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Re: [ccp4bb]: Enforcing a sigma(f) cutoff?

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Mark DePristo wrote:
> I have a general question about refinement with refmac5.  I've been 
> re-solving a protein structure against its structure factors (obtained 
> from PDB).  One consistent difference between my new structure and the 
> PDB structure is that the PDB structure uses a sigma(f) cutoff of 0.0, 
> as seen in the REMARK in the pdb file:
> REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
> My structure's PDB file, as generated by refmac5, has the line
> REMARK   3   DATA CUTOFF            (SIGMA(F)) : NONE
> For the life in me I cannot figure out how to enforce a sigma(f) cutoff 
> in refmac5.  There are some suggestions (in the archives of ccp4bb) that 
> such a cutoff can introduce artifacts, as the sigma(f) cutoff 
> disproportionately affects the weaker reflections.  Regardless, I am 
> suspicious that this cutoff accounts for the slightly higher R and 
> R-Free values (~ 2%) of my new structure.  Is this a reasonable 
> interpretation?  If so, how can I enforce a sigma(f) data cutoff?

I don't think that can be the cause of the discrepancy-
A sigma cutoff of "0.000" only rejects reflections with
negative Fobs, which in general is precisely "none".

If it were a cutoff on I, that is a different story as some
weak reflections will come up with negative measured
intensities. But all reasonable algorithms for converting
I to F avoid negative amplitudes, whether by discarding those
reflections, setting them to zero, or some more sophisticated