A secondary structure assignment was made automatically:
pdb-nuc-ss trna.pdb trna.ss
This file was then edited by hand to add a code for the `domains' of the tRNA molecule.
The *.ribbons file consists of only one filename:
ls trna.ss > trna.ribbons
This file was then edited to add a special color file, `nucleic.color'.
The *.coords file consists of only one filename:
ls trna.pdb > trna.coords
This file was then edited to add the special `nucleic' key.
The *.model file file was created,
then edited to change the menu name:
pdb-model trna.pdb trna.model
The model was displayed at this stage to color and
select the special `base-attachment' bonds:
ribbons
( display the ribbon, open Ribbon Panel.
set Sequence Color = `dom',
set Print Select = `base-A', Print File => trna_ba0.rcyl
Exit ribbons )
This cylinder file was renamed:
mv trna_ba0.rcyl trna_ba.rcyl
Created white bonds to outline the bases:
pdb-range-sph -b 0 -h trna.pdb trna.bb
( range 1,77; color 7)
sph-bond trna.bb trna_base.cyl
The *.bonds file consists of two filenames:
ls trna_ba.rcyl > trna.bonds
ls trna_base.cyl >> trna.bonds
Create the solid aromatic ring polygons:
pdb-nuc-ring trna.pdb trna-ring.tri
Create the *.polys file from this single set:
ls trna-ring.tri > trna.polys
The complete nucleic acid model is now ready for display.
Adjusted the bond radii of the `trna_base.bond' list to 0.5. The image was saved from the Geom Panel.