Disordered moieties, such as components of organic linkers with rotational freedom, manifest in crystal structures by presenting a multiplicity of conformations. To convert such a multiplicity of conformers into a single conformer to give a simulation-ready structure, we can (i) extract the disordered substructure from the MOF and define it to be the query fragment then (ii) execute a findand-replace with a replacement fragment constructed as a single conformation of the disordered moiety.