[phenixbb] R/R free reported values

Pavel Afonine pafonine at lbl.gov
Mon Oct 27 17:34:49 PDT 2014

On 10/27/14 4:43 PM, Nathaniel Echols wrote:
> On Mon, Oct 27, 2014 at 1:19 PM, George Devaniranjan 
> <devaniranjan at gmail.com <mailto:devaniranjan at gmail.com>> wrote:
>     Would you define "significant" for me (as you see it of course)?
> Pavel's definition:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906258/
> "...the difference between R factors computed using the different 
> methods is typically less than 0.01%."
> I think this is probably a typo and it is supposed to mean "1%" or 
> "0.01", which would have been my estimate. Certainly differences below 
> 0.005 are hardly worth noticing, and below 0.001 is statistical noise. 
> Differences above 0.01 are more worrisome (although not entirely 
> unheard of).

It depends what you compare and how.. Two scenarios:

1) Compute Fcalc using FFT (Fc_fft) and direct summation (Fc_direct) and 
compute R-factor(Fc_fft, Fc_direct). In this case indeed typically the 
R-factor will be below 1% (not 0.01% !). Attached script illustrates 
this (to run: phenix.python run.py).
Also, Table 4 in

Acta Cryst. (2004). A60, 19-32.
On a fast calculation of structure factors at a subatomic resolution
P. V. Afonine and A. Urzhumtsev

does exactly this comparison.

2) You run two identical refinements, in one you use FFT and in the 
other one direct summation. In this case the difference between 
R-factors is likely to be below 0.01%. This is because refinable 
parameters will absorb the differences.


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