Hi Leo,
I'm currently working on a structure with a series of ligands which have occupancies of ~80% (according to phenix.refine). So far so good, a few of these also show alternate conformations which I'd like to let phenix refine as well, but phenix.refine adjusts the occupancy of the whole ligand (conformation A+B) automatically to 1. I see that this is useful in most cases, but not in this one.
Is there a possibility to adjust the overall occupancy or another work-around that anyone can suggest?
quick answer: yes, it is possible to do and I think this is described here: "13 typical occupancy refinement scenarios and available options in phenix.refine" https://www.phenix-online.org/newsletter/ Longer answer: Make a parameter file where you explicitly state each conformer as an individual group, something like this: refinement { refine { occupancies { constrained_group { selection = chain X and resseq 123 and altloc A } constrained_group { selection = chain X and resseq 123 and altloc B } } } } In this case one occupancy will be refined for "chain X and resseq 123 and altloc A" and it will be constrained between 0 and 1. Likewise, one occupancy will be refined for "chain X and resseq 123 and altloc B" and it will be constrained between 0 and 1. The mutual relation between the two occupancies will not be constrained in any way. So if you are lucky then their sum may end up being less than 1. Let me know if you have questions or need help! I hope Billy can tell how to do this in the GUI! All the best, Pavel