![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18162 closed defect (limitation)
Unable to save MolecularSurface in session: ArrayMemoryError
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
trouble to save a considerably big session
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\junje\Documents\TTLL11 paper\video\chimerax sessions\MT map
> complex multiTTLL11gold_TTLL11s_color_views02.cxs" format session
Opened cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc as #3, grid size
480,480,480, pixel 1.35, shown at level 0.122, step 1, values float32
Opened TTLL11_gold.mrc as #4, grid size 480,480,480, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc as #17, grid size 647,645,645, pixel 1.35,1.35,1.35,
shown at level 0.077, step 1, values float32
Opened emd_25156.map as #13, grid size 512,512,512, pixel 0.92, shown at level
6.14, step 2, values float32
Opened 9TTLL11map.mrc copy as #5, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #6, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #7, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #8, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened TTLL11maps around.mrc as #9, grid size 806,799,735, pixel
1.35,1.35,1.35, shown at level 0.077, step 1, values float32
Log from Tue Jul 8 10:04:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color.cxs"
Opened cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc as #3, grid size
480,480,480, pixel 1.35, shown at level 0.0964, step 1, values float32
Opened TTLL11_gold.mrc as #4, grid size 480,480,480, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc as #17, grid size 647,645,645, pixel 1.35,1.35,1.35,
shown at level 0.077, step 1, values float32
Opened emd_25156.map as #13, grid size 512,512,512, pixel 0.92, shown at level
6.14, step 2, values float32
Opened 9TTLL11map.mrc copy as #5, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #6, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #7, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #8, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened TTLL11maps around.mrc as #9, grid size 806,799,735, pixel
1.35,1.35,1.35, shown at level 0.077, step 1, values float32
Log from Thu Jul 3 13:34:59 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\junje\Documents\TTLL11 paper\video\chimerax sessions\MT map
> complex multiTTLL11gold02.cxs" format session
Opened cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc as #3, grid size
480,480,480, pixel 1.35, shown at level 0.0964, step 1, values float32
Opened TTLL11_gold.mrc as #4, grid size 480,480,480, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc as #17, grid size 647,645,645, pixel 1.35,1.35,1.35,
shown at level 0.077, step 1, values float32
Opened emd_25156.map as #13, grid size 512,512,512, pixel 0.92, shown at level
6.14, step 2, values float32
Opened 9TTLL11map.mrc copy as #5, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #6, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #7, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #8, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened TTLL11maps around.mrc as #9, grid size 806,799,735, pixel
1.35,1.35,1.35, shown at level 0.077, step 1, values float32
Log from Thu Jul 3 10:39:52 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\junje\Documents\TTLL11 paper\video\chimerax sessions\MT map
> complex multiTTLL11gold.cxs" format session
Opened cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc as #3, grid size
480,480,480, pixel 1.35, shown at level 0.0964, step 1, values float32
Opened TTLL11_gold.mrc as #4, grid size 480,480,480, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc as #17, grid size 647,645,645, pixel 1.35,1.35,1.35,
shown at level 0.077, step 1, values float32
Opened emd_25156.map as #13, grid size 512,512,512, pixel 0.92, shown at level
6.14, step 2, values float32
Opened 9TTLL11map.mrc copy as #5, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #6, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #7, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Opened 9TTLL11map.mrc copy as #8, grid size 647,645,645, pixel 1.35, shown at
level 0.077, step 1, values float32
Log from Wed Jun 25 10:26:43 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\junje\Documents\TTLL11 paper\video\MT.cxs" format session
Log from Mon Jun 23 06:59:39 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/junje/Documents/TTLL11 paper/video/8xring_combine.cif"
Chain information for 8xring_combine.cif
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.1/C 1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.1/J 1.2/J 1.3/J 1.4/J 1.5/J 1.6/J 1.7/J 1.8/J 1.1/K 1.2/K 1.3/K 1.4/K 1.5/K 1.6/K 1.7/K 1.8/K 1.1/L 1.2/L 1.3/L 1.4/L 1.5/L 1.6/L 1.7/L 1.8/L 1.1/M 1.2/M 1.3/M 1.4/M 1.5/M 1.6/M 1.7/M 1.8/M 1.1/O 1.2/O 1.3/O 1.4/O 1.5/O 1.6/O 1.7/O 1.8/O 1.1/Q 1.2/Q 1.3/Q 1.4/Q 1.5/Q 1.6/Q 1.7/Q 1.8/Q 1.1/V 1.2/V 1.3/V 1.4/V 1.5/V 1.6/V 1.7/V 1.8/V 1.1/W 1.2/W 1.3/W 1.4/W 1.5/W 1.6/W 1.7/W 1.8/W 1.1/X 1.2/X 1.3/X 1.4/X 1.5/X 1.6/X 1.7/X 1.8/X 1.1/Y 1.2/Y 1.3/Y 1.4/Y 1.5/Y 1.6/Y 1.7/Y 1.8/Y 1.1/a 1.2/a 1.3/a 1.4/a 1.5/a 1.6/a 1.7/a 1.8/a 1.1/c 1.2/c 1.3/c 1.4/c 1.5/c 1.6/c 1.7/c 1.8/c 1.1/h 1.2/h 1.3/h 1.4/h 1.5/h 1.6/h 1.7/h 1.8/h 1.1/i 1.2/i 1.3/i 1.4/i 1.5/i 1.6/i 1.7/i 1.8/i 1.1/j 1.2/j 1.3/j 1.4/j 1.5/j 1.6/j 1.7/j 1.8/j 1.1/k 1.2/k 1.3/k 1.4/k 1.5/k 1.6/k 1.7/k 1.8/k 1.1/m 1.2/m 1.3/m 1.4/m 1.5/m 1.6/m 1.7/m 1.8/m 1.1/o 1.2/o 1.3/o 1.4/o 1.5/o 1.6/o 1.7/o 1.8/o 1.1/t 1.2/t 1.3/t 1.4/t 1.5/t 1.6/t 1.7/t 1.8/t 1.1/u 1.2/u 1.3/u 1.4/u 1.5/u 1.6/u 1.7/u 1.8/u 1.1/v 1.2/v 1.3/v 1.4/v 1.5/v 1.6/v 1.7/v 1.8/v 1.1/w 1.2/w 1.3/w 1.4/w 1.5/w 1.6/w 1.7/w 1.8/w 1.1/z 1.2/z 1.3/z 1.4/z 1.5/z 1.6/z 1.7/z 1.8/z | Tubulin alpha-1B chain
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.1/F 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F 1.7/F 1.8/F 1.1/G 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.1/H 1.2/H 1.3/H 1.4/H 1.5/H 1.6/H 1.7/H 1.8/H 1.1/I 1.2/I 1.3/I 1.4/I 1.5/I 1.6/I 1.7/I 1.8/I 1.1/N 1.2/N 1.3/N 1.4/N 1.5/N 1.6/N 1.7/N 1.8/N 1.1/P 1.2/P 1.3/P 1.4/P 1.5/P 1.6/P 1.7/P 1.8/P 1.1/R 1.2/R 1.3/R 1.4/R 1.5/R 1.6/R 1.7/R 1.8/R 1.1/S 1.2/S 1.3/S 1.4/S 1.5/S 1.6/S 1.7/S 1.8/S 1.1/T 1.2/T 1.3/T 1.4/T 1.5/T 1.6/T 1.7/T 1.8/T 1.1/U 1.2/U 1.3/U 1.4/U 1.5/U 1.6/U 1.7/U 1.8/U 1.1/Z 1.2/Z 1.3/Z 1.4/Z 1.5/Z 1.6/Z 1.7/Z 1.8/Z 1.1/b 1.2/b 1.3/b 1.4/b 1.5/b 1.6/b 1.7/b 1.8/b 1.1/d 1.2/d 1.3/d 1.4/d 1.5/d 1.6/d 1.7/d 1.8/d 1.1/e 1.2/e 1.3/e 1.4/e 1.5/e 1.6/e 1.7/e 1.8/e 1.1/f 1.2/f 1.3/f 1.4/f 1.5/f 1.6/f 1.7/f 1.8/f 1.1/g 1.2/g 1.3/g 1.4/g 1.5/g 1.6/g 1.7/g 1.8/g 1.1/l 1.2/l 1.3/l 1.4/l 1.5/l 1.6/l 1.7/l 1.8/l 1.1/n 1.2/n 1.3/n 1.4/n 1.5/n 1.6/n 1.7/n 1.8/n 1.1/p 1.2/p 1.3/p 1.4/p 1.5/p 1.6/p 1.7/p 1.8/p 1.1/q 1.2/q 1.3/q 1.4/q 1.5/q 1.6/q 1.7/q 1.8/q 1.1/r 1.2/r 1.3/r 1.4/r 1.5/r 1.6/r 1.7/r 1.8/r 1.1/s 1.2/s 1.3/s 1.4/s 1.5/s 1.6/s 1.7/s 1.8/s 1.1/x 1.2/x 1.3/x 1.4/x 1.5/x 1.6/x 1.7/x 1.8/x 1.1/y 1.2/y 1.3/y 1.4/y 1.5/y 1.6/y 1.7/y 1.8/y | Tubulin beta-3 chain
> show cartoons
> hide atoms
[Repeated 2 time(s)]
> save "C:/Users/junje/Documents/TTLL11 paper/video/MT.cxs"
——— End of log from Mon Jun 23 06:59:39 2025 ———
opened ChimeraX session
> ui mousemode right select
> select #1.6/y:268
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1.6/r:185
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #1.6/G:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> set bgColor white
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_complex_mutfix-
> coot-13.pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_complex_mutfix-coot-13.pdb
---
warnings | End residue of secondary structure not found: HELIX 25 25 ALA B 110 CYS B 124 1 15
End residue of secondary structure not found: HELIX 27 27 VAL B 180 ILE B 189
5 10
End residue of secondary structure not found: HELIX 32 32 VAL B 286 MET B 293
1 8
End residue of secondary structure not found: HELIX 60 60 ASP D 41 GLU D 45 5
5
End residue of secondary structure not found: HELIX 70 70 VAL D 286 MET D 293
1 8
Chain information for TTLL11_complex_mutfix-coot-13.pdb #2
---
Chain | Description
A C | No description available
B | No description available
D | No description available
E | No description available
> open "C:/Users/junje/Documents/TTLL11
> paper/video/deepEMhancer/cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc"
Opened cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc as #3, grid size
480,480,480, pixel 1.35, shown at level 0.0112, step 2, values float32
> ui mousemode right select
> select #3
2 models selected
Drag select of 5719 atoms, 18 bonds, 3
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc
> select #1.6/k:54
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.6/x:395
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 25 models
selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,61.349,0,1,0,71.207,0,0,1,3.0486
> view matrix models #1,1,0,0,66.842,0,1,0,71.925,0,0,1,3.1166
> view matrix models #1,1,0,0,89.838,0,1,0,78.403,0,0,1,1.8921
> show sel cartoons
> hide sel atoms
> select add #3
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 27 models
selected
> select subtract #1
2 models selected
> show atoms
> hide cartoons
> hide atoms
> show cartoons
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select subtract #3
Nothing selected
> show #!2 models
> select add #2
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!3 models
> select add #2
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 2 models selected
> show #!1 models
> ui tool show "Side View"
> view matrix models #2,1,0,0,0.62379,0,1,0,-0.20915,0,0,1,0.097311
> ui mousemode right select
> select clear
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 25 models
selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,91.874,0,1,0,72.784,0,0,1,36.467
> view matrix models #1,1,0,0,97.411,0,1,0,77.51,0,0,1,36.952
> view matrix models #1,1,0,0,97.634,0,1,0,77.262,0,0,1,38.763
> view matrix models #1,1,0,0,96.539,0,1,0,78.999,0,0,1,38.222
> hide #!1 models
> ui mousemode right select
> select #2/C:427
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/A:159
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
292 atoms, 293 bonds, 38 residues, 1 model selected
> select up
6180 atoms, 6322 bonds, 786 residues, 1 model selected
> select up
6308 atoms, 6452 bonds, 804 residues, 1 model selected
> select up
6744 atoms, 6898 bonds, 860 residues, 1 model selected
> select up
6810 atoms, 6966 bonds, 864 residues, 1 model selected
> select up
17848 atoms, 18264 bonds, 2240 residues, 1 model selected
> select down
6810 atoms, 6966 bonds, 864 residues, 1 model selected
> color sele lime green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lime green
> select clear
> select #2/D:417
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:102
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
240 atoms, 245 bonds, 28 residues, 1 model selected
> select up
6700 atoms, 6850 bonds, 853 residues, 1 model selected
> select up
6890 atoms, 7054 bonds, 859 residues, 1 model selected
> select up
17848 atoms, 18264 bonds, 2240 residues, 1 model selected
> select up
17848 atoms, 18264 bonds, 2240 residues, 4 models selected
> select down
17848 atoms, 18264 bonds, 2240 residues, 1 model selected
> select down
6890 atoms, 7054 bonds, 859 residues, 1 model selected
> color sel cyan
> select #2/E:391
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
242 atoms, 246 bonds, 30 residues, 1 model selected
> select up
2603 atoms, 2669 bonds, 324 residues, 1 model selected
> select up
2616 atoms, 2682 bonds, 326 residues, 1 model selected
> select up
4148 atoms, 4244 bonds, 517 residues, 1 model selected
> select up
17848 atoms, 18264 bonds, 2240 residues, 1 model selected
> select down
4148 atoms, 4244 bonds, 517 residues, 1 model selected
> color sel light pink
> select clear
> select #2/E:384
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
242 atoms, 246 bonds, 30 residues, 1 model selected
> select up
2603 atoms, 2669 bonds, 324 residues, 1 model selected
> color sel lightblue magenta
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel magenta
> color sel dark magenta
> select #2/E:469
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel dark magenta
> select clear
> select #2/E:495
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel dark red
> select clear
[Repeated 1 time(s)]
> select #2/E:499
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel dark red
> select #2/E:485
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/E:485
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> color sel dark red
> select clear
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex.cxs"
> show #!1 models
> fitmap #1 inMap #3
Fit molecules 8xring_combine.cif (#1.1), 8xring_combine.cif (#1.2),
8xring_combine.cif (#1.3), 8xring_combine.cif (#1.4), 8xring_combine.cif
(#1.5), 8xring_combine.cif (#1.6), 8xring_combine.cif (#1.7),
8xring_combine.cif (#1.8) to map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) using 1423264 atoms
average map value = 0.02757, steps = 556
shifted from previous position = 7.99
rotated from previous position = 4.07 degrees
atoms outside contour = 1256563, contour level = 0.011222
Position of 8xring_combine.cif (#1.1) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.2) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.3) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.4) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.5) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.6) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.7) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
Position of 8xring_combine.cif (#1.8) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99751381 -0.07023539 -0.00576030 9.19378082
0.07027991 0.99749580 0.00792876 -14.39095845
0.00518900 -0.00831388 0.99995198 -0.65489884
Axis -0.11448631 -0.07717621 0.99042249
Axis point 209.78011594 122.51115164 0.00000000
Rotation angle (degrees) 4.06781001
Shift along axis -0.59054900
> show #!3 models
> transparency #3 50
> volume #3 level 0.04748
> volume #3 step 1
> fitmap #2 inMap #3
Fit molecule TTLL11_complex_mutfix-coot-13.pdb (#2) to map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) using 17848 atoms
average map value = 0.366, steps = 96
shifted from previous position = 0.656
rotated from previous position = 0.021 degrees
atoms outside contour = 3401, contour level = 0.047483
Position of TTLL11_complex_mutfix-coot-13.pdb (#2) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99999994 -0.00024682 0.00025461 -0.01815265
0.00024679 0.99999997 0.00009378 -0.09908017
-0.00025464 -0.00009371 0.99999996 0.07323016
Axis -0.25558054 0.69420015 0.67287795
Axis point 326.86148422 0.00000000 86.29937883
Rotation angle (degrees) 0.02101541
Shift along axis -0.01486704
> volume #3 level 0.08471
> color #3 navajo white
> color #3 rosy brown
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex.cxs"
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold.mrc"
Opened TTLL11_gold.mrc as #4, grid size 480,480,480, pixel 1.35, shown at
level 8.98e-05, step 2, values float32
> volume #4 step 1
> volume #4 level 0.07705
> color #4 gold
> transparency #4 50
> volume #3 level 0.1302
Drag select of 3394 residues, 11 pseudobonds, 3
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (2).mrc"
Opened TTLL11_gold - Copy (2).mrc as #5, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (3).mrc"
Opened TTLL11_gold - Copy (3).mrc as #6, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy.mrc"
Opened TTLL11_gold - Copy.mrc as #7, grid size 480,480,480, pixel 1.35, shown
at level 8.98e-05, step 2, values float32
> select add #3
26451 atoms, 11 pseudobonds, 3394 residues, 9 models selected
> select add #2
44091 atoms, 18264 bonds, 14 pseudobonds, 5605 residues, 10 models selected
> select add #1
1441112 atoms, 1474184 bonds, 1459 pseudobonds, 182576 residues, 31 models
selected
> ui mousemode right select
> select clear
> hide #!1 models
> select clear
> hide #!2 models
> ui tool show "Volume Viewer"
> volume #5 step 1
> volume #6 step 1
> volume #7 step 1
> volume #5 level 0.077
> volume #6 level 0.077
> volume #7 level 0.077
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,56.148,0,1,0,-34.934,0,0,1,-5.0268
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99815,-0.0051721,0.060531,38.827,0.0023858,0.99894,0.046013,-49.511,-0.060705,-0.045783,0.99711,18.428
> view matrix models
> #5,0.95899,-0.27584,0.06524,100.19,0.27397,0.96106,0.036151,-98.785,-0.072671,-0.016794,0.99721,15.231
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95899,-0.27584,0.06524,105.39,0.27397,0.96106,0.036151,-102.23,-0.072671,-0.016794,0.99721,10.498
> view matrix models
> #5,0.95899,-0.27584,0.06524,110.82,0.27397,0.96106,0.036151,-97.764,-0.072671,-0.016794,0.99721,12.096
> view matrix models
> #5,0.95899,-0.27584,0.06524,106.26,0.27397,0.96106,0.036151,-98.705,-0.072671,-0.016794,0.99721,8.4361
> view matrix models
> #5,0.95899,-0.27584,0.06524,102.65,0.27397,0.96106,0.036151,-96.263,-0.072671,-0.016794,0.99721,9.0963
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.79354,-0.58636,0.16272,171.1,0.57807,0.80991,0.099425,-152.7,-0.19008,0.015163,0.98165,33.425
> view matrix models
> #5,0.82619,-0.46365,0.32007,90.555,0.43918,0.88585,0.14962,-152.83,-0.3529,0.016954,0.93551,83.291
> view matrix models
> #5,0.79938,-0.5017,0.3306,100.82,0.47299,0.86477,0.16867,-161.97,-0.37051,0.02154,0.92858,88.404
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.79938,-0.5017,0.3306,100.43,0.47299,0.86477,0.16867,-161.26,-0.37051,0.02154,0.92858,90.404
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.84975,-0.3916,0.35296,60.346,0.32925,0.91709,0.22482,-157.43,-0.41174,-0.074828,0.90823,125.1
> view matrix models
> #5,0.93242,-0.25758,0.25348,46.115,0.2399,0.96575,0.098896,-108.43,-0.27027,-0.031401,0.96227,68.445
> view matrix models
> #5,0.93491,-0.19787,0.2946,20.864,0.15013,0.97271,0.1769,-114.2,-0.32157,-0.12116,0.9391,104.91
> view matrix models
> #5,0.97592,-0.15158,0.15683,45.258,0.060538,0.87903,0.47292,-167.44,-0.20954,-0.45204,0.86704,168.78
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.97592,-0.15158,0.15683,39.893,0.060538,0.87903,0.47292,-166.35,-0.20954,-0.45204,0.86704,170.76
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #3 level 0.09216
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #5,0.97592,-0.15158,0.15683,47.236,0.060538,0.87903,0.47292,-175.96,-0.20954,-0.45204,0.86704,169.37
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.88314,-0.4643,0.066933,158.17,0.41653,0.84178,0.34337,-206.88,-0.21577,-0.27536,0.93681,113.75
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.88314,-0.4643,0.066933,154.78,0.41653,0.84178,0.34337,-201.84,-0.21577,-0.27536,0.93681,115.94
> view matrix models
> #5,0.88314,-0.4643,0.066933,160.28,0.41653,0.84178,0.34337,-199.73,-0.21577,-0.27536,0.93681,116.14
> volume #3 level 0.164
> fitmap#5 inMap #3
Unknown command: fitmap#5 inMap #3
> fitmap #5 inMap #3
Fit map TTLL11_gold - Copy (2).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.8609, correlation about mean = 0.5851, overlap = 139.3
steps = 120, shift = 3.84, angle = 20.4 degrees
Position of TTLL11_gold - Copy (2).mrc (#5) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90319830 -0.42917852 0.00621548 167.62925208
0.42917964 0.90321833 0.00121979 -107.65510029
-0.00613745 0.00156584 0.99997994 -8.09367352
Axis 0.00040311 0.01438986 0.99989638
Axis point 322.20950640 317.91591993 0.00000000
Rotation angle (degrees) 25.41829514
Shift along axis -9.57440343
> select add #5
3 models selected
> select subtract #5
Nothing selected
> select add #6
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-41.915,0,1,0,65.213,0,0,1,-10.705
> view matrix models #6,1,0,0,-40.936,0,1,0,61.027,0,0,1,5.5853
> view matrix models #6,1,0,0,-45.145,0,1,0,67.744,0,0,1,6.9794
> view matrix models #6,1,0,0,-43.781,0,1,0,65.246,0,0,1,8.5555
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99098,0.012315,0.13347,-85.629,-0.016798,0.99933,0.032511,59.008,-0.13298,-0.03446,0.99052,47.729
> view matrix models
> #6,0.93453,0.2724,0.22901,-154.86,-0.29748,0.95115,0.08258,115.05,-0.19532,-0.1453,0.96992,90.059
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93453,0.2724,0.22901,-152.76,-0.29748,0.95115,0.08258,106.37,-0.19532,-0.1453,0.96992,90.259
> fitmap #6 inMap #3
Fit map TTLL11_gold - Copy (3).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.8154, correlation about mean = 0.4842, overlap = 93.85
steps = 120, shift = 1.33, angle = 16.6 degrees
