Session save: 'PseudobondGroup' object has no attribute '_c_pointer_ref'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.14.0-162.18.1.el9_1.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.5rc202210312311 (2022-10-31 23:11:39 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> style stick

Changed 0 atom styles  
UCSF ChimeraX version: 1.5rc202210312311 (2022-10-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J807_Toxo-
> Football-DeepEM.mrc

Opened cryosparc_P36_J807_Toxo-Football-DeepEM.mrc as #1, grid size
640,640,640, pixel 0.824, shown at level 0.000684, step 4, values float32  

> volume #1 level 0.05871

> open /home/agonzalez/Desktop/PROJECTS/CPN20/CPN20-Toxoplasma-Football-
> waters-8_deleted.pdb

Chain information for CPN20-Toxoplasma-Football-waters-8_deleted.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> set bgColor white

[Repeated 1 time(s)]

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add K

14 atoms, 14 residues, 1 model selected  

> select add Mg

28 atoms, 28 residues, 1 model selected  

> select add Be

42 atoms, 42 residues, 1 model selected  

> select add F

84 atoms, 42 residues, 1 model selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> hide

> hide #!2 models

> show #!2 models

> rename #1 id #6

> rename #2 id #1

> select clear

> hide #!6 models

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add K

14 atoms, 14 residues, 1 model selected  

> select add Mg

28 atoms, 28 residues, 1 model selected  

> select add Be

42 atoms, 42 residues, 1 model selected  

> select add F

84 atoms, 42 residues, 1 model selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> select clear

> select add /C:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

45 atoms, 41 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.982911411662656 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.982911411662656 [-0.97227183 -0.15309311 -0.17677671]  

> select clear

> select zone ligand1 10

Selected 1172 atoms, 1 surfaces  

> show sel cartoons

> select clear

> delete H

> name list

ligand1 [33 atoms, 58 bonds, 2 models]  

> select clear

> select add:ADP; select add @K,Mg,BE,F1,F2,F3; name frozen ligand_all sel;
> show sel;select clear

Expected an objects specifier or a keyword  

> select clear

> select add:ADP; select add #1@K,Mg,BE,F1,F2,F3; name frozen ligand_all sel;
> show sel;select clear

Expected an objects specifier or a keyword  

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> name list

ligand1 [33 atoms, 58 bonds, 2 models]  
ligand_all [462 atoms, 812 bonds, 2 models]  

> color ~ligand_all cornflower blue

> graphics silhouettes true

> graphics silhouettes false

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> graphics silhouettes false

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select ligand1

33 atoms, 29 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -23.959808669277965 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -23.959808669277965 [-0.97227183 -0.15309311 -0.17677671]  

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add K

14 atoms, 14 residues, 1 model selected  

> select add Mg

28 atoms, 28 residues, 1 model selected  

> select add Be

42 atoms, 42 residues, 1 model selected  

> select add F

84 atoms, 42 residues, 1 model selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add K

14 atoms, 14 residues, 1 model selected  

> select add Mg

28 atoms, 28 residues, 1 model selected  

> select add Be

42 atoms, 42 residues, 1 model selected  

> select add F

84 atoms, 42 residues, 1 model selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> show sel

> style sel stick

Changed 378 atom styles  

> color sel byhetero

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v2.cxs

> close session

> open /home/agonzalez/Desktop/PROJECTS/CPN20/CPN20-Toxoplasma-Football-
> waters-8_deleted.pdb

Chain information for CPN20-Toxoplasma-Football-waters-8_deleted.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J807_Toxo-
> Football-DeepEM.mrc

Opened cryosparc_P36_J807_Toxo-Football-DeepEM.mrc as #2, grid size
640,640,640, pixel 0.824, shown at level 0.000684, step 4, values float32  

> volume #2 level 0.01809

> hide #!2 models

> rename #2 id #6

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show selselect clear

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  

> select zone ligand1 10

Selected 553 atoms, 1 surfaces  

> show sel cartoons

> select clear

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  

> select zone ligand1 10

Selected 553 atoms, 1 surfaces  

> show sel cartoons

> hide ~sel

> select clear

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  

> select zone ligand1 10

Selected 553 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

586 atoms, 29 bonds, 2 pseudobonds, 115 residues, 3 models selected  

> hide ~sel

> select clear

> show #!6 models

> hide #!6 models

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.6

moved plane near -38.64809923616906 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -38.64809923616906 [-0.97227183 -0.15309311 -0.17677671]  

> select zone ligand1 10

Selected 553 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

586 atoms, 29 bonds, 2 pseudobonds, 115 residues, 3 models selected  

> hide ~sel

> select clear

> clip help

Expected a keyword  

> help clip

> clip off

> clip

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.7

moved plane near -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -24.845206651822966 [-0.97227183 -0.15309311 -0.17677671]  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.64

moved plane near -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  

> clip near 1

> clip near 2

> clip near 0.2

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.64

moved plane near -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  

> clip help

Expected a keyword  

> clip help

Expected a keyword  

> help clip

> cclip off

Unknown command: cclip off  

> clip off

> clip near 1

> clip near 0.5

> clip near -1

[Repeated 1 time(s)]

> clip off

> clip .5

Expected a keyword  

> clip 0.5

Expected a keyword  

> clip near 0.5

> clip near -0.5

[Repeated 1 time(s)]

