Hi,

I’m working on the refinement of a protein mutated with an unnatural amino acid that contains one bromine atom. This particular amino acid is present as two rotamers. I’ve managed to introduce and do refinements with these two unnatural, brominated rotamers in Phenix, but the problem is that when shooting the protein with X-rays about 30-40% of the bromine atoms get knocked off. This means that the sum of the occupancies for the bromine atoms of the rotamers needs to be less than 1.00. However, the total occupancy of all the other rotamer atom pairs must be 1.00. Is there a way in Phenix to refine rotamers of brominated, unnatural amino acids, and at the same time have the total occupancy less than 1.00 for the Br atoms only? Any advice how to solve this is welcome.