RINGS3D(1)

📦 version 3.0-8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 RINGS3D(1) — bestie edition 💖

okay so this is the General Commands Manual page for RINGS3D(1), and I'm about to make ring-filling triangles sound as iconic as they actually are. sit down, hydrate, let's go 🫶

✨ NAME ✨

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

not me pointing out that yes, the name up there is spelled rigns3d, exactly like that, no I will not be fixing it, that's literally what the page says 💅

🌈 SYNOPSIS 🌈

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

okay so what this actually does — rings3d goes on a little scavenger hunt through a PDB file looking for residues that contain 5-membered or 6-membered rings, and then it serves up a Raster3D output file full of ring-filling triangles. so demure, so cunt, so triangles ✨

here's the tea tho — rings3d matches residue types against an internal list of residue and atom names. so if a residue isn't on the list, it just will not be found, periodt. and if an atom has a non-standard name, it won't be recognized either. the list is the list, bestie 😭

🎀 EXAMPLES 🎀

render a DNA molecule with the bases filled in — the way this eats:

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

look at her go 🦋 piping, redirecting, rendering, living her best life.

💅 OPTIONS 💅

  • -bases — fills in purine and pyrimidine rings from A C G T U residues. the nucleic-acid girlies get their rings filled in, as they deserve 💜
  • -protein — fills in the sidechain rings of HIS PHE TRP and TYR residues. aromatic crew rise up 🔥
  • -sugars — [this is the default] fills in pyranose rings of GAL GLC NAG NGA MAN SIA residues. if you don't pass anything, this is the one you get, no cap 🍓

💀 BUGS 💀

limited residue types

ngl this one is lowkey annoying — the database of residue types should be kept externally, so you don't have to rebuild the program just to add a new type. and there should be an option to search for ring systems in un-recognized residue types. as it stands, neither of those things exist. sorry bestie 😭

crinkled planes

and another one — 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. honestly? character development 🌈

🌸 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) — go read that one too, it's giving family 💖

🧚 AUTHORS 🧚

Ethan A Merritt. — the main character, obviously ✨

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

and that's the whole page, bestie — brought to you by Raster3D, filed under RINGS3D(1), and yeah that's genuinely all the version-and-date info this page gives us, so we're running with it 💅🎀🦋

📦 where this page comes from