> clip off

> clip near 0.1

> clip off

> clip near off

> clip near -5

> clip near off

> clip near 0

> clip near off

> clip near -10

> clip off

> clip near -6

> clip off

> clip near -7

> clip off

> clip near -5

> clip off

> clip near -4

> clip off

> clip near -4

> clip far 5

> clip off

> clip near -4

> clip far off

> clip far 0

> clip off

> clip near -4

> clip far off

> clip far 10

> clip off

> clip near -4

> clip far off

> clip far 10

> clip off

> clip near -4

> clip far off

> clip far 9

> clip off

> clip near -4

> clip far off

> clip far 8

> clip off

> clip near -4

> clip far off

> clip far 7

> clip off

> clip near -4

> clip far off

> clip far 5

> clip off

> clip near -4

> clip far off

> clip far 2

> clip off

> clip near -4

> clip far off

> clip far 10

> clip off

> clip near -3

> clip far off

> clip far 10

> clip off

> clip near -2

> clip far off

> clip far 10

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v3.cxs

> turn x 10

> turn x -5

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 10

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 45

> zoom 0.64

moved plane near -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  
moved plane far -32.60933373051763 [-0.97227183 -0.15309311 -0.17677671]  

> clip off

> clip near -2

> clip far off

> clip far 10

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 50

> zoom 0.64

moved plane near -32.609333744187865 [-0.97627559 -0.19253937 -0.0990685 ]  
moved plane far -32.609333744187865 [-0.97627559 -0.19253937 -0.0990685 ]  

> clip off

> clip near -2

> clip far off

> clip far 10

> vview orient; view ligand1; turn z 60; turn x 30; turn y -30; turn x 40;
> zoom 0.64

Unknown command: vview orient; view ligand1; turn z 60; turn x 30; turn y -30;
turn x 40; zoom 0.64  

> clip off

> clip near -2

> clip far off

> clip far 10

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 10

> clip off

> clip near -2

> clip far off

> clip far 8

> clip off

> clip near -2

> clip far off

> clip far 7

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v3.cxs

> color #6 blue

> show #!6 models

> volume #6 step 1

> volume #6 level 0.3232

> volume style mesh

> surfaceSmoothing

Unknown command: surfaceSmoothing  

> surfaceSmoothing true

Unknown command: surfaceSmoothing true  

> surfaceSmoothing False

Unknown command: surfaceSmoothing False  

> volume surfaceSmoothing false

> volume #6 surfaceSmoothing false

> volume #6 surfaceSmoothing true

[Repeated 1 time(s)]

> volume #6 subdivisionLevels 2

> volume #6 surfaceSmoothing true

> volume #6 subdivisionLevels 3

> volume #6 surfaceSmoothing false

> volume #6 subdivisionLevels 3

> volume #6 surfaceSmoothing false

> volume #6 subdivisionLevels 2

> volume #6 surfaceSmoothing false

> volume #6 subdivisionLevels 1

> volume #6 surfaceSmoothing false

> volume #6 subdivisionLevels 1 squareMesh true

> volume #6 surfaceSmoothing true subdivisionLevels 1 squareMesh true

> volume #6 surfaceSmoothing true subdivisionLevels 2 squareMesh true

> volume #6 surfaceSmoothing true subdivisionLevels 2 squareMesh true
> subdivideSurface true

> volume #6 surfaceSmoothing true subdivisionLevels 1 squareMesh true
> subdivideSurface true

> volume step 1

> volume step 2

> volume step 1

> volume #6 surfaceSmoothing true subdivisionLevels 2 squareMesh true
> subdivideSurface true

> volume #6 surfaceSmoothing true subdivideSurface true subdivisionLevels 2
> squareMesh true

> show #!6 models

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> volume #6 surfaceSmoothing true subdivideSurface true subdivisionLevels 2
> squareMesh false

> volume #6 surfaceSmoothing true subdivideSurface true subdivisionLevels 1
> squareMesh false

> graphics silhouettes true

> graphics silhouettes false

> volume #6 surfaceSmoothing false subdivideSurface true subdivisionLevels 1
> squareMesh false

> volume #6 surfaceSmoothing true subdivideSurface true subdivisionLevels 1
> squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 2 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 3 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 7 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false

> volume #6 level 0.2868

> color #6 #1a5fb4ff models

> color #6 #3584e4ff models

> color #6 #4065bfff models

> color #6 #4062bfff models

> color #6 #4089bfff models

> color #6 #4048bfff models

> color #6 steelblue models

> color #6 #004ad4ff models

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels1 squareMesh false

Expected a keyword  

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels1 squareMesh false

Expected a keyword  

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevelsv1 squareMesh false

Expected a keyword  

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false smoothLines true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false smoothLines false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines true
> |

Expected a keyword  

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines false

[Repeated 1 time(s)]

> transparency #6 1

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines false

> transparency #6 0.2

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines false

> transparency #6 0

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency false smoothLines false

> transparency #6 0.2

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency true smoothLines false

> transparency #6 0.2

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false dimTransparency true smoothLines false

> transparency #6 0.8

> transparency

Missing or invalid "percent" argument: Expected a number  

> transparency #6

Missing or invalid "percent" argument: Expected a number  

> transparency #6 1

> transparency #6 0.2

> transparency #6 0

[Repeated 1 time(s)]

> volume #6 dimTransparency true

> transparency #6 0.9

> volume #6 dimTransparency true

> transparency #6 0.9

> volume #6 dimTransparency false

> transparency #6 0.9

> volume #6 dimTransparency true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false smoothLines false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false twoSidedLighting
> true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false twoSidedLighting
> false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting true twoSidedLighting
> false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting true twoSidedLighting true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false

> transparency 0

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false capFaces true

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 2 squareMesh false meshLighting false capFaces false

> volume #6 surfaceSmoothing true smoothingIterations 5 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting false capFaces false

