[phenixbb] High B-factors after Phenix restrained refinement
Pavel Afonine
pafonine at lbl.gov
Fri Dec 16 08:56:48 PST 2011
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 <nechols at lbl.gov
>> <mailto:nechols at lbl.gov>> wrote:
>>
>> On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca
>> <mailto: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 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
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>>
>> <ATT00001..c>
>
> 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 <mailto:roberto.steiner at kcl.ac.uk>
>
>
>
>
>
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