ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

Karen Manalastas-Cantos; Petr V Konarev; Nelly R Hajizadeh; Alexey G Kikhney; Maxim V Petoukhov; Dmitry S Molodenskiy; Alejandro Panjkovich; Haydyn D T Mertens; Andrey Gruzinov; Clemente Borges; Cy M Jeffries; Dmitri I Svergun; Daniel Franke

doi:10.1107/S1600576720013412

ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

J Appl Crystallogr. 2021 Feb 1;54(Pt 1):343-355. doi: 10.1107/S1600576720013412.

Affiliations

¹ European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany.
² A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation.

Abstract

The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.

Keywords: ATSAS; biological macromolecules; data analysis; small-angle scattering; structural modelling.

Grants and funding

This work was funded by Russian Foundation for Basic Research grants KOMFI 17-00-00487 and 19-32-90190. Horizon 2020 grant 653706. Bundesministerium für Bildung und Forschung grants 05K16YEA (TT-SAS) and 16QK10A (SAS BSOFT). Ministry of Science and Higher Education of the Russian Federation within the State assignment FSRC ‘Crystallography and Photonics’ RAS grant .