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Opened 9 months ago
Last modified 9 months ago
#17081 feedback defect
Session restore: KeyError: "combine"
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/andymugo/Library/CloudStorage/Box-Box/Cryo-EM-2024/350
> mesh-1.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Sun Sep 15 01:46:02 2024UCSF ChimeraX version: 1.8.dev202405040553
(2024-05-04)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/Mugo/Box/Cryo-EM-2024/Publication
> preparation/350-651/350-651-Chain-A-Mesh.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "VolumeImage" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeImage" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Fri May 3 14:03:09 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and
> 651-pdb-Yellow.cxs"
Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size
432,432,432, pixel 0.825, shown at level 0.0986, step 2, values float32
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel
0.825, shown at level 0.0871, step 2, values float32
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel
0.825, shown at level 0.0858, step 2, values float32
Log from Tue Apr 30 09:24:33 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Anon/Box/Cryo-EM-2024/Publication
> preparation/Chimera/350-651-Del1.cxs"
Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size
432,432,432, pixel 0.825, shown at level 0.101, step 2, values float32
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel
0.825, shown at level 0.0871, step 2, values float32
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel
0.825, shown at level 0.0858, step 2, values float32
Log from Sun Apr 28 17:51:21 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Deferring bundle installation
> open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp-
> phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3.pdb
Summary of feedback from opening C:/Users/Anon/Box/Cryo-
EM-2024/J350/April2024/J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C3.pdb
---
warning | Ignored bad PDB record found on line 20823
END
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C3.pdb #1
---
Chain | Description
A B C D | No description available
> select #1: 551-652
3012 atoms, 3072 bonds, 4 pseudobonds, 384 residues, 2 models selected
> select #1: 551-555
136 atoms, 132 bonds, 20 residues, 1 model selected
> select #1: 651-655
184 atoms, 192 bonds, 20 residues, 1 model selected
> select #1: 651-658
292 atoms, 304 bonds, 32 residues, 1 model selected
> open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel
0.825, shown at level 0.0496, step 2, values float32
> hide #!1 models
> hide #!2 models
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J350/J350_009_C4-unsharp_volume_map_inverted.mrc
Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #3, grid size
432,432,432, pixel 0.825, shown at level 0.0473, step 2, values float32
> hide #!3 models
> show #!1 models
> select #1: 651-665
524 atoms, 540 bonds, 60 residues, 1 model selected
> color sel red
> select #1: 602-608
184 atoms, 184 bonds, 28 residues, 1 model selected
> color sel lime
> select #1: 550-557
208 atoms, 204 bonds, 32 residues, 1 model selected
> color sel cyan
> select #1: 565
48 atoms, 48 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1: 707
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1: 445
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1: 494
56 atoms, 60 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1: 704
44 atoms, 44 bonds, 4 residues, 1 model selected
> show sel atoms
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J350/J350_009_C4-unsharp_volume_map_inverted.mrc
Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #4, grid size
432,432,432, pixel 0.825, shown at level 0.0473, step 2, values float32
> volume #2 level 0.07679
> hide #!2 models
> volume #3 level 0.1024
> volume #2 level 0.1241
> hide #!2 models
> volume #2 level 0.09892
> hide #!2 models
> volume #3 level 0.1996
> hide #!3 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.1574
> select clear
> hide #!1 models
> show #!1 models
> volume #3 level 0.1151
> volume #3 level 0.08445
> volume #3 level 0.1151
> transparency #1,3 40
> set bgColor white
> transparency #1,3 20
> transparency #1,3 30
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> transparency #1,3 30
> volume #3 level 0.08956
> volume #3 level 0.119
> volume #3 level 0.09468
> volume #3 step 1
> volume #3 level 0.08651
> volume #3 level 0.1328
> volume #3 level 0.1056
> hide #!3 models
> cartoon #1
> hide atoms
> select /B:712
