RINGS3D

SYNOPSIS

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

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.

AUTHORS

Ethan A Merritt.

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