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Re: Fw: [ccp4bb]: TLS refinement: Fix B-factors?
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Florian,
I also use ccp4i (CCP4 Program Suite 4.2, CCP4Interface 1.3.7) but when I said
I use Wilson plot B-value I meant I put the numerical value, for instance 40,
which I know from running truncate before, and NOT a keyword "Wilson B". The
log-file seems to confirm what I put.
Aleks
On Oct 10, Florian Schmitzberger wrote:
> Subject: Fw: [ccp4bb]: TLS refinement: Fix B-factors?
> Dear Alex,
>
> Thanks for your reply. I forward the following message to you. Garib says
> that the Bfactor fixing to Wilson B does not work yet. Have you checked your
> log-file. Since when I fix the Bfactor to Wilson B it is much shorter,
> though it does not give any error message. But maybe that only happens to me
> since I use ccp4i, I don't know?
>
> Florian
>
>
> ----- Original Message -----
> From: "Garib N Murshudov" <garib@ysbl.york.ac.uk>
> To: "Florian Schmitzberger" <florian@cryst.bioc.cam.ac.uk>
> Sent: Thursday, October 10, 2002 12:20 PM
> Subject: Re: [ccp4bb]: TLS refinement: Fix B-factors?
>
>
> Hi Florian
>
> As I see there is a mistake (possible casued by interface). It uses keyword
> whihc is no there. Could you please just use one particular value in FIX B
> field. I.e. let say 40 (instead of Wilson B). Program does not understand
> Wilson B. Perhaps I should add in future but at the moment it does not work
> that way.
>
> Garib
>
> On Thursday 10 October 2002 12:12, you wrote:
> > Dear Garib,
> >
> > Thanks very much for your help. I enclose the two log-files. 3_
> refmac5.log
> > is the one where I did not fix B-factors in the TLS refinement.
> > 4_refmac.log is the one where I followed basically the same refinement
> > procedure, but fixing the B-factors to Wilson B in the TLS refinement.
> >
> >
> > Thanks very much for any comments.
> >
> > Florian
> >
> >
> >
> > ----- Original Message -----
> > From: "Garib N Murshudov" <garib@ysbl.york.ac.uk>
> > To: "Florian Schmitzberger" <florian@cryst.bioc.cam.ac.uk>
> > Sent: Thursday, October 10, 2002 11:54 AM
> > Subject: Re: [ccp4bb]: TLS refinement: Fix B-factors?
> >
> >
> > Dear Florian,
> >
> > There is a little bit confusion on interface. TLS parameters box FIX B
> > means set initial values to this specific value. In my experinece it does
> > not make much difference what you put there. Are you running TLS and
> > restrained.
> >
> > Can you send me two log files so that I could have a look what is going
> on.
> >
> > Regards
> > Garib
> >
> > On Thursday 10 October 2002 11:47, you wrote:
> > > Dear Garib,
> > >
> > > Oh, I think I did not make myself entirely clear. I mean I fixed the
> > > B-factors in the TLS parameters-box, not in the scaling Fobs and Fc box.
> >
> > So
> >
> > > would you turn the "Fix B-factors" field in the TLS-parameters box on or
> > > not? If you turn it on what would you fix the B-factors to?
> > >
> > > As I understand this B-factor fixing does then only influence the TLS
> > > refinement cycles, but not the Refmac cycles. Still I got the impression
> > > that Refmac is also doing something differently since the .log-files
> > > looks considerably shorter when I turn the "Fix B-factors" in the TLS
> > > parameters box. I tried to find where I can specify individual B-factors
> > > in ccp4i,
> >
> > but
> >
> > > I could not find it. Can I specify it in ccp4i or do I have do run a
> > > script?
> > >
> > >
> > > Thanks,
> > >
> > > Florian
> > >
> > >
> > >
> > > ----- Original Message -----
> > > From: "Garib N Murshudov" <garib@ysbl.york.ac.uk>
> > > To: "Florian Schmitzberger" <florian@cryst.bioc.cam.ac.uk>;
> > > <ccp4bb@dl.ac.uk>
> > > Sent: Thursday, October 10, 2002 11:17 AM
> > > Subject: Re: [ccp4bb]: TLS refinement: Fix B-factors?
> > >
> > >
> > > 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
>
>-- End of excerpt from Florian Schmitzberger
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