![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15503 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-11.7.4-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001c2fe000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000010abf7e00 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 77 in assign_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Users/james.walshe/scripts/General_XL_2.py", line 257 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 72 in _exec_python
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 95 in open_python_script
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 49 in runscript
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, PIL._webp (total: 158)
Process: ChimeraX [56138]
Path: /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.7.1 (1.7.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [56138]
User ID: 675737
Date/Time: 2024-06-26 19:32:58.028 +0200
OS Version: macOS 11.7.4 (20G1120)
Report Version: 12
Bridge OS Version: 7.2 (20P3045)
Anonymous UUID: 92899295-67F6-EE72-5EE5-E46D70D5B584
Time Awake Since Boot: 6000000 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 10fd5f000-10fd63000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff2068a91e __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff206b95bd pthread_kill + 263
2 libsystem_c.dylib 0x00007fff2059dbd5 raise + 26
3 org.python.python 0x000000010ffe95d4 faulthandler_fatal_error + 388
4 libsystem_platform.dylib 0x00007fff206fed7d _sigtramp + 29
5 ??? 000000000000000000 0 + 0
6 org.python.python 0x000000010fe641f3 dict_traverse + 195
7 org.python.python 0x000000010ffe5888 gc_collect_main + 2568
8 org.python.python 0x000000010ffe7102 _PyObject_GC_Link + 306
9 org.python.python 0x000000010ffe7197 _PyObject_GC_New + 119
10 org.python.python 0x000000010ff86d28 _PyHamt_Assoc + 168
11 org.python.python 0x000000010ff766e3 PyContextVar_Set + 387
12 org.python.python 0x000000010ff47ce1 _PyEval_EvalFrameDefault + 70945
13 org.python.python 0x000000010fe34f71 gen_send_ex2 + 209
14 org.python.python 0x000000010fe34766 gen_iternext + 22
15 org.python.python 0x000000010ff309d7 builtin_next + 71
16 org.python.python 0x000000010ff473be _PyEval_EvalFrameDefault + 68606
17 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
18 org.python.python 0x000000010fe1b816 method_vectorcall + 454
19 org.python.python 0x000000010ff43d0e _PyEval_EvalFrameDefault + 54606
20 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
21 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
22 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
23 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
24 org.python.python 0x000000010fe18165 PyObject_Vectorcall + 69
25 _multiarray_umath.cpython-311-darwin.so 0x0000000110fd8175 dispatcher_vectorcall + 757
26 org.python.python 0x000000010ff452ef _PyEval_EvalFrameDefault + 60207
27 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
28 org.python.python 0x000000010fe1b71f method_vectorcall + 207
29 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
30 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
31 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
32 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
33 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
34 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
35 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
36 org.python.python 0x000000010fe1b71f method_vectorcall + 207
37 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
38 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
39 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
40 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
41 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
42 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
43 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
44 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
45 org.python.python 0x000000010fe17670 _PyObject_FastCallDictTstate + 96
46 org.python.python 0x000000010fea5995 slot_tp_init + 181
47 org.python.python 0x000000010fe9bb4a type_call + 122
48 org.python.python 0x000000010fe173b1 _PyObject_MakeTpCall + 129
49 org.python.python 0x000000010ff453e7 _PyEval_EvalFrameDefault + 60455
50 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
51 org.python.python 0x000000010fe17670 _PyObject_FastCallDictTstate + 96
52 org.python.python 0x000000010fea5995 slot_tp_init + 181
53 org.python.python 0x000000010fe9bb4a type_call + 122
54 org.python.python 0x000000010fe173b1 _PyObject_MakeTpCall + 129
55 org.python.python 0x000000010ff453e7 _PyEval_EvalFrameDefault + 60455
56 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
57 org.python.python 0x000000010fe1b79e method_vectorcall + 334
58 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
59 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
60 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
61 org.python.python 0x000000010fe176e6 _PyObject_FastCallDictTstate + 214
62 org.python.python 0x000000010fea5995 slot_tp_init + 181
63 org.python.python 0x000000010fe9bb4a type_call + 122
64 org.python.python 0x000000010fe173b1 _PyObject_MakeTpCall + 129
65 org.python.python 0x000000010ff453e7 _PyEval_EvalFrameDefault + 60455
66 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
67 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
68 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
69 org.python.python 0x000000010ff3547a PyEval_EvalCode + 282
70 org.python.python 0x000000010ff2fce3 builtin_exec + 483
71 org.python.python 0x000000010ff475ab _PyEval_EvalFrameDefault + 69099
72 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
73 org.python.python 0x000000010fe17f78 _PyVectorcall_Call + 120
74 org.python.python 0x000000010ff4854a _PyEval_EvalFrameDefault + 73098
75 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
76 org.python.python 0x000000010fe1b816 method_vectorcall + 454
77 QtCore.abi3.so 0x000000011ee4cf98 PyQtSlot::call(_object*, _object*) const + 40
78 QtCore.abi3.so 0x000000011ee4ce9a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362
79 QtCore.abi3.so 0x000000011ee4dde5 PyQtSlotProxy::unislot(void**) + 85
80 QtCore.abi3.so 0x000000011ee4dd5a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
81 QtCore 0x000000012746cd67 0x1273af000 + 777575
82 QtWidgets 0x0000000129fcb2c9 0x129e34000 + 1667785
83 QtCore 0x000000012746d022 0x1273af000 + 778274
84 QtWidgets 0x0000000129fd21c4 QWidgetLineControl::processKeyEvent(QKeyEvent*) + 532
85 QtWidgets 0x0000000129fc4b8a QLineEdit::keyPressEvent(QKeyEvent*) + 26
86 QtWidgets 0x0000000129e93027 QWidget::event(QEvent*) + 471
87 QtWidgets 0x0000000129fc422c QLineEdit::event(QEvent*) + 524
88 QtWidgets 0x0000000129f84a9c QComboBox::keyPressEvent(QKeyEvent*) + 572
89 QtWidgets.abi3.so 0x0000000129a3c239 meth_QComboBox_keyPressEvent(_object*, _object*) + 169
90 org.python.python 0x000000010fe7c7ea cfunction_call + 90
91 org.python.python 0x000000010fe173b1 _PyObject_MakeTpCall + 129
92 org.python.python 0x000000010ff453e7 _PyEval_EvalFrameDefault + 60455
93 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
94 org.python.python 0x000000010fe1b71f method_vectorcall + 207
95 sip.cpython-311-darwin.so 0x000000011f0ff367 sip_api_call_procedure_method + 199
96 QtWidgets.abi3.so 0x00000001299419e8 sipQComboBox::keyPressEvent(QKeyEvent*) + 104
97 QtWidgets 0x0000000129e93027 QWidget::event(QEvent*) + 471
98 QtWidgets 0x0000000129f84597 QComboBox::event(QEvent*) + 311
99 QtWidgets.abi3.so 0x0000000129940eef sipQComboBox::event(QEvent*) + 191
100 QtWidgets 0x0000000129e40a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
101 QtWidgets 0x0000000129e41c62 QApplication::notify(QObject*, QEvent*) + 1042
102 QtWidgets.abi3.so 0x000000012995d1e6 sipQApplication::notify(QObject*, QEvent*) + 230
103 QtCore 0x000000012741cc3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
104 QtWidgets 0x0000000129ea86db 0x129e34000 + 476891
105 QtWidgets 0x0000000129e40a87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
106 QtWidgets 0x0000000129e41a43 QApplication::notify(QObject*, QEvent*) + 499
107 QtWidgets.abi3.so 0x000000012995d1e6 sipQApplication::notify(QObject*, QEvent*) + 230
108 QtCore 0x000000012741cc3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
109 QtGui 0x000000012a4d0fc4 QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 292
110 QtGui 0x000000012a52829c QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 444
111 QtGui 0x000000012a527e8c QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 476
112 libqcocoa.dylib 0x0000000136dcbec9 0x136d5c000 + 458441
113 com.apple.AppKit 0x00007fff2323f7cc -[NSResponder tryToPerform:with:] + 53
114 libqcocoa.dylib 0x0000000136dce106 0x136d5c000 + 467206
115 com.apple.AppKit 0x00007fff232c41b6 -[NSTextInputContext(NSInputContext_WithCompletion) doCommandBySelector:completionHandler:] + 236
116 com.apple.AppKit 0x00007fff231e177f -[NSKeyBindingManager(NSKeyBindingManager_MultiClients) interpretEventAsCommand:forClient:] + 2129
117 com.apple.AppKit 0x00007fff231eac12 __84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_5 + 533
118 com.apple.AppKit 0x00007fff23994988 __84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_3.816 + 74
119 com.apple.AppKit 0x00007fff231ea9dd -[NSTextInputContext tryHandleEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 87
120 com.apple.AppKit 0x00007fff2399490e __84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke.813 + 237
121 com.apple.HIToolbox 0x00007fff28a31ab1 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_5 + 70
122 com.apple.HIToolbox 0x00007fff28a43aeb invocation function for block in DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 110
123 com.apple.AppKit 0x00007fff23990022 __55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke.290 + 885
124 com.apple.AppKit 0x00007fff231e35c8 __55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke_2 + 74
125 com.apple.AppKit 0x00007fff231e3550 -[NSTextInputContext tryHandleTSMEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 87
126 com.apple.AppKit 0x00007fff231e2aa8 -[NSTextInputContext handleTSMEvent:completionHandler:] + 1889
127 com.apple.AppKit 0x00007fff231e22d2 _NSTSMEventHandler + 299
128 com.apple.HIToolbox 0x00007fff289d1da1 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1362
129 com.apple.HIToolbox 0x00007fff289d11c3 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 331
130 com.apple.HIToolbox 0x00007fff289d106c SendEventToEventTargetWithOptions + 45
131 com.apple.HIToolbox 0x00007fff28a2df26 SendTSMEvent_WithCompletionHandler + 381
132 com.apple.HIToolbox 0x00007fff28a2e3d1 __SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler_block_invoke + 387
133 com.apple.HIToolbox 0x00007fff28a2e229 __SendFilterTextEvent_WithCompletionHandler_block_invoke + 182
