Hi Havier, You got the formula right alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X You may have also some water include in the model correspond to alternate loop A" occupancy = X I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well . you do not need something specific in a parameter file for the protein atom. The PDB file look like the following. ATOM 258 CA AGLN A 35 2.979 -4.265 69.678 0.40 46.35 C ANISOU 258 CA AGLN A 35 4942 7133 5533 0 946 -219 C ATOM 259 CA BGLN A 35 3.127 -4.246 69.643 0.60 47.74 C ANISOU 259 CA BGLN A 35 5152 7285 5702 0 930 -219 C The alternative atom specified with letter A and B before the amino acid three letters. Regards, George From: [email protected] [mailto:[email protected]] On Behalf Of Xavier Brazzolotto Sent: Tuesday, July 24, 2018 9:50 AM To: [email protected] Subject: [phenixbb] Ligand occupancy and conformational change I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet. As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear. How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ? Thank you for your help Xavier