We now consider building on this example of a partially occupied ligand with conformational heterogeneity in the protein. The interplay between conformational and compositional heterogeneity is often inferred from the ligand clashing with some protein conformations (Figure ). In this example, the ligand binding is compatible with the "loop in", but not the "loop out" conformation. In addition, there are individual residues in each loop state. The complexity of this interlinked conformational and compositional heterogeneity would be completely lost in the legacy PDB format (Supplementary File 1). We would have to encode the conformational heterogeneity of the protein with at least four altlocs ids and make copies of the ligand that match the altloc ids of the compatible conformations. There would be no link between how the conformational heterogeneity interacts with the compositional heterogeneity. Furthermore, the hierarchy of conformational heterogeneity is also lost.