134 com.apple.HIToolbox 0x00007fff28a2df74 SendTSMEvent_WithCompletionHandler + 459
135 com.apple.HIToolbox 0x00007fff28a2dd7c SendFilterTextEvent_WithCompletionHandler + 225
136 com.apple.HIToolbox 0x00007fff28a2da59 SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler + 277
137 com.apple.HIToolbox 0x00007fff28a2d806 __utDeliverTSMEvent_WithCompletionHandler_block_invoke_2 + 281
138 com.apple.HIToolbox 0x00007fff28a2d666 __utDeliverTSMEvent_WithCompletionHandler_block_invoke + 354
139 com.apple.HIToolbox 0x00007fff28a2d4ba TSMKeyEvent_WithCompletionHandler + 591
140 com.apple.HIToolbox 0x00007fff28a2d250 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_4 + 250
141 com.apple.HIToolbox 0x00007fff28a2d0cf __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_3 + 257
142 com.apple.HIToolbox 0x00007fff28a2ce9b __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_2 + 282
143 com.apple.HIToolbox 0x00007fff28a2cc4e __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke + 274
144 com.apple.HIToolbox 0x00007fff28a1ba43 TSMProcessRawKeyEventWithOptionsAndCompletionHandler + 3449
145 com.apple.AppKit 0x00007fff2399480c __84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_3.811 + 110
146 com.apple.AppKit 0x00007fff23994563 __204-[NSTextInputContext tryTSMProcessRawKeyEvent_orSubstitution:dispatchCondition:setupForDispatch:furtherCondition:doubleSpaceSubstitutionCondition:doubleSpaceSubstitutionWork:dispatchTSMWork:continuation:]_block_invoke.768 + 120
147 com.apple.AppKit 0x00007fff231e0dcf -[NSTextInputContext tryTSMProcessRawKeyEvent_orSubstitution:dispatchCondition:setupForDispatch:furtherCondition:doubleSpaceSubstitutionCondition:doubleSpaceSubstitutionWork:dispatchTSMWork:continuation:] + 245
148 com.apple.AppKit 0x00007fff231e07db -[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:] + 1424
149 com.apple.AppKit 0x00007fff231e020e -[NSTextInputContext _handleEvent:allowingSyntheticEvent:] + 105
150 com.apple.AppKit 0x00007fff231e0103 -[NSView interpretKeyEvents:] + 209
151 libqcocoa.dylib 0x0000000136dc9901 0x136d5c000 + 448769
152 libqcocoa.dylib 0x0000000136dca933 0x136d5c000 + 452915
153 com.apple.AppKit 0x00007fff23143ef8 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6482
154 com.apple.AppKit 0x00007fff23142386 -[NSWindow(NSEventRouting) sendEvent:] + 347
155 libqcocoa.dylib 0x0000000136dd2b4f 0x136d5c000 + 486223
156 com.apple.AppKit 0x00007fff23141201 -[NSApplication(NSEvent) sendEvent:] + 3021
157 libqcocoa.dylib 0x0000000136d6740a 0x136d5c000 + 46090
158 com.apple.AppKit 0x00007fff23419531 -[NSApplication _handleEvent:] + 65
159 com.apple.AppKit 0x00007fff22fa962e -[NSApplication run] + 623
160 libqcocoa.dylib 0x0000000136d750ac 0x136d5c000 + 102572
161 QtCore 0x0000000127426326 QEventLoop::exec(QFlags) + 486
162 QtCore 0x000000012741d235 QCoreApplication::exec() + 133
163 QtWidgets.abi3.so 0x0000000129a49d9a meth_QApplication_exec(_object*, _object*) + 90
164 org.python.python 0x000000010fe7c7ea cfunction_call + 90
165 org.python.python 0x000000010fe173b1 _PyObject_MakeTpCall + 129
166 org.python.python 0x000000010ff453e7 _PyEval_EvalFrameDefault + 60455
167 org.python.python 0x000000010ff3547a PyEval_EvalCode + 282
168 org.python.python 0x000000010ff2fce3 builtin_exec + 483
169 org.python.python 0x000000010fe7d144 cfunction_vectorcall_FASTCALL_KEYWORDS + 68
170 org.python.python 0x000000010ff452ef _PyEval_EvalFrameDefault + 60207
171 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
172 org.python.python 0x000000010ffe26fd pymain_run_module + 253
173 org.python.python 0x000000010ffe21c1 Py_RunMain + 2225
174 org.python.python 0x000000010ffe317b pymain_main + 43
175 org.python.python 0x000000010ffe314a Py_Main + 42
176 edu.ucsf.cgl.ChimeraX 0x000000010fd62d9a main + 122
177 libdyld.dylib 0x00007fff206d4f3d start + 1
Thread 1:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff2068d1c2 kevent64 + 10
1 QtWebEngineCore 0x000000012f23ca2a 0x12b2dc000 + 66456106
2 QtWebEngineCore 0x000000012f23c927 0x12b2dc000 + 66455847
3 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
4 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
5 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
6 QtWebEngineCore 0x000000012f1c32ad 0x12b2dc000 + 65958573
7 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
8 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
9 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 2:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1d026c 0x12b2dc000 + 66011756
5 QtWebEngineCore 0x000000012f1cfddd 0x12b2dc000 + 66010589
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff2068d1c2 kevent64 + 10
1 QtWebEngineCore 0x000000012f23ca2a 0x12b2dc000 + 66456106
2 QtWebEngineCore 0x000000012f23c927 0x12b2dc000 + 66455847
3 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
4 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
5 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
6 QtWebEngineCore 0x000000012e1013a2 0x12b2dc000 + 48386978
7 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
8 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
9 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 5:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 QtWebEngineCore 0x000000012f202d1b 0x12b2dc000 + 66219291
3 QtWebEngineCore 0x00000001312d092d 0x12b2dc000 + 100616493
4 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
5 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 6:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 7:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff2068d1c2 kevent64 + 10
1 QtWebEngineCore 0x000000012f23ca2a 0x12b2dc000 + 66456106
2 QtWebEngineCore 0x000000012f23c927 0x12b2dc000 + 66455847
3 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
4 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
5 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
6 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
7 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
8 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 9:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 10:: NetworkService
0 libsystem_kernel.dylib 0x00007fff2068d1c2 kevent64 + 10
1 QtWebEngineCore 0x000000012f23ca2a 0x12b2dc000 + 66456106
2 QtWebEngineCore 0x000000012f23c927 0x12b2dc000 + 66455847
3 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
4 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
5 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
6 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
7 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
8 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1d026c 0x12b2dc000 + 66011756
5 QtWebEngineCore 0x000000012f1cfecd 0x12b2dc000 + 66010829
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 14:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff207b1f0f __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff207b05ef __CFRunLoopRun + 1328
4 com.apple.CoreFoundation 0x00007fff207af9fc CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff2313ebba _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 15:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 16:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1cff9a 0x12b2dc000 + 66011034
5 QtWebEngineCore 0x000000012f1cfe0d 0x12b2dc000 + 66010637
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 interpreter.cpython-311-darwin.so 0x0000000156acbd63 th_worker(void*) + 131
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 31:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001116f667f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 32:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1d026c 0x12b2dc000 + 66011756
5 QtWebEngineCore 0x000000012f1cfe6d 0x12b2dc000 + 66010733
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 33:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1d026c 0x12b2dc000 + 66011756
5 QtWebEngineCore 0x000000012f1cfddd 0x12b2dc000 + 66010589
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 34:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f20abef 0x12b2dc000 + 66251759
4 QtWebEngineCore 0x000000012f1401c9 0x12b2dc000 + 65421769
5 QtWebEngineCore 0x000000012f1b9a5c 0x12b2dc000 + 65919580
6 QtWebEngineCore 0x000000012f171998 0x12b2dc000 + 65624472
7 QtWebEngineCore 0x000000012f1dbeb8 0x12b2dc000 + 66059960
8 QtWebEngineCore 0x000000012f1dc04a 0x12b2dc000 + 66060362
9 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
10 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 35:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff206842aa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2068461c mach_msg + 60
2 QtWebEngineCore 0x000000012f20ae26 0x12b2dc000 + 66252326
3 QtWebEngineCore 0x000000012f1cf7bf 0x12b2dc000 + 66009023
4 QtWebEngineCore 0x000000012f1d026c 0x12b2dc000 + 66011756
5 QtWebEngineCore 0x000000012f1cfe6d 0x12b2dc000 + 66010733
6 QtWebEngineCore 0x000000012f203908 0x12b2dc000 + 66222344
7 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 36:
0 libsystem_pthread.dylib 0x00007fff206b5420 start_wqthread + 0
Thread 37:
0 libsystem_kernel.dylib 0x00007fff20686cce __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff206b9e49 _pthread_cond_wait + 1298
2 org.python.python 0x000000010ffcf214 PyThread_acquire_lock_timed + 340
3 org.python.python 0x0000000110052d9e acquire_timed + 318
4 org.python.python 0x0000000110052fdc lock_PyThread_acquire_lock + 44
5 org.python.python 0x000000010fe28b07 method_vectorcall_VARARGS_KEYWORDS + 167
6 org.python.python 0x000000010ff452ef _PyEval_EvalFrameDefault + 60207
7 org.python.python 0x000000010ff4b4d0 _PyEval_Vector + 128
8 org.python.python 0x000000010fe1b816 method_vectorcall + 454
9 org.python.python 0x0000000110053b26 thread_run + 230
10 org.python.python 0x000000010ffceea4 pythread_wrapper + 36
11 libsystem_pthread.dylib 0x00007fff206b98fc _pthread_start + 224
12 libsystem_pthread.dylib 0x00007fff206b5443 thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011f36ee00 rcx: 0x00007fe5f00579e8 rdx: 0x0000000000000000
rdi: 0x0000000000000103 rsi: 0x000000000000000b rbp: 0x00007fe5f0057a10 rsp: 0x00007fe5f00579e8
r8: 0x0000000000000003 r9: 0xcccccccccccccccd r10: 0x000000011f36ee00 r11: 0x0000000000000246
r12: 0x0000000000000103 r13: 0x000000010ffe6801 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff2068a91e rfl: 0x0000000000000246 cr2: 0x00007fe5f0056e80
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
ff ff ff ff 48 89 d8 48-8b 00 48 ff c2 48 39 c3 ....H..H..H..H9.
75 f5 48 8d 3d c5 12 16-00 48 8d b5 70 ff ff ff u.H.=....H..p...
31 c0 e8 bf 83 fe ff 48-8b 05 68 e7 16 00 48 8b 1......H..h...H.
00 48 3b 45 d8 75 0d 48-83 c4 70 5b 41 5c 41 5e .H;E.u.H..p[A\A^
41 5f 5d c3 e8 cd ae 0e-00 66 2e 0f 1f 84 00 00 A_]......f......
00 00 00 0f 1f 00 55 48-89 e5 53 50 48 8b 47 08 ......UH..SPH.G.
