The following bug report has been submitted:
Platform: macOS-11.1-arm64-arm-64bit
ChimeraX Version: 1.7.dev202307200302 (2023-07-20 03:02:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002df6df000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000296853000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000295847000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029483b000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029382f000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000292823000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000291817000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029080b000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028f7ff000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028e7f3000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028d7e7000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028c7db000 (most recent call first):
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001044b3d40 (most recent call first):
Garbage-collecting
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2786 in set_matrix
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 775 in set_projection_matrix
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 683 in _use_shader
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 759 in _opengl_shader
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 656 in shader
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 807 in _draw_geometry
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 776 in draw_self
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 769 in draw
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1556 in _draw_multiple
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1543 in draw_opaque
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
File "/Volumes/ChimeraX Installer/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 53)
Process: ChimeraX [9953]
Path: /Volumes/VOLUME/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.7.0 (1.7.0.0)
Code Type: ARM-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [9953]
User ID: 501
Date/Time: 2023-07-22 21:26:59.456 +0800
OS Version: macOS 11.1 (20C69)
Report Version: 12
Anonymous UUID: 878EC3D7-E023-830B-FB3F-0AFCBAB32A09
Sleep/Wake UUID: 245B39DF-D355-437A-8B1C-8AA2B25F7BE0
Time Awake Since Boot: 72000 seconds
Time Since Wake: 940 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 0x00000000000000a9
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0xa9:
-->
__TEXT 10420c000-104210000 [ 16K] r-x/r-x SM=COW /Volumes/*/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x000000018d547cec __pthread_kill + 8
1 libsystem_pthread.dylib 0x000000018d578c24 pthread_kill + 292
2 libsystem_c.dylib 0x000000018d4584d0 raise + 32
3 org.python.python 0x00000001047563c4 faulthandler_fatal_error + 392
4 libsystem_platform.dylib 0x000000018d5c0c44 _sigtramp + 56
5 org.python.python 0x00000001045e4db0 dict_traverse + 204
6 org.python.python 0x00000001045e4db0 dict_traverse + 204
7 org.python.python 0x00000001047524e0 gc_collect_main + 1968
8 org.python.python 0x0000000104753dc4 _PyObject_GC_Link + 316
9 org.python.python 0x000000010462d4cc _PyType_AllocNoTrack + 116
10 org.python.python 0x00000001046206ec PyType_GenericAlloc + 20
11 _ctypes.cpython-311-darwin.so 0x0000000107fbe668 GenericPyCData_new + 120
12 org.python.python 0x000000010461d470 type_call + 84
13 org.python.python 0x0000000104599700 _PyObject_MakeTpCall + 128
14 org.python.python 0x00000001046bcc88 _PyEval_EvalFrameDefault + 53048
15 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
16 arraydatatype.cpython-311-darwin.so 0x000000016bf890a8 __pyx_pw_17OpenGL_accelerate_13arraydatatype_13ArrayDatatype_17asArray + 620
17 wrapper.cpython-311-darwin.so 0x000000016f24f040 __pyx_f_17OpenGL_accelerate_7wrapper_19CallFuncPyConverter_c_call + 168
18 wrapper.cpython-311-darwin.so 0x000000016f24cc90 __pyx_f_17OpenGL_accelerate_7wrapper_22PyArgCalculatorElement_c_call + 616
19 wrapper.cpython-311-darwin.so 0x000000016f24d5e8 __pyx_f_17OpenGL_accelerate_7wrapper_15PyArgCalculator_c_call + 236
20 wrapper.cpython-311-darwin.so 0x000000016f25ebfc __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 124
21 latebind.cpython-311-darwin.so 0x000000016f2a50ac __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 444
22 org.python.python 0x0000000104599700 _PyObject_MakeTpCall + 128
23 org.python.python 0x00000001046bcc88 _PyEval_EvalFrameDefault + 53048
24 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
25 org.python.python 0x000000010459dab8 method_vectorcall + 388
26 QtCore.abi3.so 0x0000000120147140 PyQtSlot::call(_object*, _object*) const + 68
27 QtCore.abi3.so 0x0000000120146fc8 PyQtSlot::invoke(void**, _object*, void*, bool) const + 292
28 QtCore.abi3.so 0x0000000120147fbc PyQtSlotProxy::unislot(void**) + 92
29 QtCore.abi3.so 0x0000000120147f2c PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 68
30 QtCore 0x00000001204414f4 0x12038c000 + 742644
31 QtCore 0x0000000120455cb0 QTimer::timerEvent(QTimerEvent*) + 208
32 QtCore.abi3.so 0x00000001200268d8 sipQTimer::timerEvent(QTimerEvent*) + 148
33 QtCore 0x0000000120439cbc QObject::event(QEvent*) + 88
34 QtCore.abi3.so 0x0000000120026724 sipQTimer::event(QEvent*) + 220
35 QtWidgets 0x000000012180cfec QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
