[phenixbb] WAS: changing TLS groups mid refinement

Pavel Afonine PAfonine at lbl.gov
Mon May 17 19:52:44 PDT 2010

Dear Phil,

> 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).


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