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Opened 3 years ago
Closed 3 years ago
#8791 closed defect (not a bug)
read_full_array: Device not configured
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/Current/040523/Figure1.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #1, grid size 220,220,220,
pixel 1.67, shown at level 0.0215, step 1, values float32
Opened deepemhancer_highres_flip.mrc as #2, grid size 220,220,220, pixel 1.68,
shown at level 0.0433, step 1, values float32
Log from Wed Apr 5 13:12:12 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/cxs_figures/figure1.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0215, step 1, values float32
Opened deepemhancer_highres_flip.mrc as #11, grid size 220,220,220, pixel
1.68, shown at level 0.075, step 1, values float32
Log from Tue Jan 31 13:12:49 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/013023.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0215, step 1, values float32
Opened deepemhancer_highres_flip.mrc as #11, grid size 220,220,220, pixel
1.68, shown at level 0.015, step 1, values float32
Log from Mon Jan 30 14:22:52 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/012523.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Opened deepemhancer_highres_flip.mrc as #11, grid size 220,220,220, pixel
1.68, shown at level 0.111, step 1, values float32
Log from Wed Jan 25 14:54:26 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/012323.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Log from Mon Jan 23 15:29:22 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Log from Fri Jan 20 15:36:51 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Log from Mon Jan 16 15:41:27 2023
> lighting soft
> set bgColor white
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_19/NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb
Chain information for NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb
#1
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb
Chain information for 01123_real_space_refined_021.pdb #2
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_22/01123_real_space_refined_022.pdb
Chain information for 01123_real_space_refined_022.pdb #3
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open /Users/amberms/Desktop/group/Modeling/122122/01123.pdb
Summary of feedback from opening
/Users/amberms/Desktop/group/Modeling/122122/01123.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
23743 messages similar to the above omitted
Chain information for 01123.pdb #4
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide atoms
> show cartoons
> select #1:A:402,411,412,414,471,474,478,481
517 atoms, 525 bonds, 24 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select #1/A:402,411,412,414,471,474,478,481
124 atoms, 120 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 124 atom styles
> color sel yellow
> select #1/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 135 atom styles
> style sel ball
Changed 135 atom styles
> color sel yellow
> select #A/C:402,411,412,414,471,474,478,481
Expected an objects specifier or a keyword
> show #!2 models
> show #!3 models
> show #!4 models
> select #2/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel cyan
> select #2/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel cyan
> select #3/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff9300ff
> select #3/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff2600ff
> color sel #ff9300ff
> select #4/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff2f92ff
> select #4/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff40ffff
> color sel #ff2f92ff
> select clear
> select H
75541 atoms, 9172 residues, 4 models selected
> hide sel target a
> hide sel cartoons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!1 models
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select #1,2,3,4/A,C:402,411,412,414,471,474,478,481
1069 atoms, 1037 bonds, 64 residues, 4 models selected
> color sel byhetero
> select clear
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!2 cartoons
> show #!4 models
> show #!2,4 cartoons
> hide #!4 models
> show #!4 models
> open
> /Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.00879, step 1, values float32
> volume #5 level 0.01524
> lighting soft
> transparency 50
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!2 cartoons
> graphics silhouettes true
> ui tool show Distances
> select add #2/A:474@NH1
1 atom, 1 residue, 1 model selected
> select add #2/A:478@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/A:474@NH1 #2/A:478@OE1
Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NH1 and GLU 478
OE1: 2.424Å
> select clear
> select add #2/A:474@NE
1 atom, 1 residue, 1 model selected
> select add #2/A:471@OD1
2 atoms, 2 residues, 1 model selected
> distance #2/A:474@NE #2/A:471@OD1
Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NE and ASP 471
OD1: 3.466Å
> select clear
> select add #2/A:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/A:474@NH2
2 atoms, 2 residues, 1 model selected
> distance #2/A:471@OD1 #2/A:474@NH2
Distance between 01123_real_space_refined_021.pdb #2/A ASP 471 OD1 and ARG 474
NH2: 3.419Å
> select clear
> select add #2/C:474@NH2
1 atom, 1 residue, 1 model selected
> select add #2/C:478@OE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:474@NH2 #2/C:478@OE2
Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH2 and GLU 478
OE2: 3.263Å
> select clear
> select add #2/C:474@NH1
1 atom, 1 residue, 1 model selected
> select add #2/C:478@OE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:474@NH1 #2/C:478@OE2
Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH1 and GLU 478
OE2: 4.710Å
> select clear
> select add #2/C:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/C:474@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/C:471@OD1 #2/C:474@NH1
Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and ARG 474
NH1: 5.085Å
> show #!1 models
> hide #!1 models
> select clear
> select add #2/C:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/A:474@NE
2 atoms, 2 residues, 1 model selected
> distance #2/C:471@OD1 #2/A:474@NE
Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and /A ARG
474 NE: 5.557Å
> distance style symbol false
> distance style symbol true
> show sel cartoons
> hide #!6 models
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/E
Alignment identifier is 2/E
> hide #!2 models
> show #!2 models
> select #2
40815 atoms, 41357 bonds, 7 pseudobonds, 2637 residues, 2 models selected
> show sel cartoons
> select clear
> show #!5 models
> show #!3 models
> show #!2-3 cartoons
> hide #!5 models
> show #!4 models
> hide #6.1 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2-4 cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!4 models
> select add #2/C:471@CG
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
01123_real_space_refined_021.pdb #2/C ASP 471: phi -62.9, psi -41.8 trans
Changed 90 bond radii
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> hide sel atoms
> select clear
> hide #!2 atoms
> show #!2 cartoons
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #ff2f92ff
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #531b93ff
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #009193ff
> select clear
> show #!5 models
> color zone #5 near #2 distance 5
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> hide #!5 models
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #ff2f92ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdffff
> select clear
> show #!5 models
> color zone #5 near #2 distance 5
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_1
> view list
Named views: figure_1
> view figure_1
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdff33
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #00fdff05
> color sel #00fdff33
> color sel #ff2f92ff
> color sel #ff2f9233
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> color sel #531b9333
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> color sel #ff930033
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 246 atom styles
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #0433ffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #00f900ff
> color (#!2 & sel) #8efa00ff
> color (#!2 & sel) #00f900ff
> color sel byhetero
> select H
75541 atoms, 9172 residues, 4 models selected
> hide (#!2 & sel) target a
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #a9a9a9ff
> color (#!2 & sel) #a9a9a933
> color (#!2 & sel) #a9a9a900
> color (#!2 & sel) #a9a9a980
> color (#!2 & sel) #a9a9a9b3
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #00f900ff
> color sel byhetero
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #009193ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #005493ff
> color (#!2 & sel) #fffb00ff
> select #2/B,E,D,H, G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color sel byhetero
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #fffc79ff
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #fffb00ff
> color sel byhetero
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> select H
75541 atoms, 9172 residues, 4 models selected
> hide (#!2 & sel) target a
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel #00fa92ff
> color sel #00fdffff
> color sel byhetero
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #2/A,C:402,411,412,414,474,478,481,471
270 atoms, 262 bonds, 7 pseudobonds, 16 residues, 2 models selected
> graphics silhouettes true
> select clear
> view name figure_2a
> view list
Named views: figure_1, figure_2a
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png" width 1704
> height 1146 supersample 3
> show #!5 models
> transparency 50
> hide #!5 models
> show #!5 models
> transparency 90
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #929292ff
> color (#!2 & sel) #a9a9a9ff
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #fffb00ff
> color sel byhetero
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel #0096ffff
> color sel #00fdffff
> color sel byhetero
> select clear
> view name figure_2b
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_2c
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> transparency 70
> transparency 80
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> show #!2 cartoons
> hide #!2 atoms
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #a9a9a9ff
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #ff2f92ff
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #0096ffff
> color sel #00fdffff
> select clear
> select #2/D,H,E,B,G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> open 5DIS
Summary of feedback from opening 5DIS fetched from pdb
---
warnings | Unknown polymer entity '6' near line 18113
Atom OXT is not in the residue template for PRO /C:301
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
5dis title:
Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino
acid FG-repeat containing fragment of Nup214 [more info...]
