Unable to save MolecularSurface in session: ArrayMemoryError

[nedvedova@…]

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

[Eric Pettersen]

Reported by Jana Campbell

[Tom Goddard]

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.