Software:GRASP General Description
GRASP is a graphics program written for Silicon Graphics computers that is widely used by the structural biology community to visualize macromolecules. Its particular strengths compared to other such programs is its facility with surfaces and with electrostatics. The program contains extremely rapid algorithms for the construction of rendered molecular surfaces and for solving the Poisson-Boltzmann equation. The latter enables a description of the electrostatic field generated by charges within a molecule (typically assigned to atom centers) such that the difference in dielectric between water (dielectric = 80) and the molecule (dielectric = 4), and also the influence of mobile ions (salt), is taken into account. There is now considerable experimental evidence that such a description has physical validity.
GRASP's surface can be molecular or accessible and can be color coded by electrostatic potential derived from its internal Poisson-Boltzmann solver or external programs such as DelPhi. This representation has become a standard tool in assessing electrostatic character of large, typically protein, molecules. Surfaces can also be colored by other properties, such as any of those of the underlying atoms (e.g. hydrophobicity) or by its own intrinsic properties, such as local curvature.
The program also contains several other unique data representational forms in addition to standard ones such as "ball and stick" for atoms and bonds, and backbone splines, or "worms", to indicate secondary structure. For instance, one can construct ellipsoids to represent arbitrary collections of atoms, represent the dihedral plane as a box with electrostatic polarity or site-site interactions with variable width tubes.
GRASP accepts atom information in Protein Brookhaven Data (PDB) format. It interprets only ATOM, HETATM and CONECT lines from the file. It will also accept certain modified formats as associated with the program DelPhi, which allow additional fields of information, such as atom radii and charge. All interactions with the program are via command line input, hot key or menu selection. The program is completely documented.
GRASP is supported by a funding from the National Science Foundation Grant # DBI-9904841
Developed in the Honig Lab