[phenixbb] phenix.refine and R free values

[Pavel Afonine]

Hello,

> 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"
or
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.

Pavel

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