Real-space refinement in Phenix for cryo-EM and crystallography
Real-space refinement in Phenix for cryo-EM and crystallography
Abstract This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 ? or better shows significant improvement of models and the fit of these models to the target maps. SynopsisA description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.
Read Randy J.、Poon Billy K.、Terwilliger Thomas C.、Adams Paul D.、Urzhumtsev Alexandre、Sobolev Oleg V.、Afonine Pavel V.
Cambridge Institute for Medical Research, University o f CambridgeMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBioscience Division, Los Alamos National Laboratory||New Mexico ConsortiumMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory||Department o f Bioengineering, University of California BerkeleyCentre for Integrative Biology, Institut de G¨|n¨|tique et de Biologie Mol¨|culaire et Cellulaire||Universit¨| de Lorraine, Facult¨| des Sciences et TechnologiesMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory
生物科学研究方法、生物科学研究技术生物物理学计算技术、计算机技术
real-space refinementcrystallographycryo-EMmap interpolationPhenix
Read Randy J.,Poon Billy K.,Terwilliger Thomas C.,Adams Paul D.,Urzhumtsev Alexandre,Sobolev Oleg V.,Afonine Pavel V..Real-space refinement in Phenix for cryo-EM and crystallography[EB/OL].(2025-03-28)[2025-08-10].https://www.biorxiv.org/content/10.1101/249607.点此复制
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