This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid?

I am currently refining (for 5 cycles) a pdb with the occupancy of atoms of a specific residue set to 0, and then looking at the difference density map contoured to 3 sigma for extra density. Is this somewhat correct? What else could/should I do? Would using OMIT maps help? (What are OMIT maps, and how do I generate them?)

Thanks,

Alex (not a crystallographer)