Model-building and reduction of model bias in electron density maps

Abstract

Model-building is a key element of interpretation of electron density maps. Once a model is built it can then be used to further improve the map and hence improve the quality of a new model. It is helpful in this process to have effective methods for automated model-building and for ensuring that the resulting maps are minimally biased by the model. Many powerful methods for automatic interpretation of macromolecular electron density maps have been developed recently. Here we describe one method based on the identification of regular secondary structure and extension with fragments from known structures. We then describe the use of density modification procedures ("prime-and- switch") to reduce the model bias in maps calculated from models. Finally we describe how these prime-and-switch maps can be used as part of procedures to improve molecular replacement models just after initial placement and how this can extend the range of molecular replacement. © 2013 Springer Science+Business Media Dordrecht.