These results were obtained for ribonuclease by the following commands:
Get the PDB file
Type: setup ribbons
To make a single colored surface:
Make the binary *.vet polyhedral surface file by reading in the
atomic coordinates
Type: msroll -m pro.pdb -f 0.5 -t pro.vet
(msroll is part of the MSP)
Convert the MSP *.vet file to ribbons format
Type: vet-rib pro.vet pro.tri
Create *.model file
Type: pdb-model pro.pdb pro.model
To view the model
Type: ribbons -n pro
To get the surface colored as nearest atom:
Create spheres by 'residue type'
Type: pdb-res-sph -b 6 pro.pdb res.sph
where the backbone atoms are set to color 6
To color the surface by the nearest sphere
Type: sph-color-tri pro.tri res.sph > colored.tri
Rename the output file to pro.tri
Type: mv colored.tri pro.tri
To view the colored model
Type: ribbons -n pro
For making the ball and stick model of the peptide with RNS,
Get the peptide PDB file
Create the atomic atom-colored sphere file *.sph
Type: pdb-atom-sph pep.pdb pep.sph
To create the bond list file *.cyl from the PDB file
Type: pdb-bond pep.pdb pep.cyl
To link the files
Type: ls pep.sph > pro.atoms
Type : ls pep.cyl > pro.bonds
To view the final image
Type: ribbons -n pro