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PROGRAM:
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
[email protected]
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