Acta Crystallographica Section D

Biological Crystallography

Volume 67, Part 4 (April 2011)


From crystal to structure with CCP4

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Human Thr160-phospho-CDK2-cyclin A complexed with a bis-anilino-pyrimidine inhibitor, PDB entry 2iw6. Drawn using CCP4mg (p. 386).

introduction


 

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Acta Cryst. (2011). D67, 233-234  [ doi:10.1107/S0907444911007578 ]

From crystal to structure with CCP4

K. Cowtan, P. Emsley and K. S. Wilson

Synopsis: An introduction to the proceedings of the CCP4 study weekend is given.

Online 18 March 2011


research papers


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Acta Cryst. (2011). D67, 235-242  [ doi:10.1107/S0907444910045749 ]

Overview of the CCP4 suite and current developments

M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin and K. S. Wilson

Synopsis: An overview of the CCP4 software suite for macromolecular crystallography is given.

Online 18 March 2011


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Acta Cryst. (2011). D67, 243-248  [ doi:10.1107/S0907444911007797 ]

It's all in the crystals...

Z. S. Derewenda

Synopsis: Protein surface engineering is increasingly used as a routine tool to enhance the crystallization propensity of proteins. Future possibilities include the use of multi-site protein variants, rational modulation of solubility and the development of strategies to tackle membrane proteins.

Online 18 March 2011


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Acta Cryst. (2011). D67, 249-260  [ doi:10.1107/S0907444911007943 ]

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

C. Morris, A. Pajon, S. L. Griffiths, E. Daniel, M. Savitsky, B. Lin, J. M. Diprose, A. Wilter da Silva, K. Pilicheva, P. Troshin, J. van Niekerk, N. Isaacs, J. Naismith, C. Nave, R. Blake, K. S. Wilson, D. I. Stuart, K. Henrick and R. M. Esnouf

Synopsis: The Protein Information Management System (PiMS) is described together with a discussion of how its features make it well suited to laboratories of all sizes.

Online 18 March 2011


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Acta Cryst. (2011). D67, 261-270  [ doi:10.1107/S0907444911007608 ]

The design of macromolecular crystallography diffraction experiments

G. Evans, D. Axford and R. L. Owen

Synopsis: Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented.

Online 18 March 2011


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Acta Cryst. (2011). D67, 271-281  [ doi:10.1107/S0907444910048675 ]

iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM

T. G. G. Battye, L. Kontogiannis, O. Johnson, H. R. Powell and A. G. W. Leslie

Synopsis: A new graphical user interface to the MOSFLM program has been developed to simplify the processing of macromolecular diffraction data. The interface, iMOSFLM, allows data processing via a series of clearly defined tasks and provides visual feedback on the progress of each stage.

Online 18 March 2011


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Acta Cryst. (2011). D67, 282-292  [ doi:10.1107/S090744491003982X ]

An introduction to data reduction: space-group determination, scaling and intensity statistics

P. R. Evans

Synopsis: A summary of how to run the data-reduction programs in the CCP4 suite.

Online 18 March 2011


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Acta Cryst. (2011). D67, 293-302  [ doi:10.1107/S0907444911007773 ]

Data processing and analysis with the autoPROC toolbox

C. Vonrhein, C. Flensburg, P. Keller, A. Sharff, O. Smart, W. Paciorek, T. Womack and G. Bricogne

Synopsis: Typical topics and problems encountered during data processing of diffraction experiments are discussed and the tools provided in the autoPROC software are described.

Online 18 March 2011


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Acta Cryst. (2011). D67, 303-312  [ doi:10.1107/S0907444910051218 ]

Improvement of molecular-replacement models with Sculptor

G. Bunkóczi and R. J. Read

Synopsis: The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used.

Online 18 March 2011


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Acta Cryst. (2011). D67, 313-323  [ doi:10.1107/S0907444911007530 ]

Evaluating the solution from MrBUMP and BALBES

R. M. Keegan, F. Long, V. J. Fazio, M. D. Winn, G. N. Murshudov and A. A. Vagin

Synopsis: The automated pipelines for molecular replacement MrBUMP and BALBES are reviewed, with an emphasis on understanding their output. Conclusions are drawn from their performance in extensive trials.

Online 18 March 2011


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Acta Cryst. (2011). D67, 324-330  [ doi:10.1107/S090744491004117X ]

The Protein Data Bank in Europe (PDBe): bringing structure to biology

S. Velankar and G. J. Kleywegt

Synopsis: Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described.

Online 18 March 2011


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Acta Cryst. (2011). D67, 331-337  [ doi:10.1107/S0907444910052224 ]

Recent advances in the CRANK software suite for experimental phasing

N. S. Pannu, W.-J. Waterreus, P. Skubák, I. Sikharulidze, J. P. Abrahams and R. A. G. de Graaff

Synopsis: Recent developments in the CRANK software suite for experimental phasing have led to many more structures being built automatically.

Online 18 March 2011


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2011). D67, 338-344  [ doi:10.1107/S0907444910051371 ]

Using SAD data in Phaser

R. J. Read and A. J. McCoy

Synopsis: SAD data can be used in Phaser to solve novel structures, supplement molecular-replacement phase information or identify anomalous scatterers from a final refined model.

Online 5 March 2011


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Acta Cryst. (2011). D67, 345-354  [ doi:10.1107/S0907444911002083 ]

Reduction of density-modification bias by [beta] correction

P. Skubák and N. S. Pannu

Synopsis: A cross-validation-based method for bias reduction in `classical' iterative density modification of experimental X-ray crystallography maps provides significantly more accurate phase-quality estimates and leads to improved automated model building.

Online 18 March 2011


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Acta Cryst. (2011). D67, 355-367  [ doi:10.1107/S0907444911001314 ]

REFMAC5 for the refinement of macromolecular crystal structures

G. N. Murshudov, P. Skubák, A. A. Lebedev, N. S. Pannu, R. A. Steiner, R. A. Nicholls, M. D. Winn, F. Long and A. A. Vagin

Synopsis: The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.

Online 18 March 2011


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2011). D67, 368-375  [ doi:10.1107/S0907444910039934 ]

Distributed structure determination at the JCSG

H. van den Bedem, G. Wolf, Q. Xu and A. M. Deacon

Synopsis: The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures.

Online 18 March 2011


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Acta Cryst. (2011). D67, 376-385  [ doi:10.1107/S0907444911007232 ]

Macromolecular complexes in crystals and solutions

E. Krissinel

Synopsis: Methods for the analysis of the relationship between macromolecular complexes and interactions and their manifestation in crystal packing are described and discussed.

Online 18 March 2011


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Acta Cryst. (2011). D67, 386-394  [ doi:10.1107/S0907444911007281 ]

Presenting your structures: the CCP4mg molecular-graphics software

S. McNicholas, E. Potterton, K. S. Wilson and M. E. M. Noble

Synopsis: The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment.

Online 18 March 2011


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