Making the most of your search model

In cases with high sequence homology, Molecular Replacement (MR) is usually a trivial exercise. But, as the structural homology gets lower and lower, solving the structure by means of MR becomes increasingly difficult. Conventional wisdom holds that an RMSD of about 1.5Å between the search model and the actual structure constitutes the limit at which MR can still be used. Fortunately, the MR programs get better, and crystallographers think of new and clever tricks, thereby pushing the limits of the method further and further. On the program end, Axel Brünger has introduced PC-refinement into X-PLOR [1], which is a useful tool to sort the rotation function boys from the rotation function men, and to improve the orientation of the entire molecule or of individual domains prior to the translation function. More recently, he has introduced a direct rotation function [2] which may help in cases where other approaches fail. Liang Tong has developed a locked rotation function [3], which uses knowledge of the rotational relationships between NCS-related molecules to increase the signal-to-noise ratio of the rotation function. More recently, he has also implemented a locked translation function [4]. Jorge Navaza, finally, has carefully redone the mathematics of the fast rotation and translation functions, and his package AMoRe [5] has solved numerous problems which could not be solved by other programs. In this article we will address some of the tricks that the crystallographer can use in order to produce a more suitable search model in cases where the standard approach is not immediately successfull. We shall also discuss some software tools that can be of help in this process.