RIBBON(1)

✨ RIBBON ✨

okay bestie, gather round, because this is the ribbon page from section 1 of the manual — the Raster3D molecular graphics package ribbon-drawer, and she is serving protein backbone realness 💅

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🎀 NAME 🎀

ribbon — Raster3D molecular graphics package ribbon-drawer

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🌸 SYNOPSIS 🌸

"ribbon" [-h] [-d[0123456]] pdbfile

or

"ribbon" [-h] -d[0123456] -     (to take PDB records from stdin)

So here's the vibe: ribbon reads a PDB coordinate file and spits out a file on stdout full of Raster3D descriptor records for a ribbon representation built out of a triangular mesh. And the file she makes? You can feed it straight to render, or you can smoosh it together with descriptor files from other Raster3D utilities. versatile icon ✨

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🦋 EXAMPLES 🦋

Wanna describe the entire protein chain as one single ribbon, colored all smooth from blue at the N-terminus to red at the C-terminus? say less:

ribbon -d2 protein.pdb | render > chain_picture.png

Wanna color a multi-chain protein with specific colors for each chain? obsessed:

cat chaincolors.pdb protein.pdb | ribbon -d5 - > chains.r3d

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💖 OPTIONS 💖

• -h — Suppress header records in output. So by default ribbon makes an output file that starts with header records containing a default set of scaling and processing options. The -h flag yeets those header records away so your output file has only triangle descriptors. This one's for when you're producing files that describe just part of a scene, and you're gonna combine them later with descriptor files from other programs. teamwork fr 🫶
• -d[0123456] — By default ribbon wants interactive input to pick ribbon parameters and coloring info. BUT. Five default coloring schemes are implemented, and you can select one as a command line option to completely bypass the interactive part. no cap:
  • -d or -d0 — same as -d2 below
  • -d1 — solid color ribbon (defaults to blue)
  • -d2 — shade from blue at N-terminus to red at C-terminus
  • -d3 — one surface of ribbon is blue, other surface is grey
  • -d4 — shade front surface from blue to red, back surface is grey
  • -d5 — color separate chains using successive color cards from input stream. Note that pattern matching on the color records is not done; colors are simply taken sequentially as new chains are encountered.
  • -d6 — Color by nearest CA atom as taken from the COLOUR records at the head of the input file

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🌈 DESCRIPTION 🌈

The input to ribbon is a single text file containing colour information [optional] plus atomic coordinates in PDB data bank format. Only CA and carbonyl O atom records are required — all other input atoms are just ignored, they're not the main character 💀

Ribbon parameters and colouring get specified interactively when the program runs. But keyboard interaction may be bypassed by selecting one of the default colouring schemes using the -d flag. A triangular mesh ribbon is output as Raster3D descriptor records. By default the output file contains a set of header records as required by the render program. And the header is constructed to include a TMAT matrix corresponding to the transformation matrix contained in file setup.matrix (if it exists), or to the Eulerian angles contained in file setup.angles (if it exists). it's giving configured ✨

ribbon produces a continuous smooth trace of the protein backbone. For more complicated representations of protein secondary structure it is better to use a different program, e.g. MOLSCRIPT, rather than ribbon. know your limits bestie, that's growth 🌱

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🧚 ENVIRONMENT 🧚

The files setup.matrix and setup.angles, if they exist, affect the header records produced by ribbon.

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⭐ SOURCE ⭐

anonymous ftp site:

ftp.bmsc.washington.edu

web URL:

http://www.bmsc.washington.edu/raster3d/raster3d.html

contact:

Ethan A Merritt
University of Washington, Seattle WA 98195
merritt@u.washington.edu

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👑 SEE ALSO 👑

MOLSCRIPT(l), render(l), rods(l), balls(l)

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💜 AUTHORS 💜

Original ribbon code written by Phil Evans for the CCP4 version of FRODO. Modification to describe solid ribbons as triangular mesh for Phong shading in Raster3D package by Ethan A Merritt.

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and that's the whole page, bestie 🎀 this was Raster3D, dated 8 May 1999, and it ate, no crumbs left. go make something gorgeous with your triangular mesh, you've got this 💖✨🦋