id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20180 Crash in swap_buffers exposing status line during Mac wakeup chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x0000000207ab7100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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""6246d6a916a70b047e454124"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000010 }, { ""rolloutId"" : ""66d35d7fe4d6bf7664f40ddf"", ""factorPackIds"" : [ ""68c1a34bd359577bbe8f2182"" ], ""deploymentId"" : 240000069 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > /Applications/ChimeraX.app/Contents/MacOS/ChimeraX Unknown command: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX > open > /Users/lucychappell/Downloads/fold_citrus_clementina_acd15/fold_citrus_clementina_acd15_model_0.cif > format mmcif Chain information for fold_citrus_clementina_acd15_model_0.cif #1 --- Chain | Description A | . Computing secondary structure > open > /Users/lucychappell/Downloads/fold_citrus_clementina_acd21/fold_citrus_clementina_acd21_model_0.cif > format mmcif Chain information for fold_citrus_clementina_acd21_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > open > /Users/lucychappell/Downloads/fold_citrus_clementina_mbd6/fold_citrus_clementina_mbd6_model_1.cif Chain information for fold_citrus_clementina_mbd6_model_1.cif #3 --- Chain | Description A | . Computing secondary structure > select add #1 1089 atoms, 1112 bonds, 141 residues, 1 model selected > select add #2 4470 atoms, 4492 bonds, 756 residues, 2 models selected > select add #3 6384 atoms, 6450 bonds, 1004 residues, 3 models selected > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A > select subtract #3 4470 atoms, 4492 bonds, 756 residues, 2 models selected > select subtract #2 1089 atoms, 1112 bonds, 141 residues, 1 model selected > select subtract #1 Nothing selected > mlp Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > show surfaces > undo > select #2/A:61 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:61-265 1150 atoms, 1149 bonds, 205 residues, 1 model selected > select #2/A:265-266 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:228-265 216 atoms, 215 bonds, 38 residues, 1 model selected > select #1/A:120 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:80-120 325 atoms, 336 bonds, 41 residues, 1 model selected > select add #1 1089 atoms, 1112 bonds, 141 residues, 2 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 To also show corresponding color key, enter the above coulombic command and add key true > select add #2 4470 atoms, 4492 bonds, 756 residues, 3 models selected > select subtract #1 3381 atoms, 3380 bonds, 615 residues, 3 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > select subtract #2 1 model selected > select add #3 1914 atoms, 1958 bonds, 248 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > select add #1 3003 atoms, 3070 bonds, 389 residues, 3 models selected > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true Desktop color scheme is dark Desktop color scheme is light Desktop color scheme is dark Desktop color scheme is light > select subtract #3 1089 atoms, 1112 bonds, 141 residues, 3 models selected > select subtract #1 1 model selected > select add #2 3381 atoms, 3380 bonds, 615 residues, 1 model selected > coulombic sel Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 To also show corresponding color key, enter the above coulombic command and add key true > select subtract #2 1 model selected > select add #2 3381 atoms, 3380 bonds, 615 residues, 1 model selected > select subtract #2 1 model selected > hide #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > show #!3 models > mlp #!1,3 Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!1,3 Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!1,3 Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!1,3 Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!1,3 Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!1,3 Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!1,3 Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!1,3 Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1,3 surfaces > show #!1,3 surfaces > hide #!1,3 surfaces > show #!1,3 surfaces > hide #!1,3 surfaces > show #!2 models > hide surfaces > select #1/A:17-20,34-38,42-48,60-63,68-75,99-106,116-120,125-131 377 atoms, 378 bonds, 48 residues, 1 model selected > select #3/A:121-160 333 atoms, 339 bonds, 40 residues, 1 model selected > select #1/A:18 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:18-19 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:17-20,34-38,42-48,60-63,68-75,99-106,116-120,125-131 377 atoms, 378 bonds, 48 residues, 1 model selected > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > select #2/A:169 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:169 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:170 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:170 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:170 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:169-170 12 atoms, 11 bonds, 2 residues, 1 model selected > select #2/A:169 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:168-169 12 atoms, 11 bonds, 2 residues, 1 model selected > select #2/A:168-169 12 atoms, 11 bonds, 2 residues, 1 model selected > select #2/A:168-170 19 atoms, 18 bonds, 3 residues, 1 model selected > select #2/A:168-170,189-191,353-355,376-378,480-482,498-502,518-521 148 atoms, 141 bonds, 24 residues, 1 model selected > mlp