Figure 2.

Illustration of typical scenarios for occupancy refinement that phenix.refine handles automatically. (a) Residue having several alternative conformations marked with altLoc identifiers (two in this example, A and B). It is essential that all conformers have identical chain identifiers and residue numbers, while residue names can be different as shown in example (e). All atoms within each conformer must have identical occupancies. The sum of occupancies over all conformers is constrained to 1. (b) Single atoms with occupancy not equal to 0 or 1. (c) Exchangeable H/D sites (used in refinement against neutron data collected from partially deuterated sample). (d) Single-residue molecule with identical occupancies for all atoms (but not equal to 1 or 0). A user can overwrite this behavior or/and define constraints for any number of selected atoms or groups of atoms.