id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17326 Crash accessing StructureSeq.structure chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 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 0x00000001ec214f40 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 91 in get_prop File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1254 in _changes_cb File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1069 in proxy_handler File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 54 in check_for_changes File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py"", line 77 in File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3318 in command_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 144 in __exit__ File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3203 in run File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 225 in delete File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 308 in _key_closed File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py"", line 105 in delete File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 1010 in close File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/close.py"", line 43 in close File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File 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""79a693f0a8679649194168fe5ce9328363112f00"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { ""NETWORK_SERVICE_PROXY_CONFIG_UPDATE"" : ""6401414cc679dd6bc5828183"" }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_4.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_3.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_2.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_1.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_4.cif #1 --- Chain | Description A | . B | . C | . Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_3.cif #2 --- Chain | Description A | . B | . C | . Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_2.cif #3 --- Chain | Description A | . B | . C | . Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_1.cif #4 --- Chain | Description A | . B | . C | . Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif #5 --- Chain | Description A | . B | . C | . > ui tool show ""AlphaFold Error Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #5 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_0.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #5 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_0.json > color bfactor #5 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.2 to 97 > color bfactor #5 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.2 to 97 > alphafold pae #5 colorDomains true > hide #1 models > hide #2 models > hide #3 models > hide #4 models > save /Users/vincent/Desktop/image5.png supersample 3 > color #5/A:1-98 lime > save /Users/vincent/Desktop/image6.png supersample 3 > color #5/B:65-429 lime > save /Users/vincent/Desktop/image7.png supersample 3 > color #5/C:7-339 lime > save /Users/vincent/Desktop/image8.png supersample 3 > color #5/B:4-428 lime > color #5/C:6-71 lime > color #5/A:4-97 magenta > save /Users/vincent/Desktop/image9.png supersample 3 > save /Users/vincent/Desktop/image10.png supersample 3 > color #5/A:1-98 lime > color #5/C:3-57 magenta > color #5/C:46-121 lime > color #5/B:68-432 magenta > save /Users/vincent/Desktop/image11.png supersample 3 > color #5/C:169 lime > color #5/B:181 magenta > color #5/C:182-245 lime > color #5/B:68-421 magenta > save /Users/vincent/Desktop/image12.png supersample 3 > color bfactor #5 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.2 to 97 > color bfactor #5 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.2 to 97 > help help:user/tools/alphafold.html#pae The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #5/C:186 lime > color #5/C:322 magenta > color #5/B:18 lime > color #5/B:5 magenta > color #5/A:5-98 lime > color #5/B:60-438/C:1-3 lime > color #5/C:4-341 lime > color #5/C:4-105 lime > color #5/A:6-88 magenta > color #5/C:17-152 lime > color #5/B:72-414 magenta > color #5/C:189-244 lime > color #5/B:75-407 magenta > view name fixed_view > rainbow chains palette silver:orchid:cornflower > 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95 > 2dlabels create #2 text USP27X color orchid size 24 xpos 0.8 ypos 0.90 > 2dlabels create #3 text ATXN7L3 color orchid size 24 xpos 0.8 ypos 0.85 > 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos > 0.85 Label ""#3"" already exists > 2dlabels #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos 0.85 > save /Users/vincent/Desktop/image13.png supersample 3 > 2dlabels delete > hide #5 models > show #1 models > show #5 models > hide #5 models > view name fixed_view > 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95 > 2dlabels create #2 text USP27X color orchid size 24 xpos 0.8 ypos 0.90 > 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos > 0.85 > save /Users/vincent/Desktop/image5.png supersample 3 > alphafold pae #4 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_1.