[phenixbb] omit map
pafonine at lbl.gov
Fri Jun 3 14:40:31 PDT 2011
there was almost exactly the same question on phenixbb a couple of days ago.
Try doing it differently and see what happens:
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
run SA refinement using phenix.refine:
phenix.refine model.pdb data.mtz model_no_ligand.pdb
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?
I will add a test that will assert that both ways (the above one and
using phenix.autobuild) give similar results.
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
> But the 2Fo density around the ligand is very poor.
> Any help is appreciated.
> 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).
> phenixbb mailing list
> phenixbb at phenix-online.org
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