> volume #6 surfaceSmoothing true smoothingIterations 10 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting false capFaces false

> hide #!6 models

> show #!6 models

> volume #6 level 0.2686

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 7

> clip front 1

> clip front 2

> clip front -2

> clip front -1

[Repeated 1 time(s)]

> clip back off

> clip back 1

> clip front -1

> clip back off

> clip back 5

> clip front -1

> clip back off

> clip back 7

> clip off

> clip near -2

> clip far off

> clip far 7

> clip off

> clip near -2

> clip far off

> clip far 7

> clip off

> clip near -2

> clip far off

> clip far 8

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 7

> clip off

> clip near -2

> clip far off

> clip far 7

> clip front off

> clip front 1

> clip off

> clip near -2

> clip far off

> clip far 7

> clip front off

> clip front 5

> clip off

> clip near -2

> clip far off

> clip far 7

> clip front off

> clip front -1

> clip off

> clip near -2

> clip far off

> clip far 7

> clip front off

> clip front -2

> help clip

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 7

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 7

> clip model #6 near 1

Expected true or false or a keyword  

> clip off

> clip near -2

> clip far off

> clip far 7

> clip model #6 true

> clip off

> clip near -2

> clip far off

> clip far 7

> clip model #6 false

> help clip

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -2

> clip far off

> clip far 7

> volume #6 surfaceSmoothing true smoothingIterations 10 subdivideSurface true
> subdivisionLevels 1 squareMesh false meshLighting false

> clip off

> clip near -2

> clip far off

> clip far 9

> clip off

> clip near -2

> clip far off

> clip far 7

> clip off

> clip near -2

> clip far off

> clip far 7

> color #6 #192e54ff models

> color #6 #0038a1ff models

> clip off

> clip near -2

> clip far off

> clip far 7

> clip off

> clip near -2.5

> clip far off

> clip far 7

> clip off

> clip near -1.8 clip far off; clip far 7;

Expected a keyword  

> clip off

> clip near -1.8

> clip far off

> clip far 7

> clip off

> clip near -1.7

> clip far off

> clip far 7

> clip off

> clip near -1

> clip far off

> clip far 7

> clip off

> clip near -1.3

> clip far off

> clip far 7

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -1.3

> clip far off

> clip far 7

> volume #6 level 0.2503

> volume #6 level 0.2276

> volume #6 level 0.1957

> volume #6 level 0.1729

> volume #6 level 0.09551

> clip off

> clip near -1.3

> clip far off

> clip far 8

> volume #6 style mesh color #0038A1 surfaceSmoothing true smoothingIterations
> 10 subdivideSurface true subdivisionLevels 1 squareMesh false meshLighting
> false

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -1.3

> clip far off

> clip far 7

> clip off

> clip near -1.3

> clip far off

> clip far 8

> clip off

> clip near -0

> clip far off

> clip far 8

> clip off

> clip near -1

> clip far off

> clip far 8

> clip off

> clip near -0.5

> clip far off

> clip far 8

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v3.cxs

> volume step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> volume step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v3.cxs

> close session

> open /home/agonzalez/Desktop/PROJECTS/CPN20/CPN20-Toxoplasma-Football-
> waters-8_deleted.pdb

Chain information for CPN20-Toxoplasma-Football-waters-8_deleted.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 10

Selected 553 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

586 atoms, 29 bonds, 2 pseudobonds, 115 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> volume #2 level 0.22

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.22 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> select clear

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.22 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> select clear

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> show sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select add @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> color :HOH red

> style sel sphere

Changed 84 atom styles  

> show sel

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.22 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> select clear

> name ame list

"list": invalid atom specifier  

> name list

ligand1 [33 atoms, 58 bonds, 2 models]  
ligand_all [462 atoms, 812 bonds, 2 models]  

> ligand1

Unknown command: ligand1  

> select ligand1

33 atoms, 29 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> show sel

> clip off

> clip near -0.5

> clip far off

> clip far 8

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> clip off

> clip near -2

> clip far off

> clip far 8

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> clip off

> clip near -0.5

> clip far off

> clip far 8

> view list

No named views.  

> view ligand1

> zoom 0.64

moved plane near -38.418270769065096 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -38.418270769065096 [-0.96086849 -0.11248171 -0.25313954]  

> zoom 0.7

moved plane near -45.7360367782975 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -45.7360367782975 [-0.96086849 -0.11248171 -0.25313954]  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> clip help

Expected a keyword  

> help clip

> clip off

> clip position ligand1

> clip near -0.5

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip position ligand1

> clip near -10

> clip far 10

> clip off

> clip position ligand1

> clip near -0

> clip far 10

> clip off

> clip position ligand1

> clip off

> clip position ligand1 near 10

> clip off

> clip position ligand1 near 0

> clip off

> clip position ligand1 near 0 far 9o

Invalid "far" argument: Expected 'off' or a number  

> clip off

> clip position ligand1 near 0 far 0

clip far plane is in front of near plane  

> clip off

> clip position ligand1 near 0 far 10

> clip off

> clip position ligand1 near -5 far 10

> clip off

> clip position ligand1 near -5 far 5

> select clear

> volume #2 level 0.3248

> volume #2 level 0.3824

> volume #2 level 0.4086

> volume #2 level 0.4505

> view camera matrix

Expected an objects specifier or a view name or a keyword  

> view matrix camera

Missing "camera" keyword's argument  

> view matrix

view matrix camera
0.15856,-0.076441,0.98439,343.5,-0.92284,0.34298,0.17528,226.16,-0.35102,-0.93623,-0.016162,281.78  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> view matrix

view matrix camera
0.21651,0.17279,0.96087,341.55,-0.875,0.47087,0.11248,220.96,-0.43301,-0.86511,0.25314,304.08  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> turn y 1'

