[33] AMoRe: An automated molecular replacement program package

This chapter discusses the automated molecular replacement (AMoRe) program package. The basic problem of molecular replacement is to determine the positions of the molecules within a crystal cell. This is achieved by generating model crystal structures with molecular models placed at tentative positions and then selecting the configurations that give an acceptable agreement between the calculated structure factors and the observed ones. It constitutes a step toward the resolution of the crystal structure to be followed by model building and refinement procedures. The molecular replacement and a posteriori analysis of solved structures led to the optimization of the different parameters that define the rotation and translation functions to enhance the signal-to-noise ratio of the rotation function (RF) and translation function (TF) peaks. The success of the package, originally designed to deal with difficult problems, is a result of the combined action of its main characteristics: (1) many potential solutions, determined by revised or novel functions, are explored by means of fast algorithms, (2) correlation coefficients are used as the main criteria of selection, (3) the information coming from already positioned models is automatically incorporated into the procedure, and (4) there is a high degree of automation. The chapter describes the positional variables used in the package and discusses the strategy and results of AMoRe.