[phenixbb] Re : Re: Does PHENIX exclude Rfree reflections in maps?

Tom Terwilliger terwilliger at lanl.gov
Thu Oct 1 08:11:34 PDT 2009

Hi Sacha,
Yes, that would help.

In parallel, to get a little more data on the practical aspects of all  
this, I think I will do a test to see how much difference taking out a  
super-test-set of reflections completely makes in overall structure  
determination from start to finish using fully automated structure  
determination with phenix.autosol and phenix.autobuild.

All the best,
Tom T

On Oct 1, 2009, at 1:56 AM, Alexandre OURJOUMTSEV wrote:

> Hi, Tom, Pavel and Joe,
> > I'm glad you put that option in, Pavel.  However for model-
> > building it is not so straightforward. Normally we are building  
> into density-modified
> > maps. Density modification works poorly when a significant set of
> > reflections is excluded, so this becomes impractical.
> As I remember it was a paper (by Blanc, ..., Bricogne ? am I wrong?  
> Ifailed to find it right now) where they faced exactly this  
> problem.Again, as I remember they suggested to exclude the test-set  
> reflectionsfrom the map calculation but , to minimize the map  
> deformation, insteadof them include average Fobs for the  
> corresponding resolution shell.
> Is it a way to answer the original question / problem ?
> As I understand, a similar technique Pavel already uses to calculate  
> the maps with Fobs missed.
> Best regards,
> Sacha

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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