36 QtWidgets 0x000000012180de50 QApplication::notify(QObject*, QEvent*) + 512
37 QtWidgets.abi3.so 0x0000000120a36548 sipQApplication::notify(QObject*, QEvent*) + 248
38 QtCore 0x00000001203f7f88 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 292
39 QtCore 0x000000012056670c QTimerInfoList::activateTimers() + 944
40 libqcocoa.dylib 0x00000001667bda98 0x1667a8000 + 88728
41 com.apple.CoreFoundation 0x000000018d673c14 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 28
42 com.apple.CoreFoundation 0x000000018d673b60 __CFRunLoopDoSource0 + 208
43 com.apple.CoreFoundation 0x000000018d67384c __CFRunLoopDoSources0 + 268
44 com.apple.CoreFoundation 0x000000018d6721e4 __CFRunLoopRun + 824
45 com.apple.CoreFoundation 0x000000018d671740 CFRunLoopRunSpecific + 600
46 com.apple.HIToolbox 0x000000019518e678 RunCurrentEventLoopInMode + 292
47 com.apple.HIToolbox 0x000000019518e4a8 ReceiveNextEventCommon + 688
48 com.apple.HIToolbox 0x000000019518e1d8 _BlockUntilNextEventMatchingListInModeWithFilter + 76
49 com.apple.AppKit 0x000000018fe49da4 _DPSNextEvent + 868
50 com.apple.AppKit 0x000000018fe48724 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1312
51 com.apple.AppKit 0x000000018fe3a60c -[NSApplication run] + 600
52 libqcocoa.dylib 0x00000001667be644 0x1667a8000 + 91716
53 QtCore 0x00000001204018fc QEventLoop::exec(QFlags) + 532
54 QtCore 0x00000001203f8614 QCoreApplication::exec() + 112
55 QtWidgets.abi3.so 0x0000000120b39cb0 meth_QApplication_exec(_object*, _object*) + 96
56 org.python.python 0x00000001045fda64 cfunction_call + 96
57 org.python.python 0x0000000104599700 _PyObject_MakeTpCall + 128
58 org.python.python 0x00000001046bcc88 _PyEval_EvalFrameDefault + 53048
59 org.python.python 0x00000001046aeac4 PyEval_EvalCode + 276
60 org.python.python 0x00000001046a9320 builtin_exec + 428
61 org.python.python 0x00000001045fe450 cfunction_vectorcall_FASTCALL_KEYWORDS + 80
62 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
63 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
64 org.python.python 0x000000010474f5e0 pymain_run_module + 256
65 org.python.python 0x000000010474f080 Py_RunMain + 1784
66 org.python.python 0x0000000104750230 pymain_main + 52
67 org.python.python 0x00000001047501f0 Py_Main + 36
68 edu.ucsf.cgl.ChimeraX 0x000000010420fd54 main + 128
69 libdyld.dylib 0x000000018d594f34 start + 4
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x000000018d54ae50 kevent64 + 8
1 QtWebEngineCore 0x000000015dc24b60 0x159cc4000 + 66456416
2 QtWebEngineCore 0x000000015dc249f8 0x159cc4000 + 66456056
3 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
4 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
5 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
6 QtWebEngineCore 0x000000015dbd98a4 0x159cc4000 + 66148516
7 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
8 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
9 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 2:: Chrome_IOThread
0 libsystem_kernel.dylib 0x000000018d54ae50 kevent64 + 8
1 QtWebEngineCore 0x000000015dc24b60 0x159cc4000 + 66456416
2 QtWebEngineCore 0x000000015dc249f8 0x159cc4000 + 66456056
3 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
4 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
5 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
6 QtWebEngineCore 0x000000015c509d50 0x159cc4000 + 42229072
7 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
8 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
9 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 3:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 4:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 5:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x000000018d54ae50 kevent64 + 8
1 QtWebEngineCore 0x000000015dc24b60 0x159cc4000 + 66456416
2 QtWebEngineCore 0x000000015dc249f8 0x159cc4000 + 66456056
3 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
4 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
5 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
6 QtWebEngineCore 0x000000016025bf34 0x159cc4000 + 106528564
7 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
8 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
9 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 6:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 QtWebEngineCore 0x000000015dc1714c 0x159cc4000 + 66400588
3 QtWebEngineCore 0x000000015fa8c598 0x159cc4000 + 98338200
4 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
5 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
6 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 7:: ThreadPoolSingleThreadSharedForeground0
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dbe4bc8 0x159cc4000 + 66194376
4 QtWebEngineCore 0x000000015dbe54b0 0x159cc4000 + 66196656
5 QtWebEngineCore 0x000000015dbe536c 0x159cc4000 + 66196332
6 QtWebEngineCore 0x000000015dbe5278 0x159cc4000 + 66196088
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 9:: VizCompositorThread
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 10:: NetworkService
0 libsystem_kernel.dylib 0x000000018d54ae50 kevent64 + 8
1 QtWebEngineCore 0x000000015dc24b60 0x159cc4000 + 66456416
2 QtWebEngineCore 0x000000015dc249f8 0x159cc4000 + 66456056
3 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
