Overview of the CCP4 suite and current developments

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

It's all in the crystals…

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.

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

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.

The design of macromolecular crystallography diffraction experiments

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

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

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.

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

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

Data processing and analysis with the autoPROC toolbox

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

Improvement of molecular-replacement models with Sculptor

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

Evaluating the solution from MrBUMP and BALBES

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.

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

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.

Recent advances in the CRANK software suite for experimental phasing

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

Using SAD data in Phaser

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.

Reduction of density-modification bias by β correction

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.

REFMAC5 for the refinement of macromolecular crystal structures

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

Distributed structure determination at the JCSG

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.

Macromolecular complexes in crystals and solutions

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

Presenting your structures: the CCP4mg molecular-graphics software

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.