![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8543 closed defect (can't reproduce)
Crash destroying QGridLayout
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [2770]
Path: /Volumes/VOLUME/ChimeraX-1.4.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.4.0 (1.4.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [2770]
User ID: 505
Date/Time: 2023-02-22 19:50:08.427 +0100
OS Version: Mac OS X 10.15.7 (19H15)
Report Version: 12
Bridge OS Version: 5.0.1 (18P2561)
Anonymous UUID: 1C80D7C0-D9D6-B7E4-ABEB-8C57BCD37ACF
Sleep/Wake UUID: CC3616DF-4E21-4C2B-B5B2-1CFCB9EE1FCD
Time Awake Since Boot: 11000 seconds
Time Since Wake: 2200 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff69c8233a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff69d3ee60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff69b9993e raise + 26
3 libsystem_platform.dylib 0x00007fff69d335fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtWidgets 0x000000011d06fdc7 QGridLayout::~QGridLayout() + 39
6 QtWidgets.abi3.so 0x000000010cc31438 non-virtual thunk to sipQGridLayout::~sipQGridLayout() + 56
7 QtWidgets 0x000000011d04b960 QBoxLayout::~QBoxLayout() + 176
8 QtWidgets.abi3.so 0x000000010cca6307 sipQVBoxLayout::~sipQVBoxLayout() + 55
9 QtWidgets 0x000000011d08098a QWidget::~QWidget() + 634
10 QtWidgets.abi3.so 0x000000010ccc3f17 sipQWidget::~sipQWidget() + 55
11 QtCore 0x000000010c5f929f QObjectPrivate::deleteChildren() + 159
12 QtWidgets 0x000000011d080c10 QWidget::~QWidget() + 1280
13 QtWidgets.abi3.so 0x000000010ccc3f17 sipQWidget::~sipQWidget() + 55
14 QtCore 0x000000010c5f929f QObjectPrivate::deleteChildren() + 159
15 QtWidgets 0x000000011d080c10 QWidget::~QWidget() + 1280
16 QtWidgets.abi3.so 0x000000010cc77407 sipQDockWidget::~sipQDockWidget() + 55
17 sip.cpython-39-darwin.so 0x000000010cb4f2e7 forgetObject + 183
18 sip.cpython-39-darwin.so 0x000000010cb4efd5 sipWrapper_dealloc + 37
19 org.python.python 0x0000000104e62b3b subtype_dealloc + 1019
20 org.python.python 0x0000000104e418c2 dict_dealloc + 162
21 org.python.python 0x0000000104e7497f subtype_clear + 239
22 org.python.python 0x0000000104f4fc29 collect + 3193
23 org.python.python 0x0000000104f50c27 gc_collect + 231
24 org.python.python 0x0000000104e4e0bd cfunction_vectorcall_FASTCALL_KEYWORDS + 125
25 org.python.python 0x0000000104ee7e0c call_function + 732
26 org.python.python 0x0000000104ee52a2 _PyEval_EvalFrameDefault + 25554
27 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
28 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
29 org.python.python 0x0000000104ee5989 _PyEval_EvalFrameDefault + 27321
30 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
31 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
32 QtCore.abi3.so 0x000000010c2ef607 PyQtSlot::call(_object*, _object*) const + 39
33 QtCore.abi3.so 0x000000010c2ef516 PyQtSlot::invoke(void**, _object*, void*, bool) const + 358
34 QtCore.abi3.so 0x000000010c2f0445 PyQtSlotProxy::unislot(void**) + 85
35 QtCore.abi3.so 0x000000010c2f03ba PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
36 QtCore 0x000000010c6019e7 0x10c545000 + 772583
37 QtCore 0x000000010c6164d7 QTimer::timerEvent(QTimerEvent*) + 199
38 QtCore.abi3.so 0x000000010c1debf9 sipQTimer::timerEvent(QTimerEvent*) + 121
39 QtCore 0x000000010c5f9bad QObject::event(QEvent*) + 109
40 QtCore.abi3.so 0x000000010c1dea7a sipQTimer::event(QEvent*) + 186
41 QtWidgets 0x000000011d03d067 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
42 QtWidgets 0x000000011d03e023 QApplication::notify(QObject*, QEvent*) + 499
43 QtWidgets.abi3.so 0x000000010ccb0829 sipQApplication::notify(QObject*, QEvent*) + 233
44 QtCore 0x000000010c5b0dca QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
45 QtCore 0x000000010c73ca01 QTimerInfoList::activateTimers() + 961
46 libqcocoa.dylib 0x0000000129ad8885 0x129ac0000 + 100485
47 com.apple.CoreFoundation 0x00007fff2fc65d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
48 com.apple.CoreFoundation 0x00007fff2fc65cf1 __CFRunLoopDoSource0 + 103
49 com.apple.CoreFoundation 0x00007fff2fc65b67 __CFRunLoopDoSources0 + 301
50 com.apple.CoreFoundation 0x00007fff2fc6483a __CFRunLoopRun + 927
51 com.apple.CoreFoundation 0x00007fff2fc63e3e CFRunLoopRunSpecific + 462
52 com.apple.HIToolbox 0x00007fff2e890abd RunCurrentEventLoopInMode + 292
53 com.apple.HIToolbox 0x00007fff2e8906f4 ReceiveNextEventCommon + 359
54 com.apple.HIToolbox 0x00007fff2e890579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
55 com.apple.AppKit 0x00007fff2ced6039 _DPSNextEvent + 883
56 com.apple.AppKit 0x00007fff2ced4880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
57 com.apple.AppKit 0x00007fff2cec658e -[NSApplication run] + 658
58 libqcocoa.dylib 0x0000000129ad948c 0x129ac0000 + 103564
59 QtCore 0x000000010c5ba516 QEventLoop::exec(QFlags) + 486
60 QtCore 0x000000010c5b13e5 QCoreApplication::exec() + 133
61 QtWidgets.abi3.so 0x000000010cd9d90a meth_QApplication_exec(_object*, _object*) + 90
62 org.python.python 0x0000000104e4e71d cfunction_call + 125
63 org.python.python 0x0000000104e0f5b7 _PyObject_MakeTpCall + 359
64 org.python.python 0x0000000104ee7e9c call_function + 876
65 org.python.python 0x0000000104ee52a2 _PyEval_EvalFrameDefault + 25554
66 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
67 org.python.python 0x0000000104e11d6a method_vectorcall + 202
68 org.python.python 0x0000000104ee7e0c call_function + 732
69 org.python.python 0x0000000104ee52a2 _PyEval_EvalFrameDefault + 25554
70 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
71 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
72 org.python.python 0x0000000104ee7e0c call_function + 732
73 org.python.python 0x0000000104ee534b _PyEval_EvalFrameDefault + 25723
74 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
75 org.python.python 0x0000000104ededab PyEval_EvalCode + 139
76 org.python.python 0x0000000104edbc12 builtin_exec + 626
77 org.python.python 0x0000000104e4e023 cfunction_vectorcall_FASTCALL + 195
78 org.python.python 0x0000000104ee7e0c call_function + 732
79 org.python.python 0x0000000104ee534b _PyEval_EvalFrameDefault + 25723
80 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
81 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
82 org.python.python 0x0000000104ee7e0c call_function + 732
83 org.python.python 0x0000000104ee534b _PyEval_EvalFrameDefault + 25723
84 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
85 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
86 org.python.python 0x0000000104f4e870 pymain_run_module + 208
87 org.python.python 0x0000000104f4df87 Py_RunMain + 1431
88 org.python.python 0x0000000104f4e58f pymain_main + 223
89 org.python.python 0x0000000104f4e49b Py_Main + 43
90 edu.ucsf.cgl.ChimeraX 0x0000000104dc2dc8 main + 120
91 libdyld.dylib 0x00007fff69b3acc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 6:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 7:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000105b9a49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 8:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff69c84b96 kevent64 + 10
1 QtWebEngineCore 0x00000001220955ca 0x11e133000 + 66463178
2 QtWebEngineCore 0x00000001220954c7 0x11e133000 + 66462919
3 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
4 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
5 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
6 QtWebEngineCore 0x000000012201b84d 0x11e133000 + 65964109
7 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
8 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
9 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 9:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x0000000122027d5f 0x11e133000 + 66014559
4 QtWebEngineCore 0x000000012202880c 0x11e133000 + 66017292
5 QtWebEngineCore 0x000000012202840d 0x11e133000 + 66016269
6 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 10:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x0000000122027d5f 0x11e133000 + 66014559
4 QtWebEngineCore 0x000000012202880c 0x11e133000 + 66017292
5 QtWebEngineCore 0x000000012202837d 0x11e133000 + 66016125
6 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 11:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff69c84b96 kevent64 + 10
1 QtWebEngineCore 0x00000001220955ca 0x11e133000 + 66463178
2 QtWebEngineCore 0x00000001220954c7 0x11e133000 + 66462919
3 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
4 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
5 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
6 QtWebEngineCore 0x0000000120f5ae32 0x11e133000 + 48397874
7 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
8 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
9 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 13:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000012205b8bb 0x11e133000 + 66226363
