Density modification: theory and practice

Abstract

Abstract Real space phasing methods are aimed at improving the agreement of a density map with a set of physically meaningful constraints. Density maps must agree simultaneously with experimental data such as the observed amplitudes and the MIR phase distribution and with physical constraints based on a-priori knowledge of the characteristics of the density function. These physical constraints include positivity; boundedness; electron density histogram; high-resolution atomicity; uniformity of solvent regions; continuity of the bio-polymer chain; and known NCS of the density distribution. A starting map to be processed by real space methods, such as an MIR map, is usually obtained from, and thus will fully agree with, the experimental data. If the map also agrees with the set of physical constraints, there is no room for real space techniques, and map interpretation should be attempted. It is more often the case, however, that the map does not fully agree with all the physical constraints. In this case there is room to improve the agreement by real space techniques. To impose the physical constraints on an experimental map, a “Density Modification (DM)* iterative algorithm has been proposed [1,2]. It alternates real and reciprocal space operations, and the procedure is outlined in the flowchart shown in figure 1, with the following steps: