id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15977 Problems with maps in sessions dinesh.indurthi@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description .mrc file does not load from the chimera session even when the session has it. Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""S:/Cryo-EM paper/Figures chimera session files/Fig1/2---Fig1a_b--- > TRPV3-WT_MAP-Model_four-colors-MAP-ChimeraX.cxs"" Error opening map ""S:\Cryo-EM paper\Figures chimera session files\Fig1\2--- Fig1a_b---TRPV3-WT_MAP-Model_four-colors-MAP-ChimeraX.cxs"": File 2---Fig1a_b ---TRPV3-WT_MAP-Model_four-colors-MAP-ChimeraX.cxs, format mrc MRC header value nsymbt (875113504) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""ZoneColor"" returned None restore_snapshot for ""Redust"" returned None restore_snapshot for ""ZoneColor"" returned None Log from Tue Aug 20 19:19:05 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:/Users/anon/Box/Cryo-EM paper/Fig1/Fig1a_b---TRPV3-WT_MAP- > Model_four-colors-Fig1-ChimeraX.cxs"" Opened MV3-WT-cryosparc_P4_J128_007_volume_map_sharp.mrc as #6, grid size 384,384,384, pixel 0.874, shown at level 0.394, step 2, values float32 Log from Mon Aug 19 12:53:56 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:/Users/anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/Fig1-WT-412S-Map_model-3.cxs"" Opened Inverted-MV3-412s-cryosparc-map2-fit-1.mrc as #3, grid size 384,384,384, pixel 0.874, shown at level 0.239, step 2, values float32 Opened MV3-WT-cryosparc_P4_J128_007_volume_map_sharp.mrc as #6, grid size 384,384,384, pixel 0.874, shown at level 0.394, step 2, values float32 Log from Thu May 23 17:58:32 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/Fig1-WT-412S-Map_model-2.cxs"" Opened Inverted-MV3-412s-cryosparc-map2-fit-1.mrc as #3, grid size 384,384,384, pixel 0.874, shown at level 0.239, step 2, values float32 Opened MV3-WT-cryosparc_P4_J128_007_volume_map_sharp.mrc as #6, grid size 384,384,384, pixel 0.874, shown at level 0.394, step 2, values float32 Log from Sun May 5 11:32:39 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"" > hide #!3 models > cartoon (#!4 & sel) > select clear > cartoon #1,4 > hide #!4 models > show #!3 models > select down Nothing selected > select down Nothing selected > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350-651-Chain- > A-MAP.cxs"" includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\session.py"", line 612, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\safesave.py"", line 130, in write self._f.write(buf) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 694, in write compressed = self._compressor.compress(data) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 258, in compress result = compress_chunk( MemoryError MemoryError File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 258, in compress result = compress_chunk( See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 162, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 379, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1285, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\toolbar\\__init__.py"", line 37, in run_provider providers.run_provider(session, name) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\toolbar\providers.py"", line 45, in run_provider what(session) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\toolbar\providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\session.py"", line 612, in save fserialize(stream, data) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\safesave.py"", line 130, in write self._f.write(buf) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 694, in write compressed = self._compressor.compress(data) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 258, in compress result = compress_chunk( MemoryError MemoryError File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\lz4\frame\\__init__.py"", line 