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 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.

       -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 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.

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