Chain information for 5dis #7
---
Chain | Description
A | Exportin-1
B | GTP-binding nuclear protein Ran
C | Snurportin-1
D | Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214
Non-standard residues in 5dis #7
---
GLC — alpha-D-glucopyranose
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> mmaker #7/A to #2/A
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 01123_real_space_refined_021.pdb, chain A (#2) with 5dis, chain A
(#7), sequence alignment score = 5346.9
RMSD between 980 pruned atom pairs is 0.691 angstroms; (across all 1030 pairs:
1.266)
> select #7/B,D,C
6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> hide #!2 models
> hide sel atoms
> select #7/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #7/A:1101,499,491
36 atoms, 38 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb
Chain information for 01123_real_space_refined_021.pdb #8
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide #!7-8 atoms
> show #!7-8 cartoons
> select #7/B,D,C
6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected
> hide sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!2 models
> show #!8 models
> hide #!2 models
> mmaker #8/C to #2/A
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 01123_real_space_refined_021.pdb, chain A (#2) with
01123_real_space_refined_021.pdb, chain C (#8), sequence alignment score =
5413.4
RMSD between 1025 pruned atom pairs is 0.435 angstroms; (across all 1050
pairs: 1.023)
> hide #!8 models
> show #!8 models
> show #!2 models
> hide #!8 models
> show #!8 models
> select #8/A,B,D,E,H,G
23748 atoms, 24114 bonds, 1587 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> select #2/C,B,D,E,H,G
23748 atoms, 24114 bonds, 3 pseudobonds, 1587 residues, 2 models selected
> hide sel cartoons
> hide #!8 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!3 cartoons
> hide #!3 models
> show #!7 models
> view name figure_3_1
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!7 models
> show #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!2 models
> show #!8 models
> show #!2 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!8 models
> show #!2 models
> show #!8 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select #8/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #2/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!8 models
> hide #!8 models
> show #!2 cartoons
> select #2/B,E,D,H,G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> select #2/C
17067 atoms, 17243 bonds, 3 pseudobonds, 1050 residues, 2 models selected
> color (#!2 & sel) #797979ff
> select clear
> select #2/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> view name figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> view name figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> show #!2 surfaces
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> select #2/B,E,G
3885 atoms, 4007 bonds, 193 residues, 1 model selected
> hide sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
01123_real_space_refined_021.pdb #2/G A 119 O5'
01123_real_space_refined_021.pdb #2/G G 171 OP1
01123_real_space_refined_021.pdb #2/G G 171 P
01123_real_space_refined_021.pdb #2/G G 171 O5'
01123_real_space_refined_021.pdb #2/G G 171 OP2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3:
minimum, -12.25, mean 5.44, maximum 22.90
Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6:
minimum, -8.00, mean 3.96, maximum 20.57
Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7:
minimum, -28.79, mean -14.78, maximum -1.19
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> coulombic #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 01123_real_space_refined_021.pdb_A SES surface #2.2:
minimum, -29.56, mean -1.13, maximum 19.93
Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3:
minimum, -12.25, mean 5.44, maximum 22.90
Coulombic values for 01123_real_space_refined_021.pdb_C SES surface #2.4:
minimum, -19.04, mean -1.19, maximum 18.78
Coulombic values for 01123_real_space_refined_021.pdb_D SES surface #2.5:
minimum, -11.36, mean 2.56, maximum 16.39
Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6:
minimum, -8.00, mean 3.96, maximum 20.57
Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7:
minimum, -28.79, mean -14.78, maximum -1.19
Coulombic values for 01123_real_space_refined_021.pdb_H SES surface #2.8:
minimum, -10.42, mean 2.57, maximum 18.49
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2/B,E,G
3885 atoms, 4007 bonds, 193 residues, 1 model selected
> hide sel surfaces
> view name figure_3_3
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> view name figure_3_4
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 3
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_3_5
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> hide #!2 surfaces
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #00fdff80
> color (#!2 & sel) #00fdff00
> color (#!2 & sel) #00fdff4d
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color (#!2 & sel) #ff2f92ff
> color (#!2 & sel) #ff2f924d
> select clear
> view name figure_3_6
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_RevBS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
——— End of log from Mon Jan 16 15:41:27 2023 ———
opened ChimeraX session
> open "/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"
Chain information for NEC_011923.pdb #9
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open "/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"
Chain information for NEC_011923.pdb #10
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
> hide #9-10#!2 atoms
> show #9-10#!2 cartoons
> mmaker #10/C to #9/A
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 NEC_011923.pdb, chain A (#9) with NEC_011923.pdb, chain C (#10),
sequence alignment score = 5399.6
RMSD between 1025 pruned atom pairs is 0.429 angstroms; (across all 1050
pairs: 1.010)
> hide #10 models
> hide #9 models
> hide #!2 models
> show #!7 models
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_2
> coulombic #!7
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5dis #7/A GLU 1048 OXT
5dis #7/D GLY 2027 OXT
5dis #7/C GLY 287 OXT
5dis #7/B MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of 5dis #/B MET 179 H bonded to atom that should not have
hydrogens (copy of 5dis #/B MET 179 C)
> select H
132205 atoms, 16051 residues, 7 models selected
> select #7/B
1440 atoms, 1466 bonds, 6 pseudobonds, 183 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> coulombic #!7
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5dis #7/A GLU 1048 OXT
5dis #7/D GLY 2027 OXT
5dis #7/C GLY 287 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5dis_A SES surface #7.3: minimum, -25.78, mean -2.95,
maximum 10.90
Coulombic values for 5dis_C SES surface #7.4: minimum, -32.04, mean -0.55,
maximum 10.32
Coulombic values for 5dis_D SES surface #7.5: minimum, -18.89, mean -2.55,
maximum 13.38
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7/C,D
5151 atoms, 5274 bonds, 14 pseudobonds, 660 residues, 2 models selected
> hide sel surfaces
> view figure_3_2
> hide #!7 models
> select #7
13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected
> select clear
> select #7
13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected
> view figure_3_3
> show #!2 models
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_4
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_6
> show #9 models
> show #10 models
> hide #10 models
> ~select #7
3 models selected
> hide #!2 models
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #797979ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color sel #531b93ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color sel #ff2f92ff
> select #9/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color sel #ff2f92ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color sel #531b93ff
> select clear
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select clear
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> select #9/E:13-26
253 atoms, 254 bonds, 14 residues, 1 model selected
> color sel #9437ffff
> color sel #7a81ffff
> color sel #531b93ff
> color sel #875093ff
> color sel #875093ff
> color sel #8f5f93ff
> color sel #8f5f93ff
> color sel #937392ff
> color sel #937392ff
> color sel #835b93ff
> color sel #835b93ff
> color sel #935b90ff
> color sel #935b90ff
> color sel #934f81ff
> color sel #934f81ff
> color sel #936791ff
> color sel #936791ff
> select #9/E:51-60
171 atoms, 171 bonds, 10 residues, 1 model selected
> color sel #011993ff
> color sel #936791ff
> select clear
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_2
> view figure_3_3
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_5
> select #9/E:13-26,51-60
424 atoms, 425 bonds, 24 residues, 1 model selected
> color sel #ff85ffff
> color sel #ff8ad8ff
> color sel #d783ffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure3_c
> view name figure3_C_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view list
Named views: figure3_C_2, figure3_c, figure_1, figure_2a, figure_2b,
figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5,
figure_3_6
> view figure3_C_2
> select #9/E:51-60
171 atoms, 171 bonds, 10 residues, 1 model selected
> color sel #531b93ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> select #9/G,B
2572 atoms, 2682 bonds, 118 residues, 1 model selected
> color sel #c0c0c0ff
> color sel #d6d6d6ff
> color sel #c0c0c0ff
> select #9/A,C,D,H
36930 atoms, 37350 bonds, 2444 residues, 1 model selected
> color sel #a9a9a9ff
> color sel #c0c0c0ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select clear
> view figure3_C_2
> view figure_3_1
> select #9/B,C,D,E,G,H
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #d6d6d6ff
> color sel #ebebebff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #9 models
> show #10 models
> select #10/B,A,D,E,G,H
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> select #10/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #797979ff
> select #10/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_4.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #9 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_5.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #9 models
> hide #10 models
> show #!7 models
> hide #!7 surfaces