Expected a number or a keyword  

> turn y 10

> turn y -10

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -5

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> select ligand1

33 atoms, 29 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> cofr sel

> cofr ligand1

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -20

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip front off

> select clear

> cofr ligand1

> cofr view orient; view ligand1;cofr ligand1; turn z 60; turn x 30; turn y
> -30; turn x 40; zoom 0.7;turn y -10

Expected some numbers or a keyword  

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1

> clip near -2

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -5

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip back off

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -5

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -5

> clip far off

> clip far 0

> clip front off

> clip off

> clip position ligand1

> clip near -5

> clip far off

> clip far 3

> clip front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -15

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -20

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -20

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -26

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -25

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip off

> clip position ligand1

> clip near -10

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -20

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -15

> clip far off

> clip far 8

> clip front off

> clip off

> clip position ligand1

> clip near -15

> clip far off

> clip far 0

> clip front off

> help clip

> clip off

> clip position liugand1 near -10 far 8 front off;

Invalid "position" argument: Expected 3 floats or object specifier  

> clip off

> clip position ligand1 near -10 far 8 front off

> clip off

> clip position ligand1 near -8 far 8 front off

> clip off

> clip position ligand1 near -5 far 8 front off

> clip off

> clip position ligand1 near -4 far 8 front off

> clip off

> clip position ligand1 near -4 far 4 front off

> clip off

> clip position ligand1 near -3 far 4 front off

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -28

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -28

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -20

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -20

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -18

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -18

> clip off

> clip position ligand1 near -2.5 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -18

> clip off

> clip position ligand1 near -2.8 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -18

> clip off

> clip position ligand1 near -2.6 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -18

> clip off

> clip position ligand1 near -2.5 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -15

> clip off

> clip position ligand1 near -2.5 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -15

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -12

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -3 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -3.2 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -3.6 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -5 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip off

> clip position ligand1 near -4 far 6 front off

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v4.cxs

> volume #2 level 0.4348

> volume #2 level 0.3824

> volume #2 level 0.25

> view matrix

view matrix camera
0.046364,0.17279,0.98387,343.46,-0.88124,0.47087,-0.041169,208.24,-0.47039,-0.86511,0.1741,297.54  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view camera matrix
> 0.046364,0.17279,0.98387,343.46,-0.88124,0.47087,-0.041169,208.24,-0.47039,-0.86511,0.1741,297.54

Expected an objects specifier or a view name or a keyword  

> view camera
> 0.046364,0.17279,0.98387,343.46,-0.88124,0.47087,-0.041169,208.24,-0.47039,-0.86511,0.1741,297.54

Expected an objects specifier or a view name or a keyword  

> view matrix
> 0.046364,0.17279,0.98387,343.46,-0.88124,0.47087,-0.041169,208.24,-0.47039,-0.86511,0.1741,297.54

Expected a keyword  

> help camera

> view orient

[Repeated 1 time(s)]

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> volume #2 level 0.22

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> volume #2 level 0.33

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> volume #2 level 0.5553

> volume #2 level 0.4505

> volume #2 level 0.461

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -23

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 near -4 far 6 front off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 near -4 far 6 front off

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v5.cxs

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1 squareMesh
> false meshLighting false

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_NBS-v5.cxs

> show :HOH

> select :HOH

67 atoms, 67 residues, 1 model selected  

> style sel sphere

Changed 67 atom styles  

> style sel ball

Changed 67 atom styles  

> style sel stick

Changed 67 atom styles  

> style sel ball

Changed 67 atom styles  

> style :HOH ball

Changed 67 atom styles  

> close session

> open /home/agonzalez/Desktop/PROJECTS/CPN20/CPN20-Toxoplasma-Football-
> waters-8_deleted.pdb

Chain information for CPN20-Toxoplasma-Football-waters-8_deleted.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 67 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> clip position ligand1 near -5 far 6 front off

> clip position ligand1 near -4 far 6 front off

> clip position ligand1 near -4 far 6 front off back off

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_Toxo_NBS.cxs

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Plasmodium_Football/CPN20-Plasmodium-
> Football.pdb

Chain information for CPN20-Plasmodium-Football.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Plasmodium_Football/cryosparc_P72_J362_Plas-
> Football-DeepEM.mrc

Opened cryosparc_P72_J362_Plas-Football-DeepEM.mrc as #2, grid size
648,648,648, pixel 0.824, shown at step 1, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 56 residues, 1 model selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 42 residues, 1 model selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 4 residues, 1 model selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1259 atoms  

> show sel cartoons

> select add ligand1

1292 atoms, 29 bonds, 207 residues, 1 model selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -20.80129482069199 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -20.80129482069199 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 56 residues, 1 model selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 42 residues, 1 model selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 4 residues, 1 model selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1259 atoms  

> show sel cartoons

> select add ligand1

1292 atoms, 29 bonds, 207 residues, 1 model selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -20.80129482069199 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -20.80129482069199 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> help clip

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football.pdb
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Chain information for CPN20-Toxoplasma-Football.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  
Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

Invalid "position" argument: Expected 3 floats or object specifier  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1234 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1267 atoms, 29 bonds, 2 pseudobonds, 206 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> clip off

