Automatic model building based on flexible fragment formalism. The case of high-resolution protein structures

A concept of flexible fragments has been developed for automatic building of crystal structures. Six monopeptides were designed as search fragments in a phased rotation and translation function for protein building. Electron density in crystal and in molecular fragments is expanded in spherical harmonics and normalized spherical Bessel functions. A fast rotation function, which is calculated at each grid point of the asymmetric unit, is used to find the fragment orientation. Position, orientation and internal torsion angles are refined. An algorithm for chain building is simplified using generalized atoms and virtual bonds. The structure is built from molecular structure units rather than from individual atoms. A polyalanine model is built with a high accuracy at resolutions 1.2-2.1 Å.