id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15023 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-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 0x00000002d8ecb000 (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 0x00000001e08e5000 (most recent call first): Garbage-collecting File """", line 729 in _compile_bytecode File """", line 1069 in get_code File """", line 936 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File """", line 241 in _call_with_frames_removed File """", line 1234 in _handle_fromlist File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/special/__init__.py"", line 780 in File """", line 241 in _call_with_frames_removed File """", line 940 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/interpolate/_interpolate.py"", line 9 in File """", line 241 in _call_with_frames_removed File """", line 940 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/interpolate/__init__.py"", line 167 in File """", line 241 in _call_with_frames_removed File """", line 940 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File """", line 1206 in _gcd_import File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py"", line 126 in import_module File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/__init__.py"", line 189 in __getattr__ File """", line 1231 in _handle_fromlist File ""/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/manipulations/register_shift.py"", line 15 in File """", line 241 in _call_with_frames_removed File """", line 940 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File ""/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/manipulations/__init__.py"", line 12 in File """", line 241 in _call_with_frames_removed File """", line 940 in exec_module File """", line 690 in _load_unlocked File """", line 1149 in _find_and_load_unlocked File """", line 1178 in _find_and_load File """", line 241 in _call_with_frames_removed File """", line 1128 in _find_and_load_unlocked File """", line 1178 in _find_and_load File ""/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/cmd/cmd.py"", line 478 in register_isolde File ""/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/__init__.py"", line 170 in register_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1286 in register_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 330 in _register_cmd File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 320 in cb 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 2158 in call 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 2227 in lazy_register 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 2579 in _find_command_name 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 2843 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/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/toolbar.py"", line 19 in toolbar_command File ""/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/__init__.py"", line 183 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback 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 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======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1504K 71 \nColorSync 608K 30 \nCoreAnimation 3760K 233 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5520K 52 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 8.4G 148 \nMALLOC guard page 384K 24 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 182.6M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 400.1M 240 \nVM_ALLOCATE (reserved) 352.0M 4 reserved VM address space (unallocated)\n__AUTH 3030K 432 \n__AUTH_CONST 34.3M 662 \n__CTF 824 1 \n__DATA 27.1M 859 \n__DATA_CONST 44.8M 867 \n__DATA_DIRTY 2027K 238 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 931.8M 201 \n__OBJC_RO 71.1M 1 \n__OBJC_RW 2168K 1 \n__TEXT 1.0G 885 \ndyld private memory 736K 8 \nmapped file 912.9M 93 \nshared memory 3328K 34 \n=========== ======= ======= \nTOTAL 12.4G 5202 \nTOTAL, minus reserved VM space 12.1G 5202 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""582e2a7c64e7ba7536134a4882ffc72813ae2ede"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { }, ""deploymentId"" : 240000019 }, { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000535 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 > open /Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_alignedcoil_04162024.cxs > format session Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > lighting flat > close #3 > color #8 #a2ff35 > lighting full > open /Users/ethancrofut/Downloads/EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb Summary of feedback from opening /Users/ethancrofut/Downloads/EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 380 UNP A0A7S3WEM8 A0A7S3WEM8_EMIHU 1 380 EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for hypothetical protein (A0A7S3WEM8) [more info...] Chain information for EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb #3 --- Chain | Description A | hypothetical protein > select add #3 2961 atoms, 2997 bonds, 380 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,392.59,0,1,0,220.83,0,0,1,72.867 > view matrix models #3,1,0,0,415.44,0,1,0,204.22,0,0,1,343.2 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.85059,-0.085848,0.51877,411.5,0.0030118,0.98736,0.15845,202.83,-0.52582,-0.13322,0.8401,346.58 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.85059,-0.085848,0.51877,400.15,0.0030118,0.98736,0.15845,202.02,-0.52582,-0.13322,0.8401,318.83 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.20162,-0.96988,-0.13665,412.42,0.93223,0.14721,0.33058,202.89,-0.3005,-0.19404,0.93383,317.78 > view matrix models > #3,0.18607,-0.97739,-0.10044,412.17,0.92943,0.14194,0.3406,202.83,-0.31865,-0.15673,0.93483,317.61 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.18607,-0.97739,-0.10044,391.7,0.92943,0.14194,0.3406,275.88,-0.31865,-0.15673,0.93483,352.4 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.24072,-0.95371,-0.18025,392.18,0.80442,0.09212,0.58688,274.18,-0.5431,-0.28628,0.78936,354.94 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.24072,-0.95371,-0.18025,386.85,0.80442,0.09212,0.58688,276.47,-0.5431,-0.28628,0.78936,354.57 > view matrix models > #3,0.24072,-0.95371,-0.18025,392.84,0.80442,0.09212,0.58688,270.61,-0.5431,-0.28628,0.78936,318.86 > view matrix models > #3,0.24072,-0.95371,-0.18025,412.63,0.80442,0.09212,0.58688,276.28,-0.5431,-0.28628,0.78936,326.52 > ui mousemode right select Drag select of 51 residues > ui mousemode right ""translate selected models"" > view matrix models > #3,0.24072,-0.95371,-0.18025,395.87,0.80442,0.09212,0.58688,271.51,-0.5431,-0.28628,0.78936,320.35 > view matrix models > #3,0.24072,-0.95371,-0.18025,391.28,0.80442,0.09212,0.58688,278.87,-0.5431,-0.28628,0.78936,321.28 > ui tool show ""Fit in Map"" > fitmap sel inMap #11 Fit molecule EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) to map cryosparc_P9_J1527_map_sharp.mrc (#11) using 414 atoms average map value = 0.1112, steps = 64 shifted from previous position = 2.88 rotated from previous position = 8.48 degrees atoms outside contour = 246, contour level = 0.12883 Position of EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) relative to cryosparc_P9_J1527_map_sharp.mrc (#11) coordinates: Matrix rotation and translation 0.17748944 -0.94353524 -0.27971191 394.02099492 0.77654551 -0.04032251 0.62876956 274.31309170 -0.60454493 -0.32880898 0.72554124 324.85849974 Axis -0.47992137 0.16280054 0.86207393 Axis point 150.86045413 355.06826931 0.00000000 Rotation angle (degrees) 93.93621678 Shift along axis 135.61127000 > color #3 #dfdfdf > select clear > select add #3 2961 atoms, 2997 bonds, 380 residues, 1 model selected > select #3/A:185 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/A:315 13 atoms, 11 bonds, 2 residues, 1 model selected > select up 1606 atoms, 1621 bonds, 193 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.11897,-0.97295,-0.19805,393.57,0.81292,-0.019083,0.58206,274.54,-0.57009,-0.23025,0.78866,323.67 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.11897,-0.97295,-0.19805,385.26,0.81292,-0.019083,0.58206,279.52,-0.57009,-0.23025,0.78866,323.44 > view matrix models > #3,0.11897,-0.97295,-0.19805,389.2,0.81292,-0.019083,0.58206,281.32,-0.57009,-0.23025,0.78866,325.83 > fitmap sel inMap #11 Fit molecule EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) to map cryosparc_P9_J1527_map_sharp.mrc (#11) using 1606 atoms average map value = 0.08517, steps = 268 shifted from previous position = 2.97 rotated from previous position = 9.8 degrees atoms outside contour = 1105, contour level = 0.12883 Position of EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) relative to cryosparc_P9_J1527_map_sharp.mrc (#11) coordinates: Matrix rotation and translation 0.01522549 -0.95284833 -0.30306476 388.99981659 0.86750665 -0.13812812 0.47786278 285.41423032 -0.49719251 -0.27018639 0.82449919 327.57234644 Axis -0.37825851 0.09816263 0.92048063 Axis point 136.77681352 339.29774694 0.00000000 Rotation angle (degrees) 98.58066763 Shift along axis 182.39852067 > select clear > show #3-8,12-13 target ab > hide #3-8,12-13 target a > cartoon #3-8,12-13 > show #9 models > show #10 models > color bfactor #3,4,5,6,7,8 palette alphafold 14952 atoms, 1848 residues, atom bfactor range 30 to 98.8 > hide #12 models > hide #13 models > windowsize 1000 500 > hide #3-10 target a > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > lighting full > lighting soft > lighting full > hide #3 models > show #6 models > windowsize 1000 400 > hide #6 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #10 models > hide #10 models > windowsize 1000 500 > show #10 models > hide #10 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > hide #4 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #6 models > hide #6 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #7 models > hide #7 models > show #6 models > hide #6 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #10 models > hide #10 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #7 models > hide #7 models > show #3 models > ui tool show ""Side View"" > save ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - > TVMT/Johnson_TvMT/tvmt_figure_making/homology_AF_montage_04222024.cxs"" > close session > open ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - > TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs"" format > session No such file/path: /Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. Research/Project #4 - TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs > open ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - > TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs"" format > session No such file/path: /Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. Research/Project #4 - TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs > open /Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024-0.cxs > format session No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive- ecrofut@g.ucla.edu/.shortcut-targets-by- id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024-0.cxs > open /Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_04162024-0.cxs > format session No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive- ecrofut@g.ucla.edu/.shortcut-targets-by- id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_04162024-0.cxs > open /Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024.cxs > format session No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive- ecrofut@g.ucla.edu/.shortcut-targets-by- id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024.cxs > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_kink_04192024-0.cxs"" Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > ui mousemode right select Drag select of 437 residues, 38 atoms, 32 bonds > hide sel target ab > select clear > windowsize 1000 500 > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/superimposition_tbinding_04232024.tif"" width 1000 height 500 > supersample 3 transparentBackground true > select #2/F:203 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/F:203-210 75 atoms, 74 bonds, 8 residues, 1 model selected > hide #12 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/F #13/F Alignment identifier is 1 > select #2/F:203 #13/F:203 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:203-207 #13/F:203-207 88 atoms, 86 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [189-193] RMSD: 115.258 > select #2/F:202 #13/F:202 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:202-203 #13/F:202-203 32 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [188-189] RMSD: 113.455 > show (#13 & sel) target ab > select #2/F:205 #13/F:205 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:205-206 #13/F:205-206 38 atoms, 36 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [191-192] RMSD: 117.252 > show (#13 & sel) target ab > select #2/F:212 #13/F:212 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:212-213 #13/F:212-213 30 atoms, 28 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [198-199] RMSD: 119.137 > show (#13 & sel) target ab > select #2/F:218 #13/F:218 24 atoms, 24 bonds, 2 residues, 2 models selected > select #2/F:218 #13/F:218 24 atoms, 24 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [204] RMSD: 121.553 > show (#13 & sel) target ab > select #2/F:220 #13/F:220 18 atoms, 16 bonds, 2 residues, 2 models selected > select #2/F:220-221 #13/F:220-221 28 atoms, 26 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [206-207] RMSD: 118.698 > show (#13 & sel) target ab > view name tbinding > select #2/F:225 #13/F:225 20 atoms, 20 bonds, 2 residues, 2 models selected > select #2/F:225 #13/F:225 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [211] RMSD: 120.382 > show (#13 & sel) target ab > select #2/F:231 #13/F:231 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:231-232 #13/F:231-232 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [217-218] RMSD: 117.841 > show (#13 & sel) target ab > select #2/F:235 #13/F:235 18 atoms, 16 bonds, 2 residues, 2 models selected > select #2/F:235-236 #13/F:235-236 36 atoms, 34 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [221-222] RMSD: 117.727 > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/fap35only_tbdingin_04232024.tif"" width 1000 height 500 supersample 3 > transparentBackground true > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_N_04192024.cxs"" Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > select #12/B:149 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel target a > select clear > view list Named views: N_aromatic, tubulin_binding_motif > view N_aromatic > windowsize 600 600 > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/superimposition_N_04232024.tif"" width 800 height 800 supersample 3 > transparentBackground true > color #3 #dfdfdf > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/superimposition_N_04232024.tif"" width 800 height 800 supersample 3 > transparentBackground true > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_N_04232024.cxs"" > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #12 models > select #13/F:103 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select clear > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/fap35only_N_04232024.tif"" width 800 height 800 supersample 3 > transparentBackground true > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_kink_04192024-0.cxs"" format session Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > hide #3-8,12-13 target a > windowsize 1000 500 > select clear > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #3 models > hide #4 models > hide #12 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/F #13/F Alignment identifier