id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16360 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.7-arm64-arm-64bit ChimeraX Version: 1.8rc202405140121 (2024-05-14 01:21:02 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001fa46e100 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 264 in atom_residues File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 206 in molecule_from_atoms File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in split_molecule File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 63 in split File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3209 in run File ""/Applications/ChimeraX.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 285 in event_loop File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1006 in init File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1169 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 59) 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""factorPackIds"" : { }, ""deploymentId"" : 240000083 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8rc202405140121 (2024-05-14) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/adminndavey/Downloads/FAT_DOMAIN (1).pdb"" 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 19 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for FAT_DOMAIN (1).pdb --- Chain | Description 1.1/0 | 1OW6_A_D 1.2/1 | 3RF3_A_C 1.3/2 | 1OW8_C_F 1.4/3 | 1OW8_A_D 1.5/4 | 3B71_B_E 1.6/5 | 3U3F_C_G 1.7/6 | 3S90_B_D 1.8/7 | 4XEK_A_C 1.9/8 | 1OW6_C_F 1.10/9 | 3TJ6_A_B 1.1/D 1.4/D 1.11/D 1.26/D | No description available 1.2/D | No description available 1.3/D | No description available 1.5/D 1.9/D 1.27/D | No description available 1.6/D 1.28/D | No description available 1.7/D | No description available 1.8/D | No description available 1.10/D | No description available 1.12/D | No description available 1.13/D | No description available 1.14/D | No description available 1.15/D | No description available 1.16/D | No description available 1.17/D | No description available 1.18/D | No description available 1.19/D 1.20/D | No description available 1.21/D | No description available 1.22/D | No description available 1.23/D | No description available 1.24/D | No description available 1.25/D | No description available 1.11/a | 3B71_A_D 1.12/b | 4XEF_D_F 1.13/c | 3U3F_A_I 1.14/d | 1XWJ_A_B 1.15/e | 4XEF_A_C 1.16/f | 3GM1_A_F 1.17/g | 3RF3_B_D 1.18/h | 4XEV_A_C 1.19/i | 5W93_A_D 1.20/j | 5W93_B_E 1.21/k | 3U3F_B_J 1.22/l | 4R32_A_C 1.23/m | 6PW8_A_B 1.24/n | 4XEV_D_F 1.25/o | 3GM1_B_D 1.26/p | 1OW7_A_D 1.27/q | 3B71_C_F 1.28/r | 3U3F_D_H > split Split FAT_DOMAIN (1).pdb (#1.1) into 2 models Split FAT_DOMAIN (1).pdb (#1.2) into 2 models Split FAT_DOMAIN (1).pdb (#1.3) into 2 models Split FAT_DOMAIN (1).pdb (#1.4) into 2 models Split FAT_DOMAIN (1).pdb (#1.5) into 2 models Split FAT_DOMAIN (1).pdb (#1.6) into 2 models Split FAT_DOMAIN (1).pdb (#1.7) into 2 models Split FAT_DOMAIN (1).pdb (#1.8) into 2 models Split FAT_DOMAIN (1).pdb (#1.9) into 2 models Split FAT_DOMAIN (1).pdb (#1.10) into 2 models Split FAT_DOMAIN (1).pdb (#1.11) into 2 models Split FAT_DOMAIN (1).pdb (#1.12) into 2 models Split FAT_DOMAIN (1).pdb (#1.13) into 2 models Split FAT_DOMAIN (1).pdb (#1.14) into 2 models Split FAT_DOMAIN (1).pdb (#1.15) into 2 models Split FAT_DOMAIN (1).pdb (#1.16) into 2 models Split FAT_DOMAIN (1).pdb (#1.17) into 2 models Split FAT_DOMAIN (1).pdb (#1.18) into 2 models Split FAT_DOMAIN (1).pdb (#1.19) into 2 models Split FAT_DOMAIN (1).pdb (#1.20) into 2 models Split FAT_DOMAIN (1).pdb (#1.21) into 2 models Split FAT_DOMAIN (1).pdb (#1.22) into 2 models Split FAT_DOMAIN (1).pdb (#1.23) into 2 models Split FAT_DOMAIN (1).pdb (#1.24) into 2 models Split FAT_DOMAIN (1).pdb (#1.25) into 2 models Split FAT_DOMAIN (1).pdb (#1.26) into 2 models Split FAT_DOMAIN (1).pdb (#1.27) into 2 models Split FAT_DOMAIN (1).pdb (#1.28) into 2 models Chain information for FAT_DOMAIN (1).pdb 0 #1.1.1 --- Chain | Description 0 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.1.