A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.

Algorithms and software have been developed to decompose spherically symmetric oscillating functions in space into a sum of specially designed shell functions. Such decomposition allows the analytical expression of a resolution-limited atomic image as a function of the atomic coordinates, isotropic disorder parameter and local resolution associated with the atom.

The development of well ordered nanonetwork materials from basic building blocks to the bulk phase is examined by simplifying the scattering from the form factor of a sphere convoluted with the nodes of the structure factor, providing a simple methodology for studying the formation of well ordered nanonetwork materials.

Methods and considerations for the structure solution and refinement of the ATPase p97/VCP at 4.7 to 3.5 Å resolution are described.

An electron beam position and angle monitoring system, ps-BPM, has been shown to be able to measure the electron source position and angle at a single location in a beamline at a synchrotron source. This system is now shown to be capable of measuring the source size and divergence simultaneously.

More precise structures are possible through improved free R factors. Changed scaling procedures allowing reduction in the size of the validation set and use of approximations to the validation amplitudes lead to more accurate electron-density maps. Improvements are greatest for real-space refinement, but are also applicable to model building and phase refinement.

This paper describes some statistical tools for analyses of macromolecular B values.

Different examples are described on how to follow the recently published guidelines [Perez-Mato et al. (2024). Acta Cryst. B80, 219–234] when reporting a commensurate magnetic structure.

Using a novel acquisition scheme for SAXS tensor tomography to obtain complete data for a millimeter-sized sample of human trabecular bone, we investigate and quantify the impact of the missing wedge problem on the reconstruction across real and reciprocal space.

An indirect Fourier transform method is presented which describes a solution scattering profile from a reduced set of intensities. Equations are derived to fit the experimental profile using least squares and to calculate commonly used size and shape parameters directly from the reduced set of intensities, along with associated uncertainties. An analytical equation is derived enabling regularization of the real-space pair distribution function. Convenient software is provided to perform all described calculations.