Despite progress in automating the assignment and creation of PDB files with AltLoc annotations, challenges persist regarding ease of interpretation and how these annotations are used. For some software, only one of the alternative conformations is used, and there are compatibility issues with other analysis software. In NMR studies, like those shown in Figure , multiple-state models are usually refined using multiple complete copies of the entire molecule for each state. This does not easily align with the AltLoc ID usage, which also does not currently support association with the corresponding alternative chemical shift assignments.