> select #4
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel atoms
> show sel surfaces
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel surfaces
> select clear
> open 7fde
Summary of feedback from opening 7fde fetched from pdb
---
note | Fetching compressed mmCIF 7fde from
http://files.rcsb.org/download/7fde.cif
7fde title:
CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 [more info...]
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> ui tool show Matchmaker
> matchmaker #5/A#5/C#5/E to #4/A#4/C#4/E pairing ss
Parameters
---
Chain pairing | ss
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 7fda, chain A (#4) with 7fde, chain A (#5), sequence alignment
score = 2981.6
Matchmaker 7fda, chain C (#4) with 7fde, chain C (#5), sequence alignment
score = 2987.6
Matchmaker 7fda, chain E (#4) with 7fde, chain E (#5), sequence alignment
score = 2921.9
RMSD between 1762 pruned atom pairs is 0.581 angstroms; (across all 1782
pairs: 0.633)
> hide #!4 models
> select #5
39557 atoms, 40247 bonds, 5 pseudobonds, 5045 residues, 2 models selected
> hide sel atoms
> show sel surfaces
> log metadata #5
Metadata for 7fde #5
---
Title | CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 31541 — open map
Experimental method | Electron microscopy
Resolution | 3.8Å
> log chains #5
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> select #5/A:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/C:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> color sel light sea green
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> color sel orchid
> select #5/C:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> select #5/E:23-616
4587 atoms, 4686 bonds, 594 residues, 1 model selected
> select #5/B:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> select #5/D:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #5/F:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #5/G:2-232
1833 atoms, 1847 bonds, 231 residues, 1 model selected
> color sel cornflower blue
> select #5/I:7-232
1801 atoms, 1815 bonds, 226 residues, 1 model selected
> color sel cornflower blue
> log metadata #5
Metadata for 7fde #5
---
Title | CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 31541 — open map
Experimental method | Electron microscopy
Resolution | 3.8Å
> log chains #5
Chain information for 7fde #5
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Oxidation resistance protein 1 | OXR1_YEAST
> select #5/K:31-232
1613 atoms, 1626 bonds, 202 residues, 1 model selected
> color sel cornflower blue
> select #5/H:2-113
876 atoms, 881 bonds, 112 residues, 1 model selected
> color sel orange
> select #5/J:2-113
876 atoms, 881 bonds, 112 residues, 1 model selected
> color sel orange
> select #5/L:21-113
731 atoms, 735 bonds, 93 residues, 1 model selected
> color sel orange
> select #5/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #5/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #5/O:5-392
2878 atoms, 2936 bonds, 1 pseudobond, 364 residues, 2 models selected
> color sel rosy brown
> select #5/P:63-272
1418 atoms, 1455 bonds, 1 pseudobond, 181 residues, 2 models selected
> color sel red
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> hide #!5 surfaces
> show #!5 atoms
> show #!5 surfaces
[Repeated 1 time(s)]
> hide #!5 surfaces
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save name side3
Cannot determine format for 'name'
> view name side3
> lighting simple
> turn x 90
Alignment identifier is 1/D
Alignment identifier is 1/C
Alignment identifier is 1/N
Alignment identifier is 1/M
Alignment identifier is 1
Alignment identifier is 1/O
Alignment identifier is 2
Alignment identifier is 1/A
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 12
Alignment identifier is 13
Alignment identifier is 14
Alignment identifier is 15
Alignment identifier is 16
Alignment identifier is 17
Alignment identifier is 5/P
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
Destroying pre-existing alignment with identifier 1/N
Alignment identifier is 1/N
Destroying pre-existing alignment with identifier 1/M
Alignment identifier is 1/M
Alignment identifier is 18
Destroying pre-existing alignment with identifier 1/O
Alignment identifier is 1/O
Alignment identifier is 19
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 20
Alignment identifier is 21
Alignment identifier is 22
Alignment identifier is 23
Alignment identifier is 24
Alignment identifier is 25
Alignment identifier is 26
Alignment identifier is 27
Alignment identifier is 28
Alignment identifier is 29
Alignment identifier is 30
Alignment identifier is 31
Alignment identifier is 32
Alignment identifier is 33
Alignment identifier is 34
Destroying pre-existing alignment with identifier 5/P
Alignment identifier is 5/P
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/C
Alignment identifier is 4/C
> sequence chain #4/E
Alignment identifier is 4/E
> select #4/A:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/A:256-263
50 atoms, 50 bonds, 8 residues, 1 model selected
> color (#!4 & sel) red
> select clear
> select #4/C:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/C:256-263
50 atoms, 50 bonds, 8 residues, 1 model selected
> color (#!4 & sel) red
