You should be able to make a sa-omit map the same was as you make an omit map if you include the keyword composite_omit_type=sa_omit

(see http://phenix-online.org/documentation/autobuild.htm#anch173):

Make a SA-omit map around atoms in target.pdb

phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit

Let me know if that doesn't do it!

All the best,

Tom T

On Dec 7, 2012, at 3:41 AM, Appu kumar wrote:

Dear Users,
I am refining a enzyme structure with ligand. I want to make the simulated annealing omit map of ligand including with 4 Angestron radius around the ligand. I am seeking your valuable advice to help me out. I know how to make omit map but i have not come accross making simmulated annealing omit map.
I would appreciate your help.
Thank you
Appu

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