HOLLOW facilitates the production of surface images of proteins. Hollow generates fake atoms that identifies voids, pockets, channels and depressions in a protein structure specified in the PDB format.
ORTEP-III is Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations.Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.
Ortep-3 for Windows developed by Dr. Louis Farrugia is a MS-Windows version of the current release of ORTEP-III
Michael N. Burnett and Carroll K. Johnson,
ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations,
Oak Ridge National Laboratory Report ORNL-6895, 1996.
PentaPlot is a software tool that computes the dekapentagonal maps given an appropriate probability support matrix.Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree.
PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration – colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.
PovChem can export the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!