[phenixbb] R value difference in model vs data vs refinement

[Christian Roth]

Hi Nat,

I am not sure I looked into the polygon. In the log it is stated that the R 
values are calculated after a resolution and sigma cutoff applied.  If I 
understood the log correctly the values taken from the pdb header are without  
sigma cutoff. Maybe thats the reason for the difference. Does modelvsdata 
somewhere print the values without cutoff in the log file? I did not find it. 
However does this mean till firsst OHS in phenix refine a default cutoff is used 
and in than throughout the refinement no coutoff is used anymore?

Christian 

Am Donnerstag 22 März 2012 19:46:15 schrieb Nathaniel Echols:
> One other thought on this: which R-factors reported by model_vs_data
> did you use?  This will calculate R-factors with and without outlier
> removal; the latter is equivalent to phenix.refine with default
> settings, but it is maybe not the obvious one to use.  A few
> reflections with extreme values could account for the difference you
> see.
> 
> -Nat
> 
> On Mon, Mar 19, 2012 at 11:20 AM, Christian Roth
> 
> <christian.roth at bbz.uni-leipzig.de> wrote:
> > Dear all,
> >
> > I refined a structure in phenix quite good resolution (1.4 Ang.)
> > After the last refinement
> > I created the "table 1" to extract all data. Interestingly I got a
> > warning due to small changes in the R values
> > R/Rfree after Refinement. 15,46/18,16
> > Phenix modelvs.data gives me
> > R/Rfree 15,34/18,07
> > Interestingly this is nearly exactly the value which I got after the
> > first OHS scattering optimization from phenix
> > R/Rfree  15,43/18,03
> > The differences are of course very small and negeligible, but  I wonder
> > why it happens. Esspecially taking into account that it was refined with
> > phenix and in this case I would expect that both values match exactly.
> >
> > Thank you very much in advance
> >
> > Best Regards
> >
> > Christian
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> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 
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