The following bug report has been submitted:
Platform: macOS-11.6-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001029f3d40 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [38843]
Path: /Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.6.1 (1.6.1.0)
Code Type: ARM-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [38843]
User ID: 501
Date/Time: 2023-07-07 09:30:10.868 +0100
OS Version: macOS 11.6 (20G165)
Report Version: 12
Anonymous UUID: 6444E6FA-F5B9-6DDB-43A6-2F46E5AA5D30
Sleep/Wake UUID: 63FBDE17-17AC-43E0-8E15-82B7081DF731
Time Awake Since Boot: 130000 seconds
Time Since Wake: 16 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000018
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x18:
-->
__TEXT 102560000-102564000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x000000018b550e68 __pthread_kill + 8
1 libsystem_pthread.dylib 0x000000018b58343c pthread_kill + 292
2 libsystem_c.dylib 0x000000018b462e10 raise + 32
3 libsystem_platform.dylib 0x000000018b5cec44 _sigtramp + 56
4 QtGui 0x00000001227bc93c QMacCGContext::QMacCGContext(QPainter*) + 40
5 libqmacstyle.dylib 0x0000000127a8682c 0x127a7c000 + 43052
6 libqmacstyle.dylib 0x0000000127a8dfec 0x127a7c000 + 73708
7 QtWidgets 0x0000000121f2d630 QCommonStyle::drawControl(QStyle::ControlElement, QStyleOption const*, QPainter*, QWidget const*) const + 2132
8 libqmacstyle.dylib 0x0000000127a8b79c 0x127a7c000 + 63388
9 QtWidgets 0x0000000121f69580 0x121ebc000 + 710016
10 QtWidgets 0x0000000122093f58 QTabBar::paintEvent(QPaintEvent*) + 1584
11 QtWidgets 0x0000000121f101ac QWidget::event(QEvent*) + 132
12 QtWidgets 0x00000001220937b8 QTabBar::event(QEvent*) + 736
13 QtWidgets 0x0000000121ec6710 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
14 QtWidgets 0x0000000121ec81ec QApplication::notify(QObject*, QEvent*) + 3396
15 QtWidgets.abi3.so 0x000000011795c6b8 sipQApplication::notify(QObject*, QEvent*) + 248
16 QtCore 0x0000000114400e9c QCoreApplication::notifyInternal2(QObject*, QEvent*) + 292
17 QtWidgets 0x0000000121f0343c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3312
18 QtWidgets 0x0000000121f0aacc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 864
19 QtWidgets 0x0000000121f0353c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3568
20 QtWidgets 0x0000000121f0aacc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 864
21 QtWidgets 0x0000000121f0353c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3568
22 QtWidgets 0x0000000121f0aacc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 864
23 QtWidgets 0x0000000121f0353c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3568
24 QtWidgets 0x0000000121f0aacc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 864
25 QtWidgets 0x0000000121f0353c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3568
26 QtWidgets 0x0000000121f0aacc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 864
27 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
28 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
29 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
30 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
31 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
32 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
33 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
34 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
35 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
36 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
37 QtWidgets 0x0000000121f0a9bc QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList const&, int, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 592
38 QtWidgets 0x0000000121f0353c QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags, QPainter*, QWidgetRepaintManager*) + 3568
39 QtWidgets 0x0000000121f20d48 QWidgetRepaintManager::paintAndFlush() + 3904
40 QtWidgets 0x0000000121f20fcc QWidgetRepaintManager::sync() + 252
41 QtWidgets 0x0000000121f1064c QWidget::event(QEvent*) + 1316
42 QtWidgets 0x000000012202c620 QMainWindow::event(QEvent*) + 248
43 QtWidgets.abi3.so 0x00000001178a72c0 sipQMainWindow::event(QEvent*) + 224
44 QtWidgets 0x0000000121ec6710 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
45 QtWidgets 0x0000000121ec81ec QApplication::notify(QObject*, QEvent*) + 3396
46 QtWidgets.abi3.so 0x000000011795c6b8 sipQApplication::notify(QObject*, QEvent*) + 248
47 QtCore 0x0000000114400e9c QCoreApplication::notifyInternal2(QObject*, QEvent*) + 292
48 QtWidgets 0x0000000121f1da3c QWidgetRepaintManager::sendUpdateRequest(QWidget*, QWidgetRepaintManager::UpdateTime) + 604
49 QtWidgets 0x0000000121f1d77c void QWidgetRepaintManager::markDirty(QRect const&, QWidget*, QWidgetRepaintManager::UpdateTime, QWidgetRepaintManager::BufferState) + 1748
50 QtWidgets 0x0000000121f27018 0x121ebc000 + 438296
51 QtCore 0x000000011444a718 0x114398000 + 730904
52 QtGui 0x00000001225364a4 QWindowPrivate::emitScreenChangedRecursion(QScreen*) + 80
53 QtGui 0x000000012252c028 QScreen::~QScreen() + 700
54 QtGui 0x000000012252c090 QScreen::~QScreen() + 12
55 QtGui 0x000000012254095c QWindowSystemInterface::handleScreenRemoved(QPlatformScreen*) + 36
56 libqcocoa.dylib 0x0000000123dafca8 0x123d80000 + 195752
57 libqcocoa.dylib 0x0000000123dae4f8 0x123d80000 + 189688
58 libqcocoa.dylib 0x0000000123dc2fe0 0x123d80000 + 274400
59 QtCore 0x000000011440fdb4 QMetaMethod::invoke(QObject*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) const + 1072
60 libqcocoa.dylib 0x0000000123dc6454 0x123d80000 + 287828
61 com.apple.Foundation 0x000000018c3fe104 -[__NSObserver _doit:] + 348
62 com.apple.CoreFoundation 0x000000018b675f08 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 28
63 com.apple.CoreFoundation 0x000000018b717e5c ___CFXRegistrationPost_block_invoke + 52
64 com.apple.CoreFoundation 0x000000018b717dc8 _CFXRegistrationPost + 456
65 com.apple.CoreFoundation 0x000000018b6449d8 _CFXNotificationPost + 720
66 com.apple.Foundation 0x000000018c3d03c0 -[NSNotificationCenter postNotificationName:object:userInfo:] + 64
67 com.apple.AppKit 0x000000018e0b3250 __67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke + 644
68 com.apple.AppKit 0x000000018dec4cf4 NSPerformVisuallyAtomicChange + 140
69 com.apple.AppKit 0x000000018e0b2fc0 -[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:] + 96
70 com.apple.AppKit 0x000000018dec66cc -[NSWindow _setFrameCommon:display:fromServer:] + 2144
71 com.apple.AppKit 0x000000018e2b084c -[_NSWindowFullScreenContentController reshapeContentForTileFrame:fromFrame:] + 352
72 com.apple.AppKit 0x000000018e94deac -[_NSFullScreenSpace updateTileShapeAndReshapeContentsUsingTileFrame:ackServer:] + 248
73 com.apple.AppKit 0x000000018e4a6680 __47+[NSCGSSpace addTileResizeNotificationHandler:]_block_invoke + 228
74 com.apple.Foundation 0x000000018c3fe104 -[__NSObserver _doit:] + 348
75 com.apple.CoreFoundation 0x000000018b675f08 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 28
76 com.apple.CoreFoundation 0x000000018b717e5c ___CFXRegistrationPost_block_invoke + 52
77 com.apple.CoreFoundation 0x000000018b717dc8 _CFXRegistrationPost + 456
78 com.apple.CoreFoundation 0x000000018b6449d8 _CFXNotificationPost + 720
79 com.apple.Foundation 0x000000018c3d03c0 -[NSNotificationCenter postNotificationName:object:userInfo:] + 64
80 com.apple.SkyLight 0x0000000190050f40 post_coordinated_distributed_notification(CGSNotificationType, void*, unsigned int, void*) + 512
81 com.apple.SkyLight 0x000000018fe58a38 CGSPostLocalNotification + 268
82 com.apple.SkyLight 0x000000018fe585ac (anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*) + 116
83 com.apple.SkyLight 0x00000001900fe1d4 CGSDatagramReadStream::dispatchMainQueueDatagrams() + 228
84 com.apple.SkyLight 0x00000001900fe0d0 invocation function for block in CGSDatagramReadStream::mainQueueWakeup() + 28
85 libdispatch.dylib 0x000000018b3d2128 _dispatch_call_block_and_release + 32
86 libdispatch.dylib 0x000000018b3d3ec0 _dispatch_client_callout + 20
87 libdispatch.dylib 0x000000018b3e2314 _dispatch_main_queue_callback_4CF + 884
88 com.apple.CoreFoundation 0x000000018b6c18e8 __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 16
89 com.apple.CoreFoundation 0x000000018b6802fc __CFRunLoopRun + 2524
90 com.apple.CoreFoundation 0x000000018b67f1a8 CFRunLoopRunSpecific + 600
91 com.apple.HIToolbox 0x00000001935a4b40 RunCurrentEventLoopInMode + 292
92 com.apple.HIToolbox 0x00000001935a48b4 ReceiveNextEventCommon + 552
93 com.apple.HIToolbox 0x00000001935a4674 _BlockUntilNextEventMatchingListInModeWithFilter + 72
94 com.apple.AppKit 0x000000018de71660 _DPSNextEvent + 836
95 com.apple.AppKit 0x000000018de70000 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1292
96 com.apple.AppKit 0x000000018de61e4c -[NSApplication run] + 596
97 libqcocoa.dylib 0x0000000123d95010 0x123d80000 + 86032
98 QtCore 0x000000011440a2c0 QEventLoop::exec(QFlags) + 532
99 QtCore 0x0000000114401538 QCoreApplication::exec() + 128