3 QtWebEngineCore 0x000000012412c55d 0x11e133000 + 100635997
4 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
5 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 14:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 15:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff69c84b96 kevent64 + 10
1 QtWebEngineCore 0x00000001220955ca 0x11e133000 + 66463178
2 QtWebEngineCore 0x00000001220954c7 0x11e133000 + 66462919
3 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
4 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
5 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
6 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
7 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
8 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 17:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 18:: NetworkService
0 libsystem_kernel.dylib 0x00007fff69c84b96 kevent64 + 10
1 QtWebEngineCore 0x00000001220955ca 0x11e133000 + 66463178
2 QtWebEngineCore 0x00000001220954c7 0x11e133000 + 66462919
3 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
4 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
5 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
6 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
7 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
8 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 19:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 20:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x0000000122027d5f 0x11e133000 + 66014559
4 QtWebEngineCore 0x000000012202880c 0x11e133000 + 66017292
5 QtWebEngineCore 0x000000012202846d 0x11e133000 + 66016365
6 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 21:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 22:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2fc65ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2fc649c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2fc63e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2d077954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 23:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x000000012206378f 0x11e133000 + 66258831
4 QtWebEngineCore 0x0000000121f99089 0x11e133000 + 65429641
5 QtWebEngineCore 0x000000012201219c 0x11e133000 + 65925532
6 QtWebEngineCore 0x0000000121fc9ff8 0x11e133000 + 65630200
7 QtWebEngineCore 0x0000000122034458 0x11e133000 + 66065496
8 QtWebEngineCore 0x00000001220345ea 0x11e133000 + 66065898
9 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
10 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 24:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x0000000122027d5f 0x11e133000 + 66014559
4 QtWebEngineCore 0x000000012202853a 0x11e133000 + 66016570
5 QtWebEngineCore 0x00000001220283ad 0x11e133000 + 66016173
6 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 31:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 32:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x0000000144149fe3 th_worker(void*) + 115
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 33:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 34:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 35:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 36:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 37:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 38:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 39:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000145ac2a9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 40:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 QtWebEngineCore 0x00000001220639c6 0x11e133000 + 66259398
3 QtWebEngineCore 0x0000000122027d5f 0x11e133000 + 66014559
4 QtWebEngineCore 0x000000012202880c 0x11e133000 + 66017292
5 QtWebEngineCore 0x000000012202840d 0x11e133000 + 66016269
6 QtWebEngineCore 0x000000012205c4a8 0x11e133000 + 66229416
7 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 41:
0 libsystem_pthread.dylib 0x00007fff69d3ab68 start_wqthread + 0
Thread 42:: Dispatch queue: com.apple.root.user-interactive-qos
0 libsystem_kernel.dylib 0x00007fff69c7bdfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff69c7c170 mach_msg + 60
2 com.apple.QuartzCore 0x00007fff3b755825 CA::CA_BLOCKED_WAITING_FOR_CLIENT_FENCES(unsigned int, unsigned long) + 170
3 com.apple.QuartzCore 0x00007fff3b73772a CA::Context::commit_transaction(CA::Transaction*, double) + 1906
4 com.apple.QuartzCore 0x00007fff3b735cf0 CA::Transaction::commit() + 644
5 com.apple.AppKit 0x00007fff2cf2e384 NSPerformVisuallyAtomicChange + 154
6 com.apple.AppKit 0x00007fff2d17d381 -[_NSWindowTransformAnimation _stopAnimation:withDisplayLink:] + 110
7 com.apple.AppKit 0x00007fff2d0dae34 -[NSScreenDisplayLink _fire] + 180
8 com.apple.AppKit 0x00007fff2d8286c2 ___NSRunLoopTimerCreateWithHandler_block_invoke + 34
9 com.apple.CoreFoundation 0x00007fff2fc807f9 __CFRUNLOOP_IS_CALLING_OUT_TO_A_TIMER_CALLBACK_FUNCTION__ + 20
10 com.apple.CoreFoundation 0x00007fff2fc8035f __CFRunLoopDoTimer + 859
11 com.apple.CoreFoundation 0x00007fff2fc7fe47 __CFRunLoopDoTimers + 322
12 com.apple.CoreFoundation 0x00007fff2fc64bea __CFRunLoopRun + 1871
13 com.apple.CoreFoundation 0x00007fff2fc63e3e CFRunLoopRunSpecific + 462
14 com.apple.Foundation 0x00007fff322ff1c8 -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212
15 com.apple.AppKit 0x00007fff2d17d150 -[NSAnimation(NSInternal) _runBlocking] + 344
16 com.apple.AppKit 0x00007fff2d17ce2d __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 97
17 libdispatch.dylib 0x00007fff69ae06c4 _dispatch_call_block_and_release + 12
18 libdispatch.dylib 0x00007fff69ae1658 _dispatch_client_callout + 8
19 libdispatch.dylib 0x00007fff69aefaa8 _dispatch_root_queue_drain + 663
20 libdispatch.dylib 0x00007fff69af0097 _dispatch_worker_thread2 + 92
21 libsystem_pthread.dylib 0x00007fff69d3b9f7 _pthread_wqthread + 220
22 libsystem_pthread.dylib 0x00007fff69d3ab77 start_wqthread + 15
Thread 43:
0 libsystem_pthread.dylib 0x00007fff69d3ab68 start_wqthread + 0
Thread 44:
0 libsystem_pthread.dylib 0x00007fff69d3ab68 start_wqthread + 0
Thread 45:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104f3e79c PyThread_acquire_lock_timed + 700
3 org.python.python 0x0000000104f8d69f acquire_timed + 111
4 org.python.python 0x0000000104f8d7b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000104e1814e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x0000000104ee7e0c call_function + 732
7 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
9 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x0000000104ee7e0c call_function + 732
11 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
13 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x0000000104ee7e0c call_function + 732
15 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
17 org.python.python 0x0000000104ee7e0c call_function + 732
18 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
20 org.python.python 0x0000000104ee7e0c call_function + 732
21 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
23 org.python.python 0x0000000104e11db2 method_vectorcall + 274
24 org.python.python 0x0000000104f8d046 t_bootstrap + 70
25 org.python.python 0x0000000104f3e2f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 46:
0 libsystem_kernel.dylib 0x00007fff69c7e882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69d3f425 _pthread_cond_wait + 698
2 org.python.python 0x0000000104f3e79c PyThread_acquire_lock_timed + 700
3 org.python.python 0x0000000104f8d69f acquire_timed + 111
4 org.python.python 0x0000000104f8d7b0 lock_PyThread_acquire_lock + 48
5 org.python.python 0x0000000104e1814e method_vectorcall_VARARGS_KEYWORDS + 350
6 org.python.python 0x0000000104ee7e0c call_function + 732
7 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
8 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
9 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
10 org.python.python 0x0000000104ee7e0c call_function + 732
11 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
12 org.python.python 0x0000000104ee8b03 _PyEval_EvalCode + 2611
13 org.python.python 0x0000000104e0fcb1 _PyFunction_Vectorcall + 289
14 org.python.python 0x0000000104ee7e0c call_function + 732
15 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
16 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
17 org.python.python 0x0000000104ee7e0c call_function + 732
18 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
19 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
20 org.python.python 0x0000000104ee7e0c call_function + 732
21 org.python.python 0x0000000104ee527e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x0000000104e0fd28 function_code_fastcall + 104
23 org.python.python 0x0000000104e11db2 method_vectorcall + 274
24 org.python.python 0x0000000104f8d046 t_bootstrap + 70