[f6]80 a9 00 00 00 40 75-09 31 c0 48 83 c4 08 5b ......@u.1.H...[ /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
0x10fd71000 - 0x110154fff +org.python.python (3.11.2, [c] 2001-2023 Python Software Foundation. - 3.11.2) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/Python
0x1106c8000 - 0x1106d3fff +math.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/math.cpython-311-darwin.so
0x1107e4000 - 0x1107f3fff +_datetime.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_datetime.cpython-311-darwin.so
0x110808000 - 0x11080bfff +_typing.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_typing.cpython-311-darwin.so
0x110918000 - 0x11091ffff +zlib.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/zlib.cpython-311-darwin.so
0x110930000 - 0x110933fff +_bz2.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_bz2.cpython-311-darwin.so
0x110940000 - 0x11096ffff +_lzma.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_lzma.cpython-311-darwin.so
0x110984000 - 0x110987fff +_bisect.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_bisect.cpython-311-darwin.so
0x110994000 - 0x110997fff +_random.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_random.cpython-311-darwin.so
0x1109a4000 - 0x1109abfff +_sha512.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_sha512.cpython-311-darwin.so
0x110ab8000 - 0x110abffff +binascii.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/binascii.cpython-311-darwin.so
0x110acc000 - 0x110ad3fff +_struct.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_struct.cpython-311-darwin.so
0x110ae4000 - 0x110ae7fff +fcntl.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/fcntl.cpython-311-darwin.so
0x110af4000 - 0x110af7fff +_posixsubprocess.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_posixsubprocess.cpython-311-darwin.so
0x110b04000 - 0x110b0bfff +select.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/select.cpython-311-darwin.so
0x110c18000 - 0x110c1bfff +_arrays.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/arrays/_arrays.cpython-311-darwin.so
0x110c28000 - 0x110d3bfff +libarrays.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/arrays/lib/libarrays.dylib
0x110d68000 - 0x110d6ffff +_json.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_json.cpython-311-darwin.so
0x110d7c000 - 0x11122ffff +_multiarray_umath.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-darwin.so
0x1113a8000 - 0x1150c7fff +libopenblas64_.0.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libopenblas64_.0.dylib
0x115388000 - 0x1159cafff +libgfortran.5.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libgfortran.5.dylib
0x115a05000 - 0x115a52fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x115a5c000 - 0x115a6cfff +libgcc_s.1.1.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libgcc_s.1.1.dylib
0x11db7e000 - 0x11db99fff +_pickle.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_pickle.cpython-311-darwin.so
0x11dcae000 - 0x11dcb1fff +_contextvars.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_contextvars.cpython-311-darwin.so
0x11dcbe000 - 0x11dcd1fff +_multiarray_tests.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_multiarray_tests.cpython-311-darwin.so
0x11ddea000 - 0x11ddfdfff +_ctypes.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so
0x11de16000 - 0x11de35fff +_umath_linalg.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/_umath_linalg.cpython-311-darwin.so
0x11df4e000 - 0x11df61fff +_pocketfft_internal.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/fft/_pocketfft_internal.cpython-311-darwin.so
0x11df6e000 - 0x11dfe1fff +mtrand.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/mtrand.cpython-311-darwin.so
0x11e046000 - 0x11e065fff +bit_generator.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/bit_generator.cpython-311-darwin.so
0x11e08a000 - 0x11e0b9fff +_common.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_common.cpython-311-darwin.so
0x11e0da000 - 0x11e0e1fff +_hashlib.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_hashlib.cpython-311-darwin.so
0x11e0f2000 - 0x11e319fff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/libcrypto.1.1.dylib
0x11e3ba000 - 0x11e3c1fff +_blake2.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_blake2.cpython-311-darwin.so
0x11e3ce000 - 0x11e421fff +_bounded_integers.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_bounded_integers.cpython-311-darwin.so
0x11e452000 - 0x11e461fff +_mt19937.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_mt19937.cpython-311-darwin.so
0x11e476000 - 0x11e481fff +_philox.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_philox.cpython-311-darwin.so
0x11e496000 - 0x11e4a5fff +_pcg64.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_pcg64.cpython-311-darwin.so
0x11e4ba000 - 0x11e4c1fff +_sfc64.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_sfc64.cpython-311-darwin.so
0x11e4d2000 - 0x11e561fff +_generator.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_generator.cpython-311-darwin.so
0x11e6ce000 - 0x11e6d1fff +_opcode.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_opcode.cpython-311-darwin.so
0x11e7de000 - 0x11e801fff +_geometry.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/_geometry.cpython-311-darwin.so
0x11ed1a000 - 0x11ee9dfff +QtCore.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtCore.abi3.so
0x11f0f7000 - 0x11f10efff +sip.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/sip.cpython-311-darwin.so
0x11f127000 - 0x11f1b2fff +QtDBus (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtDBus.framework/Versions/A/QtDBus
0x11f1d7000 - 0x11f1e6fff +QtWebEngineWidgets.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebEngineWidgets.abi3.so
0x11f1fb000 - 0x11f20efff +QtWebEngineWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebEngineWidgets.framework/Versions/A/QtWebEngineWidgets
0x11f227000 - 0x11f25afff +QtWebChannel (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebChannel.framework/Versions/A/QtWebChannel
0x11f273000 - 0x11f27afff +QtWebChannel.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebChannel.abi3.so
0x11f297000 - 0x11f332fff dyld (852.2) /usr/lib/dyld
0x1273af000 - 0x1278b2fff +QtCore (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtCore.framework/Versions/A/QtCore
0x129824000 - 0x129acffff +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWidgets.abi3.so
0x129e34000 - 0x12a2effff +QtWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWidgets.framework/Versions/A/QtWidgets
0x12a44c000 - 0x12aaf3fff +QtGui (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtGui.framework/Versions/A/QtGui
0x12ac20000 - 0x12ad87fff +QtGui.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtGui.abi3.so
0x12b260000 - 0x12b2abfff +QtPrintSupport (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtPrintSupport.framework/Versions/A/QtPrintSupport
0x12b2dc000 - 0x135043fff +QtWebEngineCore (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebEngineCore.framework/Versions/A/QtWebEngineCore
0x135cd8000 - 0x1360bbfff +QtQuick (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQuick.framework/Versions/A/QtQuick
0x13621c000 - 0x136283fff +QtOpenGL (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtOpenGL.framework/Versions/A/QtOpenGL
0x1362b4000 - 0x13633bfff +QtQmlModels (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQmlModels.framework/Versions/A/QtQmlModels
0x13636c000 - 0x13674ffff +QtQml (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQml.framework/Versions/A/QtQml
0x13680c000 - 0x13693ffff +QtNetwork (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtNetwork.framework/Versions/A/QtNetwork
0x136990000 - 0x136a07fff +QtPositioning (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtPositioning.framework/Versions/A/QtPositioning
0x136a2c000 - 0x136a3ffff +QtQuickWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQuickWidgets.framework/Versions/A/QtQuickWidgets
0x136a58000 - 0x136ac7fff +QtNetwork.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtNetwork.abi3.so
0x136b70000 - 0x136b9ffff +QtWebEngineCore.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebEngineCore.abi3.so
0x136c04000 - 0x136c27fff +QtPrintSupport.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtPrintSupport.abi3.so
0x136d5c000 - 0x136dfbfff +libqcocoa.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/plugins/platforms/libqcocoa.dylib
0x137c05000 - 0x137c14fff libobjc-trampolines.dylib (824.1) /usr/lib/libobjc-trampolines.dylib
0x13844b000 - 0x13859efff com.apple.AMDRadeonX6000GLDriver (4.6.21 - 4.0.6) /System/Library/Extensions/AMDRadeonX6000GLDriver.bundle/Contents/MacOS/AMDRadeonX6000GLDriver
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0x1391f5000 - 0x13921cfff +libqmacstyle.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/plugins/styles/libqmacstyle.dylib
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0x7fff3cee6000 - 0x7fff3cf05fff com.apple.private.SystemPolicy (1.0 - 1) /System/Library/PrivateFrameworks/SystemPolicy.framework/Versions/A/SystemPolicy
