The static partial structure flag. If you have partial structure to input, include this flag and follow it with the name of the PDB file containing the correctly positioned partial structure. You can separate the partial structure into as many files as you wish and use this flag multiple times on the command line. The minimum packing distance calculation will treat the partial structure within a single file as a single fragment. This will be MUCH slower, but if you have a very large search molecule and a workstation with little available memory, the FFT calculation may cause excessive swapping.
Summation uses little memory.
It will report the best score for each generation. A conjugate-gradient minimization will then be performed on the best scoring solution from the final generation. For a single molecule in the asymmetric unit, expect a correlation coefficient of 0.5 or more for a correct solution with a pretty good search model. For the first of two in the asymmetric unit expect a cc above 0.30. We expect later versions of the program to have significantly enhanced performance, in addition to many new features.