100 QtWidgets.abi3.so 0x0000000117a61eac meth_QApplication_exec(_object*, _object*) + 96
101 org.python.python 0x00000001025fb1dc cfunction_call + 172
102 org.python.python 0x00000001025b8870 _PyObject_MakeTpCall + 360
103 org.python.python 0x000000010268ebc8 call_function + 512
104 org.python.python 0x000000010268c208 _PyEval_EvalFrameDefault + 23108
105 org.python.python 0x00000001025b8ffc function_code_fastcall + 112
106 org.python.python 0x00000001025baf60 method_vectorcall + 168
107 org.python.python 0x000000010268eb68 call_function + 416
108 org.python.python 0x000000010268c208 _PyEval_EvalFrameDefault + 23108
109 org.python.python 0x000000010268fa90 _PyEval_EvalCode + 2988
110 org.python.python 0x00000001025b8f80 _PyFunction_Vectorcall + 256
111 org.python.python 0x000000010268eb68 call_function + 416
112 org.python.python 0x000000010268c284 _PyEval_EvalFrameDefault + 23232
113 org.python.python 0x000000010268fa90 _PyEval_EvalCode + 2988
114 org.python.python 0x00000001026866fc PyEval_EvalCode + 80
115 org.python.python 0x00000001026834a4 builtin_exec + 672
116 org.python.python 0x00000001025fa98c cfunction_vectorcall_FASTCALL + 232
117 org.python.python 0x000000010268eb68 call_function + 416
118 org.python.python 0x000000010268c284 _PyEval_EvalFrameDefault + 23232
119 org.python.python 0x000000010268fa90 _PyEval_EvalCode + 2988
120 org.python.python 0x00000001025b8f80 _PyFunction_Vectorcall + 256
121 org.python.python 0x000000010268eb68 call_function + 416
122 org.python.python 0x000000010268c284 _PyEval_EvalFrameDefault + 23232
123 org.python.python 0x000000010268fa90 _PyEval_EvalCode + 2988
124 org.python.python 0x00000001025b8f80 _PyFunction_Vectorcall + 256
125 org.python.python 0x00000001026e9ea4 pymain_run_module + 200
126 org.python.python 0x00000001026e94e8 Py_RunMain + 764
127 org.python.python 0x00000001026e9d54 pymain_main + 340
128 org.python.python 0x00000001026e9bf4 Py_Main + 36
129 edu.ucsf.cgl.ChimeraX 0x0000000102563d54 main + 128
130 libdyld.dylib 0x000000018b5a1430 start + 4
Thread 1:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 2:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 3:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 4:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 5:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 6:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 7:
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000103765b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 8:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x000000018b553ee8 kevent64 + 8
1 QtWebEngineCore 0x000000015bb45b50 0x158000000 + 62151504
2 QtWebEngineCore 0x000000015bb459f0 0x158000000 + 62151152
3 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
4 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
5 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
6 QtWebEngineCore 0x000000015baf8778 0x158000000 + 61835128
7 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
8 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
9 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 9:: Chrome_IOThread
0 libsystem_kernel.dylib 0x000000018b553ee8 kevent64 + 8
1 QtWebEngineCore 0x000000015bb45b50 0x158000000 + 62151504
2 QtWebEngineCore 0x000000015bb459f0 0x158000000 + 62151152
3 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
4 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
5 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
6 QtWebEngineCore 0x000000015980c000 0x158000000 + 25214976
7 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
8 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
9 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 11:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 12:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x000000018b553ee8 kevent64 + 8
1 QtWebEngineCore 0x000000015bb45b50 0x158000000 + 62151504
2 QtWebEngineCore 0x000000015bb459f0 0x158000000 + 62151152
3 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
4 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
5 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
6 QtWebEngineCore 0x000000015e166fd4 0x158000000 + 102133716
7 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
8 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
9 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 13:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x000000018b54c548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018b583dac _pthread_cond_wait + 1248
2 QtWebEngineCore 0x000000015bb38344 0x158000000 + 62096196
3 QtWebEngineCore 0x000000015d8876a8 0x158000000 + 92829352
4 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
5 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
6 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 14:: ThreadPoolSingleThreadSharedForeground0
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04df8 0x158000000 + 61885944
5 QtWebEngineCore 0x000000015bb049bc 0x158000000 + 61884860
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 16:: VizCompositorThread
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015ba80170 0x158000000 + 61342064
4 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
5 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
6 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
7 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
8 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
9 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 17:: NetworkService
0 libsystem_kernel.dylib 0x000000018b553ee8 kevent64 + 8
1 QtWebEngineCore 0x000000015bb45b50 0x158000000 + 62151504
2 QtWebEngineCore 0x000000015bb459f0 0x158000000 + 62151152
3 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
4 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
5 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
6 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
7 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
8 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 19:: ThreadPoolSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04df8 0x158000000 + 61885944
5 QtWebEngineCore 0x000000015bb049e8 0x158000000 + 61884904
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 21:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 com.apple.SkyLight 0x000000018fe56fd8 CGSSnarfAndDispatchDatagrams + 164
3 com.apple.SkyLight 0x00000001900fa564 SLSGetNextEventRecordInternal + 408
4 com.apple.SkyLight 0x000000018ff4a568 SLEventCreateNextEvent + 16
5 com.apple.HIToolbox 0x00000001935b1c50 PullEventsFromWindowServerOnConnection(unsigned int, unsigned char, __CFMachPortBoost*) + 60
6 com.apple.HIToolbox 0x00000001935b1bd8 MessageHandler(__CFMachPort*, void*, long, void*) + 60
7 com.apple.CoreFoundation 0x000000018b6b0e38 __CFMachPortPerform + 260
8 com.apple.CoreFoundation 0x000000018b681f28 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE1_PERFORM_FUNCTION__ + 60
9 com.apple.CoreFoundation 0x000000018b681de4 __CFRunLoopDoSource1 + 596
10 com.apple.CoreFoundation 0x000000018b680264 __CFRunLoopRun + 2372
11 com.apple.CoreFoundation 0x000000018b67f1a8 CFRunLoopRunSpecific + 600
12 com.apple.AppKit 0x000000018dff0334 _NSEventThread + 196
13 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 22:: MemoryInfra
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb3f658 0x158000000 + 62125656
4 QtWebEngineCore 0x000000015ba801d4 0x158000000 + 61342164
5 QtWebEngineCore 0x000000015baed9ec 0x158000000 + 61790700
6 QtWebEngineCore 0x000000015baaf490 0x158000000 + 61535376
7 QtWebEngineCore 0x000000015bb10514 0x158000000 + 61932820
8 QtWebEngineCore 0x000000015bb1068c 0x158000000 + 61933196
9 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
10 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 23:: ThreadPoolSingleThreadSharedBackgroundBlocking2
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04b04 0x158000000 + 61885188
5 QtWebEngineCore 0x000000015bb04938 0x158000000 + 61884728
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 24:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04df8 0x158000000 + 61885944
5 QtWebEngineCore 0x000000015bb04990 0x158000000 + 61884816
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 25:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04df8 0x158000000 + 61885944
5 QtWebEngineCore 0x000000015bb0490c 0x158000000 + 61884684
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 26:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04df8 0x158000000 + 61885944
5 QtWebEngineCore 0x000000015bb04990 0x158000000 + 61884816
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 27:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018b548dd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018b549184 mach_msg + 76
2 QtWebEngineCore 0x000000015bb3f86c 0x158000000 + 62126188
3 QtWebEngineCore 0x000000015bb042ec 0x158000000 + 61883116
4 QtWebEngineCore 0x000000015bb04b04 0x158000000 + 61885188