sel Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > select #3/A:97-101,111-117,127-133,138-140,203-208,213-217 310 atoms, 317 bonds, 33 residues, 1 model selected > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 To also show corresponding color key, enter the above mlp command and add key true > select add #3 1914 atoms, 1958 bonds, 248 residues, 2 models selected > select subtract #3 1 model selected > select add #3 1914 atoms, 1958 bonds, 248 residues, 1 model selected > select add #2 5295 atoms, 5338 bonds, 863 residues, 3 models selected > select add #1 6384 atoms, 6450 bonds, 1004 residues, 5 models selected > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > view orient > hide #!3 models > hide #!1 models > show #!1 models > hide #!2 models > select subtract #2 3003 atoms, 3070 bonds, 389 residues, 5 models selected > select subtract #3 1089 atoms, 1112 bonds, 141 residues, 3 models selected > select subtract #1 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #1 1089 atoms, 1112 bonds, 141 residues, 2 models selected > hide sel surfaces > select subtract #1 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > mlp sel Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > select #1/A:21-23,113-115 46 atoms, 45 bonds, 6 residues, 1 model selected > mlp sel Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 To also show corresponding color key, enter the above mlp command and add key true > select #1/A:114 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:114-115 19 atoms, 18 bonds, 2 residues, 1 model selected > select #1/A:112 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:112-113 15 atoms, 15 bonds, 2 residues, 1 model selected > hide sel surfaces > select #1/A:21-23,113-115 46 atoms, 45 bonds, 6 residues, 1 model selected > select #1/A:21 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:21-23 20 atoms, 19 bonds, 3 residues, 1 model selected > hide sel surfaces > select #1/A:113 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:113-115 26 atoms, 26 bonds, 3 residues, 1 model selected > select #1/A:113-114 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/A:113-114 18 atoms, 18 bonds, 2 residues, 1 model selected > hide sel surfaces > select #1/A:21-23,113-115 46 atoms, 45 bonds, 6 residues, 1 model selected > select #1/A:21 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:21-23 20 atoms, 19 bonds, 3 residues, 1 model selected > show sel surfaces > hide sel surfaces > select #1/A:16-17 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/A:16-20 34 atoms, 33 bonds, 5 residues, 1 model selected > show sel surfaces > select #1/A:18 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:18-19 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/A:17 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:18 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:18-20 20 atoms, 19 bonds, 3 residues, 1 model selected > hide sel surfaces > select #1/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:1-14 117 atoms, 120 bonds, 14 residues, 1 model selected > show sel surfaces > select add #1 1089 atoms, 1112 bonds, 141 residues, 2 models selected > select subtract #1 1 model selected > select add #2 3381 atoms, 3380 bonds, 615 residues, 1 model selected > select subtract #2 1 model selected > select add #1 1089 atoms, 1112 bonds, 141 residues, 1 model selected > show sel surfaces > select add #3 3003 atoms, 3070 bonds, 389 residues, 3 models selected > show sel & #!1 surfaces > show #!3 models > show #!2 models > select add #2 6384 atoms, 6450 bonds, 1004 residues, 5 models selected > coulombic sel Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 models > hide #!3 models > select subtract #1 5295 atoms, 5338 bonds, 863 residues, 5 models selected > show #!2 models > show #!3 models > select subtract #2 1914 atoms, 1958 bonds, 248 residues, 3 models selected > select subtract #3 1 model selected > view orient > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > coulombic #!1,3 Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > coulombic Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for fold_citrus_clementina_acd15_model_0.cif_A SES surface #1.1: minimum, -10.59, mean 0.88, maximum 12.96 Coulombic values for fold_citrus_clementina_acd21_model_0.cif_A SES surface #2.1: minimum, -23.77, mean -0.84, maximum 8.58 Coulombic values for fold_citrus_clementina_mbd6_model_1.cif_A SES surface #3.1: minimum, -13.95, mean -0.41, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true > hide #!2 models > hide #!1 models > show #!2 models > hide #!3 models > show #!1 models > show #!3 models > mlp Map values for surface ""fold_citrus_clementina_mbd6_model_1.cif_A SES surface"": minimum -26.98, mean -6.08, maximum 23.48 Map values for surface ""fold_citrus_clementina_acd15_model_0.cif_A SES surface"": minimum -26.59, mean -4.581, maximum 20.17 Map values for surface ""fold_citrus_clementina_acd21_model_0.cif_A SES surface"": minimum -28.52, mean -8.641, maximum 13.57 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1,3 surfaces ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 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How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2H3LL/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 Performance and 4 Efficiency) Memory: 24 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (25D2128) Kernel Version: Darwin 25.3.0 Time since boot: 28 days, 12 hours, 24 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect assigned normal Window Toolkit all ChimeraX