![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Last modified 12 months ago
#16632 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/mimbert/Downloads/chimeraX_fig1.cxs
Error opening map "/Users/mimbert/Downloads/fig1.svg": File fig1.svg, format
mrc
MRC header value nsymbt (1999530350) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "/Users/mimbert/Downloads/chimeraX_fig1.cxs": File
chimeraX_fig1.cxs, format mrc
MRC header value nsymbt (1953787962) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "/Users/mimbert/Downloads/chimeraX_fig1.cxs": File
chimeraX_fig1.cxs, format mrc
MRC header value nsymbt (1953787962) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "/Users/mimbert/RadA_filament_250924.cxs": File
RadA_filament_250924.cxs, format mrc
MRC header value nsymbt (1953787962) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P12_J237_map_sharp.mrc zone as #6, grid size 256,256,256,
pixel 1.14, shown at level 0.0459, step 1, values float32
Opened cryosparc_P20_J181_map_sharp.mrc zone as #9, grid size 512,512,512,
pixel 0.504, shown at level 0.0762, step 2, values float32
Opened cryosparc_P20_J181_map_sharp.mrc zone as #10, grid size 512,512,512,
pixel 0.504, shown at level 0.0349, step 2, values float32
restore_snapshot for "ZoneColor" returned None
[Repeated 2 time(s)]Log from Thu Dec 19 16:49:36 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/cryosparc_P12_J231_017_volume_map_sharp(1).mrc
Opened cryosparc_P12_J231_017_volume_map_sharp(1).mrc as #1, grid size
256,256,256, pixel 1.14, shown at level 0.0867, step 1, values float32
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/cryosparc_P12_J239_map_locres.mrc
Opened cryosparc_P12_J239_map_locres.mrc as #2, grid size 256,256,256, pixel
1.14, shown at level 8.46, step 1, values float32
> lighting full
> hide #!2 models
> set bgColor white
> lighting full
> lighting soft
> show #!2 models
> ui tool show "Surface Color"
> color sample #1.1 map #2 palette 6,#ff0000:3,#0000ff
Map values for surface "surface": minimum 0, mean 4.526, maximum 44.21
> hide #!2 models
> color sample #1.1 map #2 palette 6,#ff0000:4.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum 0, mean 4.526, maximum 44.21
> color sample #1.1 map #2 palette 7,#ff0000:5,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum 0, mean 4.526, maximum 44.21
> color sample #1.1 map #2 palette 7,#ff0000:5,#ffffff:3,#0000ff
Map values for surface "surface": minimum 0, mean 4.526, maximum 44.21
> color sample #1.1 map #2 palette 8,#ff0000:5,#ffffff:2,#0000ff
Map values for surface "surface": minimum 0, mean 4.526, maximum 44.21
> volume #1 level 0.09199
> view
> view orient
> turn y 90
[Repeated 3 time(s)]
> turn x 90
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/resloc_3.tif width 2000
> height 1205 supersample 4 transparentBackground true
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/J240_viewing_direction_distribution.bild
Opened BILD data containing 1535 objects
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/distrib.tif width 2000
> height 1205 supersample 4 transparentBackground true
> hide #3 models
> combine #1
No structures specified
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadAWT/161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb
Chain information for
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4
---
Chain | Description
A E F G H V X | No description available
B C D | No description available
I | No description available
U | No description available
W | No description available
Y | No description available
Z | No description available
> dssp
> hide atoms
> show cartoons
> hide #!1 models
> ui mousemode right select
> select /I:153
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
83 atoms, 83 bonds, 11 residues, 1 model selected
> select up
1535 atoms, 1559 bonds, 194 residues, 1 model selected
> select up
1542 atoms, 1566 bonds, 195 residues, 1 model selected
> select down
1535 atoms, 1559 bonds, 194 residues, 1 model selected
> select up
1542 atoms, 1566 bonds, 195 residues, 1 model selected
> color sel #ae839bff
> select clear
> select /I:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /I:321
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 5 residues, 1 model selected
> select up
417 atoms, 425 bonds, 54 residues, 1 model selected
> select up
435 atoms, 443 bonds, 56 residues, 1 model selected
> select up
1952 atoms, 1984 bonds, 248 residues, 1 model selected
> color sel #ae839bff
[Repeated 1 time(s)]
> select /H:330
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #533744ff
> select clear
> select /G:156
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
1548 atoms, 1572 bonds, 196 residues, 1 model selected
> select up
1563 atoms, 1587 bonds, 198 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #ae839bff
> select /F:268
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
139 atoms, 139 bonds, 17 residues, 1 model selected
> select up
1548 atoms, 1572 bonds, 196 residues, 1 model selected
> select up
1622 atoms, 1648 bonds, 206 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #533744ff
> select clear
> select /E:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
130 atoms, 130 bonds, 16 residues, 1 model selected
> select up
1548 atoms, 1572 bonds, 196 residues, 1 model selected
> select up
1622 atoms, 1648 bonds, 206 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #ae839bff
> select /D:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #533744ff
> select /C:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #ae839bff
> select /B:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #533744ff
> select /A:330
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
486 atoms, 494 bonds, 63 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #ae839bff
> select clear
> select /U:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
139 atoms, 139 bonds, 17 residues, 1 model selected
> select up
1548 atoms, 1572 bonds, 196 residues, 1 model selected
> select up
1622 atoms, 1648 bonds, 206 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #533744ff
> select /U:219
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
73 atoms, 73 bonds, 9 residues, 1 model selected
> select up
1548 atoms, 1572 bonds, 196 residues, 1 model selected
> select up
1626 atoms, 1652 bonds, 207 residues, 1 model selected
> select up
1977 atoms, 2009 bonds, 252 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1977 atoms, 2009 bonds, 252 residues, 1 model selected
> color sel #ae839bff
> select /X:329
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
501 atoms, 509 bonds, 65 residues, 1 model selected
> select up
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1973 atoms, 2005 bonds, 251 residues, 1 model selected
> color sel #533744ff
> select /Z:330
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
486 atoms, 494 bonds, 63 residues, 1 model selected
> select up
1955 atoms, 1986 bonds, 249 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1955 atoms, 1986 bonds, 249 residues, 1 model selected
> color sel #ae839bff
> select /Y:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> select up
1868 atoms, 1901 bonds, 239 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
1868 atoms, 1901 bonds, 239 residues, 1 model selected
> color sel #533744ff
> select /W:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
777 atoms, 887 bonds, 37 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
777 atoms, 887 bonds, 37 residues, 1 model selected
> color sel #ffbc6cff
> select clear
> show #!1 models
> color zone #1 near #4 distance 6.84
> select clear
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/cryosparc_P12_J239_map_locres.mrc
Opened cryosparc_P12_J239_map_locres.mrc as #5, grid size 256,256,256, pixel
1.14, shown at level 8.46, step 1, values float32
> close #5
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/cryosparc_P12_J237_map_sharp.mrc
Opened cryosparc_P12_J237_map_sharp.mrc as #5, grid size 256,256,256, pixel
1.14, shown at level 0.0459, step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!1 models
> color zone #5 near #4 distance 6.84
> color #5 #b2b2b2ff models
> color zone #5 near #4 distance 6.84
[Repeated 1 time(s)]
> hide #!5 models
> select /I:272
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
183 atoms, 185 bonds, 22 residues, 1 model selected
> select up
1535 atoms, 1559 bonds, 194 residues, 1 model selected
> select up
1542 atoms, 1566 bonds, 195 residues, 1 model selected
> select /C:329
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> invert sel
Unknown command: invert sel
> invert select
Unknown command: invert select
> inver select
Unknown command: inver select
> inverse sel
Unknown command: inverse sel
> help sel
> ~select
Nothing selected
> select clear
[Repeated 1 time(s)]Drag select of 1102 residues, 5 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select /E:278
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
183 atoms, 185 bonds, 22 residues, 1 model selected
> select up
698 atoms, 709 bonds, 86 residues, 1 model selected
> select up
1165 atoms, 1179 bonds, 146 residues, 1 model selected
> select up
21345 atoms, 21738 bonds, 2667 residues, 1 model selected
> select down
1165 atoms, 1179 bonds, 146 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /D:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2173 atoms, 2205 bonds, 281 residues, 1 model selected
> select up
2321 atoms, 2354 bonds, 301 residues, 1 model selected
> select up
20180 atoms, 20559 bonds, 2521 residues, 1 model selected
> select down
2321 atoms, 2354 bonds, 301 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 30 residues, 7 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 1 pseudobonds
> select clear
Drag select of 649 residues, 1 pseudobonds
Drag select of 1030 residues, 2 pseudobonds
> select up
9044 atoms, 9241 bonds, 2 pseudobonds, 1119 residues, 2 models selected
> select down
8228 atoms, 2 pseudobonds, 1030 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 214 residues, 7 pseudobonds
> select up
1904 atoms, 1919 bonds, 7 pseudobonds, 247 residues, 2 models selected
Drag select of 126 residues, 11 pseudobonds
Drag select of 195 residues, 7 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 4 residues, 1 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
> select /V:247
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 6 residues, 1 model selected
> select up
84 atoms, 86 bonds, 10 residues, 1 model selected
> select up
248 atoms, 249 bonds, 32 residues, 1 model selected
> select up
283 atoms, 284 bonds, 37 residues, 1 model selected
> select up
301 atoms, 300 bonds, 39 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 11 residues, 1 pseudobonds
> select up
125 atoms, 125 bonds, 1 pseudobond, 16 residues, 2 models selected
> select up
1909 atoms, 1938 bonds, 1 pseudobond, 244 residues, 2 models selected
> select up
1918 atoms, 1946 bonds, 1 pseudobond, 245 residues, 2 models selected
> select up
7475 atoms, 7606 bonds, 9 pseudobonds, 922 residues, 2 models selected
> select down
1918 atoms, 1946 bonds, 1 pseudobond, 245 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
> select /B:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
1655 atoms, 1679 bonds, 211 residues, 1 model selected
> select up
1679 atoms, 1702 bonds, 214 residues, 1 model selected
> select up
2089 atoms, 2120 bonds, 267 residues, 1 model selected
> select up
2362 atoms, 2393 bonds, 303 residues, 1 model selected
> select up
5557 atoms, 5658 bonds, 677 residues, 1 model selected
> select down
2362 atoms, 2393 bonds, 303 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 6 residues
> delete atoms sel
> delete bonds sel
Drag select of 1 pseudobonds
No visible atoms or bonds selected
> show atoms
> select clear
Drag select of 141 atoms, 1 pseudobonds, 132 bonds
> select up
143 atoms, 141 bonds, 1 pseudobond, 14 residues, 2 models selected
> select up
149 atoms, 147 bonds, 1 pseudobond, 14 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 66 atoms, 66 bonds
> delete atoms sel
> delete bonds sel
Drag select of 131 atoms, 132 bonds
> delete atoms sel
> delete bonds sel
Drag select of 69 atoms, 66 bonds
> select up
72 atoms, 70 bonds, 8 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
2651 atoms, 2705 bonds, 2 pseudobonds, 329 residues, 2 models selected
> hide sel atoms
> select ::name="ATP"::name="CA"
99 atoms, 99 bonds, 9 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 33 atoms, 3 residues, 33 bonds
> select clear
Drag select of 33 atoms, 2 residues, 33 bonds
> select up
95 atoms, 95 bonds, 11 residues, 1 model selected
> select down
52 atoms, 33 bonds, 5 residues, 1 model selected
Drag select of 26 atoms, 30 bonds
> select up
29 atoms, 30 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 4 atoms
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 2 residues, 1 model selected
> select up
2618 atoms, 2672 bonds, 326 residues, 1 model selected
> select down
32 atoms, 33 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /M:402@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
2585 atoms, 2639 bonds, 2 pseudobonds, 323 residues, 2 models selected
> graphics silhouettes color black width 3
[Repeated 1 time(s)]
> cartoon style width 2 thickness é
Invalid "thickness" argument: Expected a number
> cartoon style width 2 thickness 2
> cartoon style width 2 thickness 1
> cartoon style width 1 thickness 1
> cartoon style width 1 thickness 2
> cartoon style width 2 thickness 1
> graphics silhouettes color black width 3
> select /C:247
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select down
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
2585 atoms, 2639 bonds, 323 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes color black width 1
> select clear
> select /W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 126 atom styles
> select clear
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/monomere.tif width 2000
> height 1162 supersample 4 transparentBackground true
> cartoon style width 3 thickness 2
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/monomere2.tif width 2000
> height 1162 supersample 4 transparentBackground true
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #4
2585 atoms, 2639 bonds, 2 pseudobonds, 323 residues, 2 models selected
> volume zone #5 nearAtoms sel newMap true
Opened cryosparc_P12_J237_map_sharp.mrc zone as #6, grid size 256,256,256,
pixel 1.14, shown at step 1, values float32
> color zone #6 near sel & #4 distance 6.84
> hide #!4 models
> select subtract #4
Nothing selected
> view orient
> turn x 90
[Repeated 4 time(s)]
> turn y 90
[Repeated 8 time(s)]
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/monomere_density.tif
> width 2000 height 1162 supersample 4 transparentBackground true
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/WT/monomere_density2.tif
> width 2000 height 1162 supersample 4 transparentBackground true
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/A136P/cryosparc_P20_J161_008_volume_map_sharp(1).mrc
Opened cryosparc_P20_J161_008_volume_map_sharp(1).mrc as #7, grid size
512,512,512, pixel 0.504, shown at level 0.0217, step 2, values float32
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Présentations/RadA_pathway/A136P/cryosparc_P20_J181_map_sharp.mrc
Opened cryosparc_P20_J181_map_sharp.mrc as #8, grid size 512,512,512, pixel
0.504, shown at level 0.0762, step 2, values float32
> close #7
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadA_mutant26_ADN/RealSpaceRefine_5/111224_optimisation_modele_radA_A136P_2_real_space_refined_005.pdb
Chain information for
111224_optimisation_modele_radA_A136P_2_real_space_refined_005.pdb #7
---
Chain | Description
A B C D E F G H I T V Z | No description available
W | No description available
b | No description available
> hide #!6 models
> hide #!8 models
> select add #7
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> dssp
> select clear
Drag select of 799 residues
> delete atoms sel
> delete bonds sel
> show #!6 models
> hide #!6 models
> select clear
> select #7/C:227
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
139 atoms, 139 bonds, 17 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> select up
20745 atoms, 21196 bonds, 2567 residues, 1 model selected
> select down
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
Drag select of 499 residues, 8 pseudobonds
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/D:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 1 model selected
> select up
331 atoms, 334 bonds, 43 residues, 1 model selected
> select up
1730 atoms, 1753 bonds, 221 residues, 1 model selected
> select up
16715 atoms, 17068 bonds, 2068 residues, 1 model selected
> select down
1730 atoms, 1753 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #7/E:277
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
62 atoms, 58 bonds, 7 residues, 1 model selected
> select up
159 atoms, 156 bonds, 18 residues, 1 model selected
> select up
14985 atoms, 15315 bonds, 1847 residues, 1 model selected
> select down
159 atoms, 156 bonds, 18 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 563 residues
> select up
5062 atoms, 5208 bonds, 602 residues, 1 model selected
> select down
4552 atoms, 563 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 593 residues, 6 pseudobonds
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/A:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 10 residues, 1 model selected
> select up
302 atoms, 307 bonds, 36 residues, 1 model selected
> select up
316 atoms, 320 bonds, 38 residues, 1 model selected
> select up
890 atoms, 895 bonds, 113 residues, 1 model selected
> select up
5543 atoms, 5650 bonds, 673 residues, 1 model selected
> select down
890 atoms, 895 bonds, 113 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/B:342
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
1983 atoms, 2018 bonds, 252 residues, 1 model selected
> select up
4653 atoms, 4752 bonds, 560 residues, 1 model selected
> select down
1983 atoms, 2018 bonds, 252 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 3 residues
> delete atoms sel
> delete bonds sel
> select #7/W:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> color sel #ffbc6cff
> select clear
> show #!8 models
> color zone #8 near #7 distance 3.02
> select add #7
2607 atoms, 2659 bonds, 305 residues, 1 model selected
> volume zone #5 nearAtoms sel newMap true
Opened cryosparc_P12_J237_map_sharp.mrc zone as #9, grid size 256,256,256,
pixel 1.14, shown at step 1, values float32
> volume zone #7 nearAtoms sel newMap true
> volume zone #8 nearAtoms sel newMap true
Opened cryosparc_P20_J181_map_sharp.mrc zone as #10, grid size 512,512,512,
pixel 0.504, shown at step 1, values float32
> close #10
> close #9
> show #!8 models
> select subtract #7
Nothing selected
> hide #!8 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> select add #7
2607 atoms, 2659 bonds, 305 residues, 1 model selected
> show sel atoms
Drag select of 169 atoms, 165 bonds
> delete atoms sel
> delete bonds sel
Drag select of 140 atoms, 132 bonds
> delete atoms sel
> delete bonds sel
Drag select of 66 atoms, 66 bonds
> delete atoms sel
> delete bonds sel
Drag select of 33 atoms, 33 bonds
> delete atoms sel
> delete bonds sel
> select add #7
2199 atoms, 2250 bonds, 268 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select ::name="ATP"
93 atoms, 99 bonds, 3 residues, 2 models selected
> select ::name="ATP"::name="CA"
99 atoms, 99 bonds, 9 residues, 2 models selected
> show sel & #!7 atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> select clear
[Repeated 1 time(s)]
> select #7/C:232
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/K:400@O3A
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 2 residues, 1 model selected
> select up
2199 atoms, 2250 bonds, 268 residues, 1 model selected
> select up
4784 atoms, 4889 bonds, 591 residues, 13 models selected
> select down
2199 atoms, 2250 bonds, 268 residues, 1 model selected
> select down
