On Monday, May 23, 2011 01:17:45 pm Hailiang Zhang wrote:
> Thanks Nat! I am not doing real space refinement. Actually I am only using
> the maps for manual model building/adjustments. In this case, if some
> Rfree reflections have strong scattering intensities, removing them may
> lead to featureless density maps. However, if we just leave them in, do
> you think we may have the so-called model-bias issue?
>
> Hailiang
In theory:
On the one hand, if you include Fobs for the Rfree reflections and then use
the map for fitting, you are contaminating your Rfree set. -> bias
On the other hand, if you omit the Rfree reflections altogether then you
suffer from possible Fourier truncation effects -> bias
Third alternative: Include Fcalc values for the Rfree reflections rather
than Fobs. -> avoids both classes of bias
In practice:
For manual fitting I doubt any of this makes very much difference.
cheers,
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