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #4 colorDomains true > color bfactor #4 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.7 to 97 > color bfactor #4 palette alphafold 6989 atoms, 886 residues, atom bfactor range 13.7 to 97 > alphafold pae #4 colorDomains true > show #4 models > hide #1 models > show #1 models > hide #4 models > show #4 models > hide #4 models > alphafold pae #1 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_4.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #1 colorDomains true > hide #!7 models > save /Users/vincent/Desktop/image6.png supersample 3 > color #1/A:1 lime > color #1/A:2 magenta > color #1/A:1-99 lime > save /Users/vincent/Desktop/image7.png supersample 3 > save /Users/vincent/Desktop/image8.png supersample 3 > color #1/B:57-431 lime > save /Users/vincent/Desktop/image9.png supersample 3 > color #1/C:4-346 lime > save /Users/vincent/Desktop/image10.png supersample 3 > color #1/C:4-109 lime > color #1/A:4-97 magenta > save /Users/vincent/Desktop/image11.png supersample 3 > color #1/C:11-120 lime > color #1/B:68-425 magenta > save /Users/vincent/Desktop/image12.png supersample 3 > color #1/C:183-250 lime > color #1/B:68-416 magenta > save /Users/vincent/Desktop/image13.png supersample 3 > hide #1 models > show #4 models > rainbow chains palette silver:orchid:cornflower > show #!7 models > hide #!7 models > show #!7 models > save /Users/vincent/Desktop/image14.png supersample 3 > alphafold pae #4 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_1.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #4 colorDomains true > save /Users/vincent/Desktop/image15.png supersample 3 > save /Users/vincent/Desktop/image16.png supersample 3 > color #4/C:208 lime > color #4/C:303 magenta > color #4/A:30 lime > color #4/A:26 magenta > color #4/A:1-97 lime > save /Users/vincent/Desktop/image17.png supersample 3 > hide #!7 models > save /Users/vincent/Desktop/image18.png supersample 3 > color #4/B:57-430 lime > save /Users/vincent/Desktop/image19.png supersample 3 > color #4/C:3-346 lime > save /Users/vincent/Desktop/image20.png supersample 3 > color #4/B:438/C:1-110 lime > color #4/A magenta > save /Users/vincent/Desktop/image21.png supersample 3 > color #4/C:8-126 lime > color #4/B:70-427 magenta > save /Users/vincent/Desktop/image22.png supersample 3 > color #4/C:188-255 lime > color #4/B:73-425 magenta > save /Users/vincent/Desktop/image23.png supersample 3 > color #4/B:12-436 lime > color #4/A:4-97 magenta > save /Users/vincent/Desktop/image24.png supersample 3 > color #4/C:188-248 lime > color #4/C:64-109 magenta > color #4/B:62-182 lime > color #4/B:258-344 magenta > color #4/B:65-431 lime > close > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_4.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_3.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_2.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_1.cif > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_4.cif #1 --- Chain | Description A | . B | . C | . D | . Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_3.cif #2 --- Chain | Description A | . B | . C | . D | . Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_2.cif #3 --- Chain | Description A | . B | . C | . D | . Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_1.cif #4 --- Chain | Description A | . B | . C | . D | . Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif #5 --- Chain | Description A | . B | . C | . D | . > hide #1 models > hide #2 models > hide #3 models > hide #4 models > select add #5 8502 atoms, 8688 bonds, 1071 residues, 1 model selected > select subtract #5 Nothing selected > rainbow chains palette silver:orchid:cornflower > rainbow chains palette silver:orchid:cornflower:green > rainbow chains palette silver:orchid:cornflower:greenyellow > view name fixed_view > 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95 > 2dlabels create #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90 > 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos > 0.85 > 2dlabels create #3 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8 Label ""#3"" already exists > 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8 > save /Users/vincent/Desktop/image25.png supersample 3 > alphafold pae #5 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_full_data_0.