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name loopcloseup
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
——— End of log from Fri Jan 20 15:36:51 2023 ———
opened ChimeraX session
> hide #!7 models
> show #9 models
> view list
Named views: figure3_C_2, figure3_c, figure_1, figure_2a, figure_2b,
figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5,
figure_3_6, loopcloseup
> view figure3_C_2
> view figure3_c
> view figure3_C_2
> show #9 cartoons
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color sel #531b93ff
> select clear
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #797979ff
> select clear
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select clear
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #00f900ff
> select clear
> select #9/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdffff
> select clear
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color sel #ff2f92ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout_2.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> view name 3C_zoomout
> view name 3C_zoomout
> save "/Users/amberms/Desktop/NEC Paper/figures/012323.cxs"
> interfaces #9/C,E
1 buried areas: C E 1485
> interfaces #9/A,E
1 buried areas: A E 602
> save "/Users/amberms/Desktop/NEC Paper/figures/012323.cxs"
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup
> view figure3_C_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomin_2.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> select #9/A,C,D,H,B,G
39502 atoms, 40032 bonds, 2562 residues, 1 model selected
> hide sel cartoons
> color sel #00f900ff
> color sel #fffb00ff
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> view figure3_C_2
> turn x 90 models #9
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> select #9/E:1-12
31 atoms, 30 bonds, 2 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/E:13-26
253 atoms, 254 bonds, 14 residues, 1 model selected
> color sel #531b93ff
> select #9/E:27-35
130 atoms, 133 bonds, 9 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/E:36-50
313 atoms, 314 bonds, 15 residues, 1 model selected
> color sel #009193ff
> select #9/E:51-60
171 atoms, 171 bonds, 10 residues, 1 model selected
> color sel #531b93ff
> select #9/E:61-75
226 atoms, 228 bonds, 15 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/E:76-88
211 atoms, 211 bonds, 13 residues, 1 model selected
> color sel #941751ff
> select #9/E:89-90
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel #a9a9a9ff
> select clear
> color sel #00f900ff
> color sel #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:389-390
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup
> view name revaloneCrm1residues
> save "/Users/amberms/Desktop/NEC Paper/figures/012323.cxs"
> show #9 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #9/D
Alignment identifier is 9/D
> select #9/D:95
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/D:95-114
175 atoms, 179 bonds, 20 residues, 1 model selected
> select clear
> select #9/D:95
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/D:95
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/B,E,G
3921 atoms, 4043 bonds, 198 residues, 1 model selected
> hide sel cartoons
> select clear
> coulombic #9
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
NEC_011923.pdb #9/A VAL 1056
NEC_011923.pdb #9/B ASN 91
NEC_011923.pdb #9/C VAL 1056
NEC_011923.pdb #9/D MET 179
NEC_011923.pdb #9/E CYS 90
NEC_011923.pdb #9/G A 119
NEC_011923.pdb #9/G G 171
NEC_011923.pdb #9/H MET 179
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for NEC_011923.pdb_A SES surface #9.1: minimum, -17.80, mean
-1.02, maximum 18.08
Coulombic values for NEC_011923.pdb_B SES surface #9.2: minimum, -14.48, mean
5.26, maximum 23.62
Coulombic values for NEC_011923.pdb_C SES surface #9.3: minimum, -16.76, mean
-1.12, maximum 13.01
Coulombic values for NEC_011923.pdb_D SES surface #9.4: minimum, -11.64, mean
2.29, maximum 17.83
Coulombic values for NEC_011923.pdb_E SES surface #9.5: minimum, -10.95, mean
3.76, maximum 21.73
Coulombic values for NEC_011923.pdb_G SES surface #9.6: minimum, -28.22, mean
-14.57, maximum 0.34
Coulombic values for NEC_011923.pdb_H SES surface #9.7: minimum, -10.41, mean
2.29, maximum 15.48
To also show corresponding color key, enter the above coulombic command and
add key true
> select #9/B,E,G
3921 atoms, 4043 bonds, 198 residues, 1 model selected
> hide sel surfaces
> select #9/B,E,G
3921 atoms, 4043 bonds, 198 residues, 1 model selected
> show sel cartoons
> select clear
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #531b93ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure4_Crm1DimerES.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/012323.cxs"
——— End of log from Mon Jan 23 15:29:22 2023 ———
opened ChimeraX session
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff2f92ff
> color (#!9 & sel) #ff344bff
> color (#!9 & sel) #ff344bff
> color (#!9 & sel) #ff6c88ff
> color (#!9 & sel) #ff6c88ff
> color (#!9 & sel) #ff9dabff
> color (#!9 & sel) #ff9dabff
> color (#!9 & sel) #ff9dabff
> color (#!9 & sel) #b65d60ff
> color (#!9 & sel) #ff9dabff
> color (#!9 & sel) #ffbdbfff
> color (#!9 & sel) #ffbdbfff
> color (#!9 & sel) #ffa296ff
> color (#!9 & sel) #ffa296ff
> color (#!9 & sel) #ff8666ff
> color (#!9 & sel) #ff8666ff
> color (#!9 & sel) #ff8048ff
> color (#!9 & sel) #ff8048ff
> color (#!9 & sel) #ff37aaff
> color (#!9 & sel) #ff37aaff
> color (#!9 & sel) #ff28c3ff
> color (#!9 & sel) #ff28c3ff
> color (#!9 & sel) #ff23f7ff
> color (#!9 & sel) #ff23f7ff
> color (#!9 & sel) #d82dffff
> color (#!9 & sel) #d72cffff
> color (#!9 & sel) #d365ffff
> color (#!9 & sel) #d365ffff
> color (#!9 & sel) #ff9dabff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure4_Crm1DimerES.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues
> view 3C_zoomout
> view figure3_C_2
> view figure3_c
> view figure_1
> view figure_3_1
> view figure_3_2
> view figure_3_3
> view figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/E,B,G
3921 atoms, 4043 bonds, 198 residues, 1 model selected
> hide sel cartoons
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide sel surfaces
> select clear
> hide #!9 surfaces
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> show sel cartoons
> select clear
> select #9/A,C
34134 atoms, 34486 bonds, 2100 residues, 1 model selected
> color (#!9 & sel) #a9a9a9ff
> select #9/B,E
2675 atoms, 2699 bonds, 159 residues, 1 model selected
> color (#!9 & sel) #ff2f92ff
> view figure_1
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!8 models
> hide #!8 models
> show #!5 models
> transparency #5.1#9.1-7 0
> color zone #5 near #9 5
Expected a keyword
> color zone #5 near #9 distance 5
> color zone #5 near #9 distance 7
> transparency #5.1#9.1-7 50
> color zone #5 near #9 distance 7
> color zone #5 near #9 distance 7
> color zone #5 near #9 distance 8
> color zone #5 near #9 distance 9
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view figure_2a
> hide #!5 models
> select #9/B,E,G,D,H
6717 atoms, 6907 bonds, 542 residues, 1 model selected
> hide sel cartoons
> select clear
> select #9/A,C:402,411,412,414,471,474,478,,481
Expected an objects specifier or a keyword
> select #9/A,C:402,411,412,414,471,474,478,481
270 atoms, 262 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 270 atom styles
> select H
132205 atoms, 16051 residues, 7 models selected
> hide (#!9 & sel) target a
> select #9/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 14 residues, 1 model selected
> color (#!9 & sel) yellow
> style sel sphere
Changed 246 atom styles
> color sel byhetero
> color sel byhetero
> color (#!9 & sel) yellow
> select #9/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 24 atom styles
> color (#!9 & sel) cyan
> select clear
> show #!5 models
> hide #!5 models
> open
> /Users/amberms/Desktop/group/Modeling/122122/deepemhancer_highres_flip.mrc
Opened deepemhancer_highres_flip.mrc as #11, grid size 220,220,220, pixel
1.68, shown at level 0.00201, step 1, values float32
> volume #11 level 0.1657
> volume #11 level 0.1427
> volume #11 level 0.1226
> volume #11 level 0.1111
> surface dust #11 size 16.8
> volume #11 color #ebebeb
> volume #11 color white
> transparency #9.1-7#11.1 0
> transparency #9.1-7#11.1 50
> volume #11 color #ebebeb
> transparency #9.1-7#11.1 0
> transparency #9.1-7#11.1 50
> transparency 90
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/A,C:402,411,412,414,474,478,481,471
270 atoms, 262 bonds, 16 residues, 1 model selected
> style sel ball
Changed 270 atom styles
> color sel byhetero
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!9 atoms
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #5e5e5eff
> color (#!9 & sel) #424242ff
> color (#!9 & sel) #5e5e5eff
> color (#!9 & sel) #424242ff
> select clear
> select #9/A,C:389-400
334 atoms, 338 bonds, 24 residues, 1 model selected
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #00f900ff
> select clear
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues
> view figure_3_1
> view figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> show #!9 surfaces
> hide #!9 surfaces
> select clear
> coulombic #!9
Coulombic values for NEC_011923.pdb_A SES surface #9.1: minimum, -17.80, mean
-1.02, maximum 18.08
Coulombic values for NEC_011923.pdb_B SES surface #9.2: minimum, -14.48, mean
5.26, maximum 23.62
Coulombic values for NEC_011923.pdb_C SES surface #9.3: minimum, -16.76, mean
-1.12, maximum 13.01
Coulombic values for NEC_011923.pdb_D SES surface #9.4: minimum, -11.64, mean
2.29, maximum 17.83
Coulombic values for NEC_011923.pdb_E SES surface #9.5: minimum, -10.95, mean
3.76, maximum 21.73
Coulombic values for NEC_011923.pdb_G SES surface #9.6: minimum, -28.22, mean
-14.57, maximum 0.34
Coulombic values for NEC_011923.pdb_H SES surface #9.7: minimum, -10.41, mean
2.29, maximum 15.48
To also show corresponding color key, enter the above coulombic command and
add key true
> select #9/D,H,E,B,G
6717 atoms, 6907 bonds, 542 residues, 1 model selected
> hide sel surfaces
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> show sel surfaces
> select clear
> select #9/B,E,G
3921 atoms, 4043 bonds, 198 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> interfaces #9/C,E
1 buried areas: C E 1485
> interfaces #9/A,E
