Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

Journal Article · Tue Jan 01 00:00:00 EST 2008 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S090744490705024X· OSTI ID:22347689

Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Moriarty, Nigel W.; Zwart, Peter H. ^[1]; Hung, Li-Wei ^[2]; Read, Randy J. ^[3]

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1. Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720 (United States)
2. Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545 (United States)
3. Department of Haematology, University of Cambridge, Cambridge CB2 0XY (United Kingdom)

The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods. The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 Å, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

• OSTI ID: 22347689
• Journal Information: Acta Crystallographica. Section D: Biological Crystallography, Vol. 64, Issue Pt 1; Other Information: PMCID: PMC2394820; PUBLISHER-ID: ba5109; PMID: 18094468; OAI: oai:pubmedcentral.nih.gov:2394820; Copyright (c) International Union of Crystallography 2008; This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
• Country of Publication: Denmark
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
ALGORITHMS
CHAINS
DENSITY
ELECTRON DENSITY
ELECTRONS
MODIFICATIONS
MOLECULES
OPTIMIZATION
R FACTORS
RESOLUTION
SOLVENTS