[phenixbb] phenix refinement question

Pavel Afonine pafonine at lbl.gov
Mon Nov 15 21:17:01 PST 2010

  Hi Katarina,

> 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)-;)

For example:

- 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 
minimizers used);
- phenix.refine uses ML target for bulk-solvent and scaling and Refmac 
uses LS;
- 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!

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