The Raster3D molecular graphics package consists of a core program
and a number of ancillary programs that read atomic coordinates from
PDB (Protein Data Bank) files to produce scene descriptions for input to render.
Raster3D can also render images composed using other programs such as
Molscript, Xfit, and coot.
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 plus one matte channel.
Raster3D does not depend on graphics hardware. The rendering program currently
supports output to files in AVS, JPEG, TIFF, PNG and SGI libimage format.
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).
The Raster3D rendering program can be integrated with ImageMagick to
expand the flexibility of output formats and interactive use.
Ancillary programs are provided for the generation of object
descriptions based on atomic coordinates stored in PDB format.
Although Raster3D is not intended as a general purpose ray-tracing package,
nothing in the rendering process is specific to molecular graphics.
Some of the algorithms used have been chosen for speed rather than generality,
however. They work well for molecular graphics images, but possibly
would produce odd results if used for very different types of image.
Raster3D currently supports rendering six object types: spheres,
triangles, planes, smooth-ended cylinders, round-ended cylinders,
and quadric surfaces. It also supports the definition of material
properties (transparency, bounding planes, color, reflectivity)
that apply to groups of objects within the rendered scene.
New in version 3.0: Dynamic array allocation, direct rendering of
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
One can alternatively use Molscript to produce a Raster3D
input file by using the -r switch. 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
The same image rendered as a side-by-side stereo pair:
molscript -r < infile.dat | stereo3d -border -png stereo_pair.png
Raster3D distribution also includes a filter utility which will convert the
24-bit color AVS output stream from render into a dithered black & white
render -avs < description.r3d | avs2ps > picture.ps
- via WWW:
- Ethan A Merritt
Biomolecular Structure Center
University of Washington
Required for full installation:
- Generation of PNG and JPEG images, as well as label processing,
requires prior installation of the
gd graphics library.
libgd itself requires other libraries, but if you have libd itself
installed then you should be all set.
- 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). However, you can only render text labels for PNG or JPEG
output, so you may be better off generating PNG images and then converting
them to TIFF afterward.
- For full functionality you should also obtain and install a copy of
Some other programs with direct Raster3D output modes:
- The contents of the current view window in a Coot session may be rendered in
Raster3D using the <F8> hotkey. More complicated scripting from Coot
is also possible. Coot web page:
- Figures composed in Molscript can be rendered in Raster3D rather than
being printed as PostScript images. The Molscript web page is
- ORTEP and the small molecule world
- ORTEX V7 (an interactive descendent of Carroll Johnson's ORTEP program)
now supports Raster3D as an output mode. ORTEX runs under DOS/Windows,
and is available from
Another small molecule package running under Windows and incorporating
Raster3D rendering options is WinGX, available from
- Biomolecular visualization tool from the Theoretical Biophysics group
at the University of Illinois,
- Figure generation and analysis tool for RNA and DNA structures.
X3DNA Web site:
- General crystallographic model building, map fitting, and
analysis program by Duncan McRee, available in both academic and
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; the proper citation for the
most recent version of the package is Merritt & Bacon (1997) as given below.
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.
Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D
Photorealistic Molecular Graphics''. Methods in Enzymology 277, 505-524.
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