[phenixbb] Questions about phenix.refine with twin_law

Peter Zwart PHZwart at lbl.gov
Fri Dec 24 21:43:11 PST 2010


Hi Keitaro,

>
> During refinement with twin_law, the log file says x-ray target
> function is set to "twin_lsq_f".
> Does it mean, we cannot use maximum likelihood target for twinned data?
> If so, is it recommended to refine without twin_law at first several cycles?

I have never done a systematic study to answer this question. How good
is your model?

>
>
> When I tried to refine using the model refined without twin_law,
> the target function was still ml, not twin_lsq_f although I specified twin_law.
> Is this a bug?

Not sure, can you send (off-list) logfile of that run?

>
>
> When I used twin_law option, in the table "R-free likelihood based estimates",
> "Scale factor" were None in all resolution bins.
> Cannot scale factor be calculated during twin refinement?

The scale factor (one per dataset) is refined during twin refinement
and subsequently fixed during positional and adp refinement. The
lsq_twin target function doesn't have a resolution dependent scale
factor.

>
>
> Thanks in advance and Wishing you the best holidays,

Same to you!

HTH

P


> Keitaro



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P.H. Zwart
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