Automatic multiple-zone rigid-body refinement with a large convergence radius

By Pavel V. Afonine, R. Grosse-Kunstleve, Alexandre Urzhumtsev, Paul D. Adams. 2009

51 citations recorded by the source corpus.

Systematic investigation of a large number of trial rigid-body refinements leads to an optimized multiple-zone protocol with a larger convergence radius.

Subfields: Materials Chemistry, Statistics and Probability

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “In Phenix, phases can be determined by experimental phasing or by molecular replacement (Adams, Afonine et al., 2009).”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “A highly optimized automatic rigid-body refinement protocol (Afonine et al., 2009) is available to facilitate initial stages of refinement when the starting model may contain large errors or as the only option at very low resolution.”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “…tasks allow optimization using simulated annealing (SA; Brunger et al., 1987), morphing (Terwilliger at al., 2013), rigid-body refinement (see Afonine et al., 2009 and references within) and systematic residue side-chain optimizations using grid searches in torsion χ-angle space (Oldfield,…”
Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition (2018, methodology): “When computational tools are developed, it is desirable to exercise the new algorithms using all available data and models (see, for example, Afonine et al., 2009; Weichenberger et al., 2015).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, background): “At very low-resolution limits it may only be appropriate to refine coordinates as rigid bodies[56].”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “In simple cases this can be achieved using rigidbody refinement (available in various packages; see, for example, Afonine et al., 2009).”
Joint X-ray and neutron refinement with phenix.refine. (2010, methodology): “…where an interatomic scatterers (IAS) model can be used to model bonding features (Afonine et al., 2007), to highly optimized automatic rigidbody refinement (Afonine et al., 2009) and torsion-angle parameterized dynamics (Grosse-Kunstleve et al., 2009), which are important at low resolution.”