[phenixbb] Phenix.model_vs_data - Rfree difference

Pavel Afonine pafonine at lbl.gov
Mon Jan 2 10:26:19 PST 2017


Hi Luca,

the differences you quote are very small and I'd say insignificant. This 
is likely due to limited precision of coordinates and B-factors in PDB 
file. 0.1720/0.2086 and 0.1715/0.2080 are really the same.

I wonder what happens if you ask phenix.refine to output model in mmCIF 
file and then use it as input to phenix.model_vs_data (mmCIF has more 
digits for coordinates and B-factor records).

Pavel

On 1/2/17 10:09, Luca Pellegrini wrote:
> Hello,
>
> I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data:
>
> phenix.refine
> R-work/R-free 0.1702/0.1974
>
> phenix.model_vs_data
> R-work/R-free 0.1728/0.1795
>
> Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy:
>
> phenix.refine
> R-work/R-free 0.1720/0.2086
>
> phenix.model_vs_data
> R-work/R-free 0.1715/0.2080
>
> Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine.
>
> Thanks for the help & happy New Year,
>
> Luca
>
> Luca Pellegrini, PhD
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge CB2 1GA
> UK
>
> Email: lp212 at cam.ac.uk
> Phone: 0044-1223-760469
>
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