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

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.

doi:10.1107/S2059798319011471

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

Journal Article · Wed Oct 02 00:00:00 EDT 2019 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798319011471· OSTI ID:1617999

;

; Baker, Matthew L.; Bunkóczi, Gábor; Chen, Vincent B.; Croll, Tristan I.;

;

; Jain, Swati; McCoy, Airlie J.;

;

; Prisant, Michael G.;

; Richardson, Jane S.; Richardson, David C.; Sammito, Massimo D.;

; Stockwell, Duncan H. more »

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH1123.; 209407/Z/17/Z; AC02-05CH11231; 89233218CNA000001; P01GM063210; AC02-05CH1123

OSTI ID:: 1617999

Alternate ID(s):: OSTI ID: 1581374; OSTI ID: 1597368

Report Number(s):: LA-UR-19-31498; ACSDAD; PII: S2059798319011471

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Vol. 75 Journal Issue: 10; ISSN 2059-7983

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 2230 works

Citation information provided by
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