Re: [ccp4bb] Stop Refmac from refining B factors?

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CCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007

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Subject: Re: Stop Refmac from refining B factors?
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2007-04-18

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Subject: Re: Stop Refmac from refining B factors?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-04-18

Subject: Re: Stop Refmac from refining B factors?
From: Eva Kirchner eva {- dot -} kirchner {- at -} UNI-TUEBINGEN {- dot -} DE
Date: 2007-04-18

Thank you Roberto, I saw that line in the log file, too. So it is as I
feared: Refmac cannot be stopped from refining B-factors ;-) Maybe I'll use
CNS...

Eva

2007/4/18, Roberto Steiner < roberto.steiner@kcl.ac.uk>:
>
>
> On 18 Apr 2007, at 14:39, Eva Kirchner wrote:
>
>
>
>
>
> (But I'm still curious about the B-factor refinement when there is no "REFI
> BREF ISOT" in the com-file...)
>
>
> Eva,
>
> Refmac internal default is REFI BREF ISOT
> that's why even if you remove the above line from the com file (or
> deselect that option from the interface) it still does ISOT BREF refinement.
>
> It does tell you that though....
> if you look at the log file there's a bit that says
>
> .......
> Method of minimisation : Sparse Matrix
> Experimental sigmas used for weighting
> Number of Bins and width: 20 0.0080
> Refinement of individual isotropic Bfactors
> ..........
> what do you have there when you deselect the B fact option from the
> interface?
>
>
> I agree with Herman that at 3.2 A isotropic B values refinement can be
> useful.
>
>
> Roberto
>
>
> Eva
>
>
>
> 2007/4/18, Mischa Machius < Mischa.Machius@utsouthwestern.edu>:
> >
> > Like Harry said, it is not justified to do individual B factor
> > refinement at that resolution. Well, you can do it, but you'll end up with
> > funny results, such as what are observing right now. Still, from a pragmatic
> > point of view, individual B factor refinement in cases like these can have a
> > positive effect on the electron density. However, keep in mind that the
> > resulting B factors may physically not be very meaningful. In the end,
> > you'll have to switch to grouped B factor refinement, or you risk nasty
> > comments from an attentive mentor or reviewer (and rightly so). Hope that
> > helps. Best - MM
> > On Apr 18, 2007, at 7:20 AM, Eva Kirchner wrote:
> >
> > Hi,
> >
> > I have a little problem with B-factor refinement. I'm using the CCP4i
> > interface, Refmac 5.2.0019 , a resolution of 30-3.2 A (I tried 8-3.2 A
> > as well, it doesn't make a big difference for this problem), and a current
> > Rfree of 30.4%.
> >
> > Refmac refines the B-factors so that they are nearly the same for main
> > chain and side chain, and I don't like that (or could it make sense in any
> > way?). Moreover, my structure is a protein complex, and Refmac is mainly
> > doing this for one component of the complex. If I take the B-factors from
> > the original uncomplexed protein (around 18, 1.75 A) and add 44 to them
> > with moleman to get them in the range they are in the complex, Refmac
> > "flattens" them remarkably in only 5 cycles of restricted refinement. Does
> > anyone have an explanation for this? I am pretty sure that the complex
> > components are in the right place, I see beautiful density and everything I
> > should see at this resolution.
> >
> > Here is what I tried further:
> >
> > * I de-selected "Refine isotropic temperature factors" in the Refmac
> > interface. There was no REFI BREF ISOT any more in the com file. But there
> > was also no difference in the B-factors compared to when there _was_ REFI
> > BREF ISOT in the com file... So does Refmac just _ignore_ my wish not to
> > refine B-factors? (The REFI keywords were as follows: type REST - resi MLKF
> > - meth CGMAT - is there any B-factor-thing hidden in this?)
> >
> > * I played around with the geometric parameters. If I select the
> > B-factor values there (the keywords are TEMP
BFAC
> > ), it does not make _any_ difference,
> > what values I fill in there, the resulting B-factors are always the same
> > (but different from when I don't use the TEMP keyword, and even "flatter").
> > Default for WBSCAL is 1.0, I tried 10, 1.0, 0.1, 0.01, and the
> > equivalent numbers for the sigbs.
> >
> > Thanks for any thoughts on this,
> >
> > Eva
> >
> >
> >
> >
> > --------------------------------------------------------------------------------
> > Mischa Machius, PhD
> > Associate Professor
> > UT Southwestern Medical Center at Dallas
> > 5323 Harry Hines Blvd.; ND10.214A
> > Dallas, TX 75390-8816; U.S.A.
> > Tel: +1 214 645 6381
> > Fax: +1 214 645 6353
> >
> >
> >
>
> ---
> Dr. Roberto Steiner
> Randall Division of Cell and Molecular Biophysics
> New Hunt's House
> King's College London
> Guy's Campus
> London, SE1 1UL
> Phone +44 (0)20-7848-8216
> Fax +44 (0)20-7848-6435
> e-mail roberto.steiner@kcl.ac.uk
>
>
>
>
>

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CCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007

Previous message:
Subject: Re: Stop Refmac from refining B factors?
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2007-04-18

Next message:
Subject: Re: Stop Refmac from refining B factors?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-04-18