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. Each element has its own dummy atom with its own radius. 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 second option is to use the cube method. In this case the protein and hydration shell are tiled with cubes. The cubes in the protein are given negative densities equal to the solvent density, while cubes in the hydration shell are given densities according to the hydration shell options. This is slower, but more accurate, because there are no gaps or overlaps of the cubes. WAXS patterns are typically calculated with the Debye formula or multipole expansion. However those two methods can only be used when all particles are spherical, so those formulas cannot be used for the cube method. Instead the scattering is calculated for a number of vectors, and the intensities are averaged.