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
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
The -h flag will suppress these header records so that the output
file contains only object 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.
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.
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.
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,
Raster3D uses a pseudo-PDB record type with the same basic
layout as the above but with COLO in the first 4 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 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.