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Macromolecular structure determination using X‐rays, neutrons and electrons: recent developments in Phenix
Author(s) -
Liebschner Dorothee,
Afonine Pavel V.,
Baker Matthew L.,
Bunkóczi Gábor,
Chen Vincent B.,
Croll Tristan I.,
Hintze Bradley,
Hung Li-Wei,
Jain Swati,
McCoy Airlie J.,
Moriarty Nigel W.,
Oeffner Robert D.,
Poon Billy K.,
Prisant Michael G.,
Read Randy J.,
Richardson Jane S.,
Richardson David C.,
Sammito Massimo D.,
Sobolev Oleg V.,
Stockwell Duncan H.,
Terwilliger Thomas C.,
Urzhumtsev Alexandre G.,
Videau Lizbeth L.,
Williams Christopher J.,
Adams Paul D.
Publication year - 2019
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798319011471
Subject(s) - software , workflow , computer science , neutron , graphical user interface , automation , computational science , physics , engineering , nuclear physics , mechanical engineering , database , operating system
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.