id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16858 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_BeFx- > coot-11.pdb"" Chain information for Drs2p_PS_BeFx-coot-11.pdb #1 --- Chain | Description A | No description available C | No description available > open 8oxa Summary of feedback from opening 8oxa fetched from pdb --- notes | Fetching compressed mmCIF 8oxa from http://files.rcsb.org/download/8oxa.cif Fetching CCD D39 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/D39/D39.cif Fetching CCD VN4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/VN4/VN4.cif 8oxa title: Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS [more info...] Chain information for 8oxa #2 --- Chain | Description | UniProt A | Phospholipid-transporting ATPase IC | AT8B1_HUMAN 1-1185 B | Cell cycle control protein 50A | CC50A_HUMAN 1-361 Non-standard residues in 8oxa #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) D39 — (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy- propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) VN4 — oxido(dioxo)vanadium > open 7bsv Summary of feedback from opening 7bsv fetched from pdb --- notes | Fetching compressed mmCIF 7bsv from http://files.rcsb.org/download/7bsv.cif Fetching CCD P5S from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/P5S/P5S.cif 7bsv title: Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF state [more info...] Chain information for 7bsv #3 --- Chain | Description A | ATP11C C | CDC50A Non-standard residues in 7bsv #3 --- ALF — tetrafluoroaluminate ion MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) > open 6k7m Summary of feedback from opening 6k7m fetched from pdb --- note | Fetching compressed mmCIF 6k7m from http://files.rcsb.org/download/6k7m.cif 6k7m title: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state) [more info...] Chain information for 6k7m #4 --- Chain | Description | UniProt A | Phospholipid-transporting ATPase | Q59EX4_HUMAN 1-1149 C | Cell cycle control protein 50A | CC50A_HUMAN 1-361 Non-standard residues in 6k7m #4 --- ALF — tetrafluoroaluminate ion D39 — (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy- propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Y01 — cholesterol hemisuccinate > ui tool show Matchmaker > matchmaker #!2-4 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 8oxa, chain A (#2), sequence alignment score = 2515.2 RMSD between 446 pruned atom pairs is 0.912 angstroms; (across all 998 pairs: 6.683) Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 7bsv, chain A (#3), sequence alignment score = 1924.9 RMSD between 425 pruned atom pairs is 1.095 angstroms; (across all 772 pairs: 6.022) Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 6k7m, chain A (#4), sequence alignment score = 2910.7 RMSD between 508 pruned atom pairs is 0.988 angstroms; (across all 978 pairs: 5.954) > hide #1 models > close #1 > open ""/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_AlFx- > coot-10.pdb"" Chain information for Drs2p_PS_AlFx-coot-10.pdb #1 --- Chain | Description A | No description available C | No description available > ui tool show Matchmaker > matchmaker #!2-4 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 8oxa, chain A (#2), sequence alignment score = 2542.6 RMSD between 759 pruned atom pairs is 1.069 angstroms; (across all 1010 pairs: 4.071) Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 7bsv, chain A (#3), sequence alignment score = 1947.7 RMSD between 570 pruned atom pairs is 1.162 angstroms; (across all 785 pairs: 2.461) Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 6k7m, chain A (#4), sequence alignment score = 2905.8 RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs: 2.322) > set bgColor white > hide atoms > select ::name=""D39"" 156 atoms, 153 bonds, 3 residues, 3 models selected > show sel atoms > select ::name=""P5S"" 136 atoms, 135 bonds, 1 residue, 1 model selected > show sel atoms > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > ui mousemode right zoom > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select add #3 20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected > select add #4 31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected > hide sel cartoons > color #1 silver > color #3 #4f8f00ff > color #3 #008f00ff > color #3 #945200ff > color #3 #941100ff > color #3 #009193ff > color #4 #00fa92ff > color #4 #8efa00ff > color #4 #fffb00ff > color #4 #ff9300ff > color #4 #0433ffff > color #4 #005493ff > color #4 #011993ff > color #4 #0433ffff > color #4 #0096ffff > color #4 #0433ffff > color #4 #929000ff > ui tool show ""Side View"" > select subtract #2 20012 atoms, 20497 bonds, 12 pseudobonds, 2467 residues, 8 models selected > select subtract #3 10591 atoms, 10844 bonds, 6 pseudobonds, 1316 residues, 4 models selected > select subtract #4 Nothing selected > color :D39 byhetero > color :P5S byhetero > select h Expected an objects specifier or a keyword > select H 11513 atoms, 1421 residues, 2 models selected > hide sel > select add #3 20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected > select subtract #3 11431 atoms, 1420 residues, 1 model selected > select add #1 22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected > select subtract #1 Nothing selected > lighting shadows false > lighting soft > graphics silhouettes true > cartoon style width 1.2 thickness 0.25 xsection oval sides 20 > save AlFx_PS_comparison.png format png width 3600 height 3600 supersample 2 > transparentBackground true > select add #1 22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected > select subtract #1 Nothing selected > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select add #3 20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected > select add #4 31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected > select add #1 54135 atoms, 55139 bonds, 26 pseudobonds, 5276 residues, 14 models selected > show sel cartoons > select /A:507-510,1047,237,245 247 atoms, 239 bonds, 23 residues, 4 models selected > show sel atoms > hide sel atoms > select #1/A:507-510,1047,237,245 105 atoms, 102 bonds, 7 residues, 1 model selected > show sel atoms > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #4/A:96 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color #4/A:96 by het Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #4/A:96 byhetero > color #3/A:86 byhetero > select #3/A:86 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:139 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color #2/A:139 byhetero > color #3/A:79 > select #3/A:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color #3/A:79 byhetero > select #4/A:88 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color #4/A:88 byhetero > select #2/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:879 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > color #4/A:879 byhetero > select #3/A:909 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color #3/A:909 byhetero > hide #!3 models > select #2/A:986 byhet Expected a keyword > select #2/A:986 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > show #!3 models > color #1/A:507-510,1047,237,245 byhetero > select H 11513 atoms, 1421 residues, 2 models selected > hide sel > select add #3 20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected > select add #1 32406 atoms, 32904 bonds, 9 pseudobonds, 2578 residues, 6 models selected > select subtract #1 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > ~label #1-4 residues > ui mousemode right select No visible residues selected > ui mousemode right translate > ui mousemode right zoom > select #4/A:356-359 29 atoms, 29 bonds, 4 residues, 1 model selected > show sel atoms > color #4/A:356-359 byhetero > select #3/A:356-359 28 atoms, 28 bonds, 4 residues, 1 model selected > color #3/A:356-359 byhetero > select #2/A:401-404 byhet Expected a keyword > select #2/A:401-404 29 atoms, 29 bonds, 4 residues, 1 model selected > color #2/A:401-404 byhetero > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select subtract #2 Nothing selected > select #2/A:401-404 29 atoms, 29 bonds, 4 residues, 1 model selected > show sel atoms > select #3/A:356-359 28 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > open /Users/amaliebenfeldt/Downloads/emd_9941.map Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level 0.0122, step 2, values float32 > volume #5 step 1 > hide #!5 models > save AlFx_PS_comparison_residue.png format png width 3600 height 3600 > supersample 2 transparentBackground true > show #!5 models > volume #5 level 0.02482 > select add #5 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.99088,0.049565,-0.12526,224.15,-0.09401,-0.92042,0.37946,184.94,-0.096486,0.38778,0.91669,-24.083 > view matrix models > #5,-0.98157,0.19111,0.0022948,192.51,-0.18143,-0.93552,0.30313,204.83,0.060077,0.29712,0.95295,-34.872 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.98157,0.19111,0.0022948,208.55,-0.18143,-0.93552,0.30313,266.6,0.060077,0.29712,0.95295,20.617 > view matrix models > #5,-0.98157,0.19111,0.0022948,251.75,-0.18143,-0.93552,0.30313,257.1,0.060077,0.29712,0.95295,22.924 > select subtract #5 Nothing selected > ui tool show ""Fit in Map"" > fitmap #4 inMap #5 Fit molecule 6k7m (#4) to map emd_9941.map (#5) using 10591 atoms average map value = 0.03523, steps = 128 shifted from previous position = 3.16 rotated from previous position = 16 degrees atoms outside contour = 4387, contour level = 0.024815 Position of 6k7m (#4) relative to emd_9941.map (#5) coordinates: Matrix rotation and translation 0.99999999 -0.00007255 -0.00002499 0.01510218 0.00007255 0.99999999 0.00001998 -0.01007013 0.00002498 -0.00001999 0.99999999 0.00530739 Axis -0.25202896 -0.31509735 0.91498364 Axis point 120.46426379 222.81896502 0.00000000 Rotation angle (degrees) 0.00454324 Shift along axis 0.00422307 > ui tool show Matchmaker > matchmaker #!1-3 to #4 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6k7m, chain A (#4) with Drs2p_PS_AlFx-coot-10.pdb, chain A (#1), sequence alignment score = 2905.8 RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs: 2.322) Matchmaker 6k7m, chain A (#4) with 8oxa, chain A (#2), sequence alignment score = 2604.3 RMSD between 777 pruned atom pairs is 0.959 angstroms; (across all 948 pairs: 2.203) Matchmaker 6k7m, chain A (#4) with 7bsv, chain A (#3), sequence alignment score = 1989 RMSD between 629 pruned atom pairs is 1.058 angstroms; (across all 755 pairs: 2.162) > volume #5 style mesh > volume #5 color #005493 > ui mousemode right zoom > hide #!3 models > hide #!2 models > hide #!1 models > volume #5 level 0.02001 > volume #5 level 0.02145 > show #!1 models > hide #!1 models > open /Users/amaliebenfeldt/Downloads/emd_17262.map Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level 2.47, step 1, values float32 > show #!1 models > show #!2 models > show #!3 models > save ""/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"" > volume #6 level 0.79 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"" Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level 0.0215, step 1, values float32 Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level 2.47, step 1, values float32 Log from Fri Feb 14 09:43:52 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_BeFx- > coot-11.pdb"" Chain information for Drs2p_PS_BeFx-coot-11.pdb #1 --- Chain | Description A | No description available C | No description available > open 8oxa Summary of feedback from opening 8oxa fetched from pdb --- notes | Fetching compressed mmCIF 8oxa from http://files.rcsb.org/download/8oxa.cif Fetching CCD D39 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/D39/D39.cif Fetching CCD VN4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/VN4/VN4.cif 8oxa title: Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS [more info...] Chain information for 8oxa #2 --- Chain | Description | UniProt A | Phospholipid-transporting ATPase IC | AT8B1_HUMAN 1-1185 B | Cell cycle control protein 50A | CC50A_HUMAN 1-361 Non-standard residues in 8oxa #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) D39 — (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy- propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) VN4 — oxido(dioxo)vanadium > open 7bsv Summary of feedback from opening 7bsv fetched from pdb --- notes | Fetching compressed mmCIF 7bsv from http://files.rcsb.org/download/7bsv.cif Fetching CCD P5S from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/P5S/P5S.cif 7bsv title: Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF state [more info...] Chain information for 7bsv #3 --- Chain | Description A | ATP11C C | CDC50A Non-standard residues in 7bsv #3 --- ALF — tetrafluoroaluminate ion MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) > open 6k7m Summary of feedback from opening 6k7m fetched from pdb --- note | Fetching compressed mmCIF 6k7m from http://files.rcsb.org/download/6k7m.cif 6k7m title: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state) [more info...] Chain information for 6k7m #4 --- Chain | Description | UniProt A | Phospholipid-transporting ATPase | Q59EX4_HUMAN 1-1149 C | Cell cycle control protein 50A | CC50A_HUMAN 1-361 Non-standard residues in 6k7m #4 --- ALF — tetrafluoroaluminate ion D39 — (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy- propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Y01 — cholesterol hemisuccinate > ui tool show Matchmaker > matchmaker #!2-4 to #1 Computing secondary structure [Repeated 3 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 8oxa, chain A (#2), sequence alignment score = 2515.2 RMSD between 446 pruned atom pairs is 