This is the command rings3d that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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