.ad l
.nh
.TH RINGS3D 1 "" "Raster3D"
.SH NAME

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

.SH SYNOPSIS

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

.PP
\fIrings3d\fP searches through a PDB file looking for residues containing
5- or 6-membered rings, then produces a Raster3D output file of ring-filling
triangles.

\fIrings3d\fP 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.
.PP
.SH EXAMPLES
.PP
render a DNA molecule with the bases filled in:
.PP
     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
.SH OPTIONS

.B "-bases"
.PP
Fills in purine and pyrimidine rings from A C G T U residues.

.B "-protein"
.PP
Fills in sidechain rings of HIS PHE TRP and TYR residues.

.B "-sugars"
.PP
[This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA
residues.

.SH BUGS
.B limited residue types
.PP
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.
.B crinkled planes
.PP
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.

.SH SOURCE
.B anonymous ftp site:	
 	ftp.bmsc.washington.edu
 
.B web URL:
 	http://www.bmsc.washington.edu/raster3d/raster3d.html

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

.SH SEE ALSO
Raster3D(l)
.PP
.SH AUTHORS

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