1 buried areas: A E 602
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #424242ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select clear
> color (#!9 & sel) #00f900ff
> color (#!9 & sel) #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_Crm1revsurface.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select clear
> hide #!9 surfaces
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues
> view figure_3_1
> select #9/D,H,C,B,E,G
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #ffffffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view figure_3_2
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure3_C_2
> view figure3_c
> view figure_1
> view loopcloseup
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1AC.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!9 models
> show #10 models
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> select #10/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #00f900ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_4.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!9 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_5.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view figure3_c
> view figure3_C_2
> view 3C_zoomout
> hide #!9 models
> show #!9 models
> hide #10 models
> show #!9 cartoons
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #424242ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff9dabff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout_2.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> view figure3_C_2
> view 3C_zoomout
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #00f900ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout_2.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> view figure3_C_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomin_2.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> view figure3_c
> view figure_3_1
> view figure_3_2
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_6
> view revaloneCrm1residues
> select #9/A,C,D,H,B,G
39502 atoms, 40032 bonds, 2562 residues, 1 model selected
> hide sel cartoons
> select #9/E:1-12,27-35,61-75,84-116
474 atoms, 477 bonds, 33 residues, 1 model selected
> color (#!9 & sel) #d783ffff
> color (#!9 & sel) #ff85ffff
> color (#!9 & sel) #a9a9a9ff
> color (#!9 & sel) #929292ff
> color (#!9 & sel) #919191ff
> color (#!9 & sel) #929292ff
> color (#!9 & sel) #a9a9a9ff
> color (#!9 & sel) #919191ff
> select #9/E:36-50
313 atoms, 314 bonds, 15 residues, 1 model selected
> color (#!9 & sel) #ff40ffff
> color (#!9 & sel) #ff7e79ff
> color (#!9 & sel) #73fcd6ff
> select clear
> select #9/E:76-83
138 atoms, 138 bonds, 8 residues, 1 model selected
> color (#!9 & sel) #941751ff
> select #9/E:36-50
313 atoms, 314 bonds, 15 residues, 1 model selected
> color (#!9 & sel) #942193ff
> color (#!9 & sel) #531b93ff
> select clear
> color (#!9 & sel) #00f900ff
> color (#!9 & sel) #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> show #!9 cartoons
> view 3C_zoomout
> view figure3_C_2
> view figure_3_2
> view figure_3_1
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_6
> view 3C_zoomout
> view figure3_C_2
> view figure3_c
> view figure_1
> view figure_2a
> view figure_2b
> view 3C_zoomout
> select #9/E:A,C
Nothing selected
> select #9/A,C
34134 atoms, 34486 bonds, 2100 residues, 1 model selected
> color (#!9 & sel) #ebebebff
> color (#!9 & sel) #ebebeb4d
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color (#!9 & sel) #ff9300ff
> color (#!9 & sel) #ff93004d
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff9dabff
> select clear
> view name revasymmetry
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ONL.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/012523.cxs"
> view list
Named views: 3C_zoomout, figure3_C_2, figure3_c, figure_1, figure_2a,
figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4,
figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues, revasymmetry
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #424242ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color (#!9 & sel) #ff9300ff
> select clear
> select #9/D:134,132,95
29 atoms, 26 bonds, 3 residues, 1 model selected
> style sel ball
Changed 29 atom styles
> select H
132205 atoms, 16051 residues, 7 models selected
> hide (#!9 & sel) target a
> select clear
> select #9/D:134,132,95
29 atoms, 26 bonds, 3 residues, 1 model selected
> style sel ball
Changed 29 atom styles
> show sel atoms
> color (#!9 & sel) #00f900ff
> color sel byhetero
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure4_Ran_RREBS_2.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select #9/D:134,132,95
29 atoms, 26 bonds, 3 residues, 1 model selected
> hide sel atoms
> color (#!9 & sel) #ff9300ff
> select clear
> select #9/C:597,556,596,594,382,458,446,1012
186 atoms, 179 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 186 atom styles
> select H
132205 atoms, 16051 residues, 7 models selected
> hide (#!9 & sel) target a
> select #9/C:597,556,596,594,382,458,446,1012
186 atoms, 179 bonds, 8 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> color sel byhetero
> select #9/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color (#!9 & sel) #00fdffff
> color (#!9 & sel) #00fdff80
> color (#!9 & sel) #00fdff4d
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure4_Crm1_RREBS_3.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/012523.cxs"
> select #9/D
1398 atoms, 1432 bonds, 172 residues, 1 model selected
> color (#!9 & sel) #ff7e79ff
> select clear
> view name Crm1postiveresidues
> save "/Users/amberms/Desktop/NEC Paper/figures/012523.cxs"
> select #9/D,h
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color (#!9 & sel) #7a81ffff
> color (#!9 & sel) #0096ffff
> color (#!9 & sel) #7a81ffff
> color (#!9 & sel) #009051ff
> color (#!9 & sel) #008f00ff
> color (#!9 & sel) #ff40ffff
> color (#!9 & sel) #7a81ffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/012523.cxs"
——— End of log from Wed Jan 25 14:54:26 2023 ———
opened ChimeraX session
> show #!8 models
> hide #!8 models
> show #!5 models
> select #9/A,C
34134 atoms, 34486 bonds, 2100 residues, 1 model selected
> color (#!9 & sel) #a9a9a9ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color (#!9 & sel) #ff9300ff
> select #9/E,B
2675 atoms, 2699 bonds, 159 residues, 1 model selected
> color (#!9 & sel) #ff2f92ff
> select #9/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> show sel cartoons
> color (#!9 & sel) #00fdffff
> hide #!9 models
> show #!9 models
> color zone #5 near #9 distance 5
> color zone #5 near #9 distance 7
> color zone #5 near #9 distance 9
> color zone #5 near #9 distance 9
> hide #!9 models
> volume #5 level 0.01948
> volume #5 level 0.01782
> volume #5 level 0.018
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues,
revasymmetry
> view figure_1
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> show #!9 models
> view figure_1
> select clear
> lighting full depthCue true
> view figure_1
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #5e5e5eff
> color (#!9 & sel) #424242ff
> color (#!9 & sel) #a9a9a9ff
> hide sel atoms
> select clear
> view figure_1
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #424242ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff9dabff
> select clear
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view figure3_C_2
> view figure3_c
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #00f900ff
> select clear
> view 3C_zoomout
> turn y 180 #9
Expected 'forever' or an integer >= 1 or a keyword
> turn y 180 models #9
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout_1.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> view figure3_c
> view figure3_C_2
> view figure3_c
> turn y 180 models #9
> turn y 180 models #9
> view figure3_C_2
> turn y 180 models #9
> view 3C_zoomout
> turn y 180 models #9
> turn y 180 models #9
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomin_2.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> turn y 180 models #9
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomin_1.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> select #9/A,C,D,H,G,B
39502 atoms, 40032 bonds, 2562 residues, 1 model selected
> hide sel cartoons
> turn x 90 models #9
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select clear
> interfaces #9/A,E
1 buried areas: A E 602
> interfaces #9/C,E
1 buried areas: C E 1485
> color (#!9 & sel) #fffb00ff
> color (#!9 & sel) #00f900ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> turn x 270 models #9
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff9dabff
> select #9/
Expected an objects specifier or a keyword
> show sel cartoons
> select clear
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> show sel cartoons
> select clear
> turn y 180 models #9
> select #9/E,G,A,C,D,H
39525 atoms, 40055 bonds, 2563 residues, 1 model selected
> hide sel cartoons
> turn x 90 models #9
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color (#!9 & sel) #d6d6d6ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone_2.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> show sel cartoons
> turn y 180 models #9
> select clear
> turn y 180 models #9
> turn x 270 models #9
> turn x 90 models #9
> turn y 180 models #9
> turn x 270 models #9
> turn x 270 models #9
> turn x 270 models #9
> turn x 90 models #9
> select #9/E,B:1-12
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #9/E,B:13-26
506 atoms, 508 bonds, 28 residues, 1 model selected
> select #9/E,B:27-35
260 atoms, 266 bonds, 18 residues, 1 model selected
> select #9/E,B:36-50
621 atoms, 623 bonds, 30 residues, 1 model selected
> select #9/E,B:51-60
347 atoms, 347 bonds, 20 residues, 1 model selected
> select #9/E,B:61-75
452 atoms, 456 bonds, 30 residues, 1 model selected
> select #9/E,B:76-83
276 atoms, 276 bonds, 16 residues, 1 model selected
> select #9/
Expected an objects specifier or a keyword
> show sel cartoons
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> show sel cartoons
> select #9/S,C,D,H,G
21109 atoms, 21451 bonds, 1433 residues, 1 model selected
> hide sel cartoons
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> open 4PMI
4pmi title:
Crystal structure of Rev and Rev-response-element RNA complex [more info...]
