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.
Thanks
Katarina
On Mon, Nov 15, 2010 at 4:50 PM, Pavel Afonine
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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