On Thursday, August 08, 2013 01:51:34 pm Omid Haji-Ghassemi wrote:
> Dear Robbie, Marcus and Reginald,
>
> Thanks again for your replies, I truly appreciate the help.
>
> The B-factors was set to 20 when performing TLS refinement so I don't
> think that is the problem.
>
> I also tried Marcus's suggestion using output from coot, with no luck.
>
> The only thing left to try is to test alternative TLS group as Reginald
> have suggested.
You have only told us about an increase in average B, not whether it is
uniformly inflated. Possibly the output from analysis by the Parvati server
http://skuld.bmsc.washington.edu/parvati
would indicate specific parts of your structure that are behaving
badly during refinement.
Ethan
>
> Cheers
> Omid
>
> > Hi Omid,
> >
> > Sometimes the choice of TLS groups and to a lesser extent the initial
> > B-factor matter a lot. You should try a few other TLS group selections and
> > see if these give nicer results. Things to try: TLSMD, including or
> > excluding ligands and carbohydrates, other common-sense or gut-feeling
> > structure partitionings. If you have a lot of different groupings to
> > test, you can reset the B-factor and do pure TLS refinement (i.e. 0 cycles
> > of restrained refinement) for all of them. You can then use the best one
> > for your 'final' refinement. It's much faster then trying your final
> > refinement with all TLS groups selections.
> >
> > Cheers,
> > Robbie
> >
> > Sent from my Windows Phone
> > ________________________________
> > Van: Omid Haji-Ghassemi
> > Verzonden: 8-8-2013 21:55
> > Aan: CCP4BB@JISCMAIL.AC.UK
> > Onderwerp: Re: [ccp4bb] TLS refinement and ANISOU records
> >
> > Dear Ethan,
> >
> > Thank you for your reply.
> >
> > I will try to review my refinement protocol once more; however, I am still
> > perplexed at what lies at the heart of the problem.
> >
> > Overestimation of average B-factor using TLS is perfectly sound, but I am
> > not sure why all my structures the average increases tremendously.
> >
> > In one case it increases from 16.36 to 73.02 for a 2.3Ang structure.
> >
> > I already tried changing weights and number of TLS rounds, which resulting
> > in only a small change in average B.
> >
> > Omid
> >
> >> On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi wrote:
> >>> Dear all,
> >>>
> >>> I was about to deposit a few structures to the pdb when I noticed the
> >>> mean
> >>> B-factors were larger than one might expect.
> >>>
> >>> All the structures were refined using TLS refinement.
> >>>
> >>> During refinement in Refmac the average temperature factors for each
> >>> structure is reasonable. For example, a structure at 2.75� has a
> >>> mean
> >>> B-factor of 40; however, after adding the ANISOU records as required by
> >>> the PDB, I noticed the average B-factors double.
> >>
> >> Please see my paper:
> >> E. A. Merritt (2011).
> >> "Some Beq are more equivalent than others". Acta Cryst. A67, 512-516.
> >> <http://skuld.bmsc.washington.edu/parvati/ActaA_67_512.pdf>
> >>
> >> In short, the quantity stored in the "B" field of a PDB file after TLS
> >> refinement is Beq, which overestimates what the isotropic B factor would
> >> have been if you had refined without TLS. So in general the "average B"
> >> after TLS refinement is always higher than the "average B" without TLS.
> >> The problem is that the two quantities marked "average B" are not
> >> directly comparable.
> >>
> >> Having said that, the overestimate is not usually as much as a factor of
> >> 2.
> >> So something else may indeed be causing a problem in your case.
> >>
> >> Ethan
> >>
> >>
> >>>
> >>> Is this normal?
> >>>
> >>> Sincerely,
> >>> Omid
> >>>
> >>> ---------------------------------------------------
> >>> ---------------------------------------------------
> >>> Omid Haji-Ghassemi, Graduate Student
> >>> Department of Biochemistry & Microbiology
> >>> University of Victoria
> >>> PO Box 3055 STN CSC
> >>> Victoria, BC, V8W 3P6
> >>> CANADA
> >>>
> >>> Tel: 250-721-8945
> >>> Fax: 250-721-8855
> >>>
> >>
> >> --
> >> Ethan A Merritt
> >> Biomolecular Structure Center, K-428 Health Sciences Bldg
> >> University of Washington, Seattle 98195-7742
> >>
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