32 atoms, 33 bonds, 2 residues, 1 model selected
> select #7/L:402@CA
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/C:277
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #7/L:402@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!6 models
> select add #7
2166 atoms, 2217 bonds, 265 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume zone #8 nearAtoms sel newMap true
Opened cryosparc_P20_J181_map_sharp.mrc zone as #9, grid size 512,512,512,
pixel 0.504, shown at step 1, values float32
> select clear
> select #9
2 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> select add #7
2166 atoms, 2217 bonds, 265 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> select #7/G:278@C
1 atom, 1 residue, 1 model selected
Drag select of 3 atoms
> delete atoms sel
> delete bonds sel
Drag select of 3 atoms
> delete atoms sel
> delete bonds sel
> select add #7
2160 atoms, 2215 bonds, 263 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> select ::name="ATP"::name="CA"
66 atoms, 66 bonds, 6 residues, 2 models selected
> show sel & #!7 atoms
> show #!8 models
> volume zone #8 nearAtoms sel newMap true
Opened cryosparc_P20_J181_map_sharp.mrc zone as #10, grid size 512,512,512,
pixel 0.504, shown at step 1, values float32
> hide #!10 models
> close #10
> select add #7
2193 atoms, 2248 bonds, 266 residues, 2 models selected
> volume zone #8 nearAtoms sel newMap true
Opened cryosparc_P20_J181_map_sharp.mrc zone as #10, grid size 512,512,512,
pixel 0.504, shown at step 1, values float32
> color zone #10 near sel & #7 distance 3.02
> volume #10 level 0.1161
> color zone #10 near sel & #7 distance 3.02
> select clear
> hide #!7 models
> volume #10 level 0.1281
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> volume #10 level 0.1015
> select #10
2 models selected
> select clear
> volume #10 level 0.08151
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/A136P/Monomère.tif" width 2000 height 1162
> supersample 4 transparentBackground true
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #10 level 0.03489
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> color zone #10 near #7 distance 3.02
[Repeated 1 time(s)]
> hide #!7 models
> hide #!10 models
> show #!6 models
Drag select of 6 cryosparc_P12_J237_map_sharp.mrc zone
> select clear
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/WT/filaments.tif" width 20000 height 11623
> supersample 4 transparentBackground true
Image size 20000 x 11623 too large, exceeds maximum OpenGL render buffer size
16384
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/WT/filaments.tif" width 2000 height 1162
> supersample 4 transparentBackground true
> hide #!6 models
> show #!6 models
> hide #!5 models
> save view1
Cannot determine format for 'view1'
> view name 1
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/WT/monomerdensity.tif" width 2000 height
> 1162 supersample 4 transparentBackground true
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> turn x 90
[Repeated 3 time(s)]
> turn y 90
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/WT/filaments90 .tif" width 2000 height 1162
> supersample 4 transparentBackground true
> hide #!5 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> hide #!8 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadA_mutant26_ADN/RealSpaceRefine_5/111224_optimisation_modele_radA_A136P_2_real_space_refined_005.pdb
Chain information for
111224_optimisation_modele_radA_A136P_2_real_space_refined_005.pdb #11
---
Chain | Description
A B C D E F G H I T V Z | No description available
W | No description available
b | No description available
> hide #11 atoms
> show #11 cartoons
> dssp
> select #11/I:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/I:256
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
203 atoms, 205 bonds, 25 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> select up
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> select down
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select clear
> select #11/H:329
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> select up
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> select down
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select #11/G:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> select up
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> select down
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select #11/F:351
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/F:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #11/F:352
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/F:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> select up
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> select down
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select #11/E:187
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
68 atoms, 68 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select #11/D:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select #11/C:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/C:187
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 10 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select #11/B:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 10 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select #11/A:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select #11/V:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
68 atoms, 68 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select #11/T:197
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #ae839bff
> select #11/Z:188
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
68 atoms, 68 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2037 bonds, 254 residues, 1 model selected
> color sel #533744ff
> select clear
[Repeated 2 time(s)]Drag select of 37 residues
> select clear
> select #11/b:216
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/b:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
130 atoms, 130 bonds, 16 residues, 1 model selected
> select up
1866 atoms, 1900 bonds, 238 residues, 1 model selected
> color sel #ae839bff
> select #11/W:19
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #ffbc6cff
> select up
777 atoms, 887 bonds, 37 residues, 1 model selected
> color sel #ffbc6cff
[Repeated 1 time(s)]
> hide #11 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!8 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
[Repeated 2 time(s)]
> hide #!8 models
> show #!8 models
> hide #!10 models
> color zone #8 near sel & #11 distance 3.02
[Repeated 1 time(s)]
> hide #11 models
> show #11 models
> hide #!8 models
> show #!8 models
> select add #11
27118 atoms, 27719 bonds, 3366 residues, 1 model selected
> color zone #8 near sel & #11 distance 3.02
> color #11 #b2b2b2ff
> hide #!8 models
> show #!8 models
> undo
[Repeated 2 time(s)]
> hide #!8 models
> show #!8 models
> color #8 #b2b2b2ff models
> color zone #8 near sel & #11 distance 3.02
> hide #11 models
> show #11 models
> hide #11 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #11 models
> color zone #10 near sel & #11 distance 3.02
[Repeated 1 time(s)]
> select clear
> hide #!10 models
> show #!10 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> view orient
> turn x 90
[Repeated 10 time(s)]
> turn y 90
[Repeated 2 time(s)]
> hide #!10 models
> show #!10 models
> hide #11 models
> turn x 90
[Repeated 1 time(s)]
> show #11 models
> hide #11 models
> turn y 90
[Repeated 4 time(s)]
> turn x 90
[Repeated 3 time(s)]
> turn y 90
> show #11 models
> hide #11 models
> show #!9 models
> hide #!9 models
> show #!8 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/A136P/Fig_RadA/fil.tif" width 2000 height
> 1162 supersample 4 transparentBackground true
> turn y 90
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/A136P/Fig_RadA/fil y90.tif" width 2000
> height 1162 supersample 4 transparentBackground true
> turn y 90
[Repeated 1 time(s)]
> hide #!8 models
> turn y 90
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Présentations/RadA_pathway/A136P/Fig_RadA/moomere.tif" width 2000
> height 1162 supersample 4 transparentBackground true
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #11 models
> hide #11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> open "/Users/mimbert/Downloads/8bq2 (1).pdb"
8bq2 (1).pdb title:
Cryoem structure of the pre-synaptic RAD51 nucleoprotein filament In the
presence of atp and CA2+ [more info...]
Chain information for 8bq2 (1).pdb #12
---
Chain | Description | UniProt
A B C D E F G H I | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
W | DNA (30-mer) |
Non-standard residues in 8bq2 (1).pdb #12
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
> select add #12
22331 atoms, 22726 bonds, 59 pseudobonds, 2847 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> mmaker #4/C to #E/5
> matchmaker #4/C to #E/5
Invalid "to" argument: invalid atoms specifier
> mmaker #4/C to #12/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8bq2 (1).pdb, chain E (#12) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C (#4),
sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
Drag select of 474 residues
> select up
4038 atoms, 4089 bonds, 526 residues, 1 model selected
> select up
4752 atoms, 4820 bonds, 620 residues, 1 model selected
> select up
4819 atoms, 4886 bonds, 627 residues, 1 model selected
> select up
22331 atoms, 22726 bonds, 2847 residues, 1 model selected
> select down
4819 atoms, 4886 bonds, 627 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 199 residues
> select up
2326 atoms, 2346 bonds, 302 residues, 1 model selected
> select up
4752 atoms, 4820 bonds, 620 residues, 1 model selected
> select up
4818 atoms, 4886 bonds, 626 residues, 1 model selected
> select up
17512 atoms, 17840 bonds, 2220 residues, 1 model selected
> select down
4818 atoms, 4886 bonds, 626 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 306 residues
> select up
3444 atoms, 3568 bonds, 393 residues, 1 model selected
Drag select of 167 residues
Drag select of 519 residues
> select up
5034 atoms, 5090 bonds, 655 residues, 1 model selected
> select up
7128 atoms, 7230 bonds, 930 residues, 1 model selected
> select up
7226 atoms, 7329 bonds, 938 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #12/F:80
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
115 atoms, 114 bonds, 16 residues, 1 model selected
> select up
1947 atoms, 1974 bonds, 253 residues, 1 model selected
> select up
1954 atoms, 1981 bonds, 254 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 13 residues
> delete atoms sel
> delete bonds sel
Drag select of 11 residues
> delete atoms sel
> delete bonds sel
> hide #!4 models
> select #12/W:16
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
130 atoms, 147 bonds, 6 residues, 1 model selected
> select up
2572 atoms, 2623 bonds, 322 residues, 1 model selected
> select down
130 atoms, 147 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 130 atom styles
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> select add #12
2572 atoms, 2623 bonds, 8 pseudobonds, 322 residues, 3 models selected
> select subtract #12
Nothing selected
> select add #12
2572 atoms, 2623 bonds, 8 pseudobonds, 322 residues, 3 models selected
> select ::name="ATP"::name="CA"
595 atoms, 594 bonds, 3 pseudobonds, 55 residues, 5 models selected
> show sel & #!12 atoms
> select clear
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadAWT/161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb
Chain information for
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #13
---
Chain | Description
A E F G H V X | No description available
B C D | No description available
I | No description available
U | No description available
W | No description available
Y | No description available
Z | No description available
> mmaker #13/C to #12/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8bq2 (1).pdb, chain E (#12) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C
(#13), sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
> hide sel atoms
> select add #13
30115 atoms, 30699 bonds, 16 pseudobonds, 3770 residues, 3 models selected
> select add #12
32684 atoms, 33321 bonds, 24 pseudobonds, 4090 residues, 5 models selected
> select subtract #12
30113 atoms, 30698 bonds, 16 pseudobonds, 3769 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> dssp
> select clear
Drag select of 118 residues, 2 pseudobonds
> select up
1139 atoms, 1150 bonds, 2 pseudobonds, 151 residues, 2 models selected
> select up
5898 atoms, 5994 bonds, 2 pseudobonds, 750 residues, 2 models selected
> select up
30113 atoms, 30698 bonds, 16 pseudobonds, 3769 residues, 2 models selected
> select down
5898 atoms, 5994 bonds, 2 pseudobonds, 750 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
Drag select of 351 residues
> select up
3175 atoms, 3221 bonds, 402 residues, 1 model selected
> select up
3946 atoms, 4010 bonds, 502 residues, 1 model selected
> select up
24215 atoms, 24701 bonds, 3019 residues, 1 model selected
> select down
3946 atoms, 4010 bonds, 502 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 86 residues
> select up
778 atoms, 786 bonds, 99 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 314 residues
Drag select of 1 residues
> select up
82 atoms, 82 bonds, 10 residues, 1 model selected
Drag select of 247 residues
> select up
3082 atoms, 3111 bonds, 389 residues, 1 model selected
> select up
5796 atoms, 5892 bonds, 739 residues, 1 model selected
> select up
17843 atoms, 18226 bonds, 2203 residues, 1 model selected
> select down
5796 atoms, 5892 bonds, 739 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 434 residues
> select up
4074 atoms, 4131 bonds, 520 residues, 1 model selected
> select up
5923 atoms, 6019 bonds, 754 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 104 residues
Drag select of 37 residues
> select up
338 atoms, 339 bonds, 44 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!12 models
> show #!12 models
> select #13/B:341
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/B:341
9 atoms, 8 bonds, 1 residue, 1 model selected
> mmaker #13/C to #12/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8bq2 (1).pdb, chain E (#12) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C
(#13), sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
> select clear
Drag select of 2 residues
> select up
98 atoms, 101 bonds, 13 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 14 residues
> select up
777 atoms, 887 bonds, 37 residues, 1 model selected
> select down
294 atoms, 14 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 2 residues
> delete atoms sel
> delete bonds sel
Drag select of 7 residues
> select up
441 atoms, 503 bonds, 21 residues, 1 model selected
> select clear
Drag select of 10 residues
> delete atoms sel
> delete bonds sel
Drag select of 4 residues
> delete atoms sel
> delete bonds sel
> select #13/W:23
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> delete atoms sel
> delete bonds sel
> show #11 models
> hide #11 models
> show #!4 models
> hide #!4 models
> select add #13
3047 atoms, 3101 bonds, 2 pseudobonds, 365 residues, 2 models selected
> select ::name="ATP"::name="CA"
1089 atoms, 1089 bonds, 3 pseudobonds, 99 residues, 6 models selected
> show sel & #!12-13 atoms
> select clear
Drag select of 198 atoms, 198 bonds
> delete atoms sel
> delete bonds sel
Drag select of 99 atoms, 99 bonds
> delete atoms sel
> delete bonds sel
Drag select of 33 atoms, 33 bonds
> delete atoms sel
> delete bonds sel
Drag select of 55 atoms, 56 bonds
Drag select of 66 atoms, 66 bonds
> delete atoms sel
> delete bonds sel
Drag select of 33 atoms, 33 bonds
> delete atoms sel
> delete bonds sel
> select add #13
2618 atoms, 2672 bonds, 2 pseudobonds, 326 residues, 2 models selected
> select subtract #13
Nothing selected
> combine #12
> combine #13
> hide #!12 models
> hide #!13 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
2409 atoms, 2443 bonds, 313 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #15/C:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #15/M:400@N9
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #15/N:402@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #14/E:401@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> mmaker #13/C to #12/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8bq2 (1).pdb, chain E (#12) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C
(#13), sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
> select #15/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> select up
2584 atoms, 2638 bonds, 322 residues, 1 model selected
> select down
126 atoms, 143 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 126 atom styles
> select add #15
2584 atoms, 2638 bonds, 1 pseudobond, 322 residues, 2 models selected
> color (#!15 & sel) #ae839bff
> hide #!14 models
> show #!14 models
> select clear
> color #14 #8ac99dff
> undo
> color #14 #6bc99dff
> color #14 #75c99dff
> color #14 #75a79dff
> select clear
> lighting soft
> rmsd #14 to #15
Number of atoms from first atom spec (2539) differs from number in second
(2584)
> rmsd #14
Missing required "to" argument
> rmsd #14 to #15
Number of atoms from first atom spec (2539) differs from number in second
(2584)
> select add #14
2539 atoms, 2590 bonds, 6 pseudobonds, 319 residues, 3 models selected
> select add #15
5123 atoms, 5228 bonds, 7 pseudobonds, 641 residues, 5 models selected
Alignment identifier is 14/E
Alignment identifier is 14/W
Alignment identifier is 15/C
Alignment identifier is 15/W
> rmsd #14 to #15:37-351
Number of atoms from first atom spec (2539) differs from number in second
(2408)
> rmsd #14:37-351 to #15
Number of atoms from first atom spec (2259) differs from number in second
(2584)
> rmsd #14:37-351 to #15:37-351
Number of atoms from first atom spec (2259) differs from number in second
(2408)
> select clear
> mmaker #14/E to #15/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C (#15)
with copy of 8bq2 (1).pdb, chain E (#14), sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1_A.tif"
> width 2000 height 1161 supersample 4 transparentBackground true
> select ::name="ATP"::name="CA"
725 atoms, 726 bonds, 5 pseudobonds, 65 residues, 9 models selected
> color (#!14-15 & sel) byelement
> select #14/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
130 atoms, 147 bonds, 6 residues, 1 model selected
> select clear
> select #15/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> color sel #ffbc6cff
> select clear
> select #14/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
2517 atoms, 2566 bonds, 6 pseudobonds, 318 residues, 3 models selected
> select down
2517 atoms, 2566 bonds, 6 pseudobonds, 318 residues, 3 models selected
Drag select of 2 residues
> select up
256 atoms, 290 bonds, 12 residues, 2 models selected
> color sel #ffbc6cff
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1_A2.tif"
> width 2000 height 1161 supersample 4 transparentBackground true
> hide #!14 models
> show #!14 models
> color #14 #b2b2b2ff
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1_A3.tif"
> width 2000 height 1161 supersample 4 transparentBackground true
[Repeated 1 time(s)]
> view name fig1
> show #11 models
> hide #11 models
> show #11 models
> hide #!14 models
> hide #!15 models
> hide #11 models
> show #11 models
> hide #11 models
> show #!14 models
> show #!15 models
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadAWT/161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb
Chain information for
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #16
---
Chain | Description
A E F G H V X | No description available
B C D | No description available
I | No description available
U | No description available
W | No description available
Y | No description available
Z | No description available
> hide #!14-16 atoms
> show #!14-16 cartoons
> open "/Users/mimbert/Downloads/8bq2 (1).pdb"
8bq2 (1).pdb title:
Cryoem structure of the pre-synaptic RAD51 nucleoprotein filament In the
presence of atp and CA2+ [more info...]