0x7fff3d0a9000 - 0x7fff3d0c6fff com.apple.sidecar-core (1.0 - 231.0.3) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff3d0c7000 - 0x7fff3d0cafff com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff3d4e2000 - 0x7fff3d4e8fff com.apple.FeatureFlagsSupport (1.0 - 28.60.1) /System/Library/PrivateFrameworks/FeatureFlagsSupport.framework/Versions/A/FeatureFlagsSupport
0x7fff3d659000 - 0x7fff3d670fff com.apple.SafariServices.framework (16611 - 16611.3.10.1.16) /System/Library/Frameworks/SafariServices.framework/Versions/A/SafariServices
0x7fff3d823000 - 0x7fff3d82efff com.apple.MallocStackLogging (1.0 - 1) /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging
0x7fff3d843000 - 0x7fff3d855fff libmis.dylib (274.140.2) /usr/lib/libmis.dylib
0x7fff3d872000 - 0x7fff3d9e1fff com.apple.CoreHandwriting (161 - 1.2) /System/Library/PrivateFrameworks/CoreHandwriting.framework/Versions/A/CoreHandwriting
0x7fff3d9e2000 - 0x7fff3dc3dfff com.apple.imageKit (3.0 - 1100) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit
0x7fff3dc3e000 - 0x7fff3dd54fff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit
0x7fff3dd55000 - 0x7fff3dd66fff com.apple.sidecar-ui (1.0 - 231.0.3) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff3e389000 - 0x7fff3e3ebfff com.apple.ImageCaptureCore (1711.5.2.1 - 1711.5.2.1) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x7fff3e3ec000 - 0x7fff3e411fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters
0x7fff3e65d000 - 0x7fff3e7bffff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer
0x7fff3e7c0000 - 0x7fff3eaa1fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud
0x7fff3eacd000 - 0x7fff3ebf5fff com.apple.AnnotationKit (1.0 - 383.6.1) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit
0x7fff3ebf6000 - 0x7fff3f096fff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x7fff3f097000 - 0x7fff3f17ffff com.apple.PDFKit (1.0 - 950.40.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit
0x7fff4107a000 - 0x7fff41083fff com.apple.IOAccelMemoryInfo (1.0 - 1) /System/Library/PrivateFrameworks/IOAccelMemoryInfo.framework/Versions/A/IOAccelMemoryInfo
0x7fff410de000 - 0x7fff410e1fff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x7fff41506000 - 0x7fff41524fff libCGInterfaces.dylib (544.6) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff42ba4000 - 0x7fff43904fff libfaceCore.dylib (4.3.1) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib
0x7fff43905000 - 0x7fff43a18fff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x7fff43a19000 - 0x7fff43a31fff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark
0x7fff43ab3000 - 0x7fff43d26fff com.apple.RawCamera.bundle (9.10.0 - 1450.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff4458f000 - 0x7fff44593fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
0x7fff45f0a000 - 0x7fff45f0dfff libpmenergy.dylib (227.140.1) /usr/lib/libpmenergy.dylib
0x7fff465f9000 - 0x7fff46604fff libGPUSupportMercury.dylib (18.5.9) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
0x7fff47c2f000 - 0x7fff47c70fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x7fff484be000 - 0x7fff484d9fff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x7fff516ff000 - 0x7fff5179efff com.apple.Symbolication (12.5 - 64544.70.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff5198e000 - 0x7fff51991fff libpmsample.dylib (227.140.1) /usr/lib/libpmsample.dylib
0x7fff54027000 - 0x7fff5405dfff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x7fff55653000 - 0x7fff55656fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff5e21a000 - 0x7fff5ec7dfff libSC.dylib (4.6.21) /System/Library/Extensions/AMDShared.bundle/Contents/PlugIns/libSC.dylib
0x7fff6974b000 - 0x7fff6974ffff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x7fff6bb96000 - 0x7fff6bb9cfff libCoreFSCache.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6bb9d000 - 0x7fff6bba1fff libCoreVMClient.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6bba2000 - 0x7fff6bbb1fff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6bbb2000 - 0x7fff6bbb4fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6bbb5000 - 0x7fff6bbbdfff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6bbbe000 - 0x7fff6bbf1fff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6bbf2000 - 0x7fff6bc2efff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6bc2f000 - 0x7fff6bdc2fff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6bdc3000 - 0x7fff6bdcdfff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6bdce000 - 0x7fff6bf4bfff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6bf4c000 - 0x7fff6bf74fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6d20d000 - 0x7fff6d265fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6e1af000 - 0x7fff6e1fefff ATIRadeonX6000SCLib.dylib (4.6.21) /System/Library/Extensions/AMDRadeonX6000GLDriver.bundle/Contents/MacOS/ATIRadeonX6000SCLib.dylib
0x7fff6e30f000 - 0x7fff6e316fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff6e317000 - 0x7fff6e3fefff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff6f984000 - 0x7fff6f996fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x7fff73cb0000 - 0x7fff73cbbfff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff73ed1000 - 0x7fff73ee9fff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff777f8000 - 0x7fff777fffff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)
Writable regions: Total=7.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 4
Activity Tracing 256K 1
CG backing stores 7200K 12
CG image 284K 23
CoreAnimation 160K 21
CoreGraphics 16K 3
CoreUI image data 4228K 40
Foundation 36K 2
Kernel Alloc Once 8K 1
MALLOC 4.7G 311
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 1.4G 16 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
Mach message 24K 4
OpenGL GLSL 384K 4
STACK GUARD 148K 37
Stack 184.8M 38
Stack Guard 56.0M 1
VM_ALLOCATE 418.8M 396
VM_ALLOCATE (reserved) 352.0M 3 reserved VM address space (unallocated)
__DATA 53.8M 764
__DATA_CONST 25.5M 305
__DATA_DIRTY 1708K 207
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 547.4M 454
__OBJC_RO 70.3M 1
__OBJC_RW 2496K 2
__TEXT 770.0M 728
__UNICODE 588K 1
mapped file 265.8M 46
shared memory 3592K 25
=========== ======= =======
TOTAL 8.9G 3463
TOTAL, minus reserved VM space 7.1G 3463
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor #ffffff00
> lighting soft
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> runscript /Users/james.walshe/scripts/General_XL_2.py -id #1 -m -i
> log clear
> windowsize 1097 680
> close
> runscript /Users/james.walshe/scripts/Color&Load.py --load_models
> ECstar_hexasome
Argparse argument "load_models" is ECstar_hexasome
These are the available structures to load:
1: ECstar
2: NCP
3: DNA
4: PEC
5: EC
6: NCP_SETD2
7: ECstar_hexasome
8: SETD2_CD
9: NCP_102bp_RU
10: NCP_SETD2_27
> open
> /Users/james.walshe/Dropbox/MPI/MPI/labwork/model_building/chimeraX/ECstar_hexasome.pdb
Chain information for ECstar_hexasome.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
e | No description available
f | No description available
g | No description available
h | No description available
j | No description available
k | No description available
> hide #1 atoms
> show #1 cartoons
> color #1 white
> hide #1 target abpcrs
> select #1
77573 atoms, 79395 bonds, 32 pseudobonds, 9436 residues, 2 models selected
Loading of ECstar_hexasome was successful!
ECstar_hexasome models was loaded into ChimeraX.
> name PolII #1/A,B,C,D,E,F,G,H,I,J,K,L
> show PolII cartoons
> color PolII dark gray
> name DNARNA #1/T,P,N
> show DNARNA surfaces
> name Template #1/T
> show Template surfaces
> color Template blue
> name NonTemplate #1/N
> show NonTemplate surfaces
> color NonTemplate cyan
> name RNA #1/P
> show RNA surfaces
> color RNA red
> name TFIIS #1/S
> show TFIIS cartoons
> color TFIIS yellow
> name PAF #1/Q,R,U,V,W
> show PAF cartoons
> name DSIF #1/Z
> show DSIF cartoons
> name SPT6 #1/M
> show SPT6 cartoons
> color SPT6 darkblue
> name CTR9 #1/Q
> show CTR9 cartoons
> color CTR9 dark orange
> name RTF1 #1/R
> show RTF1 cartoons
> color RTF1 deep pink
> name LEO1 #1/U
> show LEO1 cartoons
> color LEO1 purple
> name Paf1 #1/V
> show Paf1 cartoons
> color Paf1 green yellow
> name WDR61 #1/W
> show WDR61 cartoons
> color WDR61 teal
> name CDC73 #1/X
> show CDC73 cartoons
> color CDC73 maroon
> name SPT4 #1/Y
> show SPT4 cartoons
> color SPT4 pale green
> name SPT5 #1/Z
> show SPT5 cartoons
> color SPT5 forestgreen
> name histones #1/A-H
> show histones cartoons
> name H2A #1/c,g
> show H2A cartoons
> color H2A yellow
> name H2B #1/d,h
> show H2B cartoons
> color H2B red
> name H3 #1/a,e
> show H3 cartoons
> color H3 dodgerblue
> name H4 #1/b,f
> show H4 cartoons
> color H4 chartreuse
> name SETD2 #1/O
> show SETD2 cartoons
> color SETD2 plum
> name SSRP1 #1/k
> show SSRP1 cartoons
> color SSRP1 dark violet
> name SPT16 #1/j
> show SPT16 cartoons
> color SPT16 slate blue
> ui mousemode right "move picked models"
> view
The script has ended!
> hide atoms
> ~select
Nothing selected
> style stick
