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Re: [ccp4bb]: Enforcing a sigma(f) cutoff
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> The responses to my question, all of which have been very thoughtful and
> helpful, lead to the following question: what is a statistically
> significant difference in the R (or R-free) statistic? If the R and
> related factors can be influenced by the solvent model, and in fact
> differ substantially when calculated by different programs, should a
> difference of 2% in the R or R-free be dismissed as insignificant? Or
> is it an indication that the model can still be improved, for instance
> through careful analysis of omit maps? I am aware of Ian Tickle's work
> analyzing the properties of the R-free, but is there other work that
> discusses these issues?
> Thanks again,
In my experience in any refinement, when you change the program you
always change the R factors.. ie CNS differs from REfmac5; SFCHECK
differs from them both, often by 1-2% etc etc..
I dont think R factors are the best measure of a completed structure;
you dont say what resolutions your trials are at, but different scaling
options including Bulk solvent corrections can make a huge difference to
the lower resolution bins. ( Indeed some quoted R factors actually
exclude these terms, and only give Rfactors from 6-xA say..)
At the least you need a table of R factor v resolution, wjich you cant
ge from the PDB.
I think the reason REFMAC5 reduces the Rfactor is that it does a
better job with the temperature factors - if you did have this table of
R v resolution you would see that the outer shells have fallen, not the
lowest resln ones..
How much have the coordinates shifted? I suspect very little
Your work provides a useful leson to us all I think - dont judge
quality by R factors alone..