[phenixbb] High B-factors after Phenix restrained refinement

Nathaniel Echols nechols at lbl.gov
Fri Dec 16 08:11:29 PST 2011

On Fri, Dec 16, 2011 at 7:54 AM, Da Duan <2dd13 at queensu.ca> wrote:
> I was just looking at the average B in the refinement log files from Refmac
> and Phenix Refine. Thanks for the clarification on how Refmac and Phenix
> calculate the average B. My next question is when depositing the structure,
> is it more common to deposit structures with the "residual" B-factors or
> B-factors generated by Phenix that includes the TLS and Ucryst contribution?
> I also performed sfcheck and the average B generated by the Wilson plot is
> ~100 which seems to suggest that the Phenix average B is probably "more"
> correct?

I had thought that the PDB automatically converted Refmac PDB files to
contain full B-factors, but the link Ed posted suggests otherwise.  If
you are depositing the output file from Phenix, at least, you do not
need to take any additional steps.


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