Ab initio phasing

Abstract

The background and use of dual-space direct methods (also known as Shake-and-Bake) for the ab initio phasing of small proteins as well as the phasing of heavy-atom substructures of large proteins is described. Basic concepts include normalized structure factors, multisolution procedures, random trial structures, phase-refinement formulas, peak-picking techniques, alternation of phase improvement in reciprocal and real space, and recognizing solutions. Two independent computer programs which implement the Shake-and-Bake algorithm, SnB and SHELXD, are compared and typical parameters are given. Other topics discussed are the use of Patterson information to get better starting phases, avoiding false minima, the effects of data resolution and completeness, special features of space group P1, and refinement strategies. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr.