---
name: "balls"
section: "1"
platform: "linux"
package: "raster3d"
version: "3.0-7-2+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/balls"
---

# balls(1)

preprocessor for space-filling models in Raster3D molecular graphics package

## 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 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 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.

Several files of COLOUR 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.