[phenixbb] sigma cutoff

Joe Krahn krahn at niehs.nih.gov
Mon Nov 30 11:11:37 PST 2009

Kay Diederichs wrote:
>> 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

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