Molecular surface Triangulation

Abstract

A method is presented for triangulating the surface of a molecule. A triangulated surface is a polyhedron, all of whose faces are triangles. The triangles are created by subdividing the curved faces of an analytical molecular surface that has been precalculated by an earlier algorithm. The triangulated surface has many applications. Molecular areas and volumes may be calculated from it. Packing defects in proteins may be identified. It may be used to determine whether a particular water molecule lies in the interior of the protein or on the surface. The triangulated surface may be drawn on pen plotters, vector graphics systems and raster graphics terminals. Mathematical functions defined on the surface may be contoured. Local maxima and minima of functions may be located. While the triangulated surface is less accurate than the analytical molecular surface it is derived from, it has the advantage of being much simpler and easier to deal with. It combines the simplicity of a dot surface with the continuity of an analytical surface.