[Chimera-users] creating volume maps

Nils Becker nils.becker at ens-lyon.fr
Wed Apr 29 04:40:11 PDT 2009


I would like to use chimera for measuring the steric accessibility of
particular atoms in a structure to reactive species in solution. To do
that I had the following idea:

1. create a volume map which represents a solid sphere centered on the
atom in question (alternatively, a Gaussian blob), with some chosen radius.

2. mask this sphere using the solvent accessible surface of the protein
(for example, if the atom is at the surface and the surface is flat,
half of the sphere would be cut away)

3. measure the volume of the remaining piece of the sphere.

So now my question is: can this work, and how can I generate the sphere
in step 1. ?

thanks for any advice!

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