25 org.python.python 0x0000000104f3e2f9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff69d3f109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff69d3ab8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010d4a8dc0 rcx: 0x00007fe0f8047a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fe0f8047a80 rsp: 0x00007fe0f8047a58
r8: 0x00007fe0f8047f48 r9: 0xc1ae8bf2d61d3325 r10: 0x000000010d4a8dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff69c8233a rfl: 0x0000000000000246 cr2: 0x00007fe0f8047f48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff68aa0000 - 0x7fff68ae4ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff68ae5000 - 0x7fff68af7ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff68af8000 - 0x7fff68af9ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff68afa000 - 0x7fff68ce4ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff68dd8000 - 0x7fff68e05ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff68e87000 - 0x7fff68eb8ff7 libtidy.A.dylib (17.2) /usr/lib/libtidy.A.dylib
0x7fff68eda000 - 0x7fff68f34ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff68f35000 - 0x7fff68f38ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff68f39000 - 0x7fff68f46ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff68f4c000 - 0x7fff6902efff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff69032000 - 0x7fff6905afff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff6905b000 - 0x7fff6906dff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6991c000 - 0x7fff69921ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff69922000 - 0x7fff6992dfff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6992e000 - 0x7fff69935fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff69936000 - 0x7fff6993fff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff69940000 - 0x7fff699d2fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff69adf000 - 0x7fff69b1fff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff69b20000 - 0x7fff69b56fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff69b57000 - 0x7fff69b57ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff69b58000 - 0x7fff69b64ff3 libkxld.dylib (6153.141.2.2) /usr/lib/system/libkxld.dylib
0x7fff69b65000 - 0x7fff69b65ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff69b66000 - 0x7fff69b6bff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff69b6c000 - 0x7fff69b6eff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff69b6f000 - 0x7fff69b70ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff69b71000 - 0x7fff69b88ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff69b89000 - 0x7fff69b89ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff69b8a000 - 0x7fff69c11fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff69c12000 - 0x7fff69c15ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff69c16000 - 0x7fff69c19fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff69c1a000 - 0x7fff69c22fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff69c23000 - 0x7fff69c2afff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff69c2b000 - 0x7fff69c2cffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff69c2d000 - 0x7fff69c7aff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff69c7b000 - 0x7fff69ca7ff7 libsystem_kernel.dylib (6153.141.2.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff69ca8000 - 0x7fff69ceffff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff69cf0000 - 0x7fff69d17fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff69d18000 - 0x7fff69d25ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff69d26000 - 0x7fff69d2fff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff69d30000 - 0x7fff69d38fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff69d39000 - 0x7fff69d43fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff69d44000 - 0x7fff69d48ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff69d49000 - 0x7fff69d4bfff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff69d4c000 - 0x7fff69d53ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff69d54000 - 0x7fff69d6aff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff69d6c000 - 0x7fff69d71ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff69d72000 - 0x7fff69da7ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 3
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: 8687
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=4.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.9G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 4
Activity Tracing 256K 1
CG backing stores 6712K 13
CG image 5744K 41
CoreAnimation 8724K 73
CoreGraphics 8K 1
CoreImage 40K 6
CoreUI image data 3272K 34
Foundation 28K 2
Kernel Alloc Once 8K 1
MALLOC 3.3G 372
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 792.0M 10 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 256K 3
STACK GUARD 184K 46
Stack 189.9M 47
Stack Guard 56.0M 1
VM_ALLOCATE 108.6M 181
VM_ALLOCATE (reserved) 384.0M 2 reserved VM address space (unallocated)
__DATA 84.0M 792
__DATA_CONST 180K 10
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 442.9M 396
__OBJC_RO 32.3M 1
__OBJC_RW 1904K 1
__TEXT 758.6M 737
__UNICODE 564K 1
mapped file 133.8M 64
shared memory 2880K 30
=========== ======= =======
TOTAL 6.4G 2884
TOTAL, minus reserved VM space 5.1G 2884
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/elena/Desktop/figures_TAC/dimercomparison.cxs
Opened cryosparc_P142_J865_008_tightTarget zflip.mrc as #2, grid size
460,460,460, pixel 0.411, shown at level 0.116, step 1, values float32
Opened cryosparc_P136_J110_004_volume_map.mrc as #1, grid size 150,150,150,
pixel 2, shown at level 0.353, step 1, values float32
Log from Wed Feb 22 14:42:34 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/elena/Desktop/figures_TAC/220923.cxs
Opened cryosparc_P142_J865_008_tightTarget zflip.mrc as #2, grid size
460,460,460, pixel 0.411, shown at level 0.116, step 1, values float32
Opened cryosparc_P136_J110_004_volume_map.mrc as #1, grid size 150,150,150,
pixel 2, shown at level 0.353, step 1, values float32
Log from Fri Sep 23 13:31:56 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-2.pdb format
> pdb
refined-coot-2.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-2.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> open "/Users/elena/Documents/ccp-em_workshop_Elena/Elena data workshop/ccp-
> em_workshop_Elena/cryosparc_P142_J865_008_tightTarget zflip.mrc"
Opened cryosparc_P142_J865_008_tightTarget zflip.mrc as #2, grid size
460,460,460, pixel 0.411, shown at level 0.163, step 2, values float32
> color zone #2 near #1 distance 2.47
> hide #!1 models
> volume #2 level 0.0279
> volume #2 level 0.1569
> show #!1 models
> style stick
Changed 13329 atom styles
> style stick
Changed 13329 atom styles
> style sphere
Changed 13329 atom styles
> color bychain
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.1569
> volume #2 step 1
> volume #2 level 0.1348
> volume #2 level -0.001816
> volume #2 level 0.1397
> volume #2 level 0.09254
> ui tool show "Color Zone"
> color zone #2 near #1 distance 2.33
> color zone #2 near #1 distance 0.76
> color zone #2 near #1 distance 0.77
> color zone #2 near #1 distance 2.01
> color zone #2 near #1 distance 1.98
> color zone #2 near #1 distance 8.09
> color zone #2 near #1 distance 6.11
> color zone #2 near #1 distance 1.45
[Repeated 1 time(s)]
> color zone #2 near #1 distance 1.35
> color zone #2 near #1 distance 9.12
> color zone #2 near #1 distance 7.63
> color zone #2 near #1 distance 6.2
> close #1
> close #2
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-2.pdb format
> pdb
refined-coot-2.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-2.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> open "/Users/elena/Documents/ccp-em_workshop_Elena/Elena data workshop/ccp-
> em_workshop_Elena/cryosparc_P142_J865_008_tightTarget zflip.mrc"
Opened cryosparc_P142_J865_008_tightTarget zflip.mrc as #2, grid size
460,460,460, pixel 0.411, shown at level 0.163, step 2, values float32
> volume #2 step 1
> lighting soft
[Repeated 1 time(s)]
> color zone #2 near #1 distance 2.47
> hide #!1 models
> color zone #2 near #1 distance 2.4
> color zone #2 near #1 distance 2
> color zone #2 near #1 distance 23
> color zone #2 near #1 distance 230
> color zone #2 near #1 distance 23
> volume #2 level 0.2098
> volume #2 level 0.1741
> volume #2 level 0.229
> volume #2 level 0.3718
> volume #2 level 0.24
> volume #2 level 0.1686
> volume #2 level -0.001816
> volume #2 level 0.04487
> volume #2 level 0.06409
> hide #!2 models
> show #!1 models
> show cartoons
> show surfaces
> hide surfaces
> show cartoons
> color bypolymer
> show cartoons
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /K
Alignment identifier is 1/K
> select /K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /K:3-101
777 atoms, 792 bonds, 99 residues, 1 model selected
> select /K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /K:3-101
