[phenixbb] refinement with anomalous data

Pavel Afonine pafonine at lbl.gov
Fri Feb 6 10:46:11 PST 2015


> I have a data set for refinement at 3.8A (outshell I/sigma ~1.0). When 
> I processed the data, I kept anomalous data I+/I-. Because at that 
> time I think I might have anomalous signal. But later I found that the 
> protein coordinated with wrong metal, so I don’t really have anomalous 
> scatters. I have good model from high resolution data.
> When I refined the structure, I found that refined against I+/I- give 
> lower R/Rfree (23.0%/27.0%)  than against Imean (25.1%/28.3%). When I 
> used I+/I-, I knew I doubled reflections/parameters ratio. I also let 
> Phenix both X-ray stereochemistry/ADP weight. The refined models have 
> similar geometry. So should I use I+/I- for refinement since it gives 
> lower R factor?

you cannot compare R-factors calculated using different sets of 
reflections, they are simply not comparable. So 23.0%/27.0% versus 
25.1%/28.3% doesn't really mean anything in this case.

If data set is not anomalous then you can use 
"force_anomalous_flag_to_be_equal_to=False" so that phenix.refine uses 
Fobs_mean = (Fobs(+) - Fobs(-))/2 in refinement.


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