[phenixbb] Does PHENIX exclude Rfree reflections in maps?

Peter Grey petgxray at gmail.com
Thu Oct 1 09:43:51 PDT 2009

Hi Joe,

There  was a very fruitful discussion about R-free and its size in ccp4bb
and this was summerized (including views from Read and from Cowtan) in




On Thu, Oct 1, 2009 at 6:05 PM, Joe Krahn <krahn at niehs.nih.gov> wrote:

> I propose that the issue of using test reflections be addressed by more
> than just speculation.
> Create a 10% test set for refinement, but divide that into two 5%
> groups. One is used as a "pure" test set, and the other subgroup is
> allowed to be used in non-refinement tasks. During the course of an
> entire structure determination, one can monitor whether the unbiased
> test set differs from the biased test set.
> My concern is that if the data is weak enough that including test
> reflections is required to interpret a part of the map, then the data is
> probably too weak to distinguish a correct model from a model-bias.
> For density modification, it may be possible to converge on a good map
> if both missing and test reflections use "Fcalc" fill-in values from the
> previous density-modified transformation. Maybe the people who could not
> get good results without the test reflections used a DM method that
> reset missing values to zero on every cycle.
> Pavel Afonine wrote:
> > Hi Joe,
> >
> >> Normally, 5% for R-free is sufficient.
> >
> > did anyone studied this and came to this conclusion (publication?)?  I'm
> > not aware.
> Is there a paper showing that 10% is required or sufficient? Maybe that
> needs to be studied as well.
> ...
> >> I am sure that many people will use it when
> >> they find that real-space fitting and refinement tools lower R-free,
> >> unaware that they are cheating.
> >>
> >
> > Sure. This is why free-R flags are not used in maps calculation for
> > real-space refinement (my previous email).
> Yes, but people can still use maps from PHENIX with external real-space
> refinement.
> >
> >> With 10% test reflection, I suspect that difference maps used to find
> >> waters can easily find a few noise peaks with significant R-free
> >> contributions.
> >
> > - I'm not aware of any systematic study on this matter, although I can
> > believe it in theory;
> > - phenix.refine uses very sophisticated filtering tools;
> > - I guess at some point I will switch to using Average Kick Maps for
> > water picking. This will remove the noise peaks, and so eliminate the
> > problem (I need to test this all, though).
> I started wondering about test reflections im maps because I was
> removing some bad "waters" and found a bigger increase in Rfree than in
> Rwork. That made me wonder if they had a significant component of
> test-set density. But, I also have not checked this in detail.
> Joe Krahn
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