Acta Crystallographica Section D

Biological Crystallography

Volume 60, Part 12 Number 1 (December 2004)


Model building and refinement

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: This is a Kendrew wire model of alcohol dehydrogenase that is about to undergo a round of rebuilding by Maelle Cambillau (p. 2115).

research papers


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Acta Cryst. (2004). D60, 2115-2125  [ doi:10.1107/S0907444904023509 ]

Interactive electron-density map interpretation: from INTER to O

T. A. Jones

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2126-2132  [ doi:10.1107/S0907444904019158 ]

Coot: model-building tools for molecular graphics

P. Emsley and K. Cowtan

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2133-2143  [ doi:10.1107/S090744490402061X ]

Statistical pattern recognition for macromolecular crystallographers

R. J. Morris

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2144-2149  [ doi:10.1107/S0907444904019535 ]

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

T. C. Terwilliger

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2150-2155  [ doi:10.1107/S0907444904019055 ]

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

V. Calderone

Synopsis: 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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2156-2168  [ doi:10.1107/S090744490402356X ]

Introduction to macromolecular refinement

D. E. Tronrud

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2169-2183  [ doi:10.1107/S0907444904016038 ]

Liking likelihood

A. J. McCoy

Synopsis: An explanation of maximum likelihood in macromolecular crystallography.

Online 26 November 2004


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2004). D60, 2184-2195  [ doi:10.1107/S0907444904023510 ]

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

A. A. Vagin, R. A. Steiner, A. A. Lebedev, L. Potterton, S. McNicholas, F. Long and G. N. Murshudov

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2196-2201  [ doi:10.1107/S0907444904019079 ]

Direct incorporation of experimental phase information in model refinement

P. Skubák, G. N. Murshudov and N. S. Pannu

Synopsis: 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.

Online 26 November 2004


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2004). D60, 2202-2209  [ doi:10.1107/S0907444904008996 ]

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

S. H. W. Scheres and P. Gros

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2210-2221  [ doi:10.1107/S0907444904016427 ]

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

E. Blanc, P. Roversi, C. Vonrhein, C. Flensburg, S. M. Lea and G. Bricogne

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2222-2229  [ doi:10.1107/S0907444904027556 ]

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

S. X. Cohen, R. J. Morris, F. J. Fernandez, M. Ben Jelloul, M. Kakaris, V. Parthasarathy, V. S. Lamzin, G. J. Kleywegt and A. Perrakis

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2230-2239  [ doi:10.1107/S0907444904012995 ]

Modelling bound ligands in protein crystal structures

P. H. Zwart, G. G. Langer and V. S. Lamzin

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2240-2249  [ doi:10.1107/S0907444904013253 ]

The Uppsala Electron-Density Server

G. J. Kleywegt, M. R. Harris, J. Zou, T. C. Taylor, A. Wählby and T. A. Jones

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2250-2255  [ doi:10.1107/S0907444904027167 ]

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

E. B. Krissinel, M. D. Winn, C. C. Ballard, A. W. Ashton, P. Patel, E. A. Potterton, S. J. McNicholas, K. D. Cowtan and P. Emsley

Synopsis: Description of the new CCP4 Coordinate Library.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2256-2268  [ doi:10.1107/S0907444904026460 ]

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

E. Krissinel and K. Henrick

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2269-2275  [ doi:10.1107/S0907444904023492 ]

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

T. R. Schneider

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

Online 26 November 2004


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Acta Cryst. (2004). D60, 2276-2279  [ doi:10.1107/S0907444904025491 ]

Differential evolution for protein crystallographic optimizations

D. E. McRee

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2280-2287  [ doi:10.1107/S0907444904019171 ]

Dynamite: a simple way to gain insight into protein motions

C. P. Barrett, B. A. Hall and M. E. M. Noble

Synopsis: 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.

Online 26 November 2004


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Acta Cryst. (2004). D60, 2288-2294  [ doi:10.1107/S0907444904023716 ]

Developments in the CCP4 molecular-graphics project

L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, P. Emsley, G. N. Murshudov, S. Cohen, A. Perrakis and M. Noble

Synopsis: 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.

Online 26 November 2004


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