258, in compress result = compress_chunk( See log for complete Python traceback. > hide #!3 models > open ""S:/Cryo-EM-2024/TRPV3-publication preparation/350-ChainA-Map.mrc"" Opened 350-ChainA-Map.mrc as #6, grid size 432,432,432, pixel 0.825, shown at level 7.83e-05, step 2, values float32 > show #!4 models > hide #!1 models > hide #!4 models > 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 #7 --- Chain | Description A C D | No description available B | No description available > hide #!6 models > show #!6 models > volume #6 style mesh > volume #6 level 0.02378 > hide #!6 models > open ""S:/Cryo-EM-2024/TRPV3-publication preparation/350-ChainA-Map- > interpolated.mrc"" Opened 350-ChainA-Map-interpolated.mrc as #8, grid size 864,864,864, pixel 0.412, shown at step 1, values float32 > volume #8 region 0,0,0,863,863,863 step 4 > volume #8 region 0,0,0,863,863,863 step 4 > hide #!8 models > show #!8 models > select #7/B-D 15287 atoms, 15620 bonds, 9 pseudobonds, 1878 residues, 2 models selected > cartoon hide (#!7 & sel) > volume #8 change image level -3.265e-06,0 level 0.05567,0.8 level 0.5567,1 > volume #8 level 7.831e-05 > volume #8 step 2 > select #7 20384 atoms, 20828 bonds, 12 pseudobonds, 2504 residues, 2 models selected > ~select #7 Nothing selected > volume #8 step 4 > volume #8 level 0.02378 > volume #8 level 0.06823 > save C:\Users\Anon\Desktop\image30.png supersample 3 > save ""S:/Cryo-EM-2024/TRPV3-publication preparation/350-651-Chain- > A_Mesh.cxs"" > volume #8 color #9999bb > volume #8 color #bb22ff > volume #8 color #b2ffb2 > volume #8 color blue > volume #8 color #0055ff > volume #8 color #00aaff > volume #8 color cyan > volume #8 color #aaffff > volume #8 color cyan > volume #8 color #aaaaff > volume #8 color #55ffff > volume #8 color #5555ff > volume #8 color #bb22ff > volume #8 color #b2ffb2 > save C:\Users\Anon\Desktop\image31.png supersample 3 > volume #8 level 0.08898 > save C:\Users\Anon\Desktop\image32.png supersample 3 > volume #8 level 0.09046 > volume #8 step 2 > hide #!7 models > show #!3 models > hide #!8 models > show #!1 models > volume #3 step 2 > select #1/B-D 26475 atoms, 26736 bonds, 21 pseudobonds, 1611 residues, 2 models selected > cartoon hide (#!1 & sel) > volume #3 level 0.07132 > volume #3 step 4 > volume #3 step 2 > volume #3 level 0.07903 > save C:\Users\Anon\Desktop\image33.png supersample 3 > save C:\Users\Anon\Desktop\image34.png supersample 3 > volume #3 step 4 > save C:\Users\Anon\Desktop\image35.png supersample 3 > hide #!1 models > hide #!3 models > show #!4 models > hide #!4 models > show #!7 models > show #!8 models > volume #8 step 4 > save C:\Users\Anon\Desktop\image36.png supersample 3 > save ""S:/Cryo-EM-2024/TRPV3-publication preparation/350-651-Chain- > A_Mesh.cxs"" > hide #!8 models > hide #!7 models > show #!4 models > show #!1 models > hide #!4 models > cartoon (#!1 & sel) > select clear > show #!4 models > set bgColor black > select #1/A 8825 atoms, 8912 bonds, 7 pseudobonds, 537 residues, 2 models selected > select #4/A 5097 atoms, 5208 bonds, 3 pseudobonds, 626 residues, 2 models selected > select clear QFileSystemWatcher: FindNextChangeNotification failed for ""S:\Cryo- EM-2024\TRPV3-publication preparation"" (The specified network name is no longer available.) > hide #!1 models > select #4:584 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel target ab > color sel forest green > select #4:518 32 atoms, 28 bonds, 4 residues, 1 model selected > color sel light sea green > show sel atoms > select #4:651 48 atoms, 48 bonds, 4 residues, 1 model selected > show sel atoms > select #4:654 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > color sel lime > select #4:657 44 atoms, 44 bonds, 4 residues, 1 model selected > show sel atoms > color sel lime > select #4:518 32 atoms, 28 bonds, 4 residues, 1 model selected > select #4:521 20 atoms, 16 bonds, 