777 atoms, 792 bonds, 99 residues, 1 model selected
> select /K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> open "/Users/elena/Documents/ccp-em_workshop_Elena/Elena data workshop/ccp-
> em_workshop_Elena/4r8p_oneside_no_e2.pdb"
Chain information for 4r8p_oneside_no_e2.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> color sel bychain
> style sel stick
Changed 5 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel bychain
> color sel bypolymer
> style sel ball
Changed 5 atom styles
> style sel stick
Changed 5 atom styles
> select add #1
13329 atoms, 14158 bonds, 1 pseudobond, 1248 residues, 3 models selected
> select subtract #1
12 models selected
> hide #3 models
> show #3 models
> select add #3
13460 atoms, 14292 bonds, 1266 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide atoms
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> color #3 #e1521c transparency 0
> select add #3
13460 atoms, 14292 bonds, 1266 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> color #3 #e12a02 transparency 0
> select add #3
13460 atoms, 14292 bonds, 1266 residues, 1 model selected
> show sel cartoons
> select subtract #3
Nothing selected
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4r8p_oneside_no_e2.pdb, chain G (#3) with refined-coot-2.pdb, chain
G (#1), sequence alignment score = 534.6
RMSD between 107 pruned atom pairs is 0.464 angstroms; (across all 107 pairs:
0.464)
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/I #3/I
Alignment identifier is 1
> select #1/I:-71 #3/I:-71
38 atoms, 40 bonds, 2 residues, 2 models selected
> select #1/I:-71-72 #3/I:-71-72
5870 atoms, 6578 bonds, 288 residues, 2 models selected
1 [ID: 1] region 2 chains [1-144] RMSD: 1.249
> ui tool show "Show Sequence Viewer"
> sequence chain #1/I #3/I
Alignment identifier is 1
> select #1/I:-71--70 #3/I:-71--70
82 atoms, 90 bonds, 4 residues, 2 models selected
> select #1/I:-71-72 #3/I:-71-72
5870 atoms, 6578 bonds, 288 residues, 2 models selected
1 [ID: 1] region 2 chains [1-144] RMSD: 1.249
> ui tool show "Show Sequence Viewer"
> sequence chain #1/J #3/J
Alignment identifier is 1
> select #1/J:-72 #3/J:-72
40 atoms, 42 bonds, 2 residues, 2 models selected
> select #1/J:-72-72 #3/J:-72-72
5980 atoms, 6714 bonds, 290 residues, 2 models selected
1 [ID: 1] region 2 chains [1-145] RMSD: 1.351
> volume #2 color #329bff
> ui tool show "Color Actions"
> color sel cyan
> color sel light sea green
> color sel cadet blue
> color sel teal
> color sel steel blue
> color sel slate gray
[Repeated 1 time(s)]
> color sel cadet blue
> select clear
> show #3 models
> hide #3 models
> show #3 models
> color #3 #d4d727 transparency 0
> color #3 #b2d5d7 transparency 0
> color #3 #47d7bd transparency 0
> color #3 #d72cc5 transparency 0
> color #3 #d72639 transparency 0
> color #3 #74d77f transparency 0
> color #3 #c6d760 transparency 0
> color #3 #d73b26 transparency 0
> color #3 #d7163e transparency 0
> color #3 #d71056 transparency 0
> hide #3 models
> set bgColor white
> set bgColor #ffffff00
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/elena/Desktop/movie1.mp4
Movie saved to /Users/elena/Desktop/movie1.mp4
> set bgColor black
> set bgColor transparent
> set bgColor black
> show #!2 models
> close #1
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-2.pdb
refined-coot-2.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-2.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #!1 atoms
> hide #!2 models
> show #!2 models
> show #!1 cartoons
> volume #2 level 0.116
> color zone #2 near #1 distance 2.47
> color #2 #329bff47 models
[Repeated 1 time(s)]
> color #2 #4279b147 models
> color #2 #4077ae47 models
> color #2 #a198ae47 models
> color #2 #abacae47 models
> color #2 #86aeaa47 models
> color #2 #76acae47 models
> color #2 #adfbff47 models
> color #2 #4d6f7147 models
> color #2 #2e434447 models
> color #2 #3f5c5d47 models
> color #2 #83838347 models
> color #2 white models transparency 0
> color #2 #ffffff2e models
[Repeated 1 time(s)]
> color #2 darkgrey models transparency 0
> color #2 #a9a9a951 models
> color #2 #a9a9a960 models
> hide #!2 models
> show #3 models
> hide #3 models
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker refined-coot-2.pdb, chain G (#1) with 4r8p_oneside_no_e2.pdb, chain
G (#3), sequence alignment score = 534.6
RMSD between 107 pruned atom pairs is 0.464 angstroms; (across all 107 pairs:
0.464)
> show #3 models
> show #!2 models
> hide #!1 models
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-3.pdb
refined-coot-3.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-3.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #3#!4 atoms
> hide #3#!4 cartoons
[Repeated 1 time(s)]
> show #3#!4 cartoons
[Repeated 1 time(s)]
> hide #!4 models
> close #4
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-4.pdb
refined-coot-4.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-4.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #3#!4 atoms
> close #1
> show cartoons
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker refined-coot-4.pdb, chain G (#4) with 4r8p_oneside_no_e2.pdb, chain
G (#3), sequence alignment score = 534.6
RMSD between 107 pruned atom pairs is 0.464 angstroms; (across all 107 pairs:
0.464)
> hide #3 models
> color zone #2 near #4 distance 2.47
> hide #!4 models
> color #2 darkgrey models transparency 0
> color #2 #a9a9a95a models
> color #2 #a9a9a959 models
> color #2 #a9a9a9dd models
> color #2 #bcbcbcdd models
> color #2 #59c83add models
> hide #!2 models
> open /Users/elena/Downloads/cryosparc_P136_J110_004_volume_map.mrc
Opened cryosparc_P136_J110_004_volume_map.mrc as #1, grid size 150,150,150,
pixel 2, shown at level 0.931, step 1, values float32
> volume #1 level 0.5376
> volume #1 level 0.3527
> volume #1 style mesh
> open "/Users/elena/Documents/ccp-em_workshop_Elena/Elena data workshop/ccp-
> em_workshop_Elena/4r8p_oneside_no_e2.pdb"
Chain information for 4r8p_oneside_no_e2.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #5 atoms
> show #5 cartoons
> matchmaker #5to #1
Missing or invalid "matchAtoms" argument: only initial part "#5" of atom
specifier valid
> fitmap #5 inMap #1
Fit molecule 4r8p_oneside_no_e2.pdb (#5) to map
cryosparc_P136_J110_004_volume_map.mrc (#1) using 13460 atoms
average map value = 3.839e-05, steps = 2000
shifted from previous position = 93.4
rotated from previous position = 58.5 degrees
atoms outside contour = 13460, contour level = 0.35265
Position of 4r8p_oneside_no_e2.pdb (#5) relative to
cryosparc_P136_J110_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.85521714 0.45581838 -0.24664397 -85.34518885
-0.10287049 0.61572555 0.78121681 -73.53235313
0.50795798 -0.64273762 0.57346931 34.41150626
Axis -0.83485112 -0.44241604 -0.32755405
Axis point 0.00000000 55.02646751 68.80210478
Rotation angle (degrees) 58.51965773
Shift along axis 92.51079095
> fitmap #5 inMap #1
Fit molecule 4r8p_oneside_no_e2.pdb (#5) to map
cryosparc_P136_J110_004_volume_map.mrc (#1) using 13460 atoms
average map value = 5.129e-05, steps = 916
shifted from previous position = 20.7
rotated from previous position = 26.7 degrees
atoms outside contour = 13460, contour level = 0.35265
Position of 4r8p_oneside_no_e2.pdb (#5) relative to
cryosparc_P136_J110_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.98441808 0.17334848 0.02951868 -110.58755892
-0.10359242 0.43606077 0.89393491 -65.65295712
0.14209032 -0.88306359 0.44722369 119.74055404
Axis -0.98614265 -0.06247147 -0.15368794
Axis point 0.00000000 79.04483327 116.68637837
Rotation angle (degrees) 64.28777930
Shift along axis 94.75386664
> toolshed show
Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> view matrix models
> #5,0.98442,0.17335,0.029519,16.886,-0.10359,0.43606,0.89393,26.848,0.14209,-0.88306,0.44722,201.15
> view matrix models
> #5,0.98442,0.17335,0.029519,49.068,-0.10359,0.43606,0.89393,29.4,0.14209,-0.88306,0.44722,166.58
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> fitmap #5 inMap #1
Fit molecule 4r8p_oneside_no_e2.pdb (#5) to map
cryosparc_P136_J110_004_volume_map.mrc (#1) using 13460 atoms
average map value = 1.328, steps = 216
shifted from previous position = 17
rotated from previous position = 63.5 degrees
atoms outside contour = 628, contour level = 0.35265
Position of 4r8p_oneside_no_e2.pdb (#5) relative to
cryosparc_P136_J110_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.96535168 -0.20429317 -0.16235898 97.37972410
0.21483180 0.97536737 0.05005786 28.63249347
0.14813318 -0.08320332 0.98546120 52.87897141
Axis -0.24753251 -0.57673887 0.77852420
Axis point -78.49625845 490.64534195 0.00000000
Rotation angle (degrees) 15.61542740
Shift along axis 0.54943977
> hide #5 models
> close #5
> open /Users/elena/Downloads/4r8p.pdb
4r8p.pdb title:
Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound
to the nucleosome core particle [more info...]
