Re: [ccp4bb] weighting term in refmac

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

Previous message:
Subject: Re: practical limits of MR?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-03-05

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Subject: Re: weighting term in refmac
From: HKim {- at -} DECODE {- dot -} COM HKim {- at -} DECODE {- dot -} COM
Date: 2007-03-05

Subject: Re: weighting term in refmac
From: Leo Chavas leo {- at -} PFWEIS {- dot -} KEK {- dot -} JP
Date: 2007-03-05

Dear Li,

> There is a value of weighting term with default 0.3 in refmac5,
> what is
> the exact meaning of it?

You might want to have a look at:
http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#weig

> What is the best value of it for different resolution
> data?

I don't know exactly, but I like to use the minimum (0.01) for "bad"
data (that is high Rmerge, high mosaicity, low resolution), and
slightly higher for "good" data. Anyway, personally, I'm doing
several runs with different values of weighting, and check how it
affects the geometry (respective rmsd values).

> Does it affect the result R value much?

Well yes, if you do distort like hell your protein side chains &
atoms, you will have everything that will fit into the electron
density, resulting in decreasing largely your stats, but you'll have
little biological significance (as an example: using a somehow too
high value of weighting, a lys was disrupted in 3 parts, to fit the
blobs of density...).

Good luck.
Leo

==========================
Chavas Leonard M.G., Ph.D.
Structural Research Center
KEK,PF. 1-1 Oho
Tuskuba, Ibaraki - Japan
---------------------------------------------
PHS: +81(0)29-864-5200 (ext: 2682)
e-mail: leo@pfweis.kek.jp
URL: http://pfweis.kek.jp/~leo
==========================

CCP4bb navigation

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

Previous message:
Subject: Re: practical limits of MR?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-03-05

Next message:
Subject: Re: weighting term in refmac
From: HKim {- at -} DECODE {- dot -} COM HKim {- at -} DECODE {- dot -} COM
Date: 2007-03-05