NAME

       rigns3d - produces a file of ring-filling triangles from a PDB file

SYNOPSIS

       rings3d [-bases] [-protein] [-sugars]  < infile.pdb > outfile.r3d

       rings3d searches through a PDB file looking for residues containing 5- or 6-membered
       rings, then produces a Raster3D output file of ring-filling triangles.

       rings3d matches residue types from an internal list of residue and atom names. It will
       fail to find residues not in its list, and fail to recognize atoms with non-standard
       names.

EXAMPLES

       render a DNA molecule with the bases filled in:

            cat $R3D_LIB/dna.colours dna.pdb | rods -radius 0.05 > temp.1
            rings3d -bases < dna.pdb > temp.2
            cat temp.1 temp.2 | render -tiff dna.tiff

OPTIONS

       -bases

       Fills in purine and pyrimidine rings from A C G T U residues.

       -protein

       Fills in sidechain rings of HIS PHE TRP and TYR residues.

       -sugars

       [This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA residues.

BUGS

       limited residue types

       The database of residue types should be kept externally, so you don't have to rebuild the
       program to add a new type.  There should be an option to search for ring systems in un-
       recognized residue types.  crinkled planes

       There should be an option to do a least-squares best plane through supposedly flat rings.
       Then again, seeing a crease in a "flat" ring may force people to consider whether their
       planarity restraints are tight enough.

SOURCE

       anonymous ftp site:
            ftp.bmsc.washington.edu

       web URL:
            http://www.bmsc.washington.edu/raster3d/raster3d.html

       contact:
            Ethan A Merritt
            Dept of Biological Structure Box 357742
            University of Washington, Seattle WA 98195
            merritt@u.washington.edu

SEE ALSO

       Raster3D(l)

AUTHORS

       Ethan A Merritt.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian
       project (but may be used by others).