> clip near -0.5

> clip far off

> clip far 8

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football.pdb
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Chain information for CPN20-Toxoplasma-Football.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  
Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1234 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1267 atoms, 29 bonds, 2 pseudobonds, 206 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.7

moved plane near -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -24.845206643779882 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.64

moved plane near -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -32.60933371996108 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.73

moved plane near -21.441753678878523 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -21.441753678878523 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1234 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1267 atoms, 29 bonds, 2 pseudobonds, 206 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football.pdb
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Chain information for CPN20-Toxoplasma-Football.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  
Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 0 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1234 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1267 atoms, 29 bonds, 2 pseudobonds, 206 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> select ligand

378 atoms, 406 bonds, 14 residues, 1 model selected  

> force i in #1/

force is provided by the uninstalled bundle SEQCROW versions 1.5.4 – 1.6.1  

> close session

> open /home/agonzalez/Desktop/PROJECTS/CPN20/CPN20-Toxoplasma-Football-
> waters-8_deleted.pdb

Chain information for CPN20-Toxoplasma-Football-waters-8_deleted.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> hide

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> help select

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add zone sel 5

Expected an objects specifier or a keyword  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add select zone sel 5

Expected an objects specifier or a keyword  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add zone sel 5.

Expected an objects specifier or a keyword  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add zone sel 5.

Expected an objects specifier or a keyword  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select add zone sel 5

Expected an objects specifier or a keyword  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select zone sel 5

Selected 227 atoms  

> select /A:ADP

39 atoms, 41 bonds, 1 residue, 1 model selected  

> select zone sel 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> show sel

> select up

7881 atoms, 7905 bonds, 528 residues, 1 model selected  

> select zone /A:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> select zone /A:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /A

Chain IDs of 3 residues changed  

> select zone /B:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /B

Chain IDs of 3 residues changed  

> select zone /C:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /C

Chain IDs of 3 residues changed  

> select zone /D:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /D

Chain IDs of 3 residues changed  

> select zone /E:ADP 5

Selected 225 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /E

Chain IDs of 3 residues changed  

> select zone /F:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /F

Chain IDs of 3 residues changed  

> select zone /G:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /G

Chain IDs of 3 residues changed  

> select zone /A:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /A

Chain IDs of 0 residues changed  

> select zone /B:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /B

Chain IDs of 0 residues changed  

> select zone /C:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /C

Chain IDs of 0 residues changed  

> select zone /D:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /D

Chain IDs of 0 residues changed  

> select zone /E:ADP 5

Selected 225 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /E

Chain IDs of 0 residues changed  

> select zone /F:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /F

Chain IDs of 0 residues changed  

> select zone /G:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /G

Chain IDs of 0 residues changed  

> select zone /H:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /H

Chain IDs of 3 residues changed  

> select zone /I:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /I

Chain IDs of 3 residues changed  

> select zone /J:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /J

Chain IDs of 3 residues changed  

> select zone /K:ADP 5

Selected 222 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /K

Chain IDs of 3 residues changed  

> select zone /L:ADP 5

Selected 223 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /L

Chain IDs of 3 residues changed  

> select zone /M:ADP 5

Selected 225 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /M

Chain IDs of 3 residues changed  

> select zone /N:ADP 5

Selected 222 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel /N

Chain IDs of 3 residues changed  

> show K

> hide

> show :600-605

> hide

> show /A:600-605

> ui tool show "Change Chain IDs"

> select zone /A:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel A

Chain IDs of 3 residues changed  

> select zone /B:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel B

Chain IDs of 3 residues changed  

> select zone /C:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel C

Chain IDs of 3 residues changed  

> select zone /D:ADP 5

Selected 227 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel D

Chain IDs of 3 residues changed  

> select zone /E:ADP 5

Selected 225 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel E

Chain IDs of 3 residues changed  

> select zone /F:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel F

Chain IDs of 3 residues changed  

> select zone /G:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel G

Chain IDs of 3 residues changed  

> select zone /H:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel H

Chain IDs of 3 residues changed  

> select zone /I:ADP 5

Selected 224 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel I

Chain IDs of 3 residues changed  

> select zone /J:ADP 5

Selected 226 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel J

Chain IDs of 3 residues changed  

> select zone /K:ADP 5

Selected 222 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel K

Chain IDs of 3 residues changed  

> select zone /L:ADP 5

Selected 223 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel L

Chain IDs of 3 residues changed  

> select zone /M:ADP 5

Selected 225 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel M

Chain IDs of 3 residues changed  

> select zone /N:ADP 5

Selected 222 atoms  

> select subtract ~@K,Mg,Be,F1,F2,F3

6 atoms, 3 residues, 1 model selected  

> changechains sel N

Chain IDs of 3 residues changed  

> show /A:600++

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show /A:600+

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show /A:600-605

> save
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football_waters8.pdb relModel #1

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football_waters8.pdb
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J807_Toxo-
> Football-DeepEM.mrc

Chain information for CPN20-Toxoplasma-Football_waters8.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  
Opened cryosparc_P36_J807_Toxo-Football-DeepEM.mrc as #2, grid size
640,640,640, pixel 0.824, shown at level 0.000684, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 67 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> volume #2 level 0.1878

> select pseudobonds

Expected an objects specifier or a keyword  

> select pseudobond

Expected an objects specifier or a keyword  

> select p

Expected an objects specifier or a keyword  

> select add

65329 atoms, 65776 bonds, 27 pseudobonds, 8859 residues, 5 models selected  

> select clear

> hide #!2 models

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> lighting full

[Repeated 1 time(s)]

> lighting shadows false

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> graphics silhouettes false

> lighting shadows false

> graphics silhouettes true

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> show sel

> style sel stick

Changed 123 atom styles  

> color sel byhetero

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -5 far 6 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -10 far 6 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 6 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 8 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 10 front off back
> off