Chain information for 4r8p.pdb #5
---
Chain | Description | UniProt
A | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
E | histone H3.2 | H32_XENLA
F | histone H4 | H4_XENLA
G | histone H2A | Q6AZJ8_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
K | polycomb complex protein bmi-1 | BMI1_HUMAN
L | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
M | polycomb complex protein bmi-1 | BMI1_HUMAN
N | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
Non-standard residues in 4r8p.pdb #5
---
ZN — zinc ion
> hide #!5 models
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 atoms
> show #!5 cartoons
> ui mousemode right "translate selected models"
> select add #5
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> view matrix models #5,1,0,0,128.97,0,1,0,131.11,0,0,1,199.42
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.41546,0.15837,0.89572,206.91,0.83161,0.46511,0.30349,136.68,-0.36854,0.87097,-0.32493,123.27
> view matrix models
> #5,-0.027047,-0.091624,0.99543,207.54,0.83937,0.53871,0.072393,123.55,-0.54288,0.83749,0.062337,147.35
> select add #1
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 4 models selected
> fitmap #5 inMap #1
Fit molecule 4r8p.pdb (#5) to map cryosparc_P136_J110_004_volume_map.mrc (#1)
using 17134 atoms
average map value = 0.8914, steps = 116
shifted from previous position = 15.2
rotated from previous position = 13.4 degrees
atoms outside contour = 4136, contour level = 0.35265
Position of 4r8p.pdb (#5) relative to cryosparc_P136_J110_004_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.14296517 0.10129691 0.98453029 196.47600743
0.80712343 0.58764973 0.05674120 109.52391235
-0.57281125 0.80274948 -0.16577255 136.92636070
Axis 0.39990057 0.83481884 0.37836098
Axis point 93.76845293 0.00000000 -0.60897341
Rotation angle (degrees) 111.13360837
Shift along axis 221.81108541
> select subtract #1
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> view matrix models
> #5,-0.16415,0.036182,0.98577,198.97,0.65663,0.74976,0.08182,110.43,-0.73613,0.66072,-0.14683,146.47
> fitmap #5 inMap #1
Fit molecule 4r8p.pdb (#5) to map cryosparc_P136_J110_004_volume_map.mrc (#1)
using 17134 atoms
average map value = 0.9069, steps = 108
shifted from previous position = 2.62
rotated from previous position = 20.2 degrees
atoms outside contour = 4245, contour level = 0.35265
Position of 4r8p.pdb (#5) relative to cryosparc_P136_J110_004_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.14794715 0.08567703 0.98527717 198.74543527
0.37372921 0.92721398 -0.02450962 107.01697791
-0.91566267 0.36460072 -0.16919867 161.03391803
Axis 0.19836173 0.96906628 0.14684402
Axis point 146.24513604 0.00000000 2.25155530
Rotation angle (degrees) 101.24273271
Shift along axis 166.77690148
> select subtract #5.1
17134 atoms, 18059 bonds, 1770 residues, 1 model selected
> select add #5
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> view matrix models
> #5,-0.11755,-0.26675,0.95657,206.44,-0.20403,-0.93621,-0.28615,163.6,0.97188,-0.22881,0.055622,134.45
> view matrix models
> #5,-0.2583,-0.16242,0.95231,207.32,-0.93593,-0.20222,-0.28835,163.73,0.23941,-0.96578,-0.099781,168.76
> select subtract #5
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L
Alignment identifier is 5/L
> select #5/L:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:116-347
1070 atoms, 1103 bonds, 153 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L
Destroying pre-existing alignment with identifier 5/L
Alignment identifier is 5/L
> select #5/L:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:116-347
1070 atoms, 1103 bonds, 153 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> select #5/L:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:116-347
1070 atoms, 1103 bonds, 153 residues, 1 model selected
> select #5/L:222
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:222
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/N
Alignment identifier is 5/N
> select #5/N:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/N:115-347
1157 atoms, 1193 bonds, 154 residues, 1 model selected
> hide sel cartoons
> fitmap #5 inMap #1
Fit molecule 4r8p.pdb (#5) to map cryosparc_P136_J110_004_volume_map.mrc (#1)
using 17134 atoms
average map value = 1.087, steps = 108
shifted from previous position = 8.62
rotated from previous position = 19.2 degrees
atoms outside contour = 2912, contour level = 0.35265
Position of 4r8p.pdb (#5) relative to cryosparc_P136_J110_004_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.06079690 0.00051938 0.99815003 198.89224085
-0.90552531 -0.42072072 -0.05493625 188.69951624
0.41991386 -0.90719007 0.02604882 170.30940143
Axis -0.62130390 0.42154154 -0.66051813
Axis point 95.87786434 118.15093881 0.00000000
Rotation angle (degrees) 136.69679514
Shift along axis -156.52028695
> color #1 #fbfefe models transparency 0
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/elena/Desktop/movie2.mp4
Movie saved to /Users/elena/Desktop/movie2.mp4
> select add #5
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!1 models
> open /Users/elena/Downloads/4r8p.pdb
4r8p.pdb title:
Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound
to the nucleosome core particle [more info...]
Chain information for 4r8p.pdb #6
---
Chain | Description | UniProt
A | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
E | histone H3.2 | H32_XENLA
F | histone H4 | H4_XENLA
G | histone H2A | Q6AZJ8_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
K | polycomb complex protein bmi-1 | BMI1_HUMAN
L | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
M | polycomb complex protein bmi-1 | BMI1_HUMAN
N | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
Non-standard residues in 4r8p.pdb #6
---
ZN — zinc ion
> hide #!6 atoms
> show #!6 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L #6/L
Alignment identifier is 1
> select #5/L:116 #6/L:116
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #5/L:116-347 #6/L:116-347
2140 atoms, 2206 bonds, 306 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [102-254] RMSD: 311.067
> ui tool show "Color Actions"
> color sel indigo
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/N #6/N
Alignment identifier is 1
> select #5/N:116 #6/N:116
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #5/N:116-347 #6/N:116-347
2300 atoms, 2370 bonds, 306 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [101-253] RMSD: 307.909
> ui tool show "Color Actions"
> color sel indigo
> select #5/N:16 #6/N:16
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #5/N:16-115 #6/N:16-115
1490 atoms, 1518 bonds, 200 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [1-100] RMSD: 264.449
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right "rotate selected models"
> ui tool show "Color Actions"
> color sel yellow green
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> color sel light green
[Repeated 1 time(s)]
> color sel pale green
[Repeated 1 time(s)]
> select clear
> select #5/N:16 #6/N:16
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #5/N:16-115 #6/N:16-115
1490 atoms, 1518 bonds, 200 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [1-100] RMSD: 264.449
> ui tool show "Color Actions"
> color sel light salmon
[Repeated 1 time(s)]
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L #6/L
Alignment identifier is 2
> select #5/L:15 #6/L:15
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #5/L:15-115 #6/L:15-115
1574 atoms, 1602 bonds, 202 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [1-101] RMSD: 284.344
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel salmon
> color sel dark salmon
[Repeated 1 time(s)]
> color sel salmon
> color sel dark salmon
> color sel salmon
[Repeated 1 time(s)]
> color sel dark salmon
[Repeated 4 time(s)]
> color sel light salmon
[Repeated 2 time(s)]
> select #5/L:15-16 #6/L:15-16
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #5/L:15-114 #6/L:15-114
1560 atoms, 1586 bonds, 200 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [1-100] RMSD: 284.432
> select #5/N:16 #6/N:16
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #5/N:16-115 #6/N:16-115
1490 atoms, 1518 bonds, 200 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [1-100] RMSD: 264.449
> select #5/L:15 #6/L:15
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #5/L:15-115 #6/L:15-115
1574 atoms, 1602 bonds, 202 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [1-101] RMSD: 284.344
> ui tool show "Color Actions"
> color sel light salmon
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select #5/L:15-16 #6/L:15-16
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #5/L:15-83 #6/L:15-83
1068 atoms, 1084 bonds, 138 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [1-69] RMSD: 287.621
