Model building in SHELXE

Density modification is a standard step to provide a route for routine structure solution by any experimental phasing method -with SAD and MAD being the most popular ones- as well as to extend fragments or incomplete models into a full solution. The effect of density modification on the starting maps from either source is illustrated in the case of SHELXE. The different modes in which the program can run are reviewed; these include less well-known uses such as reading external phase values and weights or phase distributions encoded in Hendrickson-Lattman coefficients. Typically in SHELXE, initial phases are calculated from experimental data, from a partial model or map, or from a combination of both sources. The initial phase set is improved and extended by density modification and, if the resolution of the data and the type of structure permits, poly-alanine tracing. The trace now includes an extension into the gamma position or hydrophobic and aromatic side chains if a sequence is provided, which is performed in every tracing cycle. Once a correlation coefficient over 30% between the structure factors calculated from such a trace and the native data indicates that the structure has been solved, in all model building cycles sequence is docked and side chains are fitted if the map supports it. The extensions to the tracing algorithm brought in to provide a complete model are discussed. The improvement in phasing performance is assessed using a set of tests. SynopsisSide chain tracing now completes model building in SHELXE to enhance density modification. All alternative SHELXE modes, using single or combined sources of starting phase information, are described. O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD