balls is a preprocessor which prepares a description of a space-filling model
for the
Raster3D molecular graphics package
Note: balls
used to be called "setup" in previous releases of Raster3D.
The name has been changed to avoid conflicts with other programs called setup
on some systems. For compatibility with previous versions the command "setup"
may be installed as a symbolic link to balls.
balls [-h]
balls
reads a file describing atom colours and/or a Brookhaven PDB coordinate file
and produces on stdout 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.
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.
The input to balls consists of a single text file containing colour information
and atomic coordinates in Brookhaven 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 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
the same basic layout as the above but 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 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 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.
The files setup.matrix and setup.angles, if they exist, affect the header
records produced by balls.
Originally written by David J. Bacon and Wayne F. Anderson. Extensions and
revisions by Ethan A Merritt.
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