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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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

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Subject: Re: Stop Refmac from refining B factors?
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-04-18

BS"D

Dear Eva,

You should be refining an overall temperature factor at that
resolution. It's one of the choices in the list, instead of
"isotropic".

> 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

------------------------------------------------------------------------
-
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology harry.greenblatt@weizmann.ac.il
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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