Chain information for 8bq2 (1).pdb #17
---
Chain | Description | UniProt
A B C D E F G H I | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
W | DNA (30-mer) |
Non-standard residues in 8bq2 (1).pdb #17
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
> hide #!14-17 atoms
> show #!14-17 cartoons
> mmaker #16/C to #13/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb,
chain C (#13) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C
(#16), sequence alignment score = 1589.7
RMSD between 314 pruned atom pairs is 0.000 angstroms; (across all 314 pairs:
0.000)
> mmaker #17/E to #14/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 8bq2 (1).pdb, chain E (#14) with 8bq2 (1).pdb, chain E
(#17), sequence alignment score = 1691.7
RMSD between 310 pruned atom pairs is 0.000 angstroms; (across all 310 pairs:
0.000)
> hide #!17 models
> select #16/D:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> color sel #ae839bff
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #ae839bff
> select clear
> dssp
Drag select of 261 residues
> select clear
Drag select of 156 residues
> select clear
[Repeated 2 time(s)]Drag select of 199 residues
Drag select of 20 residues
> select clear
> select #16/A:141
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #16/X:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> dssp
> select clear
[Repeated 1 time(s)]Drag select of 33 residues
> select clear
> dssp
> select clear
> select #16/Z:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!16 models
> hide #!14 models
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!16 models
> show #!17 models
Drag select of 98 residues
> select up
1010 atoms, 1019 bonds, 126 residues, 1 model selected
> select up
3503 atoms, 3558 bonds, 445 residues, 1 model selected
> select up
3577 atoms, 3634 bonds, 455 residues, 1 model selected
> select up
3928 atoms, 3991 bonds, 500 residues, 1 model selected
> select up
30113 atoms, 30698 bonds, 3769 residues, 1 model selected
> select down
3928 atoms, 3991 bonds, 500 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
> select clear
> select #16/Y:219
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
124 atoms, 124 bonds, 15 residues, 1 model selected
> select up
1868 atoms, 1901 bonds, 239 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 199 residues
> select up
2184 atoms, 2208 bonds, 278 residues, 1 model selected
> select up
3950 atoms, 4014 bonds, 503 residues, 1 model selected
> select up
24317 atoms, 24802 bonds, 3030 residues, 1 model selected
> select down
3950 atoms, 4014 bonds, 503 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 85 residues
> select up
1400 atoms, 1408 bonds, 183 residues, 2 models selected
> select up
7976 atoms, 8092 bonds, 1028 residues, 2 models selected
> hide #!16 models
> show #!16 models
> select clear
Drag select of 166 residues
> select up
1811 atoms, 1829 bonds, 232 residues, 1 model selected
> select up
4399 atoms, 4467 bonds, 565 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!17 models
> hide #!17 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
Drag select of 356 residues
> select up
3480 atoms, 3518 bonds, 442 residues, 1 model selected
> select up
5919 atoms, 6015 bonds, 753 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 124 residues, 1 pseudobonds
> select up
1394 atoms, 1402 bonds, 1 pseudobond, 181 residues, 2 models selected
> select up
3925 atoms, 3989 bonds, 1 pseudobond, 499 residues, 2 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
Drag select of 7 residues
[Repeated 1 time(s)]Drag select of 10 residues
> delete atoms sel
> delete bonds sel
Drag select of 11 residues
> select up
567 atoms, 647 bonds, 27 residues, 1 model selected
> select clear
Drag select of 6 residues
> select clear
Drag select of 9 residues
> delete atoms sel
> delete bonds sel
Drag select of 7 residues
> delete atoms sel
> delete bonds sel
Drag select of 3 residues
[Repeated 1 time(s)]
> select clear
Drag select of 3 residues
> delete atoms sel
> delete bonds sel
> select #16/D:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> color sel #533744ff
> select clear
> select #16/D:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/D:343
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #533744ff
[Repeated 1 time(s)]
> select #15/C:111
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #ae839bff
[Repeated 5 time(s)]
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> select add #17
24757 atoms, 25188 bonds, 59 pseudobonds, 3161 residues, 4 models selected
> select add #16
30272 atoms, 30800 bonds, 63 pseudobonds, 3842 residues, 6 models selected
> select subtract #17
7941 atoms, 8074 bonds, 4 pseudobonds, 995 residues, 3 models selected
> select add #15
8099 atoms, 8250 bonds, 5 pseudobonds, 1003 residues, 4 models selected
> select subtract #15
5515 atoms, 5612 bonds, 4 pseudobonds, 681 residues, 2 models selected
> select subtract #16
Nothing selected
> select #16/C:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
100 atoms, 99 bonds, 14 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> color sel #ae839bff
> select #16/C:341
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #16/C:123
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #16/C:342
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #ae839bff
> select clear
> select #16/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> select up
5515 atoms, 5612 bonds, 681 residues, 1 model selected
> select down
168 atoms, 191 bonds, 8 residues, 1 model selected
> color sel #ffbc6cff
> select add #16
5515 atoms, 5612 bonds, 4 pseudobonds, 681 residues, 2 models selected
> select ::name="ATP"::name="CA"
1517 atoms, 1518 bonds, 23 pseudobonds, 137 residues, 12 models selected
> show sel & #!16 atoms
> select clear
Drag select of 99 atoms, 99 bonds
> delete atoms sel
> delete bonds sel
Drag select of 165 atoms, 165 bonds
> delete atoms sel
> delete bonds sel
Drag select of 99 atoms, 99 bonds
> delete atoms sel
> delete bonds sel
Drag select of 33 atoms, 33 bonds
[Repeated 1 time(s)]
> delete atoms sel
> delete bonds sel
> select clear
> select #16/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 168 atom styles
> select clear
> show #!17 models
Drag select of 247 residues
> select up
2638 atoms, 2666 bonds, 347 residues, 1 model selected
> select up
3894 atoms, 3948 bonds, 506 residues, 1 model selected
> select up
3908 atoms, 3962 bonds, 508 residues, 1 model selected
> select up
4752 atoms, 4820 bonds, 620 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 530 residues
> select up
4815 atoms, 4870 bonds, 626 residues, 1 model selected
> select up
8646 atoms, 8768 bonds, 1126 residues, 1 model selected
> select up
8660 atoms, 8782 bonds, 1128 residues, 1 model selected
> select up
9504 atoms, 9640 bonds, 1240 residues, 1 model selected
> select up
9635 atoms, 9772 bonds, 1251 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 66 residues
> select up
710 atoms, 713 bonds, 91 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> select up
2409 atoms, 2443 bonds, 313 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 8 residues
> delete atoms sel
> delete bonds sel
Drag select of 9 residues
> delete atoms sel
> delete bonds sel
Drag select of 4 residues
> delete atoms sel
> delete bonds sel
> select #17/W:22
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!16 models
> select add #17
5058 atoms, 5148 bonds, 17 pseudobonds, 641 residues, 3 models selected
> select ::name="ATP"::name="CA"
957 atoms, 957 bonds, 12 pseudobonds, 87 residues, 12 models selected
> show sel & #!17 atoms
> style sel & #!17 stick
Changed 133 atom styles
> select clear
Drag select of 67 atoms, 4 pseudobonds, 66 bonds
> delete atoms (#!17 & sel)
> delete bonds (#!17 & sel)
> show #!16 models
> select #17/D:285
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 2 residues, 1 model selected
> select up
5119 atoms, 5216 bonds, 645 residues, 1 model selected
> select down
32 atoms, 33 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #16/M:402@CA
1 atom, 1 residue, 1 model selected
> select #16/M:402@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #17/E:402@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!16 models
> select add #17
4990 atoms, 5082 bonds, 10 pseudobonds, 633 residues, 3 models selected
> color (#!17 & sel) #ffbc6cff
> color (#!17 & sel) #b2b2b2ff
> show #!16 models
> select clear
> select #17/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
173 atoms, 196 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 173 atom styles
> mmaker #16/C to #17/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8bq2 (1).pdb, chain E (#17) with
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb, chain C
(#16), sequence alignment score = 838.2
RMSD between 235 pruned atom pairs is 0.861 angstroms; (across all 305 pairs:
3.026)
> view fig1
Drag select of 46 residues
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1_B.tif"
> width 2000 height 1158 supersample 4 transparentBackground true
> view name fig2
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #11 models
> hide #11 models
> show #!15 models
> show #!14 models
> select ::name="ATP"::name="CA"
856 atoms, 858 bonds, 8 pseudobonds, 76 residues, 12 models selected
> show sel & #!14-15 atoms
> select #15/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> select #14/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
130 atoms, 147 bonds, 6 residues, 1 model selected
> select up
2539 atoms, 2590 bonds, 319 residues, 1 model selected
> select up
52251 atoms, 53361 bonds, 6515 residues, 24 models selected
> select #15/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> select up
2584 atoms, 2638 bonds, 322 residues, 1 model selected
> select down
126 atoms, 143 bonds, 6 residues, 1 model selected
> show sel atoms
> select #14/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
130 atoms, 147 bonds, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> select #15/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> hide #!14 models
> select clear
> select #15/C:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #15
2584 atoms, 2638 bonds, 1 pseudobond, 322 residues, 2 models selected
> hide #!15 models
> select subtract #15
Nothing selected
> show #!16 models
> combine #16
> rename #18 "Monomere RadAWT"
> select #16/D:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select down
456 atoms, 464 bonds, 59 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> undo
Undo failed, probably because structures have been modified.
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!16 models
> hide #!18 models
> show #!18 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!18 models
> select #16/D:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 90 bonds, 12 residues, 1 model selected
> select up
1970 atoms, 1997 bonds, 255 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 33 atoms, 33 bonds
> delete atoms sel
> delete bonds sel
> select #16/W:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> hide sel atoms
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/chimeraX_fig1.cxs"
——— End of log from Thu Dec 19 16:49:36 2024 ———
opened ChimeraX session
> ui mousemode right select
> select clear
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!15 models
> hide #!16 models
> hide #!17 models
> hide #!15 models
> show #!16 models
> select #15/C:37-38
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #15/C:37-48
90 atoms, 90 bonds, 12 residues, 1 model selected
> select add #15
2584 atoms, 2638 bonds, 1 pseudobond, 322 residues, 2 models selected
> select subtract #15
Nothing selected
> select add #16
2627 atoms, 2687 bonds, 2 pseudobonds, 325 residues, 2 models selected
Alignment identifier is 16/C
Alignment identifier is 16/W
> select subtract #16
Nothing selected
> select #16/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!15 models
> hide #!15 models
> show #!15 models
> select add #16
2627 atoms, 2687 bonds, 2 pseudobonds, 325 residues, 2 models selected
> select subtract #16
Nothing selected
> hide #!16 models
> select add #15
2584 atoms, 2638 bonds, 1 pseudobond, 322 residues, 2 models selected
Alignment identifier is 15/C
Alignment identifier is 15/W
> select subtract #15
Nothing selected
> select #15/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #15/C:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/C:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> show #!16 models
> hide #!16 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select add #15
2584 atoms, 2638 bonds, 1 pseudobond, 322 residues, 2 models selected
> select subtract #15
Nothing selected
> hide #!15 models
> combine #13
> show #!18 models
> hide #!18 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!13 models
> hide #!1 models
> show #!1 models
> select #1/C:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> color sel #ac849bff
> show #!4 models
> hide #!4 models
> show #!15 models
> hide #!15 models
> select #1/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
126 atoms, 143 bonds, 6 residues, 1 model selected
> color sel #f5bf79ff
> select clear
> select add #1
2618 atoms, 2672 bonds, 2 pseudobonds, 326 residues, 2 models selected
Alignment identifier is 1/C
Alignment identifier is 1/W
> rename #1 RadAWT_ATP_Ca
> select #1/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #1/C:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #1/C:311
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/C:311
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select #1/C:310
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:310
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #1/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select #1/C:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #1/C:149
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #1/C:145
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:145
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> select #1/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #1/C:332
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:332
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #1/C:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/C:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!18 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #1
2618 atoms, 2672 bonds, 2 pseudobonds, 326 residues, 3 models selected
> select subtract #1
1 model selected
> combine #18
> hide #!2 models
> show #!2 models
> hide #!18 models
> select add #2
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2/W
> select #2/C-D:185
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C-D:185
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select clear
> select #2/C-D:332
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:332
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> select #2/C-D:146
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/C-D:145-146
20 atoms, 18 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> select #2/C-D:149
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/C-D:149
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> select #2/C-D:180
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/C-D:180
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #2/C-D:178
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C-D:178
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> select #2/C-D:334
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/C-D:334
10 atoms, 8 bonds, 2 residues, 1 model selected
> select
> #2/C-D:41-43,49-58,63-67,71-78,82-95,104-113,122-128,148-159,163-165,183-193,197-203,212-230,247-251,255-279,309-312
2284 atoms, 2284 bonds, 286 residues, 1 model selected
> select #2/C-D:314
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/C-D:310
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/C-D:310-311
30 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 30 atom styles
> select #2/C-D:313
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/C-D:313
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select #2/C-D:333
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:333
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> select #2/C:154
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 9 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select down
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
Drag select of 63 residues
> select up
490 atoms, 494 bonds, 67 residues, 1 model selected
> hide sel cartoons
Drag select of 7 residues
> select up
86 atoms, 86 bonds, 10 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
86 atoms, 86 bonds, 10 residues, 1 model selected
> hide sel cartoons
Drag select of 13 residues
> select up
394 atoms, 397 bonds, 48 residues, 1 model selected
> hide sel cartoons
Drag select of 11 atoms, 9 bonds, 36 residues, 1 pseudobonds
> select up
466 atoms, 469 bonds, 1 pseudobond, 62 residues, 2 models selected
> select up
2426 atoms, 2462 bonds, 1 pseudobond, 314 residues, 2 models selected
> select down
466 atoms, 469 bonds, 1 pseudobond, 62 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/C:138
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
42 atoms, 42 bonds, 5 residues, 1 model selected
> select #2/C:303
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select clear
> select #2/C:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/C:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
45 atoms, 45 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #2/C:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
42 atoms, 42 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #2/C:289
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
21 atoms, 20 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #2/C:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
47 atoms, 46 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #2/C:249
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select #2/C:252
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
24 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #2/C:257
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #2/C:249
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
47 atoms, 48 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #2/C:245
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/C:174
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
43 atoms, 44 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #2/C:166
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select #2/C:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
34 atoms, 34 bonds, 4 residues, 1 model selected
Drag select of 1 residues
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
24 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #2/C:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #2/C:208
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
67 atoms, 68 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #2/C:153
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select #2/C:190
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 8 residues, 1 model selected
> select #2/C:190
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 8 residues, 1 model selected
> select clear
Drag select of 6 residues
> hide sel cartoons
> select #2/W:19
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 71 residues
> hide sel cartoons
Drag select of 58 atoms, 54 bonds, 106 residues, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
Drag select of 17 residues
> select up
353 atoms, 358 bonds, 45 residues, 1 model selected
> hide sel cartoons
Drag select of 22 residues
> select up
385 atoms, 387 bonds, 50 residues, 1 model selected
> hide sel cartoons
> select #2/D:350
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/D:351
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select down
30 atoms, 29 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/D:349
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 6 residues, 1 model selected
> hide sel cartoons
Drag select of 11 residues
> select up
115 atoms, 113 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/D:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #2/D:138
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #2/D:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
> select #2/D:342
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
> select #2/D:339
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/D:336
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D:335
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/D:337
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #2/C:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #2/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:310
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/D:318
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:317
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:316
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:314
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:330
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/D:340
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/C-D:333
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:333-336
60 atoms, 62 bonds, 8 residues, 1 model selected
> select #2/C-D:333
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:333-335
40 atoms, 40 bonds, 6 residues, 1 model selected
> select #2/C-D:333
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:331-333
48 atoms, 46 bonds, 6 residues, 1 model selected
> select #2/C-D:324-325
16 atoms, 14 bonds, 4 residues, 1 model selected
> select #2/C-D:324-328
70 atoms, 68 bonds, 10 residues, 1 model selected
> select #2/D:335
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C-D:335
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:335-338
64 atoms, 68 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #2/C-D:339
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C-D:339-340
26 atoms, 24 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #2/D:334
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/C:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #2/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #2/C:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/C:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #2/C:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C-D:346-347
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/C-D:332
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:332
16 atoms, 14 bonds, 2 residues, 1 model selected
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig_ATP.tif"
> width 2000 height 1526 supersample 4 transparentBackground true
> select #2/C:188
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:187
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/C:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #2/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #2/C-D:37
18 atoms, 16 bonds, 2 residues, 1 model selected
> show #!17 models
> hide #!17 models
> show #!14 models
> hide #!14 models
> show #!17 models
> hide #!17 models
> show #!17 models
> combine #17
> hide #!5 models
> show #!5 models
> hide #!17 models
> rename #5 "fig 1D"
Drag select of 27 atoms, 30 bonds, 64 residues
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
Drag select of 3 residues
> hide sel atoms
> hide sel cartoons
Drag select of 15 atoms, 12 bonds, 71 residues, 1 pseudobonds
Drag select of 31 residues
> hide sel cartoons
Drag select of 5 atoms, 2 bonds, 42 residues, 1 pseudobonds
> hide sel cartoons
Drag select of 57 residues
> select up
509 atoms, 516 bonds, 68 residues, 1 model selected
> hide sel cartoons
Drag select of 5 atoms, 2 bonds, 12 residues, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
Drag select of 31 atoms, 35 bonds, 123 residues
> select up
1168 atoms, 1203 bonds, 136 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 73 residues
> hide sel cartoons
> select #5/D:247
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
187 atoms, 189 bonds, 22 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select #5/D:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 6 residues, 1 model selected
Drag select of 9 residues
> select up
109 atoms, 108 bonds, 15 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> select down
109 atoms, 108 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select #5/D:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> select #5/D:291
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 21 residues
> select up
251 atoms, 250 bonds, 34 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
66 atoms, 66 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 12 residues
> select up
126 atoms, 128 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 1 residues
Drag select of 8 residues
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 3 residues
> select up
92 atoms, 93 bonds, 11 residues, 1 model selected
> select down
17 atoms, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 2 residues
> select up
50 atoms, 50 bonds, 6 residues, 1 model selected
> hide sel cartoons
Drag select of 11 residues
> select up
115 atoms, 116 bonds, 15 residues, 1 model selected
> select down
92 atoms, 11 residues, 1 model selected
> hide sel cartoons
> select #5/E:141
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> select up
98 atoms, 97 bonds, 13 residues, 1 model selected
Drag select of 2 residues
> select up
56 atoms, 56 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 7 residues
> select up
66 atoms, 63 bonds, 10 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> select down
66 atoms, 63 bonds, 10 residues, 1 model selected
> hide sel cartoons
Drag select of 9 residues
> select clear
Drag select of 14 residues
> select up
142 atoms, 141 bonds, 19 residues, 1 model selected
> hide sel cartoons
Drag select of 18 residues
> select up
248 atoms, 248 bonds, 30 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> select up
28 atoms, 27 bonds, 5 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 5 residues
> select clear
Drag select of 5 residues
Drag select of 2 residues
> hide sel cartoons
> select #5/E:137
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #5/E:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #5/D:314
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #5/D:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 8 atom styles
Drag select of 3 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select clear
> select #5/D:316
8 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 5/D
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/D:315-317
26 atoms, 26 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #5/D:317
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #5/D:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #5/D:296
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #5/D:297
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #5/D:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #5/D:294
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> select #5/E:163
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #5/E:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #5/E:170
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #5/E:134
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #5/E:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> hide #!5 models
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig_ATP_2.tif"
> width 2000 height 1526 supersample 4 transparentBackground true
> show #!5 models
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig_ATP_Rad51.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1_261224.cxs"
> hide #!5 models
> hide #!2 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!18 models
> combine #18
> rename #8 fig1E
> select add #8
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 8/W
> select #8/C-D:249
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select #8/C-D:290
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/C-D:290
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> select #8/C-D:261
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/C-D:261
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select #8/C-D:305
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #8/C-D:305
8 atoms, 6 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #8/C-D:262
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/C-D:262
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> select #8/C-D:291
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #8/C-D:291
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select #8/C-D:306
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #8/C-D:306
8 atoms, 6 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/C-D:249
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select #8/C-D:293
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/C-D:293
14 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #18/D:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select up
72658 atoms, 74168 bonds, 9083 residues, 21 models selected
> select up
72658 atoms, 74168 bonds, 2 pseudobonds, 9083 residues, 23 models selected
> select down
72658 atoms, 74168 bonds, 9083 residues, 22 models selected
> select down
5086 atoms, 5183 bonds, 642 residues, 2 models selected
> select down
2426 atoms, 2462 bonds, 314 residues, 2 models selected
> select down
456 atoms, 464 bonds, 59 residues, 2 models selected
> select down
425 atoms, 433 bonds, 55 residues, 1 model selected
> select down
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select #8/D:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> select up
456 atoms, 464 bonds, 59 residues, 1 model selected
> select up
2426 atoms, 2462 bonds, 314 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 3 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select down
33 atoms, 33 bonds, 3 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 3 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 3 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #18/N:401@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #8/N:401@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 2 time(s)]
> hide sel atoms
> select #18/O:402@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #8/O:402@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 16 residues, 4 atoms, 4 bonds
> select #18/W:24
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide #!18 models
> show #!18 models
> hide #!18 models
> select add #18
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #18
Nothing selected
> select #8/W:24
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8/W:23
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide #!8 models
> select add #8
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #8
Nothing selected
> show #!18 models
> select add #18
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select #18/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> show sel atoms
> select add #18
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select ::name="ATP"::name="CA"
1152 atoms, 1155 bonds, 11 pseudobonds, 102 residues, 18 models selected
> show sel & #!18 atoms
> select clear
> hide #!18 models
> show #11 models
> hide #11 models
> show #!8 models
Drag select of 2 atoms, 7 residues
> select clear
> select #8/C:105
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
51 atoms, 51 bonds, 6 residues, 1 model selected
> select #8/C:39
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select up
2016 atoms, 2044 bonds, 261 residues, 1 model selected
> select down
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
35 atoms, 34 bonds, 4 residues, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
Drag select of 70 residues
> hide sel cartoons
> select clear
Drag select of 1 residues
> hide sel cartoons
Drag select of 1 residues
Drag select of 8 residues
> select up
140 atoms, 140 bonds, 18 residues, 1 model selected
> hide sel cartoons
Drag select of 7 atoms, 5 bonds, 24 residues
Drag select of 33 atoms, 33 bonds, 170 residues
> hide sel cartoons
Drag select of 33 atoms, 33 bonds, 8 residues
> hide sel cartoons
> hide sel atoms
Drag select of 2 residues
> hide sel cartoons
> select clear
> select #8/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 6 residues
> select up
168 atoms, 170 bonds, 21 residues, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> select clear
[Repeated 1 time(s)]Drag select of 4 residues
> hide sel cartoons
> hide sel atoms
> undo
[Repeated 1 time(s)]
> select clear
> view name fig1E
> show #!17 models
> combine #17
> hide #!17 models
Drag select of 63 residues
> select up
509 atoms, 516 bonds, 68 residues, 1 model selected
> hide sel cartoons
Drag select of 52 residues
> select up
485 atoms, 489 bonds, 65 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 141 residues
> hide sel cartoons
Drag select of 18 atoms, 20 bonds, 120 residues
> hide sel cartoons
> hide sel atoms
Drag select of 13 residues
> hide sel cartoons