4 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
5 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
6 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 12:: ThreadPoolSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dbe4bc8 0x159cc4000 + 66194376
4 QtWebEngineCore 0x000000015dbe5724 0x159cc4000 + 66197284
5 QtWebEngineCore 0x000000015dbe5398 0x159cc4000 + 66196376
6 QtWebEngineCore 0x000000015dbe526c 0x159cc4000 + 66196076
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 14:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 15:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 16:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 17:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 18:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 19:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 20:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 21:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 22:
0 libsystem_kernel.dylib 0x000000018d547e04 poll + 8
1 select.cpython-311-darwin.so 0x0000000104dd954c select_poll_poll + 148
2 org.python.python 0x00000001045aad30 method_vectorcall_FASTCALL + 100
3 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
4 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
5 org.python.python 0x000000010459d9d8 method_vectorcall + 164
6 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x000000010459dab8 method_vectorcall + 388
9 org.python.python 0x00000001047bf878 thread_run + 200
10 org.python.python 0x000000010473ba44 pythread_wrapper + 48
11 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
12 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 23:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001045c952c calliter_iternext + 88
7 org.python.python 0x00000001046bb628 _PyEval_EvalFrameDefault + 47320
8 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
9 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
10 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
11 org.python.python 0x000000010459dab8 method_vectorcall + 388
12 org.python.python 0x00000001047bf878 thread_run + 200
13 org.python.python 0x000000010473ba44 pythread_wrapper + 48
14 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
15 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 24:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be4c PyThread_acquire_lock_timed + 412
3 _queue.cpython-311-darwin.so 0x00000001677eb3cc _queue_SimpleQueue_get_impl + 220
4 _queue.cpython-311-darwin.so 0x00000001677eb048 _queue_SimpleQueue_get + 224
5 org.python.python 0x00000001045fe8d4 cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD + 100
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x00000001046bf7d8 _PyEval_EvalFrameDefault + 64136
9 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
10 org.python.python 0x000000010459dab8 method_vectorcall + 388
11 org.python.python 0x00000001047bf878 thread_run + 200
12 org.python.python 0x000000010473ba44 pythread_wrapper + 48
13 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
14 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 25:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 com.apple.CoreFoundation 0x000000018d673e98 __CFRunLoopServiceMachPort + 380
3 com.apple.CoreFoundation 0x000000018d67236c __CFRunLoopRun + 1216
4 com.apple.CoreFoundation 0x000000018d671740 CFRunLoopRunSpecific + 600
5 com.apple.AppKit 0x000000018ffc9ddc _NSEventThread + 216
6 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
7 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 26:: MemoryInfra
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 27:: ThreadPoolSingleThreadSharedBackgroundBlocking2
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dbe4bc8 0x159cc4000 + 66194376
4 QtWebEngineCore 0x000000015dbe54b0 0x159cc4000 + 66196656
5 QtWebEngineCore 0x000000015dbe52e8 0x159cc4000 + 66196200
6 QtWebEngineCore 0x000000015dbe5290 0x159cc4000 + 66196112
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 28:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dc1ede0 0x159cc4000 + 66432480
4 QtWebEngineCore 0x000000015db5cedc 0x159cc4000 + 65638108
5 QtWebEngineCore 0x000000015dbccae0 0x159cc4000 + 66095840
6 QtWebEngineCore 0x000000015db8e848 0x159cc4000 + 65841224
7 QtWebEngineCore 0x000000015dbf108c 0x159cc4000 + 66244748
8 QtWebEngineCore 0x000000015dbf1204 0x159cc4000 + 66245124
9 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
10 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 29:
0 libsystem_kernel.dylib 0x000000018d540240 mach_absolute_time + 76
1 libsystem_kernel.dylib 0x000000018d541bf8 __commpage_gettimeofday_internal + 44
2 libsystem_c.dylib 0x000000018d459624 gettimeofday + 52
3 libopenblas64_.0.dylib 0x000000011016c208 blas_thread_server + 276
4 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
5 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 30:
0 libsystem_kernel.dylib 0x000000018d54023c mach_absolute_time + 72
1 libsystem_kernel.dylib 0x000000018d541bf8 __commpage_gettimeofday_internal + 44
2 libsystem_c.dylib 0x000000018d459624 gettimeofday + 52
3 libopenblas64_.0.dylib 0x000000011016c208 blas_thread_server + 276
4 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