> select #4/E:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/E:256-262
43 atoms, 43 bonds, 7 residues, 1 model selected
> color (#!4 & sel) red
> select clear
> view name ploop
> view side3
> view ploop
> view side3
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 atoms
> show #!5 surfaces
> view ploop
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> view side3
> turn y 30
> turn y -60
> view name oxr1
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 target m
> select #2
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> show sel surfaces
> hide sel atoms
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show "Color Actions"
> select #2/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #2/B:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #2/D:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #2/F:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> select #2/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #2/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #2/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #2/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #2/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel lime green
> select #2/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #2/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> select #2/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #2/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #2/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #2/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> log metadata #2
Metadata for 7fdc #2
---
Title | CryoEM Structures of Reconstituted V-ATPase, state3
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31540 — open map
Experimental method | Electron microscopy
Resolution | 6.6Å
> log chains #2
Chain information for 7fdc #2
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #2/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #2/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #2/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #2/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #2/e:212-263
403 atoms, 409 bonds, 52 residues, 1 model selected
> color sel red
> select #2/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> select clear
> view ploop
> show #!5 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf.cxs
> open 7fdb
Summary of feedback from opening 7fdb fetched from pdb
---
note | Fetching compressed mmCIF 7fdb from
http://files.rcsb.org/download/7fdb.cif
7fdb title:
CryoEM Structures of Reconstituted V-ATPase,State2 [more info...]
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show Matchmaker
> matchmaker #6/A#6/C#6/E to #4/A#4/C#4/E pairing ss
Parameters
---
Chain pairing | ss
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 7fda, chain A (#4) with 7fdb, chain A (#6), sequence alignment
score = 2879
Matchmaker 7fda, chain C (#4) with 7fdb, chain C (#6), sequence alignment
score = 2978.6
Matchmaker 7fda, chain E (#4) with 7fdb, chain E (#6), sequence alignment
score = 2896.4
RMSD between 689 pruned atom pairs is 1.293 angstroms; (across all 1782 pairs:
4.887)
> hide #!2 models
> hide #!5 models
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> ui tool show "Color Actions"
> select #6/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> select #6
64497 atoms, 65666 bonds, 6 pseudobonds, 8295 residues, 2 models selected
> hide sel atoms
> show sel surfaces
> select #6/A:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/C:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/E:23-616
4586 atoms, 4685 bonds, 594 residues, 1 model selected
> color sel orchid
> select #6/B:9-487
3699 atoms, 3768 bonds, 1 pseudobond, 470 residues, 2 models selected
> color sel light green
> select #6/D:9-487
3706 atoms, 3776 bonds, 1 pseudobond, 471 residues, 2 models selected
> color sel light green
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #6/F:9-487
3681 atoms, 3750 bonds, 1 pseudobond, 468 residues, 2 models selected
> color sel light green
> select #6/G:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/I:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/K:8-232
1802 atoms, 1817 bonds, 225 residues, 1 model selected
> color sel cornflower blue
> select #6/H:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/J:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/L:2-112
871 atoms, 876 bonds, 111 residues, 1 model selected
> color sel orange
> select #6/M:6-223
1756 atoms, 1775 bonds, 218 residues, 1 model selected
> color sel red
> select #6/N:2-116
928 atoms, 944 bonds, 115 residues, 1 model selected
> color sel light gray
> select #6/O:1-392
3121 atoms, 3184 bonds, 392 residues, 1 model selected
> color sel rosy brown
> select #6/P:1-469
3665 atoms, 3723 bonds, 1 pseudobond, 452 residues, 2 models selected
> color sel gold
> select #6/Q:3-829
6069 atoms, 6221 bonds, 2 pseudobonds, 747 residues, 2 models selected
> color sel lime green
> log metadata #6
Metadata for 7fdb #6
---
Title | CryoEM Structures of Reconstituted V-ATPase,State2
Citation | Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens,
S., Roh, S.H. (2021). CryoEM Structures of Reconstituted V-ATPase and
Oxr1-bound V1 Reveal a Novel Mechanism of Regulation. Embo J.
