[phenixbb] Does PHENIX exclude Rfree reflections in maps?
PDAdams at lbl.gov
Thu Oct 1 20:11:26 PDT 2009
Might be worth looking at:
Separating model optimization and model validation in statistical
cross-validation as applied to crystallography. Kleywegt GJ. Acta
Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):939-40
On Oct 1, 2009, at 9:05 AM, Joe Krahn wrote:
> I propose that the issue of using test reflections be addressed by
> 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
> previous density-modified transformation. Maybe the people who could
> 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
> 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-
>>> With 10% test reflection, I suspect that difference maps used to
>>> waters can easily find a few noise peaks with significant R-free
>> - I'm not aware of any systematic study on this matter, although I
>> 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
> 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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> phenixbb at phenix-online.org
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