5 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 31:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 libopenblas64_.0.dylib 0x000000011016c25c blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 32:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 libopenblas64_.0.dylib 0x000000011016c25c blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 33:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 libopenblas64_.0.dylib 0x000000011016c25c blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 34:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 libopenblas64_.0.dylib 0x000000011016c25c blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 35:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 libopenblas64_.0.dylib 0x000000011016c25c blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 36:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dbe4bc8 0x159cc4000 + 66194376
4 QtWebEngineCore 0x000000015dbe5724 0x159cc4000 + 66197284
5 QtWebEngineCore 0x000000015dbe52bc 0x159cc4000 + 66196156
6 QtWebEngineCore 0x000000015dbe5260 0x159cc4000 + 66196064
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 37:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018d53fce8 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018d540098 mach_msg + 76
2 QtWebEngineCore 0x000000015dc1efdc 0x159cc4000 + 66432988
3 QtWebEngineCore 0x000000015dbe4bc8 0x159cc4000 + 66194376
4 QtWebEngineCore 0x000000015dbe5724 0x159cc4000 + 66197284
5 QtWebEngineCore 0x000000015dbe5340 0x159cc4000 + 66196288
6 QtWebEngineCore 0x000000015dbe5230 0x159cc4000 + 66196016
7 QtWebEngineCore 0x000000015dc185bc 0x159cc4000 + 66405820
8 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 38:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 39:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 40:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 41:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 42:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 43:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 44:
0 libsystem_pthread.dylib 0x000000018d573d8c start_wqthread + 0
Thread 45:
0 libsystem_kernel.dylib 0x000000018d543488 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018d579568 _pthread_cond_wait + 1192
2 org.python.python 0x000000010473be00 PyThread_acquire_lock_timed + 336
3 org.python.python 0x00000001047bea10 acquire_timed + 312
4 org.python.python 0x00000001047bec58 lock_PyThread_acquire_lock + 56
5 org.python.python 0x00000001045aa9f4 method_vectorcall_VARARGS_KEYWORDS + 148
6 org.python.python 0x00000001046bcba0 _PyEval_EvalFrameDefault + 52816
7 org.python.python 0x00000001046c26ec _PyEval_Vector + 156
8 org.python.python 0x000000010459dab8 method_vectorcall + 388
9 org.python.python 0x00000001047bf878 thread_run + 200
10 org.python.python 0x000000010473ba44 pythread_wrapper + 48
11 libsystem_pthread.dylib 0x000000018d57906c _pthread_start + 320
12 libsystem_pthread.dylib 0x000000018d573da0 thread_start + 8
Thread 0 crashed with ARM Thread State (64-bit):
x0: 0x0000000000000000 x1: 0x0000000000000000 x2: 0x0000000000000001 x3: 0x0000000000000000
x4: 0x0000000000000065 x5: 0x0000000000000065 x6: 0x000000016bbf0470 x7: 0x0000000000001105
x8: 0x00000000000005b9 x9: 0x4135467478d32e03 x10: 0x0000000000001bbd x11: 0x00000001faf1ba6b
x12: 0x00000001faf1ba6b x13: 0x0000000000000004 x14: 0x0000000000000881 x15: 0x000000008000001f
x16: 0x0000000000000148 x17: 0x00000001f2f630b0 x18: 0x000000013d263940 x19: 0x000000000000000b
x20: 0x00000001044b3d40 x21: 0x0000000000000303 x22: 0x00000001044b3e20 x23: 0x0000000000000001
x24: 0x000000010491c630 x25: 0x0000000104753518 x26: 0x000000016bbf0950 x27: 0x0000000000000000
x28: 0x0000000104a00a48 fp: 0x0000000108047ae0 lr: 0x000000018d578c24
sp: 0x0000000108047ac0 pc: 0x000000018d547cec cpsr: 0x40000000
far: 0x00000001050b5010 esr: 0x56000080
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0x1aacd1000 - 0x1ab052fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud
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0x1ab1cd000 - 0x1ab686fff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
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0x1afb5f000 - 0x1afb65fff com.apple.SafariPlatformSupport.framework (16610 - ???) /System/Library/PrivateFrameworks/SafariPlatformSupport.framework/Versions/A/SafariPlatformSupport
0x1afb66000 - 0x1afd8ffff com.apple.RawCamera.bundle (9.10.0 - 1420.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x1b0724000 - 0x1b0728fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
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0x1b3ddc000 - 0x1b3e25fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x1b4682000 - 0x1b469dfff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x1bd9c5000 - 0x1bd9f3fff com.apple.HelpData (2.3 - 200) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x1bd9f4000 - 0x1bda0efff com.apple.shortcut (2.16 - 117) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x1bda0f000 - 0x1bdaa1fff com.apple.Symbolication (12.2 - 64541.7.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x1bdc1a000 - 0x1bdc1dfff libpmsample.dylib (227.60.1) /usr/lib/libpmsample.dylib
0x1c039e000 - 0x1c03d9fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x1c1a3c000 - 0x1c1a3ffff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x1c9617000 - 0x1c9626fff libSimplifiedChineseConverter.dylib (90) /System/Library/CoreServices/Encodings/libSimplifiedChineseConverter.dylib
