Re: [phenixbb] High B-factors after Phenix restrained refinement

Thanks to everyone who've replied to this thread. I really appreciated the help and the useful information. Merry Xmas and Happy New Year everyone!! Cheers Da On Fri, Dec 16, 2011 at 11:56 AM, Pavel Afonine wrote:

I agree, it is a matter of convention. The total ADP is: Utotal=Ucryst+Ugroup+Ulocal. You can either output the total Utotal into ATOM/ANISOU records or keep Ucryst+Ugroup in REMARKs and output Ulocal into ATOMs. Both ways are valid as long as they yield identical Utotal.

For more relevant information, summary and some review, see:

- pages 23-29 here: http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf

- article "On atomic displacement parameters (ADP) and their parameterization in PHENIX" here: http://phenix-online.org/newsletter/

Pavel

On 12/16/11 8:11 AM, Steiner, Roberto wrote:

Hi Da

Even if you deposit a structure refined with Refmac the PDB now expects the total B values being present. Have a look at http://deposit.rcsb.org/adit/REFMAC.html

What you call "more" correct does not really make much sense to me if I understand you properly. If you follow the link given above (or use TLSANL directly from the CCP4) and get 'total Bs' from Refmac I am sure they will be more or less the same and the Bs from phenix.refine.

R

On 16 Dec 2011, at 15:54, Da Duan wrote:

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

Da

On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols wrote:

...

On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <[email protected]> wrote:

...

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.

How are you calculating the average B? Refmac prints "residual" 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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