On Wed, Jul 6, 2011 at 6:30 AM, Tjaard Pijning
The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both the protein and the ligand. When I feed this into the CCP4 module FFT to generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the protein and ligand. However I need only the ligand Fo-Fc density. What is the right way to do this ?
Pavel is correct, it is easiest to do this with phenix.refine instead of AutoBuild. An alternative to the commands he suggested is simply to delete the ligand from the input model and then run refinement as usual (with simulated annealing). This gives you total control over what is omitted; I think AutoBuild may carve out a box around the omit atoms. The Fo-Fc map coefficients will still cover the entire unit cell, but if you have correctly placed all of the protein atoms and obvious solvent, it will mainly show your ligand. Otherwise, you need to use a different tool to limit how much of the map is displayed - Phenix won't do this for you, at least not if you want to use simulated annealing. (We could add a separate tool for this, of course - it's very easy to implement.) -Nat