[phenixbb] Re : Re: Does PHENIX exclude Rfree reflections in maps?
terwilliger at lanl.gov
Thu Oct 1 08:11:34 PDT 2009
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,
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,
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
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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