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).

Raster3D                                                                                              RINGS3D(1)