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Simulation of small-angle X-ray scattering data of biological macromolecules in solution

This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which m...

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Autores principales: Franke, Daniel, Hajizadeh, Nelly R., Svergun, Dmitri I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133063/
https://www.ncbi.nlm.nih.gov/pubmed/32280325
http://dx.doi.org/10.1107/S1600576720000527
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author Franke, Daniel
Hajizadeh, Nelly R.
Svergun, Dmitri I.
author_facet Franke, Daniel
Hajizadeh, Nelly R.
Svergun, Dmitri I.
author_sort Franke, Daniel
collection PubMed
description This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm(−1)]/c[mg ml(−1)], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).
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spelling pubmed-71330632020-04-10 Simulation of small-angle X-ray scattering data of biological macromolecules in solution Franke, Daniel Hajizadeh, Nelly R. Svergun, Dmitri I. J Appl Crystallogr Computer Programs This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm(−1)]/c[mg ml(−1)], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html). International Union of Crystallography 2020-02-18 /pmc/articles/PMC7133063/ /pubmed/32280325 http://dx.doi.org/10.1107/S1600576720000527 Text en © Daniel Franke et al. 2020 http://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.http://creativecommons.org/licenses/by/4.0/
spellingShingle Computer Programs
Franke, Daniel
Hajizadeh, Nelly R.
Svergun, Dmitri I.
Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title_full Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title_fullStr Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title_full_unstemmed Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title_short Simulation of small-angle X-ray scattering data of biological macromolecules in solution
title_sort simulation of small-angle x-ray scattering data of biological macromolecules in solution
topic Computer Programs
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133063/
https://www.ncbi.nlm.nih.gov/pubmed/32280325
http://dx.doi.org/10.1107/S1600576720000527
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