balls (a.k.a. setup) - Raster3D package

# BALLS

#### SYNOPSIS

balls is a preprocessor which prepares a description of a space-filling model for the Raster3D molecular graphics package

    balls [-h]

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.

#### EXAMPLES

To describe a simple space-filling model coloured by residue type:

    cat mycolours.pdb protein.pdb | balls | render > mypicture.avs

To include a pre-selected view matrix with the same model:

    cp view1.matrix setup.matrix
    cat mycolours.pdb protein.pdb | balls | render > mypicture.avs

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.avs

#### 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 COLO in the first 4 columns:

  Columns Contents
  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 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.

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 treated as a wildcard. I.e., a # in a COLO 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 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.

#### AUTHORS

Originally written by David J. Bacon and Wayne F. Anderson. Extensions and revisions by Ethan A Merritt.

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