From crystal to structure with CCP4

An introduction to the 2017 CCP4 Study Weekend Special Issue.

CCP4i2: the new graphical user interface to the CCP4 program suite

CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.

DIALS: implementation and evaluation of a new integration package

A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography.

Maximum-likelihood determination of anomalous substructures

Likelihood-based SAD substructure determination can be initiated using a fast translation-search algorithm based on a linear approximation to the SAD likelihood target, followed by log-likelihood-gradient map completion.

An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features

Experimental phasing of macromolecular crystals is described and explained, with the emphasis on its implementation in the programs SHELXC, SHELXD and SHELXE, which are also used in a number of macromolecular structure-solution pipelines.

Substructure determination using phase-retrieval techniques

The relaxed averaged alternating reflections (RAAR) phase-retrieval method has been applied to crystallography for the first time and has been shown to outperform charge flipping in anomalous substructure determination.

Macromolecular refinement by model morphing using non-atomic parameterizations

A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data.

Model validation: local diagnosis, correction and when to quit

An overview is provided of current crystallographic model validation of proteins and RNA, both foundations and criteria, at all resolution ranges, together with advice on how to correct specific types of problems and when you should not try so hard that you are overfitting.

Distributed computing for macromolecular crystallography

The paper describes recent CCP4 initiatives and projects aimed at bringing software and data services which utilize distributed computational resources to users.

Where is crystallography going?

Macromolecular crystallography has provided results that underpin much biological discovery and there is still scope for further development; however, a revolution in electron imaging now means that it can also routinely provide detailed atomic-level descriptions. This article attempts to tease out where crystallography is going and consider what its place might be in the new landscape.