rings3d(1)

rings3d1

Produces a file of ring-filling triangles from a pdb file

Usage

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

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.

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
[email protected]

Releases

Unchanged in 7 releases since Debian 7 (Wheezy).

  1. 7–13

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.

This manual page was written by Nelson A. de Oliveira <[email protected]>, for the Debian project (but may be used by others).

From raster3d 3.0-7-2+b2 in Debian 13 (Trixie). Parsed by carta from the page's man source.