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.