Phasing medium-size structures and proteins by the VLD algorithm

Abstract

The VLD algorithm is based on the properties of a new difference Fourier synthesis and allows the recovery of the correct structure starting from a random model. It has previously been applied to a set of small structures. The first aim of this paper is to extend the complexity range to medium-size molecules and to proteins, provided the data have atomic resolution. The algorithm always works in the correct space group and uses electron density maps rather than molecular models. It has been modified in order to (i) provide, at the end of the procedure, molecular models that are automatically interpreted (in a chemical sense), rather than electron density maps, and (ii) show the variety of ways in which VLD may be implemented. The applications show that VLD is able to solve large structures, in favorable cases by using a small number of attempts, and that this property also extends to some of its variants.