Position of TTLL11_gold - Copy (3).mrc (#6) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90284357 0.42995391 -0.00362121 -105.91825151
-0.42994052 0.90284862 0.00393820 168.77565622
0.00496265 -0.00199867 0.99998569 8.21647788
Axis -0.00690368 -0.00998173 -0.99992635
Axis point 320.28941484 318.87075395 0.00000000
Rotation angle (degrees) 25.46622017
Shift along axis -9.16931932
> select add #7
6 models selected
> select subtract #6
3 models selected
> view matrix models #7,1,0,0,3.2176,0,1,0,5.5049,0,0,1,87.341
> fitmap #7 inMap #3
Fit map TTLL11_gold - Copy.mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.3714, correlation about mean = 0.1847, overlap = 23.84
steps = 404, shift = 5.11, angle = 7.7 degrees
Position of TTLL11_gold - Copy.mrc (#7) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99327246 0.10834847 -0.04087089 -3.69286992
-0.10533023 0.99197647 0.06991582 8.95030608
0.04811823 -0.06514052 0.99671528 96.04899499
Axis -0.50396308 -0.33206316 -0.79734263
Axis point -189.19651307 383.71959702 -0.00000000
Rotation angle (degrees) 7.70046774
Shift along axis -77.69495519
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (10).mrc"
Opened TTLL11_gold - Copy (10).mrc as #8, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (11).mrc"
Opened TTLL11_gold - Copy (11).mrc as #9, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (12).mrc"
Opened TTLL11_gold - Copy (12).mrc as #10, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (4).mrc"
Opened TTLL11_gold - Copy (4).mrc as #11, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (5).mrc"
Opened TTLL11_gold - Copy (5).mrc as #12, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (6).mrc"
Opened TTLL11_gold - Copy (6).mrc as #13, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (7).mrc"
Opened TTLL11_gold - Copy (7).mrc as #14, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (8).mrc"
Opened TTLL11_gold - Copy (8).mrc as #15, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_gold - Copy
> (9).mrc"
Opened TTLL11_gold - Copy (9).mrc as #16, grid size 480,480,480, pixel 1.35,
shown at level 8.98e-05, step 2, values float32
> volume #8 step 1
> volume #16 step 1
> volume #15 step 1
> volume #14 step 1
> volume #13 step 1
> volume #12 step 1
> volume #10 step 1
> volume #9 step 1
> volume #8 level 0.077
> volume #9 level 0.077
> volume #11 level 0.077
> volume #12 level 0.077
> volume #13 level 0.077
> volume #14 level 0.077
> volume #15 level 0.077
> volume #16 level 0.077
> volume #10 level 0.077
> select subtract #7
Nothing selected
> select add #8
3 models selected
> view matrix models #8,1,0,0,3.3492,0,1,0,0.3725,0,0,1,-79.426
> fitmap #8 inMap #3
Fit map TTLL11_gold - Copy (10).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.3027, correlation about mean = 0.08149, overlap = 31.27
steps = 2000, shift = 18, angle = 38.3 degrees
Position of TTLL11_gold - Copy (10).mrc (#8) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.93739197 -0.09609831 -0.33475575 149.00693099
-0.09945765 0.84728999 -0.52173543 226.78476286
0.33377309 0.52236462 0.78468512 -200.00003404
Axis 0.84215666 -0.53922612 -0.00270960
Axis point 0.00000000 502.93971995 291.33153916
Rotation angle (degrees) 38.30858145
Shift along axis 3.74083048
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.93739,-0.096098,-0.33476,143.6,-0.099458,0.84729,-0.52174,223.7,0.33377,0.52236,0.78469,-204
> view matrix models
> #8,0.93739,-0.096098,-0.33476,144.63,-0.099458,0.84729,-0.52174,217.94,0.33377,0.52236,0.78469,-193.66
> fitmap #8 inMap #3
Fit map TTLL11_gold - Copy (10).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.2983, correlation about mean = 0.07084, overlap = 28.32
steps = 160, shift = 7.77, angle = 11 degrees
Position of TTLL11_gold - Copy (10).mrc (#8) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.88745427 -0.17494993 -0.42640056 200.37354306
-0.02227847 0.90779150 -0.41882963 162.31168676
0.46035702 0.38119170 0.80172583 -192.21433622
Axis 0.66445449 -0.73649292 0.12680066
Axis point 560.47478325 0.00000000 338.77568301
Rotation angle (degrees) 37.01425075
Shift along axis -10.77521421
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.88188,-0.13037,-0.45309,200.95,-0.070398,0.91383,-0.39996,165.87,0.46619,0.38461,0.79671,-192.63
> view matrix models
> #8,0.99485,0.0055149,-0.10126,39.763,-0.00082509,0.99893,0.0463,-4.8504,0.1014,-0.045978,0.99378,-87.043
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.99485,0.0055149,-0.10126,33.005,-0.00082509,0.99893,0.0463,-11.084,0.1014,-0.045978,0.99378,-88.908
> view matrix models
> #8,0.99485,0.0055149,-0.10126,34.224,-0.00082509,0.99893,0.0463,-14.604,0.1014,-0.045978,0.99378,-87.877
> view matrix models
> #8,0.99485,0.0055149,-0.10126,34.142,-0.00082509,0.99893,0.0463,-14.266,0.1014,-0.045978,0.99378,-88.585
> view matrix models
> #8,0.99485,0.0055149,-0.10126,29.86,-0.00082509,0.99893,0.0463,-17.45,0.1014,-0.045978,0.99378,-88.226
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.99485,0.0055149,-0.10126,28.86,-0.00082509,0.99893,0.0463,-15.544,0.1014,-0.045978,0.99378,-95.91
> volume #3 level 0.09639
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.99485,0.0055149,-0.10126,32.616,-0.00082509,0.99893,0.0463,-15.347,0.1014,-0.045978,0.99378,-95.486
> view matrix models
> #8,0.99485,0.0055149,-0.10126,31.49,-0.00082509,0.99893,0.0463,-14.624,0.1014,-0.045978,0.99378,-93.235
> fitmap #8 inMap #3
Fit map TTLL11_gold - Copy (10).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.7628, correlation about mean = 0.496, overlap = 51.38
steps = 92, shift = 2.15, angle = 6.29 degrees
Position of TTLL11_gold - Copy (10).mrc (#8) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99998168 -0.00573915 -0.00192586 2.21567299
0.00574086 0.99998313 0.00088406 -3.05343073
0.00192075 -0.00089510 0.99999775 -84.61991985
Axis -0.14538791 -0.31433365 0.93811338
Axis point 4838.71050575 -1624.21619497 0.00000000
Rotation angle (degrees) 0.35057611
Shift along axis -78.74541517
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> transparency #8 50
> transparency #8 80
> select add #8
3 models selected
> select add #9
6 models selected
> select subtract #8
3 models selected
> view matrix models #9,1,0,0,53.659,0,1,0,-58.934,0,0,1,74.189
> fitmap #9 inMap #3
Fit map TTLL11_gold - Copy (11).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.2845, correlation about mean = 0.08144, overlap = 11.99
steps = 604, shift = 29.5, angle = 68.4 degrees
Position of TTLL11_gold - Copy (11).mrc (#9) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.69926360 -0.69430693 -0.17020078 329.86473011
0.28847582 0.49190781 -0.82146723 258.71352323
0.65407348 0.52532332 0.54426399 -37.15748968
Axis 0.72412963 -0.44318800 0.52841335
Axis point 0.00000000 324.15057222 170.86502534
Rotation angle (degrees) 68.42506959
Shift along axis 104.57158188
> undo
> view matrix models #9,1,0,0,48.111,0,1,0,-55.408,0,0,1,77.431
> view matrix models #9,1,0,0,61.257,0,1,0,-32.501,0,0,1,73.437
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.90393,-0.42172,0.071158,144.82,0.41777,0.90629,0.064111,-125.78,-0.091526,-0.028224,0.9954,100.7
> fitmap #9 inMap #3
Fit map TTLL11_gold - Copy (11).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.6852, correlation about mean = 0.4279, overlap = 56.39
steps = 180, shift = 1.87, angle = 6 degrees
Position of TTLL11_gold - Copy (11).mrc (#9) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90815416 -0.41863524 -0.00075312 166.04793915
0.41859770 0.90809410 -0.01187737 -101.40706939
0.00565619 0.01047123 0.99992918 72.02623106
Axis 0.02668311 -0.00765240 0.99961465
Axis point 311.82712062 323.30733011 0.00000000
Rotation angle (degrees) 24.75745167
Shift along axis 77.20515948
> color #8 #ff550033 models
> select add #10
6 models selected
> select subtract #9
3 models selected
> view matrix models
> #10,0.20073,0.23366,0.95137,-165.37,-0.97837,-0.001692,0.20684,352.25,0.04994,-0.97232,0.22827,422.86
> undo
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,-9.0651,0,1,0,74.265,0,0,1,87.37
> view matrix models #10,1,0,0,-29.323,0,1,0,61.841,0,0,1,85.605
> view matrix models #10,1,0,0,-28.476,0,1,0,66.002,0,0,1,91.07
> view matrix models #10,1,0,0,-35.308,0,1,0,63.476,0,0,1,94.063
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.99761,0.0069217,0.068795,-57.491,-0.011935,0.99728,0.072737,44.106,-0.068104,-0.073384,0.99498,125.34
> view matrix models
> #10,0.92409,0.37664,0.06475,-114.04,-0.38164,0.91837,0.10462,131.58,-0.020062,-0.12139,0.9924,125.14
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.92409,0.37664,0.06475,-111.94,-0.38164,0.91837,0.10462,125.45,-0.020062,-0.12139,0.9924,123.78
> view matrix models
> #10,0.92409,0.37664,0.06475,-116.59,-0.38164,0.91837,0.10462,119.82,-0.020062,-0.12139,0.9924,122.3
> fitmap #10 inMap #3
Fit map TTLL11_gold - Copy (12).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.6235, correlation about mean = 0.3621, overlap = 26.73
steps = 228, shift = 7.44, angle = 7.78 degrees
Position of TTLL11_gold - Copy (12).mrc (#10) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90324628 0.42901000 -0.00982721 -103.54633667
-0.42898156 0.90329970 0.00494607 169.84957808
0.01099882 -0.00025183 0.99993948 91.21691054
Axis -0.00605632 -0.02426541 -0.99968721
Axis point 319.62346462 314.78176198 0.00000000
Rotation angle (degrees) 25.41236111
Shift along axis -94.68273848
> select add #11
6 models selected
> select subtract #10
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-49.665,0,1,0,43.787,0,0,1,-74.773
> view matrix models #11,1,0,0,-37.033,0,1,0,54.002,0,0,1,-76.428
> view matrix models #11,1,0,0,-33,0,1,0,60.985,0,0,1,-76.642
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99676,-0.0032277,-0.080332,-6.7753,0.0086195,0.99772,0.066863,38.873,0.079933,-0.067339,0.99452,-78.706
> view matrix models
> #11,0.99687,-0.0025914,-0.079048,-7.323,0.0081653,0.99749,0.07027,37.962,0.078668,-0.070696,0.99439,-77.719
> view matrix models
> #11,0.99917,0.015031,-0.037957,-24.076,-0.0081387,0.98443,0.17559,11.481,0.040005,-0.17513,0.98373,-45.15
> view matrix models
> #11,0.95138,0.26359,0.15934,-124.66,-0.27392,0.96063,0.046416,113.61,-0.14083,-0.087806,0.98613,-24.362
> view matrix models
> #11,0.92117,0.29186,0.25743,-154.19,-0.33862,0.92712,0.16059,98.932,-0.1918,-0.2351,0.95286,26.453
