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*To*: Mark DePristo <mdepristo@cryst.bioc.cam.ac.uk>*Subject*: Re: [ccp4bb]: Enforcing a sigma(f) cutoff*From*: "Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>*Date*: Tue, 04 Feb 2003 08:46:39 +0000*CC*: Edward Berry <eaberry@lbl.gov>, ccp4bb@dl.ac.uk*Organization*: Structural Biology Lab. , Dep. Of Chemistry, University of York*References*: <2D4C2F82-37C4-11D7-AE25-000393913572@cryst.bioc.cam.ac.uk>*Reply-To*: E.Dodson@ysbl.york.ac.uk*Sender*: owner-ccp4bb@dl.ac.uk*User-Agent*: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** > 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, > > Mark > 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.. Eleanor

**References**:**Re: [ccp4bb]: Enforcing a sigma(f) cutoff***From:*Mark DePristo <mdepristo@cryst.bioc.cam.ac.uk>

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