Changed 77573 atom styles
> size #1 stickRadius 0.8
Changed 79395 bond radii
> delete @H*
> color @NZ byhetero
> color #1/T blue
> color #1/N cyan
> color #1/P red
> cartoon style protein modeHelix tube radius 2 sides 24
> graphics quality atomTriangles default bondTriangles default ribbonDivisions
> default ribbonSides 12 colorDepth 16
> graphics bgColor black
> lighting soft depthCue true shadows false multiShadow 64
> material dull
> graphics silhouettes true width 1.8 depthJump 0.008
> close #2
11.4889048216094
Skipped: #1/X:243@NZ to #1/Q:398@NZ
4.116472519038603
Skipped: #1/X:243@NZ to #1/Q:645@NZ
19.73644671667116
Skipped: #1/X:247@NZ to #1/Q:637@NZ
4.150376488946515
Skipped: #1/X:257@NZ to #1/Q:637@NZ
18.3260024555275
Skipped: #1/X:247@NZ to #1/A:581@NZ
16.25202504305233
Skipped: #1/X:243@NZ to #1/H:146@NZ
14.02632090036442
Skipped: #1/X:247@NZ to #1/H:146@NZ
183.9555478424068
Skipped: #1/Q:188@NZ to #1/a,e:57@NZ
46.32807858092109
Skipped: #1/Q:188@NZ to #1/V:133@NZ
12.60659680484785
Skipped: #1/Q:213@NZ to #1/V:106@NZ
3.691823804029651
Skipped: #1/Q:246@NZ to #1/V:68@NZ
14.04356671219958
Skipped: #1/Q:252@NZ to #1/V:68@NZ
13.46025311797665
Skipped: #1/Q:282@NZ to #1/V:68@NZ
8.196997316090817
Skipped: #1/Q:283@NZ to #1/V:62@NZ
16.58307628276491
Skipped: #1/Q:283@NZ to #1/V:68@NZ
19.8269063900549
Skipped: #1/Q:710@NZ to #1/V:34@NZ
17.5101895192485
Skipped: #1/Q:833@NZ to #1/A:940@NZ
15.05630173714648
Skipped: #1/Q:844@NZ to #1/A:940@NZ
95.42672054513872
Skipped: #1/Q:187@NZ to #1/F:98@NZ
104.4235674213441
Skipped: #1/Q:216@NZ to #1/F:101@NZ
124.2395721740863
Skipped: #1/Q:188@NZ to #1/j:533@NZ
140.544440747402
Skipped: #1/Q:188@NZ to #1/j:696@NZ
139.8684931998626
Skipped: #1/Q:188@NZ to #1/Z:344@NZ
125.1295697307395
Skipped: #1/Q:188@NZ to #1/M:843@NZ
151.6353643514599
Skipped: #1/Q:188@NZ to #1/M:1002@NZ
16.83748374906416
Skipped: #1/Q:777@NZ to #1/W:97@NZ
13.83698251064876
Skipped: #1/Q:798@NZ to #1/W:140@NZ
10.84777378082714
Skipped: #1/c,g:16@NZ to #1/d,h:121@NZ
11.68286463158756
Skipped: #1/c,g:16@NZ to #1/d,h:126@NZ
11.16845217565979
Skipped: #1/c,g:37@NZ to #1/d,h:35@NZ
32.68359548764489
Skipped: #1/c,g:37@NZ to #1/d,h:86@NZ
12.65801362773796
Skipped: #1/c,g:96@NZ to #1/d,h:109@NZ
52.04003506916573
Skipped: #1/c,g:119@NZ to #1/d,h:47@NZ
21.79748634590695
Skipped: #1/c,g:120@NZ to #1/a,e:57@NZ
38.77489364266523
Skipped: #1/c,g:126@NZ to #1/a,e:57@NZ
13.87520302554163
Skipped: #1/c,g:96@NZ to #1/R:274@NZ
23.57027010876201
Skipped: #1/c,g:96@NZ to #1/R:278@NZ
13.79649770775177
Skipped: #1/d,h:109@NZ to #1/R:265@NZ
16.22929702728987
Skipped: #1/d,h:109@NZ to #1/R:274@NZ
16.37631234435885
Skipped: #1/d,h:117@NZ to #1/R:265@NZ
26.42649657067692
Skipped: #1/d,h:121@NZ to #1/R:265@NZ
167.8146424034566
Skipped: #1/d,h:86@NZ to #1/M:1345@NZ
17.97889779713983
Skipped: #1/a,e:57@NZ to #1/j:479@NZ
15.66155298812987
Skipped: #1/a,e:57@NZ to #1/j:904@NZ
69.74751776228314
Skipped: #1/a,e:57@NZ to #1/M:844@NZ
60.39883266256064
Skipped: #1/a,e:57@NZ to #1/k:426@NZ
6.221900192063518
Skipped: #1/A:331@NZ to #1/B:583@NZ
15.91133445063612
Skipped: #1/A:331@NZ to #1/B:584@NZ
20.90163182624745
Skipped: #1/A:331@NZ to #1/B:947@NZ
26.26204997710575
Skipped: #1/A:337@NZ to #1/B:584@NZ
30.51500858594012
Skipped: #1/A:346@NZ to #1/B:584@NZ
12.45299494097705
Skipped: #1/A:796@NZ to #1/B:337@NZ
13.8867687386231
Skipped: #1/A:853@NZ to #1/B:620@NZ
15.19748156768088
Skipped: #1/A:853@NZ to #1/B:1068@NZ
21.80481820607546
Skipped: #1/A:1125@NZ to #1/B:337@NZ
7.685201493780112
Skipped: #1/A:1125@NZ to #1/B:620@NZ
22.69277448881032
Skipped: #1/A:1132@NZ to #1/B:620@NZ
12.35279729454021
Skipped: #1/A:1135@NZ to #1/B:337@NZ
12.39394352092989
Skipped: #1/A:1135@NZ to #1/B:620@NZ
18.66257018740988
Skipped: #1/A:125@NZ to #1/E:88@NZ
19.31655901034136
Skipped: #1/A:134@NZ to #1/E:186@NZ
10.32094981094279
Skipped: #1/A:1350@NZ to #1/E:12@NZ
15.41824250684883
Skipped: #1/A:1350@NZ to #1/E:15@NZ
9.338040586761231
Skipped: #1/A:1350@NZ to #1/E:41@NZ
7.624163560679952
Skipped: #1/A:581@NZ to #1/H:146@NZ
12.29602557739696
Skipped: #1/A:758@NZ to #1/H:21@NZ
12.47304104859758
Skipped: #1/A:767@NZ to #1/H:21@NZ
11.99653474966832
Skipped: #1/A:707@NZ to #1/R:600@CA
51.05339007352988
Skipped: #1/A:285@NZ to #1/Y:102@NZ
35.7842231996169
Skipped: #1/A:42@NZ to #1/Z:274@NZ
20.61509711352336
Skipped: #1/A:42@NZ to #1/Z:287@NZ
9.183322492431605
Skipped: #1/A:212@NZ to #1/Z:258@NZ
24.4735217326808
Skipped: #1/A:285@NZ to #1/Z:183@NZ
25.63007487308612
Skipped: #1/A:285@NZ to #1/Z:185@NZ
37.36188424049301
Skipped: #1/A:285@NZ to #1/Z:274@NZ
19.15694834779276
Skipped: #1/A:434@NZ to #1/Z:578@NZ
19.50237659876356
Skipped: #1/A:434@NZ to #1/Z:579@NZ
13.09842253861129
Skipped: #1/A:434@NZ to #1/Z:597@NZ
20.43069154483029
Skipped: #1/A:445@NZ to #1/Z:627@NZ
25.89293818785346
Skipped: #1/A:445@NZ to #1/Z:628@NZ
96.26540967034833
Skipped: #1/A:346@NZ to #1/k:364@NZ
10.01633585698884
Skipped: #1/A:1317@NZ to #1/S:252@NZ
8.306821473945377
Skipped: #1/K:47@NZ to #1/C:225@NZ
5.324126031566121
Skipped: #1/K:52@NZ to #1/C:225@NZ
142.1530242977616
Skipped: #1/K:26@NZ to #1/k:105@NZ
19.37483682511933
Skipped: #1/B:1269@NZ to #1/G:81@NZ
11.9781150854381
Skipped: #1/B:221@NZ to #1/R:518@CA
7.97878449389379
Skipped: #1/B:221@NZ to #1/R:520@CA
19.72334134978151
Skipped: #1/B:272@NZ to #1/R:518@CA
23.51574589503807
Skipped: #1/B:277@NZ to #1/R:518@CA
22.36312055595105
Skipped: #1/B:946@NZ to #1/R:486@NZ
26.29433908657908
Skipped: #1/B:947@NZ to #1/R:486@NZ
12.57602902350341
Skipped: #1/B:463@NZ to #1/Z:236@NZ
5.84527518599425
Skipped: #1/B:547@NZ to #1/Z:185@NZ
49.65526906583028
Skipped: #1/B:547@NZ to #1/Z:344@NZ
4.647930507225776
Skipped: #1/B:1269@NZ to #1/Z:479@NZ
113.8631816304112
Skipped: #1/B:623@NZ to #1/M:1454@NZ
124.7484390643827
Skipped: #1/B:337@NZ to #1/k:39@NZ
60.09876708385956
Skipped: #1/B:584@NZ to #1/k:422@NZ
18.02679497303944
Skipped: #1/C:199@NZ to #1/H:20@NZ
10.86797391421234
Skipped: #1/C:155@NZ to #1/R:504@NZ
14.52320467390031
Skipped: #1/C:155@NZ to #1/R:555@CA
12.04059151370893
Skipped: #1/D:94@NZ to #1/G:73@NZ
11.1944473289216
Skipped: #1/D:45@NZ to #1/M:622@NZ
24.64752224869673
Skipped: #1/F:101@NZ to #1/M:1341@NZ
18.9817783413462
Skipped: #1/G:29@NZ to #1/Z:627@NZ
14.53567439095964
Skipped: #1/G:29@NZ to #1/Z:628@NZ
17.45990438118147
Skipped: #1/G:146@NZ to #1/Z:473@NZ
14.06438768663607
Mapping specific XL: #1/R:265@NZ to #1/j:473@NZ
> show #1/R:265#1/j:473 atoms
> style #1/R:265#1/j:473 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:473@NZ
Distance between /R LYS 265 NZ and /j LYS 473 NZ: 14.064Å
> crosslinks #1/R:265@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
32.16296461770898
Mapping specific XL: #1/R:265@NZ to #1/j:777@NZ
> show #1/R:265#1/j:777 atoms
> style #1/R:265#1/j:777 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:777@NZ
Distance between /R LYS 265 NZ and /j LYS 777 NZ: 32.163Å
> crosslinks #1/R:265@NZ #1/j:777@NZ radius 0.2 color 255,255,0,100
32.40224643446808
Mapping specific XL: #1/R:265@NZ to #1/j:781@NZ
> show #1/R:265#1/j:781 atoms
> style #1/R:265#1/j:781 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:781@NZ
Distance between /R LYS 265 NZ and /j LYS 781 NZ: 32.402Å
> crosslinks #1/R:265@NZ #1/j:781@NZ radius 0.2 color 255,255,0,100
12.77883414087529
Mapping specific XL: #1/R:277@NZ to #1/j:777@NZ
> show #1/R:277#1/j:777 atoms
> style #1/R:277#1/j:777 stick
Changed 18 atom styles
> distance #1/R:277@NZ #1/j:777@NZ
Distance between /R LYS 277 NZ and /j LYS 777 NZ: 12.779Å
> crosslinks #1/R:277@NZ #1/j:777@NZ radius 0.2 color 255,255,0,100
9.242002705041775
Mapping specific XL: #1/R:278@NZ to #1/j:473@NZ
> show #1/R:278#1/j:473 atoms
> style #1/R:278#1/j:473 stick
Changed 18 atom styles
> distance #1/R:278@NZ #1/j:473@NZ
Distance between /R LYS 278 NZ and /j LYS 473 NZ: 9.242Å
> crosslinks #1/R:278@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
19.05222490944297
Mapping specific XL: #1/R:286@NZ to #1/j:473@NZ
> show #1/R:286#1/j:473 atoms
> style #1/R:286#1/j:473 stick
Changed 18 atom styles
> distance #1/R:286@NZ #1/j:473@NZ
Distance between /R LYS 286 NZ and /j LYS 473 NZ: 19.052Å
> crosslinks #1/R:286@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
37.48139353065731
Mapping specific XL: #1/R:302@NZ to #1/j:497@NZ
> show #1/R:302#1/j:497 atoms
> style #1/R:302#1/j:497 stick
Changed 18 atom styles
> distance #1/R:302@NZ #1/j:497@NZ
Distance between /R LYS 302 NZ and /j LYS 497 NZ: 37.481Å
> crosslinks #1/R:302@NZ #1/j:497@NZ radius 0.2 color 255,255,0,100
43.93616351025654
Mapping specific XL: #1/R:303@NZ to #1/j:497@NZ
> show #1/R:303#1/j:497 atoms
> style #1/R:303#1/j:497 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:497@NZ
Distance between /R LYS 303 NZ and /j LYS 497 NZ: 43.936Å
> crosslinks #1/R:303@NZ #1/j:497@NZ radius 0.2 color 255,255,0,100
43.00328301420718
Mapping specific XL: #1/R:303@NZ to #1/j:504@NZ
> show #1/R:303#1/j:504 atoms
> style #1/R:303#1/j:504 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:504@NZ
Distance between /R LYS 303 NZ and /j LYS 504 NZ: 43.003Å
