Hi Mohamed and Tim,

I'm yet to see if using "thin-shells" vs random make a notable difference, however, for the record, I think it is worthwhile to point out this paper where authors explain and demonstrate why using "thin-shells" is important in case of high-order NCS:

Acta Cryst. (2006). D62, 227-238
Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry
F. Fabiola, A. Korostelev and M. S. Chapman

On ML and Rfree comment:

- ML is superior than LS if your model (atomic + nonatomic) misses scattering, that is incomplete, because ML takes missing scattering into account statistically;

- free set must be available for ML target calculation, so if you use ML then you get Rfree as a bonus.

Pavel


 
On 6/4/15 12:21 AM, Tim Gruene wrote:
Dear mohamed noor,

thin shells are commonly picked in cases of twinned data. As Andrew
points out in the email you link, the NCS makes the refinement behave
well, so also you will probably get away with 'normal' randomly selected
reflections.

At high resolution the data to parameter refinement also increases and
the Rfree looses its meaning. That's one of the reasons why people don't
use Rfree for small molecule structure determination and why ML
refinement show not much improvement compared to least squares
minimisation (it's different for charge density studies, when the data
to parameter goes down again).

Regards,
Tim

On 06/04/2015 01:18 AM, mohamed noor wrote:

Dear all

I found a not-so-old thread about this topic:
http://phenix-online.org/pipermail/phenixbb/2012-January/018259.html. Maybe
there has been significant changes in phenix.refine since then.

However, I couldn't find a conclusion. In my case, my data extends to 1.4 A
with the R/R free being around 23/26 %. There is also pseudo symmetry, so
there are 16 NCS copies in a lower symmetry group than what Xtriage
suggested. The map looks fine with density for some H atoms even being
visible.

On what basis should I decide whether to use (or not) thin shell
assignment? And what is the cut-off for number of NCS copies?

Thanks.



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