ribbon is a preprocessor which prepares a simple ribbon representation of a protein backbone for the Raster3D molecular graphics package.

ribbon [-h] [-d[0123456]] pdbfile
or (to take PDB records from stdin)
ribbon [-h] -d[0123456] -
Ribbon reads a PDB coordinate file and produces a stream of Raster3D object descriptor records on stdout describing a ribbon constructed from a triangular mesh. The file produced by ribbon may be fed directly to render or it may be combined with descriptor files produced by other Raster3D utilities.


To describe a the entire protein chain as a single ribbon colored smoothly from blue at the N-terminus to red at the C-terminus:
ribbon -d2 protein.pdb | render > chain_picture.png
To color a multi-chain protein with specified colors for each chain:
cat chaincolors.pdb protein.pdb | ribbon -d5 - > chains.r3d


Suppress header records in output. By default ribbon will produce an output file which starts with header records containing a default set of scaling and processing options. The -h flag will suppress these header records so that the output file contains only triangle descriptors. This option is useful for producing files which describe only part of a scene, and which are to be later combined with descriptor files produced by other programs.
By default ribbon requires interactive input to select ribbon parameters and coloring information. Five default coloring schemes are implemented, however, and these may be selected as a command line option to bypass any interactive input.
-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 Take color from nearest CA atom using color match templates from the COLOUR records at the head of the input file.


The input to ribbon consists of a single text file containing colour information [optional] and atomic coordinates in PDB data bank format. Only CA and carbonyl O atom records are required; all other input atoms are ignored. Ribbon parameters and colouring specified interactively when the program is run. 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. 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). 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.


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


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.
Back to top Raster3D homepage