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GRASP
 
GRASP: Graphical Representation and Analysis of Structural Properties

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.

To run grasp on any of the UCLA-DOE lab SGIs type grasp or
/joule2/programs/grasp/grasp.

There are several examples and scripts in /joule2/programs/grasp.

GRASP Home and Online Manual.