> view matrix models
> #11,0.82553,0.47747,0.30088,-184.19,-0.50471,0.86316,0.015025,192.67,-0.25253,-0.16426,0.95354,25.154
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.82553,0.47747,0.30088,-191.34,-0.50471,0.86316,0.015025,183.94,-0.25253,-0.16426,0.95354,21.063
> fitmap #11 inMap #3
Fit map TTLL11_gold - Copy (4).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 520 points
correlation = 0.653, correlation about mean = 0.3401, overlap = 3.122
steps = 96, shift = 6.47, angle = 18.6 degrees
Position of TTLL11_gold - Copy (4).mrc (#11) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90402722 0.42741228 -0.00731643 -104.48011759
-0.42742216 0.90405213 0.00023464 167.04490607
0.00671473 0.00291508 0.99997321 -77.80709229
Axis 0.00313519 -0.01641160 -0.99986041
Axis point 322.43915436 317.39795464 0.00000000
Rotation angle (degrees) 25.30754370
Shift along axis 74.72719226
> select add #12
6 models selected
> select subtract #11
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,65.189,0,1,0,-33.865,0,0,1,-92.511
> view matrix models #12,1,0,0,59.677,0,1,0,-41.735,0,0,1,-91.792
> fitmap #12 inMap #3
Fit map TTLL11_gold - Copy (5).mrc in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 4069 points
correlation = 0.7399, correlation about mean = 0.4243, overlap = 57.75
steps = 152, shift = 7.5, angle = 25.7 degrees
Position of TTLL11_gold - Copy (5).mrc (#12) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.90140686 -0.43297269 0.00056267 171.21700381
0.43297260 0.90140704 0.00028158 -108.92389685
-0.00062911 -0.00001020 0.99999980 -93.45647459
Axis -0.00033695 0.00137628 0.99999900
Axis point 324.48029250 321.48427607 0.00000000
Rotation angle (degrees) 25.65638798
Shift along axis -93.66398171
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex TTLL11gold.cxs"
> select add #4
6 models selected
> select add #5
9 models selected
> select add #6
12 models selected
> select add #7
15 models selected
> select add #8
18 models selected
> select add #9
21 models selected
> select add #10
24 models selected
> select subtract #12
21 models selected
> select add #12
24 models selected
> select add #11
27 models selected
> select add #13
30 models selected
> select subtract #13
27 models selected
> volume add #4,5,6,7,8,9,10,11,12
Opened volume sum as #17, grid size 647,645,645, pixel 1.35, shown at step 1,
values float32
> save "C:/Users/junje/Documents/TTLL11 paper/video/9TTLL11map.mrc" models #17
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> close #13-16
> open "C:/Users/junje/Documents/TTLL11 paper/video/emd_25156.map"
Opened emd_25156.map as #13, grid size 512,512,512, pixel 0.92, shown at level
6.14, step 2, values float32
> hide #!17 models
> select add #13
20 models selected
> select subtract #12
18 models selected
> select subtract #11
16 models selected
> select subtract #4
14 models selected
> select subtract #5
12 models selected
> select subtract #6
10 models selected
> select subtract #8
8 models selected
> select subtract #9
6 models selected
> select subtract #7
4 models selected
> view matrix models
> #10,0.90325,0.42901,-0.0098272,-25.094,-0.42898,0.9033,0.0049461,263.01,0.010999,-0.00025183,0.99994,89.106,#13,1,0,0,78.453,0,1,0,93.162,0,0,1,-2.1107
> view matrix models
> #10,0.90325,0.42901,-0.0098272,-5.4972,-0.42898,0.9033,0.0049461,241.34,0.010999,-0.00025183,0.99994,89.176,#13,1,0,0,98.049,0,1,0,71.491,0,0,1,-2.0409
> view matrix models
> #10,0.90325,0.42901,-0.0098272,-1.1237,-0.42898,0.9033,0.0049461,257.11,0.010999,-0.00025183,0.99994,208.2,#13,1,0,0,102.42,0,1,0,87.257,0,0,1,116.98
> view matrix models
> #10,0.90325,0.42901,-0.0098272,-11.004,-0.42898,0.9033,0.0049461,233.36,0.010999,-0.00025183,0.99994,157.61,#13,1,0,0,92.542,0,1,0,63.515,0,0,1,66.397
> fitmap #13 inMap #3
Fit map emd_25156.map in map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc using 167618 points
correlation = 0.411, correlation about mean = 0.1067, overlap = 9.949e+04
steps = 244, shift = 23.7, angle = 4.36 degrees
Position of emd_25156.map (#13) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99715032 -0.07514862 -0.00662825 100.04850082
0.07520883 0.99712389 0.00935830 60.21603776
0.00590592 -0.00983014 0.99993424 79.64513749
Axis -0.12616151 -0.08241052 0.98858069
Axis point -811.64200220 1464.78172140 0.00000000
Rotation angle (degrees) 4.36139025
Shift along axis 61.15093987
> select add #13
5 models selected
> select subtract #13
2 models selected
> show #!17 models
> hide #!3 models
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold.cxs"
> stereo off
Unknown command: stereo off
> camera ortho
> show #!12 models
> hide #!12 models
> select subtract #10
Nothing selected
> show #!12 models
> show #!10 models
> show #!9 models
> show #!8 models
> open "C:/Users/junje/Documents/TTLL11 paper/video/9TTLL11map - Copy.mrc"
Opened 9TTLL11map - Copy.mrc as #14, grid size 647,645,645, pixel
1.35,1.35,1.35, shown at step 1, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/9TTLL11map - Copy (2).mrc"
Opened 9TTLL11map - Copy (2).mrc as #15, grid size 647,645,645, pixel
1.35,1.35,1.35, shown at step 1, values float32
> open "C:/Users/junje/Documents/TTLL11 paper/video/9TTLL11map - Copy (3).mrc"
Opened 9TTLL11map - Copy (3).mrc as #16, grid size 647,645,645, pixel
1.35,1.35,1.35, shown at step 1, values float32
> hide #!10 models
> hide #!9 models
> show #!9 models
> hide #!12 models
> hide #!13 models
> close #5-12
> show #!13 models
> view orient
> select add #14
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,-55.867,0,1,0,137.01,0,0,1,0
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> volume sel style surface
> volume sel show
> volume sel hide
> volume sel show
> close #14-16
> show #!17 models
> volume copy #17
Opened 9TTLL11map.mrc copy as #5, grid size 647,645,645, pixel 1.35, shown at
step 1, values float32
> show #!17 models
> select add #5
2 models selected
> view orient
> view matrix models #5,1,0,0,-116.06,0,1,0,180.63,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.3707,0.92875,0.0025703,-170.82,-0.92859,0.37069,-0.017586,538.07,-0.017285,0.0041322,0.99984,3.1808
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.3707,0.92875,0.0025703,-89.971,-0.92859,0.37069,-0.017586,536.97,-0.017285,0.0041322,0.99984,4.4528
> view matrix models
> #5,0.3707,0.92875,0.0025703,-93.749,-0.92859,0.37069,-0.017586,534.74,-0.017285,0.0041322,0.99984,32.054
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.12318,0.99143,0.043494,-62.341,-0.99226,0.12236,0.021014,591.2,0.015512,-0.045747,0.99883,35.498
> view matrix models
> #5,0.12111,0.99218,0.030209,-57.904,-0.99264,0.12105,0.0037947,596.91,0.00010815,-0.030446,0.99954,35.564
> view matrix models
> #5,0.12081,0.99249,-0.019015,-42.648,-0.99146,0.12159,0.047109,583.1,0.049067,0.013161,0.99871,15.011
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.12081,0.99249,-0.019015,-32.912,-0.99146,0.12159,0.047109,575.95,0.049067,0.013161,0.99871,14.911
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.133,0.99109,0.00684,-43.459,-0.99069,0.13273,0.030165,578.62,0.028989,-0.010788,0.99952,24.503
> volume copy #5
Opened 9TTLL11map.mrc copy as #6, grid size 647,645,645, pixel 1.35, shown at
step 1, values float32
> show #!5 models
> select subtract #5
Nothing selected
> select add #6
2 models selected
> view orient
[Repeated 1 time(s)]
> view matrix models
> #6,0.27507,0.56578,-0.77732,258.27,-0.92136,-0.075849,-0.38124,734.99,-0.27466,0.82106,0.50043,70.306
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.133,0.99109,0.00684,114.59,-0.99069,0.13273,0.030165,707.13,0.028989,-0.010788,0.99952,24.503
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.96392,0.24935,-0.093177,561.03,-0.25223,-0.96746,0.020275,775.76,-0.085089,0.043045,0.99544,40.703
> view matrix models
> #6,-0.96703,0.25446,0.010251,528.6,-0.25458,-0.96695,-0.014109,786.85,0.0063217,-0.016253,0.99985,30.857
> view matrix models
> #6,-0.95978,0.26183,0.10136,497.09,-0.25935,-0.96507,0.037108,771.68,0.10754,0.0093262,0.99416,3.5381
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.95978,0.26183,0.10136,504.33,-0.25935,-0.96507,0.037108,694.72,0.10754,0.0093262,0.99416,5.1942
> view matrix models
> #6,-0.95978,0.26183,0.10136,518.6,-0.25935,-0.96507,0.037108,689.93,0.10754,0.0093262,0.99416,26.677
> view matrix models
> #6,-0.95978,0.26183,0.10136,503.52,-0.25935,-0.96507,0.037108,684.16,0.10754,0.0093262,0.99416,23.85
> view matrix models
> #6,-0.95978,0.26183,0.10136,503.44,-0.25935,-0.96507,0.037108,693.44,0.10754,0.0093262,0.99416,23.685
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.96551,0.25024,0.07194,516.39,-0.25294,-0.96698,-0.031125,713.5,0.061776,-0.048248,0.99692,45.907
> view matrix models
> #6,-0.96444,0.25784,0.058167,518.77,-0.26111,-0.96356,-0.05816,723.04,0.041051,-0.07128,0.99661,55.8
> view matrix models
> #6,-0.9779,0.20622,0.034311,540.44,-0.20884,-0.97108,-0.11573,730.34,0.0094523,-0.12034,0.99269,74.96
> view matrix models
> #6,-0.97892,0.20389,0.01204,548.08,-0.20404,-0.97359,-0.10241,725.64,-0.0091584,-0.1027,0.99467,74.872
> view matrix models
> #6,-0.97877,0.20489,-0.0057519,553.35,-0.20495,-0.97869,0.013102,691.15,-0.0029448,0.014003,0.9999,46.615
> view orient
> volume copy #6
Opened 9TTLL11map.mrc copy as #7, grid size 647,645,645, pixel 1.35, shown at
step 1, values float32
> select add #7
4 models selected
> show #!6 models
> select subtract #6
2 models selected
> view matrix models
> #7,-0.74956,-0.017296,0.66171,341.11,-0.41026,-0.77236,-0.48492,848.74,0.51947,-0.63495,0.57183,197.73
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.97877,0.20489,-0.0057519,708.41,-0.20495,-0.97869,0.013102,552.21,-0.0029448,0.014003,0.9999,46.615
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.53965,-0.84181,0.01149,826.76,0.83933,-0.53902,-0.070552,240.15,0.065585,-0.028429,0.99744,40.582
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.53965,-0.84181,0.01149,747.92,0.83933,-0.53902,-0.070552,213.09,0.065585,-0.028429,0.99744,37.511
> view matrix models
> #7,-0.53965,-0.84181,0.01149,751.98,0.83933,-0.53902,-0.070552,214.43,0.065585,-0.028429,0.99744,51.948
> view matrix models
> #7,-0.53965,-0.84181,0.01149,751.33,0.83933,-0.53902,-0.070552,213.47,0.065585,-0.028429,0.99744,60.401