> select clear

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> select up

194 atoms, 181 bonds, 32 residues, 2 models selected  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> select up

194 atoms, 181 bonds, 32 residues, 2 models selected  

> show

> style sel stick

Changed 194 atom styles  

> color sel byhetero

> hide sel atoms

> select clear

> hide atoms

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> show

> style sel stick

Changed 123 atom styles  

> color sel byhetero

> hide sel atoms

> hide sel cartoons

> select clear

> hide atoms

> hide cartoons

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> show sel

> style sel stick

Changed 123 atom styles  

> color sel byhetero

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH ball

Changed 67 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1238 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1271 atoms, 29 bonds, 2 pseudobonds, 210 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> show sel

> style sel stick

Changed 123 atom styles  

> color sel byhetero

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> select up

194 atoms, 181 bonds, 32 residues, 2 models selected  

> show sel

> style sel stick

Changed 194 atom styles  

> color sel byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 5

Selected 123 atoms, 1 surfaces  

> select up

194 atoms, 181 bonds, 32 residues, 2 models selected  

> show sel

> show ligand1

> style sel stick

Changed 194 atom styles  

> color sel byhetero

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4.5

Selected 92 atoms, 1 surfaces  

> select up

185 atoms, 172 bonds, 30 residues, 2 models selected  

> show sel

> show ligand1

> style sel stick

Changed 185 atom styles  

> color sel byhetero

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 65 atoms, 1 surfaces  

> select up

161 atoms, 150 bonds, 26 residues, 2 models selected  

> show sel

> show ligand1

> style sel stick

Changed 161 atom styles  

> color sel byhetero

> select clear

> select add ligand1

33 atoms, 29 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> select add :HOH

100 atoms, 29 bonds, 2 pseudobonds, 71 residues, 2 models selected  

> select zone ligand1 :HOH 5

Missing or invalid "range" argument: Expected a number  

> select zone ligand1 5 :HOH

Selected 3 atoms  

> select zone ligand1 20 :HOH

Selected 4 atoms  

> show

> hide

> select zone ligand1 20 :HOH

Selected 4 atoms  

> show sel

> show ligand1

> :HOH ball;color :HOH red;

Unknown command: :HOH ball;color :HOH red;  

> style :HOH ball

Changed 67 atom styles  

> color :HOH red

> style sel ball

Changed 4 atom styles  

> style sel stick

Changed 4 atom styles  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 65 atoms, 1 surfaces  

> select up

161 atoms, 150 bonds, 26 residues, 2 models selected  

> show sel

> show ligand1

> style sel stick

Changed 161 atom styles  

> color sel byhetero

> hide cartoons

> hide

> select zone ligand1 3.5

Selected 31 atoms, 1 surfaces  

> select up

105 atoms, 96 bonds, 19 residues, 2 models selected  

> show sel

> show ligand1

> style sel stick

Changed 105 atom styles  

> color sel byhetero

> select zone ligand1 4

Selected 65 atoms, 1 surfaces  

> select up

161 atoms, 150 bonds, 26 residues, 2 models selected  

> show sel

> show ligand1

> show :HOH

> close session

> open
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/CPN20-Toxoplasma-
> Football_waters675.pdb
> /home/agonzalez/Desktop/PROJECTS/CPN20/Modelo_Final/CPN20-Toxoplasma_Football/cryosparc_P36_J801_Toxo-
> Football.mrc

Chain information for CPN20-Toxoplasma-Football_waters675.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
a b c e f g | No description available  
d h | No description available  
  
Opened cryosparc_P36_J801_Toxo-Football.mrc as #2, grid size 640,640,640,
pixel 0.824, shown at level 0.0943, step 4, values float32  

> set bgColor white

> hide

> select clear

> delete H

> lighting full

> lighting shadows false

> graphics silhouettes false

> select clear

> select add :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> select add @K,Mg,BE,F1,F2,F3

462 atoms, 406 bonds, 8 pseudobonds, 56 residues, 2 models selected  

> name frozen ligand_all sel

> select clear

> color ~ligand_all cornflower blue

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH stick

Changed 364 atom styles  

> color :HOH red

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1258 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1291 atoms, 29 bonds, 2 pseudobonds, 230 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 3 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 4 models selected  

> show sel

> show ligand1

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select clear

> clip position ligand1 coordinateSystem ligand1 near -8 far 8 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select clear

> select /C:478@CD1

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

36 atoms, 37 bonds, 4 residues, 1 model selected  

> select up

3856 atoms, 3884 bonds, 524 residues, 1 model selected  

> select down

36 atoms, 37 bonds, 4 residues, 1 model selected  

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> ui tool show Distances

> select /C:602@N6

1 atom, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross resSeparation 5 ignoreHiddenModels true
> makePseudobonds false

4 contacts  

> contacts sel restrict cross resSeparation 5 ignoreHiddenModels true

4 contacts  

> select clear

> select /C:478@O

1 atom, 1 residue, 1 model selected  

> select clear

> select /C:478@O

1 atom, 1 residue, 1 model selected  

> contacts sel restrict cross resSeparation 5 ignoreHiddenModels true

2 contacts  

> select add /C:602@C2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> select /C:602@C2

1 atom, 1 residue, 1 model selected  

> select clear

> select /C:478@O

1 atom, 1 residue, 1 model selected  

> select add /C:602@C2

2 atoms, 2 residues, 1 model selected  

> distance /C:478@O /C:602@C2

Distance between /C TYR 478 O and ADP 602 C2: 3.581Å  

> select zone ligand1 3.5

Selected 35 atoms, 2 surfaces  

> select up

109 atoms, 96 bonds, 23 residues, 3 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 109 atom styles  

