[phenixbb] Finding correct Se sites with autosol

Tom Terwilliger terwilliger at lanl.gov
Thu Aug 27 08:20:20 PDT 2009

Hi Yu Seon,

A couple things to trh:

1. You might try SAD with the autosol option


which will use your SAD data in phaser along with the MR model to try  
to identify the anomalously-scattering atom locations and to phase  
including the MR model and the SAD data.

2. You might check whether the Se sites you have previously found are  
near your SD atoms of Met using phenix.emma if you have not already.  
This routine will take care of origin offsets and inversions for you  
so it is more comprehensive than simply superimposing the ha sites on  
your model.  I'm thinking of something like this:

cat mr.pdb |grep 'ATOM'|grep ' MET '| grep ' SD ' > sites_from_mr.pdb
phenix.emma sites_from_mr.pdb ha.pdb

All the best,
Tom T
On Aug 27, 2009, at 8:58 AM, YS. Chung wrote:

> Dear all,
> I have a 3 angstrom structure which I am trying to solve with MAD or
> SAD. The structure was previously solved with molecular replacement  
> but
> refinement could not continue due to poor phasing at the N-terminal
> domain of the protein. I have run solve and autosol which are able to
> find the Se sites. However, Se sites are not anywhere near the
> methionines when I superimpose the ha.pdb and the pdb file that I
> obtain from a new run of molecular replacement. The
> exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show
> any connected densities. I have also tried autobuild with the  
> solutions
> from AutoSol, but the model that it builds in is incorrect. Any
> suggestions would be appreciated.
> Thank you,
> Yu Seon Chung
> _______________________________________________
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> phenixbb at phenix-online.org
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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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