Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.