4 residues, 1 model selected > show sel atoms > color sel lime > select #4:565 48 atoms, 48 bonds, 4 residues, 1 model selected > hide sel atoms > show sel atoms > color sel blue > select #4:501 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > color sel blue > select #4:704 44 atoms, 44 bonds, 4 residues, 1 model selected > hide sel atoms > show sel atoms > color sel blue > close #8 > close #3 > close #2 > close #5 > close #6 > select #4:643 32 atoms, 28 bonds, 4 residues, 1 model selected > color sel red > color sel magenta > show sel target ab > select #4:644 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > color sel magenta > select #4:647 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > color sel magenta > select #4:657 44 atoms, 44 bonds, 4 residues, 1 model selected > color sel magenta > select #4:661 28 atoms, 24 bonds, 4 residues, 1 model selected > show sel atoms > color sel magenta > select #4:661 28 atoms, 24 bonds, 4 residues, 1 model selected > select clear > select #4:661 28 atoms, 24 bonds, 4 residues, 1 model selected > show #!1 models > close #1 > close > open C:/Users/Anon/Box/Cryo-EM-2024/WT-TRPV3/WT- > March-2024/rsr25_mTRPV3WT_Coot-24_chain-D- > refined_063-SYM_refined_068_214-217-220-223_real_space_refined_244.pdb Chain information for rsr25_mTRPV3WT_Coot-24_chain-D- refined_063-SYM_refined_068_214-217-220-223_real_space_refined_244.pdb #1 --- Chain | Description A B C D | No description available > open C:/Users/Anon/Box/Cryo- > EM-2024/412s/412S-March2024/Summary/mTRPV3-412s-refined_085-coot3_8-Lipids1-2_real_space_refined_289-coot1.pdb Chain information for mTRPV3-412s-refined_085-coot3_8-Lipids1-2_real_space_refined_289-coot1.pdb #2 --- Chain | Description A B C D | No description available > ui tool show Matchmaker > matchmaker #!2 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 rsr25_mTRPV3WT_Coot-24_chain-D- refined_063-SYM_refined_068_214-217-220-223_real_space_refined_244.pdb, chain A (#1) with mTRPV3-412s-refined_085-coot3_8-Lipids1-2_real_space_refined_289-coot1.pdb, chain A (#2), sequence alignment score = 2943.8 RMSD between 597 pruned atom pairs is 0.457 angstroms; (across all 616 pairs: 1.069) > set bgColor white > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > hide target a > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/WT-412S-All-1.cxs"" > save C:\Users\Anon\Desktop\image37.png supersample 3 > select #1/B-D 15212 atoms, 15540 bonds, 9 pseudobonds, 1862 residues, 2 models selected > cartoon hide (#!1 & sel) > select #2/B-D 15204 atoms, 15522 bonds, 12 pseudobonds, 1857 residues, 2 models selected > cartoon hide (#!2 & sel) > save C:\Users\Anon\Desktop\image38.png supersample 3 > hide #!1 models > hide #!2 models > open C:/Users/Anon/Box/Cryo-EM-2024/412s/Inverted-MV3-412s-cryosparc- > map2-fit-1.mrc Opened Inverted-MV3-412s-cryosparc-map2-fit-1.mrc as #3, grid size 384,384,384, pixel 0.874, shown at level 0.148, step 2, values float32 > show #!2 models > hide #!2 models > volume #3 level 0.5049 > volume #3 step 4 > volume #3 step 2 > volume #3 level 0.3109 > preset ""overall look"" interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f > set bgColor white > volume #3 level 0.4273 > open C:/Users/Anon/Box/Cryo- > EM-2024/412s/412S-March2024/Summary/mTRPV3-412s-refined_085-coot3_8-Lipids1-2_real_space_refined_289-coot1.pdb Chain information for mTRPV3-412s-refined_085-coot3_8-Lipids1-2_real_space_refined_289-coot1.pdb #4 --- Chain | Description A B C D | No description available > volume #3 level 0.2643 > volume #3 step 1 > volume #3 level 0.2955 > ui tool show ""Hide Dust"" > ui tool show ""Hide Dust"" > volume #3 level 0.4407 > volume #3 step 2 > volume #3 level 0.2545 > hide #3-4 target a > volume #3 level 0.2933 > transparency #3-4 30 > volume #3 step 4 > volume #3 step 2 > ui tool show ""Volume Viewer"" > surface dust #3 size 5.24 