In order to correct for the presence of solvent the average electron density of the solution needs to be subtracted from every point in the protein. For water this is about 0.334 e/A3. There are two options for subtracting the solvent density from protein. The fastest method is to place dummy atoms with density equal to the negative of the solvent on top of the protein atoms. This is not a very accurate method. If this option is used the user can choose between two different sets of radii used for the dummy atoms. One is a set developed so as to avoid gaps and overlaps between the atoms, the other is the set of radii developed by Fraser, MacRae, and Suzuki. The default values are:
Hydrogen: 0.90
Carbon: 1.44
Nitrogen: 1.25
Oxygen: 1.22
Sulfur: 2.20

The Fraser-MacRea-Suzuki values are:
Hydrogen: 1.07
Carbon: 1.58
Nitrogen: 0.84
Oxygen: 1.30
Sulfur: 1.68