On Tuesday, January 10, 2012 02:46:21 pm Ian Tickle wrote:
> Jacob,
>
> Actually the R factors including the Bijvoet pairs would be higher,
> because the uncertainties in F(+) and F(-) are higher than that of
> F(mean) by a factor of about sqrt(2). R factors will always be higher
> for unmerged data because averaging always reduces the uncertainty.
> This means that we are in effect 'cheating' by throwing away the
> relatively imprecise anomalous differences and getting falsely lower R
> factors as a result! But as you imply the model would improve if we
> included the anomalous data in the refinement (assuming of course that
> it is meaningful data).
This has been an option in refmac refinement for some while now.
If you are using the GUI, select the option for "using SAD data directly"
rather than the default option "using no prior phase information".
Of course you must also make sure that appropriate scattering
factors are picked up by the program.
In my limited experience this has not led to improved refinement if
the anomalous differences are due only to sulfur, but has on occasion
led to noticeable improvement for true SeMet/SAD data.
Ethan
> This just demonstrates that low R factors do
> not necessarily equate to a better model - especially if you
> deliberately throw away the less precise data! The model would
> improve (marginally) because the anomalous differences would obviously
> provide additional information about the anomalous scatterers and
> therefore increase their precision, but wouldn't affect the precision
> of the lighter atoms. But is imprecision in the parameters of the
> heavy (or heavier) atoms usually an issue? - since these have bigger
> real scattering factors they will be more precisely determined than
> the lighter atoms anyway. So I don't think you would gain very much,
> except maybe more truthful R factors!
>
> Cheers
>
> -- Ian
>
> On 10 January 2012 20:00, Jacob Keller <j-kell...@fsm.northwestern.edu> wrote:
> > Dear Crystallographers,
> >
> > it seems to me that on a certain level we are always throwing away
> > (sort of) about half of our data when we merge Bijvoet pairs--why
> > shouldn't we keep them separate, since we know that they should be a
> > little bit different, especially in light of the higher multiplicities
> > which are more common now? Shouldn't modelling them give better
> > R-values, and wouldn't it just be more true? I guess a sort of proof
> > for this is that sulfurs are almost always detectable on anomalous
> > difference maps, implying that we are actually measuring those
> > differences accurately enough to see them (I don't think these things
> > can arise from model bias, as anomalous differences are not modeled.)
> > At least maybe at the final steps of refinement...?
> >
> > JPK
> >
> > --
> > *******************************************
> > Jacob Pearson Keller
> > Northwestern University
> > Medical Scientist Training Program
> > email: j-kell...@northwestern.edu
> > *******************************************
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
