[phenixbb] picking Rfree set
PHZwart at lbl.gov
Tue Jan 22 09:52:14 PST 2008
yes, it will.
This is useful for when the data is twinned.
2008/1/22, David Garboczi <dgarboczi at niaid.nih.gov>:
> So, for instance, when addition of a ligand to a P212121 cell (1 mol)
> changes the symmetry to P21 (almost same cell, but 2 mol), the
> selection of the Rfree set from the P21 data by phenix.refine will
> take the higher almost symmetry into account?
> >btw3: the lattice symmetry is taken into account when choosing an free
> >set in phenix.refine (unless specified otherwise). If all NCS
> >rotational operators are approximately parallel to twin laws, you
> >should be fine.
> >2008/1/22, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>:
> >> > Does phenix.refine take NCS into account when picking the Rfree set?
> >> > Thin shells, or other strategy...
> >> The short answer is no.
> >> We had long internal discussions about this without reaching a final
> >> conclusion. In the long run we may integrate alternative R-free set
> >> distributions in phenix.refine; in the meantime you have to use
> >> an external program (e.g. dataman or sftools).
> >> BTW 1: just to prove that we have thought about this subject, we have a
> >> simple tool for "visualizing" distributions of R-free flags:
> >> iotbx.r_free_flags_accumulation your.mtz
> >> It writes a file with x,y pairs which you can plot with e.g. Excel
> >> or any other 2D plotting program.
> >> BTW 2: The free reflections aren't as free as one may think. When
> >> using a maximum likelihood target (any program), the free reflections
> >> are used in the estimatation of the error model. This estimation
> >> becomes more tricky if the reflections are distributed in thin
> >> shells. I.e. if you go to thin shells you may in fact account to some
> >> degree for the NCS, but at the same time you compromise the error
> >> model estimation.
> >> Ralf
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> David N. Garboczi, PhD
> Phone: 301-496-4773
> Investigator, Structural Biology Section (SBS)
> Laboratory of Immunogenetics (LIG)
> National Institute of Allergy and Infectious Diseases (NIAID)
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