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!3 models
> volume #3 level 0.09876
> volume #3 step 4
> volume #3 level 0.08879
> transparency #1,3 20
> volume #3 step 2
> volume #3 level 0.1093
> volume #3 level 0.1029
> transparency #1,3 30
> volume #3 level 0.1003
> save C:\Users\Anon\Desktop\image1.png supersample 3
> close #4
> hide #!3 models
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
> EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb
Chain information for J651-refine_320-C1-Chain-A-SYM-
EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb #4
---
Chain | Description
A B C D | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3.pdb, chain A (#1) with J651-refine_320-C1-Chain-A-SYM-
EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb, chain A
(#4), sequence alignment score = 2373.2
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs:
2.353)
> hide #!1 models
> show #!2 models
> volume #2 level 0.07779
> volume #2 level 0.07679
> close #2
> open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel
0.825, shown at level 0.0496, step 2, values float32
> volume #3 level 0.153
> volume #2 level 0.09498
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> show #!3 models
> volume #3 level 0.1018
> volume #3 level 0.1005
> close #2
> close #4
> save "S:/Cryo-EM paper/Structures/J350.cxs"
> hide #!1 models
> hide #!3 models
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
> EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb
Chain information for J651-refine_320-C1-Chain-A-SYM-
EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb #2
---
Chain | Description
A B C D | No description available
> open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #4, grid size 432,432,432, pixel
0.825, shown at level 0.0496, step 2, values float32
> volume #4 level 0.08019
> transparency #2,4 30
> volume #4 level 0.093
> transparency #2,4 30
> volume #4 level 0.08906
> volume #4 level 0.08709
> volume #4 level 0.07625
> volume #4 level 0.08709
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and
> 651.cxs"
> save C:\Users\Anon\Desktop\image2.png supersample 3
> volume #4 level 0.08512
> save C:\Users\Anon\Desktop\image3.png supersample 3
> volume #4 level 0.08906
> volume #4 level 0.08709
> save C:\Users\Anon\Desktop\image4.png supersample 3
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J651-refine_320-C1-Chain-A-SYM-
EXG_refined_321-C2_refined_327-C1_refined_328-C2_refined_339-C1.pdb, chain A
(#2) with J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3.pdb, chain A (#1), sequence alignment score = 2373.2
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs:
2.353)
> save C:\Users\Anon\Desktop\image5.png supersample 3
> save C:\Users\Anon\Desktop\image6.png supersample 3
> save C:\Users\Anon\Desktop\image7.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and
> 651-super imposition.cxs"
> hide #!1 models
> delete #2?B-D
Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid
> delete #2/B-D
> save C:\Users\Anon\Desktop\image8.png supersample 3
> select #2:611-609
Nothing selected
> select #2:636-639
59 atoms, 58 bonds, 4 residues, 1 model selected
> select #2:636-649
59 atoms, 58 bonds, 4 residues, 1 model selected
> select #2:626-649
192 atoms, 192 bonds, 12 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> select #2:600-610
146 atoms, 146 bonds, 11 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> select #2:651-660
188 atoms, 191 bonds, 10 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> save C:\Users\Anon\Desktop\image9.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication
> preparation/Chimera/651-Chain-A-1.cxs"
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> delete #1/B-D
> save C:\Users\Anon\Desktop\image10.png supersample 3
> set bgColor black
> open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp-
> phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C2.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C2.pdb #5
---
Chain | Description
A B C D | No description available
> hide #!1 models
> open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp-
> phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C3-DEL.pdb #6
---
Chain | Description
A B C D | No description available
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> close #5
> show #!6 models
> open C:/Users/Anon/Box/Cryo-EM-2024/WT-TRPV3/WT-
> March-2024/rsr25_mTRPV3WT_Coot-25_Lipid-chain-
> D_063-SYM_refined_068-coot-0.pdb
Chain information for rsr25_mTRPV3WT_Coot-25_Lipid-chain-
D_063-SYM_refined_068-coot-0.pdb #5
---
Chain | Description