> select #5/N:16 #6/N:16
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #5/N:16-115 #6/N:16-115
1490 atoms, 1518 bonds, 200 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [1-100] RMSD: 264.449
> color sel light salmon
[Repeated 1 time(s)]
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select clear
> ui tool show "Show Sequence Viewer"
> select #5/N:117 #6/N:117
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #5/N:117-347 #6/N:117-347
2288 atoms, 2358 bonds, 304 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [102-253] RMSD: 308.193
> select #5/L:117 #6/L:117
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #5/L:117-347 #6/L:117-347
2128 atoms, 2194 bonds, 304 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [103-254] RMSD: 311.288
> ui tool show "Color Actions"
[Repeated 2 time(s)]
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
[Repeated 1 time(s)]
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel rosy brown
> color sel gray
> color sel dark gray
[Repeated 1 time(s)]
> color sel gainsboro
> color sel light gray
[Repeated 5 time(s)]
> color sel light goldenrod yellow
> color sel gray
> color sel dim gray
> color sel dark gray
> color sel light gray
[Repeated 1 time(s)]
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select #5/N:117 #6/N:117
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #5/N:117-347 #6/N:117-347
2288 atoms, 2358 bonds, 304 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [102-253] RMSD: 308.193
> color sel light gray
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> color sel pale violet red
> color sel orchid
> color sel rebecca purple
> color sel dark slate blue
> color sel medium slate blue
> color sel dark sea green
> color sel wheat
> color sel rosy brown
[Repeated 2 time(s)]
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select #5/N:117 #6/N:117
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #5/N:117-346 #6/N:117-346
2270 atoms, 2340 bonds, 302 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [102-252] RMSD: 308.012
> select #5/N:115 #6/N:115
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #5/N:115-347 #6/N:115-347
2314 atoms, 2386 bonds, 308 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [100-253] RMSD: 307.609
> color sel rosy brown
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select #5/L:117-258 #6/L:117-258
896 atoms, 924 bonds, 126 residues, 2 models selected
> select #5/L:117-347 #6/L:117-347
2128 atoms, 2194 bonds, 304 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [103-254] RMSD: 311.288
> select #5/L:115 #6/L:115
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #5/L:115-347 #6/L:115-347
2154 atoms, 2222 bonds, 308 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [101-254] RMSD: 310.848
> select #5/L:114 #6/L:114
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #5/L:114-347 #6/L:114-347
2178 atoms, 2248 bonds, 310 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [100-254] RMSD: 310.663
> color sel rosy brown
> ui tool show "Show Sequence Viewer"
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> sequence chain #6/I
Alignment identifier is 6/I
> sequence chain #6/J
Alignment identifier is 6/J
> select #6/J:-72
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate gray
> color sel gray
[Repeated 1 time(s)]
> select clear
> select #5/N:16-23 #6/N:16-23
124 atoms, 128 bonds, 16 residues, 2 models selected
> select #5/N:16-114 #6/N:16-114
1476 atoms, 1502 bonds, 198 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [1-99] RMSD: 264.518
> color sel green
> color sel dark orange
> color sel dark slate gray
[Repeated 1 time(s)]
> select #5/L:15-18 #6/L:15-18
78 atoms, 80 bonds, 8 residues, 2 models selected
> select #5/L:15-115 #6/L:15-115
1574 atoms, 1602 bonds, 202 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [1-101] RMSD: 284.344
> color sel dark slate gray
> select #5/N:115-251 #6/N:115-251
804 atoms, 828 bonds, 116 residues, 2 models selected
> select #5/N:115-347 #6/N:115-347
2314 atoms, 2386 bonds, 308 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 1]
region 2 chains [100-253] RMSD: 307.609
> color sel wheat
> select #5/L:116-256 #6/L:116-256
880 atoms, 906 bonds, 124 residues, 2 models selected
> select #5/L:116-347 #6/L:116-347
2140 atoms, 2206 bonds, 306 residues, 2 models selected
E3 Ubiquitin-Protein Ligase RING2, Ubiquitin-Conjugating Enzyme E2 D3 [ID: 2]
region 2 chains [102-254] RMSD: 311.067
> color sel wheat
> ui tool show "Show Sequence Viewer"
> sequence chain #6/M
Alignment identifier is 6/M
> sequence chain #6/K
Alignment identifier is 6/K
> select #6/M:92-102
87 atoms, 90 bonds, 11 residues, 1 model selected
> select #6/M:6-102
744 atoms, 761 bonds, 97 residues, 1 model selected
> select #6/K:47-98
427 atoms, 435 bonds, 52 residues, 1 model selected
> select #6/K:3-47
347 atoms, 353 bonds, 45 residues, 1 model selected
> select #6/K:107
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/K:3-107
819 atoms, 836 bonds, 105 residues, 1 model selected
> color sel tomato
> color sel fire brick
> color sel coral
> color sel indian red
> select #6/M:102
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/M:6-102
744 atoms, 761 bonds, 97 residues, 1 model selected
> color sel indian red
> ui tool show "Show Sequence Viewer"
> sequence chain #6/G
Alignment identifier is 6/G
> sequence chain #6/H
Alignment identifier is 6/H
> sequence chain #6/F
Alignment identifier is 6/F
> sequence chain #6/E
Alignment identifier is 6/E
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #6/C
Alignment identifier is 6/C
> sequence chain #6/B
Alignment identifier is 6/B
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/H:31
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/H:31-90
459 atoms, 467 bonds, 60 residues, 1 model selected
> color sel light blue
> select #6/D:31-58
206 atoms, 210 bonds, 28 residues, 1 model selected
> select #6/D:31-90
461 atoms, 469 bonds, 60 residues, 1 model selected
> color sel light blue
> select #6/G:12-17
38 atoms, 37 bonds, 6 residues, 1 model selected
> select #6/G:12-118
793 atoms, 803 bonds, 107 residues, 1 model selected
> color sel rosy brown
> select #6/C:16-22
44 atoms, 43 bonds, 7 residues, 1 model selected
> select #6/C:16-75
439 atoms, 445 bonds, 60 residues, 1 model selected
> color sel medium slate blue
> hide #7 models
> hide #6.1 models
> hide #!6 models
> show #3 models
> hide #3 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select add #6
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> select subtract #6.1
17134 atoms, 18059 bonds, 1770 residues, 1 model selected
> hide #!6 models
> show #!6 models
> hide #!6 models
> select add #6
17134 atoms, 18059 bonds, 32 pseudobonds, 1770 residues, 2 models selected
> show #!6 models
> close #6
> close #7
> open /Users/elena/Downloads/4r8p.pdb format pdb
4r8p.pdb title:
Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound
to the nucleosome core particle [more info...]
Chain information for 4r8p.pdb #6
---
Chain | Description | UniProt
A | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
E | histone H3.2 | H32_XENLA
F | histone H4 | H4_XENLA
G | histone H2A | Q6AZJ8_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
K | polycomb complex protein bmi-1 | BMI1_HUMAN
L | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
M | polycomb complex protein bmi-1 | BMI1_HUMAN
N | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
Non-standard residues in 4r8p.pdb #6
---
ZN — zinc ion
> close #5
> show #!6 cartoons
[Repeated 1 time(s)]
> show #!6 target m
> close #6
> open /Users/elena/Downloads/4r8p.pdb format pdb
4r8p.pdb title:
Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound
to the nucleosome core particle [more info...]
Chain information for 4r8p.pdb #5
---
Chain | Description | UniProt
A | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
E | histone H3.2 | H32_XENLA
F | histone H4 | H4_XENLA
G | histone H2A | Q6AZJ8_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
K | polycomb complex protein bmi-1 | BMI1_HUMAN
L | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
M | polycomb complex protein bmi-1 | BMI1_HUMAN
N | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
Non-standard residues in 4r8p.pdb #5
---
ZN — zinc ion
> close #5
> show #!4 models
> hide #!4 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #3 models
> show #!2 models
> show #!1 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> hide #3 models
> hide #!4 models
> open /Users/elena/Downloads/4r8p.pdb format pdb
4r8p.pdb title:
Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound
to the nucleosome core particle [more info...]
Chain information for 4r8p.pdb #5
---
Chain | Description | UniProt
A | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
E | histone H3.2 | H32_XENLA
F | histone H4 | H4_XENLA
G | histone H2A | Q6AZJ8_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
K | polycomb complex protein bmi-1 | BMI1_HUMAN
L | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
M | polycomb complex protein bmi-1 | BMI1_HUMAN
N | E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 |
UB2D3_HUMAN
Non-standard residues in 4r8p.pdb #5
---
ZN — zinc ion
> hide #!5 atoms
> show #!5 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #5/M
Alignment identifier is 5/M
> sequence chain #5/N
Alignment identifier is 5/N
> sequence chain #5/L
Alignment identifier is 5/L
> sequence chain #5/K
Alignment identifier is 5/K
> sequence chain #5/J
Alignment identifier is 5/J
> sequence chain #5/I
Alignment identifier is 5/I
> sequence chain #5/H
Alignment identifier is 5/H
> sequence chain #5/G
Alignment identifier is 5/G
> sequence chain #5/F
Alignment identifier is 5/F
> sequence chain #5/E
Alignment identifier is 5/E
> sequence chain #5/D
Alignment identifier is 5/D
> sequence chain #5/C
Alignment identifier is 5/C
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/A
Alignment identifier is 5/A
> ui tool show "Color Actions"
> select #5/L:15-209
897 atoms, 911 bonds, 116 residues, 1 model selected
> select #5/L:15-58
342 atoms, 348 bonds, 44 residues, 1 model selected
> select #5/L:18
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:18-315
1622 atoms, 1662 bonds, 219 residues, 1 model selected
> select #5/L:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:15-109
737 atoms, 749 bonds, 95 residues, 1 model selected
> select #5/L:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:15-115
787 atoms, 801 bonds, 101 residues, 1 model selected
> color sel light sea green
> select #5/N:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/N:16-115
745 atoms, 759 bonds, 100 residues, 1 model selected
> color sel light sea green
> select #5/K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/K:3-107
819 atoms, 836 bonds, 105 residues, 1 model selected
> color sel khaki
> color sel pale goldenrod
[Repeated 1 time(s)]
> select #5/M:6-13
55 atoms, 54 bonds, 8 residues, 1 model selected
> select #5/M:6-102
744 atoms, 761 bonds, 97 residues, 1 model selected
> color sel pale goldenrod
> select #5/N:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/N:116-347
1150 atoms, 1185 bonds, 153 residues, 1 model selected
> select #5/N:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/N:115-347
1157 atoms, 1193 bonds, 154 residues, 1 model selected
> view matrix models
> #5,0.99702,0.043572,-0.063582,-4.124,-0.049213,0.99472,-0.090033,-2.6735,0.059324,0.092894,0.99391,-4.5892
> color sel light blue
> select #5/K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/K:3-93
713 atoms, 726 bonds, 91 residues, 1 model selected
> color sel light blue
> undo
> select #5/L:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:15-343
1836 atoms, 1884 bonds, 250 residues, 1 model selected
> undo
> select #5/L:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:116-307
810 atoms, 835 bonds, 113 residues, 1 model selected
> select #5/L:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:115-343
1056 atoms, 1090 bonds, 150 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/J
Alignment identifier is 5/J
> select #5/J:-72--71
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #5/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> color sel dim gray
> select clear
> select #5/J:72
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #5/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cadet blue
> color sel forest green
> color sel sea green
> color sel cadet blue
> select clear
> select #5/J:-72
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sea green
> color sel dark salmon
> color sel light salmon
> color sel navajo white
> color sel peach puff
> color sel pink
> color sel lavender blush
> color sel khaki
> color sel pale goldenrod
> color sel azure
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting flat
> save /Users/elena/Desktop/image1.png supersample 3
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> ui tool show "Model Panel"
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> set bgColor black
> set bgColor transparent
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> sequence chain #4/K
Alignment identifier is 4/K
> select #4/K:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/K:5-98
754 atoms, 769 bonds, 94 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select #4/K:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/K:5-98
754 atoms, 769 bonds, 94 residues, 1 model selected
> select clear
> select #4/L:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:15-115
787 atoms, 801 bonds, 101 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sea green
> ui tool show "Show Sequence Viewer"
> sequence chain #4/J
Alignment identifier is 4/J
> select #4/J:-72
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan
> color sel lavender
[Repeated 1 time(s)]
> select clear
> hide #!5 models
> show #!2 models
> color #2 #cc8fa2dd models
> color #2 #c688ccdd models
> color #2 #38cccadd models
> color #2 #38ccca80 models
> color #2 #594ecc80 models
> color #2 #92a4cc80 models
> color #2 #cc2fb580 models
> color #2 #ccc48780 models
> color #2 #90ccba80 models
> color #2 #942192 models transparency 0
> color #2 #fffb00 models transparency 0
> color #2 #00f900 models transparency 0
> color #2 #aa7942 models transparency 0
> color #2 #0433ff models transparency 0
> color #2 #a5f5e6 models transparency 0
> color #2 #a5f5e668 models
Populating font family aliases took 358 ms. Replace uses of missing font
family "Menlo" with one that exists to avoid this cost.
> save /Users/elena/Desktop/figures_TAC/chimera.cxs includeMaps true
> color zone #2 near #4 distance 2.47
> color #2 #abfff068 models
> color zone #2 near #4 distance 2.47
> hide #!2 models
> show #!2 models
> color #2 #abfff000 models
> color #2 #abfff05f models
> color zone #2 near #4 distance 2.47
> transparency #2.1 0
> transparency #2.1 50
> color #2 #abfff000 models
> color #2 #abfff06d models
> color zone #2 near #4 distance 2.47
> transparency #2.1 0
> transparency #2.1 50
> transparency #2.1 0
> ui tool show "Surface Color"
> transparency #2.1 50
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C
Alignment identifier is 4/C
> select #4/C:17-20,27-35,47-72,80-88,91-96,113-115
436 atoms, 436 bonds, 57 residues, 1 model selected
> view matrix models
> #4,0.99857,-0.037929,-0.037752,7.6475,0.037699,0.99927,-0.0067874,-3.56,0.037982,0.0053545,0.99926,-4.7927
> view matrix models
> #4,0.99234,-0.089706,-0.084929,18.149,0.091078,0.99577,0.012414,-11.159,0.083456,-0.020054,0.99631,-7.1339
> select #4/C:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/C:16-119
766 atoms, 776 bonds, 104 residues, 1 model selected
> select #4/C:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/C:16-119
766 atoms, 776 bonds, 104 residues, 1 model selected
> select #4/C:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/C:16-119
766 atoms, 776 bonds, 104 residues, 1 model selected
> select clear
> open /Users/elena/Desktop/Ring1b-BMI1-models-coot/refined-coot-5.pdb
refined-coot-5.pdb title:
Molrep --- /vers 11.9.02; 28.02.2022/ [more info...]