Chain information for 4pmi #12
---
Chain | Description
A | Rev-Response-Element RNA
B C | Protein Rev
Non-standard residues in 4pmi #12
---
PO4 — phosphate ion
4pmi mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #12/B to #9/E
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 NEC_011923.pdb, chain E (#9) with 4pmi, chain B (#12), sequence
alignment score = 283.1
RMSD between 44 pruned atom pairs is 1.211 angstroms; (across all 53 pairs:
1.542)
> select #12/A
855 atoms, 953 bonds, 38 pseudobonds, 42 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select clear
> select #12
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> color (#!12 & sel) #c0c0c0ff
> color (#!12 & sel) #d6d6d6ff
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color (#!9 & sel) #ff2f92ff
> select clear
> save "/Users/amberms/Desktop/NEC
> Paper/figures/Figure4_4PMIDimerComparison.png" width 1704 height 1146
> supersample 4 transparentBackground true
> select #9/B,E
2675 atoms, 2699 bonds, 159 residues, 1 model selected
> color (#!9 & sel) #ff40ffff
> color (#!9 & sel) #ff2f92ff
> select clear
> select #12
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> hide sel atoms
> select clear
> save "/Users/amberms/Desktop/NEC
> Paper/figures/Figure4_4PMIDimerComparison_2.png" width 1704 height 1146
> supersample 4 transparentBackground true
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color (#!9 & sel) #ff9dabff
> select clear
> save "/Users/amberms/Desktop/NEC
> Paper/figures/Figure4_4PMIDimerComparison.png" width 1704 height 1146
> supersample 4 transparentBackground true
> select #912
Nothing selected
> select #12
1717 atoms, 1832 bonds, 38 pseudobonds, 147 residues, 2 models selected
> hide sel cartoons
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> hide sel cartoons
> color (#!9 & sel) #fffb00ff
> color (#!9 & sel) #00f900ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone1.1.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> hide sel cartoons
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> show sel cartoons
> turn y 180 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn y 90 models #9
> turn x 180 models #9
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_revalone_2.1.png"
> width 1704 height 1146 supersample 4 transparentBackground true
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> save "/Users/amberms/Desktop/NEC Paper/figures/013023.cxs"
> show sel cartoons
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, revaloneCrm1residues,
revasymmetry
> view loopcloseup
> select #9/C,D,H,E,B,G
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> show #!8 models
> hide #!8 models
> show #!5 models
> transparency sel 50
> transparency sel 0
> hide #!12 models
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> ~select #9
7 models selected
> select #5
2 models selected
> transparency sel 50
> hide #!5 models
> show #!11 models
> transparency #9.1-7#11.1 0
> hide #!11 models
> show #!11 models
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> show sel cartoons
> hide #!11 models
> show #!5 models
> volume #5 level 0.0215
> transparency sel 50
> select clear
> transparency #5.1#9.1-7 0
> select #5
2 models selected
> transparency sel 50
> show #!11 models
> hide #!5 models
> show #!5 models
> select clear
> hide #!11 models
> transparency #5.1#9.1-7 50
> transparency #5 90
> show #!11 models
> volume #11 level 0.1312
> volume #11 level 0.03934
> ui mousemode right "play map series"
> ui mousemode right "play map series"
> ui mousemode right "play map series"
> ui mousemode right "move planes"
> volume #11 region 0,0,0,219,219,219
> volume #11 region 0,0,0,219,219,219
> volume #11 region 0,0,0,219,219,219
> ui tool show "Side View"
> show #!5 models
> hide #!5 models
> fitmap #9 inMap #11
Fit molecule NEC_011923.pdb (#9) to map deepemhancer_highres_flip.mrc (#11)
using 40851 atoms
average map value = 0.2367, steps = 52
shifted from previous position = 1.87
rotated from previous position = 0.0659 degrees
atoms outside contour = 10529, contour level = 0.039337
Position of NEC_011923.pdb (#9) relative to deepemhancer_highres_flip.mrc
(#11) coordinates:
Matrix rotation and translation
0.99999940 0.00106549 -0.00023425 0.93792088
-0.00106541 0.99999937 0.00036177 1.23151768
0.00023463 -0.00036152 0.99999991 1.06646644
Axis -0.31466289 -0.20398077 -0.92702703
Axis point 862.28284561 -426.47668623 0.00000000
Rotation angle (degrees) 0.06585108
Shift along axis -1.53497804
> hide #!11 models
> show #!5 models
> transparency #5.1#9.1-7 0
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 48
shifted from previous position = 1.92
rotated from previous position = 0.036 degrees
atoms outside contour = 13510, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999987 0.00050304 0.00001169 -0.09172938
-0.00050304 0.99999975 0.00049382 0.00640708
-0.00001144 -0.00049383 0.99999988 -0.00663930
Axis -0.70044510 0.01640822 -0.71351765
Axis point 10.44037125 86.14499803 0.00000000
Rotation angle (degrees) 0.04039449
Shift along axis 0.06909379
> hide #!5 models
> show #!11 models
> hide #!11 models
> show #!5 models
> transparency #5.1#9.1-7 50
> volume #5 region 0,0,0,219,219,219
> transparency #5.1#9.1-7 0
> transparency #5.1#9.1-7 50
> volume #5 region 0,0,0,219,219,219
> volume #5 region 0,0,0,219,219,219
> volume #5 region 0,0,0,219,219,219
> show #!11 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> transparency #5 90
> transparency #5 80
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #a9a9a9ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #fffb00ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color (#!9 & sel) #424242ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color (#!9 & sel) #00f900ff
> view name loopsmap
> hide #!5 models
> hide #!11 models
> show #!11 models
> show #!5 models
> transparency sel 50
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> select #5
4 models selected
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> select #5
4 models selected
> transparency sel 0
> volume sel style mesh
> volume sel step 2
> volume sel step 1
> volume sel style mesh
> volume sel step 2
> volume sel step 1
> select clear
> hide #!5 models
> show #!5 models
> volume step 2
> volume step 1
> hide #!5 models
> loopsmap
Unknown command: loopsmap
> view loopsmap
> view name loopsmap
> show #!5 models
> select clear
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> view name loopsmap
> volume style mesh
> volume style surface
> hide #!11 models
> transparency #5.1#9.1-7 0
> select #5
4 models selected
> transparency sel 50
> view loopsmap
> transparency #5 90
> transparency #5 80
> select clear
> show #!11 models
> volume style surface
> hide #!11 models
> volume #!5 style surface
> volume #!5 style surface
> hide #!5 models
> show #!5 models
> volume #!5 style surface
> volume #!5 style mesh
> volume #!5 style surface
> transparency #5.1#9.1-7 0
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, loopsmap,
revaloneCrm1residues, revasymmetry
> view 3C_zoomout
> view figure_1
> hide #!5 models
> show #!5 models
> transparency #5.1#9.1-7 50
> transparency #5.1#9.1-7 0
> turn x 180 #5
Expected 'forever' or an integer >= 1 or a keyword
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> turn x 180 models #5
> show #!11 models
> select #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,1,-3.6184e-08,-4.1354e-09,12.739,-3.6184e-08,1,3.1566e-08,-2.8309,-4.1354e-09,3.1566e-08,1,-0.40006
> hide #!11 models
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 76
shifted from previous position = 13.1
