Following the introduction of the program DENFERT[Koutsioubas & Pérez (2013). J. Appl. Cryst. 46, 1884–1888], which takes into account the hydration layer around solvated biological molecules during ab initiorestorations of low-resolution molecular envelopes from small-angle X-ray scattering data, the present work introduces the second version of the program, which provides the ability to treat neutron scattering data sets. By considering a fully interconnected and hydrated model during the entire minimization process, it has been possible to simplify the user input and reach more objective shape reconstructions. Additionally, a new method is implemented for the subtraction of the contribution of internal inhomogeneities of biomolecules to the measured scattering. Validation of the overall approach is performed by successfully recovering the shape of various protein molecules from experimental neutron and X-ray solution scattering data.