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #5 colorDomains true > save /Users/vincent/Desktop/image26.png supersample 3 > hide #!6 models > save /Users/vincent/Desktop/image27.png supersample 3 > color #5/C:267 lime > color #5/D:70 magenta > color #5/A:2-95 lime > save /Users/vincent/Desktop/image28.png supersample 3 > color #5/B:13-519 lime > save /Users/vincent/Desktop/image29.png supersample 3 > color #5/C:8-341 lime > save /Users/vincent/Desktop/image30.png supersample 3 > color #5/C:346-347/D lime > save /Users/vincent/Desktop/image31.png supersample 3 > color #5/B:15-519 lime > color #5/A:5-94 magenta > save /Users/vincent/Desktop/image32.png supersample 3 > color #5/C:3-342 lime > color #5/A:1-94 magenta > color #5/C:285 lime > color #5/A:76 magenta > color #5/C:10-120 lime > color #5/A:7-85 magenta > color #5/C:190-246 lime > color #5/A:16-87 magenta > color #5/C:5-120 lime > color #5/A:7-100 magenta > save /Users/vincent/Desktop/image33.png supersample 3 > color #5/C:190-255 lime > color #5/A:7-94 magenta > save /Users/vincent/Desktop/image34.png supersample 3 > color #5/D:1-97 lime > color #5/A:3-92 magenta > save /Users/vincent/Desktop/image35.png supersample 3 > save /Users/vincent/Desktop/image36.png supersample 3 > color #5/C:10-118 lime > color #5/B:21-513 magenta > save /Users/vincent/Desktop/image37.png supersample 3 > color #5/C:180-255 lime > color #5/A:7-87 magenta > color #5/D lime > color #5/A:1-87 magenta > color #5/C:6-125 lime > color #5/B:17-509 magenta > color #5/C:185-251 lime > color #5/B:23-513 magenta > save /Users/vincent/Desktop/image38.png supersample 3 > color #5/D:4-97 lime > color #5/B:25-513 magenta > save /Users/vincent/Desktop/image39.png supersample 3 > color #5/D:8-98 lime > color #5/C:194-253 magenta > save /Users/vincent/Desktop/image40.png supersample 3 > close > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_UBTF2L3_ATXN7short/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_model_0.cif Chain information for fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . > rainbow chains palette silver:orchid:cornflower:greenyellow > select /d 786 atoms, 807 bonds, 98 residues, 1 model selected > select /c 7669 atoms, 7823 bonds, 945 residues, 1 model selected > /c Unknown command: sequence /c > sequence chain /c Alignment identifier is 1/C > select /C:598-599 17 atoms, 16 bonds, 2 residues, 1 model selected > select /C:374-599 1887 atoms, 1922 bonds, 226 residues, 1 model selected > select /C:598-599 17 atoms, 16 bonds, 2 residues, 1 model selected > select /C:1-599 4973 atoms, 5077 bonds, 599 residues, 1 model selected > sequence chain /c 1:600 Expected a keyword > select :1-600.c Expected an objects specifier or a keyword > select /c 1-600 Expected a keyword > select /1-600.c Expected an objects specifier or a keyword > select /c.1-600 Expected an objects specifier or a keyword > select /c#1-600 13467 atoms, 13758 bonds, 1669 residues, 1 model selected > select subtract #1 Nothing selected > select /C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:1-598 4965 atoms, 5069 bonds, 598 residues, 1 model selected > color sel orange > color sel gray > select add #1 13467 atoms, 13758 bonds, 1669 residues, 1 model selected > select subtract #1 Nothing selected > view name fixed_view > 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95 > 2dlabels create #3 text UBTF2::ATXN7L3 color cornflowerblue size 24 xpos 0.8 > ypos 0.85 > 2dlabels create #2 text USP22 color cornflowerblue size 24 xpos 0.8 ypos > 0.90 > 2dlabels #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90 > 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.80 > save /Users/vincent/Desktop/image5.png supersample 3 > alphafold pae #1 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_UBTF2L3_ATXN7short/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_full_data_0.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #1 colorDomains true > hide #!2 models > save /Users/vincent/Desktop/image6.png supersample 3 > color bfactor #1 palette alphafold 13467 atoms, 1669 residues, atom bfactor range 14.1 to 97.2 > h-key true Unknown command: h-key true > h-key truekey true Unknown command: h-key truekey true Fetching url https://www.colourlovers.com/api/palettes?keywords=true&format=json&numResults=100 failed: HTTP Error 522: > color bfactor palette > 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff > key true > key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90 > #106dff:90 #106dff:100 showTool true > ui mousemode right ""color key"" 13467 atoms, 1669 residues, atom bfactor range 14.1 to 97.2 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/vincent/Desktop/image7.png supersample 3 > key delete > ui mousemode right translate > color /C:435 lime > color /B:82 magenta > color /A:8-101/B:1-4 lime > color /A:3-97 lime > color /A/B:1 lime > save /Users/vincent/Desktop/image8.png supersample 3 > color /B:165 lime > color /C:3 magenta > color /B:14-523 lime > save /Users/vincent/Desktop/image9.png supersample 3 > color /C:22 lime > color /C:43 magenta > color /C:19-349 lime > color /C:329 lime > color /C:361 magenta > color /C:222-347 lime > color /C:435-513 magenta > color /C:6-854 lime > color /C:16-182 lime > color /C:206-339 lime > color /C:365-429 lime > color /C:212-329 lime > color /C:445-506 magenta > color /C:440-513 lime > color /C:513-602 lime > color /C:591-711 lime > color /C:617-721 lime > color /C:790-837 magenta > color /C:768-843 lime > color /C:17-856 lime > color /C:206-349 lime > color /C:368-432 lime > color /C:445-513 lime > color /C:521-601 lime > color /C:596-716 lime > color /C:768-861 lime > color /C:6-861 lime > save /Users/vincent/Desktop/image10.png supersample 3 > color /D lime > save /Users/vincent/Desktop/image11.png supersample 3 > color /C:22 lime > color /C:270-273 magenta > color /C:16-188 lime > save /Users/vincent/Desktop/image12.png supersample 3 > color /C:240 lime > color /C:300 magenta > color /C:222-347 lime > save /Users/vincent/Desktop/image13.png supersample 3 > color /C:362-433 lime > save /Users/vincent/Desktop/image14.png supersample 3 > color /C:594 lime > color /C:327-331 magenta > color /C:440-511 lime > save /Users/vincent/Desktop/image15.png supersample 3 > color /C:404 lime > color /C:648 magenta > color /C:518-608 lime > save /Users/vincent/Desktop/image16.png supersample 3 > color /C:732 lime > color /C:449 magenta > color /C:604-713 lime > save /Users/vincent/Desktop/image17.png supersample 3 > color /C:778 lime > color /C:746 magenta > color /C:773-854 lime > save /Users/vincent/Desktop/image18.png supersample 3 > color /C:438-518 lime > color /C:223-341 magenta > save /Users/vincent/Desktop/image19.png supersample 3 > color /C:791 lime > color /C:560 magenta > color /C:833 lime > color /C:537 magenta > color /C:781-859 lime > color /C:611-709 magenta > color /C:602-734 lime > color /C:777-834 magenta > color /C:773-846 lime > color /C:608-712 magenta > save /Users/vincent/Desktop/image20.png supersample 3 > color /D:10-98 lime > color /C:783-837 magenta > color /C:513-531 lime > color /A:1-88 magenta > color /C:583-721 lime > color /A:1-85 magenta > save /Users/vincent/Desktop/image21.png supersample 3 > color /C:776-849 lime > color /A:4-88 magenta > save /Users/vincent/Desktop/image22.png supersample 3 > color /D:2-98 lime > color /A:4-85 magenta > save /Users/vincent/Desktop/image23.png supersample 3 > color /C:425 lime > color /B:379 magenta > color /C:589-719 lime > color /B:25-511 magenta > save /Users/vincent/Desktop/image24.png supersample 3 > color /C:810 lime > color /B:68 magenta > color /C:781-851 lime > color /B:21-521 magenta > save /Users/vincent/Desktop/image25.png supersample 3 > save /Users/vincent/Desktop/image26.png supersample 3 > color /D:2-91 lime > color /B:18-518 magenta > color /D:91 lime > color /B:518 magenta > color /C:942-945/D lime > color /B:14-525/C:1-6 magenta > save /Users/vincent/Desktop/image27.png supersample 3 > color /D:2-91 lime > color /A/B:1-521 magenta > view fixed_view > color /D:5-93 lime > color /C:601-692 magenta > color /A-D lime > color /C:308 lime > color /B:109 magenta > color /C:9-498 lime > color /A:11-88 magenta > color /C:446 lime > color /B:89 magenta > close > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif Chain information for fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . > rainbow chains palette silver:orchid:cornflower:greenyellow > color bfactor palette > 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff > key true > key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90 > #106dff:90 #106dff:100 showTool true > ui mousemode right ""color key"" 8502 atoms, 1071 residues, atom bfactor range 10.8 to 97.2 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/vincent/Desktop/image28.png supersample 3 > close > ui mousemode right translate > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif #1 --- Chain | Description A | . B | . C | . > rainbow chains palette silver:orchid:cornflower > color bfactor palette > 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff > key true > key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90 > #106dff:90 #106dff:100 showTool true > ui mousemode right ""color key"" 6989 atoms, 886 residues, atom bfactor range 13.2 to 97 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/vincent/Desktop/image29.png supersample 3 > close > ui mousemode right translate > open > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/EN2_USP22_UBTF1L3_ATXN7short/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_model_0.cif Chain information for fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . > rainbow chains palette silver:orchid:cornflower:greenyellow > 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95 > 2dlabels create #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90 > 2dlabels create #3 text UBTF1::ATXN7L3 color cornflowerblue size 24 xpos 0.8 > ypos 0.85 > 2dlabels create #3 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8 