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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
approach.
Ed