Drag select of 32 atoms, 33 bonds, 38 residues, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
Drag select of 10 residues
Drag select of 26 residues
> select up
454 atoms, 457 bonds, 57 residues, 1 model selected
> select down
209 atoms, 26 residues, 1 model selected
> hide sel cartoons
Drag select of 3 atoms, 1 bonds, 13 residues
> hide sel cartoons
Drag select of 35 residues
> hide sel cartoons
> select #19/D:239
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 3 time(s)]
> style sel stick
Changed 6 atom styles
> select #19/D:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #19/D:239
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/D:288
4 atoms, 3 bonds, 1 residue, 1 model selected
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!18 models
> select #18/D:291
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #18/D:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #18/C:306
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #19/E:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #18/C:307
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> hide sel atoms
> select #18/C:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> hide sel atoms
> hide #!19 models
> show #!19 models
> hide #!18 models
> select #19/D:239
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select #19/D:229
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 15 atoms, 12 bonds, 23 residues, 4 pseudobonds
> hide sel cartoons
> hide sel atoms
> select #19/D:295
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 9 residues, 1 pseudobonds
> select down
67 atoms, 1 pseudobond, 9 residues, 2 models selected
> select down
67 atoms, 1 pseudobond, 9 residues, 2 models selected
> select up
2376 atoms, 2410 bonds, 1 pseudobond, 310 residues, 2 models selected
> select down
67 atoms, 1 pseudobond, 9 residues, 2 models selected
> hide sel cartoons
> select #19/D:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 7 residues, 1 model selected
> select up
429 atoms, 436 bonds, 57 residues, 1 model selected
> hide sel cartoons
> select #19/D:246
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #19/E:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #19/E:294
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 7 residues, 1 model selected
> select #19/E:295
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 7 residues, 1 model selected
> select #19/E:295
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #19/E:294
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #19/E:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/E:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #19/E:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> select #19/E:228
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
> select #8/C:262
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #8/C:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #19/W:21
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #19/D:239
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/D:235
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> select up
1947 atoms, 1974 bonds, 253 residues, 1 model selected
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig_
> PRO_LEU_Ludo.tif" width 2000 height 1526 supersample 4 transparentBackground
> true
Drag select of 6 atoms, 6 bonds, 12 residues
> hide sel cartoons
> hide sel atoms
> view fig1E
> hide #!19 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1E_RadA.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #!19 models
> select #19/E:270
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #19/E:273
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #19/E:229
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #19/E:242
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #19/E:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> hide sel atoms
> select #19/E:241
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #19/E:271
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> view fig1E
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1E_Rad51.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> hide #!19 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1_261224.cxs"
> show #!19 models
> rename #19 Fig1F_Rad51_ADN_RadA
> hide #!19 models
> show #!19 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!19 models
> show #!18 models
> combine #18
> hide #!18 models
> show #!6 models
> hide #!6 models
> select add #20
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 20/W
> select #20/C-D:105
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #20/C-D:105
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> select #20/C-D:202
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #20/C-D:202
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel stick
Changed 18 atom styles
> show sel atoms
> style sel stick
Changed 18 atom styles
> ui mousemode right label
> ui mousemode right distance
> ui tool show Contacts
> contacts interModel false ignoreHiddenModels true select true color #a46c8a
> reveal true
2235 contacts
> undo
[Repeated 2 time(s)]
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide #21 models
> show #21 models
> hide #21 models
> hide #!20 models
> show #!20 models
> select add #20
5086 atoms, 5183 bonds, 2239 pseudobonds, 642 residues, 3 models selected
> hide sel atoms
> show #21 models
> close #21
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true select true
> color #a46c8a reveal true
No contacts
> contacts intraMol false ignoreHiddenModels true select true color #a46c8a
> reveal true
339 contacts
> hide #21 models
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> select add #20
5086 atoms, 5183 bonds, 362 pseudobonds, 642 residues, 4 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> show #21 models
> select subtract #20
Nothing selected
> hide #!20 models
> show #!20 models
> close #21
> select add #20
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> ui tool show Contacts
> contacts ignoreHiddenModels true select true color #a46c8a reveal true
2235 contacts
> contacts intraModel false ignoreHiddenModels true select true color #a46c8a
> reveal true
No contacts
> contacts intraModel false ignoreHiddenModels true select true color #a46c8a
> reveal true
No contacts
> contacts ignoreHiddenModels true
2235 contacts
> hide #21 models
> select add #20
5086 atoms, 5183 bonds, 2239 pseudobonds, 642 residues, 3 models selected
> hide sel atoms
> show #21 models
> hide #!20 models
> close #21
> show #!20 models
> ui tool show Contacts
> contacts intraModel false ignoreHiddenModels true color #8dab8e
No contacts
> contacts intraModel false ignoreHiddenModels true color #8dab8e
No contacts
> contacts intraRes true intraModel false intraMol false ignoreHiddenModels
> true color #8dab8e
No contacts
> contacts intraRes true intraModel false intraMol false ignoreHiddenModels
> true color #8dab8e
No contacts
> contacts ignoreHiddenModels true
2235 contacts
> close #21
> ui tool show Contacts
> contacts intraRes true intraModel false intraMol false ignoreHiddenModels
> true
No contacts
> contacts intraRes true intraModel false intraMol false ignoreHiddenModels
> true
No contacts
> hide #21 models
> show #21 models
> close #21
> contacts interModel false intraMol false ignoreHiddenModels true
339 contacts
> close #21
> ui tool show Distances
> ui tool show Contacts
> contacts interModel false intraModel false ignoreHiddenModels true
No contacts
> contacts interModel false intraModel false ignoreHiddenModels true
No contacts
> close #21
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true
No contacts
> hide #!20 models
> show #!20 models
> hide #21 models
> show #21 models
> hide #21 models
> select subtract #21
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> show #!19 models
> hide #!19 models
> combine #20
> hide #!20 models
> select subtract #20
Nothing selected
> select subtract #21
Nothing selected
> select #20/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #20/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> show #!22 atoms
> style #!22 stick
Changed 5086 atom styles
> undo
[Repeated 1 time(s)]
> select subtract #21
8 atoms, 6 bonds, 2 residues, 1 model selected
> select add #20
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #20
Nothing selected
> select subtract #21
Nothing selected
> select add #21
Nothing selected
> select subtract #21
Nothing selected
> select #20/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #20/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> select subtract #21
8 atoms, 6 bonds, 2 residues, 1 model selected
> select add #20
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #20
Nothing selected
> select subtract #21
Nothing selected
> close #21
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 11/b
Alignment identifier is 4
Alignment identifier is 5
> select add #22
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 22/W
> select #22/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byelement
> select #22/C-D:101
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #22/C-D:101
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byelement
> select #22/C-D:102-103
38 atoms, 36 bonds, 4 residues, 1 model selected
> select #22/C-D:102-104
48 atoms, 46 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 48 atom styles
> color sel byhetero
> color sel bynucleotide
> color sel byelement
> select #22/C-D:101
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #22/C-D:101-104
70 atoms, 70 bonds, 8 residues, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> undo
[Repeated 9 time(s)]
> select #22/C-D:100-101
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #22/C-D:100-103
74 atoms, 74 bonds, 8 residues, 1 model selected
> select #22/C-D:103
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:103
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:101
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #22/C-D:101-103
60 atoms, 60 bonds, 6 residues, 1 model selected
> select #22/C-D:104
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C-D:101-104
70 atoms, 70 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 70 atom styles
> color sel byhetero
> ui mousemode right select
> select #22/D:101
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #482c3dff
> color sel byhetero
> select clear
> select #22/C-D:108
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:108
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select
> #22/C-D:41-43,49-58,63-67,71-78,82-95,104-113,122-128,148-159,163-165,183-193,197-203,212-230,247-251,255-279,309-312
2284 atoms, 2284 bonds, 286 residues, 1 model selected
> select #22/C-D:111
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:111
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byhetero
> select #22/C-D:133
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:133
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel stick
Changed 18 atom styles
> color sel byhetero
> show sel atoms
> select #22/C-D:182
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:182
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> color sel byhetero
> select #22/C-D:336
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:336
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select #22/D:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/C-D:211
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:211
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:201
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:201-202
34 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 34 atom styles
> color sel byhetero
> select #22/C-D:204
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:204-206
54 atoms, 54 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 54 atom styles
> color sel byhetero
> select #22/C-D:214
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:214
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select clear
> select #22/D:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/D:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/D:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select #22/D:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #22/C-D:263
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:263
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select #22/C:254
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> color sel byhetero
> select #22/C-D:270
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C-D:270
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select #22/C-D:288
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:288
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select #22/C-D:311
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:311
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select #22/C-D:316
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:316
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byhetero
> select #22/C-D:144
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #22/C-D:144
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select #22/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #22/C-D:99
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #22/D:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #22/D:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #22/D:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/D:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> select #22/C-D:218
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:218
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select #22/D:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/C-D:108
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:108
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #22/C-D:111
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:111
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:201
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:201
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:263
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:263
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:266
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C-D:266
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select #22/C-D:266
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C-D:266
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #22/C-D:270
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C-D:270
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #22/C:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #22/C-D:288
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:288
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/C-D:311
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:311
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:316
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/C-D:316
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #22/W:21
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> show sel atoms
> rename #22 figG
> hide #!22 models
> show #!19 models
> hide #!19 models
> show #!18 models
> show #!19 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> hide #!19 models
> show #!22 models
> select clear
> select #22/D:92
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
100 atoms, 99 bonds, 14 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
100 atoms, 99 bonds, 14 residues, 1 model selected
> select #22/D:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
62 atoms, 62 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
62 atoms, 62 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #22/D:67
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
35 atoms, 34 bonds, 5 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select #22/D:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
25 atoms, 24 bonds, 3 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
25 atoms, 24 bonds, 3 residues, 1 model selected
> select clear
Drag select of 26 residues
> hide sel cartoons
Drag select of 14 residues
> hide sel cartoons
> select #22/D:115
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #22/D:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #22/D:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/D:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/D:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #22/D:117
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #22/D:119
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #22/D:120
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add #22/D:122
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #22/D:123
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #22/D:121
46 atoms, 39 bonds, 7 residues, 1 model selected
> select add #22/D:124
54 atoms, 46 bonds, 8 residues, 1 model selected
> select add #22/D:126
63 atoms, 54 bonds, 9 residues, 1 model selected
> select add #22/D:125
71 atoms, 61 bonds, 10 residues, 1 model selected
> select add #22/D:127
79 atoms, 68 bonds, 11 residues, 1 model selected
> select add #22/D:128
87 atoms, 75 bonds, 12 residues, 1 model selected
> select add #22/D:129
91 atoms, 78 bonds, 13 residues, 1 model selected
> select add #22/D:130
95 atoms, 81 bonds, 14 residues, 1 model selected
> select add #22/D:131
99 atoms, 84 bonds, 15 residues, 1 model selected
> select add #22/D:132
107 atoms, 91 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select #22/D:134
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select add #22/D:136
21 atoms, 10 bonds, 3 residues, 1 model selected
> select add #22/D:138
28 atoms, 16 bonds, 4 residues, 1 model selected
> select add #22/D:139
37 atoms, 24 bonds, 5 residues, 1 model selected
> select add #22/D:137
45 atoms, 31 bonds, 6 residues, 1 model selected
Drag select of 2 residues
> select add #22/D:141
71 atoms, 42 bonds, 9 residues, 1 model selected
Drag select of 1 residues
> select add #22/D:142
84 atoms, 45 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select clear
> select #22/D:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #22/D:145
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #22/D:146
21 atoms, 19 bonds, 3 residues, 1 model selected
> select add #22/D:147
25 atoms, 22 bonds, 4 residues, 1 model selected
> select add #22/D:149
32 atoms, 28 bonds, 5 residues, 1 model selected
> select add #22/D:148
41 atoms, 36 bonds, 6 residues, 1 model selected
> select add #22/D:150
50 atoms, 44 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select add #22/D:152
55 atoms, 48 bonds, 8 residues, 1 model selected
> select add #22/D:153
65 atoms, 58 bonds, 9 residues, 1 model selected
> select add #22/D:151
73 atoms, 65 bonds, 10 residues, 1 model selected
> select add #22/D:154
80 atoms, 71 bonds, 11 residues, 1 model selected
> select add #22/D:156
85 atoms, 75 bonds, 12 residues, 1 model selected
> select add #22/D:157
92 atoms, 81 bonds, 13 residues, 1 model selected
> select add #22/D:158
100 atoms, 88 bonds, 14 residues, 1 model selected
Drag select of 1 residues
[Repeated 1 time(s)]
> select add #22/D:167
121 atoms, 91 bonds, 17 residues, 1 model selected
> select add #22/D:166
125 atoms, 94 bonds, 18 residues, 1 model selected
> select add #22/D:165
134 atoms, 102 bonds, 19 residues, 1 model selected
> select add #22/D:163
141 atoms, 109 bonds, 20 residues, 1 model selected
> select add #22/D:169
149 atoms, 116 bonds, 21 residues, 1 model selected
> select add #22/D:164
158 atoms, 124 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select add #22/D:155
166 atoms, 131 bonds, 23 residues, 1 model selected
> select add #22/D:159
173 atoms, 137 bonds, 24 residues, 1 model selected
> select add #22/D:162
180 atoms, 144 bonds, 25 residues, 1 model selected
> select add #22/D:161
188 atoms, 151 bonds, 26 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 49 atoms, 73 residues, 43 bonds
> select clear
Drag select of 9 residues
> select clear
Drag select of 40 atoms, 40 residues, 34 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 15 residues
Drag select of 12 atoms, 17 residues, 10 bonds
Drag select of 12 atoms, 22 residues, 10 bonds
> select clear
Drag select of 12 atoms, 16 residues, 10 bonds
> select up
141 atoms, 140 bonds, 17 residues, 1 model selected
> select up
163 atoms, 164 bonds, 20 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 12 residues
> select up
130 atoms, 129 bonds, 18 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
130 atoms, 129 bonds, 18 residues, 1 model selected
> hide sel cartoons
> select #22/D:248
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 5 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
47 atoms, 48 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #22/D:252
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #22/D:242
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #22/D:243
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #22/D:244
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #22/D:245
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #22/D:246
35 atoms, 30 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select add #22/D:279
47 atoms, 42 bonds, 6 residues, 1 model selected
> select add #22/D:281
55 atoms, 49 bonds, 7 residues, 1 model selected
> select add #22/D:282
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #22/D:280
69 atoms, 61 bonds, 9 residues, 1 model selected
> select add #22/D:283
76 atoms, 67 bonds, 10 residues, 1 model selected
> select add #22/D:284
87 atoms, 78 bonds, 11 residues, 1 model selected
> select add #22/D:285
94 atoms, 84 bonds, 12 residues, 1 model selected
> select add #22/D:286
101 atoms, 90 bonds, 13 residues, 1 model selected
> select add #22/D:287
109 atoms, 97 bonds, 14 residues, 1 model selected
> select add #22/D:289
116 atoms, 104 bonds, 15 residues, 1 model selected
> select add #22/D:291
121 atoms, 108 bonds, 16 residues, 1 model selected
> select add #22/D:290
130 atoms, 116 bonds, 17 residues, 1 model selected
> select up
132 atoms, 130 bonds, 18 residues, 1 model selected
> select up
139 atoms, 139 bonds, 18 residues, 1 model selected
> select up
310 atoms, 312 bonds, 39 residues, 1 model selected
> select down
139 atoms, 139 bonds, 18 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #22/D:307
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #22/D:304
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #22/C:301
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #22/D:305
29 atoms, 26 bonds, 4 residues, 1 model selected