Label ""#3"" already exists > 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8 > save /Users/vincent/Desktop/image30.png supersample 3 > select /c 7985 atoms, 8145 bonds, 982 residues, 1 model selected > sequence chain /C:1-600 Alignment identifier is 1/C > select /C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:1-635 5281 atoms, 5391 bonds, 635 residues, 1 model selected > color sel gray > 2dlabels create #5 text UBTF1 color gray size 24 xpos 0.8 ypos 0.8 > 2dlabels #5 text UBTF1 color gray size 24 xpos 0.8 ypos 0.75 > 2dlabels create #6 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos > 0.70 > save /Users/vincent/Desktop/image31.png supersample 3 > select add #1 13783 atoms, 14080 bonds, 1706 residues, 1 model selected > select subtract #1 Nothing selected > save /Users/vincent/Desktop/image32.png supersample 3 > color bfactor palette > 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff > key true > key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90 > #106dff:90 #106dff:100 showTool true > ui mousemode right ""color key"" 13783 atoms, 1706 residues, atom bfactor range 15.7 to 96.7 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!2 models > save /Users/vincent/Desktop/image33.png supersample 3 > alphafold pae #1 file > /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/EN2_USP22_UBTF1L3_ATXN7short/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_full_data_0.json The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #1 colorDomains true > hide #3 models > save /Users/vincent/Desktop/image34.png supersample 3 > color /A:1-97 lime > save /Users/vincent/Desktop/image35.png supersample 3 > color /B:10-521 lime > save /Users/vincent/Desktop/image36.png supersample 3 > color /B:234 lime > color /C:321 magenta > color /C:20-896 lime > save /Users/vincent/Desktop/image37.png supersample 3 > color /C:978-982/D lime > save /Users/vincent/Desktop/image38.png supersample 3 > color /C:623-751 lime > color /A:1-83 magenta > color /C:558-572 lime > color /A:1-76 magenta > color /C:626-748 lime > color /A:1-80 magenta > save /Users/vincent/Desktop/image39.png supersample 3 > color /C:243 lime > color /B:245 magenta > color /C:819-887 lime > color /A:1-90 magenta > save /Users/vincent/Desktop/image40.png supersample 3 > color /D:2-96 lime > color /A:1-87 magenta > save /Users/vincent/Desktop/image41.png supersample 3 > color /C:629-751 lime > color /B:20-521 magenta > save /Users/vincent/Desktop/image42.png supersample 3 > color /C:819-890 lime > color /B:20-507 magenta > save /Users/vincent/Desktop/image43.png supersample 3 > color /C:981-982/D lime > color /B:13-525 magenta > save /Users/vincent/Desktop/image44.png supersample 3 > color /D:11 lime > color /C:728 magenta > color /D:2-98 lime > color /C:638-742 magenta > save /Users/vincent/Desktop/image45.png supersample 3 > color /C:357 lime > color /C:228 magenta > color /D:11-93 lime > color /C:821-873 magenta > save /Users/vincent/Desktop/image46.png supersample 3 > color /C:16-98 lime > save /Users/vincent/Desktop/image47.png supersample 3 > color /C:98-179 lime > save /Users/vincent/Desktop/image48.png supersample 3 > color /C:404-479 lime > save /Users/vincent/Desktop/image49.png supersample 3 > color /C:646 lime > color /C:580 magenta > color /C:482-558 lime > save /Users/vincent/Desktop/image50.png supersample 3 > color /C:555-646 lime > save /Users/vincent/Desktop/image51.png supersample 3 > color /C:638-754 lime > save /Users/vincent/Desktop/image52.png supersample 3 > color /C:811-894 lime > save /Users/vincent/Desktop/image53.png supersample 3 > color /C:107-195 lime > color /C:17-103 magenta > save /Users/vincent/Desktop/image54.png supersample 3 > color /C:544 lime > color /C:269 magenta > color /C:817-890 lime > color /C:649-735 magenta > save /Users/vincent/Desktop/image55.png supersample 3 > close > ui mousemode right translate ===== Log before crash end ===== Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 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: Mac15,6 Model Number: Z1AU001VTFN/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 6 heures et 57 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 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 P2719H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL P2719H: 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: 0.1.4 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: 14.0.5 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: 1.2.4 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: 1.8rc202405202242 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: 1.2.3 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 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: 3.0.4 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: 4.2.2 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