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Algorithms and programs for the shell decomposition of oscillating functions in spaceстатья
Статья опубликована в высокорейтинговом журнале
Статья опубликована в журнале из списка Web of Science и/или Scopus- Авторы: Urzhumtseva Ludmila, Lunin Vladimir, Urzhumtsev Alexandre
- Журнал: Journal of Applied Crystallography
- Том: 56
- Номер: 1
- Год издания: 2023
- Издательство: Blackwell Publishing Inc.
- Местоположение издательства: United Kingdom
- Первая страница: 302
- Последняя страница: 311
- DOI: 10.1107/s160057672201144x
- Аннотация: Real-space refinement of atomic models in macromolecular crystallography and in cryo electron microscopy fits a model to a map obtained with experimental data. To do so, the atomic model is converted into a map of a limited resolution and then this map is compared quantitatively with the experimental one. For an appropriate comparison, the atomic contributions composing the model map should reflect the resolution of the experimental map and the atomic displacement parameter values, ADPs. Such contributions are spherically symmetric oscillating functions, different for different chemical kinds of atoms, ADPs and resolution values, and their derivatives with respect to atomic parameters rule the model refinement. For given parameter values, every contribution may be calculated numerically using two Fourier transforms, which is highly time-consuming and makes calculation of the respective derivatives problematic. Alternatively, for an atom of each required type we can express its contribution in an analytical form as a sum of specially designed terms. Each term is different from zero essentially inside a spherical shell and changing the ADP value does not change its form but rather the value of one of its arguments. In general, these terms become a convenient tool for the decomposition of oscillating spherically symmetric functions. This work describes the algorithms and respective software, dec3D, to carry out such a shell decomposition for density contributions of different kinds of atoms and ions.
- Добавил в систему: Лунин Владимир Юрьевич