---
name: "rings3d"
section: "1"
platform: "linux"
package: "raster3d"
version: "3.0-7-2+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/rings3d"
---

# rings3d(1)

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

## 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).