0x1cd9fd000 - 0x1cda01fff libmetal_timestamp.dylib (31001.160) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x1cfc56000 - 0x1cfc5cfff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x1cfc5d000 - 0x1cfc62fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x1cfc63000 - 0x1cfc72fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x1cfc73000 - 0x1cfc75fff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x1cfc76000 - 0x1cfc7efff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x1cfc7f000 - 0x1cfcb7fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x1cfcb8000 - 0x1cfcf0fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x1cfcf1000 - 0x1cfe5ffff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x1cfe60000 - 0x1cfe6afff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x1cfe6b000 - 0x1cffd4fff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x1cffd5000 - 0x1cfffafff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x1cfffb000 - 0x1d005afff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x1d0b00000 - 0x1d0b07fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
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0x1d8a8a000 - 0x1d8aa3fff com.apple.SymptomPresentationFeed (1.0 - 1431.60.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x1de3c6000 - 0x1de3cdfff libRosetta.dylib (203.13.2) /usr/lib/libRosetta.dylib
0x298094000 - 0x2980a7fff +numpy_formathandler.cpython-311-darwin.so (0) /Volumes/VOLUME/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL_accelerate/numpy_formathandler.cpython-311-darwin.so
0x298350000 - 0x29835bfff +nones_formathandler.cpython-311-darwin.so (0) /Volumes/VOLUME/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL_accelerate/nones_formathandler.cpython-311-darwin.so
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 174
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: 290543
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=2.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.5G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 3264K 6
CG image 2480K 72
CoreAnimation 2720K 89
CoreGraphics 48K 3
CoreServices 624K 2
CoreUI image data 5472K 41
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 1.0G 482
MALLOC guard page 192K 10
MALLOC_MEDIUM (reserved) 648.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 96K 4
OpenGL GLSL 384K 4
STACK GUARD 720K 45
Stack 352.6M 46
Stack Guard 56.0M 1
VM_ALLOCATE 383.7M 350
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__AUTH 1047K 277
__AUTH_CONST 15.8M 473
__CTF 759 1
__DATA 26.0M 623
__DATA_CONST 26.4M 621
__DATA_DIRTY 1823K 223
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 509.3M 158
__OBJC_CONST 3378K 267
__OBJC_RO 64.5M 1
__OBJC_RW 2544K 1
__TEXT 599.4M 642
__UNICODE 588K 1
mapped file 611.4M 87
shared memory 2480K 14
=========== ======= =======
TOTAL 4.4G 4565
TOTAL, minus reserved VM space 3.6G 4565
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.dev202307200302 (2023-07-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/课题/synvida/SV004/无锡佰翱得/Factor_IX-coot-10_refined_005.pdb
> format pdb
Chain information for Factor_IX-coot-10_refined_005.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
K | No description available
> sequence chain #1/A
Alignment identifier is 1/A
> show target m
> select /A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:131-137
53 atoms, 52 bonds, 7 residues, 1 model selected
> select /B:2-212
1614 atoms, 1650 bonds, 211 residues, 1 model selected
> lighting full
> lighting simple
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> volume style surface
No volumes specified
> select /A:131-461
1685 atoms, 1719 bonds, 5 pseudobonds, 216 residues, 2 models selected
> color sel bychain
> color sel byhetero
> select add #1
5829 atoms, 5962 bonds, 6 pseudobonds, 762 residues, 2 models selected
> view clip false
> color sel byhetero
> color sel bychain
> color sel byhetero
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/B LYS 40
/B LYS 43
/D LYS 5
/D LYS 66
/D THR 75
/D THR 142
/D SER 168
/D SER 193
/D SER 194
/D SER 195
/D LEU 196
/D THR 198
/D LYS 199
/D LYS 208
/D LYS 213
/D HIS 220
/K LYS 76
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -4) with am1-bcc method
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.in.mol2);
atoms read (13), bonds read (12).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 62; net charge: -4`
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(HIS) `/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber: Fatal
Error!`
(HIS) `Cannot properly run ""/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpsocbcox4/ante.in.mol2);
atoms read (13), bonds read (12).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 62; net charge: -4`
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT"
-s 2 -j 1`
(HIS) ``
(HIS) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HIS) ``
Charges for residue HIS determined
Coulombic values for Factor_IX-coot-10_refined_005.pdb_A SES surface #1.2:
minimum, -16.44, mean -0.82, maximum 12.51
Coulombic values for Factor_IX-coot-10_refined_005.pdb_B SES surface #1.3:
minimum, -16.83, mean -1.13, maximum 11.62
Coulombic values for Factor_IX-coot-10_refined_005.pdb_D SES surface #1.4:
minimum, -29.36, mean -2.42, maximum 7.49
