[phenixbb] why are my B factors being "refined"
Pavel Afonine
pafonine at lbl.gov
Tue Apr 5 23:19:43 PDT 2011
Hi Scott,
yes, I just reproduced it using a fake one-atom model and generated Fobs...
The output B-factors are different because of anisotropic scaling: the
trace of overall scale matrix is subtracted from it and is added to Bsol
and all atomic B-factors. This is described in details in:
http://www.phenix-online.org/newsletter/
see "On atomic displacement..." article.
I agree, strictly speaking you are right: you did not ask phenix.refine
to do anything with atomic B-factors, so they must be the same in input
and output files. I guess I make this sure in most of other case, but I
most likely overlooked rigid-body refinement case (it has its own
bulk-solvent correction and scaling step).
I just made this change, so B-factors will stay the same in your case.
It will be available in a next build (in a day or two).
Pavel.
> Hello Phenix community,
>
> I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too.
>
> I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such:
>
> modify_start_model {
> selection = None
> adp {
> atom_selection = None
> randomize = None
> set_b_iso = 55
> convert_to_isotropic = None
> convert_to_anisotropic = None
> shift_b_iso = None
> scale_adp = None
> }
>
>
> Yet the output PDB file has all b-factors in the 100s.
>
> Whazzup with that?
>
> Thanks,
> Scott
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