The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000119b4adc0 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [21781]
Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [21781]
User ID: 501
Date/Time: 2023-02-01 15:57:07.648 -0500
OS Version: Mac OS X 10.15.7 (19H2026)
Report Version: 12
Bridge OS Version: 7.1 (20P2059)
Anonymous UUID: 61E580C7-5D45-4263-2295-2F14C708A704
Sleep/Wake UUID: 6CC32D0D-8DA6-408C-80CE-EDF3F3DB4382
Time Awake Since Boot: 110000 seconds
Time Since Wake: 4000 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 0x0000307c02636e08
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x307c02636e08:
__LINKEDIT 0000000166603000-0000000166606000 [ 12K] rw-/rwx SM=NUL /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/scipy/cluster/_optimal_leaf_ordering.cpython-39-darwin.so
-->
MALLOC_NANO 0000600000000000-0000600008000000 [128.0M] rw-/rwx SM=PRV
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6f23a32a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6f2f6e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6f15193e raise + 26
3 libsystem_platform.dylib 0x00007fff6f2eb5fd _sigtramp + 29
4 ??? 0x358d48137e40413b 0 + 3858819704286101819
5 QtWidgets 0x0000000123f166d7 QGridLayout::~QGridLayout() + 39
6 QtWidgets.abi3.so 0x0000000123983f18 non-virtual thunk to sipQGridLayout::~sipQGridLayout() + 56
7 QtWidgets 0x0000000123ef38c0 QBoxLayout::~QBoxLayout() + 176
8 QtWidgets.abi3.so 0x00000001239f7d57 sipQVBoxLayout::~sipQVBoxLayout() + 55
9 QtWidgets 0x0000000123f2729a QWidget::~QWidget() + 634
10 QtWidgets.abi3.so 0x0000000123a15537 sipQWidget::~sipQWidget() + 55
11 QtCore 0x00000001191ea89f QObjectPrivate::deleteChildren() + 159
12 QtWidgets 0x0000000123f27520 QWidget::~QWidget() + 1280
13 QtWidgets.abi3.so 0x0000000123a15537 sipQWidget::~sipQWidget() + 55
14 QtCore 0x00000001191ea89f QObjectPrivate::deleteChildren() + 159
15 QtWidgets 0x0000000123f27520 QWidget::~QWidget() + 1280
16 QtWidgets.abi3.so 0x00000001239c99e7 sipQDockWidget::~sipQDockWidget() + 55
17 QtCore 0x00000001191eb770 QObject::event(QEvent*) + 784
18 QtWidgets 0x0000000123f38f3a QWidget::event(QEvent*) + 4330
19 QtWidgets 0x0000000124051df7 QDockWidget::event(QEvent*) + 775
20 QtWidgets.abi3.so 0x00000001239ca0df sipQDockWidget::event(QEvent*) + 191
21 QtWidgets 0x0000000123ee5a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
22 QtWidgets 0x0000000123ee6a43 QApplication::notify(QObject*, QEvent*) + 499
23 QtWidgets.abi3.so 0x0000000123a021e6 sipQApplication::notify(QObject*, QEvent*) + 230
24 QtCore 0x00000001191a2c3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
25 QtCore 0x00000001191a3d52 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 802
26 libqcocoa.dylib 0x0000000130906b8b 0x1308ed000 + 105355
27 libqcocoa.dylib 0x000000013090729b 0x1308ed000 + 107163
28 com.apple.CoreFoundation 0x00007fff3546df92 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
29 com.apple.CoreFoundation 0x00007fff3546df31 __CFRunLoopDoSource0 + 103
30 com.apple.CoreFoundation 0x00007fff3546dd4b __CFRunLoopDoSources0 + 209
31 com.apple.CoreFoundation 0x00007fff3546ca7a __CFRunLoopRun + 927
32 com.apple.CoreFoundation 0x00007fff3546c07e CFRunLoopRunSpecific + 462
33 com.apple.HIToolbox 0x00007fff34098aad RunCurrentEventLoopInMode + 292
34 com.apple.HIToolbox 0x00007fff340987c5 ReceiveNextEventCommon + 584
35 com.apple.HIToolbox 0x00007fff34098569 _BlockUntilNextEventMatchingListInModeWithFilter + 64
36 com.apple.AppKit 0x00007fff326e13c9 _DPSNextEvent + 883
37 com.apple.AppKit 0x00007fff326dfc10 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
38 com.apple.AppKit 0x00007fff326d191e -[NSApplication run] + 658
39 libqcocoa.dylib 0x00000001309060ac 0x1308ed000 + 102572
40 QtCore 0x00000001191ac326 QEventLoop::exec(QFlags) + 486
41 QtCore 0x00000001191a3235 QCoreApplication::exec() + 133
42 QtWidgets.abi3.so 0x0000000123aeed9a meth_QApplication_exec(_object*, _object*) + 90
43 org.python.python 0x000000010b79d71d cfunction_call + 125
44 org.python.python 0x000000010b75e5b7 _PyObject_MakeTpCall + 359
45 org.python.python 0x000000010b836e9c call_function + 876
46 org.python.python 0x000000010b8342a2 _PyEval_EvalFrameDefault + 25554
47 org.python.python 0x000000010b75ed28 function_code_fastcall + 104
48 org.python.python 0x000000010b760d6a method_vectorcall + 202
49 org.python.python 0x000000010b836e0c call_function + 732
50 org.python.python 0x000000010b8342a2 _PyEval_EvalFrameDefault + 25554
51 org.python.python 0x000000010b837b03 _PyEval_EvalCode + 2611
52 org.python.python 0x000000010b75ecb1 _PyFunction_Vectorcall + 289
53 org.python.python 0x000000010b836e0c call_function + 732
54 org.python.python 0x000000010b83434b _PyEval_EvalFrameDefault + 25723
55 org.python.python 0x000000010b837b03 _PyEval_EvalCode + 2611
56 org.python.python 0x000000010b82ddab PyEval_EvalCode + 139
57 org.python.python 0x000000010b82ac12 builtin_exec + 626
58 org.python.python 0x000000010b79d023 cfunction_vectorcall_FASTCALL + 195
59 org.python.python 0x000000010b836e0c call_function + 732
60 org.python.python 0x000000010b83434b _PyEval_EvalFrameDefault + 25723
61 org.python.python 0x000000010b837b03 _PyEval_EvalCode + 2611
62 org.python.python 0x000000010b75ecb1 _PyFunction_Vectorcall + 289
63 org.python.python 0x000000010b836e0c call_function + 732
64 org.python.python 0x000000010b83434b _PyEval_EvalFrameDefault + 25723
