[phenixbb] Can I limit the model's B factor range during refinement
PAfonine at lbl.gov
Thu Jun 18 08:22:34 PDT 2009
message from Ralf: Ralf apologizes for the accidental reply.
> But the model's B factors in some region are very high, higher than
> 150 or more.
> I remembered that the B factor can be limited in the refinement using
> Refmac. Can I do the similar thing in Phenix
The quick answer - no (and it is intentional).
phenix.refine uses restraints in ADP refinement, as all other programs.
The upper limit for B-factors that they can refine to is set somewhere
in the code to prevent numerical issues and it is ~500 (if I re-call
If your B-factors refine to 150 or more that means there is a reason for
this: disorder or misplaced atoms. In this case artificially restricting
B-factors doesn't seem like a good idea. Using TLS (with properly
selected TLS groups) or reviewing these model regions look like a much
better idea. You can also experiment trying to repeat your refinement
after re-setting all B-factors to some constant value (Wilson B, for
instance), and allowing enough of refinement macro-cycles to achieve the
previous R-factor values.
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