Section 25.2.1.6.3. Rigid-group refinement

Although GREF can be used to refine individual heavy-atom or anomalous-scatterer parameters against isomorphous or anomalous structure-factor difference magnitudes, it is actually a group refinement program. Thus, all entities to be refined are treated as rigid bodies such that only group orientations, positions, scaling and temperature parameters can be refined. The groups, however, can be defined arbitrarily. For individual heavy-atom sites, they are simply defined as single atom `groups', and no orientation parameters are selected for refinement. This enables the program to serve two additional roles. In the case where the heavy-atom reagent is known to contain a rigid group, it can be properly treated. Also, if one chooses the target values to be native structure-factor amplitudes instead of difference magnitudes and inputs an entire protein molecule or domain, then conventional rigid-body or segmented rigid-body refinement can be carried out. The output consists of the refined parameters and a Fourier-coefficient file suitable for map or phase combination calculations.