issue contents

Journal logoSTRUCTURAL

ISSN: 2059-7983

CCP4 Study Weekend 2020

Model building, validation and representation in MX and cryoEM
Edited by Jon Agirre, Robbie Joosten and Alan Roseman

This virtual issue contains articles from the 2020 CCP4 Study Weekend.

Highlighted illustration

Cover illustration: Structural Biology - The lost structure is a creative work that shows how solving a new structure is like an adventure, full of riddles and traps. The easier path never shows up the most amazing view of a landscape, like a revelation to human eyes for the first time. By Marco Salamina, Newcastle University.

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The prerequisites for density modification of maps from electron cryomicroscopy are examined and a procedure for incorporating model-based information is presented.

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This study shows the usefulness of integrating automated crystallographic model-building pipelines. We ran the four most used pipelines (ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE) alone and in pairwise combinations, and compared the structures that they produced based on structure completeness and Rfree.

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Two neural networks were trained to predict the correctness of protein residues by combining multiple validation metrics in Coot. Using the predicted correctness to automatically prune models led to significant improvements in the Buccaneer pipeline.

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A possible connection is discussed between hierarchical and other structures which maintain gender disparities in science and two instances where barriers to collaboration have hindered scientific progress.

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Atomic models derived from cryo-EM data with map resolutions of better than 5 Å were automatically re-refined. The results of the computations are publicly available on a web page.

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Virtual reality-specific tools for model building are possible, and can provide an order-of-magnitude speedup over mouse-and-keyboard tools in certain situations.

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TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is presented.

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The web server performs an assignment of nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids.

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Macromolecular atomic B-value distributions have been modelled using a mixture of shifted inverse-gamma distributions. B-value and resolution-dependent local ADP differences have also been applied for the validation of heavy atoms and ligands.

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This article provides a survey of available web services and tools for data delivery and visualization of macromolecular structures.

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The geometry of arginine shows more complexity than is accommodated by the standard restraints.

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