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