rotated from previous position = 0.0385 degrees
atoms outside contour = 13514, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999997 0.00054508 -0.00001779 -0.09016380
-0.00054500 0.99999981 0.00039170 0.03980959
0.00001801 -0.00039176 0.99999991 -0.02885586
Axis -0.58341138 -0.02666310 -0.81173902
Axis point 76.67247804 85.20447448 0.00000000
Rotation angle (degrees) 0.03847100
Shift along axis 0.07496457
> show #!11 models
> hide #!5 models
> fitmap #9 inMap #11
Fit molecule NEC_011923.pdb (#9) to map deepemhancer_highres_flip.mrc (#11)
using 40851 atoms
average map value = 0.2367, steps = 80
shifted from previous position = 12.4
rotated from previous position = 0.0296 degrees
atoms outside contour = 10531, contour level = 0.039337
Position of NEC_011923.pdb (#9) relative to deepemhancer_highres_flip.mrc
(#11) coordinates:
Matrix rotation and translation
0.99999947 0.00102660 -0.00007223 0.92656434
-0.00102658 0.99999945 0.00021036 1.25601121
0.00007244 -0.00021029 0.99999998 1.07137730
Axis -0.20023131 -0.06886232 -0.97732564
Axis point 1135.35037261 -644.69119302 0.00000000
Rotation angle (degrees) 0.06018381
Shift along axis -1.31910354
> show #!5 models
> view matrix models
> #5,1,-3.6184e-08,-4.1354e-09,0.11257,-3.6184e-08,1,3.1566e-08,-2.2092,-4.1354e-09,3.1566e-08,1,2.1014
> mmaker #11 to #5
No 'to' model specified
> hide #!9 models
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.8821, correlation about mean = 0.8875, overlap = 567.6
steps = 64, shift = 3.59, angle = 0.0296 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999974 0.00042324 -0.00029760 1.07633338
-0.00042331 0.99999988 -0.00000600 1.18600537
0.00029759 0.00000619 0.99999997 1.10219823
Axis 0.01177392 -0.57511280 -0.81798939
Axis point 667.97083112 -2586.37704825 0.00000000
Rotation angle (degrees) 0.02964800
Shift along axis -1.57100067
> select clear
> show #!9 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!5 models
> fitmap #9 inMap #11
Fit molecule NEC_011923.pdb (#9) to map deepemhancer_highres_flip.mrc (#11)
using 40851 atoms
average map value = 0.2367, steps = 48
shifted from previous position = 0.0171
rotated from previous position = 0.00417 degrees
atoms outside contour = 10530, contour level = 0.039337
Position of NEC_011923.pdb (#9) relative to deepemhancer_highres_flip.mrc
(#11) coordinates:
Matrix rotation and translation
0.99999942 0.00108100 -0.00002468 0.90284497
-0.00108100 0.99999939 0.00021966 1.28047840
0.00002491 -0.00021963 0.99999998 1.08378530
Axis -0.19906624 -0.02247282 -0.97972833
Axis point 1158.46336717 -600.63701440 0.00000000
Rotation angle (degrees) 0.06321831
Shift along axis -1.27031707
> graphics silhouettes true
> select clear
> color zone #11 near #9 distance 5
> view name loopsmap_2
> hide #!11 models
> show #!5 models
> transparency #5.1#9.1-7 50
> transparency #5.1#9.1-7 0
> show #!11 models
> view figure_1
> hide #!11 models
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 48
shifted from previous position = 1.92
rotated from previous position = 0.0235 degrees
atoms outside contour = 13525, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999971 0.00074183 -0.00014257 -0.09210773
-0.00074177 0.99999964 0.00041700 0.08331265
0.00014288 -0.00041690 0.99999990 -0.04293492
Axis -0.48322960 -0.16541110 -0.85972572
Axis point 127.35970331 80.15021754 0.00000000
Rotation angle (degrees) 0.04943697
Shift along axis 0.06764060
> hide #!9 models
> show #!11 models
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.882, correlation about mean = 0.8876, overlap = 567.7
steps = 44, shift = 1.93, angle = 0.0237 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999993 0.00019895 -0.00030334 1.10845424
-0.00019889 0.99999996 0.00019782 1.10189106
0.00030338 -0.00019776 0.99999993 1.13490066
Axis -0.47869117 -0.73420812 -0.48144906
Axis point -747.68759388 0.00000000 678.05641763
Rotation angle (degrees) 0.02367343
Shift along axis -1.88602147
> show #!9 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!11 models
> color zone #5 near #9 distance 5
> color zone #5 near #9 distance 3
> color zone #5 near #9 distance 3
> color zone #5 near #9 distance 2
> turn x 180 models #5
> turn x 180 models #5
> show #!11 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> select #5
2 models selected
> view matrix models
> #5,0.99916,0.031044,-0.026843,9.1609,-0.031004,0.99952,0.0019107,6.5822,0.026889,-0.0010768,0.99964,-2.6982
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!9 models
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.5026, correlation about mean = 0.1299, overlap = 168.4
steps = 188, shift = 2.5, angle = 5.07 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999975 -0.00042871 -0.00061330 12.22749457
0.00038030 0.99704190 -0.07685897 16.83743684
0.00064443 0.07685872 0.99704179 -11.89197843
Axis 0.99995268 -0.00818172 0.00526269
Axis point 0.00000000 163.78706571 214.04575337
Rotation angle (degrees) 4.40824364
Shift along axis 12.02657302
> ~select #5
Nothing selected
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.5023, correlation about mean = 0.1298, overlap = 168.4
steps = 44, shift = 0.0225, angle = 0.0167 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999989 -0.00026722 -0.00047449 12.19153926
0.00022986 0.99702665 -0.07705722 16.91563099
0.00049367 0.07705709 0.99702656 -11.89756871
Axis 0.99997507 -0.00628190 0.00322536
Axis point 0.00000000 163.16931512 214.20637464
Rotation angle (degrees) 4.41954109
Shift along axis 12.04659906
> show #!9 models
> hide #!11 models
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 96
shifted from previous position = 12.4
rotated from previous position = 4.41 degrees
atoms outside contour = 13529, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999967 0.00076302 0.00007352 -0.15153117
-0.00076306 0.99999957 0.00052771 0.04309689
-0.00007311 -0.00052776 0.99999986 0.01193304
Axis -0.56706099 0.07878049 -0.81989967
Axis point 48.18880832 139.50146384 0.00000000
Rotation angle (degrees) 0.05332211
Shift along axis 0.07953871
> show #!11 models
> hide #!9 models
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.5024, correlation about mean = 0.1297, overlap = 168.4
steps = 44, shift = 0.00987, angle = 0.0158 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999984 -0.00018976 -0.00059599 12.19571291
0.00014312 0.99700848 -0.07729206 16.96878765
0.00060887 0.07729196 0.99700832 -11.96125545
Axis 0.99996731 -0.00779394 0.00215330
Axis point 0.00000000 163.38938591 214.43113299
Rotation angle (degrees) 4.43307234
Shift along axis 12.03730431
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.5024, correlation about mean = 0.1297, overlap = 168.4
steps = 44, shift = 0.00984, angle = 0.0152 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999971 -0.00020652 -0.00077803 12.22966355
0.00014561 0.99699360 -0.07748378 17.01523780
0.00079169 0.07748364 0.99699331 -12.02458486
Axis 0.99994612 -0.01012876 0.00227218
Axis point 0.00000000 163.87704167 214.81142998
Rotation angle (degrees) 4.44418355
Shift along axis 12.02933935
> hide #!11 models
> show #!11 models
> select #11
2 models selected
> view matrix models #11,1,0,0,11.102,0,1,0,-0.37895,0,0,1,1.6263
> ~select #11
Nothing selected
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.8819, correlation about mean = 0.8875, overlap = 567.7
steps = 56, shift = 1.94, angle = 4.45 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999993 0.00037260 -0.00025747 1.05907500
-0.00037258 0.99999993 0.00007403 1.14679822
0.00025749 -0.00007394 0.99999996 1.11747912
