BALLS(1)						      General Commands Manual							  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 descrip-
       tors.  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.	Coordi-
       nates 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 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.

       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 used as a wildcard. I.e. a # in
       a COLOUR 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 pro-
       vide a colour for any atom whose ATOM/HETA record fails to match any previous COLOUR record.  This idea of matching masks for colour speci-
       fications is due to Colin Broughton.

       Several files of COLOUR records, including one based on Bob Fletterick's "Shapely Models" and another mimicking CPK model parts, are pro-
       vided 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)