[phenixbb] phenix refinement question
pafonine at lbl.gov
Mon Nov 15 21:17:01 PST 2010
> 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.
yes, in general, any crystallographic program that is in common use
today utilizes similar principles, which are outlined here (for example):
But the evil in the details and their amount (especially those that make
available refinement programs different)-;)
- outliers detection and removing: available in phenix.refine, not in
- 2nd derivatives based minimizer: used in Refmac and not in phenix.refine;
- anisotropic scaling applied to a different term;
- mask calculation parameters are pretty different between two programs;
- weight optimization is VERY different (including because of different
- phenix.refine uses ML target for bulk-solvent and scaling and Refmac
- ML targets parametrized differently;
- ... I can name 100+ more differences, but it's 21:09 and the dinner is
still waiting for me -:) so I guess I stop here.
We also know that even small change somewhere can turn refinement into a
different pathway and result in refined model in different local minimum:
Also, developing phenix.refine we almost always try to implement the
best currently available technology (or develop it ourselves) and we
make sure it works the way we expect it to work by re-refining the whole
PDB (in fact, its subset where experimental data is available).
So having said all the above, I'm not too surprised that you are getting
different results, and I'm not worried since the results are better
using PHENIX (I would ask for more details otherwise).
> I am sorry for asking basic questions and please do not bother to
> reply if it is too silly.
Not a problem. Please keep asking as many questions as you need.
All the best!
More information about the phenixbb