A B C D | No description available
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #!6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rsr25_mTRPV3WT_Coot-25_Lipid-chain-
D_063-SYM_refined_068-coot-0.pdb, chain A (#5) with J350-6dvw-C4_unsharp-
phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL.pdb, chain B
(#6), sequence alignment score = 2924.7
RMSD between 368 pruned atom pairs is 1.357 angstroms; (across all 620 pairs:
2.148)
> hide #!6 models
> show #!6 models
> close #5
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
> EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb
Chain information for J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb #5
---
Chain | Description
A B C D | No description available
> hide #!2 models
> set bgColor white
> show #!6 models
> hide #!5 models
> show #!3 models
> ui tool show "Fit in Map"
Fit molecule J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb (#6) to map
J350_009_C4-unsharp_volume_map_inverted.mrc (#3) using 20632 atoms
average map value = 0.04263, steps = 120
shifted from previous position = 6.07
rotated from previous position = 6.07 degrees
atoms outside contour = 18069, contour level = 0.10051
Position of J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb (#6) relative to
J350_009_C4-unsharp_volume_map_inverted.mrc (#3) coordinates:
Matrix rotation and translation
0.99881314 -0.01633320 -0.04588611 7.41119432
-0.01910814 -0.99797302 -0.06070194 357.63323973
-0.04480164 0.06150669 -0.99710067 339.43075599
Axis 0.99970296 -0.00887126 -0.02269990
Axis point 0.00000000 173.65759994 175.27064473
Rotation angle (degrees) 176.49575605
Shift along axis -3.46870759
> hide #!3 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!5 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb, chain A (#6) with J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#5), sequence
alignment score = 2373.2
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs:
2.353)
> hide #!6 models
> set bgColor black
> select #5:600
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel target a
> cartoon hide sel
> show #!4 models
> hide #!4 models
> open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #7, grid size 432,432,432, pixel
0.825, shown at level 0.0496, step 2, values float32
> hide #!5 models
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
> EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb
Chain information for J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb #8
---
Chain | Description
A B C D | No description available
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume #7 level 0.08575
> transparency #7-8 30
> transparency #7-8 20
> hide #!7 models
> select #8:600
32 atoms, 28 bonds, 4 residues, 1 model selected
> cartoon hide sel
> select #8:660
76 atoms, 72 bonds, 4 residues, 1 model selected
> cartoon hide sel
> show #!7 models
> set bgColor white
> save C:\Users\Anon\Desktop\image11.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication
> preparation/Chimera/651-Del1.cxs"
> hide #!7 models
> hide #!8 models
> show #!2 models
> set bgColor black
> cartoon #2
> set bgColor white
> save C:\Users\Anon\Desktop\image12.png supersample 3
> hide #!2 models
> show #!8 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #!6 to #8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8) with
J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb, chain A (#6), sequence alignment score = 4
Fewer than 3 residues aligned; cannot match J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A with
J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb, chain A
> ui tool show Matchmaker
> matchmaker #!6 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8) with
J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL.pdb, chain A (#6), sequence alignment score = 2373.2
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 536 pairs:
2.353)
> save C:\Users\Anon\Desktop\image13.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication
> preparation/Chimera/350-651-Del1.cxs"
——— End of log from Sun Apr 28 17:51:21 2024 ———
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!1 models
> hide #!8 models
> hide #!1 models
> open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp-
> phenix-coot-36-chain-B-refined_301-SYM-EXG_refined_309-C3-DEL2-C2.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C3-DEL2-C2.pdb #9
---
Chain | Description
A C D | No description available
B | No description available
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!3 models
> volume #3 level 0.09856
> hide #!3 models
> open C:/Users/Anon/Box/Cryo-EM-2024/J350/April2024/J350-6dvw-C4_unsharp-
> phenix-coot-36-chain-B-refined_301-SYM-
> EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-
refined_301-SYM-EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb #10
---
Chain | Description
A C D | No description available
B | No description available
> hide #!9 models
> show #!3 models
> show #!9 models
> hide #!3 models
> hide #!10 models
> show #!3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!8 models
> save C:\Users\Anon\Desktop\image17.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350-.cxs"
> hide #!3 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!8 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-refined_301-SYM-
EXG_refined_309-C3-DEL2-C2_real_space_refined_344.pdb, chain A (#10) with
J651-refine_320-C1-Chain-A-SYM-
EXG_321-C2_327-C1__328-C2_refined_339-C1-Del.pdb, chain A (#8), sequence
alignment score = 2370.6
RMSD between 412 pruned atom pairs is 0.616 angstroms; (across all 536 pairs:
2.358)
> save C:\Users\Anon\Desktop\image18.png supersample 3
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350 and
> 651-pdb-Yellow.cxs"
——— End of log from Tue Apr 30 09:24:33 2024 ———
opened ChimeraX session
> set bgColor gray
> set bgColor black
> close
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
> EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb
Summary of feedback from opening C:/Users/Anon/Box/Cryo-
EM-2024/J651/April-2024/651-Summary/J651-refine_320-C1-Chain-A-SYM-
EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 29 29 GLY A 601 SER A 608 1 8
Start residue of secondary structure not found: HELIX 61 61 GLY B 601 SER B
608 1 8
Start residue of secondary structure not found: HELIX 93 93 GLY C 601 SER C
608 1 8
Start residue of secondary structure not found: HELIX 125 125 GLY D 601 SER D
608 1 8
Chain information for J651-refine_320-C1-Chain-A-SYM-
EXG_321C2_327C1_328C2_339C1-Del-Helix_refined_345-C1.pdb #1
---
Chain | Description
A B C D | No description available
> set bgColor gray
> open C:/Users/Anon/Box/Cryo-EM-2024/J651/C4-J651_012_volume_map_inv_2_7A.mrc
Opened C4-J651_012_volume_map_inv_2_7A.mrc as #2, grid size 432,432,432, pixel
0.825, shown at level 0.0496, step 2, values float32
> volume #2 level 0.07958
> surface style mesh
> set bgColor white
> volume #2 style image maximumIntensityProjection true
> volume #2 style mesh maximumIntensityProjection false
> lighting simple
> graphics silhouettes false
> hide #!2 models
> open S:/Cryo-EM-2024/651-S1-mask.mrc
Opened 651-S1-mask.mrc as #3, grid size 432,432,432, pixel 0.825, shown at
level 7.52e-06, step 2, values float32
> volume #2 change image level -0.009322,0 level 0.0496,0.8 level 0.4772,1
> volume #2 level 0.08535
> hide #!2 models
> volume #3 level 0.07492
> volume #3 style mesh
> volume #3 level 0.0896
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> lighting simple
> graphics silhouettes false
> hide #!3 models
> open S:/Cryo-EM-2024/651-S1-mask-interpolated.mrc
Opened 651-S1-mask-interpolated.mrc as #4, grid size 540,540,540, pixel 0.66,
shown at level 1.89e-05, step 4, values float32
> volume #4 level 0.04861
> volume #4 step 2
> volume #4 style mesh
> volume #4 level 0.0887
> volume #4 level 0.1082
> volume #4 level 0.0907
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:438-456
339 atoms, 347 bonds, 19 residues, 1 model selected
> show sel target ab
> set bgColor gray
> hide sel target a
> show sel target ab
> hide sel target a
> select clear
> set bgColor white
> select #1/A:438-456
339 atoms, 347 bonds, 19 residues, 1 model selected
> show sel target ab
> cartoon hide sel
> hide sel target a
> cartoon sel
> select clear
> volume #3 level 0.1331
> volume #3 level 0.1487
> show #!2 models
> volume #2 level 0.07355
> volume #2 level 0.08535
> hide #!3 models
> hide #!2 models
> hide #!4 models
> set bgColor gray
> open "S:/Cryo-EM-2024/TRPV3-publication preparation/651-ARD-Map.mrc"
Opened 651-ARD-Map.mrc as #5, grid size 432,432,432, pixel 0.825, shown at
level 1.61e-05, step 2, values float32
> volume #5 style mesh
> volume #5 level 0.03423
> volume #5 level 0.06372
> set bgColor white
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting simple
> volume #5 level 0.0767
> select #1/B-D
26475 atoms, 26736 bonds, 21 pseudobonds, 1611 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide #!5 models
> show #!5 models
> close #3
> close #4
> open "S:/Cryo-EM-2024/TRPV3-publication preparation/651-ARD-Map-
> interpolated.mrc"
Opened 651-ARD-Map-interpolated.mrc as #3, grid size 864,864,864, pixel 0.412,
