[phenixbb] Can I limit the model's B factor range during refinement

Pavel Afonine PAfonine at lbl.gov
Thu Jun 18 08:22:34 PDT 2009

Hi Leo,

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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