65 org.python.python 0x000000010b837b03 _PyEval_EvalCode + 2611
66 org.python.python 0x000000010b75ecb1 _PyFunction_Vectorcall + 289
67 org.python.python 0x000000010b89d870 pymain_run_module + 208
68 org.python.python 0x000000010b89cf87 Py_RunMain + 1431
69 org.python.python 0x000000010b89d58f pymain_main + 223
70 org.python.python 0x000000010b89d49b Py_Main + 43
71 edu.ucsf.cgl.ChimeraX 0x000000010b6dcdc8 main + 120
72 libdyld.dylib 0x00007fff6f0f2cc9 start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6f23cb86 kevent64 + 10
1 QtWebEngineCore 0x0000000128f65a2a 0x125005000 + 66456106
2 QtWebEngineCore 0x0000000128f65927 0x125005000 + 66455847
3 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
4 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
5 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
6 QtWebEngineCore 0x0000000128eec2ad 0x125005000 + 65958573
7 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
8 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef926c 0x125005000 + 66011756
5 QtWebEngineCore 0x0000000128ef8ddd 0x125005000 + 66010589
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6f23cb86 kevent64 + 10
1 QtWebEngineCore 0x0000000128f65a2a 0x125005000 + 66456106
2 QtWebEngineCore 0x0000000128f65927 0x125005000 + 66455847
3 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
4 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
5 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
6 QtWebEngineCore 0x0000000127e2a3a2 0x125005000 + 48386978
7 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
8 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 5:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef926c 0x125005000 + 66011756
5 QtWebEngineCore 0x0000000128ef8e6d 0x125005000 + 66010733
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 6:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000128f2bd1b 0x125005000 + 66219291
3 QtWebEngineCore 0x000000012aff992d 0x125005000 + 100616493
4 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
5 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 7:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 com.apple.framework.IOKit 0x00007fff381e8583 io_connect_method + 383
3 com.apple.framework.IOKit 0x00007fff381e83dc IOConnectCallMethod + 244
4 com.apple.framework.IOKit 0x00007fff381e9214 IOConnectCallStructMethod + 35
5 com.apple.IOAccelerator 0x00007fff59f9aedf IOAccelContextSubmitDataBuffersExt2 + 253
6 libGPUSupportMercury.dylib 0x00007fff5672053f gpusSubmitDataBuffers + 136
7 com.apple.AMDRadeonX6000GLDriver 0x000000013199c3cb glrATI_Hwl_SubmitPacketsWithToken + 101
8 QtWebEngineCore 0x000000012a97f17d 0x125005000 + 93823357
9 QtWebEngineCore 0x000000012946c3ad 0x125005000 + 71725997
10 QtWebEngineCore 0x0000000129327071 0x125005000 + 70393969
11 QtWebEngineCore 0x0000000129311bb4 0x125005000 + 70306740
12 QtWebEngineCore 0x0000000129311710 0x125005000 + 70305552
13 QtWebEngineCore 0x000000012931206d 0x125005000 + 70307949
14 QtWebEngineCore 0x000000012930a971 0x125005000 + 70277489
15 QtWebEngineCore 0x00000001293db689 0x125005000 + 71132809
16 QtWebEngineCore 0x000000012b5ab546 0x125005000 + 106587462
17 QtWebEngineCore 0x000000012b5aed88 0x125005000 + 106601864
18 QtWebEngineCore 0x000000012b5a64c9 0x125005000 + 106566857
19 QtWebEngineCore 0x000000012b5a8dcc 0x125005000 + 106577356
20 QtWebEngineCore 0x000000012b0be408 0x125005000 + 101422088
21 QtWebEngineCore 0x000000012b6f9252 0x125005000 + 107954770
22 QtWebEngineCore 0x000000012b6f8f67 0x125005000 + 107954023
23 QtWebEngineCore 0x000000012b6ffbdc 0x125005000 + 107981788
24 QtWebEngineCore 0x000000012b709a34 0x125005000 + 108022324
25 QtWebEngineCore 0x000000012b0c4f55 0x125005000 + 101449557
26 QtWebEngineCore 0x0000000128ec9689 0x125005000 + 65816201
27 QtWebEngineCore 0x0000000128ee228f 0x125005000 + 65917583
28 QtWebEngineCore 0x0000000128ee1fca 0x125005000 + 65916874
29 QtWebEngineCore 0x0000000128ee2812 0x125005000 + 65918994
30 QtWebEngineCore 0x0000000128e6918c 0x125005000 + 65421708
31 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
32 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
33 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
34 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
35 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
36 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
37 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 8:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6f23cb86 kevent64 + 10
1 QtWebEngineCore 0x0000000128f65a2a 0x125005000 + 66456106
2 QtWebEngineCore 0x0000000128f65927 0x125005000 + 66455847
3 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
4 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
5 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
6 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
7 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
8 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 10:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128e69168 0x125005000 + 65421672
4 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
5 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
6 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
7 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
8 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
9 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 11:: NetworkService
