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Boxes of Model Building and Visualization

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Protein Crystallography

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1607))

Abstract

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user’s push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

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Acknowledgments

This work is dedicated to my PhD supervisor Robert Huber at the occasion of his 80s anniversary. Jürgen Plitzko, Tom Goddard, and Tristan Croll are gratefully acknowledged for generation of several figures. Jürgen Plitzko wrote parts of the text concerning the EM structure determination. My coworker Ajda Taler Verčič helped me with formatting the text and sorting out references. Funding was provided by the Structural Biology grant P1-0048 and by the Infrastructural Funds to Centre of Excellence CIPKeBiP, both provided by Slovenian Research Agency.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia

    Dušan Turk

  2. Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia

    Dušan Turk

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  1. Dušan Turk
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Correspondence to Dušan Turk .

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Editors and Affiliations

  1. Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, USA

    Alexander Wlodawer

  2. Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois, USA

    Zbigniew Dauter

  3. Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland

    Mariusz Jaskolski

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Turk, D. (2017). Boxes of Model Building and Visualization. In: Wlodawer, A., Dauter, Z., Jaskolski, M. (eds) Protein Crystallography. Methods in Molecular Biology, vol 1607. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7000-1_21

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  • DOI: https://doi.org/10.1007/978-1-4939-7000-1_21

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