Source (natural) | Saccharomyces cerevisiae S288C
Gene sources | Saccharomyces cerevisiae S288C
Homo sapiens (human)
CryoEM Map | EMDB 31539 — open map
Experimental method | Electron microscopy
Resolution | 4.8Å
> log chains #6
Chain information for 7fdb #6
---
Chain | Description | UniProt
A C E | Yeast Vacuolar ATPase A subunit |
B D F | V-type proton ATPase subunit B | VATB_YEAST
G I K | V-type proton ATPase subunit E | VATE_YEAST
H J L | V-type proton ATPase subunit G |
M | V-type proton ATPase subunit D | VATD_YEAST
N | V-type proton ATPase subunit F | VATF_YEAST
O | V-type proton ATPase subunit C | VATC_YEAST
P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton
ATPase subunit H(CT) | VATH_HUMAN
Q | Yeast Vacuolar ATPase a subunit | VPH1_YEAST
S | V-type proton ATPase subunit d | VA0D_YEAST
T | V-type proton ATPase subunit c'' | VATO_YEAST
U | V-type proton ATPase subunit c' | VATL2_YEAST
V W X Y Z a b c | V-type proton ATPase subunit c | VATL1_YEAST
d | V-type proton ATPase subunit e | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | Yeast Vacuolar ATPase f subunit | YP17B_YEAST
> select #6/S:2-345
2793 atoms, 2852 bonds, 344 residues, 1 model selected
> color sel deep sky blue
> select #6/T:14-213
1492 atoms, 1523 bonds, 200 residues, 1 model selected
> color sel yellow
> select #6/U:7-163
1139 atoms, 1162 bonds, 157 residues, 1 model selected
> color sel orange
> select #6/V:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/W:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/X:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/Y:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #6/Z:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/a:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/b:1-160
1146 atoms, 1164 bonds, 160 residues, 1 model selected
> color sel hot pink
> select #6/c:1-159
1140 atoms, 1158 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #6/d:1-69
553 atoms, 569 bonds, 69 residues, 1 model selected
> color sel blue
> select #6/e:212-263
403 atoms, 409 bonds, 52 residues, 1 model selected
> color sel red
> select #6/f:2-77
583 atoms, 600 bonds, 76 residues, 1 model selected
> color sel purple
> select clear
> hide #!6 atoms
> view side3
> view ploop
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> save
> /Users/wilkenslab/Papers_to_be/2022Dec23_EMBO/Figures/6m0r_7fdc_comp_surf2.cxs
——— End of log from Tue Dec 27 23:06:39 2022 ———
opened ChimeraX session
OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GTX 775M OpenGL Engine
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac14,2
Processor Name: Intel Core i7
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 433.140.2.0.0
SMC Version (system): 2.15f7
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G103)
Kernel Version: Darwin 18.7.0
Time since boot: 5 days 2:11
Graphics/Displays:
NVIDIA GeForce GTX 775M:
Chipset Model: NVIDIA GeForce GTX 775M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: NVIDIA (0x10de)
Device ID: 0x119d
Revision ID: 0x00a2
ROM Revision: 3782
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
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 → Crash during redraw |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash during redraw → Graphics crash, macOS 10.14.6, NVIDIA GeForce GTX 775M |
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Apple Nvidia graphics driver crash.