Methodology and applications of automatic electron-density map interpretation by six-dimensional rotational and translational search for molecular fragments

The electron density for a search fragment and for the crystal is expanded in the space of spherical harmonics Bessel functions. The fast rotation function is evaluated for each grid point to test if the fragment can be orientated there. For the best scoring points, the six-dimensional coordinates of the fragment are refined by the second-derivative block-diagonal procedure. The method is able to locate fragments precisely over a wide range of resolutions for structure types from small organic molecules to proteins.