> color sel byhetero

> select clear

> hide cartoons

> hide

> select zone ligand1 3.55

Selected 39 atoms, 2 surfaces  

> select up

109 atoms, 96 bonds, 23 residues, 3 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 109 atom styles  

> color sel byhetero

> select clear

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 182 atom styles  

> color sel byhetero

> select clear

> select clear

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH stick

Changed 364 atom styles  

> color :HOH red

> select clear

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 2 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 3 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 4 models selected  

> name frozen ligand_full sel

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -15.768421084932978 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -15.768421084932978 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide #3.1 models

> show #3.1 models

> hide cartoons

> hide

> select zone ligand1 3.5

Selected 35 atoms, 2 surfaces  

> select up

109 atoms, 96 bonds, 23 residues, 3 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 109 atom styles  

> color sel byhetero

> select add ligand1

142 atoms, 125 bonds, 2 pseudobonds, 27 residues, 4 models selected  

> name frozen ligand_full sel

> show sel

> hide cartoons

> hide

> select zone ligand1 3.55

Selected 39 atoms, 1 surfaces  

> select up

109 atoms, 96 bonds, 23 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 109 atom styles  

> color sel byhetero

> select add ligand1

142 atoms, 125 bonds, 2 pseudobonds, 27 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> select clear

> select /C:33@CB

1 atom, 1 residue, 1 model selected  

> select /C:602@C4

1 atom, 1 residue, 1 model selected  

> select add /C:33@CB

2 atoms, 2 residues, 1 model selected  

> distance /C:602@C4 /C:33@CB

Distance between /C ADP 602 C4 and PRO 33 CB: 4.831Å  

> select add /C:602@N7

3 atoms, 2 residues, 1 model selected  

> select clear

> select /C:602@N7

1 atom, 1 residue, 1 model selected  

> select add /C:33@CB

2 atoms, 2 residues, 1 model selected  

> distance /C:602@N7 /C:33@CB

Distance between /C ADP 602 N7 and PRO 33 CB: 3.955Å  

> select clear

> close #3

> close #1.3

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross resSeparation 5 ignoreHiddenModels true

74 contacts  

> close #1.3

> hide cartoons

> hide

> select zone ligand1 5

Selected 128 atoms, 1 surfaces  

> select up

199 atoms, 181 bonds, 37 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 199 atom styles  

> color sel byhetero

> select add ligand1

232 atoms, 210 bonds, 2 pseudobonds, 41 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> select /C:601@K

1 atom, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross resSeparation 5 ignoreHiddenModels true

2 contacts  

> close #1.3

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #f9f06b restrict cross

18 hydrogen bonds found  

> hbonds sel color #ffdf00 restrict cross

18 hydrogen bonds found  

> hbonds sel color #ffdf00 restrict cross

18 hydrogen bonds found  

> hbonds sel color #dc8add restrict cross

18 hydrogen bonds found  

> hbonds sel color #ffdf00 restrict cross

18 hydrogen bonds found  

> hbonds sel color #ffe700 restrict cross

18 hydrogen bonds found  

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting simple

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select up

3889 atoms, 3913 bonds, 528 residues, 1 model selected  

> select down

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C:600@MG

28 atoms, 29 bonds, 2 residues, 1 model selected  

> select add /C:603@F2

29 atoms, 29 bonds, 3 residues, 1 model selected  

> select add /C:603@BE

30 atoms, 29 bonds, 3 residues, 1 model selected  

> select add /C:603@F3

31 atoms, 29 bonds, 3 residues, 1 model selected  

> select add /C:603@F1

32 atoms, 29 bonds, 3 residues, 1 model selected  

> select add /C:601@K

33 atoms, 29 bonds, 4 residues, 1 model selected  

> hbonds sel color #ffe700 restrict cross

18 hydrogen bonds found  

> hbonds sel color #ffe700

18 hydrogen bonds found  

> ui tool show "Check Waters"

> hbonds /P interModel false reveal true restrict any name "water H-bonds"

828 hydrogen bonds found  

> show #2 models

> select /P

364 atoms, 101 pseudobonds, 364 residues, 2 models selected  

> display /P :<4

> view /P @<4

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> color #1.4 #ffe700ff models

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> select ligand1

33 atoms, 29 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> select subtract /C:603@F2

32 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

149 atoms, 136 bonds, 28 residues, 2 models selected  

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> color Mg #A6FC4E atoms

> color K #8444CC atoms

> color F #74FAFD atoms

> color Be #F9D848 atoms

> size Mg atomRadius 0.57

Changed 14 atom radii  

> size K atomRadius 0.9

Changed 14 atom radii  

> size F atomRadius 0.5

Changed 42 atom radii  

> size Be atomRadius 0.57

Changed 14 atom radii  

> select @K,Mg,Be,F1,F2,F3

84 atoms, 8 pseudobonds, 42 residues, 2 models selected  

> style sel sphere

Changed 84 atom styles  

> show sel

> style :HOH stick

Changed 364 atom styles  

> color :HOH red

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

149 atoms, 136 bonds, 28 residues, 2 models selected  

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> color #1.4 #c061cbff models

> color #1.4 #f9f06bff models

> color #1.4 #ffe700ff models

Drag select of 170 atoms, 35 pseudobonds, 152 bonds  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

149 atoms, 136 bonds, 28 residues, 2 models selected  

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off .

Expected a keyword  

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 3.8

Selected 60 atoms, 1 surfaces  

> select up

149 atoms, 136 bonds, 28 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

149 atoms, 136 bonds, 28 residues, 2 models selected  

> style sel stick

Changed 149 atom styles  

> color sel byhetero

> select add ligand1

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> close #1.3-4

> name list

ligand1 [33 atoms, 58 bonds, 2 models]  
ligand_all [462 atoms, 812 bonds, 2 models]  
ligand_full [182 atoms, 330 bonds, 3 models]  
ligand_zone [149 atoms, 272 bonds, 2 models]  

> select ligand_full

182 atoms, 165 bonds, 2 pseudobonds, 32 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel color #ffe700 restrict both

32 hydrogen bonds found  

> select clear

> save /home/agonzalez/Desktop/image1.png supersample 3

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x 10

> turn x -10

[Repeated 3 time(s)]

> turn x 10

> turn y 10

> turn y -10

[Repeated 2 time(s)]

> turn y 10

[Repeated 2 time(s)]

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hbonds sel color #ffe700 restrict both

Atom specifier selects no atoms  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> select /P:301@O

1 atom, 1 residue, 1 model selected  
Drag select of 186 atoms, 34 pseudobonds, 166 bonds  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> select clear

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn y

[Repeated 3 time(s)]

> turn y 10

[Repeated 1 time(s)]

> turn y -10

[Repeated 1 time(s)]

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x 30

> turn y -10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x 30

[Repeated 1 time(s)]

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -10

> turn y 10

[Repeated 1 time(s)]

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn y 5

> turn x 5

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -25

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -25

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -25

> turn y 10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -25

> turn y 5

> select clear

Drag select of 186 atoms, 35 pseudobonds, 166 bonds  

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 10

> turn x 10

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 5

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 5

> turn x 10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 5

> turn x 10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 5

> turn x 20

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y 5

> turn x 10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 10

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 15 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 20 front off back
> off

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> select clear

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

[Repeated 1 time(s)]

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

[Repeated 1 time(s)]

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1258 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1291 atoms, 29 bonds, 2 pseudobonds, 230 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> show #!2 models

> hide #!2 models

> hide #1.3 models

> show #!2 models

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1258 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1291 atoms, 29 bonds, 2 pseudobonds, 230 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> graphics silhouettes false

> hide

> hide cartoons

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1258 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1291 atoms, 29 bonds, 2 pseudobonds, 230 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> graphics silhouettes false

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 2
> meshLighting false

> select clear

> graphics silhouettes false

> volume #2 level 0.22

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> hide

> hide cartoons

> select clear

> select :ADP

378 atoms, 406 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 378 atom styles  

> show sel

> color sel byhetero

> select clear

> select add /C:ADP

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add /C@K,Mg,BE,F1,F2,F3

33 atoms, 29 bonds, 1 pseudobond, 4 residues, 2 models selected  

> name frozen ligand1 sel

> show sel

> select clear

> select zone ligand1 15

Selected 1258 atoms, 1 surfaces  

> show sel cartoons

> select add ligand1

1291 atoms, 29 bonds, 2 pseudobonds, 230 residues, 3 models selected  

> hide ~sel

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> clip position ligand1 coordinateSystem ligand1 near -4 far 6 front off back
> off

> volume #2 level 0.461 step 1 style mesh color #0038A1 surfaceSmoothing true
> smoothingIterations 10 subdivideSurface true subdivisionLevels 1
> meshLighting false

> select clear

> graphics silhouettes false

> hide #!2 models

> graphics silhouettes true

> lighting full

> lighting shadows false

> hide cartoons

> hide

> select zone ligand1 4

Selected 69 atoms, 1 surfaces  

> select up

165 atoms, 150 bonds, 30 residues, 2 models selected  

> name frozen ligand_zone sel

> show ligand_zone

> select subtract ligand1

165 atoms, 150 bonds, 30 residues, 2 models selected  

> style sel stick

Changed 165 atom styles  

> color sel byhetero

> select add ligand1

198 atoms, 179 bonds, 2 pseudobonds, 34 residues, 3 models selected  

> name frozen ligand_full sel

> show sel

> hide :478

> select clear

> select ligand_full

198 atoms, 179 bonds, 35 pseudobonds, 34 residues, 4 models selected  

> hbonds sel color #ffe700 restrict both

33 hydrogen bonds found  

> select clear

> view orient

> view ligand1

> cofr ligand1

> turn z 60

> turn x 30

> turn y -30

> turn x 40

> zoom 0.78

moved plane near -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  
moved plane far -16.351118902316667 [-0.96086849 -0.11248171 -0.25313954]  

> turn y -10

> turn x -30

> turn y -5

> turn x 5

> clip position ligand1 coordinateSystem ligand1 near -8 far 12 front off back
> off

> show #1.3 models

> save
> /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_Toxo_NBS_closeup.cxs

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_Toxo_NBS_close.cxs

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /home/agonzalez/Desktop/PROJECTS/CPN20/ChimeraX/CPN20_Toxo_NBS2.cxs

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 161, in _get_name  
return self._category  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 80, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbaae1ed60> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb77d02850> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x7fbb77c6a970>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbaae1ed60> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb77d02850> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x7fbb77c6a970>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 530.30.02
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.1 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700F
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        12Gi        15Gi       607Mi       4.7Gi        18Gi
	Swap:          476Gi       6.8Gi       470Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117 [GeForce GTX 1650] [10de:1f82] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:3fcb]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210312311
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0

[Eric Pettersen]

Something is referencing a dead pseuodbond group. Thought it might be "Contacts", but can't reproduce the problem.