> select subtract #22/D:305
25 atoms, 23 bonds, 3 residues, 1 model selected
> select subtract #22/C:301
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #22/D:305
22 atoms, 20 bonds, 3 residues, 1 model selected
> select add #22/D:303
29 atoms, 27 bonds, 4 residues, 1 model selected
> select add #22/D:301
36 atoms, 33 bonds, 5 residues, 1 model selected
> select add #22/D:302
47 atoms, 43 bonds, 6 residues, 1 model selected
> select add #22/D:299
55 atoms, 50 bonds, 7 residues, 1 model selected
> select add #22/D:300
62 atoms, 57 bonds, 8 residues, 1 model selected
> select add #22/D:295
67 atoms, 61 bonds, 9 residues, 1 model selected
> select subtract #22/D:295
62 atoms, 57 bonds, 8 residues, 1 model selected
> select add #22/D:294
70 atoms, 64 bonds, 9 residues, 1 model selected
> select add #22/D:292
81 atoms, 74 bonds, 10 residues, 1 model selected
> select add #22/D:293
88 atoms, 81 bonds, 11 residues, 1 model selected
> select add #22/D:295
93 atoms, 85 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select add #22/D:306
97 atoms, 88 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select #22/C:139
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 21 residues
> select up
225 atoms, 225 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select #22/D:340
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #22/D:339
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #22/D:337
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #22/D:338
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #22/D:332
36 atoms, 32 bonds, 5 residues, 1 model selected
> select add #22/D:333
44 atoms, 39 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select add #22/D:277
52 atoms, 46 bonds, 7 residues, 1 model selected
> select add #22/D:278
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #22/D:276
65 atoms, 57 bonds, 9 residues, 1 model selected
> select add #22/D:274
76 atoms, 67 bonds, 10 residues, 1 model selected
> select add #22/D:275
84 atoms, 74 bonds, 11 residues, 1 model selected
> select add #22/D:272
92 atoms, 81 bonds, 12 residues, 1 model selected
> select add #22/D:273
102 atoms, 91 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select add #22/D:268
112 atoms, 101 bonds, 14 residues, 1 model selected
> select #22/D:260
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #22/D:258
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #22/D:257
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #22/D:256
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #22/D:254
30 atoms, 25 bonds, 5 residues, 1 model selected
> select add #22/D:259
35 atoms, 29 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select add #22/D:255
46 atoms, 39 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #22/W:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select down
168 atoms, 191 bonds, 8 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 63 residues
> hide sel cartoons
Drag select of 32 atoms, 12 residues, 27 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 33 residues
> select up
308 atoms, 310 bonds, 39 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #22/C:129
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #22/C:130
8 atoms, 6 bonds, 2 residues, 1 model selected
> select add #22/C:131
12 atoms, 9 bonds, 3 residues, 1 model selected
> select add #22/C:133
21 atoms, 17 bonds, 4 residues, 1 model selected
> select add #22/C:132
29 atoms, 24 bonds, 5 residues, 1 model selected
> select add #22/C:134
36 atoms, 30 bonds, 6 residues, 1 model selected
> select add #22/C:135
45 atoms, 38 bonds, 7 residues, 1 model selected
> select add #22/C:138
52 atoms, 44 bonds, 8 residues, 1 model selected
> select add #22/C:137
60 atoms, 51 bonds, 9 residues, 1 model selected
> select add #22/C:136
65 atoms, 55 bonds, 10 residues, 1 model selected
> select add #22/C:139
74 atoms, 63 bonds, 11 residues, 1 model selected
> select add #22/C:140
81 atoms, 69 bonds, 12 residues, 1 model selected
> select add #22/C:141
92 atoms, 80 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select add #22/C:145
96 atoms, 83 bonds, 14 residues, 1 model selected
> select add #22/C:147
100 atoms, 86 bonds, 15 residues, 1 model selected
> select add #22/C:146
106 atoms, 91 bonds, 16 residues, 1 model selected
> select add #22/C:285
113 atoms, 97 bonds, 17 residues, 1 model selected
> select subtract #22/C:285
106 atoms, 91 bonds, 16 residues, 1 model selected
> select add #22/C:274
117 atoms, 101 bonds, 17 residues, 1 model selected
> select add #22/C:148
126 atoms, 109 bonds, 18 residues, 1 model selected
> select subtract #22/C:274
115 atoms, 99 bonds, 17 residues, 1 model selected
> select add #22/C:284
126 atoms, 110 bonds, 18 residues, 1 model selected
> select subtract #22/C:284
115 atoms, 99 bonds, 17 residues, 1 model selected
> select add #22/C:149
122 atoms, 105 bonds, 18 residues, 1 model selected
> select add #22/C:150
131 atoms, 113 bonds, 19 residues, 1 model selected
> select add #22/C:152
136 atoms, 117 bonds, 20 residues, 1 model selected
> select add #22/C:151
144 atoms, 124 bonds, 21 residues, 1 model selected
> select add #22/C:153
154 atoms, 134 bonds, 22 residues, 1 model selected
> select add #22/C:154
161 atoms, 140 bonds, 23 residues, 1 model selected
> select add #22/C:156
166 atoms, 144 bonds, 24 residues, 1 model selected
> select add #22/C:155
174 atoms, 151 bonds, 25 residues, 1 model selected
> select add #22/C:158
182 atoms, 158 bonds, 26 residues, 1 model selected
> select add #22/C:157
189 atoms, 164 bonds, 27 residues, 1 model selected
> hide sel cartoons
Drag select of 19 residues
> select up
526 atoms, 531 bonds, 66 residues, 1 model selected
> select clear
> select add #22/C:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #22/C:160
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #22/C:161
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #22/C:162
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #22/C:163
38 atoms, 35 bonds, 5 residues, 1 model selected
> select add #22/C:165
47 atoms, 43 bonds, 6 residues, 1 model selected
> select subtract #22/C:165
38 atoms, 35 bonds, 5 residues, 1 model selected
> select add #22/C:165
47 atoms, 43 bonds, 6 residues, 1 model selected
> select subtract #22/C:165
38 atoms, 35 bonds, 5 residues, 1 model selected
> select add #22/C:165
47 atoms, 43 bonds, 6 residues, 1 model selected
> select add #22/C:166
51 atoms, 46 bonds, 7 residues, 1 model selected
> select add #22/C:167
55 atoms, 49 bonds, 8 residues, 1 model selected
> select add #22/C:169
63 atoms, 56 bonds, 9 residues, 1 model selected
> select add #22/C:168
71 atoms, 63 bonds, 10 residues, 1 model selected
> select add #22/C:164
80 atoms, 71 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select add #22/C:171
86 atoms, 76 bonds, 12 residues, 1 model selected
> select add #22/C:170
90 atoms, 79 bonds, 13 residues, 1 model selected
> select add #22/C:173
98 atoms, 86 bonds, 14 residues, 1 model selected
> select add #22/C:172
105 atoms, 92 bonds, 15 residues, 1 model selected
> select add #22/C:174
119 atoms, 107 bonds, 16 residues, 1 model selected
> select add #22/C:176
127 atoms, 114 bonds, 17 residues, 1 model selected
> select add #22/C:175
135 atoms, 121 bonds, 18 residues, 1 model selected
> select add #22/C:177
142 atoms, 127 bonds, 19 residues, 1 model selected
> select add #22/C:133@CA
143 atoms, 127 bonds, 20 residues, 1 model selected
> select add #22/C:179
151 atoms, 134 bonds, 21 residues, 1 model selected
> select add #22/C:178
160 atoms, 142 bonds, 22 residues, 1 model selected
> select add #22/C:181
171 atoms, 153 bonds, 23 residues, 1 model selected
> select clear
> select add #22/C:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #22/C:350
15 atoms, 14 bonds, 2 residues, 1 model selected
> select subtract #22/C:350
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #22/C:179
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #22/C:180
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add #22/C:178
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #22/C:177
42 atoms, 38 bonds, 5 residues, 1 model selected
> select add #22/C:176
50 atoms, 45 bonds, 6 residues, 1 model selected
> select add #22/C:175
58 atoms, 52 bonds, 7 residues, 1 model selected
> select add #22/C:174
72 atoms, 67 bonds, 8 residues, 1 model selected
> select add #22/C:172
79 atoms, 73 bonds, 9 residues, 1 model selected
> select add #22/C:173
87 atoms, 80 bonds, 10 residues, 1 model selected
> select add #22/C:171
93 atoms, 85 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select add #22/C:170
97 atoms, 88 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select add #22/C:113
103 atoms, 93 bonds, 13 residues, 1 model selected
> select add #22/C:114
111 atoms, 100 bonds, 14 residues, 1 model selected
> select up
293 atoms, 297 bonds, 38 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select add #22/C:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 8 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
54 atoms, 53 bonds, 8 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #22/C:316
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #22/C:315
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add #22/C:314
35 atoms, 31 bonds, 4 residues, 1 model selected
> select add #22/C:312
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add #22/C:313
46 atoms, 40 bonds, 6 residues, 1 model selected
> select subtract #22/C:313
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add #22/C:313
46 atoms, 40 bonds, 6 residues, 1 model selected
> select add #22/C:311
56 atoms, 50 bonds, 7 residues, 1 model selected
> select subtract #22/C:311
46 atoms, 40 bonds, 6 residues, 1 model selected
> select add #22/C:310
51 atoms, 44 bonds, 7 residues, 1 model selected
> select add #22/C:311
61 atoms, 54 bonds, 8 residues, 1 model selected
> select add #22/C:309
69 atoms, 61 bonds, 9 residues, 1 model selected
> select add #22/C:308
77 atoms, 68 bonds, 10 residues, 1 model selected
> select add #22/C:307
87 atoms, 78 bonds, 11 residues, 1 model selected
> select subtract #22/C:307
77 atoms, 68 bonds, 10 residues, 1 model selected
> select add #22/C:307
87 atoms, 78 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select add #22/C:306
91 atoms, 81 bonds, 12 residues, 1 model selected
> select add #22/C:305
95 atoms, 84 bonds, 13 residues, 1 model selected
> select add #22/C:304
103 atoms, 91 bonds, 14 residues, 1 model selected
> select add #22/C:303
110 atoms, 98 bonds, 15 residues, 1 model selected
Drag select of 3 residues
> select add #22/C:301
147 atoms, 104 bonds, 19 residues, 1 model selected
> select add #22/C:300
154 atoms, 111 bonds, 20 residues, 1 model selected
> select add #22/C:299
162 atoms, 118 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select add #22/C:290
171 atoms, 126 bonds, 22 residues, 1 model selected
Drag select of 1 residues
[Repeated 1 time(s)]
> select add #22/C:293
194 atoms, 133 bonds, 25 residues, 1 model selected
Drag select of 1 residues
> select add #22/C:295
207 atoms, 137 bonds, 27 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]Drag select of 21 atoms, 20 bonds
> hide sel atoms
Drag select of 4 atoms, 11 residues, 5 bonds
> select up
94 atoms, 92 bonds, 12 residues, 1 model selected
> select up
98 atoms, 96 bonds, 12 residues, 1 model selected
> select up
183 atoms, 185 bonds, 22 residues, 1 model selected
> select up
2001 atoms, 2029 bonds, 259 residues, 1 model selected
> select down
183 atoms, 185 bonds, 22 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select add #22/C:257
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #22/C:256
9 atoms, 7 bonds, 2 residues, 1 model selected
> select add #22/C:255
20 atoms, 17 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select add #22/C:280
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #22/C:282
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #22/C:283
41 atoms, 35 bonds, 6 residues, 1 model selected
> select add #22/C:285
48 atoms, 41 bonds, 7 residues, 1 model selected
> select add #22/C:281
56 atoms, 48 bonds, 8 residues, 1 model selected
> select add #22/C:286
63 atoms, 54 bonds, 9 residues, 1 model selected
> select add #22/C:284
74 atoms, 65 bonds, 10 residues, 1 model selected
> select add #22/C:287
82 atoms, 72 bonds, 11 residues, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
> select #22/C:289
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #22/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #22/C:289
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #22/C:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/D:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #22/C-D:170-171
20 atoms, 18 bonds, 4 residues, 1 model selected
> select #22/C-D:133-171
566 atoms, 574 bonds, 78 residues, 1 model selected
> select clear
> select #22/D:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/C-D:69-114
694 atoms, 698 bonds, 92 residues, 1 model selected
> select #22/C-D:69-133
956 atoms, 960 bonds, 130 residues, 1 model selected
> select #22/C-D:114
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:114-126
188 atoms, 186 bonds, 26 residues, 1 model selected
> show sel cartoons
> select #22/C-D:127
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:127-133
90 atoms, 88 bonds, 14 residues, 1 model selected
> show sel cartoons
> select clear
Drag select of 20 residues
> hide sel cartoons
> select #22/D:334
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #22/D:314
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/C-D:314-315
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #22/C-D:314-334
332 atoms, 332 bonds, 42 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> select clear
Drag select of 14 residues
Drag select of 10 residues
> select up
199 atoms, 201 bonds, 25 residues, 1 model selected
> select up
425 atoms, 433 bonds, 55 residues, 1 model selected
> hide sel cartoons
> select #22/C:288@CA
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #22/C:142
4 atoms, 3 bonds, 1 residue, 1 model selected
> combine #22
> hide #!21 models
> select add #22
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #22
Nothing selected
> select clear
> select #22/C:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #22/C:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #22/C-D:144
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #22/C-D:144-185
646 atoms, 660 bonds, 84 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> undo
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/C:144
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #22/C:142
15 atoms, 14 bonds, 2 residues, 1 model selected
> select subtract #22/C:142
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #22/C:142
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #22/C:143
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #22/C:288
33 atoms, 30 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 7 atoms, 6 residues, 7 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 8 atoms, 21 residues, 7 bonds
> hide sel atoms
> hide sel cartoons
> select clear
> select #22/D:335
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select clear
> select #22/D:336
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #22/D:101@CA
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/mimbert/Desktop/image5.png supersample 3
> show #!17 models
> hide #!17 models
> show #!17 models
> combine #17
> hide #!17 models
> save view test
Cannot determine format for 'view'
> view name test
Drag select of 67 residues
> hide sel atoms
> hide sel cartoons
Drag select of 63 residues
> hide sel cartoons
Drag select of 33 atoms, 33 bonds, 109 residues, 1 pseudobonds
> select up
1303 atoms, 1339 bonds, 1 pseudobond, 153 residues, 2 models selected
> select up
2581 atoms, 2639 bonds, 1 pseudobond, 320 residues, 2 models selected
> select down
1303 atoms, 1339 bonds, 1 pseudobond, 153 residues, 2 models selected
Drag select of 23 residues
> hide sel atoms
> hide sel cartoons
> select #23/W:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
173 atoms, 196 bonds, 8 residues, 1 model selected
> select up
4990 atoms, 5082 bonds, 633 residues, 1 model selected
> select down
173 atoms, 196 bonds, 8 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 13 atoms, 11 bonds, 66 residues, 1 pseudobonds
> hide sel cartoons
Drag select of 32 atoms, 33 bonds, 8 residues, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]Drag select of 15 residues
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
> select #23/D:139
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 21 residues
> hide sel cartoons
Drag select of 10 residues
> hide sel atoms
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
> select #23/D:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 2 residues
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 24 residues
> select up
213 atoms, 216 bonds, 28 residues, 1 model selected
> hide sel cartoons
Drag select of 25 residues
> select up
213 atoms, 211 bonds, 29 residues, 1 model selected
> select down
185 atoms, 25 residues, 1 model selected
> select up
213 atoms, 211 bonds, 29 residues, 1 model selected
> select down
185 atoms, 25 residues, 1 model selected
> hide sel cartoons
> select clear
> select #23/D:51
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #23/D:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select #23/D:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 5 atom styles
> hide sel atoms
Drag select of 20 residues
> select up
384 atoms, 386 bonds, 49 residues, 1 model selected
> hide sel cartoons
> select #23/E:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #23/E:123
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #23/E:126
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add #23/E:285
35 atoms, 32 bonds, 4 residues, 1 model selected
> select up
72 atoms, 72 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select add #23/E:263
79 atoms, 78 bonds, 10 residues, 1 model selected
> select add #23/E:270
86 atoms, 84 bonds, 11 residues, 1 model selected
> select up
133 atoms, 131 bonds, 18 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues, 1 pseudobonds
> hide sel cartoons
> select #23/E:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #23/E:305
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
97 atoms, 97 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
2408 atoms, 2443 bonds, 312 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #23/D:320
39 atoms, 40 bonds, 2 residues, 1 model selected
> select add #23/D:322
48 atoms, 48 bonds, 3 residues, 1 model selected
> select add #23/D:324
57 atoms, 56 bonds, 4 residues, 1 model selected
> select add #23/D:323
62 atoms, 60 bonds, 5 residues, 1 model selected
Drag select of 1 residues
> select subtract #23/D:321
62 atoms, 60 bonds, 5 residues, 1 model selected
> select add #23/D:321
69 atoms, 67 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #23/D:319
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #23/D:318
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #23/D:316
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #23/D:315
27 atoms, 26 bonds, 3 residues, 1 model selected
> select add #23/D:317
33 atoms, 31 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select add #23/D:297
40 atoms, 37 bonds, 5 residues, 1 model selected
> select add #23/E:236
44 atoms, 40 bonds, 6 residues, 1 model selected
> select subtract #23/E:236
40 atoms, 37 bonds, 5 residues, 1 model selected
> select add #23/D:290
48 atoms, 44 bonds, 6 residues, 1 model selected
> select up
178 atoms, 180 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select add #23/D:298
185 atoms, 186 bonds, 25 residues, 1 model selected
> select add #23/D:286
192 atoms, 193 bonds, 26 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 1 atoms
> select add #23/D:402@CA
14 atoms, 4 residues, 1 model selected
> hide sel atoms
> select add #23/D:257
22 atoms, 7 bonds, 5 residues, 1 model selected
Drag select of 1 residues
> select add #23/D:255
35 atoms, 14 bonds, 7 residues, 1 model selected
> select add #23/D:253
43 atoms, 21 bonds, 8 residues, 1 model selected
> select add #23/D:252
51 atoms, 28 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select #23/D:254
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select add #23/E:145
30 atoms, 8 bonds, 4 residues, 1 model selected
> select add #23/E:128
39 atoms, 16 bonds, 5 residues, 1 model selected
> select up
85 atoms, 82 bonds, 11 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> select down
85 atoms, 82 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select add #23/E:142
92 atoms, 88 bonds, 12 residues, 1 model selected
> select add #23/E:133
101 atoms, 96 bonds, 13 residues, 1 model selected
> select up
161 atoms, 160 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select add #23/E:334
168 atoms, 166 bonds, 22 residues, 1 model selected
> select add #23/E:328
173 atoms, 170 bonds, 23 residues, 1 model selected
> select up
230 atoms, 228 bonds, 31 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> select down
230 atoms, 228 bonds, 31 residues, 1 model selected
> hide sel cartoons
> select add #23/E:332
238 atoms, 235 bonds, 32 residues, 1 model selected
> select add #23/E:331
243 atoms, 239 bonds, 33 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select add #23/E:156
252 atoms, 247 bonds, 34 residues, 1 model selected
> select add #23/E:155
256 atoms, 250 bonds, 35 residues, 1 model selected
> select add #23/E:157
261 atoms, 254 bonds, 36 residues, 1 model selected
> select add #23/E:159
273 atoms, 266 bonds, 37 residues, 1 model selected
Drag select of 1 residues
> select add #23/E:160
289 atoms, 273 bonds, 39 residues, 1 model selected
Drag select of 1 residues
> select add #23/E:162
304 atoms, 279 bonds, 41 residues, 1 model selected
Drag select of 1 residues
> select add #23/E:165
320 atoms, 285 bonds, 43 residues, 1 model selected
> select add #23/E:166
331 atoms, 296 bonds, 44 residues, 1 model selected
> select add #23/E:164
335 atoms, 299 bonds, 45 residues, 1 model selected
> hide sel cartoons
> select add #23/E:235
346 atoms, 309 bonds, 46 residues, 1 model selected
> select add #23/E:236
350 atoms, 312 bonds, 47 residues, 1 model selected
> select add #23/E:237
359 atoms, 320 bonds, 48 residues, 1 model selected
> hide sel cartoons
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1_070124.cxs"
> select #23/D:243