0.912 angstroms; (across all 998 pairs: 6.683) Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 7bsv, chain A (#3), sequence alignment score = 1924.9 RMSD between 425 pruned atom pairs is 1.095 angstroms; (across all 772 pairs: 6.022) Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 6k7m, chain A (#4), sequence alignment score = 2910.7 RMSD between 508 pruned atom pairs is 0.988 angstroms; (across all 978 pairs: 5.954) > hide #1 models > close #1 > open ""/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_AlFx- > coot-10.pdb"" Chain information for Drs2p_PS_AlFx-coot-10.pdb #1 --- Chain | Description A | No description available C | No description available > ui tool show Matchmaker > matchmaker #!2-4 to #1 Computing secondary structure [Repeated 3 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 8oxa, chain A (#2), sequence alignment score = 2542.6 RMSD between 759 pruned atom pairs is 1.069 angstroms; (across all 1010 pairs: 4.071) Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 7bsv, chain A (#3), sequence alignment score = 1947.7 RMSD between 570 pruned atom pairs is 1.162 angstroms; (across all 785 pairs: 2.461) Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 6k7m, chain A (#4), sequence alignment score = 2905.8 RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs: 2.322) > set bgColor white > hide atoms > select ::name=""D39"" 156 atoms, 153 bonds, 3 residues, 3 models selected > show sel atoms > select ::name=""P5S"" 136 atoms, 135 bonds, 1 residue, 1 model selected > show sel atoms > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > ui mousemode right zoom > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select add #3 20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected > select add #4 31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected > hide sel cartoons > color #1 silver > color #3 #4f8f00ff > color #3 #008f00ff > color #3 #945200ff > color #3 #941100ff > color #3 #009193ff > color #4 #00fa92ff > color #4 #8efa00ff > color #4 #fffb00ff > color #4 #ff9300ff > color #4 #0433ffff > color #4 #005493ff > color #4 #011993ff > color #4 #0433ffff > color #4 #0096ffff > color #4 #0433ffff > color #4 #929000ff > ui tool show ""Side View"" > select subtract #2 20012 atoms, 20497 bonds, 12 pseudobonds, 2467 residues, 8 models selected > select subtract #3 10591 atoms, 10844 bonds, 6 pseudobonds, 1316 residues, 4 models selected > select subtract #4 Nothing selected > color :D39 byhetero > color :P5S byhetero > select h Expected an objects specifier or a keyword > select H 11513 atoms, 1421 residues, 2 models selected > hide sel > select add #3 20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected > select subtract #3 11431 atoms, 1420 residues, 1 model selected > select add #1 22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected > select subtract #1 Nothing selected > lighting shadows false > lighting soft > graphics silhouettes true > cartoon style width 1.2 thickness 0.25 xsection oval sides 20 > save AlFx_PS_comparison.png format png width 3600 height 3600 supersample 2 > transparentBackground true > select add #1 22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected > select subtract #1 Nothing selected > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select add #3 20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected > select add #4 31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected > select add #1 54135 atoms, 55139 bonds, 26 pseudobonds, 5276 residues, 14 models selected > show sel cartoons > select /A:507-510,1047,237,245 247 atoms, 239 bonds, 23 residues, 4 models selected > show sel atoms > hide sel atoms > select #1/A:507-510,1047,237,245 105 atoms, 102 bonds, 7 residues, 1 model selected > show sel atoms > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #4/A:96 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color #4/A:96 by het Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #4/A:96 byhetero > color #3/A:86 byhetero > select #3/A:86 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:139 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color #2/A:139 byhetero > color #3/A:79 > select #3/A:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color #3/A:79 byhetero > select #4/A:88 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color #4/A:88 byhetero > select #2/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:879 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > color #4/A:879 byhetero > select #3/A:909 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color #3/A:909 byhetero > hide #!3 models > select #2/A:986 byhet Expected a keyword > select #2/A:986 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > show #!3 models > color #1/A:507-510,1047,237,245 byhetero > select H 11513 atoms, 1421 residues, 2 models selected > hide sel > select add #3 20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected > select add #1 32406 atoms, 32904 bonds, 9 pseudobonds, 2578 residues, 6 models selected > select subtract #1 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > ~label #1-4 residues [Repeated 1 time(s)] > ui mousemode right select No visible residues selected > ui mousemode right translate > ui mousemode right zoom > select #4/A:356-359 29 atoms, 29 bonds, 4 residues, 1 model selected > show sel atoms > color #4/A:356-359 byhetero > select #3/A:356-359 28 atoms, 28 bonds, 4 residues, 1 model selected > color #3/A:356-359 byhetero > select #2/A:401-404 byhet Expected a keyword > select #2/A:401-404 29 atoms, 29 bonds, 4 residues, 1 model selected > color #2/A:401-404 byhetero > select add #2 11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected > select subtract #2 Nothing selected > select #2/A:401-404 29 atoms, 29 bonds, 4 residues, 1 model selected > show sel atoms > select #3/A:356-359 28 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > select add #3 9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected > select subtract #3 Nothing selected > open /Users/amaliebenfeldt/Downloads/emd_9941.map Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level 0.0122, step 2, values float32 > volume #5 step 1 > hide #!5 models > save AlFx_PS_comparison_residue.png format png width 3600 height 3600 > supersample 2 transparentBackground true > show #!5 models > volume #5 level 0.02482 > select add #5 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.99088,0.049565,-0.12526,224.15,-0.09401,-0.92042,0.37946,184.94,-0.096486,0.38778,0.91669,-24.083 > view matrix models > #5,-0.98157,0.19111,0.0022948,192.51,-0.18143,-0.93552,0.30313,204.83,0.060077,0.29712,0.95295,-34.872 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.98157,0.19111,0.0022948,208.55,-0.18143,-0.93552,0.30313,266.6,0.060077,0.29712,0.95295,20.617 > view matrix models > #5,-0.98157,0.19111,0.0022948,251.75,-0.18143,-0.93552,0.30313,257.1,0.060077,0.29712,0.95295,22.924 > select subtract #5 Nothing selected > ui tool show ""Fit in Map"" > fitmap #4 inMap #5 Fit molecule 6k7m (#4) to map emd_9941.map (#5) using 10591 atoms average map value = 0.03523, steps = 128 shifted from previous position = 3.16 rotated from previous position = 16 degrees atoms outside contour = 4387, contour level = 0.024815 Position of 6k7m (#4) relative to emd_9941.map (#5) coordinates: Matrix rotation and translation 0.99999999 -0.00007255 -0.00002499 0.01510218 0.00007255 0.99999999 0.00001998 -0.01007013 0.00002498 -0.00001999 0.99999999 0.00530739 Axis -0.25202896 -0.31509735 0.91498364 Axis point 120.46426379 222.81896502 0.00000000 Rotation angle (degrees) 0.00454324 Shift along axis 0.00422307 > ui tool show Matchmaker > matchmaker #!1-3 to #4 Computing secondary structure [Repeated 3 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6k7m, chain A (#4) with Drs2p_PS_AlFx-coot-10.pdb, chain A (#1), sequence alignment score = 2905.8 RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs: 2.322) Matchmaker 6k7m, chain A (#4) with 8oxa, chain A (#2), sequence alignment score = 2604.3 RMSD between 777 pruned atom pairs is 0.959 angstroms; (across all 948 pairs: 2.203) Matchmaker 6k7m, chain A (#4) with 7bsv, chain A (#3), sequence alignment score = 1989 RMSD between 629 pruned atom pairs is 1.058 angstroms; (across all 755 pairs: 2.162) > volume #5 style mesh > volume #5 color #005493 > ui mousemode right zoom > hide #!3 models > hide #!2 models > hide #!1 models > volume #5 level 0.02001 > volume #5 level 0.02145 > show #!1 models > hide #!1 models > open /Users/amaliebenfeldt/Downloads/emd_17262.map Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level 2.47, step 1, values float32 > show #!1 models > show #!2 models > show #!3 models > save ""/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"" ——— End of log from Fri Feb 14 09:43:52 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYDC2DK/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 10 dage og 12 minutter Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 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 HP E24m G4: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX