[phenixbb] Validation question: R-factor (all) and # of unique reflections (all)

Nathaniel Echols nechols at lbl.gov
Tue Jul 5 11:33:28 PDT 2011

On Tue, Jul 5, 2011 at 11:17 AM, Young-Jin Cho <yjcho at brandeis.edu> wrote:
> While I am trying to deposit, I am faced with several things that I am not
> sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool)
> in the PDB bank.
> Most values are came from pdb file that was made from phenix.refine but it
> asks me "R-factor (all)" that satisfy the limits established by high & low
> resolution cut off and "number of unique reflections (all)".
> My simple question is if phenix has those kind of information, if so where I
> can find them.

It looks like these aren't included in the PDB header of the files
phenix.refine writes.  I think "R-factor (all)" is an artifact from
the era when crystallographers would do a final refinement with all
reflections included (a Very Bad Idea), and I think I always left this
blank in PDB depositions.  Assuming you didn't truncate the
resolution, "Number of unique reflections (all)" is probably whatever
is in the MTZ file - depending on the outlier removal, it may be
slightly more than phenix.refine reports.

> Another question is if I changed water (deletion or changed occupancy) based
> on 'precheck', should I run phenix.refine again to get R/Rfree values in
> correct? I am not sure if these are captured by PDB automatically or not.
> (seemingly they do like that at this point but not 100% sure yet.)

You can run phenix.model_vs_data or the validation GUI to determine
new R-factors.  Unless the PDB has made huge improvements in the last
half-year, their recalculation of R-factors isn't at all robust.


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