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Toward Real Real-Space Refinement of Atomic Models

High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map w...

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Detalles Bibliográficos
Autores principales: Urzhumtsev, Alexandre G., Lunin, Vladimir Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9603565/
https://www.ncbi.nlm.nih.gov/pubmed/36292954
http://dx.doi.org/10.3390/ijms232012101
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author Urzhumtsev, Alexandre G.
Lunin, Vladimir Y.
author_facet Urzhumtsev, Alexandre G.
Lunin, Vladimir Y.
author_sort Urzhumtsev, Alexandre G.
collection PubMed
description High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples. These atomic images and, consequently, the maps for the respective models, can be expressed analytically as functions of coordinates, atomic displacement parameters, and the local resolution. This work discusses the practical feasibility of such calculation for the real-space refinement of macromolecular atomic models.
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spelling pubmed-96035652022-10-27 Toward Real Real-Space Refinement of Atomic Models Urzhumtsev, Alexandre G. Lunin, Vladimir Y. Int J Mol Sci Article High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples. These atomic images and, consequently, the maps for the respective models, can be expressed analytically as functions of coordinates, atomic displacement parameters, and the local resolution. This work discusses the practical feasibility of such calculation for the real-space refinement of macromolecular atomic models. MDPI 2022-10-11 /pmc/articles/PMC9603565/ /pubmed/36292954 http://dx.doi.org/10.3390/ijms232012101 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Urzhumtsev, Alexandre G.
Lunin, Vladimir Y.
Toward Real Real-Space Refinement of Atomic Models
title Toward Real Real-Space Refinement of Atomic Models
title_full Toward Real Real-Space Refinement of Atomic Models
title_fullStr Toward Real Real-Space Refinement of Atomic Models
title_full_unstemmed Toward Real Real-Space Refinement of Atomic Models
title_short Toward Real Real-Space Refinement of Atomic Models
title_sort toward real real-space refinement of atomic models
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9603565/
https://www.ncbi.nlm.nih.gov/pubmed/36292954
http://dx.doi.org/10.3390/ijms232012101
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