Acta Crystallographica Section D

Biological Crystallography

Volume 68, Part 4 (April 2012)


Model building, refinement and validation

Proceedings of the CCP4 study weekend

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


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Speakers at the 2011 CCP4 Study Weekend.

introduction


 

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Acta Cryst. (2012). D68, 325-327  [ doi:10.1107/S0907444912002090 ]

Model building, refinement and validation

R. A. Steiner and B. Rupp

Synopsis: An introduction to the proceedings of the CCP4 Study Weekend held at the University of Warwick on the 6-7 January 2011.

Online 16 March 2012


research papers


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Acta Cryst. (2012). D68, 328-335  [ doi:10.1107/S0907444911039655 ]

Completion of autobuilt protein models using a database of protein fragments

K. Cowtan

Synopsis: Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules.

Online 16 March 2012


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Acta Cryst. (2012). D68, 336-343  [ doi:10.1107/S0907444911056071 ]

Practical structure solution with ARCIMBOLDO

D. Rodríguez, M. Sammito, K. Meindl, I. M. de Ilarduya, M. Potratz, G. M. Sheldrick and I. Usón

Synopsis: ARCIMBOLDO combines the location of small fragments with Phaser and density modification with SHELXE of all possible Phaser solutions. Its uses are explained and illustrated through practical test cases.

Online 16 March 2012


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

Acta Cryst. (2012). D68, 344-351  [ doi:10.1107/S0907444911049791 ]

Conventions and workflows for using Situs

W. Wriggers

Synopsis: Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described.

Online 16 March 2012


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Acta Cryst. (2012). D68, 352-367  [ doi:10.1107/S0907444912001308 ]

Towards automated crystallographic structure refinement with phenix.refine

P. V. Afonine, R. W. Grosse-Kunstleve, N. Echols, J. J. Headd, N. W. Moriarty, M. Mustyakimov, T. C. Terwilliger, A. Urzhumtsev, P. H. Zwart and P. D. Adams

Synopsis: phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

Online 16 March 2012


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

Acta Cryst. (2012). D68, 368-380  [ doi:10.1107/S0907444911056058 ]

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

O. S. Smart, T. O. Womack, C. Flensburg, P. Keller, W. Paciorek, A. Sharff, C. Vonrhein and G. Bricogne

Synopsis: Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled.

PDB references: 3syu, 3urp and 3v56

Online 16 March 2012


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Acta Cryst. (2012). D68, 381-390  [ doi:10.1107/S0907444911047834 ]

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

J. J. Headd, N. Echols, P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, N. W. Moriarty, D. C. Richardson, J. S. Richardson and P. D. Adams

Synopsis: Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.

Online 16 March 2012


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Acta Cryst. (2012). D68, 391-403  [ doi:10.1107/S090744491104978X ]

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

A. T. Brunger, D. Das, A. M. Deacon, J. Grant, T. C. Terwilliger, R. J. Read, P. D. Adams, M. Levitt and G. F. Schröder

Synopsis: DEN refinement and automated model building with AutoBuild were used to determine the structure of a putative succinyl-diaminopimelate desuccinylase from C. glutamicum. This difficult case of molecular-replacement phasing shows that the synergism between DEN refinement and AutoBuild outperforms standard refinement protocols.

PDB reference: 3tx8

Online 16 March 2012


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Acta Cryst. (2012). D68, 404-417  [ doi:10.1107/S090744491105606X ]

Low-resolution refinement tools in REFMAC5

R. A. Nicholls, F. Long and G. N. Murshudov

Synopsis: Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening.

Online 16 March 2012


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Acta Cryst. (2012). D68, 418-424  [ doi:10.1107/S0907444912006737 ]

Tetartohedral twinning could happen to you too

P. Roversi, E. Blanc, S. Johnson and S. M. Lea

Synopsis: A review of published tetartohedrally twinned macromolecular structures is presented, together with details of the recent structure determination of triclinic tetartohedrally twinned crystals of human complement factor I.

Online 16 March 2012


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Acta Cryst. (2012). D68, 425-430  [ doi:10.1107/S0907444912000200 ]

Handling ligands with Coot

J. É. Debreczeni and P. Emsley

Synopsis: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of ligand tools is presented.

Online 16 March 2012


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Acta Cryst. (2012). D68, 431-440  [ doi:10.1107/S090744491200251X ]

JLigand: a graphical tool for the CCP4 template-restraint library

A. A. Lebedev, P. Young, M. N. Isupov, O. V. Moroz, A. A. Vagin and G. N. Murshudov

Synopsis: The CCP4 template-restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages.

Online 17 March 2012


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Acta Cryst. (2012). D68, 441-445  [ doi:10.1107/S0907444912001084 ]

Challenges and surprises that arise with nucleic acids during model building and refinement

W. G. Scott

Synopsis: The challenges that arise in nucleic acid model building as a consequence of their simpler and more symmetric super-secondary structures are addressed.

Online 16 March 2012


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Acta Cryst. (2012). D68, 446-453  [ doi:10.1107/S0907444911050712 ]

Use of noncrystallographic symmetry for automated model building at medium to low resolution

T. Wiegels and V. S. Lamzin

Synopsis: Noncrystallographic symmetry is automatically detected and used to achieve higher completeness and greater accuracy of automatically built protein structures at resolutions of 2.3 Å or poorer.

Online 16 March 2012


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Acta Cryst. (2012). D68, 454-467  [ doi:10.1107/S0907444911035918 ]

Statistical quality indicators for electron-density maps

I. J. Tickle

Synopsis: A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described.

Online 16 March 2012


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Acta Cryst. (2012). D68, 468-477  [ doi:10.1107/S0907444911028320 ]

To B or not to B: a question of resolution?

E. A. Merritt

Synopsis: A simple rule of thumb based on resolution is not adequate to identify the best treatment of atomic displacements in macromolecular structural models. The choice to use isotropic B factors, anisotropic B factors, TLS models or some combination of the three should be validated through statistical analysis of the model refinement.

Online 16 March 2012


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Acta Cryst. (2012). D68, 478-483  [ doi:10.1107/S0907444911050359 ]

Implementing an X-ray validation pipeline for the Protein Data Bank

S. Gore, S. Velankar and G. J. Kleywegt

Synopsis: The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described.

Online 16 March 2012


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Acta Cryst. (2012). D68, 484-496  [ doi:10.1107/S0907444911054515 ]

PDB_REDO: constructive validation, more than just looking for errors

R. P. Joosten, K. Joosten, G. N. Murshudov and A. Perrakis

Synopsis: The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.

Online 16 March 2012


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