0 libsystem_kernel.dylib 0x00007fff6f23cb86 kevent64 + 10
1 QtWebEngineCore 0x0000000128f65a2a 0x125005000 + 66456106
2 QtWebEngineCore 0x0000000128f65927 0x125005000 + 66455847
3 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
4 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
5 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
6 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
7 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
8 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 13:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef926c 0x125005000 + 66011756
5 QtWebEngineCore 0x0000000128ef8ecd 0x125005000 + 66010829
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 15:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3546e135 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff3546cc02 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff3546c07e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff32882bf4 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 16:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef8f9a 0x125005000 + 66011034
5 QtWebEngineCore 0x0000000128ef8e0d 0x125005000 + 66010637
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128f33bef 0x125005000 + 66251759
4 QtWebEngineCore 0x0000000128e691c9 0x125005000 + 65421769
5 QtWebEngineCore 0x0000000128ee2a5c 0x125005000 + 65919580
6 QtWebEngineCore 0x0000000128e9a998 0x125005000 + 65624472
7 QtWebEngineCore 0x0000000128f04eb8 0x125005000 + 66059960
8 QtWebEngineCore 0x0000000128f0504a 0x125005000 + 66060362
9 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
10 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
11 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 interpreter.cpython-39-darwin.so 0x00000001456d6e53 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 31:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 32:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 33:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x00000001521dd70f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 34:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 35:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 36:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 37:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 38:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 39:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 40:
0 libsystem_kernel.dylib 0x00007fff6f236872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6f2f7425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x000000010c6f623f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 41:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef926c 0x125005000 + 66011756
5 QtWebEngineCore 0x0000000128ef8e6d 0x125005000 + 66010733
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 42:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6f233dea mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6f234160 mach_msg + 60
2 QtWebEngineCore 0x0000000128f33e26 0x125005000 + 66252326
3 QtWebEngineCore 0x0000000128ef87bf 0x125005000 + 66009023
4 QtWebEngineCore 0x0000000128ef926c 0x125005000 + 66011756
5 QtWebEngineCore 0x0000000128ef8ddd 0x125005000 + 66010589
6 QtWebEngineCore 0x0000000128f2c908 0x125005000 + 66222344
7 libsystem_pthread.dylib 0x00007fff6f2f7109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6f2f2b8b thread_start + 15
Thread 43:
0 libsystem_pthread.dylib 0x00007fff6f2f2b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000119b4adc0 rcx: 0x00007feb20047a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007feb20047a80 rsp: 0x00007feb20047a58
r8: 0x00007feb20047f48 r9: 0xb1a941cd2adcae43 r10: 0x0000000119b4adc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000600007318300 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6f23a32a rfl: 0x0000000000000246 cr2: 0x0000000137dbc000
Logical CPU: 0
Error Code: 0x0100001f
Trap Number: 133
Binary Images:
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0x10bc18000 - 0x10bd22ff7 +unicodedata.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/unicodedata.cpython-39-darwin.so
0x10bd31000 - 0x10bd31fff +_arrays.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/_arrays.cpython-39-darwin.so
0x10bd3b000 - 0x10bddcff7 +libarrays.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/lib/libarrays.dylib
0x10be02000 - 0x10be07fff +_json.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_json.cpython-39-darwin.so
0x10be11000 - 0x10c254ffb +_multiarray_umath.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so
0x10c3ad000 - 0x1100b9e47 +libopenblas64_.0.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libopenblas64_.0.dylib
0x110379000 - 0x110490ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x1104ff000 - 0x110535fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x11054b000 - 0x110560ff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x118572000 - 0x118581fff +_datetime.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_datetime.cpython-39-darwin.so
0x118595000 - 0x1185acfff +_pickle.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_pickle.cpython-39-darwin.so
0x1185bf000 - 0x1185d2ffb +_multiarray_tests.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_tests.cpython-39-darwin.so
0x1185ef000 - 0x1185f1fff +_posixsubprocess.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_posixsubprocess.cpython-39-darwin.so
