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.
Highlights
Small-angle scattering (SAS) of X-rays (SAXS) or neutrons (SANS) provides low-resolution structural information about various nanostructured systems, including biological macromolecules in solution (Svergun et al, 2013)
Of particular note are the approaches for lipid and nucleic acid structure analysis developed in response to the increased use of SAS to characterize these types of macromolecules
The ATSAS 3.0 release introduces a set of new functionalities, which include modelling tools for lipids and nucleic acids, and expanded options for polydisperse systems
Summary
Small-angle scattering (SAS) of X-rays (SAXS) or neutrons (SANS) provides low-resolution structural information about various nanostructured systems, including biological macromolecules in solution (Svergun et al, 2013). The software tools developed by the SAS community offer access to various data analysis and modelling options. These include the multipurpose packages SASTBX (Liu et al, 2012), BioXTAS RAW (Hopkins et al, 2017), Sasview (http:// www.sasview.org) and ScAtter, which contain utilities for data handling and analysis in the form of radial averaging of 2D detector images to 1D scattering profiles, calculation of modelindependent structural parameters, SEC-SAXS data processing and deconvolution (for BioXTAS RAW), and model fitting and refinement (for SASTBX). We focus on the changes made since the ATSAS 2.8 release, which include major improvements in the existing tools, technological and standardization updates, new modules for data simulation, and modelling programs for specific systems such as membrane proteins, liposomes and nucleic acids
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