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.36248,-0.93061,0.050674,717.12,0.93015,-0.36465,-0.043134,146.2,0.058619,0.031499,0.99778,48.982
> view matrix models
> #7,-0.36996,-0.92744,0.054604,716.95,0.92733,-0.37221,-0.038996,147.2,0.056491,0.036208,0.99775,48.473
> view matrix models
> #7,-0.30419,-0.95228,-0.025325,731.77,0.95256,-0.30434,0.0020641,113.96,-0.0096728,-0.023496,0.99968,76.163
> view matrix models
> #7,-0.30419,-0.95258,-0.0080355,726.48,0.95255,-0.30425,0.0086751,111.89,-0.010709,-0.0050154,0.99993,72.337
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.30419,-0.95258,-0.0080355,727.02,0.95255,-0.30425,0.0086751,114.96,-0.010709,-0.0050154,0.99993,72.316
> view matrix models
> #7,-0.30419,-0.95258,-0.0080355,725.02,0.95255,-0.30425,0.0086751,110.48,-0.010709,-0.0050154,0.99993,72.42
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.19443,-0.98088,-0.0086394,705.76,0.98088,-0.19449,0.0066877,80.807,-0.0082401,-0.0071739,0.99994,72.308
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.19443,-0.98088,-0.0086394,696.73,0.98088,-0.19449,0.0066877,87.378,-0.0082401,-0.0071739,0.99994,71.989
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.35749,-0.93388,-0.0078197,724.29,0.93384,-0.35756,0.0096875,132.59,-0.011843,-0.0038392,0.99992,72.114
> view matrix models
> #7,-0.35344,-0.93545,-0.0032358,722.26,0.93528,-0.35343,0.018117,128.76,-0.018091,0.0033768,0.99983,72.039
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.35749,-0.93388,-0.0078197,728.99,0.93384,-0.35756,0.0096875,140.06,-0.011843,-0.0038392,0.99992,72.066
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.3987,-0.91705,0.0077124,730.14,0.91692,-0.39846,0.022195,148.95,-0.017281,0.015921,0.99972,69.129
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.3987,-0.91705,0.0077124,725.89,0.91692,-0.39846,0.022195,146.84,-0.017281,0.015921,0.99972,69.142
> view matrix models
> #7,-0.3987,-0.91705,0.0077124,725.72,0.91692,-0.39846,0.022195,146.74,-0.017281,0.015921,0.99972,73.297
> volume copy #17
Opened 9TTLL11map.mrc copy as #8, grid size 647,645,645, pixel 1.35, shown at
step 1, values float32
> select subtract #7
Nothing selected
> select add #8
2 models selected
> show #!17 models
> hide #!17 models
> show #!17 models
> view matrix models #8,1,0,0,155.53,0,1,0,-108.27,0,0,1,-9.9749
> view matrix models #8,1,0,0,191.89,0,1,0,-161.21,0,0,1,-11.423
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
[Repeated 6 time(s)]
> select subtract #8
Nothing selected
> select add #9
1 model selected
Can only have one displayed volume when erasing
[Repeated 5 time(s)]
> ui mousemode right select
Drag select of eraser sphere, 6 of 1000 triangles, 8 9TTLL11map.mrc copy
> select #9
1 model selected
> select clear
> select #9
1 model selected
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold.cxs"
——— End of log from Wed Jun 25 10:26:43 2025 ———
opened ChimeraX session
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!13 models
> hide #!17 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!8 models
> volume erase #8 center 430.94,0.12706,398.78 radius 83.789
> volume erase #8 center 432.46,-0.10253,396.53 radius 83.789
> volume erase #8 center 448.39,26.26,422.19 radius 83.789
> volume erase #8 center 458.38,39.064,321.27 radius 83.789
> volume erase #8 center 450.97,22.847,227.4 radius 83.789
> show #!13 models
Can only have one displayed volume when erasing
> hide #!13 models
> volume erase #8 center 374.12,61.781,196.15 radius 83.789
> show #!17 models
> show #!13 models
> show #!7 models
> show #!6 models
> show #!5 models
> select add #8
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.14609,-0.98306,-0.11065,688.31,0.97813,-0.16028,0.13257,-77.569,-0.14806,-0.088869,0.98498,43.032
> view matrix models
> #8,-0.21911,-0.97554,-0.017568,665.48,0.97337,-0.2198,0.065091,-36.847,-0.06736,-0.002838,0.99772,1.9067
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.21911,-0.97554,-0.017568,659.82,0.97337,-0.2198,0.065091,37.838,-0.06736,-0.002838,0.99772,-0.26997
> view matrix models
> #8,-0.21911,-0.97554,-0.017568,650.73,0.97337,-0.2198,0.065091,33.077,-0.06736,-0.002838,0.99772,-9.3514
> view matrix models
> #8,-0.21911,-0.97554,-0.017568,648.6,0.97337,-0.2198,0.065091,33.826,-0.06736,-0.002838,0.99772,-2.0439
> view matrix models
> #8,-0.21911,-0.97554,-0.017568,649.88,0.97337,-0.2198,0.065091,34.445,-0.06736,-0.002838,0.99772,-2.581
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.10189,-0.99448,-0.025185,637.08,0.99212,-0.10344,0.070695,-1.1819,-0.072909,-0.017783,0.99718,2.4805
> view matrix models
> #8,-0.099646,-0.99288,-0.065312,650.77,0.99205,-0.10421,0.070581,-0.92955,-0.076885,-0.05776,0.99537,14.25
> view matrix models
> #8,0.041639,-0.99402,-0.10095,639.26,0.99898,0.039658,0.021553,-21.925,-0.01742,-0.10174,0.99466,15.581
> view matrix models
> #8,0.10287,-0.9854,-0.13569,638.87,0.99425,0.10596,-0.015687,-24.924,0.029835,-0.13329,0.99063,17.005
> view matrix models
> #8,0.05092,-0.99675,-0.062392,624.42,0.99867,0.050335,0.010921,-20.813,-0.0077451,-0.062866,0.99799,2.5533
> view matrix models
> #8,0.091816,-0.99071,-0.10035,629.42,0.99547,0.093813,-0.01536,-22.091,0.024631,-0.098482,0.99483,7.3212
> view matrix models
> #8,0.19302,-0.97563,-0.10438,609.26,0.98056,0.19563,-0.01527,-46.055,0.035318,-0.099403,0.99442,5.8437
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.15948,-0.98249,-0.096307,613.99,0.98663,0.16193,-0.018156,-37.292,0.033433,-0.092124,0.99519,3.9992
> view matrix models
> #8,0.093787,-0.99491,0.0368,580.62,0.99554,0.093336,-0.013806,-22.54,0.010301,0.037931,0.99923,-27.317
> view matrix models
> #8,0.092821,-0.99528,0.028308,583.95,0.99566,0.092604,-0.0089037,-24.142,0.0062402,0.029012,0.99956,-24.403
> view matrix models
> #8,0.082864,-0.99615,0.028785,585.75,0.99656,0.082923,0.00088185,-25.31,-0.0032654,0.028613,0.99959,-22.648
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.082864,-0.99615,0.028785,587.71,0.99656,0.082923,0.00088185,-26.221,-0.0032654,0.028613,0.99959,-27.408
> select subtract #8
Nothing selected
> ui mousemode right select
> volume add #5,6,7,8,13,17
Opened volume sum as #9, grid size 806,799,735, pixel 1.35, shown at step 1,
values float32
> volume #9 level 1.316
> close #9
> show #!17 models
> show #!13 models
> show #!8 models
> show #!7 models
> show #!5 models
> show #!6 models
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold.cxs"
> volume add #5,6,7,8,17
Opened volume sum as #9, grid size 806,799,735, pixel 1.35, shown at step 1,
values float32
> hide #!13 models
> save "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11maps around.mrc"
> models #9
> show #!13 models
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 12 time(s)]
> color #13 cyan models
> color #13 #55ffffff models
> color #13 cyan models
> show #!1 models
No model chosen to save relative to
> save "C:/Users/junje/Documents/TTLL11 paper/video/MT long.cif" models #1
> relModel #2
> hide #!9 models
> hide #!13 models
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 25 models
selected
> save "C:/Users/junje/Documents/TTLL11 paper/video/MT long 01.cif" models #1
> selectedOnly true relModel #2
> hide #2.1 models
> save "C:/Users/junje/Documents/TTLL11 paper/video/MT long 02.cif" models
> #1.1-3 relModel #2
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold02.cxs"
——— End of log from Thu Jul 3 10:39:52 2025 ———
opened ChimeraX session
> save C:/Users/junje/Desktop/MT4.pdb models #1.1-4 relModel #2
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 25 models
selected
> select subtract #1
Nothing selected
> show #!2 models
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy
> (3).pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy (3).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy (3).pdb #10
---
Chain | Description
E | No description available
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy
> (4).pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy (4).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy (4).pdb #11
---
Chain | Description
E | No description available
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy
> (5).pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy (5).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy (5).pdb #12
---
Chain | Description
E | No description available
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy
> (6).pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy (6).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy (6).pdb #14
---
Chain | Description
E | No description available
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy.pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy.pdb #15
---
Chain | Description
E | No description available
> open "C:/Users/junje/Documents/TTLL11 paper/video/TTLL11_alone - Copy
> (2).pdb"
Summary of feedback from opening C:/Users/junje/Documents/TTLL11
paper/video/TTLL11_alone - Copy (2).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 10 HIS A 28 1 19
Start residue of secondary structure not found: HELIX 2 2 PRO A 72 ARG A 79 1
8
Start residue of secondary structure not found: HELIX 3 3 ARG A 84 LEU A 86 5
3
Start residue of secondary structure not found: HELIX 4 4 PRO A 89 GLN A 91 5
3
Start residue of secondary structure not found: HELIX 5 5 TYR A 103 TYR A 108
1 6
117 messages similar to the above omitted
Chain information for TTLL11_alone - Copy (2).pdb #16
---
Chain | Description
E | No description available
> hide #!2 models
> select add #10
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,4.4403,0,1,0,-2.5489,0,0,1,80.211
> view matrix models #10,1,0,0,4.9394,0,1,0,-2.0702,0,0,1,80.38
> view matrix models #10,1,0,0,4.1304,0,1,0,-3.4353,0,0,1,83.644
> select add #11
8296 atoms, 8488 bonds, 2 pseudobonds, 1034 residues, 4 models selected
> select subtract #10
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> view matrix models #11,1,0,0,-4.7786,0,1,0,62.287,0,0,1,-64.591
> view matrix models #11,1,0,0,-17.299,0,1,0,49.256,0,0,1,-62.918
> show #!3 models
> view matrix models #11,1,0,0,-37.419,0,1,0,60.343,0,0,1,-71.149
> fitmap #11 inMap #3
Fit molecule TTLL11_alone - Copy (4).pdb (#11) to map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) using 4148 atoms
average map value = 0.0743, steps = 156
shifted from previous position = 24.4
rotated from previous position = 14 degrees