Axis -0.16122171 -0.56107869 -0.81191025
Axis point 485.96895309 -2097.38822509 0.00000000
Rotation angle (degrees) 0.02629331
Shift along axis -1.72148268
> hide #!11 models
> show #!11 models
> hide #!5 models
> show #!9 models
> view loopsmap_2
> volume #11 level 0.045
> volume #11 level 0.03
> volume #11 level 0.02
> view loopsmap_2
> volume #11 level 0.015
> view name loopsmap_2
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_deepemhancermap.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> hide #!11 models
> show #!5 models
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, loopsmap, loopsmap_2,
revaloneCrm1residues, revasymmetry
> view figure_1
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 48
shifted from previous position = 1.92
rotated from previous position = 0.0235 degrees
atoms outside contour = 13525, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999971 0.00074183 -0.00014257 -0.09210773
-0.00074177 0.99999964 0.00041700 0.08331265
0.00014288 -0.00041690 0.99999990 -0.04293492
Axis -0.48322960 -0.16541110 -0.85972572
Axis point 127.35970331 80.15021754 0.00000000
Rotation angle (degrees) 0.04943697
Shift along axis 0.06764060
> hide #!5 models
> show #!11 models
> view loopsmap
> view loopsmap_2
> view figure_1
> hide #!11 models
> show #!5 models
> fitmap #9 inMap #5
Fit molecule NEC_011923.pdb (#9) to map cryosparc_P183_J130_locfilter_flip.mrc
(#5) using 40851 atoms
average map value = 0.02929, steps = 48
shifted from previous position = 1.92
rotated from previous position = 0.0235 degrees
atoms outside contour = 13525, contour level = 0.021502
Position of NEC_011923.pdb (#9) relative to
cryosparc_P183_J130_locfilter_flip.mrc (#5) coordinates:
Matrix rotation and translation
0.99999971 0.00074183 -0.00014257 -0.09210773
-0.00074177 0.99999964 0.00041700 0.08331265
0.00014288 -0.00041690 0.99999990 -0.04293492
Axis -0.48322960 -0.16541110 -0.85972572
Axis point 127.35970331 80.15021754 0.00000000
Rotation angle (degrees) 0.04943697
Shift along axis 0.06764060
> hide #!5 models
> show #!5 models
> transparency #5.1#9.1-7 50
> transparency #5.1#9.1-7 0
> hide #!5 models
> show #!5 models
> transparency #5.1#9.1-7 50
> transparency #5.1#9.1-7 0
> transparency #5.1#9.1-7 50
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_cryosparcmap.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> turn x 180
> turn x 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_cryosparcmap_2.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> turn y 180
> turn y 180
> turn y 180
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_cryosparcmap.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> transparency #5 90
> transparency #5 80
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_cryosparcmap_2.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> turn y 180
> save "/Users/amberms/Desktop/NEC
> Paper/figures/supplemental/Sup_loops_cryosparcmap.png" width 1704 height
> 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/013023.cxs"
——— End of log from Mon Jan 30 14:22:52 2023 ———
opened ChimeraX session
> hide #!5 models
> select #9
40851 atoms, 41393 bonds, 2642 residues, 1 model selected
> show sel cartoons
> select #9/A,C
34134 atoms, 34486 bonds, 2100 residues, 1 model selected
> color (#!9 & sel) #a9a9a9ff
> select #9/B,E
2675 atoms, 2699 bonds, 159 residues, 1 model selected
> color (#!9 & sel) #ff2f92ff
> select clear
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, loopsmap, loopsmap_2,
revaloneCrm1residues, revasymmetry
> view figure_1
> show #!5 models
> transparency #5.1#9.1-7 0
> color zone #5 near #9 distance 7
> lighting soft
> hide #!9 models
> view figure_1
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> show #!9 models
> show #!11 models
> volume #11 level 0.04371
> surface dust #11 size 16.8
> volume #11 level 0.045
> hide #!9 models
> show #!5 models
> hide #!5 models
> hide #!11 models
> show #!5 models
> transparency #5.1 50
> show #!11 models
> transparency #5 90
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.882, correlation about mean = 0.8876, overlap = 567.7
steps = 44, shift = 1.93, angle = 0.0237 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999993 0.00019895 -0.00030334 1.10845424
-0.00019889 0.99999996 0.00019782 1.10189106
0.00030338 -0.00019776 0.99999993 1.13490066
Axis -0.47869117 -0.73420812 -0.48144906
Axis point -747.68759388 0.00000000 678.05641763
Rotation angle (degrees) 0.02367343
Shift along axis -1.88602147
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> lighting soft
> graphics silhouettes false
> transparency #5 80
> transparency #5 75
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> volume #5 color #d6d6d6
> volume #5 color #ebebeb
> transparency #5.1 50
> transparency #5.1 0
> transparency #5.1 50
> graphics silhouettes true
> transparency #5 75
> transparency #5 50
> volume #5 color #d6d6d6
> transparency #5.1 50
> graphics silhouettes false
> transparency #5.1 0
> transparency #5.1 50
> transparency #5.1 0
> volume #5 color darkgrey
> transparency #5.1 50
> transparency #5 75
> transparency #5 80
> transparency #5 90
> transparency #5 80
> transparency #5 75
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> volume #11 level 0.055
> volume #11 level 0.075
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view list
Named views: 3C_zoomout, Crm1postiveresidues, figure3_C_2, figure3_c,
figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3,
figure_3_4, figure_3_5, figure_3_6, loopcloseup, loopsmap, loopsmap_2,
revaloneCrm1residues, revasymmetry
> view delete 3C_zoomout
> view figure_1
> view delete Crm1postiveresidues, figure3_C_2, figure3_c,
Expected fewer arguments
> view delete Crm1postiveresidues, figure3_C_2, figure3_c,
Expected fewer arguments
> view delete figure3_C_2
> view delete figure3_c
> view delete figure_2a
> view delete figure_2b
> view delete figure_2c
> view delete figure_3_1
> view delete figure_3_2
> view delete figure_3_3
> view delete figure_3_4
> view delete figure_3_5
> view delete figure_3_6
> view delete loopscloseup
> view delete loopsmap
> view delete loopsmap_2
> view delete revaloneCrm1residues
> view delete revasymmetry
> view list
Named views: Crm1postiveresidues, figure_1, loopcloseup
> view delete loopcloseup
> view delete Crm1positiveresidues
> view list
Named views: Crm1postiveresidues, figure_1
> view delete Crm1postiveresidues
> view list
Named views: figure_1
> save "/Users/amberms/Desktop/NEC Paper/figures/cxs_figures/figure1.cxs"
——— End of log from Tue Jan 31 13:12:49 2023 ———
opened ChimeraX session
> hide #!5 models
> show #!5 models
> hide #!11 models
> open /Users/amberms/Desktop/group/EMDA/rcc/XYZOUT.pdb
XYZOUT.pdb title:
\--- [more info...]
Chain information for XYZOUT.pdb #13
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide #!13 atoms
> show #!13 cartoons
> show #10 models
> hide #10 models
> show #!9 models
> hide #!5 models
> show #!11 models
> close #12
> close #10
> close #9
> open /Users/amberms/Desktop/group/EMDA/rcc/XYZOUT.pdb
XYZOUT.pdb title:
\--- [more info...]
Chain information for XYZOUT.pdb #9
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide #!9,13 atoms
> show #!9,13 cartoons
> show #!7 models
> hide #!9 models
> hide #!11 models
> hide #!13 models
> select #7
13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected
> show sel cartoons
> show #!13 models
> select clear
> hide #!13 models
> show #!13 models
> open 5DIS
5dis title:
Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino
acid FG-repeat containing fragment of Nup214 [more info...]
