id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17081 "Session restore: KeyError: ""combine""" anmugo@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/andymugo/Library/CloudStorage/Box-Box/Cryo-EM-2024/350 > mesh-1.cxs"" restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Log from Sun Sep 15 01:46:02 2024UCSF ChimeraX version: 1.8.dev202405040553 (2024-05-04) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:/Users/Mugo/Box/Cryo-EM-2024/Publication > preparation/350-651/350-651-Chain-A-Mesh.cxs"" restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""VolumeImage"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeImage"" returned None restore_snapshot for ""VolumeSurface"" returned None Log from Fri May 3 14:03:09 2024UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and > 651-pdb-Yellow.cxs"" Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size 432,432,432, pixel 0.825, shown at level 0.0986, step 2, values float32 Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel 0.825, shown at level 0.0871, step 2, values float32 Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel 0.825, shown at level 0.0858, step 2, values float32 Log from Tue Apr 30 09:24:33 2024UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/350-651-Del1.cxs"" Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size 432,432,432, pixel 0.825, shown at level 0.101, step 2, values float32 Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel 0.825, shown at level 0.0871, step 2, values float32 Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel 0.825, shown at level 0.0858, step 2, values float32 Log from Sun Apr 28 17:51:21 2024UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Deferring bundle installation > open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp- > phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3.pdb Summary of feedback from opening C:/Users/Anon/Box/Cryo- EM-2024/J350/April2024/J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C3.pdb --- warning | Ignored bad PDB record found on line 20823 END Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C3.pdb #1 --- Chain | Description A B C D | No description available > select #1: 551-652 3012 atoms, 3072 bonds, 4 pseudobonds, 384 residues, 2 models selected > select #1: 551-555 136 atoms, 132 bonds, 20 residues, 1 model selected > select #1: 651-655 184 atoms, 192 bonds, 20 residues, 1 model selected > select #1: 651-658 292 atoms, 304 bonds, 32 residues, 1 model selected > open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel 0.825, shown at level 0.0496, step 2, values float32 > hide #!1 models > hide #!2 models > open C:/Users/Anon/Box/Cryo- > EM-2024/J350/J350_009_C4-unsharp_volume_map_inverted.mrc Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size 432,432,432, pixel 0.825, shown at level 0.0473, step 2, values float32 > hide #!3 models > show #!1 models > select #1: 651-665 524 atoms, 540 bonds, 60 residues, 1 model selected > color sel red > select #1: 602-608 184 atoms, 184 bonds, 28 residues, 1 model selected > color sel lime > select #1: 550-557 208 atoms, 204 bonds, 32 residues, 1 model selected > color sel cyan > select #1: 565 48 atoms, 48 bonds, 4 residues, 1 model selected > show sel atoms > select #1: 707 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > select #1: 445 24 atoms, 20 bonds, 4 residues, 1 model selected > show sel atoms > select #1: 494 56 atoms, 60 bonds, 4 residues, 1 model selected > show sel atoms > select #1: 704 44 atoms, 44 bonds, 4 residues, 1 model selected > show sel atoms > open C:/Users/Anon/Box/Cryo- > EM-2024/J350/J350_009_C4-unsharp_volume_map_inverted.mrc Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #4, grid size 432,432,432, pixel 0.825, shown at level 0.0473, step 2, values float32 > volume #2 level 0.07679 > hide #!2 models > volume #3 level 0.1024 > volume #2 level 0.1241 > hide #!2 models > volume #2 level 0.09892 > hide #!2 models > volume #3 level 0.1996 > hide #!3 models > show #!3 models > hide #!4 models > volume #3 level 0.1574 > select clear > hide #!1 models > show #!1 models > volume #3 level 0.1151 > volume #3 level 0.08445 > volume #3 level 0.1151 > transparency #1,3 40 > set bgColor white > transparency #1,3 20 > transparency #1,3 30 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > transparency #1,3 30 > volume #3 level 0.08956 > volume #3 level 0.119 > volume #3 level 0.09468 > volume #3 step 1 > volume #3 level 0.08651 > volume #3 level 0.1328 > volume #3 level 0.1056 > hide #!3 models > cartoon #1 > hide atoms > select /B:712 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > show #!3 models > volume #3 level 0.09876 > volume #3 step 4 > volume #3 level 0.08879 > transparency #1,3 20 > volume #3 step 2 > volume #3 level 0.1093 > volume #3 level 0.1029 > transparency #1,3 30 > volume #3 level 0.1003 > save C:\Users\Anon\Desktop\image1.png supersample 3 > close #4 > hide #!3 models > open C:/Users/Anon/Box/Cryo- > EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- > EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb Chain information for J651-refine_320-C1-Chain-A-SYM- EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb #4 --- Chain | Description A B C D | No description available > ui tool show Matchmaker > matchmaker #!4 to #1 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 J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3.pdb, chain A (#1) with J651-refine_320-C1-Chain-A-SYM- EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb, chain A (#4), sequence alignment score = 2373.2 RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs: 2.353) > hide #!1 models > show #!2 models > volume #2 level 0.07779 > volume #2 level 0.07679 > close #2 > open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel 0.825, shown at level 0.0496, step 2, values float32 > volume #3 level 0.153 > volume #2 level 0.09498 > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!4 models > show #!3 models > volume #3 level 0.1018 > volume #3 level 0.1005 > close #2 > close #4 > save ""S:/Cryo-EM paper/Structures/J350.cxs"" > hide #!1 models > hide #!3 models > open C:/Users/Anon/Box/Cryo- > EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- > EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb Chain information for J651-refine_320-C1-Chain-A-SYM- EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb #2 --- Chain | Description A B C D | No description available > open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel 0.825, shown at level 0.0496, step 2, values float32 > volume #4 level 0.08019 > transparency #2,4 30 > volume #4 level 0.093 > transparency #2,4 30 > volume #4 level 0.08906 > volume #4 level 0.08709 > volume #4 level 0.07625 > volume #4 level 0.08709 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and > 651.cxs"" > save C:\Users\Anon\Desktop\image2.png supersample 3 > volume #4 level 0.08512 > save C:\Users\Anon\Desktop\image3.png supersample 3 > volume #4 level 0.08906 > volume #4 level 0.08709 > save C:\Users\Anon\Desktop\image4.png supersample 3 > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show Matchmaker > matchmaker #!1 to #2 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 J651-refine_320-C1-Chain-A-SYM- EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb, chain A (#2) with J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3.pdb, chain A (#1), sequence alignment score = 2373.2 RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs: 2.353) > save C:\Users\Anon\Desktop\image5.png supersample 3 > save C:\Users\Anon\Desktop\image6.png supersample 3 > save C:\Users\Anon\Desktop\image7.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and > 651-super imposition.cxs"" > hide #!1 models > delete #2?B-D Missing or invalid ""atoms"" argument: only initial part ""#2"" of atom specifier valid > delete #2/B-D > save C:\Users\Anon\Desktop\image8.png supersample 3 > select #2:611-609 Nothing selected > select #2:636-639 59 atoms, 58 bonds, 4 residues, 1 model selected > select #2:636-649 59 atoms, 58 bonds, 4 residues, 1 model selected > select #2:626-649 192 atoms, 192 bonds, 12 residues, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select clear > select #2:600-610 146 atoms, 146 bonds, 11 residues, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select clear > select #2:651-660 188 atoms, 191 bonds, 10 residues, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select clear > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > save C:\Users\Anon\Desktop\image9.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/651-Chain-A-1.cxs"" > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!1 models > delete #1/B-D > save C:\Users\Anon\Desktop\image10.png supersample 3 > set bgColor black > open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp- > phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C2.pdb Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C2.pdb #5 --- Chain | Description A B C D | No description available > hide #!1 models > open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp- > phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL.pdb Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C3-DEL.pdb #6 --- Chain | Description A B C D | No description available > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > hide #!6 models > show #!5 models > close #5 > show #!6 models > open C:/Users/Anon/Box/Cryo-EM-2024/WT-TRPV3/WT- > March-2024/rsr25_mTRPV3WT_Coot-25_Lipid-chain- > D_063-SYM_refined_068-coot-0.pdb Chain information for rsr25_mTRPV3WT_Coot-25_Lipid-chain- D_063-SYM_refined_068-coot-0.pdb #5 --- Chain | Description A B C D | No description available > ui tool show Matchmaker > ui tool show Matchmaker > matchmaker #!6 to #5 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 rsr25_mTRPV3WT_Coot-25_Lipid-chain- D_063-SYM_refined_068-coot-0.pdb, chain A (#5) with J350-6dvw-C4_unsharp- phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL.pdb, chain B (#6), sequence alignment score = 2924.7 RMSD between 368 pruned atom pairs is 1.357 angstroms; (across all 620 pairs: 2.148) > hide #!6 models > show #!6 models > close #5 > hide #!6 models > show #!2 models > hide #!2 models > show #!2 models > open C:/Users/Anon/Box/Cryo- > EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- > EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb Chain information for J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb #5 --- Chain | Description A B C D | No description available > hide #!2 models > set bgColor white > show #!6 models > hide #!5 models > show #!3 models > ui tool show ""Fit in Map"" Fit molecule J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb (#6) to map J350_009_C4-unsharp_volume_map_inverted.mrc (#3) using 20632 atoms average map value = 0.04263, steps = 120 shifted from previous position = 6.07 rotated from previous position = 6.07 degrees atoms outside contour = 18069, contour level = 0.10051 Position of J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb (#6) relative to J350_009_C4-unsharp_volume_map_inverted.mrc (#3) coordinates: Matrix rotation and translation 0.99881314 -0.01633320 -0.04588611 7.41119432 -0.01910814 -0.99797302 -0.06070194 357.63323973 -0.04480164 0.06150669 -0.99710067 339.43075599 Axis 0.99970296 -0.00887126 -0.02269990 Axis point 0.00000000 173.65759994 175.27064473 Rotation angle (degrees) 176.49575605 Shift along axis -3.46870759 > hide #!3 models > show #!5 models > ui tool show Matchmaker > matchmaker #!5 to #6 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 J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb, chain A (#6) with J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#5), sequence alignment score = 2373.2 RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs: 2.353) > hide #!6 models > set bgColor black > select #5:600 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > hide sel target a > cartoon hide sel > show #!4 models > hide #!4 models > open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel 0.825, shown at level 0.0496, step 2, values float32 > hide #!5 models > open C:/Users/Anon/Box/Cryo- > EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- > EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb Chain information for J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb #8 --- Chain | Description A B C D | No description available > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > volume #7 level 0.08575 > transparency #7-8 30 > transparency #7-8 20 > hide #!7 models > select #8:600 32 atoms, 28 bonds, 4 residues, 1 model selected > cartoon hide sel > select #8:660 76 atoms, 72 bonds, 4 residues, 1 model selected > cartoon hide sel > show #!7 models > set bgColor white > save C:\Users\Anon\Desktop\image11.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/651-Del1.cxs"" > hide #!7 models > hide #!8 models > show #!2 models > set bgColor black > cartoon #2 > set bgColor white > save C:\Users\Anon\Desktop\image12.png supersample 3 > hide #!2 models > show #!8 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!6 models > ui tool show Matchmaker > matchmaker #!6 to #8 & sel 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 J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8) with J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb, chain A (#6), sequence alignment score = 4 Fewer than 3 residues aligned; cannot match J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A with J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb, chain A > ui tool show Matchmaker > matchmaker #!6 to #8 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 J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8) with J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL.pdb, chain A (#6), sequence alignment score = 2373.2 RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs: 2.353) > save C:\Users\Anon\Desktop\image13.