On Mon, May 14, 2012 at 11:13 AM, Nora Cronin
A refine input file with strategy selecting individual adp refinement has a selection of excluded residues as follows:
adp { individual { isotropic = not ((chain A and resseq 1500:1501) or (chain B and resseq 1500:1501) or (chain X)) anisotropic = none
The isotropic B factors of the above excluded residues are however refined. The selection has been ignored.
I believe this is because of the overall B-factor for the entire crystal ("Ucryst") being refined, which will happen no matter what. Because phenix.refine reports the total atomic B-factors including all contributions, this change will propagate to the atoms you've excluded, even if their individual B-factors aren't being refined. (Although it is also unclear why you wouldn't want to refine those B-factors too - this is almost always recommended.) I guess we need to add this to the phenix.refine FAQ list. PS. please post with a new subject instead of replying to a previous post, it makes a big difference for some email clients and our mailing list archives. -Nat