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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...

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Autores principales: Balken, Eytan, Ben-Nun, Itai, Fellig, Amos, Khaykelson, Daniel, Raviv, Uri
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
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.
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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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