[phenixbb] WAS: changing TLS groups mid refinement
PAfonine at lbl.gov
Mon May 17 19:52:44 PDT 2010
> Can we turn the argument on its head ?
well, it depends what you call "head" -:)
> Short version:
> phenix.refine throws out 2896 reflections of 48895, including 11% of
> the data in the outermost shell, compared to using TRUNCATE to prep my
> data. Using the common data subset the structure has a decreased
> R-free of 0.8% if you refine against the truncate=yes PDB file with
> the common subset of data.
> 0.8% at a 24% R-free (24.0 vs 24.8) is pretty significant IMHO.
You cannot compare the R-factors that were computed using different sets
of reflections. Therefore the above comparison is not valid, obviously.
Same applies to your "Longer version". Let's compare apples with apples.
Comparing R-factors in this case does not tell that one refinement is
better or worse than the other one. It just doesn't tell anything
because the R-factor is not a good measure when you deal with two
different datasets (datasets containing different amount of reflections).
More information about the phenixbb