weight matrix and R-FreeR gap optimization

From: james09 pruza
Date: 8 November 2011 05:39

Dear ccp4bbers,

I wonder if someone can help me defining proper weight matrix term in Refmac5 to lower the R-FreeR gap. The log file indicates weight matrix of 1.98 with a gap of 7. Thanks for suggestions in advance.

James

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From: Robbie Joosten

Hi James,

 

That is not exactly a lot of info to decide the best weight. The optimal weight is (very loosely) resolution dependent. At normal resolutions the optimal matrix weight is usually well below 1.0. Start at 0.3 and try a few weights to see what works best for your data. To close the R-free gap you can also try to optimize other refinement parameters such as NCS restraints, B-factor model (and restraint weight). Jelly body restraints sometimes work really well to keep the R-free gap sensible, especially at low resolution.

 

Cheers,

Robbie

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From: Eleanor Dodson

What is your resolution? The gap is usually wider at lower resolution.
Eleanor

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From: Bernhard Rupp (Hofkristallrat a.D.)


Here a figure displaying distribution gap stats:

http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp
hy_Fig_12-24.htm

Cheers, BR