Hi Chris, thanks for the data. I'm looking at your parameters file (test2). In the strategy keyword: strategy = *individual_sites rigid_body *individual_adp group_adp tls \ individual_occupancies *group_occupancies group_anomalous I see you are using group_occupancies which means that one occupancy per residue will be refined (unless you provide your own selections to define the groups). As I mentioned before, group_occupancies does not use any constraints and it is not aware of alternative conformations. This is why in the example below the sum of occupancies is not 1.0. I think this is not what you want to do. I will add the constrains to group_occupancies option so you get equal occupancies within each conformer and the sum of occupancies computed for all conformers is 1.0. Currently, if you choose individual_occupancies then you will get the constraints, that is the sum of occupancies for "523 SE AMSE A 32" and "530 SE BMSE A 32" will be one, but the occupancies for atoms within each conformer will be different, which is, as Paul correctly pointed out, not 100% right. I will keep you posted about the progress. Pavel.
In that case, then the occ of alt conf's tends to refine to greater than 1: ATOM 523 SE AMSE A 32 23.654 11.792 6.216 0.56 14.04 Se ATOM 530 SE BMSE A 32 23.570 12.284 6.796 0.46 13.91 Se