A multi-component description of the unit-cell content is introduced. Efficient algorithms to define the contribution of these components to structure factors are described and implemented in CCTBX and Phenix.

Partitioning of small amphiphilic molecules into biomembranes and other lamellar structures induces structural changes and impacts the properties of the membrane. This work presents a model to describe the amount of co-solvent within the bilayer, its localization and the induced changes to the bilayer structure. The implementation of this model is shared as a fitting algorithm within SasView.

Using synchrotron radiation, diffraction data extending to 0.70 Å resolution were collected from crystals of the small protein crambin at room temperature (297 K), and the structure was refined with spherical-atom approximation to an R factor of 0.0591, revealing (i) protein regions with multiple conformations, (ii) extended water networks correlated with protein conformations and (iii) minimal radiation damage. The structure sets a standard for room-temperature refinement of macromolecular targets and provides accurate data for modeling protein–solvent interactions.

The fast Fourier transform is implemented to compute small- and near-wide-angle X-ray scattering profiles of biomacromolecules in solution. This approach can substantially improve the computational efficiency of solution scattering modeling using an explicit solvent model.

fullrmc is an open-source framework to model and optimize atomic and molecular materials. It is enabled with reinforcement machine learning and designed to solve complex crystalline, amorphous atomic or molecular structures up to the nanoscopic scale.

Residual OMIT maps can be improved by the selective exclusion of bulk solvent from the OMIT region.

Based on the molecular-dynamics simulation platform Amber, a refinement algorithm has been developed to obtain structural models of protein crystals in the form of a fully hydrated unit cell. These models typically yield better R_free values and MolProbity scores compared with the PDB-deposited or Phenix-refined coordinates. The new algorithm has a favorable radius of convergence, is simple to use and is fast.

Data from multiple solvent-soaked crystal structures were used to improve model quality, to identify bound organic molecules at sites involved in protein–protein interactions and to identify a conserved water network that governs DNA binding. A differential B-factor analysis identifies the regiospecific effects of various solvents on protein mobility.

D+ is a computer program that calculates both monochromatic and anomalous X-ray scattering curves from solutions of complex structures, using a hierarchical reciprocal grid algorithm.

A procedure is presented to model the truncated low pixel counts in micro-electron diffraction (MicroED) images. The correction could extend to any conventional macromolecular X-ray crystallography or X-ray free-electron laser measurements.