Coulombic values for Factor_IX-coot-10_refined_005.pdb_K SES surface #1.5:
minimum, -11.01, mean -0.62, maximum 9.04
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for Factor_IX-coot-10_refined_005.pdb_A SES surface #1.2:
minimum, -16.44, mean -0.82, maximum 12.51
Coulombic values for Factor_IX-coot-10_refined_005.pdb_B SES surface #1.3:
minimum, -16.83, mean -1.13, maximum 11.62
Coulombic values for Factor_IX-coot-10_refined_005.pdb_D SES surface #1.4:
minimum, -29.36, mean -2.42, maximum 7.49
Coulombic values for Factor_IX-coot-10_refined_005.pdb_K SES surface #1.5:
minimum, -11.01, mean -0.62, maximum 9.04
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
> color sel byhetero
> color sel bychain
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/D
Alignment identifier is 1/K
> undo
> color sel bychain
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-252
37 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:311-314
39 atoms, 40 bonds, 4 residues, 1 model selected
> select /A
1685 atoms, 1719 bonds, 5 pseudobonds, 216 residues, 2 models selected
> select /K
921 atoms, 940 bonds, 120 residues, 1 model selected
> select clear
> select /K
921 atoms, 940 bonds, 120 residues, 1 model selected
> cartoon hide (#!1 & sel)
> name frozen VHH sel
> select clear
> lighting simple
> volume showOutlineBox true
No volumes specified
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> select /A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:445-454
89 atoms, 91 bonds, 10 residues, 1 model selected
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 1/B:1 1/D:1 numModels 5 fast false multichain
> true hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> rainbow sel
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:445-455
98 atoms, 100 bonds, 11 residues, 1 model selected
> select /A
1685 atoms, 1719 bonds, 5 pseudobonds, 216 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> ui tool show "Color Actions"
> color sel light gray
> color sel white
> color sel gray
> color sel dark gray
> color sel gray
> color sel dim gray
> color sel gray
> select clear
> select /D
1609 atoms, 1653 bonds, 1 pseudobond, 215 residues, 2 models selected
> ui tool show "Color Actions"
> ui tool show "Render By Attribute"
> ui tool show "Basic Actions"
> color (#!1 & sel) dark gray
> cofr sel
> color (#!1 & sel) byelement
> undo
> surface style #1.4 mesh
> undo
> ui tool show "Selection Inspector"
> undo
> select /D
1609 atoms, 1653 bonds, 1 pseudobond, 215 residues, 2 models selected
> color (#!1 & sel) byhetero
> undo
> interfaces select /A & ::polymer_type>0 contacting /D & ::polymer_type>0
> areaCutoff 0
11 contacting residues
> undo
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select backbone
3049 atoms, 3039 bonds, 6 pseudobonds, 762 residues, 2 models selected
> undo
> select clear
> interfaces ~solvent
4 buried areas: B D 1690, B K 719, A D 577, A B 382
> select /A:183
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:183-281
348 atoms, 354 bonds, 1 pseudobond, 47 residues, 2 models selected
> select /A
1685 atoms, 1719 bonds, 5 pseudobonds, 216 residues, 2 models selected
> ui tool show "Selection Inspector"
> style sel ball
Changed 1685 atom styles
> select clear
> select /D
1609 atoms, 1653 bonds, 1 pseudobond, 215 residues, 2 models selected
> color (#!1 & sel) light gray
> select /B
1614 atoms, 1650 bonds, 211 residues, 1 model selected
> color (#!1 & sel) light gray
> select clear
> select /A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:446
9 atoms, 8 bonds, 1 residue, 1 model selected
> rainbow sel
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> rainbow sel
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:388
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:388-389
18 atoms, 18 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> select /A:388
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:388-394
62 atoms, 63 bonds, 7 residues, 1 model selected
> color (#!1 & sel) red
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:445-455
98 atoms, 100 bonds, 11 residues, 1 model selected
> rainbow sel
> color (#!1 & sel) orange
> select /A:338
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:338-345
72 atoms, 73 bonds, 8 residues, 1 model selected
> color (#!1 & sel) yellow
> select
> /A:144-147,153-156,161-163,170-172,241-245,252-255,261-264,276-279,292-301,317-321,394-397,414-419,422-431,442-446
554 atoms, 553 bonds, 71 residues, 1 model selected
> select /A:137-140,266-268,339-348,447-458
252 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:267
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:267-268
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:267
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) hot pink
> select /A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select /A:411
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:411
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> select /A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:315-318
29 atoms, 28 bonds, 4 residues, 1 model selected
> select /A:313
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:313-316
34 atoms, 34 bonds, 4 residues, 1 model selected
> select /A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> open /Users/xuemeifan/Downloads/1pfx.pdb
1pfx.pdb title:
Porcine factor ixa [more info...]