5 QtWebEngineCore 0x000000015bb04990 0x158000000 + 61884816
6 QtWebEngineCore 0x000000015bb397a8 0x158000000 + 62101416
7 libsystem_pthread.dylib 0x000000018b583878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018b57e5e0 thread_start + 8
Thread 28:
0 libsystem_pthread.dylib 0x000000018b57e5cc start_wqthread + 0
Thread 29:
0 libsystem_pthread.dylib 0x000000018b57e5cc start_wqthread + 0
Thread 30:
0 libsystem_pthread.dylib 0x000000018b57e5cc start_wqthread + 0
Thread 0 crashed with ARM Thread State (64-bit):
x0: 0x0000000000000000 x1: 0x0000000000000000 x2: 0x0000000000000001 x3: 0x000000018b5cbead
x4: 0x000000016d8967a8 x5: 0x6edbb36701631ee6 x6: 0x0000000000000000 x7: 0x000000016d895f68
x8: 0xc083a1eed87e7138 x9: 0xc083a1efdae14c78 x10: 0x0000000000001bba x11: 0x00000002024dbb5e
x12: 0x00000002024dbb5e x13: 0x0000000000000004 x14: 0x0000000000000881 x15: 0x000000008000001f
x16: 0x0000000000000148 x17: 0x00000001fa00ae90 x18: 0x00000001407e43cc x19: 0x000000000000000b
x20: 0x00000001029f3d40 x21: 0x0000000000000103 x22: 0x00000001029f3e20 x23: 0x00000001468498b0
x24: 0x0000000000000001 x25: 0x0000000000008001 x26: 0x0000000000008000 x27: 0x00000001f69d9848
x28: 0x0000000000000001 fp: 0x000000016d8966e0 lr: 0x000000018b58343c
sp: 0x000000016d8966c0 pc: 0x000000018b550e68 cpsr: 0x40000000
far: 0x00000001548c8000 esr: 0x56000080
Binary Images:
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0x104ba0000 - 0x104e97fff +libgfortran.5.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.5.dylib
0x104ec4000 - 0x104ecffff +libgcc_s.2.dylib (0) /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.2.dylib
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0x1a7d1e000 - 0x1a7e28fff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit
0x1a7e29000 - 0x1a7e3afff com.apple.sidecar-ui (1.0 - 231) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x1a848e000 - 0x1a84e7fff com.apple.ImageCaptureCore (1711.5.2 - 1711.5.2) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x1a84e8000 - 0x1a850dfff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters
0x1a86e4000 - 0x1a875afff com.apple.Safari.Core (16611 - 16611.3.10.1.6) /System/Library/PrivateFrameworks/SafariCore.framework/Versions/A/SafariCore
0x1a875b000 - 0x1a88cdfff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer
0x1a88ce000 - 0x1a8b92fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud
0x1a8be6000 - 0x1a8d02fff com.apple.AnnotationKit (1.0 - 383.6) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit
0x1a8d03000 - 0x1a91bbfff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x1a91bc000 - 0x1a929cfff com.apple.PDFKit (1.0 - 950.40.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit
0x1a9ff9000 - 0x1aa07bfff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput
0x1ab0a6000 - 0x1ab0a9fff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x1ab3a5000 - 0x1ab3befff libCGInterfaces.dylib (544.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x1aca77000 - 0x1ad662fff libfaceCore.dylib (4.3.1) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib
0x1ad663000 - 0x1ad75efff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x1ad75f000 - 0x1ad776fff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark
0x1ad777000 - 0x1ad7d7fff com.apple.DifferentialPrivacy (1.0 - 1) /System/Library/PrivateFrameworks/DifferentialPrivacy.framework/Versions/A/DifferentialPrivacy
0x1ad7d8000 - 0x1ad7f3fff com.apple.SafariFoundation (16611 - 16611.3.10.1.6) /System/Library/PrivateFrameworks/SafariFoundation.framework/Versions/A/SafariFoundation
0x1ad7f4000 - 0x1ad7fafff com.apple.SafariPlatformSupport.framework (16611 - ???) /System/Library/PrivateFrameworks/SafariPlatformSupport.framework/Versions/A/SafariPlatformSupport
0x1ad7fb000 - 0x1ada1afff com.apple.RawCamera.bundle (9.10.0 - 1450.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x1ae2c3000 - 0x1ae2c7fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
0x1afbe7000 - 0x1afbeafff libpmenergy.dylib (227.140.1) /usr/lib/libpmenergy.dylib
0x1b1877000 - 0x1b18b2fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x1b20fc000 - 0x1b2117fff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x1bb148000 - 0x1bb175fff com.apple.HelpData (2.3 - 201) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x1bb176000 - 0x1bb190fff com.apple.shortcut (2.16 - 118) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x1bb191000 - 0x1bb22ffff com.apple.Symbolication (12.5 - 64544.70.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x1bb42d000 - 0x1bb430fff libpmsample.dylib (227.140.1) /usr/lib/libpmsample.dylib
0x1bd952000 - 0x1bd98cfff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x1befd2000 - 0x1befd5fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x1cb3e6000 - 0x1cb3eafff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x1cd638000 - 0x1cd63efff libCoreFSCache.dylib (200.11) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x1cd63f000 - 0x1cd644fff libCoreVMClient.dylib (200.11) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x1cd645000 - 0x1cd654fff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x1cd655000 - 0x1cd657fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x1cd658000 - 0x1cd660fff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x1cd661000 - 0x1cd699fff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x1cd69a000 - 0x1cd6d2fff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x1cd6d3000 - 0x1cd83ffff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x1cd840000 - 0x1cd84afff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x1cd84b000 - 0x1cd9b5fff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x1cd9b6000 - 0x1cd9dafff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x1cd9db000 - 0x1cda3afff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x1ce4b9000 - 0x1ce4c0fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x1ce4c1000 - 0x1ce5a7fff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x1d0a89000 - 0x1d0a94fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x1d6c94000 - 0x1d6c9ffff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x1d6eb9000 - 0x1d6ed2fff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x1deaae000 - 0x1deab5fff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
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: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)
Writable regions: Total=15.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=15.4G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 1408K 11
Activity Tracing 256K 1
CG backing stores 3072K 13
CG image 1280K 61
CoreAnimation 2384K 141
CoreGraphics 64K 4
CoreUI image data 2224K 28
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 14.2G 1100
MALLOC guard page 192K 10
MALLOC_MEDIUM (reserved) 576.0M 8 reserved VM address space (unallocated)
Mach message 64K 4
OpenGL GLSL 384K 4
STACK GUARD 56.5M 31
Stack 166.1M 31
VM_ALLOCATE 338.3M 623
VM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)
__AUTH 1074K 275
__AUTH_CONST 15.8M 467
__DATA 18.6M 604
__DATA_CONST 26.0M 607
__DATA_DIRTY 1833K 222
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 518.6M 149
__OBJC_CONST 3411K 264
__OBJC_RO 75.1M 1
__OBJC_RW 2576K 1
__TEXT 586.8M 628
__UNICODE 588K 1
mapped file 658.8M 110
shared memory 3216K 24
=========== ======= =======
TOTAL 17.3G 5429
TOTAL, minus reserved VM space 16.6G 5429
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked /alpha2macroglobulin_emd_32052.map"
> format ccp4
Opened alpha2macroglobulin_emd_32052.map as #1, grid size 256,256,256, pixel
1.04, shown at level 0.443, step 1, values float32
> ui tool show "Volume Viewer"
> ui tool show "Map Statistics"
> measure mapstats
Map alpha2macroglobulin_emd_32052.map #1, minimum -1.328, maximum 2.244, mean
0.007262, SD 0.08849, RMS 0.08878
> toolshed show
> ui tool show "Show Volume Menu"
> toolshed show
> close #1
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked /7M0R_emd_23613.map" format ccp4
Opened 7M0R_emd_23613.map as #1, grid size 280,280,280, pixel 1.08, shown at
level 0.0107, step 2, values float32
> set bgColor white
> lighting soft
> lighting full
> lighting soft
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked
> /cryosparc_P986_J127_003_volume_map_sharp.mrc"
Opened cryosparc_P986_J127_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 2.06, shown at level 0.307, step 1, values float32
> select add #2
2 models selected
> volume #2 level 0.4999
> volume #2 step 2
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98185,-0.18968,-0.0013861,55.253,0.18966,0.98156,0.023768,-48.53,-0.0031476,-0.023599,0.99972,7.1247
> view matrix models
> #2,0.99724,0.074199,-0.00068878,-18.838,-0.074202,0.9972,-0.0092524,21.634,3.2911e-07,0.009278,0.99996,-2.4527
> view matrix models
> #2,0.97271,-0.23201,-0.0023301,69.014,0.23197,0.97229,0.029095,-57.994,-0.0044846,-0.028841,0.99957,8.8869
> view matrix models