0x1185fb000 - 0x1185ffff7 +select.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/select.cpython-39-darwin.so
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0x118633000 - 0x11864efff +_umath_linalg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-39-darwin.so
0x11866b000 - 0x11867efff +_pocketfft_internal.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/fft/_pocketfft_internal.cpython-39-darwin.so
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0x118763000 - 0x118782ff3 +bit_generator.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/bit_generator.cpython-39-darwin.so
0x1187a7000 - 0x1187dafff +_common.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/random/_common.cpython-39-darwin.so
0x1187fb000 - 0x118801fff +_hashlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_hashlib.cpython-39-darwin.so
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0x7fff63164000 - 0x7fff63182ff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff63183000 - 0x7fff631a3ff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff631a4000 - 0x7fff631b6ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff64520000 - 0x7fff64816fff com.apple.SkyLight (1.600.0 - 451.6) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff65063000 - 0x7fff65071ffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff65133000 - 0x7fff653bfff6 com.apple.spotlight.index (10.7.0 - 2076.7.2) /System/Library/PrivateFrameworks/SpotlightIndex.framework/Versions/A/SpotlightIndex
0x7fff6574d000 - 0x7fff6578eff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff658a5000 - 0x7fff658aeff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.2) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff6591f000 - 0x7fff65949ffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff65b65000 - 0x7fff65b75ff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff65f1c000 - 0x7fff66077ff5 com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff6609a000 - 0x7fff66160ff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff662f7000 - 0x7fff662f8fff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff66330000 - 0x7fff66588ff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff6661f000 - 0x7fff66625ffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff66fb7000 - 0x7fff66fd7ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff67d83000 - 0x7fff67e6eff2 com.apple.ViewBridge (468 - 468) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff68014000 - 0x7fff68015fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff683a4000 - 0x7fff683dffff libAWDSupport.dylib (949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupport.dylib
0x7fff683e0000 - 0x7fff686c0ff7 libAWDSupportFramework.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libAWDSupportFramework.dylib
0x7fff686c1000 - 0x7fff686d2fff libprotobuf-lite.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf-lite.dylib
0x7fff686d3000 - 0x7fff6872cffb libprotobuf.dylib (3541.2) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/Libraries/libprotobuf.dylib
0x7fff6872d000 - 0x7fff68771ff6 com.apple.awd (1.0 - 949) /System/Library/PrivateFrameworks/WirelessDiagnostics.framework/Versions/A/WirelessDiagnostics
0x7fff68c45000 - 0x7fff68c48ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff68cc2000 - 0x7fff68cd0ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff68e98000 - 0x7fff68ecdffe com.apple.iCalendar (7.0 - 810.6.1) /System/Library/PrivateFrameworks/iCalendar.framework/Versions/A/iCalendar
0x7fff69012000 - 0x7fff69014ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff69015000 - 0x7fff69028ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff6905a000 - 0x7fff69066ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff69067000 - 0x7fff69098ffd com.apple.contacts.vCard (1.0 - 3455.18) /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
0x7fff6baeb000 - 0x7fff6baf7ff9 libAudioStatistics.dylib (1104.104) /usr/lib/libAudioStatistics.dylib
0x7fff6baf8000 - 0x7fff6bb2bffa libAudioToolboxUtility.dylib (1104.104) /usr/lib/libAudioToolboxUtility.dylib
0x7fff6bb32000 - 0x7fff6bb66fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff6bb69000 - 0x7fff6bb73fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff6bb74000 - 0x7fff6bbfcfff libCoreStorage.dylib (551.0.1) /usr/lib/libCoreStorage.dylib
0x7fff6bbff000 - 0x7fff6bc01ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff6bc47000 - 0x7fff6bdfeffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff6be25000 - 0x7fff6be2bff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff6bf0d000 - 0x7fff6bf14fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff6bf43000 - 0x7fff6bf63ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff6bfe3000 - 0x7fff6c0c0ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff6c0d5000 - 0x7fff6c0d6fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff6c0d7000 - 0x7fff6c162ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff6c163000 - 0x7fff6c164fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff6c17c000 - 0x7fff6c192fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff6c1c7000 - 0x7fff6c239ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib
