scholarly journals ATSAS2.1, a program package for small-angle scattering data analysis

2006 ◽  
Vol 39 (2) ◽  
pp. 277-286 ◽  
Author(s):  
Petr V. Konarev ◽  
Maxim V. Petoukhov ◽  
Vladimir V. Volkov ◽  
Dmitri I. Svergun
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Three Dimensional ◽  
Program Package ◽  
Scattering Data ◽  
Primary Data ◽  
Biological Macromolecules ◽  
Colloidal Solutions ◽  
Angle Scattering ◽  
Recent Developments

The program packageATSAS2.1 for small-angle X-ray and neutron scattering data analysis is presented. The programs included in the package cover the major processing and interpretation steps from primary data reduction to three-dimensional modelling. This system is primarily oriented towards the analysis of biological macromolecules, but could also be used for non-biological isotropic and partially ordered objects (nanoparticle systems, colloidal solutions, polymers in solution and bulk). Recent developments in the programs included inATSAS2.1 are highlighted. The main programs run on multiple hardware platforms, including Windows PC, Linux RedHat and Suse, DEC Alpha, SGI IRIX and Mac OSX.

scholarly journals Small Angle Scattering Data Analysis Assisted by Machine Learning Methods

MRS Advances ◽  
2020 ◽  
Vol 5 (29-30) ◽  
pp. 1577-1584
Author(s):  
Changwoo Do ◽  
Wei-Ren Chen ◽  
Sangkeun Lee
Keyword(s):  
Machine Learning ◽  
Data Analysis ◽  
Small Angle ◽  
Confusion Matrix ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Search Spaces ◽  
Angle Scattering ◽  
Analysis Workflow ◽  
The Right

ABSTRACTSmall angle scattering (SAS) is a widely used technique for characterizing structures of wide ranges of materials. For such wide ranges of applications of SAS, there exist a large number of ways to model the scattering data. While such analysis models are often available from various suites of SAS data analysis software packages, selecting the right model to start with poses a big challenge for beginners to SAS data analysis. Here, we present machine learning (ML) methods that can assist users by suggesting scattering models for data analysis. A series of one-dimensional scattering curves have been generated by using different models to train the algorithms. The performance of the ML method is studied for various types of ML algorithms, resolution of the dataset, and the number of the dataset. The degree of similarities among selected scattering models is presented in terms of the confusion matrix. The scattering model suggestions with prediction scores provide a list of scattering models that are likely to succeed. Therefore, if implemented with extensive libraries of scattering models, this method can speed up the data analysis workflow by reducing search spaces for appropriate scattering models.

scholarly journals New developments in theATSASprogram package for small-angle scattering data analysis

2012 ◽  
Vol 45 (2) ◽  
pp. 342-350 ◽  
Author(s):  
Maxim V. Petoukhov ◽  
Daniel Franke ◽  
Alexander V. Shkumatov ◽  
Giancarlo Tria ◽  
Alexey G. Kikhney ◽  
...  
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Scattering Data ◽  
New Developments ◽  
Angle Scattering ◽  
Automated Data Processing ◽  
Analyse Data ◽  
Three Dimensional Models ◽  
Structural Methods ◽  
New Algorithms

New developments in the program packageATSAS(version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The newATSASrelease includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to runATSASprograms, are also presented.

Small-angle scattering data analysis for dense polydisperse systems: the FLAC program

2000 ◽  
Vol 133 (1) ◽  
pp. 66-75 ◽  
Author(s):  
Flavio Carsughi ◽  
Achille Giacometti ◽  
Domenico Gazzillo
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Angle Scattering

Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions

2018 ◽  
Vol 2 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Martin A. Schroer ◽  
Dmitri I. Svergun
Keyword(s):  
Small Angle ◽  
Scattering Data ◽  
Quality Data ◽  
Biological Macromolecules ◽  
Ambient Conditions ◽  
X Ray ◽  
X Ray Scattering ◽  
Analysis Methods ◽  
Recent Developments ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.

scholarly journals Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints

2015 ◽  
Vol 71 (1) ◽  
pp. 57-66 ◽  
Author(s):  
Henry S. Kim ◽  
Frank Gabel
Keyword(s):  
Small Angle ◽  
Hydration Shell ◽  
Small Angle Scattering ◽  
Conformational Space ◽  
Scattering Data ◽  
Body System ◽  
Angle Scattering ◽  
Recent Developments ◽  
The Impact ◽  
Nmr Restraints

Small-angle scattering (SAS) has witnessed a breathtaking renaissance and expansion over the past 15 years regarding the determination of biomacromolecular structures in solution. While important issues such as sample quality, good experimental practice and guidelines for data analysis, interpretation, presentation, publication and deposition are increasingly being recognized, crucial topics such as the uniqueness, precision and accuracy of the structural models obtained by SAS are still only poorly understood and addressed. The present article provides an overview of recent developments in these fields with a focus on the influence of complementary NMR restraints and of a hydration shell on the uniqueness of biomacromolecular models. As a first topic, the impact of incorporating NMR orientational restraints in addition to SAS distance restraints is discussed using a quantitative visual representation that illustrates how the possible conformational space of a two-body system is reduced as a function of the available data. As a second topic, the impact of a hydration shell on modelling parameters of a two-body system is illustrated, in particular on its inter-body distance. Finally, practical recommendations are provided to take both effects into account and promising future perspectives of SAS approaches are discussed.

Three-dimensional reconstruction of liquid phases in disordered mesopores usingin situsmall-angle scattering

2013 ◽  
Vol 46 (2) ◽  
pp. 493-504 ◽  
Author(s):  
Cedric J. Gommes
Keyword(s):  
Mesoporous Materials ◽  
Small Angle ◽  
Solid Phase ◽  
Gaussian Random Field ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Wetting Transition ◽  
X Rays ◽  
Angle Scattering

Small-angle scattering of X-rays (SAXS) or neutrons is one of the few experimental methods currently available for thein situanalysis of phenomena in mesoporous materials at the mesoscopic scale. In the case of disordered mesoporous materials, however, the main difficulty of the method lies in the data analysis. A stochastic model is presented, which enables one to reconstruct the three-dimensional nanostructure of liquids confined in disordered mesopores starting from small-angle scattering data. This so-called plurigaussian model is a multi-phase generalization of clipped Gaussian random field models. Its potential is illustrated through the synchrotron SAXS analysis of a gel permeated with a critical nitrobenzene/hexane solution that is progressively cooled below its consolute temperature. The reconstruction brings to light a wetting transition whereby the nanostructure of the pore-filling liquids passes from wetting layers that uniformly cover the solid phase of the gel to plugs that locally occlude the pores. Using the plurigaussian model, the dewetting phenomenon is analyzed quantitatively at the nanometre scale in terms of changing specific interface areas, contact angle and specific length of the triple line.

scholarly journals ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

2007 ◽  
Vol 40 (s1) ◽  
pp. s223-s228 ◽  
Author(s):  
Maxim V. Petoukhov ◽  
Peter V. Konarev ◽  
Alexey G. Kikhney ◽  
Dmitri I. Svergun
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Angle Scattering
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