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<title> rings3d - Raster3D package </title>
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<h1 align=center>RINGS3D</h1>
<h4>SYNOPSIS</h4>
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.
<pre>
rings3d [-bases] [-protein] [-sugars] < infile.pdb > outfile.r3d
</pre>
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.
<a href="r3d_example6.jpeg">
<img src="r3d_example6.gif" align=right></a>
<h4>EXAMPLES</h4>
render a DNA molecule with the bases filled in:
<pre>
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
</pre>
<h4>OPTIONS</h4>
<dl>
<dt><i>-bases</i>
<dd>Fills in purine and pyrimidine rings from A C G T U residues.
<dt><i>-protein</i>
<dd>Fills in sidechain rings of HIS PHE TRP and TYR residues.
<dt><i>-sugars</i>
<dd>[This is the default]
Fills in pyranose rings of GAL GLC NAG NGA MAN SIA residues.
</dl>
<h4>BUGS</h4>
<dl>
<dt>limited residue types
<dd>The database of residue types should be kept externally, so you
don't have to rebuild the program to add a new type.
<dd>There should be an option to search for ring systems in un-recognized
residue types.
<dt>crinkled planes
<dd>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.
</dl>
<h4>AUTHORS</h4>
Ethan A Merritt.
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