Section 25.2.1.6.2.3. Using external phase information

When using either the conventional phase refinement or approximate-likelihood methods, protein phase estimates are required. In the former case, only a single value is used, whereas in the latter, information about all possibilities is provided by way of the phase probability distribution. Normally, this information comes from a prior phasing calculation; thus, the estimates are typically SIR, SAS, MIR etc. phases. However, in PHASIT, an option allows one to read in the protein phase information from an external source. This enables parameter refinement (by either conventional or approximate-likelihood methods) using protein phase estimates that are improvements over the initial ones. For example, one could get the best phases by one of the previously described methods, but then improve them by density-modification procedures, such as solvent flattening or negative-density truncation and/or NC symmetry averaging. Using these improved phases in the calculation of when refining should then lead to more accurate heavy-atom and scaling parameters, which in turn will produce still better protein phases. These new protein phases can either be treated as final and used to produce an electron-density map for interpretation, or be used to initiate another round of phase improvement by density modification. There are several cases where this type of refinement has been beneficial, and it is particularly useful for the refinement of derivative-to-native scaling parameters.