RODS(1) General Commands Manual RODS(1)
NAME
rods - Raster3D preprocessor for ball-and-stick models
SYNOPSIS
rods [-h] [-b] [-radius R] [-Bcolor Bmin Bmax]
Rods reads a file describing atom colours and/or a PDB coordinate file and produces a file containing Raster3D descriptor records. The
file produced by rods may be fed directly to render or it may be combined with descriptor files produced by other Raster3D utilities.
EXAMPLES
To describe a simple bonds-only model coloured by residue type:
cat mycolours.pdb protein.pdb | rods | render > mypicture.png
To render the same molecule as ball-and-stick:
cat mycolours.pdb protein.pdb | rods -b | render > mypicture.png
OPTIONS
-h
Suppress header records in output. By default rods 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 object 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.
-b
By default rods will describe bonds only; the -b flag will cause it to include spheres at the atom positions also, yielding a ball-and-
stick representation.
-radius R
By default rods will draw bonds as cylinders with a 0.2A radius. The radius option allows you to change this cylindrical radius.
-Bcolor Bmin Bmax
Assign colors based on B values rather than from atom or residue types. Atoms with B <= Bmin will be colored dark blue; atoms with B >=
Bmax will be colored light red; atoms with Bmin < B < Bmax will be assigned colors shading smoothly through the spectrum from blue to red.
DESCRIPTION
The input to rods 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. Ball-and-
stick figures have atoms drawn at 0.2 * VanderWaals radius, connected by rods with a default 0.2A cylindrical radius. Bonds are drawn for
atoms which lie closer to each other than 0.6 * (sum of VanderWaals radii). 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. If no COLOUR records are
present in the input file, atoms will receive default CPK colors (C=grey, O=red, N=blue, S=yellow, P=green, other=magenta). Raster3D uses
a pseudo-PDB record type with the same basic layout as the above but 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 pro-
vide a colour for any atom whose ATOM/HETA record fails to match any previous COLO record. This idea of matching masks for colour specifi-
cations is due to Colin Broughton.
ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the header records produced by rods.
SOURCE
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), ribbon(l), balls(l)
AUTHORS
Ethan A Merritt
Raster3D 8 May 1999 RODS(1)