How SOLVE works

MAD structure determination

The real power of the SOLVE package is the automated solution of MAD and MIR datasets. For a MAD dataset, all you need to do is tell the program about your space group and cell dimensions, where the unscaled intensity data files are, and what the scattering factors are for the MAD dataset. The program scales the data using localscaling in SCALE_MAD , calculates difference Patterson maps, compresses the MAD data into SIRAS-like data using MADMRG, calculates an optimized Bayesian heavy-atom Patterson using MADBST, and iteratively builds up and scores potential heavy-atom solutions for the MAD dataset with the SOLVE routine. Potential solutions are scored on the basis of (1) agreement with the Patterson, (2) "free" difference Fouriers, (3) the presence of "solvent" and "protein" regions in a native electron density map, and (4) the figure of merit of phasing. SOLVE carries out the search for heavy-atom solutions in steps of resolution (the number of which can be specified with the "resolution_steps" keyword). This makes the search much faster than it might otherwise be, because many times the heavy atom solution can be found at low resolution and then simply refined and used to calculate phases at high resolution. Final phases for the top solutions are written out along with Hendrickson-Lattman coefficients for calculating maps and solvent flattening.

MIR structure determination

MIR structure determination is almost the same as for MAD structure determination. The program scales the data using localscaling in SCALE_NATIVE and SCALE_MIR , calculates difference Patterson maps, and iteratively builds up and scores potential heavy-atom solutions for the MAD dataset with the SOLVE routine.

Combinations of multiple MAD or MIR datasets

SOLVE can treat multiple MAD or MIR datasets by converting them into one super-dataset that uses each native dataset other than the first one as a pseudo- derivative with no heavy atom. Then it uses correlated bayesian phasing to take into account any non-isomorphisms among the different datasets. In this way you can combine several MAD datasets, several MIR datasets, or MAD and MIR datasets. See the command COMBINE.

Datasets with anomalously-scattering native

SOLVE treats native datasets with anomalously-scattering atoms as two datasets. You enter the same data twice, once as a "native", and again as a "derivative" for which you specify a new heavy atom type with a zero real part and a non-zero imaginary part.