Chain information for refined-coot-5.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #!4,6 atoms
> show #!4,6 cartoons
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:45-54,64-77,86-113,121-131
512 atoms, 515 bonds, 63 residues, 1 model selected
> view matrix models
> #4,0.67565,0.6387,0.3682,-63.033,-0.38927,0.73321,-0.55756,125.42,-0.62608,0.23338,0.74402,72.808
> undo
> select add #4
13306 atoms, 14135 bonds, 1 pseudobond, 1243 residues, 2 models selected
> select subtract #4
Nothing selected
> select #4/A:45
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:45-54
89 atoms, 89 bonds, 10 residues, 1 model selected
> select #4/A:37-38
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/A:37-47
80 atoms, 83 bonds, 11 residues, 1 model selected
> view matrix models
> #4,0.97834,-0.20459,-0.03154,26.082,0.20628,0.9763,0.065492,-27.495,0.017393,-0.070579,0.99735,5.3633
> undo
> view matrix models
> #4,0.99261,-0.090198,-0.081233,17.808,0.091392,0.99575,0.011095,-11.065,0.079887,-0.018437,0.99663,-6.9212
> view matrix models
> #4,0.94214,0.24824,-0.22525,3.5953,-0.31135,0.89705,-0.31364,76.341,0.12421,0.36562,0.92244,-43.311
> undo
> select add #4
13306 atoms, 14135 bonds, 1 pseudobond, 1243 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!6 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/J
Alignment identifier is 6/J
> select #6/J:-72
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel moccasin
[Repeated 1 time(s)]
> view matrix models
> #6,0.9996,-0.028311,-0.00092523,2.9786,0.028292,0.99627,0.081578,-10.791,-0.0013878,-0.081571,0.99667,8.6734
> undo
> select add #6
13305 atoms, 14134 bonds, 1 pseudobond, 1242 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/C
Alignment identifier is 6/C
> sequence chain #6/G
Alignment identifier is 6/G
> select #6/C:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/C:16-118
765 atoms, 775 bonds, 103 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale green
> select #6/G:12
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/G:12-118
793 atoms, 803 bonds, 107 residues, 1 model selected
> color sel pale green
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/K
Alignment identifier is 3/K
> select #3/K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/K:3-107
819 atoms, 836 bonds, 105 residues, 1 model selected
> select #3/K:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/K:3-107
819 atoms, 836 bonds, 105 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #6/K
Alignment identifier is 6/K
> select #6/K:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/K:5-98
754 atoms, 769 bonds, 94 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #6/L
Alignment identifier is 6/L
> select #6/L:15-16
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/L:15-115
787 atoms, 801 bonds, 101 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sea green
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> view matrix models
> #6,0.99942,0.028979,-0.017676,-1.1233,-0.028869,0.99956,0.0064805,2.7016,0.017856,-0.0059665,0.99982,-1.4177
> undo
> hide #!2 models
> select add #6
13305 atoms, 14134 bonds, 1 pseudobond, 1242 residues, 2 models selected
> select subtract #6
Nothing selected
> show #!2 models
> color #2 #e3fcf26d models
> color #2 #edfcf36d models
> color #2 #f7fce96d models
> color #2 #f7fce96e models
> fitmap #6 inMap #2
Fit molecule refined-coot-5.pdb (#6) to map
cryosparc_P142_J865_008_tightTarget zflip.mrc (#2) using 13305 atoms
average map value = 0.4001, steps = 44
shifted from previous position = 0.074
rotated from previous position = 0.0548 degrees
atoms outside contour = 3305, contour level = 0.116
Position of refined-coot-5.pdb (#6) relative to
cryosparc_P142_J865_008_tightTarget zflip.mrc (#2) coordinates:
Matrix rotation and translation
0.99999955 0.00080285 0.00049737 -0.07172228
-0.00080277 0.99999967 -0.00015108 0.12230438
-0.00049749 0.00015068 0.99999986 -0.00974949
Axis 0.15775419 0.52010993 -0.83940412
Axis point 113.12556371 101.28211964 0.00000000
Rotation angle (degrees) 0.05479780
Shift along axis 0.06048100
> color zone #2 near #6 distance 2.47
> transparency #2.1 0
> transparency #2.1 50
> ui tool show "Show Sequence Viewer"
> sequence chain #6/J
Alignment identifier is 6/J
> select #6/J:-72--71
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #6/J:-72-72
2990 atoms, 3357 bonds, 145 residues, 1 model selected
> ui tool show "Color Actions"
> color sel beige
> color sel alice blue
[Repeated 3 time(s)]
> select clear
> color zone #2 near #6 distance 2.47
> transparency #2.1 0
> transparency #2.1 50
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> view
[Repeated 1 time(s)]
> view orient
[Repeated 2 time(s)]
> view
> undo
[Repeated 1 time(s)]
> ui tool show "Side View"
> save /Users/elena/Desktop/figures_TAC/220923.cxs
——— End of log from Fri Sep 23 13:31:56 2022 ———
opened ChimeraX session
> show #3 models
> hide #!2 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4r8p_oneside_no_e2.pdb, chain G (#3) with refined-coot-5.pdb, chain
G (#6), sequence alignment score = 534.6
RMSD between 107 pruned atom pairs is 0.464 angstroms; (across all 107 pairs:
0.464)
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> save /Users/elena/Desktop/image29.png supersample 3
> set bgColor black
> set bgColor transparent
> save /Users/elena/Desktop/image30.png supersample 3
> set bgColor white
> set bgColor #ffffff00
> hide #3 models
> open /Users/elena/Downloads/2ckl.pdb
2ckl.pdb title:
RING1B-BMI1 E3 catalytic domain structure [more info...]
Chain information for 2ckl.pdb #7
---
Chain | Description | UniProt
A | polycomb group ring finger protein 4 | PCGF4_MOUSE
B | ubiquitin ligase protein RING2 | RING2_MOUSE
Non-standard residues in 2ckl.pdb #7
---
IOD — iodide ion
ZN — zinc ion
> mmaker #7 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4r8p_oneside_no_e2.pdb, chain K (#3) with 2ckl.pdb, chain A (#7),
sequence alignment score = 497.3
RMSD between 97 pruned atom pairs is 0.410 angstroms; (across all 98 pairs:
0.472)
> show #3 models
> hide #3 models
> color #7 #b5ed21 transparency 0
> color #7 #56ed69 transparency 0
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> show #3 models
> hide #!6 models
> show #!6 models
> select protein
35059 atoms, 35626 bonds, 3 pseudobonds, 4551 residues, 8 models selected
> select nucleic-acid
23700 atoms, 26584 bonds, 1156 residues, 4 models selected
> hide sel & #3#!6 atoms
> hide sel & #3#!6 cartoons
> select #3/A#4/A#6/A
2367 atoms, 2403 bonds, 294 residues, 3 models selected
> hide sel & #3#!6 atoms
> hide sel & #3#!6 cartoons
> select #3/B#4/B#6/B
1933 atoms, 1952 bonds, 2 pseudobonds, 248 residues, 5 models selected
> hide sel & #3#!6 atoms
> hide sel & #3#!6 cartoons
> select #3/C#4/C#6/C
2297 atoms, 2327 bonds, 311 residues, 3 models selected
> hide sel & #3#!6 atoms
> hide sel & #3#!6 cartoons
> select #3/C#4/C#6/C
2297 atoms, 2327 bonds, 311 residues, 3 models selected
> hide sel & #3#!6 cartoons
> hide sel & #3#!6 atoms
> select #3/C#4/C#6/C
2297 atoms, 2327 bonds, 311 residues, 3 models selected
> select #3/D#4/D#6/D
2163 atoms, 2196 bonds, 285 residues, 3 models selected
> hide sel & #3#!6 cartoons
> select #3/E#4/E#6/E
2364 atoms, 2400 bonds, 291 residues, 3 models selected
> hide sel & #3#!6 cartoons
> select #3/G#4/G#6/G
2379 atoms, 2409 bonds, 321 residues, 3 models selected
> hide sel & #3#!6 cartoons
> select #3/H#4/H#6/H
2157 atoms, 2190 bonds, 285 residues, 3 models selected
> hide sel & #3#!6 cartoons
> select #3/F#4/F#6/F
1905 atoms, 1926 bonds, 246 residues, 3 models selected
> hide sel & #3#!6 cartoons
> hide sel & #3#!6 atoms
> color #7 #71e3e9 transparency 0
> undo
> color #7 #e791e9 transparency 0
> color #7 #b657e9 transparency 0
> color #7 #e586e9 transparency 0
> color #7 #e9735a transparency 0
> color #7 #e945a3 transparency 0
> color #7 #e9bfbf transparency 0
> color #7 #e944c0 transparency 0
> color #7 #b03ee9 transparency 0
> color #7 #e9bfe6 transparency 0
> color #7 #ada4e9 transparency 0
> color #7 #719fe9 transparency 0
> color #7 #b6e0e9 transparency 0
> color #7 #b438e9 transparency 0
> color #7 #e941d6 transparency 0
> color #7 #e9a6bb transparency 0
> color #7 #e96578 transparency 0
> color #7 #e93798 transparency 0
> color #7 #b392e9 transparency 0
> color #7 #c2bde9 transparency 0
> color #7 #b6cae9 transparency 0
> color #7 #bf71e9 transparency 0
> color #7 #e97cd4 transparency 0
> color #7 #d14de9 transparency 0
> color #7 #e8b1e9 transparency 0
> cd /Users/elena/Desktop/figures_TAC
Current working directory is: /Users/elena/Desktop/figures_TAC
Populating font family aliases took 381 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
> save /Users/elena/Desktop/figures_TAC/dimercomparison.cxs includeMaps true
——— End of log from Wed Feb 22 14:42:34 2023 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1554.50.3.0.0 (iBridge: 18.16.12561.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 3:50
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG HDR 4K:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
et-xmlfile: 1.1.0
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openpyxl: 3.0.10
openvr: 1.16.802
packaging: 21.0
pandas: 1.5.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
seaborn: 0.12.0
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash destroying QGridLayout |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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XMAS was installed