Kay Diederichs wrote:

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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.

HTH,

Kay

We were initially puzzled by Fobs/Sigma_Fobs of about 1.9, for data processed with XDS. It turns out that the data was culled at processing time, by software applying a 2-sigma cutoff. Joe Krahn