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 1 #1.2.1 --- Chain | Description 1 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.2.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 2 #1.3.1 --- Chain | Description 2 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.3.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 3 #1.4.1 --- Chain | Description 3 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.4.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 4 #1.5.1 --- Chain | Description 4 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.5.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 5 #1.6.1 --- Chain | Description 5 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.6.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 6 #1.7.1 --- Chain | Description 6 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.7.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 7 #1.8.1 --- Chain | Description 7 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.8.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 8 #1.9.1 --- Chain | Description 8 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.9.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 9 #1.10.1 --- Chain | Description 9 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.10.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb D #1.11.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb a #1.11.2 --- Chain | Description a | No description available Chain information for FAT_DOMAIN (1).pdb D #1.12.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb b #1.12.2 --- Chain | Description b | No description available Chain information for FAT_DOMAIN (1).pdb D #1.13.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb c #1.13.2 --- Chain | Description c | No description available Chain information for FAT_DOMAIN (1).pdb D #1.14.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb d #1.14.2 --- Chain | Description d | No description available Chain information for FAT_DOMAIN (1).pdb D #1.15.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb e #1.15.2 --- Chain | Description e | No description available Chain information for FAT_DOMAIN (1).pdb D #1.16.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb f #1.16.2 --- Chain | Description f | No description available Chain information for FAT_DOMAIN (1).pdb D #1.17.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb g #1.17.2 --- Chain | Description g | No description available Chain information for FAT_DOMAIN (1).pdb D #1.18.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb h #1.18.2 --- Chain | Description h | No description available Chain information for FAT_DOMAIN (1).pdb D #1.19.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb i #1.19.2 --- Chain | Description i | No description available Chain information for FAT_DOMAIN (1).pdb D #1.20.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb j #1.20.2 --- Chain | Description j | No description available Chain information for FAT_DOMAIN (1).pdb D #1.21.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb k #1.21.2 --- Chain | Description k | No description available Chain information for FAT_DOMAIN (1).pdb D #1.22.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb l #1.22.2 --- Chain | Description l | No description available Chain information for FAT_DOMAIN (1).pdb D #1.23.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb m #1.23.2 --- Chain | Description m | No description available Chain information for FAT_DOMAIN (1).pdb D #1.24.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb n #1.24.2 --- Chain | Description n | No description available Chain information for FAT_DOMAIN (1).pdb D #1.25.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb o #1.25.2 --- Chain | Description o | No description available Chain information for FAT_DOMAIN (1).pdb D #1.26.