Fitting molecular fragments into electron density

Abstract

Molecular replacement is a powerful tool for the location of large models using structure-factor magnitudes alone. When phase information is available, it becomes possible to locate smaller fragments of the structure ranging in size from a few atoms to a single domain. The calculation is demanding, requiring a six-dimensional rotation and translation search. A number of approaches have been developed to this problem and a selection of these are reviewed in this paper. The application of one of these techniques to the problem of automated model building is explored in more detail, with particular reference to the problem of sequencing a protein main-chain trace.

Figure 1

Success rates in sequencing fragments of different lengths for two structures using two different chain traces for generating the fragments. (a) 1vkn at 2.45 Å, using chain fragments taken from the true model. (b) 1vkn at 2.45 Å, using chain fragments taken from the Buccaneer auto-built model. (c) 1vrb at 3.2 Å, using chain fragments taken from the true model. (d) 1vrb at 3.2 Å, using chain fragments taken from the Buccaneer auto-built model.