title: The Phenix software for automated determination of macromolecular structures.
abstract: X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. PDAdams@lbl.gov
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.forename: Gábor
authors.initials: G
authors.lastname: Bunkóczi
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Chen
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Echols
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Headd
authors.forename: Li-Wei
authors.initials: LW
authors.lastname: Hung
authors.forename: Swati
authors.initials: S
authors.lastname: Jain
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Kapral
authors.forename: Ralf W
authors.initials: RW
authors.lastname: Grosse Kunstleve
authors.forename: Airlie J
authors.initials: AJ
authors.lastname: McCoy
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Moriarty
authors.forename: Robert D
authors.initials: RD
authors.lastname: Oeffner
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Read
authors.forename: David C
authors.initials: DC
authors.lastname: Richardson
authors.forename: Jane S
authors.initials: JS
authors.lastname: Richardson
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Terwilliger
authors.forename: Peter H
authors.initials: PH
authors.lastname: Zwart
mesh_terms: D000465:Algorithms; D057205:Automation, Laboratory / Q000295:instrumentation / Q000379:methods*; D018360:Crystallography, X-Ray / Q000295:instrumentation / Q000379:methods; D003625:Data Collection / Q000379:methods*; D057166:High-Throughput Screening Assays; D015394:Molecular Structure; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins