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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/20/12101 |
| _version_ | 1797472813400981504 |
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| author | Alexandre G. Urzhumtsev Vladimir Y. Lunin |
| author_facet | Alexandre G. Urzhumtsev Vladimir Y. Lunin |
| author_sort | Alexandre G. Urzhumtsev |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T20:06:29Z |
| format | Article |
| id | doaj.art-1fdeda4e5624445ea3423b9d7179b6f4 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T20:06:29Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1fdeda4e5624445ea3423b9d7179b6f42023-11-24T00:28:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-10-0123201210110.3390/ijms232012101Toward Real Real-Space Refinement of Atomic ModelsAlexandre G. Urzhumtsev0Vladimir Y. Lunin1Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM-UdS, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, FranceInstitute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, RussiaHigh-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.https://www.mdpi.com/1422-0067/23/20/12101real-space refinementrefinement programsatomic imagesmap calculationshell decompositioninhomogeneous resolution |
| spellingShingle | Alexandre G. Urzhumtsev Vladimir Y. Lunin Toward Real Real-Space Refinement of Atomic Models International Journal of Molecular Sciences real-space refinement refinement programs atomic images map calculation shell decomposition inhomogeneous resolution |
| 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 | real-space refinement refinement programs atomic images map calculation shell decomposition inhomogeneous resolution |
| url | https://www.mdpi.com/1422-0067/23/20/12101 |
| work_keys_str_mv | AT alexandregurzhumtsev towardrealrealspacerefinementofatomicmodels AT vladimirylunin towardrealrealspacerefinementofatomicmodels |