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Advancing Methods for Biomolecular Crystallography pp 193–203Cite as

Model-Building and Reduction of Model Bias in Electron Density Maps

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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.

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Acknowledgments

The author is most grateful to the entire crystallographic community for feedback on methods development and to the other members of the Phenix team for development of the algorithms and software that form a foundation for the methods described here, and to the NIH for generous support of the Phenix project (PI, Paul Adams).

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Authors and Affiliations

  1. Los Alamos National Laboratory, Bioscience Division and Los Alamos Institutes, Los Alamos, NM, 87545, USA

    Thomas C. Terwilliger

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  1. Thomas C. Terwilliger
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Correspondence to Thomas C. Terwilliger .

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Editors and Affiliations

  1. , Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, United Kingdom

    Randy Read

  2. Fac.des Sciences et des Technologies, Physics Department, Université de Lorraine, Blvd. des Aiguillettes 1, Vandoeuvre-lès-Nancy, 54506, France

    Alexandre G. Urzhumtsev

  3. , Institute of Mathematical Problems of Bi, Russian Academy of Sciences, Institutskaya st. 4, Pushchino, 142290, Russia

    Vladimir Y. Lunin

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Terwilliger, T.C. (2013). Model-Building and Reduction of Model Bias in Electron Density Maps. In: Read, R., Urzhumtsev, A., Lunin, V. (eds) Advancing Methods for Biomolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6232-9_18

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