Dear Qixu Cai,
it is a misconception that Rfree was not free anymore. The gap does
not close when you swap the reflections in Rfree set. The 'free'
reflections are freed when you do proper refinement, i.e., when the
value of the target function becomes stationary.
See https://doi.org/10.1107/S0907444997013875 and
https://doi.org/10.1107/S0907444999016868 for the mathematical
background, https://doi.org/10.1073/pnas.1502136112 for an experimental
treatment, and Ian Tickle's explanations on this topic here on the
CCP4bb.
Best wishes,
Tim
On Fri, 28 Apr 2023 16:54:07 +0800 Qixu Cai <caiq...@gmail.com> wrote:
> Dear Robbie and Tim，
>
> Thanks a lot for your reply. I just do not understand that if we can
> change the R free set during different rounds of refinement, the gap
> between Rwork and Rfree would be small, and Rfree would be
> meaningless, as R-free set is not "free".
>
> Best regards,
>
> Qixu Cai
> Email: caiq...@gmail.com
>
>
>
> Robbie Joosten <robbie_joos...@hotmail.com> 于2023年4月28日周五
> 15:26写道：
>
> > Hi Qixu,
> >
> > PDB-REDO tries to have a minimum number test set reflections to
> > reduce the error margin in R-free. As Tim says this is not a
> > problem but if you reach out privately we can change your
> > calculation to use your current testset. That is not recommended
> > though.
> >
> > Cheers,
> > Robbie
> >
> > On 28 Apr 2023 04:51, Qixu Cai <caiq...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I'm using the PDB-REDO server to refine my structure. I found that
> > PDB-REDO said that 5% R-free set is too small and it created a new
> > R-free set.
> >
> > Is possible for the PDB-REDO server to keep the original R-free set
> > to make final Rfree value comparable?
> >
> > Best regards,
> >
> > Qixu Cai
> > Email: caiq...@gmail.com
> >
> >
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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
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