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb p #1.26.2 --- Chain | Description p | No description available Chain information for FAT_DOMAIN (1).pdb D #1.27.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb q #1.27.2 --- Chain | Description q | No description available Chain information for FAT_DOMAIN (1).pdb D #1.28.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb r #1.28.2 --- Chain | Description r | No description available > close session > open ""/Users/adminndavey/Downloads/FAT_DOMAIN (1).pdb"" 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 19 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for FAT_DOMAIN (1).pdb --- Chain | Description 1.1/0 | 1OW6_A_D 1.2/1 | 3RF3_A_C 1.3/2 | 1OW8_C_F 1.4/3 | 1OW8_A_D 1.5/4 | 3B71_B_E 1.6/5 | 3U3F_C_G 1.7/6 | 3S90_B_D 1.8/7 | 4XEK_A_C 1.9/8 | 1OW6_C_F 1.10/9 | 3TJ6_A_B 1.1/D 1.4/D 1.11/D 1.26/D | No description available 1.2/D | No description available 1.3/D | No description available 1.5/D 1.9/D 1.27/D | No description available 1.6/D 1.28/D | No description available 1.7/D | No description available 1.8/D | No description available 1.10/D | No description available 1.12/D | No description available 1.13/D | No description available 1.14/D | No description available 1.15/D | No description available 1.16/D | No description available 1.17/D | No description available 1.18/D | No description available 1.19/D 1.20/D | No description available 1.21/D | No description available 1.22/D | No description available 1.23/D | No description available 1.24/D | No description available 1.25/D | No description available 1.11/a | 3B71_A_D 1.12/b | 4XEF_D_F 1.13/c | 3U3F_A_I 1.14/d | 1XWJ_A_B 1.15/e | 4XEF_A_C 1.16/f | 3GM1_A_F 1.17/g | 3RF3_B_D 1.18/h | 4XEV_A_C 1.19/i | 5W93_A_D 1.20/j | 5W93_B_E 1.21/k | 3U3F_B_J 1.22/l | 4R32_A_C 1.23/m | 6PW8_A_B 1.24/n | 4XEV_D_F 1.25/o | 3GM1_B_D 1.26/p | 1OW7_A_D 1.27/q | 3B71_C_F 1.28/r | 3U3F_D_H > hide #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1-9,11-17,19-23,25-28#!1#!1.10,18,24 target m > show #!1.10 models > hide #!1.10 models > show #1.9 models > hide #1.9 models > show #1.9 models > show #1.8 models > show #1.7 models > show #!1.10 models > show #1.11 models > show #1.13 models > hide #1.13 models > show #1.14 models > show #1.16 models > show #1.12 models > show #1.13 models > show #1.15 models > color #1.7-9,11-16#!1.10 byhetero > color #1.7-9,11-16#!1.10 bychain > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #1.11 models > select add #1.13 1049 atoms, 1052 bonds, 142 residues, 1 model selected > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > select add #1.15 2165 atoms, 2167 bonds, 297 residues, 2 models selected > hide #1.14 models > show #1.14 models > hide #1.14 models > hide #1.16 models > hide #1.7 models > show #1.7 models > hide #1.7 models > hide #1.8 models > show #1.8 models > hide #1.8 models > hide #1.9 models > hide #!1.10 models > show #!1.10 models > hide #1.12 models > rename #1.10 3TJ6 > rename #1.13 3U3F > rename #1.15 4XEF > select subtract #1.13 1116 atoms, 1115 bonds, 155 residues, 1 model selected > select subtract #1.15 Nothing selected > select add #1.10 2291 atoms, 2175 bonds, 1 pseudobond, 417 residues, 2 models selected > select subtract #1.10 Nothing selected > select add #1.10 2291 atoms, 2175 bonds, 1 pseudobond, 417 residues, 2 models selected > select subtract #1.10 Nothing selected > sequence chain #1.10/D Alignment identifier is 1.10/D > select #1.10/D:217-257 327 atoms, 329 bonds, 41 residues, 1 model selected > select #1.10/D:135-257 977 atoms, 986 bonds, 123 residues, 1 model selected > cartoon hide sel > save ""/Users/adminndavey/Desktop/Structures/FAT domain.cxs"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #1.11-12 > close #1.1-9 > close #1.14 > close #1.16-17,19-23,25-28#1.18,24 > save ""/Users/adminndavey/Desktop/Structures/FAT domain.cxs"" > split ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8rc202405140121 (2024-05-14) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/adminndavey/Desktop/Structures/FAT