atoms outside contour = 3301, contour level = 0.09639
Position of TTLL11_alone - Copy (4).pdb (#11) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.97037061 0.22069175 -0.09836685 -21.40659761
-0.22199519 0.97504488 -0.00237119 119.73620273
0.09538879 0.02413790 0.99514740 -86.46799500
Axis 0.05477556 -0.40035600 -0.91472111
Axis point 573.05023794 181.37579937 0.00000000
Rotation angle (degrees) 14.00338298
Shift along axis 29.98443444
> view matrix models
> #11,0.97037,0.22069,-0.098367,-46.755,-0.222,0.97504,-0.0023712,112.4,0.095389,0.024138,0.99515,-86.906
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s.cxs"
> fitmap #11 inMap #3
Fit molecule TTLL11_alone - Copy (4).pdb (#11) to map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) using 4148 atoms
average map value = 0.09626, steps = 324
shifted from previous position = 37
rotated from previous position = 3.14 degrees
atoms outside contour = 3037, contour level = 0.09639
Position of TTLL11_alone - Copy (4).pdb (#11) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.95661349 0.27168856 -0.10524238 -15.90029553
-0.27420863 0.96161838 -0.00998616 134.67040078
0.09848988 0.03841126 0.99439646 -82.52205147
Axis 0.08277565 -0.34844978 -0.93366533
Axis point 506.97656825 148.26046163 0.00000000
Rotation angle (degrees) 16.99815637
Shift along axis 28.80594936
> undo
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-35.652,0,1,0,53.576,0,0,1,-62.213
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99234,0.11818,-0.036015,-46.37,-0.12189,0.9841,-0.1292,122.81,0.020173,0.1326,0.99096,-90.104
> view matrix models
> #11,0.99434,0.10075,-0.033592,-44.095,-0.10389,0.98841,-0.1107,112.37,0.02205,0.11356,0.99329,-87.452
> hide #!3 models
> view matrix models
> #11,0.95623,0.22009,-0.19284,-10.696,-0.24703,0.9604,-0.12886,154.64,0.15684,0.17086,0.97273,-121.86
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.95623,0.22009,-0.19284,-11.056,-0.24703,0.9604,-0.12886,155.61,0.15684,0.17086,0.97273,-126.31
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.95623,0.22009,-0.19284,-10.015,-0.24703,0.9604,-0.12886,159.39,0.15684,0.17086,0.97273,-126.33
> select add #12
8296 atoms, 8488 bonds, 2 pseudobonds, 1034 residues, 4 models selected
> select subtract #11
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> view matrix models #12,1,0,0,-149.04,0,1,0,57.341,0,0,1,-63.122
> view matrix models #12,1,0,0,-43.677,0,1,0,128.66,0,0,1,-77.99
> view matrix models #12,1,0,0,-66.026,0,1,0,121.15,0,0,1,-129.5
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.99882,0.0018591,0.048451,-80.967,-0.0045827,0.99841,0.056162,105.27,-0.048269,-0.056318,0.99725,-106.99
> view matrix models
> #12,0.84221,0.52957,0.1012,-167.54,-0.537,0.84068,0.069914,248.22,-0.048052,-0.11323,0.99241,-94.286
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.84221,0.52957,0.1012,-152.9,-0.537,0.84068,0.069914,253,-0.048052,-0.11323,0.99241,-94.255
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.73421,0.6595,0.16124,-173.5,-0.67493,0.73473,0.068149,304.55,-0.073525,-0.15886,0.98456,-77.268
> view matrix models
> #12,0.72844,0.64118,0.24136,-193.14,-0.67354,0.73469,0.081058,300.31,-0.12536,-0.22161,0.96704,-48.193
> view matrix models
> #12,0.62685,0.71645,0.30621,-205.77,-0.77277,0.62183,0.12705,330.19,-0.099383,-0.31627,0.94345,-27.879
> select subtract #12
Nothing selected
> select add #14
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> view matrix models
> #14,0.07311,0.93797,0.33891,-87.71,-0.99003,0.027237,0.13819,365.93,0.12039,-0.34564,0.93061,63.486
> view matrix models
> #14,0.94671,0.15762,0.28087,-105.58,-0.31013,0.68141,0.66294,-72.271,-0.086894,-0.71472,0.69399,254.14
> view matrix models
> #14,0.73501,-0.27799,0.61845,-76.523,-0.37515,0.59305,0.71243,-55.758,-0.56482,-0.75565,0.33162,477.2
> view matrix models
> #14,0.93902,0.26098,0.22389,-106.94,-0.33864,0.58894,0.73381,-69.435,0.059651,-0.76488,0.6414,248.26
> view matrix models
> #14,0.85257,0.52241,-0.014851,-66.829,-0.30469,0.51994,0.79801,-82.809,0.42461,-0.67583,0.60246,163.09
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.85257,0.52241,-0.014851,-41.063,-0.30469,0.51994,0.79801,-21.468,0.42461,-0.67583,0.60246,185.15
> view matrix models
> #14,0.85257,0.52241,-0.014851,-108.27,-0.30469,0.51994,0.79801,36.254,0.42461,-0.67583,0.60246,184.04
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.82328,0.50009,0.26855,-184.21,-0.48979,0.38672,0.78138,108.03,0.2869,-0.77483,0.56332,245.6
> view matrix models
> #14,0.75627,0.36334,0.54409,-226.86,-0.57112,0.77232,0.27809,203.39,-0.31917,-0.52106,0.7916,257.42
> view matrix models
> #14,0.76725,0.36843,0.52497,-224.41,-0.59481,0.7149,0.36758,192.53,-0.23987,-0.59428,0.76765,261.99
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.76725,0.36843,0.52497,-237.37,-0.59481,0.7149,0.36758,198.9,-0.23987,-0.59428,0.76765,261.72
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.6236,0.40878,0.66635,-257.36,-0.7546,0.53741,0.37651,266.11,-0.20419,-0.73762,0.6436,320.31
> view matrix models
> #14,0.65387,0.72545,-0.21488,-56.977,-0.63142,0.67968,0.37329,212.1,0.41685,-0.10841,0.90249,-18.76
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.65387,0.72545,-0.21488,-60.878,-0.63142,0.67968,0.37329,209.75,0.41685,-0.10841,0.90249,-22.98
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.87054,0.43176,0.23609,-187.9,-0.48344,0.83995,0.24653,184.59,-0.091858,-0.32875,0.93994,119.95
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.74568,0.58903,0.31145,-214.93,-0.6532,0.73849,0.16724,265.91,-0.13149,-0.32815,0.93543,129.84
> view matrix models
> #14,0.75027,0.57296,0.32987,-218.38,-0.63867,0.75707,0.13763,268.13,-0.17088,-0.31393,0.93394,136.06
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.60515,0.71011,0.35991,-223.14,-0.77442,0.62988,0.059341,346.83,-0.18456,-0.31463,0.9311,140.05
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #14,0.60515,0.71011,0.35991,-218.82,-0.77442,0.62988,0.059341,356.45,-0.18456,-0.31463,0.9311,139.96
> view matrix models
> #14,0.60515,0.71011,0.35991,-212.51,-0.77442,0.62988,0.059341,355.85,-0.18456,-0.31463,0.9311,151.18
> view matrix models
> #14,0.60515,0.71011,0.35991,-209.56,-0.77442,0.62988,0.059341,344.59,-0.18456,-0.31463,0.9311,149.93
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.60515,0.71011,0.35991,-212.32,-0.77442,0.62988,0.059341,343.16,-0.18456,-0.31463,0.9311,146.51
> view matrix models
> #14,0.60515,0.71011,0.35991,-212.26,-0.77442,0.62988,0.059341,351.14,-0.18456,-0.31463,0.9311,146.36
> select add #15
8296 atoms, 8488 bonds, 2 pseudobonds, 1034 residues, 4 models selected
> select subtract #14
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> view matrix models #15,1,0,0,0.057944,0,1,0,69.31,0,0,1,90.997
> view matrix models #15,1,0,0,-8.3344,0,1,0,123.74,0,0,1,134.74
> view matrix models #15,1,0,0,-16.551,0,1,0,126.81,0,0,1,111.76
> view matrix models #15,1,0,0,12.58,0,1,0,68.09,0,0,1,127.51
> view matrix models #15,1,0,0,-32.551,0,1,0,52.018,0,0,1,126.26
> view matrix models #15,1,0,0,-32.763,0,1,0,53.228,0,0,1,168.85
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.94308,0.33065,0.035477,-96.722,-0.33123,0.94348,0.011631,132.98,-0.029626,-0.02272,0.9993,180.01
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.94308,0.33065,0.035477,-100.98,-0.33123,0.94348,0.011631,137.56,-0.029626,-0.02272,0.9993,179.48
> view matrix models
> #15,0.94308,0.33065,0.035477,-101.62,-0.33123,0.94348,0.011631,139.24,-0.029626,-0.02272,0.9993,179.7
> view matrix models
> #15,0.94308,0.33065,0.035477,-101.2,-0.33123,0.94348,0.011631,138.67,-0.029626,-0.02272,0.9993,177.23
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.91099,0.40771,0.062175,-117.64,-0.41072,0.91056,0.046803,151.74,-0.037532,-0.068173,0.99697,188.67
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.91099,0.40771,0.062175,-120.59,-0.41072,0.91056,0.046803,150.76,-0.037532,-0.068173,0.99697,188.67
> select add #16
8296 atoms, 8488 bonds, 2 pseudobonds, 1034 residues, 4 models selected
> select subtract #15
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> view matrix models #16,1,0,0,-88.456,0,1,0,31.096,0,0,1,-100.69
> undo
> view matrix models #16,1,0,0,0.86491,0,1,0,-0.67299,0,0,1,0.70392
> undo
> select subtract #16
Nothing selected
> ui mousemode right select
> select add #10
4148 atoms, 4244 bonds, 1 pseudobond, 517 residues, 2 models selected
> select add #11
8296 atoms, 8488 bonds, 2 pseudobonds, 1034 residues, 4 models selected
> select add #12
12444 atoms, 12732 bonds, 3 pseudobonds, 1551 residues, 6 models selected
> select add #16
16592 atoms, 16976 bonds, 4 pseudobonds, 2068 residues, 8 models selected
> select add #15
20740 atoms, 21220 bonds, 5 pseudobonds, 2585 residues, 10 models selected
> select add #14
24888 atoms, 25464 bonds, 6 pseudobonds, 3102 residues, 12 models selected
> hide #!11 models
> show #!11 models
> color #10 white
> color #10 #aa00ffff
> color #10 #ce1effff
> color #10 #ac1effff
> color #10 #b41dffff
> color #10 #ac1cffff
> color #10 #ab1affff
> color #10 #aa17ffff
> color #10 white
> color #10 #8019ffff
> color #10 #9819ffff
> color #10 #a513ffff
> color #11 #a513ffff
> color #12 #a513ffff
> color #14 #a513ffff
> color #15 #a513ffff
> color #16 #a513ffff
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select #16/E:592
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/E:591
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
150 atoms, 152 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> color sele hot pink
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel hot pink
> color sel light pink
> color sel pink
> color sel voilet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel violet
> select #10/E:646
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select up
4148 atoms, 4244 bonds, 517 residues, 1 model selected
> select down
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> color sel violet
> undo
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
143 atoms, 144 bonds, 18 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #10/E:647
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/E:646
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select up
4148 atoms, 4244 bonds, 517 residues, 1 model selected
> select down
