PVMR: assembling small helix fragments as structural solutions for molecular replacement

A new real-space implementation of the molecular-replacement method is described. The method locates the search model in the target crystal by maximizing the matching between the search-model vectors and the Patterson self and cross vectors. In previous work, a new rotation function was introduced for the molecular-replacement method [Jiang (2008). Acta Cryst. D64, 561-566]. This rotation function is calculated by matching the search model directly with both the Patterson self and cross vectors in real space. All the matches are summed and averaged to enhance the overall signal-to-noise ratio for a given orientation of the search model. Recently, to avoid the dependence of the weights derived from the linear regression on the properties of the search model and the target crystal structure, such as secondary structures, space groups and cell parameters, a dynamic correlation coefficient has been designed and used as the total rotation function score [Jiang & Ding (2010). Chin. Phys. B, 19, 106101]. This work further extends this idea to the implementation of translation search. A new real- or direct-space translation function has been implemented by matching the cross vectors between the symmetry mates of the search model to the Patterson cross vectors. This method enables effective searching for small helix fragments in the target crystal. Although the solution model assembled by using multiple fragments of helix is insufficient to start ab initio phasing of the target crystal, it can be used to identify the known protein folds in the Protein Data Bank that are homologous to the target structure. It can also be combined with other experimental and theoretical models to screen and select for better search models for molecular replacement.