domain.cxs"" Log from Fri Nov 22 18:14:17 2024UCSF ChimeraX version: 1.8rc202405140121 (2024-05-14) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/adminndavey/Downloads/FAT_DOMAIN (1).pdb"" 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 19 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for FAT_DOMAIN (1).pdb --- Chain | Description 1.1/0 | 1OW6_A_D 1.2/1 | 3RF3_A_C 1.3/2 | 1OW8_C_F 1.4/3 | 1OW8_A_D 1.5/4 | 3B71_B_E 1.6/5 | 3U3F_C_G 1.7/6 | 3S90_B_D 1.8/7 | 4XEK_A_C 1.9/8 | 1OW6_C_F 1.10/9 | 3TJ6_A_B 1.1/D 1.4/D 1.11/D 1.26/D | No description available 1.2/D | No description available 1.3/D | No description available 1.5/D 1.9/D 1.27/D | No description available 1.6/D 1.28/D | No description available 1.7/D | No description available 1.8/D | No description available 1.10/D | No description available 1.12/D | No description available 1.13/D | No description available 1.14/D | No description available 1.15/D | No description available 1.16/D | No description available 1.17/D | No description available 1.18/D | No description available 1.19/D 1.20/D | No description available 1.21/D | No description available 1.22/D | No description available 1.23/D | No description available 1.24/D | No description available 1.25/D | No description available 1.11/a | 3B71_A_D 1.12/b | 4XEF_D_F 1.13/c | 3U3F_A_I 1.14/d | 1XWJ_A_B 1.15/e | 4XEF_A_C 1.16/f | 3GM1_A_F 1.17/g | 3RF3_B_D 1.18/h | 4XEV_A_C 1.19/i | 5W93_A_D 1.20/j | 5W93_B_E 1.21/k | 3U3F_B_J 1.22/l | 4R32_A_C 1.23/m | 6PW8_A_B 1.24/n | 4XEV_D_F 1.25/o | 3GM1_B_D 1.26/p | 1OW7_A_D 1.27/q | 3B71_C_F 1.28/r | 3U3F_D_H > split Split FAT_DOMAIN (1).pdb (#1.1) into 2 models Split FAT_DOMAIN (1).pdb (#1.2) into 2 models Split FAT_DOMAIN (1).pdb (#1.3) into 2 models Split FAT_DOMAIN (1).pdb (#1.4) into 2 models Split FAT_DOMAIN (1).pdb (#1.5) into 2 models Split FAT_DOMAIN (1).pdb (#1.6) into 2 models Split FAT_DOMAIN (1).pdb (#1.7) into 2 models Split FAT_DOMAIN (1).pdb (#1.8) into 2 models Split FAT_DOMAIN (1).pdb (#1.9) into 2 models Split FAT_DOMAIN (1).pdb (#1.10) into 2 models Split FAT_DOMAIN (1).pdb (#1.11) into 2 models Split FAT_DOMAIN (1).pdb (#1.12) into 2 models Split FAT_DOMAIN (1).pdb (#1.13) into 2 models Split FAT_DOMAIN (1).pdb (#1.14) into 2 models Split FAT_DOMAIN (1).pdb (#1.15) into 2 models Split FAT_DOMAIN (1).pdb (#1.16) into 2 models Split FAT_DOMAIN (1).pdb (#1.17) into 2 models Split FAT_DOMAIN (1).pdb (#1.18) into 2 models Split FAT_DOMAIN (1).pdb (#1.19) into 2 models Split FAT_DOMAIN (1).pdb (#1.20) into 2 models Split FAT_DOMAIN (1).pdb (#1.21) into 2 models Split FAT_DOMAIN (1).pdb (#1.22) into 2 models Split FAT_DOMAIN (1).pdb (#1.23) into 2 models Split FAT_DOMAIN (1).pdb (#1.24) into 2 models Split FAT_DOMAIN (1).pdb (#1.25) into 2 models Split FAT_DOMAIN (1).pdb (#1.26) into 2 models Split FAT_DOMAIN (1).pdb (#1.27) into 2 models Split FAT_DOMAIN (1).pdb (#1.28) into 2 models Chain information for FAT_DOMAIN (1).pdb 0 #1.1.1 --- Chain | Description 0 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.1.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 1 #1.2.1 --- Chain | Description 1 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.2.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 2 #1.3.1 --- Chain | Description 2 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.3.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 3 #1.4.1 --- Chain | Description 3 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.4.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 4 #1.5.1 --- Chain | Description 4 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.5.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 5 #1.6.1 --- Chain | Description 5 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.6.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 6 #1.7.1 --- Chain | Description 6 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.7.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 7 #1.8.1 --- Chain | Description 7 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.8.