is 1 > select #2/F:56-69,83-98,103-184,201-214,218-304 > #13/F:56-69,83-98,103-184,201-214,218-304 3542 atoms, 3560 bonds, 426 residues, 2 models selected > select #2/F:202 #13/F:202 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:202-203 #13/F:202-203 32 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [188-189] RMSD: 113.455 > show (#13 & sel) target ab > select #2/F:205 #13/F:205 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:205-206 #13/F:205-206 38 atoms, 36 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [191-192] RMSD: 117.252 > show (#13 & sel) target ab > select #2/F:212 #13/F:212 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:212-213 #13/F:212-213 30 atoms, 28 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [198-199] RMSD: 119.137 > show (#13 & sel) target ab > select #2/F:218 #13/F:218 24 atoms, 24 bonds, 2 residues, 2 models selected > select #2/F:218 #13/F:218 24 atoms, 24 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [204] RMSD: 121.553 > show (#13 & sel) target ab > select #2/F:220 #13/F:220 18 atoms, 16 bonds, 2 residues, 2 models selected > select #2/F:220-221 #13/F:220-221 28 atoms, 26 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [206-207] RMSD: 118.698 > show (#13 & sel) target ab > select #2/F:225 #13/F:225 20 atoms, 20 bonds, 2 residues, 2 models selected > select #2/F:225 #13/F:225 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [211] RMSD: 120.382 > show (#13 & sel) target ab > select #2/F:231 #13/F:231 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/F:231-232 #13/F:231-232 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [217-218] RMSD: 117.841 > show (#13 & sel) target ab > select clear > windowsize 1000 500 > view list Named views: tbinding_04192024, tubulin_binding_motif > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/fap35only_tbdingin_04232024-0.tif"" width 1000 height 500 supersample > 3 transparentBackground true > show #8 models > show #7 models > show #6 models > show #5 models > show #4 models > show #3 models > show #12 models > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/superimposition_tbinding_04232024-0.tif"" width 1000 height 500 > supersample 3 transparentBackground true > hide #3-8,12-13 target a > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/superimposition_tbinding_04232024-0.tif"" width 1000 height 500 > supersample 3 transparentBackground true > windowsize 1000 500 > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #7 models > hide #8 models > hide #12 models > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_N_04192024.cxs"" format session Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/homology_cxs/homology_figure_kink_04192024-0.cxs"" format session Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel 1.1, shown at level 0.129, step 1, values float32 opened ChimeraX session > hide #12 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > select #13/F:203 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #13/F:202 16 atoms, 14 bonds, 2 residues, 1 model selected > hide sel target a > select clear Drag select of 16 atoms, 10 residues, 16 bonds > show sel target ab > undo > select #13/F:208 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #13/F:206 22 atoms, 20 bonds, 2 residues, 1 model selected > show sel target ab > select #13/F:208 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel target a > select #13/F:206 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel target a > select clear > save ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology > figure/fap35_only_tbinding_closeup_04242024.tif"" width 1000 height 500 > supersample 3 transparentBackground true > close session > open /Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/MIPS_fit_figure/supplemental_mip_figures.cxs Opened 16nm_Bmap_UD2_sharp_J1506.mrc as #1, grid size 640,640,640, pixel 1.1, shown at level 0.0929, step 1, values float32 opened ChimeraX session > select clear > hide #!1 models > show #!1 models > volume copy #1 Opened 16nm_Bmap_UD2_sharp_J1506.mrc copy as #3, grid size 640,640,640, pixel 1.1, shown at step 1, values float32 > combine #2 > color #3 darkgrey models > hide #2 models > hide #4 models > show #4 models > clipper associate #3 toModel #4 Opened 16nm_Bmap_UD2_sharp_J1506.mrc copy as #3.1.1.1, grid size 640,640,640, pixel 1.1, shown at level 0.143, step 1, values float32 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 Metal - 88 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z127000FLLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 108 days, 20 hours, 40 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2714H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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-Clipper: 0.22.4 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-ISOLDE: 1.7.1 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-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 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 openvr: 1.23.701 packaging: 21.3 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 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 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 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX