help with sigma value in electronic maps

Dr. Artem Evdokimov eudokima at ncifcrf.gov
Thu Sep 14 10:36:22 EST 2000


Hello,

Sigma value is literally an estimated standard deviation of the electron
density.
Normally crystallographers contour the maps in 'sigmas'. Hence, map
contoured at 0.5 sigma is of very low quality (noisy) map contoured at
10 sigma is of exceptional quality but usually does not contain anything
but (perhaps) heavy atom peaks. For different kinds of maps, different
cut off criteria are selected - for instance |2Fo-Fc| maps are usually
contoured around 1.5 sigma, whereas difference maps (|Fo-Fc|) are
considered meaningful around 3 sigma and higher. One always has to apply
reason and to be guided by what one needs the map for - if you're
looking for heavy atoms then you obviously should look at high contours,
whereas if you are looking for ommitted 'light' atoms then you would
expect intermediate height of difference e.d. and so forth.

Hope it helps,

A.G.E.

-- 
|Dr. Artem Evdokimov   Protein Engineering |
| NCI-FCRF             Tel. (301)846-1843  |
|              FAX (301)846-7148           |
|        eudokima at mail.ncifcrf.gov         |
|      http://www.ncifcrf.gov/plague       |







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