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
187 atoms, 189 bonds, 22 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #23/E:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #23/D:250
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #22/D:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #23/D:80
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> select #23/D:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #23/E:199
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select #23/E:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select #23/D:86
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #23/D:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> select #23/E:190
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> color sel byhetero
Drag select of 1 atoms, 10 residues
> select clear
> select #23/E:191
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel byhetero
> select #23/E:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #23/E:187
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #23/D:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #23/E:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #23/D:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #23/D:90
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select #23/D:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #23/D:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #23/D:93
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select clear
> select #22/C:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #23/E:168
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #23/D:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #23/E:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #23/D:119
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #23/D:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #23/E:233
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/E:234
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/C:254
4 atoms, 3 bonds, 1 residue, 1 model selected
> test
Unknown command: test
> view test
> select #23/D:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
26 atoms, 25 bonds, 3 residues, 1 model selected
> select up
1947 atoms, 1974 bonds, 253 residues, 1 model selected
> select up
1954 atoms, 1981 bonds, 254 residues, 1 model selected
> select up
2376 atoms, 2410 bonds, 310 residues, 1 model selected
> color sel dark gray
> color sel dim gray
> color sel byhetero
> select clear
> select #22/C-D:201
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/C-D:201
16 atoms, 14 bonds, 2 residues, 1 model selected
Drag select of 2 residues
> select #22/C:251
9 atoms, 8 bonds, 1 residue, 1 model selected
> combine #22,23
Remapping chain ID 'D' in copy of 8bq2 (1).pdb #23 to 'F'
Remapping chain ID 'W' in copy of 8bq2 (1).pdb #23 to 'X'
> hide #!22 models
> hide #!23 models
> select add #22
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 2 models selected
> select subtract #22
Nothing selected
Drag select of 13 atoms, 12 bonds, 3 residues
> select clear
Drag select of 13 atoms, 12 bonds, 1 residues
Drag select of 24 atoms, 19 bonds, 38 residues
> hide sel cartoons
> hide sel atoms
Drag select of 33 atoms, 31 bonds, 70 residues
> hide sel atoms
> hide sel cartoons
Drag select of 55 atoms, 48 bonds, 28 residues
> hide sel atoms
> hide sel cartoons
Drag select of 28 atoms, 22 bonds, 48 residues
Drag select of 25 atoms, 19 bonds, 26 residues
> hide sel atoms
> hide sel cartoons
Drag select of 18 residues
Drag select of 12 residues
> hide sel atoms
> hide sel cartoons
> select #24/F:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #24/F:120
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #24/F:119
17 atoms, 14 bonds, 3 residues, 1 model selected
> select subtract #24/F:119
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel cartoons
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/figG_1.tif"
> width 2000 height 1526 supersample 4 transparentBackground true
> rename #24 G1
> hide #!24 models
> show #!23 models
> show #!22 models
> combine #22,23
Remapping chain ID 'D' in copy of 8bq2 (1).pdb #23 to 'F'
Remapping chain ID 'W' in copy of 8bq2 (1).pdb #23 to 'X'
> hide #!22 models
> hide #!23 models
> select add #24
10076 atoms, 10265 bonds, 14 pseudobonds, 1275 residues, 3 models selected
> select subtract #24
Nothing selected
Drag select of 25 atoms, 22 bonds, 42 residues
> hide sel cartoons
> hide sel atoms
> select #25/F:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 53 atoms, 49 bonds, 25 residues
> hide sel cartoons
> hide sel atoms
Drag select of 28 atoms, 22 bonds, 39 residues
> hide sel atoms
> hide sel cartoons
Drag select of 15 residues
Drag select of 1 residues
Drag select of 14 residues
> hide sel cartoons
> hide sel atoms
Drag select of 23 residues
> hide sel cartoons
Drag select of 15 residues
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
> view name 1
> view test
> view 1
[Repeated 1 time(s)]
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/figG_2.tif"
> width 2000 height 1526 supersample 4 transparentBackground true
> rename #25 G2
> hide #!25 models
> combine #22,23
Remapping chain ID 'D' in copy of 8bq2 (1).pdb #23 to 'F'
Remapping chain ID 'W' in copy of 8bq2 (1).pdb #23 to 'X'
Drag select of 208 atoms, 182 bonds, 206 residues
> hide sel atoms
> hide sel cartoons
> select #26/D:270
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #26/D:270
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #26/F:250
16 atoms, 14 bonds, 2 residues, 1 model selected
Drag select of 2 residues
> select add #26/D:264
42 atoms, 22 bonds, 5 residues, 1 model selected
> select subtract #26/D:264
33 atoms, 14 bonds, 4 residues, 1 model selected
> select add #26/E:230
40 atoms, 20 bonds, 5 residues, 1 model selected
> select up
42 atoms, 36 bonds, 6 residues, 1 model selected
> select up
46 atoms, 40 bonds, 6 residues, 1 model selected
> label sel attribute name
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
[Repeated 1 time(s)]
> ui mousemode right label
> label delete residues
> ui mousemode right label
> undo
[Repeated 2 time(s)]
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label delete residues
> ui mousemode right label
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right distance
> ui mousemode right "move label"
> ui mousemode right distance
> ui mousemode right "move label"
[Repeated 1 time(s)]
> style sel stick
Changed 46 atom styles
> ui mousemode right select
> select #26/C:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26/C:249
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #26/E:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #26/C:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26/C:250@CB
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/FigG_3.tif"
> width 2000 height 1526 supersample 4 transparentBackground true
> rename #26 G3
> hide #!26 models
> show #!25 models
> view 1
> select #25/C:218
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #25/D:94
17 atoms, 18 bonds, 2 residues, 1 model selected
> select add #25/F:80
26 atoms, 26 bonds, 3 residues, 1 model selected
> select add #25/D:101
37 atoms, 37 bonds, 4 residues, 1 model selected
> select add #25/F:86
48 atoms, 48 bonds, 5 residues, 1 model selected
> select add #25/E:190
53 atoms, 52 bonds, 6 residues, 1 model selected
> select add #25/F:87
60 atoms, 59 bonds, 7 residues, 1 model selected
> select add #25/F:88
67 atoms, 67 bonds, 8 residues, 1 model selected
> select add #25/E:189@CB
68 atoms, 69 bonds, 9 residues, 1 model selected
> select add #25/C:202
77 atoms, 78 bonds, 10 residues, 1 model selected
> select add #25/C:201@CG
78 atoms, 78 bonds, 11 residues, 1 model selected
> select add #25/C:198
86 atoms, 86 bonds, 12 residues, 1 model selected
> select add #25/E:182
90 atoms, 89 bonds, 13 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right label
> label delete residues
> label #25/C:202
> select up
106 atoms, 88 bonds, 22 residues, 1 model selected
> select up
193 atoms, 185 bonds, 22 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right select
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> label #25/E:203
> label delete residues
> ui mousemode right select
> select add #25/C:218
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #25/E:199
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #25/F:86@CE2
1 atom, 1 residue, 1 model selected
> select add #25/E:203
9 atoms, 7 bonds, 2 residues, 1 model selected
> select clear
> select add #25/C:218
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #25/C:214
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #25/D:101
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #25/C:201@CB
30 atoms, 28 bonds, 4 residues, 1 model selected
> select add #25/C:204
38 atoms, 35 bonds, 5 residues, 1 model selected
> label sel atoms attribute name
> undo
> ui mousemode right label
> label delete residues
[Repeated 2 time(s)]
> label delete atoms
> label sel attribute name
> label delete residues
> label sel attribute name
> ui mousemode right select
> select clear
> ui mousemode right "move label"
> ui mousemode right select
> select #25/E:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel attribute name
> select clear
> select #25/D:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #25/F:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #25/C:205
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #25/E:190
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #25/F:80
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #25/D:94
18 atoms, 16 bonds, 2 residues, 1 model selected
> select clear
> select add #25/F:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #25/D:93
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #25/C:205@CA
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #25/D:102
25 atoms, 22 bonds, 4 residues, 1 model selected
> select add #25/F:87
32 atoms, 28 bonds, 5 residues, 1 model selected
> select add #25/E:191
44 atoms, 40 bonds, 6 residues, 1 model selected
> select add #25/C:202
53 atoms, 51 bonds, 7 residues, 1 model selected
> select add #25/E:187
61 atoms, 58 bonds, 8 residues, 1 model selected
> select up
69 atoms, 58 bonds, 12 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view 1
> select clear
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/figG_2_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> hide #!25 models
> show #!24 models
> ui mousemode right select
> select #24/D:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #24/C:182
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #24/D:111
31 atoms, 28 bonds, 3 residues, 1 model selected
> select up
33 atoms, 29 bonds, 4 residues, 1 model selected
> select up
38 atoms, 36 bonds, 4 residues, 1 model selected
> label sel attribute name
> select clear
> select add #24/D:336
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #24/F:93
20 atoms, 21 bonds, 2 residues, 1 model selected
> select add #24/D:108
28 atoms, 28 bonds, 3 residues, 1 model selected
> select up
30 atoms, 28 bonds, 4 residues, 1 model selected
> select up
34 atoms, 32 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig_1_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> ui mousemode right select
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig_1_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> rename #23 FigG_Rad51
> hide #!23 models
> show #!22 models
> rename #22 figG_RadA
> hide #!22 models
> show #!21 models
> show #!20 models
> hide #!21 models
> hide #!20 models
> show #!21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!22 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #!8 models
> select #8/W:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
168 atoms, 191 bonds, 8 residues, 1 model selected
> select up
5086 atoms, 5183 bonds, 642 residues, 1 model selected
> select down
168 atoms, 191 bonds, 8 residues, 1 model selected
> color sel byhetero
> select #19/W:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
173 atoms, 196 bonds, 8 residues, 1 model selected
> color sel byhetero
> select clear
> select #19/E:273
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> select add #8/C:262
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #19/E:229
20 atoms, 19 bonds, 2 residues, 2 models selected
> select up
22 atoms, 19 bonds, 3 residues, 2 models selected
> select up
31 atoms, 29 bonds, 3 residues, 2 models selected
> select up
221 atoms, 223 bonds, 26 residues, 2 models selected
> label sel attribute name
> undo
> ui mousemode right label
> label delete residues
> ui mousemode right select
> select clear
> select #8/C:262@CG
1 atom, 1 residue, 1 model selected
> select add #8/C:262
9 atoms, 9 bonds, 1 residue, 2 models selected
> select add #19/E:229
20 atoms, 19 bonds, 2 residues, 2 models selected
> select up
22 atoms, 19 bonds, 3 residues, 2 models selected
> label sel attribute name
> select #19/E:270@CA
1 atom, 1 residue, 1 model selected
> select add #8/C:290
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
14 atoms, 10 bonds, 4 residues, 2 models selected
> select up
30 atoms, 27 bonds, 4 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> view fig1E
[Repeated 1 time(s)]
> select clear
> ui mousemode right "move label"
> view name fig1E1
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1E_Rad51 et
> RadA.tif" width 2000 height 1526 supersample 4 transparentBackground true
> hide #!19 models
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1E_RadA_090125.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> hide #!8 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> rename #2 "fig1D RadA"
> ui mousemode right select
> select #2/D:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/D:293
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #5/D:296
19 atoms, 16 bonds, 3 residues, 2 models selected
> select up
21 atoms, 17 bonds, 4 residues, 2 models selected
> select up
29 atoms, 27 bonds, 4 residues, 2 models selected
> select add #2/C:180
36 atoms, 34 bonds, 5 residues, 2 models selected
> select add #2/C:149
43 atoms, 40 bonds, 6 residues, 2 models selected
Drag select of 3 residues
> select subtract #5/E:170
63 atoms, 40 bonds, 8 residues, 2 models selected
> select up
65 atoms, 48 bonds, 9 residues, 2 models selected
> select up
72 atoms, 55 bonds, 9 residues, 2 models selected
> select up
468 atoms, 473 bonds, 60 residues, 2 models selected
> select down
72 atoms, 55 bonds, 9 residues, 2 models selected
> label sel attribute name
Drag select of 1 residues
> select add #5/E:131
19 atoms, 7 bonds, 2 residues, 2 models selected
> select add #2/C:146
25 atoms, 12 bonds, 3 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
66 atoms, 68 bonds, 9 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view fig1D
Expected an objects specifier or a view name or a keyword
> view fig1d
Expected an objects specifier or a view name or a keyword
> view fig1
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui mousemode right "move label"
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> ui mousemode right select
> select add #2/C:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/D:313
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #2/D:311
24 atoms, 22 bonds, 3 residues, 1 model selected
> select up
26 atoms, 23 bonds, 4 residues, 1 model selected
> select add #2/D:332
34 atoms, 30 bonds, 5 residues, 1 model selected
> select add #2/D:333
42 atoms, 37 bonds, 6 residues, 1 model selected
> select add #2/C:180
49 atoms, 43 bonds, 7 residues, 1 model selected
> select add #2/C:185
60 atoms, 54 bonds, 8 residues, 1 model selected
> select add #2/C:146
66 atoms, 59 bonds, 9 residues, 1 model selected
> select up
68 atoms, 60 bonds, 10 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #!5 models
> hide #!2 models
> undo
> hide #!5 models
> view name fig1D
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #!5 models
> ui mousemode right label
> label delete residues
> label #5/E:134
[Repeated 1 time(s)]
> ui mousemode right label
> label delete residues
> ui mousemode right select
> select add #2/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5/E:163
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #5/E:134
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #5/E:169
32 atoms, 28 bonds, 4 residues, 2 models selected
> select subtract #5/E:169
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #5/E:170
34 atoms, 30 bonds, 4 residues, 2 models selected
> select add #5/D:293
39 atoms, 34 bonds, 5 residues, 2 models selected
> select add #5/D:316
47 atoms, 42 bonds, 6 residues, 2 models selected
> select add #5/E:169
56 atoms, 50 bonds, 7 residues, 2 models selected
> select subtract #5/E:170
45 atoms, 40 bonds, 6 residues, 2 models selected
> select up
47 atoms, 40 bonds, 7 residues, 2 models selected
> label sel attribute name
> select clear
> select add #5/E:169
9 atoms, 9 bonds, 1 residue, 2 models selected
Drag select of 4 residues
> select clear
> select add #5/E:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/C:185@CG
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #5/E:170@CD
11 atoms, 8 bonds, 3 residues, 2 models selected
> select up
31 atoms, 29 bonds, 3 residues, 2 models selected
> select up
161 atoms, 161 bonds, 19 residues, 2 models selected
> select add #5/D:315
173 atoms, 173 bonds, 20 residues, 2 models selected
> select add #2/D:332@CB
174 atoms, 173 bonds, 21 residues, 2 models selected
> select add #2/D:313
179 atoms, 177 bonds, 22 residues, 2 models selected
> select up
181 atoms, 178 bonds, 23 residues, 2 models selected
> select up
192 atoms, 189 bonds, 23 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right "move label"
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> ui mousemode right "move label"
> ui mousemode right select
> select add #2/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5/E:169
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #2/C:183
25 atoms, 23 bonds, 3 residues, 2 models selected
> select add #5/E:168
32 atoms, 30 bonds, 4 residues, 2 models selected
> select subtract #5/E:169
23 atoms, 22 bonds, 3 residues, 2 models selected
> ui mousemode right label
> label delete residues
> ui mousemode right select
> select add #2/C:178
32 atoms, 30 bonds, 4 residues, 2 models selected
> select add #2/C:180
39 atoms, 36 bonds, 5 residues, 2 models selected
> select clear
> select add #2/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/C:178
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #5/D:293
21 atoms, 20 bonds, 3 residues, 2 models selected
> select add #5/D:295
26 atoms, 24 bonds, 4 residues, 2 models selected
> select subtract #5/D:295
21 atoms, 20 bonds, 3 residues, 2 models selected
> select up
27 atoms, 21 bonds, 6 residues, 2 models selected
> select up
46 atoms, 42 bonds, 6 residues, 2 models selected
> select up
248 atoms, 249 bonds, 32 residues, 2 models selected
> select down
46 atoms, 42 bonds, 6 residues, 2 models selected
> label sel attribute name
> select clear
Drag select of 1 residues
> select add #2/D:313@CA
7 atoms, 2 residues, 2 models selected
> select add #2/C:185@CD
8 atoms, 3 residues, 2 models selected
> select add #5/E:131@CB
9 atoms, 1 bond, 4 residues, 2 models selected
> select up
13 atoms, 7 bonds, 6 residues, 2 models selected
> select up
46 atoms, 40 bonds, 6 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view fig1D
> select clear
> ui mousemode right "move label"
> ui mousemode right select
Drag select of 2 residues
> select up
146 atoms, 147 bonds, 17 residues, 1 model selected
> ~label sel residues
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel attribute name
> select clear
[Repeated 4 time(s)]
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> select up
20 atoms, 19 bonds, 2 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #5/E:165@CA
1 atom, 1 residue, 1 model selected
> select add #5/E:163
10 atoms, 8 bonds, 2 residues, 1 model selected
> label sel attribute name
> view fig1D
> select clear
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_Rad51.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> hide #!5 models
> hide #!2 models
> show #!8 models
> show #!5 models
> hide #!5 models
> show #11 models
> hide #11 models
> show #!19 models
> view fig1E1
> hide #!19 models
> ui mousemode right select
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/090124.cxs"
> select add #8/C:262
9 atoms, 9 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select add #8/C:249
22 atoms, 19 bonds, 2 residues, 1 model selected
> select add #8/C:290
31 atoms, 27 bonds, 3 residues, 1 model selected
> select add #8/C:291
36 atoms, 31 bonds, 4 residues, 1 model selected
> select up
47 atoms, 43 bonds, 6 residues, 1 model selected
> select up
52 atoms, 49 bonds, 6 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view fig1E1
> select clear
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1E_RadA_090125.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #!19 models
> ui mousemode right label
> label delete residues
> label #19/E:229
> label delete residues
> ui mousemode right select
> select #19/E:229
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #8/C:262
20 atoms, 18 bonds, 2 residues, 2 models selected
> select add #8/C:261@CD
21 atoms, 18 bonds, 3 residues, 2 models selected
> select up
31 atoms, 29 bonds, 3 residues, 2 models selected
> label sel attribute name
> select add #19/E:273@CB
1 atom, 2 bonds, 1 residue, 2 models selected
> select up
7 atoms, 3 bonds, 4 residues, 2 models selected
> select up
30 atoms, 27 bonds, 4 residues, 2 models selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view fig1E1
[Repeated 2 time(s)]
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> view fig1E1
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1E_Rad51 et
> RadA.tif" width 2000 height 1526 supersample 3 transparentBackground true
> hide #!19 models
> select add #8/C:293
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/C:291
12 atoms, 11 bonds, 2 residues, 1 model selected
> select add #8/C:290
21 atoms, 19 bonds, 3 residues, 1 model selected
> select add #8/C:249
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #8/C:261
43 atoms, 39 bonds, 5 residues, 1 model selected
> select add #8/C:262
52 atoms, 47 bonds, 6 residues, 1 model selected
> color sel byhetero
> select clear
> select #8/C:291
5 atoms, 4 bonds, 1 residue, 1 model selected
> label sel attribute name
> select add #8/C:262