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
143 atoms, 144 bonds, 18 residues, 1 model selected
> select #10/E:591
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/E:591
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/E:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/E:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
150 atoms, 152 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> color sel violet
> select #11/E:595
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
150 atoms, 152 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> color sel violet
> select #14/E:643
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> color sel violet
> select #15/E:643
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> color sel violet
> select #12/E:642
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:642
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
143 atoms, 144 bonds, 18 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select up
4148 atoms, 4244 bonds, 517 residues, 1 model selected
> select down
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> color sel violet
> select #12/E:475
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:475
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:475
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select up
1607 atoms, 1637 bonds, 201 residues, 1 model selected
> select down
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel #a513ff
> select #12/E:495
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel #a513ff
> select #12/E:510
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/u:393
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/E:503
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:503
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> select #11/E:496
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel #a513ff
> select #11/E:479
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/E:479
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #a513ff
> select #11/E:472
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/E:472
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel pink
> color sel #a513ff
> select #1.1/q:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/E:505
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> select #16/E:483
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select down
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel #a513ff
> select #16/E:493
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/E:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> select #16/E:491
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel #a513ff
> select clear
> select #16/E:524
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> select #10/E:496
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel #a513ff
> select #10/E:483
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> select up
1545 atoms, 1575 bonds, 193 residues, 1 model selected
> color sel #a513ff
> undo
> select #10/E:144
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #10/E:481
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/E:481
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel #a513ff
> select clear
[Repeated 1 time(s)]
> select #10/E:505
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> select #14/E:495
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel #a513ff
> select #14/E:505
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> select #14/E:471
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/E:472
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel #a513ff
> select #15/E:479
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 136 bonds, 17 residues, 1 model selected
> color sel #a513ff
> select #15/E:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #a513ff
> select #15/E:496
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 95 bonds, 11 residues, 1 model selected
> color sel pink
> color sel #a513ff
> select #1.4/p:193
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.4/p:418
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.4/x:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/E:519
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
392 atoms, 402 bonds, 50 residues, 1 model selected
> color sel #a513ff
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color.cxs"
——— End of log from Thu Jul 3 13:34:59 2025 ———
opened ChimeraX session
> view
> center #1
Unknown command: center #1
> view
> view orient
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> turn y 90
[Repeated 1 time(s)]
> turn z 90
> turn x 90
> view
> turn x 90
[Repeated 1 time(s)]
> turn y 90
[Repeated 1 time(s)]
> turn x 90
> turn y 90
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!13 models
> hide #!13 models
> turn z 90
[Repeated 1 time(s)]
> turn y 90
[Repeated 1 time(s)]
> show surfaces
> view name p1
> show #!12 models
> show #!8 models
> hide #!12 models
> show #!5 models
> show #!7 models
> show #!6 models
> hide #!8 models
> view name p2
> roll x 3 120 center #1
> view name p2
> view name p3
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> volume #3 level 0.04143
> hide #!1 models
> volume #3 level 0.08371
> volume #3 level 0.1218
> view
> center #3
Unknown command: center #3
> view center #3
Expected an objects specifier or a view name or a keyword
> volume #3 color #55aa7f80
> view name p4
> movie record
> fly p1 p2
> show #!1 models
> roll x 3 120 center #1
> fly p3
> crossfade
> show #5,6,7,8
> fly p4
> show #!17 models
> hide #!17 models
> show #!17 models
> roll x 3 120 center #1
> fly p1
> movie encode C:\Users\junje\Documents\MT01.mp4
Movie saved to \C:Users\\...\Documents\MT01.mp4
> hide #!17 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!3 models
> view name p1
> roll y 3 120 center #1
> roll y 4 120 center #1
> show #!6 models
> roll x 1 360 center #1
> view name p2
> hide #!6 models
> show #!6 models
Unknown or unsupported skia image format
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views.cxs"
Ran out of memory trying to save a session including 4 maps (4.0 Gbytes).
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.
#5 "9TTLL11map.mrc copy" (1026 MB)
#6 "9TTLL11map.mrc copy" (1026 MB)
#7 "9TTLL11map.mrc copy" (1026 MB)
#8 "9TTLL11map.mrc copy" (1026 MB)
[Repeated 1 time(s)]
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views.cxs"
> fly p1
> view name p1
> fly p1
[Repeated 2 time(s)]
> fly p3
> zoom 3 frames 20
> fly p3
> show #!2 models
> hide #!2#!1.1-8 surfaces
> select add #2
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,-0.00024682,0.00025461,17.004,0.00024679,1,9.3775e-05,207.09,-0.00025464,-9.3712e-05,1,36.369
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.51085,0.85572,0.082348,170.56,-0.8571,-0.51438,0.028064,743.51,0.066373,-0.056244,0.99621,33.731
> view matrix models
> #2,-0.45198,0.88255,0.12969,135.15,-0.88305,-0.46325,0.07492,723.61,0.1262,-0.080661,0.98872,26.898
> undo
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.097854,0.98964,0.10508,32.658,-0.99006,-0.10752,0.090616,665.93,0.10098,-0.095173,0.99033,35.771
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.51085,0.85572,0.082348,177.57,-0.8571,-0.51438,0.028064,721.18,0.066373,-0.056244,0.99621,38.829
> show #!7 models
> show #!5 models
> view matrix models
> #2,-0.51085,0.85572,0.082348,157.71,-0.8571,-0.51438,0.028064,730.53,0.066373,-0.056244,0.99621,26.714
> hide #!7 models
> hide #!6 models
> view matrix models
> #2,-0.51085,0.85572,0.082348,150.27,-0.8571,-0.51438,0.028064,735,0.066373,-0.056244,0.99621,34.802
> fitmap #2 inMap #5
Fit molecule TTLL11_complex_mutfix-coot-13.pdb (#2) to map 9TTLL11map.mrc copy
(#5) using 17848 atoms
average map value = 0.009177, steps = 236
shifted from previous position = 3.89
rotated from previous position = 6.41 degrees
atoms outside contour = 17124, contour level = 0.077045
Position of TTLL11_complex_mutfix-coot-13.pdb (#2) relative to 9TTLL11map.mrc
copy (#5) coordinates:
Matrix rotation and translation
0.79865005 0.59837451 -0.06407853 -101.36521460
-0.58506311 0.79696410 0.15016455 178.46887659
0.14092292 -0.08243895 0.98658227 1.03082161
Axis -0.19013210 -0.16756995 -0.96735211
Axis point 216.37390023 245.90520193 0.00000000
Rotation angle (degrees) 37.71174120
Shift along axis -11.63040685
> fitmap #2 inMap #5
Fit molecule TTLL11_complex_mutfix-coot-13.pdb (#2) to map 9TTLL11map.mrc copy
(#5) using 17848 atoms
average map value = 0.009176, steps = 48
shifted from previous position = 0.0705
rotated from previous position = 0.217 degrees
atoms outside contour = 17120, contour level = 0.077045
Position of TTLL11_complex_mutfix-coot-13.pdb (#2) relative to 9TTLL11map.mrc
copy (#5) coordinates:
Matrix rotation and translation
0.79845081 0.59826289 -0.06751177 -100.20744791
-0.58490242 0.79738361 0.14855493 178.85266921
0.14270768 -0.07912600 0.98659699 -0.07616476
Axis -0.18615460 -0.17187789 -0.96736986
Axis point 217.54604104 244.52455514 0.00000000
Rotation angle (degrees) 37.70073474
Shift along axis -12.01306316
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views02.cxs"
——— End of log from Tue Jul 8 10:04:14 2025 ———
opened ChimeraX session
> show #!3 models
> hide #!1 models
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.47253,0.86931,0.145,94.608,-0.86435,-0.48924,0.11636,600.95,0.1721,-0.070348,0.98257,-14.721
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.51038,0.82079,0.25655,-170.46,-0.85941,0.47624,0.18605,363.55,0.03053,-0.31544,0.94846,85.075
> view matrix models
> #2,0.50248,0.84522,0.18196,-150.21,-0.86435,0.48611,0.12885,380.77,0.020459,-0.22202,0.97483,58.438
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.50248,0.84522,0.18196,-172.91,-0.86435,0.48611,0.12885,391.81,0.020459,-0.22202,0.97483,58.476
> view matrix models
> #2,0.50248,0.84522,0.18196,-174.45,-0.86435,0.48611,0.12885,384.95,0.020459,-0.22202,0.97483,71.686
> fitmap #2 inMap #5
Fit molecule TTLL11_complex_mutfix-coot-13.pdb (#2) to map 9TTLL11map.mrc copy
(#5) using 17848 atoms
average map value = 0.01304, steps = 148
shifted from previous position = 2.47
rotated from previous position = 12 degrees
atoms outside contour = 16772, contour level = 0.077045
Position of TTLL11_complex_mutfix-coot-13.pdb (#2) relative to 9TTLL11map.mrc
copy (#5) coordinates:
