title: Towards automated crystallographic structure refinement with phenix.refine.
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.
authors.affiliation: Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA. pafonine@lbl.gov
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.forename: Ralf W
authors.initials: RW
authors.lastname: Grosse-Kunstleve
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Echols
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Headd
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Moriarty
authors.forename: Marat
authors.initials: M
authors.lastname: Mustyakimov
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Terwilliger
authors.forename: Alexandre
authors.initials: A
authors.lastname: Urzhumtsev
authors.forename: Peter H
authors.initials: PH
authors.lastname: Zwart
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D012984:Software