1. Number of water molecules around other waters. This algorithm is the default. For each water molecule within specified cutoff R c of non-solvent molecules (default value for R c is 5 Å) the number of water atoms N atoms HOH within a sphere of radius R (default value is 10 Å) is calculated. For waters outside of the protein this number is large (around 400), while for waters inside the molecule this number will be smaller than than N cutoff = 120 (Figure ). The latter water molecules are thus removed.