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

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Mark DePristo wrote:
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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.  

  IN any maximum likelihood procedure using a Sigma  cutoff is 
completely inappropriate. The weighting depends on the intensity 
distribution following the Wilson expectations, and this will most 
certainly NOT be so if you impose a Sima cutoff. I am sure this must be 
true in CNS as well..

  If you are using a different data set the R and Rfree will be 
different; however a more important factor is the scaling algorithm. You 
do not say what the resolution is - the differences are less important 
the higher the resln,
What you really should be comparing is the DISTRIBUTION of R factor 
against resolution but I dont think is deposited with the PDB so it is 
hard to compare..

  Eleanor