Re: [ccp4bb] Choosing weighing term

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

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Subject: Re: Choosing weighing term
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-04-01

On Apr 1, 2009, at 7:12, conancao wrote:

> Dear All:
>
> Hi. I have a question about selecting weighing term during
> restrained refinement using Refmac5 of CCP4 packages.
>
> For a 300kDa homodimer protein structure at 2.5A, 91%
> complete. I obtain optimal R and Rfree by using NCS tight restraints
> of the peptides of the two monomers. Weighing term 0.15 gives
> (R=0.22, Rfree=0.28) and weighing term 0.1 gives(R=0.23,
> Rfree=0.28). Higher weighing term gives larger difference between R
> and Rfree.
>
> Is there a criteria or special range of choosing weighing
> term? Is weighing term 0.1 too small? I read the references by Ian
> Tickle (Acta Cryst D, 1998 and 2000)on R and Rfree ratio, those
> helped a lot but I still do not know the key of weighing term.

The absolute value of the weighing term is rather irrelevant - it has
no physical meaning.
A term of 0.1 for 2.5 A data sounds about right in my experience, and
from what you say.

What you could try to do is to play a bit with the Bweight as well
(look at ccp4i under the Restraints panel).

At 2.5 you might want to try and relaxing NCS restraints (use medium
or exclude some regions that have a reason to be different, if they
are eg in a different crystal contact environment in each copy) and
see if they lower the Rfree. I also presume you use TLS.

Tassos

>
>
> Thanks so much.
>
> Best,
> Hongnan Cao
> Biochemistry Department
> UC Riverside
>
> °ÑMSN×°½øÊÖ»ú£¬¸ü¶àÁÄÌìÀÖÈ¤µÈÄãÍÚ¾ò£¡ Á¢¿ÌÏÂÔØ£¡

P please don't print this e-mail unless you really need to
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Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
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CCP4bb navigation

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

Previous message:
Subject: New human genome policy - please read.
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-04-01

Next message:
Subject: Re: Building structure in COOT
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-04-01