Automatic multiple-zone rigid-body refinement with a large convergence radius
Pavel V. Afonine,Ralf W. Grosse-Kunstleve,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +5 more
TLDR
Systematic investigation of a large number of trial rigid-body refinements leads to an optimized multiple-zone protocol with a larger convergence radius.Abstract:
Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.read more
Citations
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Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Towards automated crystallographic structure refinement with phenix.refine
Pavel V. Afonine,Ralf W. Grosse-Kunstleve,Nathaniel Echols,Jeffrey J. Headd,Nigel W. Moriarty,Marat Mustyakimov,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Peter H. Zwart,Paul D. Adams,Paul D. Adams +11 more
TL;DR: 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.
Journal ArticleDOI
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Dorothee Liebschner,Pavel V. Afonine,Matthew L. Baker,Gábor Bunkóczi,Vincent B. Chen,Tristan I. Croll,Bradley J. Hintze,Li-Wei Hung,Swati Jain,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Billy K. Poon,Michael G. Prisant,Randy J. Read,Jane S. Richardson,David S. Richardson,Sammito,Oleg V. Sobolev,Duncan H. Stockwell,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Lizbeth L. Videau,Carmen J. Williams,Paul D. Adams,Paul D. Adams +26 more
TL;DR: Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
Journal ArticleDOI
Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
TL;DR: In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.
References
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