[phenixbb] sigma cutoff

Kay Diederichs kay.diederichs at uni-konstanz.de
Fri Jul 24 11:44:54 PDT 2009

> Hi,
> According to the Phenix manual, phenix.refine uses no sigma cutoff by
> default. Since I haven't changed this manually, why do I see in my pdb
> file  MIN(FOBS/SIGMA_FOBS) 1.340?
> Thanks for help,
> Karolina

This one I can answer because I asked myself the same question recently.

The answer is that Phenix does not impose any sigma cutoff, but rather 
your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 .

You can verify this for yourself by going through your reflection file, 
line by line, and calculating Fobs/Sigma_Fobs for each reflection. You 
will find that all your reflections have a Fobs/Sigma_Fobs larger or 
equal to 1.34 . So it has nothing to with phenix; phenix just reports a 
property of your data.

An easier way than doing it "manually" is using CCP4 sftools for 
calculating a new column "ratio", writing out the resulting MTZ file, 
and looking at this with mtzdmp.


Kay Diederichs                 http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de     Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
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