Interactive electron-density map interpretation: from INTER to O

A review of the author's computer-graphics developments is presented, as well as a description of a secondary-structure template-building system that works in conjunction with a new sequence-decoration scheme.

Coot: model-building tools for molecular graphics

Coot provides both a set of libraries and a stand-alone application for model building and map fitting using molecular graphics.

Statistical pattern recognition for macromolecular crystallographers

An overview of statistical pattern-recognition techniques is given with a bias towards crystallographic applications, especially automated model building.

Using prime-and-switch phasing to reduce model bias in molecular replacement

Prime-and-switch phasing can reduce atomic model bias in model-based electron-density maps.

Practical aspects of the integration of different software in protein structure solution

A few examples are presented on the use of different programs to achieve the goal of structure solution and the associated practicalities that can make the difference between solving or not solving a structure

Introduction to macromolecular refinement

A general introduction to the models and methods used in contemporary macromolecular refinement programs.

Liking likelihood

An explanation of maximum likelihood in macromolecular crystallography.

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

The organization and use of a dictionary of monomers and links for restrained macromolecular refinement with application in the program REFMAC5 is described.

Direct incorporation of experimental phase information in model refinement

A multivariate likelihood function that directly and dynamically incorporates experimental phase information in model refinement leads to an automatically built model when current functions fail.

The potentials of conditional optimization in phasing and model building of protein crystal structures

The N-particle modelling method of conditional optimization is discussed. Its model-building potential at medium to low (2.4–3.0 Å) resolution is compared with ARP/wARP and RESOLVE and preliminary results indicate its potential for phasing by ab initio modelling.

Refinement of severely incomplete structures with maximum likelihood in BUSTER–TNT

BUSTER–TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the unbuilt parts of the structure through low-resolution probability distributions for the random positions of the missing atoms.

Towards complete validated models in the next generation of ARP/wARP

The new ARP/wARP control system, rebuilding and validation modules are described.

Modelling bound ligands in protein crystal structures

Algorithms and scoring functions for automated interpretation of electron density of protein-bound ligands are described.

The Uppsala Electron-Density Server

Details of the Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) are described, including the methods and programs that are used to calculate the maps and the files and information that are made available through the server.

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

Description of the new CCP4 Coordinate Library.

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

A description of a new tool for the comparison of protein structures in three dimensions and analysis of structure similarity scores.

Domain identification by iterative analysis of error-scaled difference distance matrices

The identification of the four structural domains of Src kinase by iterative analysis of error-scaled difference distance matrices is described.

Differential evolution for protein crystallographic optimizations

Genetic algorithms have been implemented for real-space optimizations in a new fitting program, MIfit, for real-space refinement of protein models and heavy-atom searches. Some programming tips and examples are presented to aid others who might want to use genetic algorithms in their own work.

Dynamite: a simple way to gain insight into protein motions

A public web-based facility to infer, analyse and graphically represent the likely modes of a protein motion, starting from a static structure, is presented.

Developments in the CCP4 molecular-graphics project

The CCP4 molecular-graphics project will provide a wide range of graphics-related functionality for crystallography and related disciplines. The current status and future plans are presented.