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      Towards automated crystallographic structure refinement with phenix.refine

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          Abstract

          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.

          Abstract

          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. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. 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.

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          Author and article information

          Conference
          Acta Crystallogr D Biol Crystallogr
          Acta Crystallogr. D Biol. Crystallogr
          Acta Cryst. D
          Acta Crystallographica Section D: Biological Crystallography
          International Union of Crystallography
          0907-4449
          1399-0047
          01 April 2012
          16 March 2012
          16 March 2012
          : 68
          : Pt 4 ( publisher-idID: d120400 )
          : 352-367
          Affiliations
          [a ]simpleLawrence Berkeley National Laboratory , One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
          [b ]simpleLos Alamos National Laboratory , M888, Los Alamos, NM 87545, USA
          [c ]IGBMC, simpleCNRS–INSERM–UdS , 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
          [d ]Département de Physique, Faculté des Sciences et des Technologies, simpleUniversité Henri Poincaré, Nancy 1 , BP 239, 54506 Vandoeuvre-lès-Nancy, France
          [e ]Department of Bioengineering, simpleUniversity of California Berkeley , Berkeley, CA 94720, USA
          Author notes
          Correspondence e-mail: pafonine@ 123456lbl.gov
          Article
          ba5180 ABCRE6 S0907444912001308
          10.1107/S0907444912001308
          3322595
          22505256
          © Afonine et al. 2012

          This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

          Model building, refinement and validation
          Categories
          Research Papers

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