Chain information for 1pfx.pdb #2
---
Chain | Description | UniProt
C | christmas factor | FA9_PIG 16-237
L | christmas factor | FA9_PIG 7-146
Non-standard residues in 1pfx.pdb #2
---
0G6 —
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
(PPACK)
> undo
> hide #2 models
> hide #!1 models
> show #2 models
> color #2 bychain
> color #2 byhetero
> color #2 bychain
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CGU (net charge -2) with am1-bcc method
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmp9f21i2lr/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmp9f21i2lr/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(CGU) ``
(CGU) `Welcome to antechamber 20.0: molecular input file processor.`
(CGU) ``
(CGU) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmp9f21i2lr/ante.in.mol2);
atoms read (29), bonds read (28).`
(CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CGU) ``
(CGU) ``
(CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CGU) `Info: Total number of electrons: 130; net charge: -2`
(CGU) ``
(CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(CGU) ``
(CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT"
-s 2 -j 1`
(CGU) ``
(CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CGU) ``
Charges for residue CGU determined
Assigning partial charges to residue BHD (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpdkegzas7/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpdkegzas7/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(BHD) ``
(BHD) `Welcome to antechamber 20.0: molecular input file processor.`
(BHD) ``
(BHD) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpdkegzas7/ante.in.mol2);
atoms read (25), bonds read (24).`
(BHD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(BHD) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(BHD) ``
(BHD) ``
(BHD) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(BHD) `Info: Total number of electrons: 108; net charge: -1`
(BHD) ``
(BHD) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(BHD) ``
(BHD) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT"
-s 2 -j 1`
(BHD) ``
(BHD) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(BHD) ``
Charges for residue BHD determined
Assigning partial charges to residue CGU+CGU (net charge -4) with am1-bcc
method
2 tautomers of CGU+CGU; charging separately
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpxijc7sfy/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpxijc7sfy/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(CGU+CGU) ``
(CGU+CGU) `Welcome to antechamber 20.0: molecular input file processor.`
(CGU+CGU) ``
(CGU+CGU) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmpxijc7sfy/ante.in.mol2);
atoms read (46), bonds read (45).`
(CGU+CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CGU+CGU) ``
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CGU+CGU) `Info: Total number of electrons: 220; net charge: -4`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT"
-s 2 -j 1`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CGU+CGU) ``
Charges for residue CGU+CGU determined
Running ANTECHAMBER command: /Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmppelvs3ti/ante.in.mol2 -fi
mol2 -o
/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmppelvs3ti/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(CGU+CGU) ``
(CGU+CGU) `Welcome to antechamber 20.0: molecular input file processor.`
(CGU+CGU) ``
(CGU+CGU) `Info: Finished reading file
(/var/folders/x1/y30n4l6x1xbf4bl68y0zm2mc0000gn/T/tmppelvs3ti/ante.in.mol2);
atoms read (46), bonds read (45).`
(CGU+CGU) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CGU+CGU) ``
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CGU+CGU) `Info: Total number of electrons: 220; net charge: -4`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm" -O -i sqm.in -o
sqm.out`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT"
-s 2 -j 1`
(CGU+CGU) ``
(CGU+CGU) `Running: "/Volumes/ChimeraX
Installer/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype" -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CGU+CGU) ``
Charges for residue CGU+CGU determined
Coulombic values for 1pfx.pdb_C SES surface #2.1: minimum, -21.35, mean 1.43,
maximum 24.23
Coulombic values for 1pfx.pdb_L SES surface #2.2: minimum, -30.45, mean -4.88,
maximum 13.64
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!2 bychain
> show target m
> hide #!1 models
> show #!1 models
> hide #!1 models
> view #1 clip false
> select sequence TKVSRYVNMI
Nothing selected
> select #2/C
2287 atoms, 2336 bonds, 236 residues, 1 model selected
> select #2/C
2287 atoms, 2336 bonds, 236 residues, 1 model selected
> select #2/C
2287 atoms, 2336 bonds, 236 residues, 1 model selected
> undo
> ui favorite true "Model Panel"
> hide #!2 target m
> open /Users/xuemeifan/Downloads/1pfx.pdb
1pfx.pdb title:
Porcine factor ixa [more info...]