> crosslinks #1/R:303@NZ #1/j:504@NZ radius 0.2 color 255,255,0,100
26.04891191585553
Mapping specific XL: #1/R:303@NZ to #1/j:647@NZ
> show #1/R:303#1/j:647 atoms
> style #1/R:303#1/j:647 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:647@NZ
Distance between /R LYS 303 NZ and /j LYS 647 NZ: 26.049Å
> crosslinks #1/R:303@NZ #1/j:647@NZ radius 0.2 color 255,255,0,100
6.28588641322767
Mapping specific XL: #1/R:303@NZ to #1/j:792@NZ
> show #1/R:303#1/j:792 atoms
> style #1/R:303#1/j:792 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:792@NZ
Distance between /R LYS 303 NZ and /j LYS 792 NZ: 6.286Å
> crosslinks #1/R:303@NZ #1/j:792@NZ radius 0.2 color 255,255,0,100
89.3050655562158
Mapping specific XL: #1/R:265@NZ to #1/M:838@NZ
> show #1/R:265#1/M:838 atoms
> style #1/R:265#1/M:838 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/M:838@NZ
Distance between /R LYS 265 NZ and /M LYS 838 NZ: 89.305Å
> crosslinks #1/R:265@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
77.40834650733731
Mapping specific XL: #1/R:265@NZ to #1/M:844@NZ
> show #1/R:265#1/M:844 atoms
> style #1/R:265#1/M:844 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/M:844@NZ
Distance between /R LYS 265 NZ and /M LYS 844 NZ: 77.408Å
> crosslinks #1/R:265@NZ #1/M:844@NZ radius 0.2 color 255,255,0,100
69.56037047054883
Mapping specific XL: #1/R:302@NZ to #1/M:838@NZ
> show #1/R:302#1/M:838 atoms
> style #1/R:302#1/M:838 stick
Changed 18 atom styles
> distance #1/R:302@NZ #1/M:838@NZ
Distance between /R LYS 302 NZ and /M LYS 838 NZ: 69.560Å
> crosslinks #1/R:302@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
58.86815268886906
Mapping specific XL: #1/R:303@NZ to #1/M:838@NZ
> show #1/R:303#1/M:838 atoms
> style #1/R:303#1/M:838 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/M:838@NZ
Distance between /R LYS 303 NZ and /M LYS 838 NZ: 58.868Å
> crosslinks #1/R:303@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
30.70350356229726
Mapping specific XL: #1/R:303@NZ to #1/M:1135@NZ
> show #1/R:303#1/M:1135 atoms
> style #1/R:303#1/M:1135 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/M:1135@NZ
Distance between /R LYS 303 NZ and /M LYS 1135 NZ: 30.704Å
> crosslinks #1/R:303@NZ #1/M:1135@NZ radius 0.2 color 255,255,0,100
14.97592204173087
Skipped: #1/O:2028@NZ to #1/M:1100@NZ
31.2226572059458
Skipped: #1/j:696@NZ to #1/Z:344@NZ
35.87485081502083
Skipped: #1/j:661@NZ to #1/M:838@NZ
22.99626765368676
Skipped: #1/j:661@NZ to #1/M:844@NZ
8.080834115362094
Skipped: #1/j:696@NZ to #1/M:777@NZ
14.63421145808684
Skipped: #1/j:696@NZ to #1/M:844@NZ
23.75544766995562
Skipped: #1/j:786@NZ to #1/M:1005@NZ
46.04967928227079
Skipped: #1/j:497@NZ to #1/k:105@NZ
26.06885985232191
Skipped: #1/j:504@NZ to #1/k:105@NZ
20.13935301840653
Skipped: #1/j:507@NZ to #1/k:105@NZ
10.88677679572792
Skipped: #1/j:513@NZ to #1/k:105@NZ
47.69925898795494
Skipped: #1/j:606@NZ to #1/k:396@NZ
11.15022587215166
Skipped: #1/j:626@NZ to #1/k:264@NZ
46.01420339416951
Skipped: #1/Y:102@NZ to #1/Z:344@NZ
13.29000880360883
Skipped: #1/Y:109@NZ to #1/Z:265@NZ
1.433925381601146
Skipped: #1/Y:116@NZ to #1/Z:268@NZ
9.337233209040022
Skipped: #1/Y:116@NZ to #1/Z:274@NZ
14.18636239491997
Skipped: #1/Y:116@NZ to #1/Z:276@NZ
77.89569092703397
Skipped: #1/Y:102@NZ to #1/M:838@NZ
33.68250492466379
Skipped: #1/Y:116@NZ to #1/M:1002@NZ
65.81877884768147
Skipped: #1/Z:183@NZ to #1/M:838@NZ
64.06037122902114
Skipped: #1/Z:183@NZ to #1/M:1002@NZ
55.65474140628093
Skipped: #1/Z:185@NZ to #1/M:843@NZ
27.03334559391419
Skipped: #1/Z:306@NZ to #1/M:1005@NZ
24.56814117917756
Skipped: #1/Z:317@NZ to #1/M:838@NZ
13.61775675359198
Skipped: #1/Z:317@NZ to #1/M:843@NZ
25.10195446573832
Skipped: #1/Z:317@NZ to #1/M:844@NZ
31.78610215172662
Skipped: #1/Z:317@NZ to #1/M:1002@NZ
37.44038817907744
Skipped: #1/Z:344@NZ to #1/M:838@NZ
15.9173482716186
Skipped: #1/Z:344@NZ to #1/M:1002@NZ
8.486640854896576
Skipped: #1/Z:344@NZ to #1/M:1005@NZ
20.48942288108672
Skipped: #1/Z:369@NZ to #1/M:1005@NZ
9.78836007715286
Skipped: #1/Z:579@NZ to #1/M:816@NZ
18.68985807864791
Skipped: #1/Z:601@NZ to #1/M:622@NZ
7.659518196335855
Skipped: #1/Z:601@NZ to #1/M:626@NZ
38.75339083228719
Skipped: #1/Z:601@NZ to #1/M:816@NZ
23.05639672628834
Skipped: #1/Z:601@NZ to #1/M:1319@NZ
23.70647702633185
Skipped: #1/Z:627@NZ to #1/M:626@NZ
> size #1/R:310-353 pseudobondRadius 0.9
Changed 1 pseudobond radii
> close #2
> set bgColor white
> hide atoms
> coulombic #1/j:450-500,642-1000 #1/R:200-310
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/R PRO 506
/R PRO 507
/R ASN 508
/R TYR 509
/R MET 511
/R LYS 512
/R LYS 513
/R THR 514
/R GLN 515
/R LEU 516
/R LEU 517
/R LYS 518
/R GLU 519
/R LYS 520
/R MET 522
/R GLU 524
/R ASP 525
/R LEU 526
/R ASP 528
/R GLN 529
/R ASP 530
/R LYS 531
/R LYS 533
/R GLN 534
/R ILE 535
/R GLN 536
/R ASP 537
/R GLN 538
/R LEU 539
/R ASN 540
/R GLU 541
/R LEU 542
/R GLU 543
/R GLU 544
/R ARG 545
/R GLU 547
/R LEU 549
/R ASP 550
/R ARG 551
/R GLN 552
/R ARG 553
/R THR 554
/R LYS 555
/R ASN 556
/R MET 591
/R ASP 592
/R THR 595
/R GLN 598
/R CYS 599
/R LYS 600
/j GLU 930
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ECstar_hexasome.pdb_R SES surface #1.5: minimum, -17.86,
mean 0.55, maximum 13.88
Coulombic values for ECstar_hexasome.pdb_j SES surface #1.6: minimum, -18.77,
mean -0.77, maximum 15.91
> hide #1/M,O cartoons
> hide #1/R surfaces
> hide #1/R:300-310 cartoons
> show #1/R:289,292,295 atoms
> view matrix camera
> 0.40398,-0.65577,-0.63778,-75.42,0.4043,0.75341,-0.51857,-22.381,0.82057,-0.048369,0.5695,427.76
> save
> /Users/james.walshe/Dropbox/MPI/MPI/Papers/2024_Walshe_Ochmann_SETD2_FACT/Figures/Figure3//XL_Top_electro.tiff
> format tiff supersample 4 transparentBackground true
> close #2
> set bgColor white
> hide atoms
> coulombic #1/j:450-500,642-1000 #1/R:200-310
Coulombic values for ECstar_hexasome.pdb_R SES surface #1.5: minimum, -17.86,
mean 0.55, maximum 13.88
Coulombic values for ECstar_hexasome.pdb_j SES surface #1.6: minimum, -18.77,
mean -0.77, maximum 15.91
> hide #1/M,O cartoons
> hide #1/R surfaces
> hide #1/R:300-310 cartoons
> show #1/R:289,292,295 atoms
> view matrix camera
> 0.19287,-0.94612,0.26013,218.04,0.5223,-0.12543,-0.84349,27.951,0.83066,0.29854,0.46997,285.64
> save
> /Users/james.walshe/Dropbox/MPI/MPI/Papers/2024_Walshe_Ochmann_SETD2_FACT/Figures/Figure3//XL_Side_electro.tiff
> format tiff supersample 4 transparentBackground true
> color byhetero
> runscript /Users/james.walshe/scripts/General_XL_2.py -id #1 -m -i
> log clear
> windowsize 1097 680
> close
> runscript /Users/james.walshe/scripts/Color&Load.py --load_models
> ECstar_hexasome
Argparse argument "load_models" is ECstar_hexasome
These are the available structures to load:
1: ECstar
2: NCP
3: DNA
4: PEC
5: EC
6: NCP_SETD2
7: ECstar_hexasome
8: SETD2_CD
9: NCP_102bp_RU
10: NCP_SETD2_27
> open
> /Users/james.walshe/Dropbox/MPI/MPI/labwork/model_building/chimeraX/ECstar_hexasome.pdb
Chain information for ECstar_hexasome.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
e | No description available
f | No description available
g | No description available
h | No description available
j | No description available
k | No description available
> hide #1 atoms
> show #1 cartoons
> color #1 white
> hide #1 target abpcrs
> select #1
77573 atoms, 79395 bonds, 32 pseudobonds, 9436 residues, 2 models selected
Loading of ECstar_hexasome was successful!
ECstar_hexasome models was loaded into ChimeraX.
> name PolII #1/A,B,C,D,E,F,G,H,I,J,K,L
> show PolII cartoons
> color PolII dark gray
> name DNARNA #1/T,P,N
> show DNARNA surfaces
> name Template #1/T
> show Template surfaces
> color Template blue
> name NonTemplate #1/N
> show NonTemplate surfaces
> color NonTemplate cyan
> name RNA #1/P
> show RNA surfaces
> color RNA red
> name TFIIS #1/S
> show TFIIS cartoons
> color TFIIS yellow
> name PAF #1/Q,R,U,V,W
> show PAF cartoons
> name DSIF #1/Z
> show DSIF cartoons
> name SPT6 #1/M
> show SPT6 cartoons
> color SPT6 darkblue
> name CTR9 #1/Q
> show CTR9 cartoons
> color CTR9 dark orange
> name RTF1 #1/R
> show RTF1 cartoons
> color RTF1 deep pink
> name LEO1 #1/U
> show LEO1 cartoons
> color LEO1 purple
> name Paf1 #1/V
> show Paf1 cartoons
> color Paf1 green yellow
> name WDR61 #1/W
> show WDR61 cartoons
> color WDR61 teal
> name CDC73 #1/X
> show CDC73 cartoons
> color CDC73 maroon
> name SPT4 #1/Y
> show SPT4 cartoons
> color SPT4 pale green
> name SPT5 #1/Z
> show SPT5 cartoons
> color SPT5 forestgreen
> name histones #1/A-H
> show histones cartoons
> name H2A #1/c,g
> show H2A cartoons
> color H2A yellow
> name H2B #1/d,h
> show H2B cartoons
> color H2B red
> name H3 #1/a,e
> show H3 cartoons
> color H3 dodgerblue
> name H4 #1/b,f
> show H4 cartoons
> color H4 chartreuse
> name SETD2 #1/O
> show SETD2 cartoons
> color SETD2 plum
> name SSRP1 #1/k
> show SSRP1 cartoons
> color SSRP1 dark violet
> name SPT16 #1/j
> show SPT16 cartoons
> color SPT16 slate blue
> ui mousemode right "move picked models"
> view
The script has ended!