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 8 #1.9.1 --- Chain | Description 8 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.9.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb 9 #1.10.1 --- Chain | Description 9 | No description available Chain information for FAT_DOMAIN (1).pdb D #1.10.2 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb D #1.11.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb a #1.11.2 --- Chain | Description a | No description available Chain information for FAT_DOMAIN (1).pdb D #1.12.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb b #1.12.2 --- Chain | Description b | No description available Chain information for FAT_DOMAIN (1).pdb D #1.13.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb c #1.13.2 --- Chain | Description c | No description available Chain information for FAT_DOMAIN (1).pdb D #1.14.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb d #1.14.2 --- Chain | Description d | No description available Chain information for FAT_DOMAIN (1).pdb D #1.15.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb e #1.15.2 --- Chain | Description e | No description available Chain information for FAT_DOMAIN (1).pdb D #1.16.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb f #1.16.2 --- Chain | Description f | No description available Chain information for FAT_DOMAIN (1).pdb D #1.17.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb g #1.17.2 --- Chain | Description g | No description available Chain information for FAT_DOMAIN (1).pdb D #1.18.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb h #1.18.2 --- Chain | Description h | No description available Chain information for FAT_DOMAIN (1).pdb D #1.19.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb i #1.19.2 --- Chain | Description i | No description available Chain information for FAT_DOMAIN (1).pdb D #1.20.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb j #1.20.2 --- Chain | Description j | No description available Chain information for FAT_DOMAIN (1).pdb D #1.21.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb k #1.21.2 --- Chain | Description k | No description available Chain information for FAT_DOMAIN (1).pdb D #1.22.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb l #1.22.2 --- Chain | Description l | No description available Chain information for FAT_DOMAIN (1).pdb D #1.23.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb m #1.23.2 --- Chain | Description m | No description available Chain information for FAT_DOMAIN (1).pdb D #1.24.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb n #1.24.2 --- Chain | Description n | No description available Chain information for FAT_DOMAIN (1).pdb D #1.25.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb o #1.25.2 --- Chain | Description o | No description available Chain information for FAT_DOMAIN (1).pdb D #1.26.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb p #1.26.2 --- Chain | Description p | No description available Chain information for FAT_DOMAIN (1).pdb D #1.27.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb q #1.27.2 --- Chain | Description q | No description available Chain information for FAT_DOMAIN (1).pdb D #1.28.1 --- Chain | Description D | No description available Chain information for FAT_DOMAIN (1).pdb r #1.28.2 --- Chain | Description r | No description available > close session > open ""/Users/adminndavey/Downloads/FAT_DOMAIN (1).pdb"" 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 19 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for FAT_DOMAIN (1).pdb --- Chain | Description 1.1/0 | 1OW6_A_D 1.2/1 | 3RF3_A_C 1.3/2 | 1OW8_C_F 1.4/3 | 1OW8_A_D 1.5/4 | 3B71_B_E 1.6/5 | 3U3F_C_G 1.7/6 | 3S90_B_D 1.8/7 | 4XEK_A_C 1.9/8 | 1OW6_C_F 1.10/9 | 3TJ6_A_B 1.1/D 1.4/D 1.11/D 1.26/D | No description available 1.2/D | No description available 1.3/D | No description available 1.5/D 1.9/D 1.27/D | No description