Chain information for 1pfx.pdb #3
---
Chain | Description | UniProt
C | christmas factor | FA9_PIG 16-237
L | christmas factor | FA9_PIG 7-146
Non-standard residues in 1pfx.pdb #3
---
0G6 —
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
(PPACK)
> close #2
> log metadata #1
No models had metadata
> log chains #1
Chain information for Factor_IX-coot-10_refined_005.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
K | No description available
> log metadata #3
Metadata for 1pfx.pdb #3
---
Title | Porcine factor ixa
Citation | X-ray structure of clotting factor ixa: active site andmodule
structure related to xase activity and hemophilia B. PMID: 7568220
Non-standard residue | 0G6 —
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
(PPACK)
Gene source | Sus scrofa (pig)
Experimental method | X-ray diffraction
Resolution | 3.00Å
> log chains #3
Chain information for 1pfx.pdb #3
---
Chain | Description | UniProt
C | christmas factor | FA9_PIG 16-237
L | christmas factor | FA9_PIG 7-146
> log metadata #1
No models had metadata
> log chains #1
Chain information for Factor_IX-coot-10_refined_005.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
K | No description available
> log metadata #3
Metadata for 1pfx.pdb #3
---
Title | Porcine factor ixa
Citation | X-ray structure of clotting factor ixa: active site andmodule
structure related to xase activity and hemophilia B. PMID: 7568220
Non-standard residue | 0G6 —
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
(PPACK)
Gene source | Sus scrofa (pig)
Experimental method | X-ray diffraction
Resolution | 3.00Å
> log chains #3
Chain information for 1pfx.pdb #3
---
Chain | Description | UniProt
C | christmas factor | FA9_PIG 16-237
L | christmas factor | FA9_PIG 7-146
> log metadata #1
No models had metadata
> log chains #1
Chain information for Factor_IX-coot-10_refined_005.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
K | No description available
> log metadata #3
Metadata for 1pfx.pdb #3
---
Title | Porcine factor ixa
Citation | X-ray structure of clotting factor ixa: active site andmodule
structure related to xase activity and hemophilia B. PMID: 7568220
Non-standard residue | 0G6 —
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
(PPACK)
Gene source | Sus scrofa (pig)
Experimental method | X-ray diffraction
Resolution | 3.00Å
> log chains #3
Chain information for 1pfx.pdb #3
---
Chain | Description | UniProt
C | christmas factor | FA9_PIG 16-237
L | christmas factor | FA9_PIG 7-146
> select #3/C:16-245
2249 atoms, 2296 bonds, 235 residues, 1 model selected
> select #3/C:16-245
2249 atoms, 2296 bonds, 235 residues, 1 model selected
> sequence chain #3/C
Alignment identifier is 3/C
> select #3/C:229
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:229-238
113 atoms, 115 bonds, 10 residues, 1 model selected
> color sel bychain
> select #3/C
2287 atoms, 2336 bonds, 236 residues, 1 model selected
> color sel gray
> select clear
> select #3/C:229
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:229-238
113 atoms, 115 bonds, 10 residues, 1 model selected
> color sel red
> select #3/C:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:125-130
87 atoms, 88 bonds, 8 residues, 1 model selected
> color sel orange
> select #3/C:160
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:160-167
73 atoms, 73 bonds, 8 residues, 1 model selected
> color sel yellow
> select #3/C:230
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/C:230
13 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select #3/C:233
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/C:233
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel lime
> select #3/C:174
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/C:174-175
21 atoms, 21 bonds, 2 residues, 1 model selected
> color sel lime
> select #3/C:179
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/C:179
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select #3/C:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:100-101
21 atoms, 21 bonds, 2 residues, 1 model selected
> color sel lime
> select #3/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel purple
> select #3/C:57
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/C:57
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel hot pink
> select #3/C:195
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/C:195
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1/K
921 atoms, 940 bonds, 120 residues, 1 model selected
> select #3/L
1449 atoms, 1478 bonds, 146 residues, 1 model selected
> color sel dark gray
> select clear
> select #3/L
1449 atoms, 1478 bonds, 146 residues, 1 model selected
> color sel light gray
> select clear
> select
> #3/C:20-21,30-34,42-48,51-54,65-68,81-90,104-108,135-140,156-163,180-183,199-203,206-209,212-215,226-229
679 atoms, 677 bonds, 72 residues, 1 model selected
> select #3/C:233
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/C:233
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel forest green
> undo
> select #3/C:239
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/C:239
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/C:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:169-180
128 atoms, 129 bonds, 12 residues, 1 model selected
> show #!1 models
> hide #!1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.dev202307200302 (2023-07-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 71.0.7
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.5.1, Qt 6.5.1
Qt runtime version: 6.5.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 6723.61.3
Software:
System Software Overview:
System Version: macOS 11.1 (20C69)
Kernel Version: Darwin 20.2.0
Time since boot: 2 days 11:44
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:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46.1
ChimeraX-AtomicLibrary: 10.0.8
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
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: 1.7.dev202307200302
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: 1.1.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
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: 2.1.1
ChimeraX-MCopy: 1.0
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: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.2
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: 2.9
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: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
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: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.31
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
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: 1.1.0
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: 4.41.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.9.1
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.5.1
PyQt6-Qt6: 6.5.1
PyQt6-sip: 13.5.1
PyQt6-WebEngine-commercial: 6.5.0
PyQt6-WebEngine-Qt6: 6.5.1
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
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: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
I hope this is not a new bug introduced by PyQt 6.5.1.