man rigns3d (1): 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

        [email protected]

AUTHORS

Ethan A Merritt.

This manual page was written by Nelson A. de Oliveira <[email protected]>, for the Debian project (but may be used by others).