Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Journal Article (Journal Article)

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

Full Text

Duke Authors

Cited Authors

  • Liebschner, D; Afonine, PV; Baker, ML; Bunkóczi, G; Chen, VB; Croll, TI; Hintze, B; Hung, LW; Jain, S; McCoy, AJ; Moriarty, NW; Oeffner, RD; Poon, BK; Prisant, MG; Read, RJ; Richardson, JS; Richardson, DC; Sammito, MD; Sobolev, OV; Stockwell, DH; Terwilliger, TC; Urzhumtsev, AG; Videau, LL; Williams, CJ; Adams, PD

Published Date

  • October 1, 2019

Published In

Volume / Issue

  • 75 / Pt 10

Start / End Page

  • 861 - 877

PubMed ID

  • 31588918

Pubmed Central ID

  • PMC6778852

Electronic International Standard Serial Number (EISSN)

  • 2059-7983

Digital Object Identifier (DOI)

  • 10.1107/S2059798319011471


  • eng

Conference Location

  • United States