NAME

       ribbon - Raster3D molecular graphics package ribbon-drawer

SYNOPSIS

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

       Ribbon  reads  a PDB coordinate file and produces a file on stdout containing Raster3D descriptor records
       for a ribbon representation 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.

EXAMPLES

       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

OPTIONS

       -h

       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.

       -d[0123456]

       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  Color by nearest CA atom as taken from the COLOUR
            records at the head of the input file

DESCRIPTION

       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.

ENVIRONMENT

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

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

SEE ALSO

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

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.

Raster3D                                           8 May 1999                                          RIBBON(1)