> hide atoms
> ~select
Nothing selected
> style stick
Changed 77573 atom styles
> size #1 stickRadius 0.8
Changed 79395 bond radii
> delete @H*
> color @NZ byhetero
> color #1/T blue
> color #1/N cyan
> color #1/P red
> cartoon style protein modeHelix tube radius 2 sides 24
> graphics quality atomTriangles default bondTriangles default ribbonDivisions
> default ribbonSides 12 colorDepth 16
> graphics bgColor black
> lighting soft depthCue true shadows false multiShadow 64
> material dull
> graphics silhouettes true width 1.8 depthJump 0.008
> close #2
11.4889048216094
Skipped: #1/X:243@NZ to #1/Q:398@NZ
4.116472519038603
Skipped: #1/X:243@NZ to #1/Q:645@NZ
19.73644671667116
Skipped: #1/X:247@NZ to #1/Q:637@NZ
4.150376488946515
Skipped: #1/X:257@NZ to #1/Q:637@NZ
18.3260024555275
Skipped: #1/X:247@NZ to #1/A:581@NZ
16.25202504305233
Skipped: #1/X:243@NZ to #1/H:146@NZ
14.02632090036442
Skipped: #1/X:247@NZ to #1/H:146@NZ
183.9555478424068
Skipped: #1/Q:188@NZ to #1/a,e:57@NZ
46.32807858092109
Skipped: #1/Q:188@NZ to #1/V:133@NZ
12.60659680484785
Skipped: #1/Q:213@NZ to #1/V:106@NZ
3.691823804029651
Skipped: #1/Q:246@NZ to #1/V:68@NZ
14.04356671219958
Skipped: #1/Q:252@NZ to #1/V:68@NZ
13.46025311797665
Skipped: #1/Q:282@NZ to #1/V:68@NZ
8.196997316090817
Skipped: #1/Q:283@NZ to #1/V:62@NZ
16.58307628276491
Skipped: #1/Q:283@NZ to #1/V:68@NZ
19.8269063900549
Skipped: #1/Q:710@NZ to #1/V:34@NZ
17.5101895192485
Skipped: #1/Q:833@NZ to #1/A:940@NZ
15.05630173714648
Skipped: #1/Q:844@NZ to #1/A:940@NZ
95.42672054513872
Skipped: #1/Q:187@NZ to #1/F:98@NZ
104.4235674213441
Skipped: #1/Q:216@NZ to #1/F:101@NZ
124.2395721740863
Skipped: #1/Q:188@NZ to #1/j:533@NZ
140.544440747402
Skipped: #1/Q:188@NZ to #1/j:696@NZ
139.8684931998626
Skipped: #1/Q:188@NZ to #1/Z:344@NZ
125.1295697307395
Skipped: #1/Q:188@NZ to #1/M:843@NZ
151.6353643514599
Skipped: #1/Q:188@NZ to #1/M:1002@NZ
16.83748374906416
Skipped: #1/Q:777@NZ to #1/W:97@NZ
13.83698251064876
Skipped: #1/Q:798@NZ to #1/W:140@NZ
10.84777378082714
Skipped: #1/c,g:16@NZ to #1/d,h:121@NZ
11.68286463158756
Skipped: #1/c,g:16@NZ to #1/d,h:126@NZ
11.16845217565979
Skipped: #1/c,g:37@NZ to #1/d,h:35@NZ
32.68359548764489
Skipped: #1/c,g:37@NZ to #1/d,h:86@NZ
12.65801362773796
Skipped: #1/c,g:96@NZ to #1/d,h:109@NZ
52.04003506916573
Skipped: #1/c,g:119@NZ to #1/d,h:47@NZ
21.79748634590695
Skipped: #1/c,g:120@NZ to #1/a,e:57@NZ
38.77489364266523
Skipped: #1/c,g:126@NZ to #1/a,e:57@NZ
13.87520302554163
Skipped: #1/c,g:96@NZ to #1/R:274@NZ
23.57027010876201
Skipped: #1/c,g:96@NZ to #1/R:278@NZ
13.79649770775177
Skipped: #1/d,h:109@NZ to #1/R:265@NZ
16.22929702728987
Skipped: #1/d,h:109@NZ to #1/R:274@NZ
16.37631234435885
Skipped: #1/d,h:117@NZ to #1/R:265@NZ
26.42649657067692
Skipped: #1/d,h:121@NZ to #1/R:265@NZ
167.8146424034566
Skipped: #1/d,h:86@NZ to #1/M:1345@NZ
17.97889779713983
Skipped: #1/a,e:57@NZ to #1/j:479@NZ
15.66155298812987
Skipped: #1/a,e:57@NZ to #1/j:904@NZ
69.74751776228314
Skipped: #1/a,e:57@NZ to #1/M:844@NZ
60.39883266256064
Skipped: #1/a,e:57@NZ to #1/k:426@NZ
6.221900192063518
Skipped: #1/A:331@NZ to #1/B:583@NZ
15.91133445063612
Skipped: #1/A:331@NZ to #1/B:584@NZ
20.90163182624745
Skipped: #1/A:331@NZ to #1/B:947@NZ
26.26204997710575
Skipped: #1/A:337@NZ to #1/B:584@NZ
30.51500858594012
Skipped: #1/A:346@NZ to #1/B:584@NZ
12.45299494097705
Skipped: #1/A:796@NZ to #1/B:337@NZ
13.8867687386231
Skipped: #1/A:853@NZ to #1/B:620@NZ
15.19748156768088
Skipped: #1/A:853@NZ to #1/B:1068@NZ
21.80481820607546
Skipped: #1/A:1125@NZ to #1/B:337@NZ
7.685201493780112
Skipped: #1/A:1125@NZ to #1/B:620@NZ
22.69277448881032
Skipped: #1/A:1132@NZ to #1/B:620@NZ
12.35279729454021
Skipped: #1/A:1135@NZ to #1/B:337@NZ
12.39394352092989
Skipped: #1/A:1135@NZ to #1/B:620@NZ
18.66257018740988
Skipped: #1/A:125@NZ to #1/E:88@NZ
19.31655901034136
Skipped: #1/A:134@NZ to #1/E:186@NZ
10.32094981094279
Skipped: #1/A:1350@NZ to #1/E:12@NZ
15.41824250684883
Skipped: #1/A:1350@NZ to #1/E:15@NZ
9.338040586761231
Skipped: #1/A:1350@NZ to #1/E:41@NZ
7.624163560679952
Skipped: #1/A:581@NZ to #1/H:146@NZ
12.29602557739696
Skipped: #1/A:758@NZ to #1/H:21@NZ
12.47304104859758
Skipped: #1/A:767@NZ to #1/H:21@NZ
11.99653474966832
Skipped: #1/A:707@NZ to #1/R:600@CA
51.05339007352988
Skipped: #1/A:285@NZ to #1/Y:102@NZ
35.7842231996169
Skipped: #1/A:42@NZ to #1/Z:274@NZ
20.61509711352336
Skipped: #1/A:42@NZ to #1/Z:287@NZ
9.183322492431605
Skipped: #1/A:212@NZ to #1/Z:258@NZ
24.4735217326808
Skipped: #1/A:285@NZ to #1/Z:183@NZ
25.63007487308612
Skipped: #1/A:285@NZ to #1/Z:185@NZ
37.36188424049301
Skipped: #1/A:285@NZ to #1/Z:274@NZ
19.15694834779276
Skipped: #1/A:434@NZ to #1/Z:578@NZ
19.50237659876356
Skipped: #1/A:434@NZ to #1/Z:579@NZ
13.09842253861129
Skipped: #1/A:434@NZ to #1/Z:597@NZ
20.43069154483029
Skipped: #1/A:445@NZ to #1/Z:627@NZ
25.89293818785346
Skipped: #1/A:445@NZ to #1/Z:628@NZ
96.26540967034833
Skipped: #1/A:346@NZ to #1/k:364@NZ
10.01633585698884
Skipped: #1/A:1317@NZ to #1/S:252@NZ
8.306821473945377
Skipped: #1/K:47@NZ to #1/C:225@NZ
5.324126031566121
Skipped: #1/K:52@NZ to #1/C:225@NZ
142.1530242977616
Skipped: #1/K:26@NZ to #1/k:105@NZ
19.37483682511933
Skipped: #1/B:1269@NZ to #1/G:81@NZ
11.9781150854381
Skipped: #1/B:221@NZ to #1/R:518@CA
7.97878449389379
Skipped: #1/B:221@NZ to #1/R:520@CA
19.72334134978151
Skipped: #1/B:272@NZ to #1/R:518@CA
23.51574589503807
Skipped: #1/B:277@NZ to #1/R:518@CA
22.36312055595105
Skipped: #1/B:946@NZ to #1/R:486@NZ
26.29433908657908
Skipped: #1/B:947@NZ to #1/R:486@NZ
12.57602902350341
Skipped: #1/B:463@NZ to #1/Z:236@NZ
5.84527518599425
Skipped: #1/B:547@NZ to #1/Z:185@NZ
49.65526906583028
Skipped: #1/B:547@NZ to #1/Z:344@NZ
4.647930507225776
Skipped: #1/B:1269@NZ to #1/Z:479@NZ
113.8631816304112
Skipped: #1/B:623@NZ to #1/M:1454@NZ
124.7484390643827
Skipped: #1/B:337@NZ to #1/k:39@NZ
60.09876708385956
Skipped: #1/B:584@NZ to #1/k:422@NZ
18.02679497303944
Skipped: #1/C:199@NZ to #1/H:20@NZ
10.86797391421234
Skipped: #1/C:155@NZ to #1/R:504@NZ
14.52320467390031
Skipped: #1/C:155@NZ to #1/R:555@CA
12.04059151370893
Skipped: #1/D:94@NZ to #1/G:73@NZ
11.1944473289216
Skipped: #1/D:45@NZ to #1/M:622@NZ
24.64752224869673
Skipped: #1/F:101@NZ to #1/M:1341@NZ
18.9817783413462
Skipped: #1/G:29@NZ to #1/Z:627@NZ
14.53567439095964
Skipped: #1/G:29@NZ to #1/Z:628@NZ
17.45990438118147
Skipped: #1/G:146@NZ to #1/Z:473@NZ
14.06438768663607
Mapping specific XL: #1/R:265@NZ to #1/j:473@NZ
> show #1/R:265#1/j:473 atoms
> style #1/R:265#1/j:473 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:473@NZ
Distance between /R LYS 265 NZ and /j LYS 473 NZ: 14.064Å
> crosslinks #1/R:265@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
32.16296461770898
Mapping specific XL: #1/R:265@NZ to #1/j:777@NZ
> show #1/R:265#1/j:777 atoms
> style #1/R:265#1/j:777 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:777@NZ
Distance between /R LYS 265 NZ and /j LYS 777 NZ: 32.163Å
> crosslinks #1/R:265@NZ #1/j:777@NZ radius 0.2 color 255,255,0,100
32.40224643446808
Mapping specific XL: #1/R:265@NZ to #1/j:781@NZ
> show #1/R:265#1/j:781 atoms
> style #1/R:265#1/j:781 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/j:781@NZ
Distance between /R LYS 265 NZ and /j LYS 781 NZ: 32.402Å
> crosslinks #1/R:265@NZ #1/j:781@NZ radius 0.2 color 255,255,0,100
12.77883414087529
Mapping specific XL: #1/R:277@NZ to #1/j:777@NZ
> show #1/R:277#1/j:777 atoms
> style #1/R:277#1/j:777 stick
Changed 18 atom styles
> distance #1/R:277@NZ #1/j:777@NZ
Distance between /R LYS 277 NZ and /j LYS 777 NZ: 12.779Å
> crosslinks #1/R:277@NZ #1/j:777@NZ radius 0.2 color 255,255,0,100
9.242002705041775
Mapping specific XL: #1/R:278@NZ to #1/j:473@NZ
> show #1/R:278#1/j:473 atoms
> style #1/R:278#1/j:473 stick
Changed 18 atom styles
> distance #1/R:278@NZ #1/j:473@NZ
Distance between /R LYS 278 NZ and /j LYS 473 NZ: 9.242Å
> crosslinks #1/R:278@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
