A secondary structure assignment was made based on H-bonding:
pdb-pro-pdb toxin.pdb toxin.ss
The *.ribbons file consists of only one filename:
ls toxin.ss > toxin.ribbons
This file was then edited to add a special color file, `protein.color'.
The *.coords file consists of only one filename:
ls toxin.pdb > toxin.coords
The *.model file was generated:
pdb-model toxin.pdb toxin.model
( edited the *.model file to change the menu name )
The *.atoms file will consist of two parts.
These are all created from a temporary file `tox.sph',
colored by residue with backbone atoms excluded:
pdb-res-sph -b 0 toxin.pdb tox.sph
1) create a file of SG atomic spheres:
grep sg tox.sph > toxin_sg.sph
2) create a file with only aromatic spheres:
touch toxin-arom.sph
foreach i ( F Y H W )
grep $i tox.sph >> toxin-arom.sph
end
Group atoms together:
ls toxin-arom.sph > toxin.atoms
ls toxin_sg.sph >> toxin.atoms
The model was displayed at this stage to color and
select the special `ribbon-bonds':
ribbons
( display the ribbon, open Ribbon Panel.
set Sequence Color = `seq',
set Print Select = `CB-bond', Print File => toxin_cb0.rcyl
set Print Select = `SG-bond', Print File => toxin_sg0.rcyl
Exit ribbons )
The *.bonds file will consist of three parts.
1) The disulphide bonds are set (all CYS form bridges in the toxin):
mv toxin_sg0.rcyl toxin_sg.rcyl
2) The ribbon-bonds to the aromatic residues are selected:
touch toxin_cb.sph
foreach i ( F Y H W )
grep $i toxin_cb0.rcyl >> toxin_cb.rcyl
end
3) The bonds in the aromatic side chains are calculated:
sph-bond toxin-arom.sph toxin-arom.cyl
Group bonds together:
ls toxin-arom.cyl > toxin.bonds
ls toxin_sg.rcyl >> toxin.bonds
ls toxin_cb.rcyl >> toxin.bonds
Create the solid aromatic ring polygons:
pdb-pro-ring toxin.pdb toxin-ring.tri
Create the *.polys file from this single set:
ls toxin-ring.tri > toxin.polys
The Atom Panel had the default settings except:
Sphere Radii = `0.30' ( for toxin_sg.sph )
Sphere Radii = `0.45' ( for toxin-arom.sph )
The image was saved.
-ps, this demo was used in the movie `Jurassic Park' (for about a second).