anisotropic refinement based on B values
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? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
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
Hi Yarrow, I don't see a rationale for doing this, so that's my excuse for not having this (easily) available in phenix.refine. Could you please tell why you think this may be a good thing to do? I'm just curious what am I missing here... Thanks, Pavel On 10/17/13 12:40 PM, Yarrow Madrona 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?
Thanks.
-Yarrow
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Yarrow Madrona