[phenixbb] phenix refinement question

Katarina Moravcevic katarinm at mail.med.upenn.edu
Mon Nov 15 15:24:18 PST 2010

Hi Pavel,
after reading the paper you suggested I have to admit I am still confused
with this discrepancy. In the section that describes specific reasons in
R/Rfree discrepancies that could apply to my model, REFMAC and PHENIX
supposedly use same principles. So, do these differences come from some
slight variations in how for example bulk solvent and anisotropic scaling
are treated in two programs?
I am sorry for asking basic questions and please do not bother to reply if
it is too silly.

On Mon, Nov 15, 2010 at 4:50 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hello,
>  I have only started using PHENIX and have made an interesting observation.
>>> If I run my model through PHENIX refine (individual sites, individual
>>> ADPs,
>>> occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP
>>> weight options selected) I obtain R/Rfree 0.15/0.18 and very nice
>>> geometry
>>> values (data is to 1.7A). However, if I now take this refined model and
>>> run
>>> it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21.
> sounds good to me, I would be worried otherwise.
>  Can anyone explain why is there such a big difference? Will this be an
>>> issue
>>> during PDB submission?
> Have a look at this:
> J. Appl. Cryst. (2010). 43, 669-676
> phenix.model_vs_data: a high-level tool for the calculation of
> crystallographic model and data statistics
> P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W.
> Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and
> P. D. Adams
>  Take a look at what phenix.refine reports for the number of
>> reflections used for refinement in the logfile - I believe it will
>> discard reflections that are flagged as suspicious (can't remember the
>> reference, I think it's one of Randy Read's papers),
> It is typically from zero to a few dozens of reflections and unless they
> are ~1.e+9 removing them rarely visible in terms of R-factor (if you just
> re-compute it).
> Pavel.
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