0x7fff6c23a000 - 0x7fff6c2d3fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff6c2d7000 - 0x7fff6c2d7ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff6c2d8000 - 0x7fff6c39cffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff6c39d000 - 0x7fff6c3adffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff6c3ae000 - 0x7fff6c3bafff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff6c3bb000 - 0x7fff6c40dfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6c40e000 - 0x7fff6c423ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff6c424000 - 0x7fff6c424fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff6c425000 - 0x7fff6c436fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff6c437000 - 0x7fff6c44efd7 libcompression.dylib (87.1) /usr/lib/libcompression.dylib
0x7fff6c728000 - 0x7fff6c73eff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6c73f000 - 0x7fff6c740fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff6cbe3000 - 0x7fff6cce7fcf libcrypto.44.dylib (47.140.3) /usr/lib/libcrypto.44.dylib
0x7fff6ccea000 - 0x7fff6ccf5fff libcsfde.dylib (551.0.1) /usr/lib/libcsfde.dylib
0x7fff6ccfd000 - 0x7fff6cd5cff7 libcups.2.dylib (483.9) /usr/lib/libcups.2.dylib
0x7fff6cd5e000 - 0x7fff6cdc3ff7 libcurl.4.dylib (118.120.6) /usr/lib/libcurl.4.dylib
0x7fff6ce66000 - 0x7fff6ce66fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6ce67000 - 0x7fff6ce81ff7 libexpat.1.dylib (19.60.3) /usr/lib/libexpat.1.dylib
0x7fff6ce82000 - 0x7fff6ce8effb libexslt.0.dylib (16.12) /usr/lib/libexslt.0.dylib
0x7fff6ce8f000 - 0x7fff6ce91fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6ce92000 - 0x7fff6ce97f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff6cea0000 - 0x7fff6cea5fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6cea6000 - 0x7fff6ceafff7 libheimdal-asn1.dylib (564.140.8) /usr/lib/libheimdal-asn1.dylib
0x7fff6ceb0000 - 0x7fff6cfa0fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6cfa1000 - 0x7fff6d1f8fff libicucore.A.dylib (64261.1.1) /usr/lib/libicucore.A.dylib
0x7fff6d212000 - 0x7fff6d213fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6d214000 - 0x7fff6d22cff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6d244000 - 0x7fff6d2ebff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6d2ec000 - 0x7fff6d54eff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6d8bb000 - 0x7fff6d8eafff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6da1a000 - 0x7fff6de96ff5 libnetwork.dylib (1880.120.5) /usr/lib/libnetwork.dylib
0x7fff6de97000 - 0x7fff6deaefff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6df37000 - 0x7fff6df6afde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6df6b000 - 0x7fff6df6cff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6df7d000 - 0x7fff6df81fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6df84000 - 0x7fff6dfbafff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff6dffa000 - 0x7fff6e008ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6e009000 - 0x7fff6e00cff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib
0x7fff6e00d000 - 0x7fff6e00ffff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib
0x7fff6e03e000 - 0x7fff6e056fff libresolv.9.dylib (67.40.3) /usr/lib/libresolv.9.dylib
0x7fff6e058000 - 0x7fff6e09cff7 libsandbox.1.dylib (1217.141.9) /usr/lib/libsandbox.1.dylib
0x7fff6e09d000 - 0x7fff6e0afff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6e0b0000 - 0x7fff6e0b1ff7 libspindump.dylib (281.4) /usr/lib/libspindump.dylib
0x7fff6e0b2000 - 0x7fff6e29cff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff6e390000 - 0x7fff6e3bdffb libssl.46.dylib (47.140.3) /usr/lib/libssl.46.dylib
0x7fff6e43f000 - 0x7fff6e470ff7 libtidy.A.dylib (17.3) /usr/lib/libtidy.A.dylib
0x7fff6e492000 - 0x7fff6e4ecff8 libusrtcp.dylib (1880.120.5) /usr/lib/libusrtcp.dylib
0x7fff6e4ed000 - 0x7fff6e4f0ffb libutil.dylib (57.140.1) /usr/lib/libutil.dylib
0x7fff6e4f1000 - 0x7fff6e4fefff libxar.1.dylib (425.7) /usr/lib/libxar.1.dylib
0x7fff6e504000 - 0x7fff6e5e6ff7 libxml2.2.dylib (33.14) /usr/lib/libxml2.2.dylib
0x7fff6e5ea000 - 0x7fff6e612fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff6e613000 - 0x7fff6e625ff3 libz.1.dylib (76.0.1) /usr/lib/libz.1.dylib
0x7fff6eed4000 - 0x7fff6eed9ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6eeda000 - 0x7fff6eee5fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6eee6000 - 0x7fff6eeedfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6eeee000 - 0x7fff6eef7ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6eef8000 - 0x7fff6ef8afdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff6f097000 - 0x7fff6f0d7ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6f0d8000 - 0x7fff6f10efff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff6f10f000 - 0x7fff6f10fffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6f110000 - 0x7fff6f11cff3 libkxld.dylib (6153.141.66) /usr/lib/system/libkxld.dylib
0x7fff6f11d000 - 0x7fff6f11dff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff6f11e000 - 0x7fff6f123ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6f124000 - 0x7fff6f126ff3 libquarantine.dylib (110.40.6) /usr/lib/system/libquarantine.dylib
0x7fff6f127000 - 0x7fff6f128ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6f129000 - 0x7fff6f140ff3 libsystem_asl.dylib (377.60.4) /usr/lib/system/libsystem_asl.dylib
