Subject: SAS of nucleic acids

From: Dongchul Lim <[email-masked]>
Date: Wed, 22 Nov 95 22:49:39 EST

Searching Web pages resulted in the following packages:

Naccess v2.0 - Atomic solvent accessible areas
	http://www.biochem.ucl.ac.uk/~roman/naccess/naccess.html

	Naccess calculates the accessible area of a molecule from a PDB file.
	The program uses the Lee & Richards (1971, J. Mol. Biol., 55, 379-400)
	method, whereby a probe of given radius is rolled around the surface
	of the molecule, and the path traced out by its centre is the
	accessible surface. Typically, the probe has the same radius as water
	(1.4 Angstroms) and hence the surface described is often referred to
	as the solvent accessible surface. 

Ray Casting and Protein Geometry
	http://www.chem.duke.edu/research/prisant/protein/protein.html

SURF
	http://www.cs.unc.edu/ftp/pub/projects/GRIP/SURF

	SURF is a set of programs for generating and displaying the solvent
	accessible surface of a molecule.  A representation of a typical
	protein molecule can be generated in about a second, allowing near
	real-time response to changes in the surface parameters.

RASMOL
	http://www.bio.cam.ac.uk/doc/rasmol.html

	The RasMol set solvent command is used to control the behaviour
	of the RasMol dots command. Depending upon the value of the
	solvent parameter, the dots command either generates a Van der Waal's
	or a solvent acessible surface around the currently selected set of
	atoms. Changing this parameter automatically resets the value of the
	RasMol radius parameter. The command set solvent false, the
	default value, indicates that a Van der Waal's surface should be
	generated and resets the value of radius to zero. The command set
	solvent true indicates that a `Connolly' or `Richards' solvent
	accessible surface should be drawn and sets the radius parameter, the
	solvent radius, to 1.2 Angstroms (or 300 RasMol units).

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Dongchul Lim
Department of Chemistry
Yale University