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Alpha Shape

The alpha shape is a topological construct developed by Herbert Edelsbrunner at the UIUC CS department. It constructs a solid triangulation which is dual to the molecular surface in that it has the same number of tunnels, concavities, and pockets. The `Alpha' representation calls the alpha shape programs to construct the triangulation that corresponds to the given probe radius. Since these programs have not yet been released, it is unlikely that this method is available to you so your version of VMD should not even have this option.

The only available parameter is the probe radius and it is controlled by the sphere radius. This value has almost no relation to the real probe parameter as it passes through several layers of conversion to make the dial scale nicely over the range 0 to 2. The convex hull corresponds to a value of 2 while 0 corresponds, for the most part, to the point set. A value of about 0.25 gives a pretty good representation of the surface.

Take care when using this option. It is slow. On an SGI Onyx with an R4400 procesor, it takes about 4 minutes to find the general alpha shape of a 4,000 atom molecule. However, once the spectrum of alpha shapes is computed, the shape corresponding to specific probe radius is easy to extract and does not involve recomputation.



Andrew Dalke
Tue May 14 16:49:45 CDT 1996