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

[Mark DePristo <mdepristo@cryst.bioc.cam.ac.uk>]

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Hello,

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?

Thanks,

Mark

Mark DePristo
Ph.D. Candidate
Dept. of Biochemistry
Cambridge University
mdepristo@cryst.bioc.cam.ac.uk
http://www-cryst.bioc.cam.ac.uk/~mdepristo/