shown at step 1, values float32
> volume #3 region 0,0,0,863,863,863 step 4
> volume #3 region 0,0,0,863,863,863 step 4
> hide #!5 models
> volume #3 change image level -1.233e-05,0 level 0.02694,0.8 level 0.2695,1
> volume #3 level 0.03689
> volume #3 level 0.0703
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> volume #3 level 0.0726
> show #!2 models
> hide #!2 models
> save "S:/Cryo-EM-2024/TRPV3-publication preparation/651-Chain-A_Mesh.cxs"
> save C:\Users\Anon\Desktop\image29.png supersample 3
> open C:/Users/Anon/Box/Cryo-
> EM-2024/J350/April2024/May-2024/J350-6dvw-C4_unsharp-phenix-coot-36-chain-
> B-_301-SYM-
> EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-coot-36-chain-B-_301-SYM-
EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb #4
---
Chain | Description
A C D | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J651-refine_320-C1-Chain-A-SYM-EXG_321C2_327C1_328C2_339C1-Del-
Helix_refined_345-C1.pdb, chain A (#1) with J350-6dvw-C4_unsharp-phenix-
coot-36-chain-B-_301-SYM-
EXG_309-C3-DEL2-C2-EXG309C3EXG344_348-C2_354-C1_359-C5_refined_366-C1.pdb,
chain C (#4), sequence alignment score = 2362.2
RMSD between 415 pruned atom pairs is 0.639 angstroms; (across all 534 pairs:
2.336)
> hide #!3 models
> hide #!1 models
> select #4/A,B-D
20384 atoms, 20828 bonds, 12 pseudobonds, 2504 residues, 2 models selected
> cartoon hide (#!4 & sel)
> cartoon (#!4 & sel)
> select #4/B-D
15287 atoms, 15620 bonds, 9 pseudobonds, 1878 residues, 2 models selected
> cartoon hide (#!4 & sel)
> show #!1 models
> show #!3 models
> select #4/C
5097 atoms, 5208 bonds, 3 pseudobonds, 626 residues, 2 models selected
> cartoon (#!4 & sel)
> select #4/A
5097 atoms, 5208 bonds, 3 pseudobonds, 626 residues, 2 models selected
> cartoon hide (#!4 & sel)
> save "C:/Users/Anon/Box/Cryo-EM-2024/Publication preparation/350-651-Chain-
> A-Mesh.cxs"
——— End of log from Fri May 3 14:03:09 2024 ———
opened ChimeraX session
> open "C:/Users/Mugo/Box/Cryo-EM-2024/Publication
> preparation/350-651/350-ChainA masked map.mrc"
Opened 350-ChainA masked map.mrc as #2, grid size 432,432,432, pixel 0.825,
shown at level 7.83e-05, step 2, values float32
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!4 models
> open C:/Users/Mugo/Box/Cryo-EM-2024/J350/J350-6dvw-C4_unsharp-phenix-
> coot-3-sym-2-coot-24-B-chain-A.pdb
Chain information for J350-6dvw-C4_unsharp-phenix-
coot-3-sym-2-coot-24-B-chain-A.pdb #3
---
Chain | Description
A | No description available
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> volume #2 style mesh
> volume #2 step 1
> volume #2 step 4
> volume #2 step 2
> color #2 yellow models
> save "C:/Users/Mugo/Box/Cryo-EM-2024/350 mesh-1.cxs"
——— End of log from Sun Sep 15 01:46:02 2024 ———
opened ChimeraX session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 655, in restore_snapshot
if session.restore_options['combine']:
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'combine'
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,5
Model Number: MX303LL/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 7 days, 13 hours, 5 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2410:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (4)
comment:1 by , 9 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Session restore: KeyError: "combine" |
comment:2 by , 9 months ago
| Status: | accepted → feedback |
|---|
comment:3 by , 9 months ago
Hi Eric,
Thank you for your response.
The data is unpublished, probably later on when we submit the paper, I can provide the files.
Thank you.
Best regards,
Andrew
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, March 13, 2025 5:39 PM
To: Andrew Mugo <anmugo@buffalo.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #17081: Session restore: KeyError: "combine"
#17081: Session restore: KeyError: "combine"
-------------------------------+----------------------
Reporter: anmugo@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------+----------------------
Changes (by pett):
* status: accepted => feedback
Comment:
Hi Andrew,
Thanks for reporting this problem. Looking at the relevant code
it would seem to be impossible, yet clearly somehow it isn't. Is there
any chance you could provide the session file that generates this error?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
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comment:4 by , 9 months ago
We haven't gotten any other reports of this so far, so I will be intrigued to see your session file once it's available.
--Eric
Note:
See TracTickets
for help on using tickets.
Hi Andrew,
--Eric