Biomedical Engineering Reference
In-Depth Information
RasMol, placed in the public domain in 1993 by Roger Sayle and maintained today by the University
of Massachusetts, Amherst, is the easiest-to-use molecular rendering program available on the
Internet. Although this stand-alone program has been supplanted in functionality by a host of
derivative programs, such as Chime and Protein Explorer, RasMol remains one of the standard tools
in bioinformatics visualization. RasMol is limited in functionality compared to programs introduced in
the past decade. However, it has a small footprint of less than a megabyte, runs on a standard laptop
computer, and is computationally efficient.
Cn3D, which is closely linked with NCBI's MMDB, is a browser plug-in that supports interactive
viewing of 3D protein structures in a Web browser environment. In addition to standard features such
as selective coloring of subsets of the protein structure to emphasize certain regions of interest,
Cn3D can correlate structure and sequence data to locate residues in a crystal structure that
correspond to known disease mutations and can display structure-structure alignment. Cn3D can also
export images in a variety of formats for publications and for use in other rendering engines,
including high-end commercial rendering programs.
PyMol is a Web-enabled rendering program that emphasizes power and functionality over ease of
use. PyMol is often used to produce graphics for publication, in part because of its built-in ray-tracing
function. Ray tracing is a computationally challenging method of rendering an image so that
shadows, highlights, and other photo-realistic features appear in the final image. The technique
involves calculating the color and intensity of each pixel in an image by tracing single rays of light
