MrBUMP: automated search model discovery and preparation for structure solution by molecular replacement
Martyn Winn, Ronan M. Keegan, Noah D. Stein · Acta Crystallographica Section A Foundations of Crystallography · 2006
MrBUMP is a new automated procedure for structure solution by Molecular Replacement.The aim of MrBUMP is to start from native structure factors and a target sequence, and deliver a positioned and partly refined model, suitable for further model re-building, model completion and/or refinement.In the highest level view, the process consists of three stages.In the first stage, the target sequence is used to search for related proteins in the Protein Data Bank.This gives a list of template chains, domains and multimers, which is passed to the search model preparation stage.Up to three search models are generated for each template, differing in the alignment used and the treatment of side chains.Finally, given a list of putative search models, a subset is passed to the MR stage which uses Phaser or Molrep.Initial restrained refinement of the positioned model is used to assess the putative solution.MrBUMP consists of a set of Python scripts which link together established programs.MrBUMP differs from other molecular replacement pipelines in two ways: Firstly, there is a greater emphasis on the discovery of potential search models.A list of search models is generated and many are tried in molecular replacement with the aim of finding the optimum model.Secondly, Mr Bump is intended for general use within the CCP4 software suite, and is designed to be portable and flexible.m03.o04