> #2,0.97271,-0.23201,-0.0023301,-25.088,0.23197,0.97229,0.029095,-128.85,-0.0044846,-0.028841,0.99957,-2.3767
> view matrix models
> #2,0.97271,-0.23201,-0.0023301,-55.789,0.23197,0.97229,0.029095,-146.21,-0.0044846,-0.028841,0.99957,-6.3673
> view matrix models
> #2,0.58155,-0.1631,-0.79699,226.96,0.70208,0.59553,0.39043,-256,0.41095,-0.7866,0.46084,229.04
> view matrix models
> #2,0.37457,0.2274,-0.89888,201.02,0.31905,0.87864,0.35523,-226.56,0.87058,-0.41985,0.25656,69.214
> view matrix models
> #2,0.37457,0.2274,-0.89888,222.64,0.31905,0.87864,0.35523,-239.5,0.87058,-0.41985,0.25656,-28.611
> volume #2 color #ffffb28a
> view matrix models
> #2,0.37457,0.2274,-0.89888,233.64,0.31905,0.87864,0.35523,-243.71,0.87058,-0.41985,0.25656,-33.309
> select subtract #2
Nothing selected
> volume #2 color #ffffb2
> select add #2
2 models selected
> view matrix models
> #2,0.37457,0.2274,-0.89888,154.7,0.31905,0.87864,0.35523,-207.51,0.87058,-0.41985,0.25656,-49.334
> view matrix models
> #2,0.63577,-0.27851,-0.71988,178.02,0.75603,0.41274,0.508,-231.98,0.15564,-0.86722,0.47297,192.53
> view matrix models
> #2,0.67355,-0.28813,-0.68067,161.1,0.73048,0.40006,0.55349,-233.88,0.11283,-0.87002,0.47994,202.17
> view matrix models
> #2,0.67355,-0.28813,-0.68067,172.81,0.73048,0.40006,0.55349,-240.37,0.11283,-0.87002,0.47994,202.04
> view matrix models
> #2,0.10517,0.14393,-0.98398,277.59,-0.085126,0.98714,0.1353,-85.622,0.9908,0.069532,0.11607,-173.47
> view matrix models
> #2,0.080827,-0.18678,-0.97907,370.23,-0.033428,0.98122,-0.18995,-13.704,0.99617,0.048081,0.073066,-158.1
> view matrix models
> #2,0.080827,-0.18678,-0.97907,442.15,-0.033428,0.98122,-0.18995,-38.837,0.99617,0.048081,0.073066,-156.95
> view matrix models
> #2,0.080827,-0.18678,-0.97907,441.02,-0.033428,0.98122,-0.18995,-38.663,0.99617,0.048081,0.073066,-151.12
> view matrix models
> #2,0.10506,0.25916,-0.9601,311.7,-0.031859,0.96583,0.25722,-149.43,0.99396,0.0035657,0.10972,-148.13
> volume #2 color #ffffb2cf
> volume #2 color #ffffb2b2
> volume #2 color #ffffb2b3
> view matrix models
> #2,0.10506,0.25916,-0.9601,313.82,-0.031859,0.96583,0.25722,-151.59,0.99396,0.0035657,0.10972,-155.96
> view matrix models
> #2,0.10506,0.25916,-0.9601,316.39,-0.031859,0.96583,0.25722,-156.84,0.99396,0.0035657,0.10972,-167.12
> view matrix models
> #2,0.10506,0.25916,-0.9601,315.1,-0.031859,0.96583,0.25722,-164.15,0.99396,0.0035657,0.10972,-167.02
> view matrix models
> #2,0.10694,0.25742,-0.96036,315.15,-0.043513,0.96619,0.25413,-160.55,0.99331,0.014611,0.11453,-171.02
> view matrix models
> #2,0.024997,0.27371,-0.96149,331.57,-0.0090292,0.96181,0.27357,-172.97,0.99965,0.0018432,0.026514,-146.68
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked /PlxnC1_A39R_emd_21442.map"
Opened PlxnC1_A39R_emd_21442.map as #3, grid size 360,360,360, pixel 0.828,
shown at level 0.00627, step 2, values float32
> hide #!2 models
> hide #!1 models
> select subtract #2
Nothing selected
> hide #!3 models
> show #!2 models
> show #!1 models
> open /Users/rowland_e/Downloads/cryosparc_P986_J203_map.mrc
Opened cryosparc_P986_J203_map.mrc as #4, grid size 280,280,280, pixel 1.08,
shown at level 0.0107, step 2, values float32
> hide #!2 models
> select add #4
2 models selected
> view matrix models #4,1,0,0,-4.8598,0,1,0,-0.76322,0,0,1,1.8995
> view matrix models
> #4,-0.98986,-0.142,-0.0034483,317.98,-0.1312,0.90467,0.40541,-25.114,-0.05445,0.40175,-0.91413,226.07
> select subtract #4
Nothing selected
> hide #!1 models
> show #!2 models
> select add #4
2 models selected
> view matrix models
> #4,-0.98911,-0.14334,0.033487,312.73,-0.11382,0.889,0.44354,-30.884,-0.093348,0.4349,-0.89563,224.27
> view matrix models
> #4,-0.99715,0.057326,0.048988,281.36,0.072944,0.89796,0.43398,-59.096,-0.019111,0.43632,-0.89959,213.4
> select subtract #4
Nothing selected
> hide #!4 models
> show #!1 models
> select add #1
2 models selected
> view matrix models
> #1,0.99811,-0.060977,-0.0071981,10.641,0.061032,0.99811,0.0076864,-10.155,0.0067158,-0.0081112,0.99994,0.21975
> view matrix models
> #1,0.54962,-0.82096,0.15474,167.8,-0.8351,-0.53481,0.12882,337.99,-0.023002,-0.20003,-0.97952,346.19
> view matrix models
> #1,0.88816,0.45314,0.076448,-63.671,0.44189,-0.8878,0.12863,198.32,0.12616,-0.080463,-0.98874,307.02
> view matrix models
> #1,0.88534,0.43275,0.17001,-74.931,0.40044,-0.89551,0.19417,195.4,0.23627,-0.10383,-0.96612,290.33
> view matrix models
> #1,0.77183,-0.46442,-0.43427,173.27,0.56261,0.81704,0.12617,-77.319,0.29621,-0.34171,0.8919,23.942
> view matrix models
> #1,0.82182,-0.5371,-0.19012,138.16,0.47136,0.82838,-0.30266,2.4552,0.32005,0.15912,0.93394,-62.023
> view matrix models
> #1,0.86438,-0.49468,0.090192,81.064,0.48908,0.78545,-0.3793,18.363,0.11679,0.37197,0.92087,-61.409
> view matrix models
> #1,0.87751,-0.45061,-0.1641,112.56,0.47943,0.83221,0.27851,-91.084,0.011066,-0.32307,0.94631,55.65
> view matrix models
> #1,0.91546,0.3801,-0.13209,-23.84,-0.33835,0.90478,0.25863,24.73,0.21782,-0.19208,0.9569,2.9116
> view matrix models
> #1,0.95032,-0.19108,-0.24573,75.192,0.20689,0.97755,0.03997,-34.197,0.23257,-0.088824,0.96852,-16.764
> view matrix models
> #1,0.96618,-0.14,-0.21656,60.467,0.12263,0.9882,-0.091731,-2.2785,0.22685,0.06207,0.97195,-39.257
> view matrix models
> #1,0.93982,-0.30444,-0.1551,79.615,0.32251,0.94033,0.10845,-56.861,0.11283,-0.15194,0.98193,8.7666
> view matrix models
> #1,0.99563,-0.0047867,-0.093301,16.113,0.017875,0.99,0.13995,-23.282,0.091698,-0.14101,0.98575,9.7048
> view matrix models
> #1,0.99976,-0.016473,-0.014376,4.7962,0.016101,0.99954,-0.025682,1.6891,0.014792,0.025445,0.99957,-6.0155
> select subtract #1
Nothing selected
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right zone
> ui mousemode right clip
> ui mousemode right "translate selected models"
> ui tool show "Side View"
> select add #1
5 models selected
> view matrix models
> #1,0.96691,-0.25498,-0.0083092,44.867,0.25428,0.96586,-0.049527,-25.467,0.020654,0.045776,0.99874,-9.845
> select subtract #1
Nothing selected
> select add #1
5 models selected
> view matrix models
> #1,0.96691,-0.25498,-0.0083092,45.111,0.25428,0.96586,-0.049527,-24.826,0.020654,0.045776,0.99874,-12.322
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
3 models selected
> view matrix models
> #2,0.44064,0.3821,-0.8123,160.85,-0.89171,0.29055,-0.34705,384.47,0.10341,0.87726,0.46875,-268.62
> view matrix models
> #2,0.31378,0.38203,-0.86925,207.11,-0.94451,0.21931,-0.24456,390.33,0.097201,0.89775,0.42965,-262.5
> view matrix models
> #2,0.25531,0.6092,-0.75079,131.06,-0.78633,-0.32101,-0.52787,566.84,-0.56259,0.72514,0.39708,-43.633
> view matrix models
> #2,0.25531,0.6092,-0.75079,113.47,-0.78633,-0.32101,-0.52787,546.69,-0.56259,0.72514,0.39708,-166.92
> view matrix models
> #2,0.25531,0.6092,-0.75079,77.963,-0.78633,-0.32101,-0.52787,515.92,-0.56259,0.72514,0.39708,-31.045
> view matrix models
> #2,0.25531,0.6092,-0.75079,92.233,-0.78633,-0.32101,-0.52787,523.77,-0.56259,0.72514,0.39708,-123.98
> view matrix models
> #2,0.25531,0.6092,-0.75079,118.39,-0.78633,-0.32101,-0.52787,541.76,-0.56259,0.72514,0.39708,-144.79
> view matrix models
> #2,0.5166,0.30147,-0.8014,147.84,-0.85374,0.25269,-0.45528,387.67,0.065257,0.91938,0.38792,-350.75
> view matrix models
> #2,0.50662,-0.16278,-0.84666,285.19,-0.862,-0.07607,-0.50117,488.77,0.017174,0.98373,-0.17885,-210.76
> select subtract #2
Nothing selected
> select add #2
3 models selected
> view matrix models
> #2,0.50662,-0.16278,-0.84666,302.81,-0.862,-0.07607,-0.50117,510.29,0.017174,0.98373,-0.17885,-89.414
> view matrix models
> #2,0.50662,-0.16278,-0.84666,301.32,-0.862,-0.07607,-0.50117,510.63,0.017174,0.98373,-0.17885,-61.875
> view matrix models
> #2,0.50662,-0.16278,-0.84666,286.43,-0.862,-0.07607,-0.50117,543.42,0.017174,0.98373,-0.17885,-69.187
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map 7M0R_emd_23613.map in map cryosparc_P986_J127_003_volume_map_sharp.mrc
using 27414 points
correlation = 0.559, correlation about mean = 0.09883, overlap = 257.8
steps = 112, shift = 9.97, angle = 13.3 degrees
Position of 7M0R_emd_23613.map (#1) relative to
cryosparc_P986_J127_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.23053111 -0.96443317 0.12932152 359.04726669
-0.37733381 0.03389999 0.92545664 170.28628067
-0.89692508 -0.26214393 -0.35609824 497.30171667
Axis -0.70868219 0.61239672 0.35034243
Axis point -0.00000000 427.23228795 277.91256593
Rotation angle (degrees) 123.08164538
Shift along axis 24.05824694
> view matrix models
> #2,0.50662,-0.16278,-0.84666,308.15,-0.862,-0.07607,-0.50117,552.57,0.017174,0.98373,-0.17885,-74.924
> hide #!2 models
> ui tool show "Map Statistics"
> measure mapstats #!1
Map 7M0R_emd_23613.map #1, step 2, minimum -0.01205, maximum 0.04805, mean
0.0005064, SD 0.002195, RMS 0.002253
> ui tool show "Measure and Color Blobs"
> ui tool show "Measure Volume and Area"
> ui tool show Distances
Exactly two atoms must be selected!
