NAME
balls - preprocessor for space-filling models in Raster3D molecular
graphics package
SYNOPSIS
balls [-h]
Balls reads a file describing atom colours and/or a PDB coordinate file
and produces a file containing Raster3D descriptor records for each
atom in the input file. The file produced by balls may be fed directly
to render or it may be combined with descriptor files produced by other
Raster3D utilities.
EXAMPLES
To describe a simple space-filling model coloured by residue type:
cat mycolours.pdb protein.pdb | balls | render > mypicture.png
To include a pre-selected view matrix with the same model:
cp view1.matrix setup.matrix
cat mycolours.pdb protein.pdb | balls | render > mypicture.png
To prepend header records describing a pre-selected scale and view:
cat mycolours.pdb protein.pdb | balls -h > balls.r3d
cat header.r3d balls.r3d | render > mypicture.png
OPTIONS
-h
Suppress header records in output. By default balls 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 sphere
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.
DESCRIPTION
The input to balls consists of a single text file containing colour
information and atomic coordinates in PDB data bank format.
Coordinates are output as Raster3D descriptor records with colours and
sphere radii assigned according to the COLO records described below.
By default atoms are assigned CPK colours. 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).
Colours are assigned to atoms using a matching process, using COLOUR
records prepended to the input PDB file. Raster3D uses a pseudo-PDB
record type with with COLO in the first 4 columns:
Columns
1 - 4 COLO
7 - 30 Mask (described below)
31 - 38 Red component
39 - 46 Green component
47 - 54 Blue component
55 - 60 van der Waals radius in Angstroms
61 - 80 Comments
Note that the Red, Green, and Blue components are in the same positions
as the X, Y, and Z components of an ATOM or HETA record, and the van
der Waals radius goes in place of the Occupancy. The Red, Green, and
Blue components must all be in the range 0 to 1.
The Mask field is used in the matching process as follows. First the
program reads in and stores all the ATOM, HETA, and COLO records in
input order. Then it goes through each stored ATOM/HETA record in
turn, and searches for a COLO record that matches the ATOM/HETA record
in all of columns 7 through 30. The first such COLO record to be found
determines the colour and radius of the atom.
In order that one COLO record can provide colour and radius
specifications for more than one atom (e.g., based on residue or atom
type, or any other criterion for which labels can be given somewhere in
columns 7 through 30), the "#" symbol is used as a wildcard. I.e. a #
in a COLO record matches any character in the corresponding column in
an ATOM or HETA record. All other characters must match literally to
count as a match. Note that the very last COLO record in the input
should have # symbols in all of columns 7 through 30 in order to
provide a colour for any atom whose ATOM/HETA record fails to match any
previous COLO record. This idea of matching masks for colour
specifications is due to Colin Broughton.
Several files of COLO records, including one based on Bob Fletterick’s
"Shapely Models" and another mimicking CPK model parts, are provided as
samples.
ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the
header records produced by balls.
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
render(l), rods(l), ribbon(l)
AUTHORS
Originally written by David J Bacon and Wayne F Anderson.
Extensions and revisions by Ethan A Merritt.