Joint X-ray and neutron refinement with phenix.refine.

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “Macromolecular models can be refined with phenix.refine using neutron data or X-ray and neutron data simultaneously (Adams, Mustyakimov et al., 2009; Afonine et al., 2010).”
Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase. (2013, methodology): “Joint neutron and X-ray structure refinement is in progress using both a modified version of CNS for neutrons (nCNS) and phenix.refine (Adams et al., 2009; Afonine et al., 2010).”
The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery (2014, methodology): “Recent advances in crystallographic refinement offer the opportunity to model higher-energy conformational states using direct experimental observations 3–5 , 33– 35 .”
Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition (2018, methodology): “We note that the neutron community is increasingly using programs tailored to handle neutron data, such as PHENIX (Afonine et al., 2010) and nCNS (Adams et al., 2009), which can be used for joint XN refinement (Table 3).”