> measure blob #!1.1 triangleNumber 8024 color #0000ccff outline true
Surface 7M0R_emd_23613.map #1.1 blob:
volume = 2.3632e+05
area = 1.68e+05
size = 220.83 150.17 122.72
> measure blob #!1.1 triangleNumber 7646 color #1bbaadff outline true
Surface 7M0R_emd_23613.map #1.1 blob:
volume = 6.0657
area = 22.494
size = 4.7498 2.7385 1.8665
Exactly two atoms must be selected!
> undo
> redo
> hide #!2 models
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select add #1
9 models selected
> show #!2 models
> hide #!1 models
> select subtract #1
2 models selected
> select subtract #2
Nothing selected
> color #2 #ffffb2ff models
> show #!1 models
> hide #!2 models
> ui tool show "Measure Volume and Area"
> help help:user/tools/measurevolume.html
> measure blob #!1.1 triangleNumber 66673 color #0000ccff outline true
Surface 7M0R_emd_23613.map #1.1 blob:
volume = 2.3632e+05
area = 1.68e+05
size = 220.83 150.17 122.72
> volume #1 color silver
> volume #1 color darkgrey
> ui tool show "Volume Viewer"
> toolshed show
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked /7m0r.cif"
7m0r.cif title:
Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex [more info...]
Chain information for 7m0r.cif #5
---
Chain | Description | UniProt
A B | Plexin-A4 | PLXA4_MOUSE 36-1229
C D | Semaphorin-3A | SEM3A_MOUSE 21-569
E F | Neuropilin-1 | NRP1_MOUSE 22-588
Non-standard residues in 7m0r.cif #5
---
CA — calcium ion
> hide #!1 models
> ui tool show Distances
> ui mousemode right select
> select /B:842@OG
1 atom, 1 residue, 1 model selected
> select add /A:842@CA
2 atoms, 2 residues, 1 model selected
> distance /B:842@OG /A:842@CA
Distance between /B SER 842 OG and /A SER 842 CA: 222.935Å
> select clear
> select /B:1159@CD
1 atom, 1 residue, 1 model selected
> select /D:676@CB
1 atom, 1 residue, 1 model selected
> select add /B:1202@C
2 atoms, 2 residues, 1 model selected
> distance /D:676@CB /B:1202@C
Distance between /D UNK 676 CB and /B SER 1202 C: 163.212Å
> select /A:616@CB
1 atom, 1 residue, 1 model selected
> select add /F:413@CB
2 atoms, 2 residues, 1 model selected
> distance /A:616@CB /F:413@CB
Distance between /A ALA 616 CB and /F THR 413 CB: 165.381Å
> select /A:177@ND2
1 atom, 1 residue, 1 model selected
> select add /B:206@OD1
2 atoms, 2 residues, 1 model selected
> distance /A:177@ND2 /B:206@OD1
Distance between /A ASN 177 ND2 and /B ASN 206 OD1: 117.700Å
> select /E:413@CB
1 atom, 1 residue, 1 model selected
> select add /A:840@CA
2 atoms, 2 residues, 1 model selected
> distance /E:413@CB /A:840@CA
Distance between /E THR 413 CB and /A HIS 840 CA: 241.861Å
> distance save
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked /7M0R_dimensions"
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> select subtract #5
Nothing selected
> hide #!6 models
> hide #!5 models
> show #!1 models
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked
> /cryosparc_P986_J127_003_volume_map_sharp.mrc"
Opened cryosparc_P986_J127_003_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 2.06, shown at level 0.307, step 1, values float32
> hide #!1 models
> select clear
Drag select of 7 cryosparc_P986_J127_003_volume_map_sharp.mrc
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right clip
> select add #7
5 models selected
> select subtract #7
Nothing selected
> close #7
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked
> /cryosparc_P986_J127_003_volume_map_sharp.mrc"
Opened cryosparc_P986_J127_003_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 2.06, shown at level 0.307, step 1, values float32
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right translate
> hide #!3 models
> volume #7 level 0.4885
> volume #7 step 2
> show #!5 models
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select add #6
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 5 models selected
> select subtract #6
30898 atoms, 31634 bonds, 64 pseudobonds, 4362 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,89.804,0,1,0,38.488,0,0,1,114.15
> view matrix models #5,1,0,0,119.91,0,1,0,46.623,0,0,1,124
> hide #!7 models
> show #!2 models
> color #2 silver models
> color #2 darkgrey models
> color #2 #e1d3e0ff models
> color #2 darkgrey models
> color #2 #a9a9a9c2 models
> color #2 #a9a9a9c1 models
> color #2 #a9a9a9b1 models
> color #2 #a9a9a9b3 models
> color #2 darkgrey models
> color #2 #212121ff models
> color #2 silver models
> color #2 #d6d6d6ff models
> color #2 darkgrey models
> transparency (#!5 & sel) 70
> select add #2
30898 atoms, 31634 bonds, 64 pseudobonds, 4362 residues, 7 models selected
> transparency (#!5 & sel) 70
> select subtract #5
4 models selected
> transparency #2.1 70
> view matrix models
> #2,-0.28782,-0.56877,-0.77049,594.77,0.19649,0.75235,-0.62878,101.03,0.93731,-0.33237,-0.10478,25.904
> view matrix models
> #2,-0.28782,-0.56877,-0.77049,675.8,0.19649,0.75235,-0.62878,158.15,0.93731,-0.33237,-0.10478,102.07
> view matrix models
> #2,-0.28782,-0.56877,-0.77049,697.47,0.19649,0.75235,-0.62878,122.78,0.93731,-0.33237,-0.10478,120.62
> fitmap #5 inMap #2
Fit molecule 7m0r.cif (#5) to map cryosparc_P986_J127_003_volume_map_sharp.mrc
(#2) using 30898 atoms
average map value = 0.642, steps = 296
shifted from previous position = 22.7
rotated from previous position = 37.7 degrees
atoms outside contour = 16847, contour level = 0.49994
Position of 7m0r.cif (#5) relative to
cryosparc_P986_J127_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.67960490 0.34120392 0.64939746 218.14602805
-0.57894459 0.29418691 -0.76044540 420.43052574
-0.45051118 -0.89276757 -0.00239270 470.74714619
Axis -0.09188194 0.76375520 -0.63893326
Axis point 265.41810644 0.00000000 350.51756975
Rotation angle (degrees) 133.94005169
Shift along axis 0.28631103
> view matrix models
> #2,-0.28782,-0.56877,-0.77049,694.69,0.19649,0.75235,-0.62878,129.16,0.93731,-0.33237,-0.10478,118.38
> select subtract #2
Nothing selected
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.98656,0.045982,-0.15682,135.77,-0.13097,0.79642,-0.59039,193.69,0.097747,0.60299,0.79174,28.663,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.91471,0.0056353,-0.40408,191.47,0.026531,0.99691,0.073961,35.479,0.40324,-0.078373,0.91173,66.681,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.91471,0.0056353,-0.40408,182.85,0.026531,0.99691,0.073961,37.515,0.40324,-0.078373,0.91173,86.95,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.99196,0.036911,-0.12104,122.09,-0.014534,0.98341,0.18079,29.028,0.1257,-0.17758,0.97605,133.84,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.58872,-0.77921,-0.21502,321.19,0.79132,0.50126,0.35008,-46.461,-0.16501,-0.37625,0.9117,217.92,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.58872,-0.77921,-0.21502,322.11,0.79132,0.50126,0.35008,-25.869,-0.16501,-0.37625,0.9117,214.45,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.43194,-0.86925,-0.24047,363.42,0.86952,0.33055,0.36696,-14.532,-0.2395,-0.3676,0.89862,226.46,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.39439,-0.85695,-0.3318,381.54,0.91468,0.33135,0.23145,-0.24917,-0.088394,-0.39477,0.91452,205.22,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.39439,-0.85695,-0.3318,375.01,0.91468,0.33135,0.23145,-8.4381,-0.088394,-0.39477,0.91452,208.52,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.39439,-0.85695,-0.3318,374.14,0.91468,0.33135,0.23145,-4.8152,-0.088394,-0.39477,0.91452,208.33,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #5,0.39439,-0.85695,-0.3318,374.23,0.91468,0.33135,0.23145,-4.8007,-0.088394,-0.39477,0.91452,208.19,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> lighting simple
