[phenixbb] picking Rfree set

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Jan 22 09:23:38 PST 2008

> 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.

More information about the phenixbb mailing list