Kevin Cowtan

Features and development of Coot

Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of development and available features are presented.

Overview of the CCP4 suite and current developments

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

Developments in the CCP4 molecular-graphics project

Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.

Miscellaneous algorithms for density modification.

Various algorithms are described, developed for the dm density modification package, which have not been described elsewhere. Methods are described for the following problems: determination of the absolute scale and overall temperature factor of a data set, by a method which is less dependent on data resolution than Wilson statistics; an efficient interpolation algorithm for averaging and its application to refinement of averaging operators; a method for the automatic determination of averaging masks.

Density modification for macromolecular phase improvement

Density modification provides a simple and largely automatic tool for improving phase estimates for observed structure factors. The phase information arises from a combination of the known structure factor magnitudes, the current phase estimates, and stereochemical information. The magnitudes, the current phase estimates, and stereochemical information. The addition of these phase information derived from theoretical sources renders new structures amenable to solution, and reduces the effort required to solve other structures. A diverse array of techniques which have been applied to the phase improvement problem are reviewed.

Phase combination and cross validation in iterated density-modification calculations.

A variety of density-modification techniques are now available for improving electron-density maps in accordance with known chemical information. This modification must, however, always be constrained by consistency with the experimental data. This is conventionally achieved by alternating cycles of map modification in real space with recombination with the experimental data in reciprocal space. The phase recombination is based upon the assumption that the density-modified map may be treated as a partial model of the structure which contains information independent of the experimentally derived phases. This assumption is shown to be incorrect, and an alternative procedure is investigated which as a side effect allows calculation of a free R factor.

Recent developments in classical density modification

Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation. These methods have been implemented in a new computer program, Parrot.

The CCP4 molecular-graphics project

This new package will provide easy-to-use access to crystallographic structure solution, model building and structure analysis. It will be possible for any developer to integrate scientific software into the system.

Improvement of Macromolecular Electron-Density Maps by the Simultaneous Application of Real and Reciprocal Space Constraints

A general scheme for the improvement of electron-density maps is described which combines information from real and reciprocal space. The use of Sayres equation, solvent flattening and histogram matching within this scheme has been described previously [Main (1990). Acta Cryst. A46, 372-377]. Non-crystallographic symmetry averaging, the use of a partial structure and constraints on individual structure factors have now been added. A computer program, SQUASH, is described which applies all these constraints simultaneously. Its application to the maps of several structures has been successful, particularly so when non-crystallographic symmetry is present. Uninterpretable maps have been improved to the point where a significant amount of the structure can be recognized. Applying the constraints simultaneously is more powerful than applying them all in series.

Fitting molecular fragments into electron density

A number of techniques for the location of small and medium-sized model fragments in experimentally phased electron-density maps are explored. The application of one of these techniques to automated model building is discussed.