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #8/C:249
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #8/C:250
31 atoms, 27 bonds, 4 residues, 1 model selected
> select subtract #8/C:250
25 atoms, 23 bonds, 3 residues, 1 model selected
> select up
27 atoms, 23 bonds, 4 residues, 1 model selected
> select up
36 atoms, 33 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view fig1E1
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/fig1E_RadA_090125.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #3 models
> hide #3 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> ui mousemode right select
> select add #8/C:291
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #8/C:262
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #8/C:261
25 atoms, 22 bonds, 3 residues, 1 model selected
> select up
27 atoms, 24 bonds, 4 residues, 1 model selected
> select up
36 atoms, 33 bonds, 4 residues, 1 model selected
> label sel attribute name
> show #!19 models
> select clear
> ui mousemode right "move label"
> hide #!8 models
> ui mousemode right select
> select #19/E:241
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #19/E:242
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #19/E:229
31 atoms, 28 bonds, 3 residues, 1 model selected
> select add #19/E:271
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #19/E:270
43 atoms, 38 bonds, 5 residues, 1 model selected
> select add #19/E:273
50 atoms, 44 bonds, 6 residues, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select clear
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/fig1E_Rad51 et
> RadA.tif" width 2000 height 1526 supersample 3 transparentBackground true
> hide #!8 models
> hide #!19 models
> show #!5 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> view fig1D
> select add #2/C:178
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #2/C:180@CA
10 atoms, 9 bonds, 2 residues, 1 model selected
> select add #2/D:311
20 atoms, 19 bonds, 3 residues, 1 model selected
> select add #2/D:312
26 atoms, 24 bonds, 4 residues, 1 model selected
> select add #2/D:332
34 atoms, 33 bonds, 5 residues, 1 model selected
> select add #2/C:146
40 atoms, 38 bonds, 6 residues, 1 model selected
> select add #2/C:185@CZ
41 atoms, 38 bonds, 7 residues, 1 model selected
> select subtract #2/C:185@CZ
40 atoms, 38 bonds, 6 residues, 1 model selected
> select add #2/C:185@CZ
41 atoms, 38 bonds, 7 residues, 1 model selected
> select #2/C:147
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2/C:185@NH1
5 atoms, 5 bonds, 2 residues, 1 model selected
> select add #2/C:180
12 atoms, 12 bonds, 3 residues, 1 model selected
> select add #2/C:178
21 atoms, 20 bonds, 4 residues, 1 model selected
> select add #2/D:311
31 atoms, 30 bonds, 5 residues, 1 model selected
Drag select of 1 residues
> select add #2/D:332
45 atoms, 39 bonds, 7 residues, 1 model selected
> select add #2/C:146
51 atoms, 44 bonds, 8 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/D:311@CD2
1 atom, 1 residue, 1 model selected
> select add #2/D:310
6 atoms, 4 bonds, 2 residues, 1 model selected
> select add #2/D:312
12 atoms, 9 bonds, 3 residues, 1 model selected
> select add #2/C:178
21 atoms, 17 bonds, 4 residues, 1 model selected
> select add #2/C:180@CA
22 atoms, 17 bonds, 5 residues, 1 model selected
> select add #2/C:149
29 atoms, 23 bonds, 6 residues, 1 model selected
> select add #2/C:146
35 atoms, 28 bonds, 7 residues, 1 model selected
> select add #2/D:333
43 atoms, 35 bonds, 8 residues, 1 model selected
> select add #2/D:332
51 atoms, 42 bonds, 9 residues, 1 model selected
> select add #2/C:185@CZ
52 atoms, 42 bonds, 10 residues, 1 model selected
> select subtract #2/C:185
51 atoms, 42 bonds, 9 residues, 1 model selected
> select add #2/C:185@CZ
52 atoms, 42 bonds, 10 residues, 1 model selected
> select add #2/C:185@NH1
53 atoms, 42 bonds, 10 residues, 1 model selected
> color sel byhetero
> select clear
> select add #2/D:332
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/D:310
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #2/D:310
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/D:311
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/D:312
21 atoms, 19 bonds, 3 residues, 1 model selected
> select add #2/C:178
30 atoms, 27 bonds, 4 residues, 1 model selected
> select add #2/C:180
37 atoms, 33 bonds, 5 residues, 1 model selected
> select add #2/C:185
48 atoms, 44 bonds, 6 residues, 1 model selected
> select add #2/C:146@CA
49 atoms, 44 bonds, 7 residues, 1 model selected
> select add #2/D:333
57 atoms, 51 bonds, 8 residues, 1 model selected
> select add #2/D:332
65 atoms, 58 bonds, 9 residues, 1 model selected
> select up
67 atoms, 61 bonds, 10 residues, 1 model selected
> select up
77 atoms, 71 bonds, 10 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> ui mousemode right "move label"
> undo
> ui mousemode right select
> view fig1D
> select clear
> ui mousemode right "move label"
> view fig1D
> select add #2
5086 atoms, 5183 bonds, 4 pseudobonds, 642 residues, 3 models selected
Alignment identifier is 2
Alignment identifier is 2/W
> select #2/C-D:312
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/C-D:312
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/C-D:312-313
22 atoms, 20 bonds, 4 residues, 1 model selected
> select #2/C-D:312-314
36 atoms, 34 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/C-D:312
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/C-D:310-312
42 atoms, 42 bonds, 6 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> undo
[Repeated 5 time(s)]
> ui mousemode right select
> select clear
> view fig1D
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_annoté.tif" width 2000 height 1526 supersample 3
> transparentBackground true
> show #!5 models
> hide #!2 models
> select add #5/E:163
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5/E:165
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #5/E:134
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #5/E:169
32 atoms, 28 bonds, 4 residues, 1 model selected
> select subtract #5/E:169
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #5/E:169
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #5/E:170
43 atoms, 38 bonds, 5 residues, 1 model selected
> select subtract #5/E:169
34 atoms, 30 bonds, 4 residues, 1 model selected
> select add #5/D:315
46 atoms, 42 bonds, 5 residues, 1 model selected
> select add #5/D:293
51 atoms, 46 bonds, 6 residues, 1 model selected
> select add #5/D:296
57 atoms, 51 bonds, 7 residues, 1 model selected
> select add #5/D:316
65 atoms, 58 bonds, 8 residues, 1 model selected
> select up
67 atoms, 60 bonds, 9 residues, 1 model selected
> color sel byhetero
> view fig1D
> select #5/E:400@N9
1 atom, 1 residue, 1 model selected
> select #5/E:400@N9
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 8 atoms, 9 bonds
> select clear
> ui mousemode right rotate
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
2408 atoms, 2443 bonds, 312 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select down
Nothing selected
> view fig1D
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/E:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #!5 models
> view fig1D
> select clear
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_annoté.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/E:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5/D:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #5/D:294
15 atoms, 14 bonds, 2 residues, 1 model selected
> color sel byhetero
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> select add #2/C:149
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/C:180
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #2/C:178
23 atoms, 21 bonds, 3 residues, 1 model selected
> select up
25 atoms, 21 bonds, 4 residues, 1 model selected
> select up
34 atoms, 30 bonds, 4 residues, 1 model selected
> label sel attribute name
> show #!5 models
> hide #!5 models
> select #2/D:333@CA
1 atom, 1 residue, 1 model selected
> select add #2/D:312
7 atoms, 5 bonds, 2 residues, 1 model selected
> select subtract #2/D:312
1 atom, 1 residue, 1 model selected
> select add #2/D:311
11 atoms, 10 bonds, 2 residues, 1 model selected
> select add #2/D:313
16 atoms, 14 bonds, 3 residues, 1 model selected
> select subtract #2/D:313
11 atoms, 10 bonds, 2 residues, 1 model selected
> select up
13 atoms, 11 bonds, 3 residues, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label sel attribute name
> view fig1D
> show #!5 models
> hide #!5 models
> show #!5 models
> select clear
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/E:131
19 atoms, 19 bonds, 2 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #5/D:315
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/E:131@OG1
13 atoms, 13 bonds, 2 residues, 1 model selected
> select subtract #5/E:131
12 atoms, 13 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #5/D:296
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5/E:131
13 atoms, 11 bonds, 2 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #2/D:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 2 time(s)]
> select clear
> select #5/D:296
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> label sel attribute name
> select #2/D:312
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> ui mousemode right "move label"
> ui mousemode right select
> view fig1E
> view fig1D
> ui mousemode right "move label"
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_Rad51.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> ui mousemode right select
> hide #!2 models
> select #5/E:400@C1'
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
2408 atoms, 2443 bonds, 312 residues, 1 model selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel gray
> color sel light gray
> color sel #bbbbbbff
> select clear
> show #!2 models
> view fig1D
> save "/Users/mimbert/OneDrive - Institut Pasteur
> Paris/Papers/Fig1D_RadA_Rad51.tif" width 2000 height 1526 supersample 4
> transparentBackground true
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/090125.cxs"
> hide #!5 models
> hide #!2 models
> show #!4 models
> select add #4
2585 atoms, 2639 bonds, 2 pseudobonds, 323 residues, 2 models selected
Alignment identifier is 4/C
Alignment identifier is 4/W
> select #4/C:136
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/C:136
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> show #!12 models
Drag select of 29 residues
> hide #!4 models
> select #12/E:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!4 models
> select #4/C:136
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!4 models
> select #12/E:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!15 models
> select #12/E:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/C:136
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
Drag select of 1 residues, 1 atoms
> hide #!12 models
> show #!12 models
> select add #15
2592 atoms, 2638 bonds, 1 pseudobond, 323 residues, 3 models selected
> select add #12
5155 atoms, 5261 bonds, 9 pseudobonds, 643 residues, 5 models selected
> ui mousemode right translate
> hide #!12 models
> hide #!15 models
> select subtract #15
2571 atoms, 2623 bonds, 8 pseudobonds, 321 residues, 3 models selected
> select subtract #12
Nothing selected
> show #!4 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> open /Users/mimbert/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Phenix/RadA/RadAWT/161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb
Chain information for
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27
---
Chain | Description
A E F G H V X | No description available
B C D | No description available
I | No description available
U | No description available
W | No description available
Y | No description available
Z | No description available
> hide #!4 models
> select add #27
30113 atoms, 30698 bonds, 16 pseudobonds, 3769 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> dssp
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 1
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 2
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 3
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 4
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 5
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 6
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 7
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 8
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 9
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 10
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 11
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 12
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 13
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 14
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 15
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 16
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 17
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 18
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 19
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 20
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 21
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 22
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 23
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 24
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 25
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 26
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 27
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 28
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 29
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 30
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 31
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 32
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 33
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 34
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 35
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 36
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 37
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 401, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 419, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 338, in run
f(s)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 592, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 535, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 472, in add_hydrogens
_attach_hydrogens(end, altloc_hpos_info, _type_info(end))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 909, in _attach_hydrogens
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 910, in add_altloc_hyds
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 949, in new_hydrogen
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
See log for complete Python traceback.
> show sel surfaces
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 1
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 2
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 3
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 4
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 5
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 6
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 7
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 8
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 9
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 10
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 11
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 12
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 13
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 14
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 15
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 16
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 17
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 18
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 19
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 20
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 21
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 22
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 23
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 24
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 25
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 26
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 27
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 28
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 29
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 30
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 31
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 32
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 33
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 34
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 35
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 36
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 37
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 401, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 419, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 338, in run
f(s)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 592, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 535, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 472, in add_hydrogens
_attach_hydrogens(end, altloc_hpos_info, _type_info(end))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 909, in _attach_hydrogens
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 910, in add_altloc_hyds
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 949, in new_hydrogen
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
See log for complete Python traceback.
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 1
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 2
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 3
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 4
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 5
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 6
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 7
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 8
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 9
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 10
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 11
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 12
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 13
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 14
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 15
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 16
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 17
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 18
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 19
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 20
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 21
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 22
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 23
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 24
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 25
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 26
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 27
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 28
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 29
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 30
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 31
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 32
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 33
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 34
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 35
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 36
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #27/W A 37
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 401, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 419, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 338, in run
f(s)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 592, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 535, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 472, in add_hydrogens
_attach_hydrogens(end, altloc_hpos_info, _type_info(end))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 909, in _attach_hydrogens
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 910, in add_altloc_hyds
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 949, in new_hydrogen
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/O ATP 400 N6
taken!
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
See log for complete Python traceback.
> hide #!27 models
> select subtract #27
15 models selected
> save "/Users/mimbert/OneDrive - Institut Pasteur Paris/Papers/160125.cxs"
> show #!4 models
> select add #4
2585 atoms, 2639 bonds, 2 pseudobonds, 323 residues, 2 models selected
> show sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 22 O2'
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 20 O2'
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 18 O2'
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 21 O2'
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 19 O2'
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #4/W A 17 O2'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 401, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 419, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 338, in run
f(s)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 592, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 535, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 764, in add_hydrogens
_attach_hydrogens(a, altloc_hpos_info, bonding_info)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 909, in _attach_hydrogens
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 910, in add_altloc_hyds
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 949, in new_hydrogen
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/M ATP 400 N6
taken!
ValueError: All hydrogen names for copy of
161224_optimisation_model_radAWT_ATP_real_space_refined_008.pdb #/M ATP 400 N6
taken!
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 1046, in _h_name
raise ValueError("All hydrogen names for %s taken!" % atom)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXX3FN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 76 jours, 3 heures et 32 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Note:
See TracTickets
for help on using tickets.