0x7fff6f141000 - 0x7fff6f141ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6f142000 - 0x7fff6f1c9fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff6f1ca000 - 0x7fff6f1cdffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff6f1ce000 - 0x7fff6f1d1fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6f1d2000 - 0x7fff6f1dafff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff6f1db000 - 0x7fff6f1e2fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6f1e3000 - 0x7fff6f1e4ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6f1e5000 - 0x7fff6f232ff7 libsystem_info.dylib (538.1) /usr/lib/system/libsystem_info.dylib
0x7fff6f233000 - 0x7fff6f25fff7 libsystem_kernel.dylib (6153.141.66) /usr/lib/system/libsystem_kernel.dylib
0x7fff6f260000 - 0x7fff6f2a7fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6f2a8000 - 0x7fff6f2cffff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6f2d0000 - 0x7fff6f2ddffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6f2de000 - 0x7fff6f2e7ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6f2e8000 - 0x7fff6f2f0fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6f2f1000 - 0x7fff6f2fbfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6f2fc000 - 0x7fff6f300ff3 libsystem_sandbox.dylib (1217.141.9) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6f301000 - 0x7fff6f303fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6f304000 - 0x7fff6f30bffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6f30c000 - 0x7fff6f322ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6f324000 - 0x7fff6f329ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6f32a000 - 0x7fff6f35fffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 12
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: 1678392
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=13.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=13.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 1232K 2
CG image 240K 18
CoreAnimation 528K 30
CoreGraphics 8K 1
CoreImage 32K 4
CoreUI image data 2924K 24
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 11.0G 1001
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 1.4G 16 reserved VM address space (unallocated)
Mach message 24K 4
OpenGL GLSL 384K 4
STACK GUARD 172K 43
Stack 172.3M 44
Stack Guard 56.0M 1
VM_ALLOCATE 152.7M 183
VM_ALLOCATE (reserved) 352.0M 3 reserved VM address space (unallocated)
__DATA 82.3M 772
__DATA_CONST 148K 7
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 442.4M 491
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 757.0M 764
__UNICODE 564K 1
mapped file 94.3M 53
shared memory 2848K 24
=========== ======= =======
TOTAL 14.5G 3513
TOTAL, minus reserved VM space 12.7G 3513
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.0
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/chris/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
Requirement already satisfied: ChimeraX-UI~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.24.3)
Collecting seaborn
Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 2.4 MB/s eta 0:00:00
Collecting pandas
Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 20.3 MB/s eta 0:00:00
Collecting openpyxl
Downloading openpyxl-3.1.0-py2.py3-none-any.whl (250 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 6.5 MB/s eta 0:00:00
Requirement already satisfied: ChimeraX-Core~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.5)
Collecting qtrangeslider
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
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Requirement already satisfied: ChimeraX-Graphics~=1.0 in
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packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1)
Collecting et-xmlfile
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6)
Requirement already satisfied: numpy>=1.20.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1)
Requirement already satisfied: python-dateutil>=2.8.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2)
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
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packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
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packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
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packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0.1)
Requirement already satisfied: packaging>=20.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3)
Requirement already satisfied: pillow>=6.2.0 in
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packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0)
Requirement already satisfied: cycler>=0.10 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(4.38.0)
Requirement already satisfied: pyparsing>=2.2.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9)
Requirement already satisfied: kiwisolver>=1.0.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4)
Requirement already satisfied: six>=1.5 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)
Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
seaborn, ChimeraX-XMAS
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.0
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
\---
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.0
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
Installed ChimeraX-XMAS (1.1.2)
> ui tool show XMAS
> open "/Users/chris/OneDrive -
> rockefeller.edu/Cell_Manuscript_NPC_cryoEM_SPA-
> in_situ/Double_Nuclear_Outer_Ring/7n84.pdb"
7n84.pdb title:
Double nuclear outer ring from the isolated yeast NPC [more info...]
