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, ribbon)
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. Other
output formats are possible in conjunction with ImageMagick.
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 as AVS image file
#
cat ribbon.r3d irons.r3d | render > picture.x
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:-
A similar example using xv as an image viewer, and assuming that TIFF
support has been built into the render program:
molscript -r infile.dat | render -tiff image.tif
xv image.tif
SOURCE
anonymous ftp site:
ftp.bmsc.washington.edu
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),
label3d(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.