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

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CCP4bb <-- 2007 <-- April 2007 <-- 19 April 2007
Previous message:
Subject: Hints on oil phase in the presence precipitants?
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2007-04-19 		Next message:
Subject: Re: How to run SIGMAA twice in a row? (fwd)
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2007-04-19


Subject: Re: Summary - Stop Refmac from refining B factors?
From: "Mark A {- dot -} White" white {- at -} XRAY {- dot -} UTMB {- dot -} EDU
Date: 2007-04-19
Eva,

If you do have NCS then you should be aware of a bug in the CNS1.1
release. PMB has a patch to fix this, and I hope that CNS1.2 will have
fixed it also. The problem is with the NCS restraints on B-factors in
CNS. The NCS groups, usually molecules, are restrained to have
identical B-factors. This does not allow for the affect of local
environment on the motions of the separate molecules. The PMB patch
basically applies an overall B-factor to each NCS-related group to
account for differences in the local environment of each group, such as
differing crystal contacts. The effect is sometimes quite significant
(B-factors ~10), but on other occasions the overall B-factors can be ~0,
indicating that the molecules are practically identical.

Good Luck,

Mark

On Thu, 2007-04-19 at 10:07 +0200, Eva Kirchner wrote:

> Hi all,
>
> thanks for all your help so far, and as we ended up in a more general
> discussion about temperature factor refinement at not-so-great
> resolution, here is a quick summary of what I'll try out:
>
> 1.) Refine overall B's instead of isotropic B's.
>
> 2.) Use isotropic B's with the following (combinable) options:
>
> a) Isotropic in the beginning, grouped B's in the end.
> b) Use tight geometric restraints (I'm doing this anyways).
> c) Use tight B restraints rather than grouped CNS B's (not
> geometrically restrained, and most likely not restrained by NCS).
>
> 3.) Use not so tight B restraints, but tight geometric restraints with
> individual or grouped B's, plus TLSMD server and multi-group TLS
> refinement.
>
> 4.) Use CNS and try Mark White's tools, and simulated annealing.
>
> 5.) Use phenix with weighted nearest-neighbor restraint.
>
> ...and some remarks:
> * Of course I never wanted not to refine any B factors! I just wanted
> to see their contribution/influence on the refinement and explain
> their strange behaviour.
> * Luckily, I have NCS :o) Thanks for your good wishes, Mark.
>
>
> Eva
>
>
>
>
>
> 2007/4/18, Eva Kirchner :
>
> 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

Sincerely yours,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white



CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 19 April 2007
Previous message:
Subject: Hints on oil phase in the presence precipitants?
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2007-04-19 		Next message:
Subject: Re: How to run SIGMAA twice in a row? (fwd)
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2007-04-19


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