ribbons-demo -n dna

Data Files:

An ideal 24-base pair B-DNA model was provided by Robert Tan. This file was edited to produce two pdb files, one for each strand: `bdna_1.pdb' and `bdna_2.pdb'.

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.

Image File: $RIBBONS_HOME/rgb/dna.rgb

The model was displayed with default settings on the Ribbon Panel for everything except:
Sequence Color = `chain'
Chain Color = `11' ( bdna_1 )
Chain Color = `16' ( bdna_2 )
Ribbon Style = `Circle'
Ribbon Samples = `11'

The image was saved.

-ps, this was the demo used in the movie `Jurassic Park' (for about 2 seconds).


Ribbons User Manual / UAB-CBSE / carson@uab.edu