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Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations
This article presents an upgrade of the D+ software [Ginsburg et al. (2019 ▸). J. Appl. Cryst. 52, 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal gr...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10405579/ https://www.ncbi.nlm.nih.gov/pubmed/37555208 http://dx.doi.org/10.1107/S1600576723005319 |
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author | Balken, Eytan Ben-Nun, Itai Fellig, Amos Khaykelson, Daniel Raviv, Uri |
author_facet | Balken, Eytan Ben-Nun, Itai Fellig, Amos Khaykelson, Daniel Raviv, Uri |
author_sort | Balken, Eytan |
collection | PubMed |
description | This article presents an upgrade of the D+ software [Ginsburg et al. (2019 ▸). J. Appl. Cryst. 52, 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal grid algorithm [Ginsburg et al. (2016 ▸). J. Chem. Inf. Model. 56, 1518–1527], providing D+ its computational strength. Furthermore, the extensive modifications made to the Python API of D+ are described, broadening the X-ray analysis performed with D+ to account for the effects of the instrument-resolution function and polydispersity. In addition, structure-factor and radial-distribution-function modules were added, taking into account the effects of thermal fluctuations and intermolecular interactions. Finally, numerical examples demonstrate the usage and potential of the added features. |
format | Online Article Text |
id | pubmed-10405579 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-104055792023-08-08 Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations Balken, Eytan Ben-Nun, Itai Fellig, Amos Khaykelson, Daniel Raviv, Uri J Appl Crystallogr Computer Programs This article presents an upgrade of the D+ software [Ginsburg et al. (2019 ▸). J. Appl. Cryst. 52, 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal grid algorithm [Ginsburg et al. (2016 ▸). J. Chem. Inf. Model. 56, 1518–1527], providing D+ its computational strength. Furthermore, the extensive modifications made to the Python API of D+ are described, broadening the X-ray analysis performed with D+ to account for the effects of the instrument-resolution function and polydispersity. In addition, structure-factor and radial-distribution-function modules were added, taking into account the effects of thermal fluctuations and intermolecular interactions. Finally, numerical examples demonstrate the usage and potential of the added features. International Union of Crystallography 2023-07-28 /pmc/articles/PMC10405579/ /pubmed/37555208 http://dx.doi.org/10.1107/S1600576723005319 Text en © Eytan Balken et al. 2023 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Computer Programs Balken, Eytan Ben-Nun, Itai Fellig, Amos Khaykelson, Daniel Raviv, Uri Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title | Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title_full | Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title_fullStr | Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title_full_unstemmed | Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title_short | Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations |
title_sort | upgrade of d+ software for hierarchical modeling of x-ray scattering data from complex structures in solution, fibers and single orientations |
topic | Computer Programs |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10405579/ https://www.ncbi.nlm.nih.gov/pubmed/37555208 http://dx.doi.org/10.1107/S1600576723005319 |
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