Chain information for 7n84.pdb #1
---
Chain | Description | UniProt
X | nuclear PORE protein NUP188 | NU188_YEAST
Y Z | unknown |
a l | nuclear PORE protein NUP120 | NU120_YEAST
b m | nuclear PORE protein NUP85 | NUP85_YEAST
c | nucleoporin 145C | NU145_YEAST
d o | protein transport protein SEC13 | SEC13_YEAST
e p | nucleoporin SEH1 | SEH1_YEAST
f q | nuclear PORE protein NUP84 | NUP84_YEAST
g | nuclear PORE protein NUP133 | NU133_YEAST
n | nucleoporin 145C | NU145_YEAST
r | nuclear PORE protein NUP133 | NU133_YEAST
> ui tool show XMAS
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 101, in __init__
df = self.make_df(evidence_file, delimiter, header)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 300, in make_df
df = pd.read_csv(evidence_file, sep=delimiter, header=0,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/util/_decorators.py", line 211, in wrapper
return func(*args, **kwargs)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/io/parsers/readers.py", line 611, in _read
return parser.read(nrows)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/io/parsers/readers.py", line 1778, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 230, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 808, in
pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 890, in
pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 952, in
pandas._libs.parsers.TextReader._convert_column_data
pandas.errors.ParserError: Too many columns specified: expected 22 and found
21
pandas.errors.ParserError: Too many columns specified: expected 22 and found
21
File "pandas/_libs/parsers.pyx", line 952, in
pandas._libs.parsers.TextReader._convert_column_data
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
See log for complete Python traceback.
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
See log for complete Python traceback.
> close session
> open "/Users/chris/OneDrive - rockefeller.edu/Cross-
> linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/fibrin.pdb"
Chain information for fibrin.pdb #1
---
Chain | Description
A D | No description available
B E | No description available
C F | No description available
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/demo.tsv
1 Peptide pair is disregarded due to lacking/decoy sequence
Unique peptide pairs: 4 out of 5
Unique peptide pairs with pseudobonds: 3
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/demo_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/demo_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence1.tsv
Unique peptide pairs: 345 out of 345
Unique peptide pairs with pseudobonds: 39
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence1_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence1_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence2.tsv
Unique peptide pairs: 357 out of 357
Unique peptide pairs with pseudobonds: 39
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence2_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence2_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence3.tsv
Unique peptide pairs: 447 out of 447
Unique peptide pairs with pseudobonds: 47
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence3_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/evidence3_1.tsv
> hide #5 models
> hide #4 models
> hide #3 models
> close session
> open "/Users/chris/OneDrive -
> rockefeller.edu/Cell_Manuscript_NPC_cryoEM_SPA-
> in_situ/Double_Nuclear_Outer_Ring/7n84.pdb" format pdb
7n84.pdb title:
Double nuclear outer ring from the isolated yeast NPC [more info...]
Chain information for 7n84.pdb #1
---
Chain | Description | UniProt
X | nuclear PORE protein NUP188 | NU188_YEAST
Y Z | unknown |
a l | nuclear PORE protein NUP120 | NU120_YEAST
b m | nuclear PORE protein NUP85 | NUP85_YEAST
c | nucleoporin 145C | NU145_YEAST
d o | protein transport protein SEC13 | SEC13_YEAST
e p | nucleoporin SEH1 | SEH1_YEAST
f q | nuclear PORE protein NUP84 | NUP84_YEAST
g | nuclear PORE protein NUP133 | NU133_YEAST
n | nucleoporin 145C | NU145_YEAST
r | nuclear PORE protein NUP133 | NU133_YEAST
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
AttributeError: 'Pandas' object has no attribute 'Peptide_Order'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 181, in parse_plink
ref = row.Peptide_Order
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 286, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 457, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
> close session
> open "/Users/chris/OneDrive -
> rockefeller.edu/Cell_Manuscript_NPC_cryoEM_SPA-
> in_situ/Double_Nuclear_Outer_Ring/7n9f.cif"
7n9f.cif title:
Structure of the in situ yeast NPC [more info...]
