Direct-space methods in phase extension and phase refinement. VI. PERP (phase extension and refinement program).
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.
Physics Department, University of York, England.
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Tate
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