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 \ composite_omit_type=sa_omit 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 -TomT At 01:26 PM 4/22/2008, you wrote:

Hi, 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.... ;-) ) Thanks. Have a nice day. Mathieu. ____________ Mathieu Coinçon Biochemistry PhD Student Université de Montréal (+1)514-343-6111 #5352

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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