Abstract
Summary: Complex formation and conformational transitions of biological macromolecules in solution can be effectively studied using the information about overall shape and size provided by small angle X-ray scattering (SAXS). Hybrid modeling is often applied to integrate high-resolution models into SAXS data analysis. To facilitate this task, we present SASpy, a PyMOL plugin that provides an easy-to-use graphical interface for SAXS-based hybrid modeling. Through a few mouse clicks in SASpy, low-resolution models can be superimposed to high-resolution structures, theoretical scattering profiles and fits can be calculated and displayed on-the-fly. Mouse-based manual rearrangements of complexes are conveniently applied to rapidly check and interactively refine tentative models. Interfaces to automated rigid-body and flexible refinement of macromolecular models against the experimental SAXS data are provided.Availability and implementation: SASpy is available as open source at: github.com/emblsaxs/saspy/. Working installations of both PyMOL (www.pymol.org) and ATSAS (www.embl-hamburg.de/biosaxs/download.html) are required.Contact: apanjkovich@embl-hamburg.de or svergun@embl-hamburg.de
Highlights
Small angle X-ray scattering (SAXS) can be used to obtain size, shape and oligomerization information of biological macromolecules in solution, and the method has become an important part of the structural biology toolbox (Graewert and Svergun, 2013)
Most of the ATSAS programs operate through the command line interface (CLI), but often a graphical way to interact with models can be convenient, e.g. visually rearranging subunits in a macromolecular complex may be simpler than defining a set of translations and rotations numerically
Much more elaborated manipulations including rigid-body refinement of complexes are available through the graphical interface of MASSHA (Konarev et al, 2001), which is included in ATSAS
Summary
Small angle X-ray scattering (SAXS) can be used to obtain size, shape and oligomerization information of biological macromolecules in solution, and the method has become an important part of the structural biology toolbox (Graewert and Svergun, 2013). Given the atomic or predicted models of the entire particle or of its domains/subunits, tools are available to compute theoretical scattering profiles, fits and to perform hybrid modeling and refinement (Petoukhov and Svergun, 2005). MASSHA incorporates its own three-dimensional (3D) display and refinement functions, but has some limitations Most notably, it is Windows-only; further, it uses keystrokes instead of the mouse for the manual rearrangement of complexes; MASSHA requires. To overcome the limitations mentioned above, we present the SASpy plugin that combines tools available in the ATSAS software suite with the graphical display resources of the popular PyMOL molecular visualization software (DeLano, 2015). As with other PyMOL plugins, SASpy is distributed as open source This allows the users to modify or add functions at will, extending the applicability and usefulness of SASpy to fit their particular workflows
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