Direct-space methods in phase extension and phase refinement. VI. PERP (phase extension and refinement program).

Abstract

Several techniques for extending and refining phases for macromolecular structures have been incorporated into a program package PERP. In addition to previously employed techniques such as solvent flattening and histogram matching, PERP includes a new way of applying the Sayre equation [Refaat, Tate & Woolfson (1995). Acta Cryst. D51, 1036-1040], low-density elimination [Shiono & Woolfson (1992). Acta Cryst. A48, 451-456] and two double-histogram methods [Refaat, Tate & Woolfson (1996). Acta Cryst. D52, 252-256]. PERP is an easy-to-use package controlled by keywords and provided with default parameters that usually give near-optimum results. Examples are given of refinement, and also extension and refinement, for six known protein structures with a variety of characteristics. In each case PERP gives a very satisfactory outcome as measured by improvements in the mean-phase-error and conventional map-correlation coefficient. The main conclusion is that the several methods used in sequence give more effective extension and refinement than using any single method alone.