Matrix rotation and translation
0.90056857 -0.43462756 0.00866888 168.63335743
0.43460546 0.90061028 0.00438595 -109.28448415
-0.00971354 -0.00018230 0.99995282 -7.03147031
Axis -0.00525425 0.02114284 0.99976266
Axis point 322.77444696 314.02910361 0.00000000
Rotation angle (degrees) 25.76745801
Shift along axis -10.22642692
> show #!1 models
> hide #!3 models
> ui mousemode right select
> select clear
> fitmap #1 inMap #3
Fit molecules 8xring_combine.cif (#1.1), 8xring_combine.cif (#1.2),
8xring_combine.cif (#1.3), 8xring_combine.cif (#1.4), 8xring_combine.cif
(#1.5), 8xring_combine.cif (#1.6), 8xring_combine.cif (#1.7),
8xring_combine.cif (#1.8) to map
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) using 1423264 atoms
average map value = 0.02757, steps = 48
shifted from previous position = 0.0894
rotated from previous position = 0.0304 degrees
atoms outside contour = 1374222, contour level = 0.12175
Position of 8xring_combine.cif (#1.1) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.2) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.3) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.4) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.5) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.6) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.7) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
Position of 8xring_combine.cif (#1.8) relative to
cryosparc_P35_J257_006_volume_map_hancer_highRes.mrc (#3) coordinates:
Matrix rotation and translation
0.99748331 -0.07067587 -0.00565314 9.22465859
0.07072086 0.99746244 0.00819991 -14.52683723
0.00505926 -0.00857907 0.99995040 -0.58403600
Axis -0.11750712 -0.07502142 0.99023425
Axis point 210.39847383 122.07677481 0.00000000
Rotation angle (degrees) 4.09414976
Shift along axis -0.57247151
> select add #2
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 2 models selected
> hide #!5 models
> select clear
Drag select of 5 residues
> select add #2
17863 atoms, 18264 bonds, 3 pseudobonds, 2242 residues, 5 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.4,0.99748,-0.070676,-0.0056531,12.995,0.070721,0.99746,0.0081999,-13.74,0.0050593,-0.0085791,0.99995,-2.5712,#2,0.55044,0.83478,0.012339,-125.62,-0.83479,0.55012,0.022158,397.63,0.011709,-0.022497,0.99968,21.555
> view matrix models
> #1.4,0.99748,-0.070676,-0.0056531,14.262,0.070721,0.99746,0.0081999,-2.6175,0.0050593,-0.0085791,0.99995,-22.332,#2,0.55044,0.83478,0.012339,-124.35,-0.83479,0.55012,0.022158,408.75,0.011709,-0.022497,0.99968,1.7938
> undo
> select add #1
1441112 atoms, 1474184 bonds, 1459 pseudobonds, 182576 residues, 33 models
selected
> select subtract #1
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 423 models selected
> select add #1
1441112 atoms, 1474184 bonds, 1459 pseudobonds, 182576 residues, 32 models
selected
> select subtract #1
17848 atoms, 18264 bonds, 3 pseudobonds, 2240 residues, 7 models selected
> view matrix models
> #2,0.55044,0.83478,0.012339,-125.64,-0.83479,0.55012,0.022158,397.8,0.011709,-0.022497,0.99968,20.204
> view matrix models
> #2,0.55044,0.83478,0.012339,-125.82,-0.83479,0.55012,0.022158,397.25,0.011709,-0.022497,0.99968,17.763
> hide #!2 models
> select subtract #2
5 models selected
> ui mousemode right select
> select #1.4/r:375
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1.1/u:385
14 atoms, 12 bonds, 2 residues, 3 models selected
> select add #1.4/s:150
22 atoms, 19 bonds, 3 residues, 4 models selected
> select add #1.1/v:148
26 atoms, 22 bonds, 4 residues, 4 models selected
> select up
592 atoms, 599 bonds, 75 residues, 5 models selected
> select up
12938 atoms, 13230 bonds, 1648 residues, 6 models selected
> select up
13126 atoms, 13424 bonds, 1672 residues, 6 models selected
> select up
13562 atoms, 13870 bonds, 1728 residues, 6 models selected
> select up
13684 atoms, 13998 bonds, 1734 residues, 6 models selected
> show #!2 models
> select clear
> show #!5 models
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views03.cxs"
> show #!13 models
> hide #!13 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!17 models
> select #5
2 models selected
> select #5
2 models selected
> ui mousemode right select
> transparency #5,6,7,8,17 set 50
Missing or invalid "percent" argument: Expected a number
> transparency #5,6,7,8,17 50
> view name "p3\\\"
> view name p3
> center #2
Unknown command: center #2
> view #2
> view name p4
> hide #!1 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!17 models
> show #!3 models
> hide #!3 models
> view name p5
> view name p7
> view name p8
> movie record
> movie encode C:\Users
Unrecognized movie file suffix Users, use *.ogv, *.wmv, *.png, *.avi, *.mp4,
*.webm, *.mov
> movie encode C:\Users\xx.mp4
Movie encoding failed because no images were recorded.
> hide #!2 models
> show #!1 models
> movie record
> roll y 4 120 center #1
> fly p1 p2
> zoom 3 frames 20
> center #5
Unknown command: center #5
> fly p1 p2
> zoom 3 frames 20 center #5
Expected a keyword
> select clear
> hide #!1 models
> ui tool show "Side View"
> show #!1 models
> end
Unknown command: end
> movie encode C:\Users\xx.mp4
C:\Program Files\ChimeraX 1.9\bin\ffmpeg.exe -r 25 -i
C:\Users\junje\AppData\Local\Temp\chimovie_Z3UM-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\xx.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'C:\Users\junje\AppData\Local\Temp\chimovie_Z3UM-%05d.ppm':
Duration: 00:00:10.32, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 830x606, 25 fps, 25 tbr, 25 tbn, 25 tbc
C:\Users\xx.mp4: Permission denied
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 1
Error message:
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'C:\Users\junje\AppData\Local\Temp\chimovie_Z3UM-%05d.ppm':
Duration: 00:00:10.32, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 830x606, 25 fps, 25 tbr, 25 tbn, 25 tbc
C:\Users\xx.mp4: Permission denied
\-----------------------------
> roll y 4 120 center #1
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 25 models
selected
> show sel surfaces
> fly p1 p2
> zoom 3 frames 20 center #5
Expected a keyword
> fly p1 p2
> zoom 3 frames 20
> select clear
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 297 models
selected
> select subtract #1
416 models selected
> select add #1
1423264 atoms, 1455920 bonds, 1456 pseudobonds, 180336 residues, 297 models
selected
> select subtract #1
416 models selected
> roll x 3 120 center #1
> crossfade
> show #5,6,7,8,17 models
> roll x 2 300 center #1
> crossfade, show #3 models, hide #1
Unknown command: crossfade, show #3 models, hide #1
> crossfade
> show #3 models, hide #1
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> crossfade
> show #3 models
> , hide #1
Unknown command: , hide #1
> crossfade
> show #3 models
> hide #1
> crossfade
> show #2 models
> hide #3
[Repeated 1 time(s)]
> hide #1
> hide #!1 models
> fly p4
> zoom 2 frames 5 center #2
Expected a keyword
> fly p4
> zoom 2 frames 5
> crossfade
> hide #5,6,7,8,17
> fly p5
> flyp6
Unknown command: flyp6
> fly p6
fly: Unknown position name "p6"
> fly p7
> fly p8
> fly p9
fly: Unknown position name "p9"
> crossfade
> show #1
> crossfade
> show #!1
> roll y 4 300
> zoom 0.2 frames 20
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 6 time(s)]
> select clear
> view
> fly p1
> hide #!2 models
> fly p5
> show #!2 models
> hide #!1 models
> view name p6
> fly p8
> view name p9
> fly p5
> fly p6
> fly p5
> fly p7
> fly p8
> fly p9
> show #!1 models
> hide #!2 models
> select ~sel & ##selected
Nothing selected
> fly p1
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views04.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
> save "C:/Users/junje/Documents/TTLL11 paper/video/chimerax sessions/MT map
> complex multiTTLL11gold_TTLL11s_color_views04.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy
return data.copy()
^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.88 MiB for an
array with shape (338844, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001742F6D9C90> ->
<chimerax.std_commands.view.NamedView object at 0x000001774DDDF310> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001742F552D10>
'8xring_combine.cif_G SES surface': Unable to allocate 3.88 MiB for an array
with shape (338844, 3) and data type int32
ValueError: error processing: 'named views' -> -> -> '8xring_combine.cif_G SES
surface': Unable to allocate 3.88 MiB for an array with shape (338844, 3) and
data type int32
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy
return data.copy()
^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.88 MiB for an
array with shape (338844, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001742F6D9C90> ->
<chimerax.std_commands.view.NamedView object at 0x000001774DDDF310> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001742F552D10>
'8xring_combine.cif_G SES surface': Unable to allocate 3.88 MiB for an array
with shape (338844, 3) and data type int32
ValueError: error processing: 'named views' -> -> -> '8xring_combine.cif_G SES
surface': Unable to allocate 3.88 MiB for an array with shape (338844, 3) and
data type int32
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
QWindowsWindow::setGeometry: Unable to set geometry 600x479+1620+332 (frame:
626x550+1607+274) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 590x447+1625+359 (frame:
616x518+1612+301) margins: 13, 58, 13, 13 minimum size: 600x325 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=1048600, y=1048645), mintrack=POINT(x=1226, y=721)))
[Repeated 1 time(s)]
OpenGL version: 3.3.0 - Build 31.0.101.4255
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: Zenbook UX3402ZA_UX3402ZA
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,785,965,056
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i7-1260P
OSLanguage: en-GB
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 3 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to save MolecularSurface in session: ArrayMemoryError |
comment:2 by , 3 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
Saving a ChimeraX session file ran out of memory. Your computer only has 16 GB of memory and you had 16 maps open each about 0.5 to 1 GB in size. You would need more memory to work with that many large maps and avoid out of memory errors.
Note:
See TracTickets
for help on using tickets.
Reported by Jana Campbell