Hi Mary,

there was almost exactly the same question on phenixbb a couple of days ago.

Try doing it differently and see what happens:

step 1:
remove ligand from PDB file

phenix.pdbtools model.pdb remove="chain X and resseq 123"

or set its occupancy to 0 (which is not 100% equivalent but close):

phenix.pdbtools model.pdb occupancy.set=0 selection="chain X and resseq 123"

step 2:
run SA refinement using phenix.refine:

phenix.refine model.pdb data.mtz model_no_ligand.pdb simulated_annealing=true

step 3: load a map created by above run into Coot: how different it is from the map that you get from phenix.autobuild run?

Pavel.

PS1.:
I will add a test that will assert that both ways (the above one and using phenix.autobuild) give similar results.

PS2.:
You probably meant mFo-DFc map or 2mFo-DFc (and not 2Fo)?

On 6/3/11 7:21 AM, Desi Mail wrote:

Hi everybody,

I would like to calculate the omit map around the ligand. I followed the documentation
http://www.phenix-online.org/documentation/autobuild.htm#anch159

But the 2Fo density around the ligand is very poor.

Any help is appreciated.

Thanks
Mary

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
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).
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