Re: [ccp4bb]: TLS refinement: Fix B-factors?

["M.D.Winn" <M.D.Winn@dl.ac.uk>]

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Assuming you are refining Bs after TLS, check that the
refinement has converged in the second case. Since you are
starting from uniform Bs, the refinement has further to
go, so to speak.

The value you choose for the starting point of Bs doesn't
matter.

Martyn

> Refmac does not fix B values. It sets initial value to whatever you give and 
> then refines from that point. If you don't use individual atomic B value 
> refinement then all B values will be equal not necessarily to that given by 
> user.  If you use individual B refinement then program will refine TLS and 
> then residual B values. Check if you are using individual B refinement after 
> TLS. That may make difference. 
> 
> 
> Garib
> On Thursday 10 October 2002 11:09, Florian Schmitzberger wrote:
> > Dear all,
> >
> > I am refining a structure with two protomers in the asymmetric unit;
> > resolution range 25-2.0 Angstroem; hexagonal space group P6122; total
> > number of reflections: 22 000; total number of atoms to refine: ~2800.
> >
> > I have been using TLS refinement in the last stage of refinement and got a
> > nice drop in Rfree and Rcryst: before TLS: Rfree=19.3 Rcryst=17.3. after
> > TLS refinement: Rfree=18.2 Rcryst=16.6. I used two TLS groups for the two
> > protomers in the asymmetic unit respectively, 5 cycles of TLS refinement+9
> > cycles of normal Refmac refinement. However I did not turn the "Fix
> > B-factors" field on, though I entered Wilson B in the respective field.
> > When going back and runnning the same refinement procedure as above, this
> > time fixing B-factors to Wilson B I get: Rfree=18.5 Rcryst= 17.3. i.e
> > little worse than above.
> >
> > Since I am not very experienced in using TLS refinement my question is
> > whether it is necessary to fix the B-factors. It makes more sense to me,
> > but I would like to have some competent advice on that. If fixing is
> > advicable: to what should I fix it  (with this particular refinement
> > problem).
> >
> >
> > Thanks very much,
> >
> > Florian
> >
> > -------------------------------------
> > Florian Schmitzberger
> > University of Cambridge
> > Department of Biochemistry
> > 80 Tennis Court Road
> > CB2 1GA Cambridge
> > Tel: 0044-1223-766029
> 
> -- 
> Dr. Garib N Murshudov, YSBL, Chemistry Dp, Univerisyt of York
> Tel: (01904) 328252
> 


-- 


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*                                                                        *
*                  Dr. Martyn Winn                                       *
*                                                                        *
*      Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND     *
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