[phenixbb] refinement with anomalous data

Guangyu Zhu gzhu at hwi.buffalo.edu
Fri Feb 6 11:09:34 PST 2015


I use same data set for refinement, so Rfree is also marked for same reflection. The only difference is that I chose “Data labels” from Phenix IMEAN or I(+) I(-). By the way, I use version 1.8.2 for refinement. Newer versions gives higher R/Rfree.


From: Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>>
Date: Friday, February 6, 2015 at 1:46 PM
To: Guangyu Zhu <gzhu at hwi.buffalo.edu<mailto:gzhu at hwi.buffalo.edu>>, "phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] refinement with anomalous data


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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