Provided by: raster3d_3.0-2-3_amd64 bug

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.