A secondary structure assignment was made automatically:
foreach i ( 1 2 )
pdb-nuc-ss bdna_$i.pdb bdna_$i.ss
end
The *.ribbons file consists of two filenames:
ls bdna_1.ss > dna.ribbons
ls bdna_2.ss >> dna.ribbons
This file was then edited to add a special color file, 'nucleic.color'.
The *.coords file consists of two filenames:
ls bdna_1.pdb > dna.coords
ls bdna_2.pdb >> dna.coords
This file was then edited to add the special 'nucleic' keys.
The *.model file file was created, then edited to change the menu name:
pdb-model dna.pdb dna.model
The model was displayed at this stage to color and
select the special 'base-Hydrogen bonding' bonds:
ribbons
( display the ribbon, open Ribbon Panel.
set Sequence Color = 'seq',
set Print Select = 'base-H', Print File = 'dna_bh0.rcyl'
Exit ribbons )
This cylinder file was renamed:
mv dna_bh0.rcyl dna_base.cyl
The *.bonds file consists of only one filename:
ls dna_base.cyl > dna.bonds
The complete double-stranded nucleic acid model is now ready for display.
The image was saved.
-ps, this was the demo used in the movie 'Jurassic Park' (for about 2 seconds).