Re: [ccp4bb]: How big is my active site?

[Charlie Bond <C.S.Bond@dundee.ac.uk>]

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James Naismith wrote:
> Does anyone know of a good way to look at the volume of an active site? 

Jim,
I haven't used it for a very long time, but Roman Laskowski's Surfnet 
http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
might be of use:
"The SURFNET program generates surfaces and void regions between
surfaces from coordinate data supplied in a PDB file. It can compute:-

         van der Waals surfaces
         Gaps between molecules
         Clefts, cavities and binding sites
         3D density distributions and sidechain-sidechain interactions
         Planes, paraboloids and boxes"

Cheers,
Charlie
-- 
Dr Charles S. Bond            MSI/WTB Complex    Tel: +44-1382-348325
BBSRC David Phillips Fellow   Dow St.  Dundee    Fax: +44-1382-345764  
School of Life Sciences       DD1 5EH Scotland  C.S.Bond@dundee.ac.uk
University of Dundee         http://stein.bioch.dundee.ac.uk/~charlie