[phenixbb] Questions about phenix.refine with twin_law

Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp
Mon Dec 27 05:40:52 PST 2010

Dear Pavel and Peter,

> Here is the typical distribution of Rfree, Rwork and Rfree-Rwork for structures in PDB refined at 2.5A resolution:

Are their statistics applied to twinning cases?
I think such kind of statistics should be (slightly) different from
normal cases.. not?

> Did you use PHENIX to select free-R flags? It is important.

Yes, I used phenix to select R-free-flags with use_lattice_symmetry=true.
But, my data have pseudo-translation, too (~20% of origin height in patterson).
I'm afraid I should have considered pseudo-translation as well as
twinning when selecting R-free-flags, e.g. use_dataman_shells=true.

Do you have any way to know the refinement is biased or not because of
wrong R-free-flags selections?

> ML is better than LS because ML better account for model errors and incompleteness taking the latter into account statistically.

Do they come from sigma-A estimation?

> phenix.model_vs_data model.pdb data.mtz
> does it suggest that you have twinning?

Yes, it says:
    twinned                 : -k,-h,-l

> I do not know what's implemented in Refmac - I'm not aware of a
> corresponding publication.

FYI, I think No. 13 of this slide describes the likelihood function in
case of twin..

> Typically, when people send us the "reproducer" (all inputs that are enough
> to reproduce the problem) then we can work much more efficiently, otherwise
> it takes a lot of emails before one can start having a clue about the
> problem.

I fully understand it, but I'm sorry I couldn't..
I will do my best to give you sufficient information.

Thank you for giving me the solution!


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