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Dear Melanie,
you don't need to bother about using the same set of reflections for Rfree. As
long as you refine to convergence, the memory effect will be removed from the
reported Rfree (I call this Tickle's conjection and provided a method to test
the conjection in my work on Rcomplete).
If your Rfree set is small, there will be fluctuation. In that case, you can
use each set of flagged reflections one after the other and calculated an
average Rfree.
The better way (if your Rfree set is small), of course, would be to calculate
Rcomplete instead of Rfree as
it is calculated using all reflections, hence no variation problems. PDB_REDO
reports the value for you, but for programs other than Refmac and shelxl you
would have to convince the respective developers to not only print Rfree, but
also the numerator and denominator of Rfree - it's only one line of extra code
and it's a shame that authors of refinement programs do not report the extra
two numbers.
Cheers,
Tim
On Friday, June 24, 2016 10:41:21 AM [log in to unmask] wrote:
> Hi all,
>
> I am a little confused and I am looking for some advice and clarification
> here...
>
> I processed the same data with different integration programs. In order to
> be able to compare the refinement I want the two resulting reflection files
> to use the same Rfree. My worry is that if I pick the Rfree created from
> one integration result and copy it to the other I am biased in some way.
>
> If there would be any bias, will creating an Rfree set with 50% of
> reflections from one integration result and 50% of the other be a good
> idea? And if so, has anyone done this in the past and could give me some
> advice on that?
>
> And if this is all bollocks can someone give a reasonable explanation for
> this please?
>
> Thank you
>
> Best
>
> Melanie
>
> Dr Melanie Vollmar
> Diamond Light Source Ltd.
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> United Kingdom
> Tel: +44 (0)1235 778492
> www.diamond.ac.uk
- --
- --
Paul Scherrer Institut
Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
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