balls(1)

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.

Raster3D 8 May 1999 BALLS(1)