[phenixbb] R/Rfree discrepancy Phenix vs Refmac

[Nathaniel Echols]

On Fri, Aug 12, 2011 at 6:15 AM, David Goldstone
<david.goldstone at nimr.mrc.ac.uk> wrote:
> I am by no means an expert in such things and I am sure that you will get a
> comprehensive answer at some point. My understanding is that differences in
> weightings, and the treatment of the solvent correction means reproducing
> R-factors across different programs is not really possible.

Correct, although we can usually come close.  See Pavel's paper on
phenix.model_vs_data for more details:

http://www.ncbi.nlm.nih.gov/pubmed/20648263

I'm not sure if the use of total vs. residual B-factors in Phenix and
Refmac will also contribute - although if model_vs_data detects that a
PDB file was refined with Refmac, it will automatically adjust its
treatment of B-factors to compensate.

In general, the R-factors from Refmac and Phenix recalculated in the
other program will be fairly similar - this discrepancy is on the
upper end of the range, but it's not unheard of.

-Nat