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Re: [ccp4bb] weighting term in refmac |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: 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 navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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