Biomedical subjects

K D Cowtan

Publications and source records attributed to K D Cowtan.

5 recordsLinked to original sources

PubMed2006

SPINE workshop on automated X-ray analysis: a progress report.

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.

Algorithms↗

PubMed2004

The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography.

The new CCP4 Coordinate Library is a development aiming to provide a common layer of coordinate-related functionality to the existing applications in the CCP4 suite, as well as a variety of tools that can simplify the design of new applications where they relate to atomic coordinates. The Library comprises a wide spectrum of useful functions, ranging from parsing coordinate formats and elementary editing operations on the coordinate hierarchy of biomolecules, to high-level functionality such as calculation of secondary structure, interatomic bonds, atomic contacts, symmetry transformations, structure superposition and many others. Most of the functions are available in a C++ object interface; however, a Fortran interface is provided for compatibility with older CCP4 applications. The paper describes the general principles of the Library design and the most important functionality. The Library, together with documentation, is available under the LGPL license from the CCP4 suite version 5.0 and higher.

Computer Graphics↗

PubMed1999

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.

Algorithms↗

PubMed1996

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.

Journal Article↗

PubMed1993

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 Sayre's 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.

Journal Article↗