The Raster3D molecular graphics package consists of a core program
and a number of ancillary programs
which produce input files
for rendering from Brookhaven PDB files of atomic coordinates. Raster3D can
also render images composed using version 1.4 of
Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images
featuring two light sources, specular highlighting, Phong shaded surfaces, and
shadowing. Output is in the form of a pixel image with 24 bits of color
information per pixel.
Raster3D does not depend on graphics hardware for operation. Four image output
formats are supported: AVS, TIFF, SGI libimage, and a private format which is
backwards-compatible with earlier versions of Raster3D. 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).
Ancillary programs are provided for the generation of object
descriptions based on atomic coordinates stored in Brookhaven PDB format.
Although the rendering program is not specific to molecular graphics, Raster3D
is not intended as a general purpose ray-tracing program.
Some of the algorithms used have been chosen for speed rather than generality;
that is, they happen to work well for the types of images the program is
intended for, but may produce odd results if used for very different types of
Raster3d currently supports rendering five object types: spheres,
triangles, planes, smooth-ended cylinders, and round-ended cylinders.
Version 2.1 added support for two additional "object types" which are
really modifiers for characteristic properties of existing objects. One
of these allows specification of explicit surface normals at triangle
vertices; the other allows specification of surface reflectance
properties specific to individual objects.
Version 2.2: The major new feature in Raster3D Version 2.2 is support
for transparent objects.
This permits Raster3D rendering of transparent molecular surfaces
in combination with the existing provisions for depicting molecular structures.
In keeping with the philosophy of the package, the intention is not to
duplicate the power of more general programs for composing or describing
such surfaces. The idea rather is to provide a tool for creating images with
greater resolution and photorealism than is generally possible using a
graphics workstation screen.
Also new in this version is the
utility, a tool to facilitate merging Raster3D input files created by different
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
can alternatively use Molscript Version 1.4 to produce a Raster3D input file by
using the -r switch. Raster3D is not able, however, to render any labels
specified by the Molscript input. 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 avs:-
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
Raster3D distribution also includes a filter utility which will convert the
24-bit color output stream from render into a dithered black & white
render < description.r3d | avs2ps > picture.ps
In order to build in support for the direct output of TIFF image files, you
must separately obtain and install a copy of the TIFF library (libtiff.a).
Several implementations are available, including one by Sam Leffler which may
be obtained via anonymous ftp from
- anonymous ftp site:
- ftp.bmsc.washington.edu /pub/raster3d/
- via WWW:
- Ethan A Merritt
Dept of Biological Structure
University of Washington,
Seattle WA 98195-7742
In order to view the rendered images on a workstation screen you must also
obtain and install an image viewer. Two commonly available viewers are John
(also available via anonymous ftp from
ftp.x.org ) and John Bradley's xv.
The avs2ps utility for direct production of black & white PostScript images
is now included in the Raster3D distribution. It replaces earlier
machine-dependent programs in the viewtools kit.
Several auxiliary programs are available from the ftp site above which may be
useful, though they have not been kept up to date with the current Raster3D
version. These include two attempts to aid in the composition of Raster3D
images (atoms, preras3d) and tools for conversion to half-toned monochrome
images and annotation and display of the images (viewtools). Most of the code
was written specifically for SGI workstations, and may not transport well to
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.
If you use the package to prepare figures for
publication, please give proper credit to the authors: (Bacon and Anderson,
1988; Merritt and Murphy, 1994).
Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for Rendering
Space-Filling Molecule Pictures''. (abstract of paper presented at the Seventh
Annual Meeting of the Molecular Graphics Society). J. Molec. Graphics 6,
Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed and
schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.
Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program
for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.
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