Chain information for 7n9f.cif #1
---
Chain | Description | UniProt
0 Y | Nucleoporin NUP170 | NU170_YEAST
1 Z | Nucleoporin NUP157 | NU157_YEAST
5 6 | orphans bound to Nup192 NTD |
A D G J y z | Nucleoporin NSP1 | NSP1_YEAST
B E H K | Nucleoporin NUP57 | NUP57_YEAST
C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST
M O | Nucleoporin NUP192 | NU192_YEAST
N P | Nucleoporin NUP188 | NU188_YEAST
Q R S T | Nucleoporin NIC96 | NIC96_YEAST
U W | Nucleoporin NUP53 | NUP53_YEAST
V X | Nucleoporin ASM4 | NUP59_YEAST
a h | Nucleoporin NUP120 | NU120_YEAST
b i | Nucleoporin NUP85 | NUP85_YEAST
c j | Nucleoporin 145c | NU145_YEAST
d k | Protein transport protein SEC13 | SEC13_YEAST
e l | Nucleoporin SEH1 | SEH1_YEAST
f m | Nucleoporin NUP84 | NUP84_YEAST
g n | Nucleoporin NUP133 | NU133_YEAST
o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST
u v | Nucleoporin NUP82 | NUP82_YEAST
w x | Nucleoporin NUP159 | NU159_YEAST
7n9f.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1.csv
Unique peptide pairs: 1 out of 1
Unique peptide pairs with pseudobonds: 0
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1.csv
Unique peptide pairs: 1 out of 1
Unique peptide pairs with pseudobonds: 0
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1.csv
Unique peptide pairs: 2 out of 2
Unique peptide pairs with pseudobonds: 0
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1.csv
Unique peptide pairs: 2 out of 2
Unique peptide pairs with pseudobonds: 2
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.tsv
> hide #2 models
> show #2 models
Please check one or more files
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1.csv
Unique peptide pairs: 2 out of 2
Unique peptide pairs with pseudobonds: 2
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-
linking_Mass_Spec/ChimeraX_XMAS_Plugin_Manual_and_Tutorial/media-2/Test_1_1.tsv
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-linking_Mass_Spec/XMAS_Test/20210326 Nup214 IP CX
final_TVtest.xlsx
Unique peptide pairs: 270 out of 271
Unique peptide pairs with pseudobonds: 0
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-linking_Mass_Spec/XMAS_Test/20210326 Nup214 IP CX
final_TVtest_1.tsv
> close session
> open "/Users/chris/OneDrive - rockefeller.edu/Cross-
> linking_Mass_Spec/XMAS_Test/7r5j.cif"
7r5j.cif title:
Human nuclear pore complex (dilated) [more info...]
Chain information for 7r5j.cif #1
---
Chain | Description | UniProt
00 01 02 03 04 | E3 SUMO-protein ligase RanBP2 | RBP2_HUMAN
10 11 12 13 14 15 16 17 | Nuclear pore membrane glycoprotein 210 | PO210_HUMAN
40 41 | Aladin | AAAS_HUMAN
A0 A1 A2 A3 A4 A5 A6 | Nuclear pore complex protein Nup93 | NUP93_HUMAN
B0 B1 | Nucleoporin NUP188 homolog | NU188_HUMAN
C0 C1 C2 C3 C4 | Nuclear pore complex protein Nup205 | NU205_HUMAN
D0 D1 D2 D3 D4 D5 | Nuclear pore complex protein Nup155 | NU155_HUMAN
E0 E1 | Nucleoporin NDC1 | NDC1_HUMAN
F0 F1 F2 F3 | Nucleoporin NUP35 | NUP35_HUMAN
H0 H1 H2 H3 | Nucleoporin p54 | NUP54_HUMAN
I0 I1 I2 I3 | Nucleoporin p58/p45 | NUP58_HUMAN
J0 J1 J2 J3 J4 | Nuclear pore glycoprotein p62 | NUP62_HUMAN
K0 K1 K2 K3 | Nuclear pore complex protein Nup133 | NU133_HUMAN
L0 L1 L2 L3 | Nuclear pore complex protein Nup107 | NU107_HUMAN
M0 M1 M2 M3 | Nuclear pore complex protein Nup96 | NUP98_HUMAN
N0 N1 N2 N3 | Protein SEC13 homolog | SEC13_HUMAN
O0 O1 O2 O3 | Nucleoporin SEH1 | SEH1_HUMAN
P0 P1 P2 P3 | Nuclear pore complex protein Nup85 | NUP85_HUMAN
Q0 Q1 Q2 Q3 | Nucleoporin Nup43 | NUP43_HUMAN
R0 R1 R2 R3 | Nuclear pore complex protein Nup160 | NU160_HUMAN
S0 S1 S2 S3 | Nucleoporin Nup37 | NUP37_HUMAN
T0 T1 | Protein ELYS | ELYS_HUMAN
U0 U1 U2 U3 U4 U5 U6 | Nuclear pore complex protein Nup98 | NUP98_HUMAN
V0 | Nuclear pore complex protein Nup214 | NU214_HUMAN
W0 | Nuclear pore complex protein Nup88 | NUP88_HUMAN
7r5j.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
Peptide pair mapping of XlinkX evidence file: /Users/chris/OneDrive -
rockefeller.edu/Cross-linking_Mass_Spec/XMAS_Test/20210326 Nup214 IP CX
final_TVtest.xlsx
Unique peptide pairs: 270 out of 271
Unique peptide pairs with pseudobonds: 188
Pseudobonds are stored in /Users/chris/OneDrive - rockefeller.edu/Cross-
linking_Mass_Spec/XMAS_Test/20210326 Nup214 IP CX final_TVtest_1.pb
Mapping information is stored in /Users/chris/OneDrive -
rockefeller.edu/Cross-linking_Mass_Spec/XMAS_Test/20210326 Nup214 IP CX
final_TVtest_1.tsv
Please select pseudobonds
/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
/Users/chris/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
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: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2026)
Kernel Version: Darwin 19.6.0
Time since boot: 6 days 7:25
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
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
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: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openpyxl: 3.1.0
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
seaborn: 0.12.2
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed with newest release of XMAS (1.1.3)