Journal of Applied Crystallography

Volume 42, Part 4 (August 2009)

research papers

J. Appl. Cryst. (2009). 42, 607-615 [ doi:10.1107/S0021889809023528 ]

Automatic multiple-zone rigid-body refinement with a large convergence radius

P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams

Abstract: Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.

Keywords: rigid-body refinement; multiple-zone protocols.