> lighting full
> lighting soft
> lighting flat
> open
> "/Users/rowland_e/Documents/University/Postgrad/DPhil_in_Clinical_Medicine/Results/Cryo-
> EM/ER36-ER26-ER39/230530_Crosslinked
> /cryosparc_P986_J177_002_volume_map_sharp.mrc"
Opened cryosparc_P986_J177_002_volume_map_sharp.mrc as #8, grid size
128,128,128, pixel 2.4, shown at level 1.53, step 1, values float32
> select add #8
3 models selected
> view matrix models #8,1,0,0,22.021,0,1,0,114.86,0,0,1,95.024
> view matrix models
> #8,-0.094697,-0.71448,-0.69322,412.7,-0.12904,-0.68166,0.7202,269.73,-0.98711,0.15765,-0.027646,392.68
> view matrix models
> #8,-0.8719,-0.43451,-0.22581,415.37,-0.089077,-0.31271,0.94566,171.36,-0.48151,0.84464,0.23394,168.24
> view matrix models
> #8,0.93606,-0.22518,-0.27033,109.87,0.27246,-0.022172,0.96191,68.859,-0.2226,-0.97406,0.040599,432.37
> view matrix models
> #8,0.83967,-0.060252,0.53975,-32.066,-0.49291,0.33272,0.80395,160.5,-0.22803,-0.9411,0.24968,394.15
> view matrix models
> #8,-0.010374,-0.7584,0.6517,186.7,-0.10423,0.64901,0.75361,60.77,-0.9945,-0.060109,-0.085781,435.99
> view matrix models
> #8,0.30885,-0.53891,0.7837,82.548,-0.30067,0.7264,0.61801,101.86,-0.90233,-0.42651,0.062316,452.45
> view matrix models
> #8,-0.24921,-0.91593,0.31459,302.51,-0.93022,0.31676,0.18535,331.89,-0.26942,-0.24645,-0.93095,489.03
> view matrix models
> #8,0.31198,-0.37008,0.87505,41.825,-0.88431,-0.44984,0.12503,449.61,0.34736,-0.81282,-0.46761,402.41
> view matrix models
> #8,-0.85478,-0.49086,0.16854,356.81,-0.50233,0.70088,-0.50639,320.55,0.13044,-0.51751,-0.84567,453.55
> view matrix models
> #8,-0.84619,0.49415,-0.19946,267.73,-0.50888,-0.63824,0.57767,345.59,0.15815,0.59032,0.79153,15.863
> view matrix models
> #8,0.39816,-0.87442,0.27724,201.63,0.0063452,0.30484,0.95238,62.763,-0.9173,-0.37744,0.12692,436.87
> view matrix models
> #8,0.20824,-0.92699,0.31198,233.41,0.095631,0.33674,0.93673,46.637,-0.97339,-0.16523,0.15877,408.57
> view matrix models
> #8,0.092157,-0.91552,0.39157,236.76,-0.15836,0.37477,0.91349,84.249,-0.98307,-0.14619,-0.11044,451.15
> view matrix models
> #8,0.14748,-0.92138,0.35961,234.25,-0.044193,0.35708,0.93303,65.949,-0.98808,-0.15349,0.011944,433.05
> view matrix models
> #8,0.067881,-0.92621,0.37084,245.53,-0.0045078,0.37141,0.92846,58.369,-0.99768,-0.064697,0.021037,419.74
> view matrix models
> #8,0.067881,-0.92621,0.37084,313.15,-0.0045078,0.37141,0.92846,-8.9416,-0.99768,-0.064697,0.021037,422.55
> view matrix models
> #8,-0.028611,-0.87737,0.47896,303.2,-0.0735,0.4797,0.87435,-5.6227,-0.99688,-0.010187,-0.078212,430.44
> view matrix models
> #8,-0.091915,-0.82714,0.55442,293.2,-0.10092,0.56165,0.82119,-4.977,-0.99064,0.019525,-0.1351,434.29
> view matrix models
> #8,0.22834,-0.6856,0.69124,199.8,-0.40725,0.57763,0.70745,58.857,-0.88431,-0.44305,-0.14731,489.14
> hide #!5 models
> show #!5 models
> hide #!2 models
> color #8 darkgrey models
> transparency #8.1 70
> color #8 #919191ff models
> color #8 #929292ff models
> color #8 darkgrey models
> color #8 #929292ff models
> transparency #8.1.1#!8.1 70
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting full
> lighting soft
> view matrix models
> #8,0.56448,-0.61668,0.54869,160.41,-0.32687,0.44338,0.83461,45.742,-0.75797,-0.65047,0.048704,468.62
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 7 models selected
> select add #8
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 8 models selected
> select add #6
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 9 models selected
> select subtract #8
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 5 models selected
> select subtract #6
30898 atoms, 31634 bonds, 64 pseudobonds, 4362 residues, 3 models selected
> view matrix models
> #5,0.39439,-0.85695,-0.3318,352.63,0.91468,0.33135,0.23145,-23.629,-0.088394,-0.39477,0.91452,207.04
> view matrix models
> #5,0.40966,-0.86803,-0.28053,343.96,0.90848,0.36033,0.21171,-23.983,-0.082692,-0.34159,0.93621,194.74
> view matrix models
> #5,0.36601,-0.87492,-0.31709,357.33,0.93041,0.35111,0.10517,-9.212,0.019321,-0.33351,0.94255,177.1
> view #8 clip false
> view matrix models
> #5,0.36601,-0.87492,-0.31709,355.29,0.93041,0.35111,0.10517,-12.632,0.019321,-0.33351,0.94255,175.43
> select subtract #5
Nothing selected
> ui tool show "Side View"
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.60645,-0.69407,-0.38792,302.69,0.76721,0.63892,0.056248,-23.803,0.20881,-0.33173,0.91998,150.04,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> view orient
> select add #5
30898 atoms, 31634 bonds, 69 pseudobonds, 4362 residues, 4 models selected
> view matrix models
> #5,0.83591,-0.28288,-0.47035,218.74,0.26225,0.95865,-0.11049,30.341,0.48216,-0.030992,0.87553,70.198,#6,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #5
Nothing selected
> hide #!5 models
> show #!1 models
> color #8 #d783ffff models
> select add #8
2 models selected
> view matrix models
> #8,0.56448,-0.61668,0.54869,78.415,-0.32687,0.44338,0.83461,31.622,-0.75797,-0.65047,0.048704,505.16
> view matrix models
> #8,0.56448,-0.61668,0.54869,62.913,-0.32687,0.44338,0.83461,27.371,-0.75797,-0.65047,0.048704,358.86
> hide #!1 models
> view matrix models
> #8,-0.23576,-0.84123,0.48657,231.27,-0.42898,0.53935,0.72462,46.81,-0.87201,-0.037893,-0.48803,372.29
> show #!1 models
> view matrix models
> #8,-0.23576,-0.84123,0.48657,229.29,-0.42898,0.53935,0.72462,40.168,-0.87201,-0.037893,-0.48803,351.45
> view matrix models
> #8,-0.058747,-0.8505,0.52268,197.25,-0.2681,0.51779,0.81241,4.0408,-0.9616,-0.092406,-0.25844,336.11
> select add #8
3 models selected
> select subtract #8
Nothing selected
> select add #8
3 models selected
> view matrix models
> #8,0.41563,-0.76893,0.48579,117.2,-0.7133,-0.60696,-0.35044,431.83,0.56432,-0.20086,-0.80075,203.41
> view matrix models
> #8,0.10834,-0.99225,0.060891,267.87,-0.9768,-0.094873,0.19201,307.49,-0.18474,-0.080281,-0.9795,331.06
> view matrix models
> #8,0.51011,-0.38504,0.76911,-1.3286,0.056878,-0.87714,-0.47685,373.14,0.85823,0.28699,-0.42554,23.252
> view matrix models
> #8,0.56416,0.53436,0.62943,-124.89,0.43144,-0.84077,0.32707,178.21,0.70398,0.087044,-0.70487,122.84
> view matrix models
> #8,0.48249,-0.097494,0.87046,-56.712,-0.64185,-0.71558,0.27563,334.85,0.59601,-0.69169,-0.40784,208.01
> view matrix models
> #8,0.48249,-0.097494,0.87046,-57.556,-0.64185,-0.71558,0.27563,321.1,0.59601,-0.69169,-0.40784,244.34
> view matrix models
> #8,0.48431,0.050603,0.87343,-80.544,-0.41862,-0.86323,0.28213,307.45,0.76825,-0.50227,-0.39689,187.33
> view matrix models
> #8,0.69085,0.31079,0.65279,-115.72,-0.29552,-0.70264,0.64728,204.62,0.65985,-0.64008,-0.39357,224.34
> view matrix models
> #8,0.69085,0.31079,0.65279,-107.93,-0.29552,-0.70264,0.64728,205.26,0.65985,-0.64008,-0.39357,241.68
> view matrix models
> #8,0.58467,0.39573,0.7082,-113.19,-0.33954,-0.67346,0.65663,206.21,0.7368,-0.62438,-0.25938,205.45
> view matrix models
> #8,0.58467,0.39573,0.7082,-109.33,-0.33954,-0.67346,0.65663,208.57,0.7368,-0.62438,-0.25938,192.93
> view matrix models
> #8,0.58467,0.39573,0.7082,-120.21,-0.33954,-0.67346,0.65663,207.72,0.7368,-0.62438,-0.25938,182.91
> fitmap #8 inMap #1
Fit map cryosparc_P986_J177_002_volume_map_sharp.mrc in map 7M0R_emd_23613.map
using 20963 points
correlation = 0.5858, correlation about mean = 0.07976, overlap = 239.7
steps = 176, shift = 21.6, angle = 14.4 degrees
Position of cryosparc_P986_J177_002_volume_map_sharp.mrc (#8) relative to
7M0R_emd_23613.map (#1) coordinates:
Matrix rotation and translation
0.23607270 0.07878752 0.96853613 -50.26959665
-0.50990732 -0.83841682 0.19248840 312.85031349
0.82720265 -0.53930491 -0.15775299 145.78257152
Axis -0.77049736 0.14880850 -0.61983050
Axis point 0.00000000 174.95123410 41.70669191
Rotation angle (degrees) 151.64822034
Shift along axis -5.07310571
> view matrix models
> #8,0.53911,0.18538,0.82158,-85.286,-0.42642,-0.78114,0.45606,256.38,0.72631,-0.5962,-0.34207,189.59
> fitmap #8 inMap #1
Fit map cryosparc_P986_J177_002_volume_map_sharp.mrc in map 7M0R_emd_23613.map
using 20963 points
correlation = 0.5858, correlation about mean = 0.07977, overlap = 239.7
steps = 104, shift = 4.49, angle = 0.00216 degrees
Position of cryosparc_P986_J177_002_volume_map_sharp.mrc (#8) relative to
7M0R_emd_23613.map (#1) coordinates:
Matrix rotation and translation
0.23610312 0.07879854 0.96852781 -50.27502374
-0.50991560 -0.83840528 0.19251670 312.84373867
0.82718886 -0.53932123 -0.15776950 145.78993420
Axis -0.77050608 0.14880688 -0.61982005
Axis point 0.00000000 174.94981018 41.71074919
Rotation angle (degrees) 151.64668515
Shift along axis -5.07301335
> select subtract #8
Nothing selected
> select add #8
3 models selected
> view matrix models
> #8,0.53914,0.18538,0.82156,-81.293,-0.42642,-0.78112,0.45609,257.69,0.72629,-0.59622,-0.34208,190.84
> view matrix models
> #8,-0.33744,-0.47567,0.81232,155.81,0.13199,0.83051,0.54115,-84.894,-0.93205,0.28982,-0.21747,295.63
> view matrix models
> #8,-0.33744,-0.47567,0.81232,148.09,0.13199,0.83051,0.54115,-92.478,-0.93205,0.28982,-0.21747,276.14
> view matrix models
> #8,-0.51513,-0.29487,0.80479,149.84,0.25217,0.84526,0.47111,-101.97,-0.81918,0.44563,-0.36106,258.63
> view matrix models
> #8,-0.64303,-0.51209,0.56945,240.74,0.11542,0.67027,0.73309,-97.18,-0.75709,0.53713,-0.3719,237.01
> view matrix models
> #8,-0.38915,-0.68128,0.62002,218.36,0.24379,0.5729,0.78252,-110.62,-0.88833,0.45567,-0.056851,218.24
> view matrix models
> #8,-0.43094,-0.65919,0.61625,222.17,0.22456,0.58309,0.78076,-108.86,-0.87399,0.47485,-0.10325,220.71
> view matrix models
> #8,-0.43094,-0.65919,0.61625,219.55,0.22456,0.58309,0.78076,-101.44,-0.87399,0.47485,-0.10325,222.6
> view matrix models
> #8,-0.44318,-0.7902,0.4233,272.59,0.084445,0.4333,0.89728,-76.179,-0.89245,0.4334,-0.1253,235.29
> view matrix models
> #8,-0.44318,-0.7902,0.4233,267.62,0.084445,0.4333,0.89728,-70.539,-0.89245,0.4334,-0.1253,235.03
> view matrix models
> #8,-0.44318,-0.7902,0.4233,267.81,0.084445,0.4333,0.89728,-69.981,-0.89245,0.4334,-0.1253,230.62
> view matrix models
> #8,-0.4418,-0.73608,0.51283,244.86,0.095675,0.52972,0.84276,-77.298,-0.892,0.42139,-0.16361,238.6
> volume #1 step 1
> select subtract #8
Nothing selected
> view
> view name 7M0R_J177_bottom
> view list
Named views: 7M0R_J177_bottom
> view name 7M0R_J177_frog
> hide #!8 models
> hide #!1 models
> show #!1 models
> show #!5 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!7 models
> volume #7 step 1
> volume #7 level 0.5887
> select add #8
2 models selected
> select add #7
4 models selected
> select subtract #8
2 models selected
> view matrix models #7,1,0,0,-22.812,0,1,0,-87.851,0,0,1,-75.302
> view matrix models #7,1,0,0,-43.596,0,1,0,-129.24,0,0,1,-89.492
> hide #!1 models
> view matrix models
> #7,0.17849,0.016195,-0.98381,417.13,-0.021902,0.99968,0.012482,-126.88,0.9837,0.01932,0.17879,-128.59
> view matrix models
> #7,0.34358,-0.060122,-0.9372,381.72,0.095706,0.99499,-0.028743,-144.73,0.93423,-0.07982,0.34761,-136.1
> show #!1 models
> view matrix models
> #7,0.34358,-0.060122,-0.9372,341.13,0.095706,0.99499,-0.028743,-148.7,0.93423,-0.07982,0.34761,-187.11
> view matrix models
> #7,0.3086,-0.45671,-0.83437,419.37,-0.040921,0.87,-0.49135,36.974,0.95031,0.18577,0.24979,-230.09
> view matrix models
> #7,0.24406,-0.46316,-0.85201,441.86,-0.063729,0.86902,-0.49066,42.803,0.96766,0.17405,0.18257,-214.08
> view matrix models
> #7,0.24406,-0.46316,-0.85201,437.3,-0.063729,0.86902,-0.49066,69.392,0.96766,0.17405,0.18257,-208.08
> select add #7
3 models selected
> select subtract #7
Nothing selected
> select add #7
3 models selected
> select subtract #7
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.93761,-0.27218,0.21637,19.09,0.2795,0.96014,-0.0034069,-27.069,-0.20682,0.06367,0.97631,15.677
> view matrix models
> #1,0.64383,-0.73206,0.22265,132.05,0.7542,0.65624,-0.023209,-49.771,-0.12912,0.18286,0.97462,-13.828
> view matrix models
> #1,0.64623,-0.73138,0.21786,132.34,0.75363,0.65655,-0.03134,-48.45,-0.12012,0.18444,0.97548,-15.562
> view matrix models
> #1,0.64623,-0.73138,0.21786,128.05,0.75363,0.65655,-0.03134,-54.552,-0.12012,0.18444,0.97548,-14.456
> view matrix models
> #1,0.73005,-0.64276,0.23214,99.721,0.66593,0.74539,-0.030401,-54.873,-0.1535,0.17679,0.97221,-7.7358
> view matrix models
> #1,0.60538,-0.76797,0.20914,141.13,0.78989,0.61199,-0.039189,-52.06,-0.097897,0.18892,0.9771,-18.749
> view matrix models
> #1,0.60538,-0.76797,0.20914,143.94,0.78989,0.61199,-0.039189,-52.857,-0.097897,0.18892,0.9771,-6.3615
> view matrix models
> #1,0.60538,-0.76797,0.20914,143.94,0.78989,0.61199,-0.039189,-60.105,-0.097897,0.18892,0.9771,0.86983
> view matrix models
> #1,0.60538,-0.76797,0.20914,140.24,0.78989,0.61199,-0.039189,-56.966,-0.097897,0.18892,0.9771,-6.2259
