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Raster3D(1)            DragonFly General Commands Manual           Raster3D(1)


NAME

       Raster3D molecular graphics package


SYNOPSIS

       The Raster3D molecular graphics package consists of a core program
       render and a number of ancillary programs (balls, rastep, rods) which
       produce input files for rendering from PDB (Protein Data Bank) files of
       atomic coordinates.  Raster3D can also render images composed using
       other programs such as MOLSCRIPT [Per Kraulis (1991), J. Appl. Cryst.
       24, 946-950].

       Raster3D is freely available. If you use the package to prepare figures
       for publication, please give proper credit to the authors.  The proper
       citation for the current version is Merritt & Bacon (1997).

            Bacon & Anderson (1988) J. Molec. Graphics 6, 219-220.
            Merritt & Murphy (1994) Acta Cryst. D50, 869-873.
            Merritt & Bacon  (1997) Meth. Enzymol. 277, 505-524.


DESCRIPTION

       Raster3D uses a fast Z-buffer algorithm to produce high quality pixel
       images featuring one shadowing light source, additional non-shadowing
       light sources, specular highlighting, transparency, and Phong shaded
       surfaces.  Output is in the form of a pixel image with 24 bits of color
       information per pixel.  Raster3D does not depend on graphics hardware.

       The following image output formats are supported: AVS, JPEG, PNG, TIFF,
       and SGI libimage.  To actually view or manipulate the images produced,
       you must also have installed an image viewing package (e.g. John
       Cristy's ImageMagick or the SGI libimage utilities).  A filter utility
       avs2ps is included in the package which can convert an AVS format
       output stream directly to a dithered monochrome PostScript image.

       Although Raster3D is not intended as a general purpose ray-tracing
       package, nothing in the rendering process is specific to molecular
       graphics.


EXAMPLES

       Using only programs included in the Raster3D distribution one can
       create and render space-filling models, ball-and-stick models, ribbon
       models, and figures composed of any combination of these.  The
       following set of commands would produce a composite figure of an Fe-
       containing metalloprotein with a smoothly shaded ribbon representation
       of the protein and spheres drawn for the Fe atoms:

            #
            # Draw smooth ribbon with default color scheme 2,
            # save description (with header records) in ribbon.r3d
            #
            cat protein.pdb | ribbon -d2 > ribbon.r3d
            #
            # Extract Fe atoms only, and draw as spheres.
            # Color info is taken from colorfile.
            # Save description (with no header records) in irons.r3d
            #
            grep "FE" protein.pdb | cat colorfile - | balls -h > irons.r3d
            #
            # combine the two descriptions and render to a PNG image
            #
            cat ribbon.r3d irons.r3d | render > picture.png

       Integrated use of MOLSCRIPT/Raster3D/ImageMagick allows one to
       describe, render, and view 3D representations of existing MOLSCRIPT
       figures:

            molscript -r infile.dat | render | display png:-


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), rastep(l), rods(l), ribbon(l), balls(l), avs2ps(l),
       stereo3d(l)


AUTHORS

        Originally written by David J Bacon and Wayne F Anderson.
        Ancillary programs by Mark Israel, Stephen Samuel, Michael Murphy,
       Albert Berghuis, and Ethan A Merritt.  Extensions, revisions, and
       modifications by Ethan A Merritt.

Raster3D V3.0                  14 December 2010                    Raster3D(1)

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