On Thu, Oct 17, 2013 at 12:40 PM, Yarrow Madrona <amadrona@uci.edu> wrote:

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