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/350-651-Del1.cxs"" ——— End of log from Sun Apr 28 17:51:21 2024 ——— opened ChimeraX session > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!1 models > hide #!8 models > hide #!1 models > open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp- > phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL2-C2.pdb Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C3-DEL2-C2.pdb #9 --- Chain | Description A C D | No description available B | No description available > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > show #!8 models > hide #!8 models > show #!3 models > volume #3 level 0.09856 > hide #!3 models > open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp- > phenix-coot-36-chain-B-refined_301-SYM- > EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B- refined_301-SYM-EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb #10 --- Chain | Description A C D | No description available B | No description available > hide #!9 models > show #!3 models > show #!9 models > hide #!3 models > hide #!10 models > show #!3 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!3 models > show #!3 models > hide #!8 models > save C:\Users\Anon\Desktop\image17.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350-.cxs"" > hide #!3 models > show #!8 models > ui tool show Matchmaker > matchmaker #!8 to #10 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 J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM- EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb, chain A (#10) with J651-refine_320-C1-Chain-A-SYM- EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8), sequence alignment score = 2370.6 RMSD between 412 pruned atom pairs is 0.616 angstroms; (across all 536 pairs: 2.358) > save C:\Users\Anon\Desktop\image18.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and > 651-pdb-Yellow.cxs"" ——— End of log from Tue Apr 30 09:24:33 2024 ——— opened ChimeraX session > set bgColor gray > set bgColor black > close > open C:/Users/Anon/Box/Cryo- > EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- > EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb Summary of feedback from opening C:/Users/Anon/Box/Cryo- EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM- EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb --- warnings | Start residue of secondary structure not found: HELIX 29 29 GLY A 601 SER A 608 1 8 Start residue of secondary structure not found: HELIX 61 61 GLY B 601 SER B 608 1 8 Start residue of secondary structure not found: HELIX 93 93 GLY C 601 SER C 608 1 8 Start residue of secondary structure not found: HELIX 125 125 GLY D 601 SER D 608 1 8 Chain information for J651-refine_320-C1-Chain-A-SYM- EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb #1 --- Chain | Description A B C D | No description available > set bgColor gray > open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel 0.825, shown at level 0.0496, step 2, values float32 > volume #2 level 0.07958 > surface style mesh > set bgColor white > volume #2 style image maximumIntensityProjection true > volume #2 style mesh maximumIntensityProjection false > lighting simple > graphics silhouettes false > hide #!2 models > open S:/Cryo-EM-2024/651-S1-mask.mrc Opened 651-S1-mask.mrc as #3, grid size 432,432,432, pixel 0.825, shown at level 7.52e-06, step 2, values float32 > volume #2 change image level -0.009322,0 level 0.0496,0.8 level 0.4772,1 > volume #2 level 0.08535 > hide #!2 models > volume #3 level 0.07492 > volume #3 style mesh > volume #3 level 0.0896 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > lighting simple > graphics silhouettes false > hide #!3 models > open S:/Cryo-EM-2024/651-S1-mask-interpolated.mrc Opened 651-S1-mask-interpolated.mrc as #4, grid size 540,540,540, pixel 0.66, shown at level 1.89e-05, step 4, values float32 > volume #4 level 0.04861 > volume #4 step 2 > volume #4 style mesh > volume #4 level 0.0887 > volume #4 level 0.1082 > volume #4 level 0.0907 > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > select #1/A:438-456 339 atoms, 347 bonds, 19 residues, 1 model selected > show sel target ab > set bgColor gray > hide sel target a > show sel target ab > hide sel target a > select clear > set bgColor white > select #1/A:438-456 339 atoms, 347 bonds, 19 residues, 1 model selected > show sel target ab > cartoon hide sel > hide sel target a > cartoon sel > select clear > volume #3 level 0.1331 > volume #3 level 0.1487 > show #!2 models > volume #2 level 0.07355 > volume #2 level 0.08535 > hide #!3 models > hide #!2 models > hide #!4 models > set bgColor gray > open ""S:/Cryo-EM-2024/TRPV3-publication preparation/651-ARD-Map.mrc"" Opened 651-ARD-Map.mrc as #5, grid size 432,432,432, pixel 0.825, shown at level 1.61e-05, step 2, values float32 > volume #5 style mesh > volume #5 level 0.03423 > volume #5 level 0.06372 > set bgColor white > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting flat > lighting flat > graphics silhouettes false > lighting flat > lighting flat > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting simple > lighting soft > graphics silhouettes false > lighting simple > volume #5 level 0.0767 > select #1/B-D 26475 atoms, 26736 bonds, 21 pseudobonds, 1611 residues, 2 models selected > cartoon hide (#!1 & sel) > hide #!5 models > show #!5 models > close #3 > close #4 > open ""S:/Cryo-EM-2024/TRPV3-publication preparation/651-ARD-Map- > interpolated.mrc"" Opened 651-ARD-Map-interpolated.mrc as #3, grid size 864,864,864, pixel 0.412, shown at step 1, values float32 > volume #3 region 0,0,0,863,863,863 step 4 > volume #3 region 0,0,0,863,863,863 step 4 > hide #!5 models > volume #3 change image level -1.233e-05,0 level 0.02694,0.8 level 0.2695,1 > volume #3 level 0.03689 > volume #3 level 0.0703 > show #!5 models > hide #!3 models > show #!3 models > hide #!5 models > volume #3 level 0.0726 > show #!2 models > hide #!2 models > save ""S:/Cryo-EM-2024/TRPV3-publication preparation/651-Chain-A_Mesh.cxs"" > save C:\Users\Anon\Desktop\image29.png supersample 3 > open C:/Users/Anon/Box/Cryo- > EM-2024/J350/April2024/May-2024/J350-6dvw-C4_unsharp-phenix-coot-36-chain- > B-_301-SYM- > EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-_301-SYM- EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb #4 --- Chain | Description A C D | No description available B | No description available > ui tool show Matchmaker > matchmaker #!4 to #1 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 J651-refine_320-C1-Chain-A-SYM-EXG_321C2_327C1_328C2_339C1-Del- Helix_refined_345-C1.pdb, chain A (#1) with J350-6dvw-C4_unsharp-phenix- coot-36-chain-B-_301-SYM- EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb, chain C (#4), sequence alignment score = 2362.2 RMSD between 415 pruned atom pairs is 0.639 angstroms; (across all 534 pairs: 2.336) > hide #!3 models > hide #!1 models > select #4/A,B-D 20384 atoms, 20828 bonds, 12 pseudobonds, 2504 residues, 2 models selected > cartoon hide (#!4 & sel) > cartoon (#!4 & sel) > select #4/B-D 15287 atoms, 15620 bonds, 9 pseudobonds, 1878 residues, 2 models selected > cartoon hide (#!4 & sel) > show #!1 models > show #!3 models > select #4/C 5097 atoms, 5208 bonds, 3 pseudobonds, 626 residues, 2 models selected > cartoon (#!4 & sel) > select #4/A 5097 atoms, 5208 bonds, 3 pseudobonds, 626 residues, 2 models selected > cartoon hide (#!4 & sel) > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350-651-Chain- > A-Mesh.cxs"" ——— End of log from Fri May 3 14:03:09 2024 ——— opened ChimeraX session > open ""C:/Users/Mugo/Box/Cryo-EM-2024/Publication > preparation/350-651/350-ChainA masked map.mrc"" Opened 350-ChainA masked map.mrc as #2, grid size 432,432,432, pixel 0.825, shown at level 7.83e-05, step 2, values float32 > hide #!4 models > hide #!2 models > hide #!1 models > show #!2 models > show #!4 models > open C:/Users/Mugo/Box/Cryo-EM-2024/J350/J350-6dvw-C4_unsharp-phenix- > coot-3-sym-2-coot-24-B-chain-A.pdb Chain information for J350-6dvw-C4_unsharp-phenix- coot-3-sym-2-coot-24-B-chain-A.pdb #3 --- Chain | Description A | No description available > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > volume #2 style mesh > volume #2 step 1 > volume #2 step 4 > volume #2 step 2 > color #2 yellow models > save ""C:/Users/Mugo/Box/Cryo-EM-2024/350 mesh-1.cxs"" ——— End of log from Sun Sep 15 01:46:02 2024 ——— opened ChimeraX session restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 655, in restore_snapshot if session.restore_options['combine']: ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ KeyError: 'combine' opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Max 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: Mac16,5 Model Number: MX303LL/A Chip: Apple M4 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 7 days, 13 hours, 5 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2410: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 feedback normal Sessions all ChimeraX