[phenixbb] Phaser heavy atom sites - question

Tom Terwilliger terwilliger at lanl.gov
Tue Jul 6 08:11:06 PDT 2010

Hi Peter,
You can do this with phenix.solve using a script like this:

#!/bin/csh -f
phenix.solve --giant <<EOD
symfile $PHENIX/solve_resolve/ext_ref_files/p21.sym
CELL 25.0 25. 25. 90 100. 90
resolution 5 20.0
infile(1)  ha.pdb      !  input file with coordinates to be mapped
infile(2)  coords.pdb     !  pdb file with object that we want to be  
close to
outfile    atoms.mapped   !  atoms mapped close to object
dismin     0.0            !  Only atoms with a closest distance to an  
dismax 1000.0             !  in object between dismin and dismax will be
                           !  written out. Default= 0 to 1000000.
maptoobject                 !  map them as close to the object as  

All the best,
Tom T

On Jul 6, 2010, at 6:11 AM, Peter Grey wrote:

> Dear all,
> Phaser SAD module found roughly 200 sites of my heavy atom. Phaser  
> writes the location of the sites within an ASU.
> I am looking for a tool that can transform these sites to the  
> corresponding sites within and just around my model.
> Thank you in advance for any suggestions,
> Peter.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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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