Hi Nat
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?
Thanks again
DaOn Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <[email protected]> wrote:
On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <[email protected]> wrote:How are you calculating the average B? Refmac prints "residual"
> I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of
> rigidbody refinement with Phenix Refine I proceeded to restrained
> refinement. The R/Rfree from the refinement decreased nicely as expected but
> the B average is at ~100 (using Group B factor refinement option). I took
> the same model and mtz through Refmac and the B average is about ~40. Has
> anyone experienced this before? I am almost positive it maybe a setting
> issue in Phenix Refine that i should be looking at to get the B factors to
> refine correctly.
B-factors in the B column of ATOM records - these do not include the
contribution from TLS and Ucryst (an overall B-factor for the entire
crystal). In Phenix, the ATOM records always have the total isotropic
B-factor, and this will always be higher than the equivalent in
Refmac. So it's quite likely that both programs are correct, they're
just reporting very different things. (And for what it's worth, a
mean B-factor of 100 is totally normal at 3.3A resolution.)
-Nat
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