The program takes as input an mtz file containing the Fourier coefficients of the map to be searched, and a search model in the form of a pdb file, map, or maximum likelihood target. A `fragment mask' is generated to cover the fragment density, and orientations and translations are searched to find those transformations which give a good fit between the fragment density and map density within the fragment mask.
The program has been highly optimised using reciprocal-space rotations and grid-doubling FFT's, and crystallographic symmetry (Rossman+Arnold, 1993) giving 4-50 times speed improvement over the results published in 1998. The speed of the calculation is almost independent of the size of the model, thus the program may also be used for molecular replacement calculations where weak phases are available.
A maximum likelihood search function is provided in the current beta release, which allows searches for helices in even poorer maps than the conventional target. The likelihood weights take over the role of fragment mask and are determined directly from the database.