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > volume #3 level 0.3088 > volume #3 level 0.239 > save C:\Users\Anon\Desktop\image39.png supersample 3 > hide #!3 models > hide #!4 models > open C:/Users/Anon/Box/Cryo-EM-2024/WT-TRPV3/WT- > March-2024/rsr25_mTRPV3WT_Coot-24_chain-D- > refined_063-SYM_refined_068_214-217-220-223_real_space_refined_244.pdb Chain information for rsr25_mTRPV3WT_Coot-24_chain-D- refined_063-SYM_refined_068_214-217-220-223_real_space_refined_244.pdb #5 --- Chain | Description A B C D | No description available > open C:/Users/Anon/Box/Cryo-EM-2024/WT-TRPV3/MV3-WT- > cryosparc_P4_J128_007_volume_map_sharp.mrc Opened MV3-WT-cryosparc_P4_J128_007_volume_map_sharp.mrc as #6, grid size 384,384,384, pixel 0.874, shown at level 0.202, step 2, values float32 > surface dust #6 size 5.24 > volume #6 level -0.1302 > volume #6 level 0.2682 > volume #6 level 0.4453 > transparency #5-6 30 > close #1 > close #2 > volume #6 level 0.4011 > volume #6 level 0.3125 > transparency #5-6 20 > show #!3 models > show #!4 models > hide #!5 models > hide #!6 models > transparency #3-4 30 > hide #!4 models > hide #!3 models > show #!5 models > show #!6 models > volume #6 level 0.3679 > volume #6 level 0.3236 > volume #6 level 0.239 > volume #6 level 0.3165 > volume #6 level 0.2833 > volume #6 level 0.394 > save C:\Users\Anon\Desktop\image40.png supersample 3 > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/WT-412S-Map_model-2.cxs"" ——— End of log from Sun May 5 11:32:39 2024 ——— opened ChimeraX session > hide #!6 models > select #5 20320 atoms, 20756 bonds, 12 pseudobonds, 2484 residues, 2 models selected > surface (#!5 & sel) > hide #!5 models > ~select #5 4 models selected > show #!3 models > hide #!3 models > show #!4 models > select #4/A 5068 atoms, 5175 bonds, 4 pseudobonds, 619 residues, 2 models selected > surface (#!4 & sel) > color (#!4 & sel) purple > select #4/B 5068 atoms, 5174 bonds, 4 pseudobonds, 619 residues, 2 models selected > surface (#!4 & sel) > color (#!4 & sel) orange red > select #4/c 5068 atoms, 5174 bonds, 4 pseudobonds, 619 residues, 2 models selected > surface (#!4 & sel) > color (#!4 & sel) hot pink > select #4/d 5068 atoms, 5174 bonds, 4 pseudobonds, 619 residues, 2 models selected > surface (#!4 & sel) > color (#!4 & sel) yellow > select #4/b 5068 atoms, 5174 bonds, 4 pseudobonds, 619 residues, 2 models selected > select #4/c 5068 atoms, 5174 bonds, 4 pseudobonds, 619 residues, 2 models selected > color (#!4 & sel) cornflower blue > select clear > save C:\Users\Anon\Desktop\image1.png supersample 3 > select #4 20272 atoms, 20697 bonds, 16 pseudobonds, 2476 residues, 2 models selected > surface hidePatches (#!4 & sel) > ~select #4 4 models selected > select #4 20272 atoms, 20697 bonds, 16 pseudobonds, 2476 residues, 2 models selected > ~select #4 4 models selected > select #4/a 5068 atoms, 5175 bonds, 4 pseudobonds, 619 residues, 2 models selected > color (#!4 & sel) #ff55ffff > surface (#!4 & sel) > select clear > surface #4 > save C:\Users\Anon\Desktop\image2.png supersample 3 > hide #!4 models > show #!5 models > select #5/a 5108 atoms, 5216 bonds, 3 pseudobonds, 622 residues, 2 models selected > color (#!5 & sel) cyan > select clear > hide #!5 atoms > show #!5 atoms > hide #!5 atoms > save C:\Users\Anon\Desktop\image3.png supersample 3 > surface hidePatches #5 > show #!4 models > hide #!5 models > show #!4 cartoons > surface hidePatches #4 > save C:\Users\Anon\Desktop\image4.png supersample 3 > hide #!4 models > show #!5 models > surface #5 > show #!5 cartoons > surface hidePatches #5 Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. > show #!6 models > color zone #6 near #5 distance 5.24 > color zone #6 near #5 distance 5.24 > color zone #6 near #5 distance 5.24 > hide #!6 models > select #5/b 5080 atoms, 5189 bonds, 3 pseudobonds, 621 residues, 2 models selected > color (#!5 & sel) orange > color (#!5 & sel) byhetero > ui tool show ""Color Actions"" > color sel salmon > select #5/c 5052 atoms, 5162 bonds, 3 pseudobonds, 620 residues, 2 models selected > color sel olive drab > select #5/d 5080 atoms, 5189 bonds, 3 pseudobonds, 621 residues, 2 models selected > color sel dark khaki > select clear > select #5/c 5052 atoms, 5162 bonds, 3 pseudobonds, 620 residues, 2 models selected > ui tool show ""Color Actions"" > color sel olive drab > color sel green > color sel olive drab > color sel medium sea green > color sel sea green > color sel sea green > color sel olive drab > color sel green yellow > color sel olive drab > select clear > select #5/c 5052 atoms, 5162 bonds, 3 pseudobonds, 620 residues, 2 models selected > color sel teal > color sel green > color sel sea green > color sel olive drab > color sel cadet blue > color sel sea green > color sel olive drab > color sel medium sea green > color sel olive drab > surface (#!5 & sel) > color sel yellow green > color sel green > color sel spring green > color sel lime green > color sel forest green > color sel green > color sel olive drab > color sel green > surface hidePatches (#!5 & sel) > select clear > save C:\Users\Anon\Desktop\image5.png supersample 3 > save C:\Users\Anon\Desktop\image6.png supersample 3 > surface #5 > save C:\Users\Anon\Desktop\image7.png supersample 3 > surface hidePatches #5 > show #!4 models > hide #!5 models > save ""C:/Users/Anon/Box/Cryo-EM-2024/Publication > preparation/Chimera/Fig1-WT-412S-Map_model-3.cxs"" ——— End of log from Thu May 23 17:58:32 2024 ——— opened ChimeraX session > close #3 > close #4 > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > save ""S:/Cryo-EM paper/TRPV3-Structures_Raw-data/TRPV3-WT/TRPV3-WT_MAP- > Model_four-colors-Fig1-ChimeraX.cxs"" ——— End of log from Mon Aug 19 12:53:56 2024 ——— opened ChimeraX session > show #!6 models > color zone #6 near #5 distance 5.24 > hide #!6 models > hide #!5 models > show #!6 models > save ""C:/Users/anon/Box/Cryo-EM paper/Fig1/New figures/Fig1a_b--- > TRPV3-WT_MAP-Model_four-colors-MAP-ChimeraX.cxs"" > save C:\Users\anon/Desktop\image22.png supersample 3 > save ""S:/Cryo-EM paper/Figures chimera session files/Fig1/2---Fig1a_b--- > TRPV3-WT_MAP-Model_four-colors-MAP-ChimeraX.cxs"" ——— End of log from Tue Aug 20 19:19:05 2024 ——— opened ChimeraX session OpenGL version: 3.3.0 - Build 30.0.101.1338 OpenGL renderer: Intel(R) Iris(R) Plus Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: Dell Inc. Model: XPS 13 7390 2-in-1 OS: Microsoft Windows 11 Pro (Build 22631) Memory: 16,938,192,896 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 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: 2024.6.2 cftime: 1.6.4 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: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 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: 1.2.7 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: 1.0.5 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: 1.8 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: 1.2.4 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.13.5 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: 3.0.15 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: 1.16.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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 comtypes: 1.4.1 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: 4.53.0 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: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 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: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 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 pywin32: 306 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 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: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1 }}} " defect closed normal Sessions not a bug all ChimeraX