Chain information for 5dis #10
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_HUMAN
B | GTP-binding nuclear protein Ran | RAN_HUMAN
C | Snurportin-1 | SPN1_HUMAN
D | Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214 |
NU214_HUMAN
Non-standard residues in 5dis #10
---
GLC — alpha-D-glucopyranose
GTP — guanosine-5'-triphosphate
MG — magnesium ion
PRO — proline
> hide #!7 models
> hide #!13 models
> show #!9 models
> ui mousemode right zoom
> show #!7 models
> hide #!7 models
> mmaker #7/A to #9/C
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 XYZOUT.pdb, chain C (#9) with 5dis, chain A (#7), sequence
alignment score = 5310.3
RMSD between 976 pruned atom pairs is 0.703 angstroms; (across all 1030 pairs:
1.275)
> show #!7 models
> mmaker #10/A to #9/C
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 XYZOUT.pdb, chain C (#9) with 5dis, chain A (#10), sequence
alignment score = 5310.3
RMSD between 976 pruned atom pairs is 0.703 angstroms; (across all 1030 pairs:
1.275)
> hide #!7 models
> color #9 black
> close #6
> close #4
> close #3
> close #2
> close #1
> save "/Users/amberms/Desktop/NEC Paper/figures/Current/040523/Figure1.cxs"
> view list
Named views: figure_1
> view figure_1
> hide #!10 models
> select #9/A,C
17012 atoms, 17364 bonds, 2100 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #9/E,B
1325 atoms, 1349 bonds, 159 residues, 1 model selected
> color sel #ff2f92ff
> select #9/G
830 atoms, 928 bonds, 1 pseudobond, 39 residues, 2 models selected
> color (#!9 & sel) #00fdffff
> select clear
> hide pseudobonds target p #9/G
Expected a keyword
> hide pseudobonds target p
> show #!5 models
> hide #!5 models
> show #!11 models
> fitmap #9 inMap #11
Fit molecule XYZOUT.pdb (#9) to map deepemhancer_highres_flip.mrc (#11) using
21963 atoms
average map value = 0.3106, steps = 64
shifted from previous position = 1.96
rotated from previous position = 0.0647 degrees
atoms outside contour = 5400, contour level = 0.075
Position of XYZOUT.pdb (#9) relative to deepemhancer_highres_flip.mrc (#11)
coordinates:
Matrix rotation and translation
0.99999941 -0.00094296 -0.00053492 1.35888589
0.00094279 0.99999950 -0.00031904 0.99715852
0.00053522 0.00031854 0.99999981 1.03399338
Axis 0.28211279 -0.47350284 0.83439045
Axis point -1445.74066446 1210.43564913 0.00000000
Rotation angle (degrees) 0.06474518
Shift along axis 0.77395590
> hide #!9 models
> show #!5 models
> transparency #5.1#11.1 0
> fitmap #5 inMap #11
Fit map cryosparc_P183_J130_locfilter_flip.mrc in map
deepemhancer_highres_flip.mrc using 44741 points
correlation = 0.882, correlation about mean = 0.8876, overlap = 567.7
steps = 44, shift = 1.93, angle = 0.0237 degrees
Position of cryosparc_P183_J130_locfilter_flip.mrc (#5) relative to
deepemhancer_highres_flip.mrc (#11) coordinates:
Matrix rotation and translation
0.99999993 0.00019895 -0.00030334 1.10845424
-0.00019889 0.99999996 0.00019782 1.10189106
0.00030338 -0.00019776 0.99999993 1.13490066
Axis -0.47869117 -0.73420812 -0.48144906
Axis point -747.68759388 0.00000000 678.05641763
Rotation angle (degrees) 0.02367343
Shift along axis -1.88602147
> hide #!5 models
> show #!13 models
> hide #!13 models
> show #!9 models
> fitmap #9 inMap #11
Fit molecule XYZOUT.pdb (#9) to map deepemhancer_highres_flip.mrc (#11) using
21963 atoms
average map value = 0.3106, steps = 36
shifted from previous position = 0.0173
rotated from previous position = 0.00628 degrees
atoms outside contour = 5402, contour level = 0.075
Position of XYZOUT.pdb (#9) relative to deepemhancer_highres_flip.mrc (#11)
coordinates:
Matrix rotation and translation
0.99999945 -0.00095558 -0.00043585 1.32802119
0.00095546 0.99999951 -0.00027390 0.97913132
0.00043611 0.00027348 0.99999987 1.05621378
Axis 0.25216394 -0.40168950 0.88037429
Axis point -1390.53391530 1160.59358409 0.00000000
Rotation angle (degrees) 0.06218658
Shift along axis 0.87143575
> fitmap #9 inMap #11
Fit molecule XYZOUT.pdb (#9) to map deepemhancer_highres_flip.mrc (#11) using
21963 atoms
average map value = 0.3106, steps = 48
shifted from previous position = 0.0277
rotated from previous position = 0.00812 degrees
atoms outside contour = 5403, contour level = 0.075
Position of XYZOUT.pdb (#9) relative to deepemhancer_highres_flip.mrc (#11)
coordinates:
Matrix rotation and translation
0.99999934 -0.00099696 -0.00056576 1.38638956
0.00099678 0.99999945 -0.00031266 0.98151321
0.00056607 0.00031209 0.99999979 1.03081878
Axis 0.26291783 -0.47632039 0.83904297
Axis point -1348.10486644 1190.57900892 0.00000000
Rotation angle (degrees) 0.06807347
Shift along axis 0.76189302
> transparency #11.1 50
> hide #!11 models
> show #!11 models
> select #9/B,E,G
2155 atoms, 2277 bonds, 1 pseudobond, 198 residues, 2 models selected
> hide sel cartoons
> hide #!11 models
> select #9/A,C:402,411,412,414,471,474,478,481
142 atoms, 134 bonds, 16 residues, 1 model selected
> style sel ball
Changed 142 atom styles
> show sel atoms
> color sel yellow
> select clear
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #11 level 0.04328
> save "/Users/amberms/Desktop/NEC Paper/figures/Current/040523/Figure1.cxs"
> rename #9 rcc.pdb
> rename #13 rcc.pdb
> rename #5 id #1
> rename #11 id #2
> rename #9 id #3
> rename #13 id #4
> rename #10 id #5
> rename #7 id #6
> close #8
> save "/Users/amberms/Desktop/NEC Paper/figures/Current/040523/Figure1.cxs"
——— End of log from Wed Apr 5 13:12:12 2023 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 4021, in _update_drawings
v.update_drawings()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 785, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 808, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 2088, in update_surface
matrix = v.matrix()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 84, in read_full_array
file.readinto(b)
OSError: [Errno 6] Device not configured
Error processing trigger "graphics update":
OSError: [Errno 6] Device not configured
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 84, in read_full_array
file.readinto(b)
See log for complete Python traceback.
> hide #!3 cartoons
> select #3/A
8506 atoms, 8682 bonds, 1050 residues, 1 model selected
> hide sel atoms
> select #3/C
8506 atoms, 8682 bonds, 1050 residues, 1 model selected
> color sel #a9a9a9ff
> select clear
> volume zone #2 nearAtoms #3/C:402,411,412,414,471,474,478,481 range 5 newMap
> map false
Invalid "newMap" argument: Expected true or false (or 1 or 0)
> volume zone #2 nearAtoms #3/C:402,411,412,414,471,474,478,481 range 5 newMap
> false
> transparency #2.1 50
[Repeated 1 time(s)]
> volume unzone #2
> hide #!2 models
> show #!2 models
> ui mousemode right zoom
> show #!1 models
> hide #!2 models
> hide #!3 models
> volume show
> hide #!1 models
> volume show
> volume hide
> volume show
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2153, in mousePressEvent
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 366, in select_marker_cb
cb(self.markers[i])
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2222, in selected_marker_cb
self.select_data_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2155, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2162, in mouseReleaseEvent
self._drag(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2159, in _drag
cb(event)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2230, in moved_marker_cb
self.select_data_cb() # Causes redisplay using GUI settings
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2216, in select_data_cb
d.redisplay_needed_cb()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb
self.redisplay_needed()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed
self.show_using_dialog_settings(self.active_volume)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings
dr.show()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 751, in show
self._keep_displayed_data = self.displayed_matrices() if show else None
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1746, in displayed_matrices
matrices.append(self.matrix(read_matrix))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1231, in matrix
m = self.region_matrix(r, read_matrix)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1255, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 306, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix
matrix = read_array(self.path, self.data_offset,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 27, in read_array
m = read_full_array(path, byte_offset, full_size,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
OSError: [Errno 6] Device not configured:
'/Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 74, in read_full_array
file = open(path, 'rb')
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 476.0.0.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 12.6.3 (21G419)
Kernel Version: Darwin 21.6.0
Time since boot: 16 minutes
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2416D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: TN5PP6CO174S
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → read_full_array: Device not configured |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
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User opened MRC map and later when ChimeraX tried to read data (probably at smaller step) the disk apparently was not connected. It is a bit strange that the file appears to be under the Desktop directory so it does not look like it is on a detachable USB drive. Maybe the path is a symbollic link to such a drive.