All hydrogen names for ATP N6

[chimerax-bug-report@…]

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)  
  

[deleted to fit within ticket limits]

> 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

[Eric Pettersen]

In the user's structure, ATP N6 must be being typed as something other than Npl.