available 1.6/D 1.28/D | No description available 1.7/D | No description available 1.8/D | No description available 1.10/D | No description available 1.12/D | No description available 1.13/D | No description available 1.14/D | No description available 1.15/D | No description available 1.16/D | No description available 1.17/D | No description available 1.18/D | No description available 1.19/D 1.20/D | No description available 1.21/D | No description available 1.22/D | No description available 1.23/D | No description available 1.24/D | No description available 1.25/D | No description available 1.11/a | 3B71_A_D 1.12/b | 4XEF_D_F 1.13/c | 3U3F_A_I 1.14/d | 1XWJ_A_B 1.15/e | 4XEF_A_C 1.16/f | 3GM1_A_F 1.17/g | 3RF3_B_D 1.18/h | 4XEV_A_C 1.19/i | 5W93_A_D 1.20/j | 5W93_B_E 1.21/k | 3U3F_B_J 1.22/l | 4R32_A_C 1.23/m | 6PW8_A_B 1.24/n | 4XEV_D_F 1.25/o | 3GM1_B_D 1.26/p | 1OW7_A_D 1.27/q | 3B71_C_F 1.28/r | 3U3F_D_H > hide #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1-9,11-17,19-23,25-28#!1#!1.10,18,24 target m > show #!1.10 models > hide #!1.10 models > show #1.9 models > hide #1.9 models > show #1.9 models > show #1.8 models > show #1.7 models > show #!1.10 models > show #1.11 models > show #1.13 models > hide #1.13 models > show #1.14 models > show #1.16 models > show #1.12 models > show #1.13 models > show #1.15 models > color #1.7-9,11-16#!1.10 byhetero > color #1.7-9,11-16#!1.10 bychain > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #1.11 models > select add #1.13 1049 atoms, 1052 bonds, 142 residues, 1 model selected > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > hide #1.15 models > show #1.15 models > select add #1.15 2165 atoms, 2167 bonds, 297 residues, 2 models selected > hide #1.14 models > show #1.14 models > hide #1.14 models > hide #1.16 models > hide #1.7 models > show #1.7 models > hide #1.7 models > hide #1.8 models > show #1.8 models > hide #1.8 models > hide #1.9 models > hide #!1.10 models > show #!1.10 models > hide #1.12 models > rename #1.10 3TJ6 > rename #1.13 3U3F > rename #1.15 4XEF > select subtract #1.13 1116 atoms, 1115 bonds, 155 residues, 1 model selected > select subtract #1.15 Nothing selected > select add #1.10 2291 atoms, 2175 bonds, 1 pseudobond, 417 residues, 2 models selected > select subtract #1.10 Nothing selected > select add #1.10 2291 atoms, 2175 bonds, 1 pseudobond, 417 residues, 2 models selected > select subtract #1.10 Nothing selected > sequence chain #1.10/D Alignment identifier is 1.10/D > select #1.10/D:217-257 327 atoms, 329 bonds, 41 residues, 1 model selected > select #1.10/D:135-257 977 atoms, 986 bonds, 123 residues, 1 model selected > cartoon hide sel > save ""/Users/adminndavey/Desktop/Structures/FAT domain.cxs"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #1.11-12 > close #1.1-9 > close #1.14 > close #1.16-17,19-23,25-28#1.18,24 > save ""/Users/adminndavey/Desktop/Structures/FAT domain.cxs"" ——— End of log from Fri Nov 22 18:14:17 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17K001T0B/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.1.1 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.7 (22H123) Kernel Version: Darwin 22.6.0 Time since boot: 1 day, 5 hours, 25 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 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: Yes Connection Type: Internal DELL P2418D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.3 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202405140121 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.1 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 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-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 1.3.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 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 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: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.1 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate all ChimeraX