Using Parallel Computers To Solve the Phase Problem of X-Ray Crystallography

Abstract

Direct methods are commonly used by crystallographers to determine relatively small crystal structures.However, existing techniques do not appear to be extensible to larger structures. The recent development of a solution strategy called Shake-and-Bake, aimed at determining structures via local minimization and repeated Fourier transformations, allows for implicit constraints to be included. In this article, a description of the Shake-and-Bake algorithm is given, along with a detailed description of master/slave MIMD implementations on a network of Sun workstations, an Intel iPSC/860 Hypercube, and a Connection Machine CM-5. Our experimental results on known structures, including gramicidin A, are extremely encouraging. For example, based on efficient implementations of Shakeand-Bake on the iPSC/860 and CM-5, for known structures of 28, 84, and 127 nonhydrogen atoms, we obtain success rates of 19%, 1%, and 0.2%, as opposed to existing methods, which yield success rates of approximately 6%, 0.006%, and 0.0002%, respectively.

Now we’re cooking: new successes for shake-and-bake

“…1). This approach was successfully implemented by Miller and Weeks in the form of a computer algorithm called SnB [10][11][12] and applied to a number of large, small molecules and proteins [13]. The name of the computer algorithm, SnB, was derived from the two distinct steps: a reciprocal space phase refinement step (shake) and a real-space filtering step (bake).…”

A minimal principle in X-ray crystallography: starting in a small way

“…The formulation of the minimal principle as the solution of the phase problem was first proposed in 1988 (Hauptman) and further progress reported in the following years (Hauptman 1989(Hauptman , 1991Hauptman et al 1990 ;DeTitta et al 1991;Weeks et al 1992Chang et al 1993;Miller et al 1993). Here some definitions are given first and then the present status of this approach to the phase problem is briefly summarized.…”