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Re: [ccp4bb] weighting term in refmac
 

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Subject: Re: weighting term in refmac
From: Leo Chavas leo {- at -} PFWEIS {- dot -} KEK {- dot -} JP
Date: 2007-03-05 		Next message:
Subject: Re: MTZ format conversion
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-06


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

Check out this post by Tassos regarding the MATRIX weight
http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-10/msg00592.html Good
luck,



Hidong











Leo Chavas
Sent by: CCP4 bulletin board
03/05/2007 06:27 PM
Please respond to
Leo Chavas


To
CCP4BB@JISCMAIL.AC.UK
cc

Subject
Re: [ccp4bb] weighting term in refmac






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
==========================




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