[phenixbb] High B-factors after Phenix restrained refinement
2dd13 at queensu.ca
Sun Dec 18 07:49:13 PST 2011
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!!
On Fri, Dec 16, 2011 at 11:56 AM, Pavel Afonine <pafonine at lbl.gov> 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:
> - article "On atomic displacement parameters (ADP) and their
> parameterization in PHENIX" here:
> 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
> 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.
> 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
> On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols at lbl.gov>wrote:
>> On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca> 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
>> > the same model and mtz through Refmac and the B average is about ~40.
>> > 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
>> > 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.)
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Roberto Steiner, PhD
> Randall Division of Cell and Molecular Biophysics Group Leader
> King's College London
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL, London, UK
> Tel 0044-20-78488216
> Fax 0044-20-78486435
> roberto.steiner at kcl.ac.uk
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
> phenixbb mailing list
> phenixbb at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb