[phenixbb] Omit map around a ligand

Tom Terwilliger terwilliger at lanl.gov
Tue Apr 22 12:44:00 PDT 2008

Hi Mathieu,

Can you possibly just try this: replace HETATM 
with ATOM in your ligand-to-be-omitted-around 
file. This is fixed in the current version but 
your version ignores all the HETATM records in 
the omit_around_pdb file. I'm sorry about 
that.  If that doesn't do it, please ask again...

Otherwise this (from the documentation) should work:

phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=ligand.pdb \

Coefficients for the output omit map will be in 
the file resolve_composite_map.mtz in the 
subdirectory OMIT/ . An additional map 
coefficients file omit_region.mtz will show you 
the region that has been omitted. (Note: be sure 
to use the weights in both resolve_composite_map.mtz and omit_region.mtz).

All the best


At 01:26 PM 4/22/2008, you wrote:
>I tried to use phenix.autobuild to generate a SA-omit map around a
>non-protein residue but I didn't succeed.
>Can someone give me a recipe? (perhaps with file from the ligand fit
>examples.... ;-)  )
>Have a nice day.
>Mathieu Coinçon
>Biochemistry PhD Student
>Université de Montréal
>(+1)514-343-6111 #5352
>phenixbb mailing list
>phenixbb at phenix-online.org

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

More information about the phenixbb mailing list