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<title> balls (a.k.a. setup) - Raster3D package </title>
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<h1 align=center>
<a name="RTFToC30">BALLS</a></h1>
<h4>
<a name="RTFToC31">SYNOPSIS</a></h4>
balls is a preprocessor which prepares a description of a space-filling model
for the
<a href="raster3d.html">Raster3D</a> molecular graphics package <p>
<pre>
balls [-h]
</pre>
balls
reads a file describing atom colours and/or a PDB coordinate file
and produces a stream of Raster3D object descriptors on stdout, one sphere
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.
<h4>
<a name="RTFToC32">EXAMPLES</a></h4>
To describe a simple space-filling model coloured by residue type:
<pre>
cat mycolours.pdb protein.pdb | balls | render > mypicture.png
</pre>
To
include a pre-selected view matrix with the same model:
<pre>
cp view1.matrix setup.matrix
cat mycolours.pdb protein.pdb | balls | render > mypicture.png
</pre>
To
prepend header records describing a pre-selected scale and view:
<pre>
cat mycolours.pdb protein.pdb | balls -h > balls.r3d
cat header.r3d balls.r3d | render > mypicture.png
</pre>
<H4>OPTIONS</H4>
<dl>
<dt><i>-h</i><dd>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.</dl><h4>
<a name="RTFToC33">DESCRIPTION</a></h4>
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 COLOUR records described below. By default atoms are assigned
CPK colours.
<p>
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).<p>
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
COLO in the first 4 columns:
<dl>
<dt><b><i></i></b><dd>Columns Contents
<br> 1 - 4 COLO
<br> 7 - 30 Mask (described below)
<br> 31 - 38 Red component
<br> 39 - 46 Green component
<br> 47 - 54 Blue component
<br> 55 - 60 van der Waals radius in Angstroms
<br> 61 - 80 Comments</dl>Note that the Red, Green, and Blue components are
in the same positions as the X, Y, and Z components of a PDB 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.<p>
The Mask field is used in the matching process as follows. First the program
reads in and stores all the ATOM, HETA, and COLOUR records in input order. Then
it goes through each stored ATOM/HETA record in turn, and searches for a COLOUR
record that matches the ATOM/HETA record in all of columns 7 through 30. The
first such COLOUR record to be found determines the colour and radius of the
atom.<p>
In order that one COLOUR 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 treated as a wildcard. I.e., a # in a COLOUR record matches any character
found in the corresponding column in an ATOM or HETA record. All other
characters must match exactly. Note that the very last COLOUR 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 COLOUR
record. This idea of matching masks for colour specifications is due to Colin
Broughton.<p>
Several files of COLOUR records, including one based on Bob Fletterick's
``Shapely Models'' and another mimicking CPK model parts, are provided as
samples.
<h4>
<a name="RTFToC34">ENVIRONMENT</a></h4>
The files setup.matrix and setup.angles, if they exist, affect the header
records produced by balls.
<h4>
<a name="RTFToC35">AUTHORS
</a></h4>
Originally written by David J. Bacon and Wayne F. Anderson. Extensions and
revisions by Ethan A Merritt.<p>
<p>
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