[phenixbb] phenix.refine and R free values

Pavel Afonine pafonine at lbl.gov
Sat Aug 30 09:45:58 PDT 2014


> Hi Phenix users,
> I was trying to experiment with phenix.refine using default parameters 
> (2Y78.pdb) and I got the following message.
> Multiple equally suitable arrays of observed X-ray data found.
> Possible choices:
>   2Y78.mtz:IOBS,SIGIOBS
>   2Y78.mtz:I(+),SIGI(+),I(-),SIGI(-)
> Please use refinement.input.xray_data.labels
> to specify an unambiguous substring of the target label.
> Anyway, two questions related to this:
> 1) How does one pick of the two options above?

If your question is about the syntax:

phenix.refine model.pdb data.mtz xray_data.labels="IOBS,SIGIOBS"
phenix.refine model.pdb data.mtz xray_data.labels="I(+),SIGI(+"
(sub-string should work).

If your question is about choice anomalous vs non-anomalous data to be 
used: I would use anomalous because it is a richer source of 
information, you will get anomalous difference map, you can refine 
anomalous f'&f'', etc.

> 2) If R work/R free went from 0.1044/0.1142  to 0.1096/0.1200 is that 
> bad or is it acceptable?

R-factors look similar to me. Systematic slight increase may mean you 
need to adjust target weights or choose refinement strategy more 
tailored to the quality of input data and model.


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