[phenixbb] anisotropic refinement based on B values

Nathaniel Echols nechols at lbl.gov
Thu Oct 17 19:25:48 PDT 2013

On Thu, Oct 17, 2013 at 12:40 PM, Yarrow Madrona <amadrona at 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.

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