> select subtract #1
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.60538,-0.76797,0.20914,140.47,0.78989,0.61199,-0.039189,-55.91,-0.097897,0.18892,0.9771,-0.36939
> select subtract #1
Nothing selected
> view name 7M0R_J127_bottom
> view orient
> view name 7M0R_J127_side
> view name 7M0R_J127_top
> select add #7
3 models selected
> view matrix models
> #7,-0.10053,0.20007,-0.97461,395.53,-0.37764,-0.91394,-0.14867,492.15,-0.92048,0.35311,0.16743,230.01
> view matrix models
> #7,-0.16942,0.17356,-0.97014,418.23,-0.089298,-0.98303,-0.16027,439.01,-0.98149,0.059478,0.18204,312.88
> view matrix models
> #7,-0.16942,0.17356,-0.97014,413.26,-0.089298,-0.98303,-0.16027,435.78,-0.98149,0.059478,0.18204,358.33
> view matrix models
> #7,-0.16942,0.17356,-0.97014,413.23,-0.089298,-0.98303,-0.16027,483.51,-0.98149,0.059478,0.18204,357.15
> view matrix models
> #7,-0.16942,0.17356,-0.97014,414.37,-0.089298,-0.98303,-0.16027,484.74,-0.98149,0.059478,0.18204,367.86
> view matrix models
> #7,-0.20317,-0.50196,-0.84069,553.03,-0.10896,-0.84167,0.52888,275.48,-0.97306,0.19906,0.11631,349.02
> hide #!7 models
> select subtract #7
Nothing selected
> show #!7 models
> select add #7
2 models selected
> select subtract #7
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.20317,-0.50196,-0.84069,558.75,-0.10896,-0.84167,0.52888,258.18,-0.97306,0.19906,0.11631,347.18
> select subtract #7
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.23831,-0.64952,0.72204,195.43,-0.034095,0.74859,0.66215,-181.45,-0.97059,0.13318,-0.20054,445.27
> view matrix models
> #7,-0.23831,-0.64952,0.72204,194.2,-0.034095,0.74859,0.66215,-197.39,-0.97059,0.13318,-0.20054,446.47
> select subtract #7
Nothing selected
> view 7M0R_J127_top
> hide #!7 models
> show #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.38131,-0.76312,0.52177,238.05,0.16512,0.49911,0.85066,-84.802,-0.90958,0.41052,-0.064311,226.77
> view matrix models
> #8,-0.38985,-0.92034,-0.031447,353.24,-0.0067296,-0.0313,0.99949,-2.763,-0.92085,0.38987,0.0060091,220.14
> select subtract #8
Nothing selected
> view 7M0R_J177_top
Expected an objects specifier or a view name or a keyword
> view 7M0R_J177_bottom
> view 7M0R_J127_bottom
> show #!7 models
> hide #!8 models
> open /Users/rowland_e/Downloads/cryosparc_P986_J215_map.mrc
Opened cryosparc_P986_J215_map.mrc as #9, grid size 256,256,256, pixel 2.06,
shown at level 0.253, step 1, values float32
> select add #9
2 models selected
> view matrix models #9,1,0,0,-76.521,0,1,0,15.988,0,0,1,-26.946
> select subtract #9
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,0.12702,-0.72071,-0.6815,503.95,0.30957,0.68155,-0.66307,196.11,0.94235,-0.12675,0.30968,-45.223
> view matrix models
> #9,0.12702,-0.72071,-0.6815,489.96,0.30957,0.68155,-0.66307,90.844,0.94235,-0.12675,0.30968,-147.15
> view matrix models
> #9,0.1073,-0.74147,-0.66235,495.35,0.39498,0.64316,-0.656,78.357,0.9124,-0.19123,0.36188,-136.19
> view matrix models
> #9,0.14914,-0.72494,-0.67247,483.35,0.29438,0.68179,-0.6697,96.204,0.94398,-0.098082,0.31509,-156.55
> view matrix models
> #9,0.097609,-0.73114,-0.67521,498.29,0.31091,0.6669,-0.67719,98.055,0.94542,-0.14383,0.29241,-138.9
> view matrix models
> #9,0.014757,-0.72701,-0.68647,520.33,0.18758,0.67637,-0.71228,134.71,0.98214,-0.11826,0.14635,-116.96
> view matrix models
> #9,-0.059877,-0.71427,-0.69731,537.97,0.18151,0.67912,-0.71123,135.2,0.98157,-0.16915,0.08898,-88.495
> select add #9
3 models selected
> select subtract #9
Nothing selected
> hide #!7 models
> volume #9 level 0.297
> volume #9 level 0.2838
> volume #9 step 2
> volume #9 level 0.2838
> select add #9
3 models selected
> view matrix models
> #9,0.065481,-0.67989,-0.73038,502.88,0.095768,0.73286,-0.67361,134.82,0.99325,-0.025839,0.1131,-135.98
> view matrix models
> #9,0.06562,-0.6814,-0.72896,502.88,0.09554,0.73147,-0.67515,135.64,0.99326,-0.025342,0.1131,-136.12
> view matrix models
> #9,0.1865,-0.63469,-0.74993,462.62,0.035938,0.76722,-0.64038,133.59,0.9818,0.092483,0.1659,-177.87
> view matrix models
> #9,0.093988,-0.75066,-0.65397,494.11,0.028988,0.65866,-0.75188,193.09,0.99515,0.051711,0.083666,-149.5
> view matrix models
> #9,-0.0074792,-0.75231,-0.65876,523.71,-0.099257,0.65609,-0.74813,228.1,0.99503,0.059791,-0.079579,-109.49
> view matrix models
> #9,-0.0074792,-0.75231,-0.65876,504.88,-0.099257,0.65609,-0.74813,204.08,0.99503,0.059791,-0.079579,-105.79
> view matrix models
> #9,0.43937,0.72417,-0.53154,-42.909,-0.54421,-0.2562,-0.79887,581.83,-0.7147,0.64027,0.28153,117.43
> view matrix models
> #9,-0.269,0.92757,-0.25932,27.782,0.019948,-0.26382,-0.96437,471.3,-0.96293,-0.26459,0.052465,485.08
> select subtract #9
Nothing selected
> select add #9
3 models selected
> view matrix models
> #9,-0.269,0.92757,-0.25932,37.484,0.019948,-0.26382,-0.96437,460.73,-0.96293,-0.26459,0.052465,482
> view matrix models
> #9,-0.26936,0.86917,-0.4147,93.185,0.01761,-0.4261,-0.9045,489.01,-0.96288,-0.25094,0.09947,466.23
> view matrix models
> #9,-0.24248,0.76233,-0.60004,161.98,0.0053165,-0.61745,-0.78659,512.76,-0.97014,-0.19393,0.14567,441.17
> view matrix models
> #9,-0.24248,0.76233,-0.60004,171.56,0.0053165,-0.61745,-0.78659,519.16,-0.97014,-0.19393,0.14567,437.32
> view matrix models
> #9,-0.24208,0.72863,-0.6407,190.89,0.010865,-0.65827,-0.75271,519.72,-0.97019,-0.18918,0.15144,434.58
> select subtract #9
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select add #9
2 models selected
> view matrix models
> #9,-0.24208,0.72863,-0.6407,185.41,0.010865,-0.65827,-0.75271,516.71,-0.97019,-0.18918,0.15144,435.35
> select subtract #9
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 6723.140.2
OS Loader Version: 6723.140.2
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 4 days 1:41
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Resolution: 2880 x 1800
UI Looks like: 1440 x 900 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
There is an identical crash that gives the same stack trace in the Qt bug tracker
https://bugreports.qt.io/browse/QTBUG-114908
Notices that ~QScreen() is in the crash report, and the reporter in the Qt bug report says it happens when logging back into the mac after it sleeps with the app running.
Also the comment in that Qt bug report "Volker Hilsheimer added a comment - 28 Jun '23 18:09" lists five other related Qt bug reports, that he claims should be fixed in Qt 6.4.3.
It looks like the discussions in those bug reports might be sufficient for us to figure out how to reproduce the crash in ChimeraX and allow us to test fixes that may already be in Qt newer than the 6.4.2 we are using.
Since this is a reported Qt bug which is getting some attention it would be a very useful step to update our Qt to the current 6.5.1 which may resolve the problem.