19.05222490944297
Mapping specific XL: #1/R:286@NZ to #1/j:473@NZ
> show #1/R:286#1/j:473 atoms
> style #1/R:286#1/j:473 stick
Changed 18 atom styles
> distance #1/R:286@NZ #1/j:473@NZ
Distance between /R LYS 286 NZ and /j LYS 473 NZ: 19.052Å
> crosslinks #1/R:286@NZ #1/j:473@NZ radius 0.2 color 255,255,0,100
37.48139353065731
Mapping specific XL: #1/R:302@NZ to #1/j:497@NZ
> show #1/R:302#1/j:497 atoms
> style #1/R:302#1/j:497 stick
Changed 18 atom styles
> distance #1/R:302@NZ #1/j:497@NZ
Distance between /R LYS 302 NZ and /j LYS 497 NZ: 37.481Å
> crosslinks #1/R:302@NZ #1/j:497@NZ radius 0.2 color 255,255,0,100
43.93616351025654
Mapping specific XL: #1/R:303@NZ to #1/j:497@NZ
> show #1/R:303#1/j:497 atoms
> style #1/R:303#1/j:497 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:497@NZ
Distance between /R LYS 303 NZ and /j LYS 497 NZ: 43.936Å
> crosslinks #1/R:303@NZ #1/j:497@NZ radius 0.2 color 255,255,0,100
43.00328301420718
Mapping specific XL: #1/R:303@NZ to #1/j:504@NZ
> show #1/R:303#1/j:504 atoms
> style #1/R:303#1/j:504 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:504@NZ
Distance between /R LYS 303 NZ and /j LYS 504 NZ: 43.003Å
> crosslinks #1/R:303@NZ #1/j:504@NZ radius 0.2 color 255,255,0,100
26.04891191585553
Mapping specific XL: #1/R:303@NZ to #1/j:647@NZ
> show #1/R:303#1/j:647 atoms
> style #1/R:303#1/j:647 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:647@NZ
Distance between /R LYS 303 NZ and /j LYS 647 NZ: 26.049Å
> crosslinks #1/R:303@NZ #1/j:647@NZ radius 0.2 color 255,255,0,100
6.28588641322767
Mapping specific XL: #1/R:303@NZ to #1/j:792@NZ
> show #1/R:303#1/j:792 atoms
> style #1/R:303#1/j:792 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/j:792@NZ
Distance between /R LYS 303 NZ and /j LYS 792 NZ: 6.286Å
> crosslinks #1/R:303@NZ #1/j:792@NZ radius 0.2 color 255,255,0,100
89.3050655562158
Mapping specific XL: #1/R:265@NZ to #1/M:838@NZ
> show #1/R:265#1/M:838 atoms
> style #1/R:265#1/M:838 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/M:838@NZ
Distance between /R LYS 265 NZ and /M LYS 838 NZ: 89.305Å
> crosslinks #1/R:265@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
77.40834650733731
Mapping specific XL: #1/R:265@NZ to #1/M:844@NZ
> show #1/R:265#1/M:844 atoms
> style #1/R:265#1/M:844 stick
Changed 18 atom styles
> distance #1/R:265@NZ #1/M:844@NZ
Distance between /R LYS 265 NZ and /M LYS 844 NZ: 77.408Å
> crosslinks #1/R:265@NZ #1/M:844@NZ radius 0.2 color 255,255,0,100
69.56037047054883
Mapping specific XL: #1/R:302@NZ to #1/M:838@NZ
> show #1/R:302#1/M:838 atoms
> style #1/R:302#1/M:838 stick
Changed 18 atom styles
> distance #1/R:302@NZ #1/M:838@NZ
Distance between /R LYS 302 NZ and /M LYS 838 NZ: 69.560Å
> crosslinks #1/R:302@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
58.86815268886906
Mapping specific XL: #1/R:303@NZ to #1/M:838@NZ
> show #1/R:303#1/M:838 atoms
> style #1/R:303#1/M:838 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/M:838@NZ
Distance between /R LYS 303 NZ and /M LYS 838 NZ: 58.868Å
> crosslinks #1/R:303@NZ #1/M:838@NZ radius 0.2 color 255,255,0,100
30.70350356229726
Mapping specific XL: #1/R:303@NZ to #1/M:1135@NZ
> show #1/R:303#1/M:1135 atoms
> style #1/R:303#1/M:1135 stick
Changed 18 atom styles
> distance #1/R:303@NZ #1/M:1135@NZ
Distance between /R LYS 303 NZ and /M LYS 1135 NZ: 30.704Å
> crosslinks #1/R:303@NZ #1/M:1135@NZ radius 0.2 color 255,255,0,100
14.97592204173087
Skipped: #1/O:2028@NZ to #1/M:1100@NZ
31.2226572059458
Skipped: #1/j:696@NZ to #1/Z:344@NZ
35.87485081502083
Skipped: #1/j:661@NZ to #1/M:838@NZ
22.99626765368676
Skipped: #1/j:661@NZ to #1/M:844@NZ
8.080834115362094
Skipped: #1/j:696@NZ to #1/M:777@NZ
14.63421145808684
Skipped: #1/j:696@NZ to #1/M:844@NZ
23.75544766995562
Skipped: #1/j:786@NZ to #1/M:1005@NZ
46.04967928227079
Skipped: #1/j:497@NZ to #1/k:105@NZ
26.06885985232191
Skipped: #1/j:504@NZ to #1/k:105@NZ
20.13935301840653
Skipped: #1/j:507@NZ to #1/k:105@NZ
10.88677679572792
Skipped: #1/j:513@NZ to #1/k:105@NZ
47.69925898795494
Skipped: #1/j:606@NZ to #1/k:396@NZ
11.15022587215166
Skipped: #1/j:626@NZ to #1/k:264@NZ
46.01420339416951
Skipped: #1/Y:102@NZ to #1/Z:344@NZ
13.29000880360883
Skipped: #1/Y:109@NZ to #1/Z:265@NZ
1.433925381601146
Skipped: #1/Y:116@NZ to #1/Z:268@NZ
9.337233209040022
Skipped: #1/Y:116@NZ to #1/Z:274@NZ
14.18636239491997
Skipped: #1/Y:116@NZ to #1/Z:276@NZ
77.89569092703397
Skipped: #1/Y:102@NZ to #1/M:838@NZ
33.68250492466379
Skipped: #1/Y:116@NZ to #1/M:1002@NZ
65.81877884768147
Skipped: #1/Z:183@NZ to #1/M:838@NZ
64.06037122902114
Skipped: #1/Z:183@NZ to #1/M:1002@NZ
55.65474140628093
Skipped: #1/Z:185@NZ to #1/M:843@NZ
27.03334559391419
Skipped: #1/Z:306@NZ to #1/M:1005@NZ
24.56814117917756
Skipped: #1/Z:317@NZ to #1/M:838@NZ
13.61775675359198
Skipped: #1/Z:317@NZ to #1/M:843@NZ
25.10195446573832
Skipped: #1/Z:317@NZ to #1/M:844@NZ
31.78610215172662
Skipped: #1/Z:317@NZ to #1/M:1002@NZ
37.44038817907744
Skipped: #1/Z:344@NZ to #1/M:838@NZ
15.9173482716186
Skipped: #1/Z:344@NZ to #1/M:1002@NZ
8.486640854896576
Skipped: #1/Z:344@NZ to #1/M:1005@NZ
20.48942288108672
Skipped: #1/Z:369@NZ to #1/M:1005@NZ
9.78836007715286
Skipped: #1/Z:579@NZ to #1/M:816@NZ
18.68985807864791
Skipped: #1/Z:601@NZ to #1/M:622@NZ
7.659518196335855
Skipped: #1/Z:601@NZ to #1/M:626@NZ
38.75339083228719
Skipped: #1/Z:601@NZ to #1/M:816@NZ
23.05639672628834
Skipped: #1/Z:601@NZ to #1/M:1319@NZ
23.70647702633185
Skipped: #1/Z:627@NZ to #1/M:626@NZ
> size #1/R:310-353 pseudobondRadius 0.9
Changed 1 pseudobond radii
> close #2
> set bgColor white
> hide atoms
> coulombic #1/j:450-500,642-1000 #1/R:200-310
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/R PRO 506
/R PRO 507
/R ASN 508
/R TYR 509
/R MET 511
/R LYS 512
/R LYS 513
/R THR 514
/R GLN 515
/R LEU 516
/R LEU 517
/R LYS 518
/R GLU 519
/R LYS 520
/R MET 522
/R GLU 524
/R ASP 525
/R LEU 526
/R ASP 528
/R GLN 529
/R ASP 530
/R LYS 531
/R LYS 533
/R GLN 534
/R ILE 535
/R GLN 536
/R ASP 537
/R GLN 538
/R LEU 539
/R ASN 540
/R GLU 541
/R LEU 542
/R GLU 543
/R GLU 544
/R ARG 545
/R GLU 547
/R LEU 549
/R ASP 550
/R ARG 551
/R GLN 552
/R ARG 553
/R THR 554
/R LYS 555
/R ASN 556
/R MET 591
/R ASP 592
/R THR 595
/R GLN 598
/R CYS 599
/R LYS 600
/j GLU 930
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor #ffffff00
> lighting soft
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.6.21
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,2
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.7.4 (20G1120)
Kernel Version: Darwin 20.6.0
Time since boot: 70 days 1:42
Graphics/Displays:
AMD Radeon Pro 5700:
Chipset Model: AMD Radeon Pro 5700
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x731b
Revision ID: 0x0040
ROM Revision: 113-D1820Q-231
VBIOS Version: 113-D182A2XG-013
Option ROM Version: 113-D182A2XG-013
EFI Driver Version: 01.01.231
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2418D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: MY3ND91S1Q1T
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C Digital AV Adapter
Automatically Adjust Brightness: Yes
Adapter Firmware Version: 2.35
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
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: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.2.2
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
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: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
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: 1.1.2
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: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openpyxl: 3.1.3
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
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: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.13.2
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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