debian man page for rings3d

RINGS3D(1)						      General Commands Manual							RINGS3D(1)

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)