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Opened 13 months ago
Closed 13 months ago
#15977 closed defect (not a bug)
Problems with maps in sessions
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problems with maps in sessions |
comment:2 by , 13 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
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See TracTickets
for help on using tickets.
ChimeraX sessions include a file path to map (.mrc) files when the session used a map opened from a file. If you later move or remove that .mrc file then when you open the session it will ask you to choose in a File browser the original .mrc file (if it was just moved somewhere). It appears you instead chose the ".cxs" file. That is not what it is asking for. You have to either choose the original .mrc file (located in some new location on your computer), or you can press cancel on the file chooser and it will open the rest of your session but not that map.
When you save a session if you would instead like to include the maps in the session (.cxs) file you can click the "Copy maps into session file option" on the Save dialog. This will make the session file much larger since the map files are usually large.