On Thu, Oct 17, 2013 at 12:40 PM, Yarrow Madrona
I'm sure that this has probably already been covered but I am having some problem finding out how to tell phenix to make a decision whether to refine isotropically or anisotropically based on B factor values. Is this something you can do with a python script?
Not easily, I think. But it was extremely easy to modify the atom selection code to support a "bfactor" keyword, which has been on the todo list since as long as I can remember. Starting tomorrow (or whenever the next usable build is), syntax like this will be possible: bfactor < 20 chain A and bfactor > 20 (resname HOH) and (bfactor = 0) Only ">", "<", and "=" are supported as operators right now (but keep in mind "not (bfactor = 0)" is also possible). So in the phenix.refine GUI, the atom selections for anisotropic and isotropic could be set this way. Just make sure they don't overlap. -Nat