Hi Manoj,
you can do it this way:
1) remove ligand from PDB file;
2) compute mFo-DFc map. This is your ligand-omit map.
Some would advise to do a round of refinement between steps 1-2 above in order to remove "memory from the ligand". I'm not convinced this is critical though.
Pavel
On 11/15/15 12:18, Manoj saxena wrote:
Greetings,
I would be very grateful if someone can help
me to explain in I can get F0-Fc omit maps of a particular
ligands using Phenix.
I am trying to generate an omit map
for the ligands in my protein model using the
composite omit map GUI feature of phenix version 1.10.1-2155.
I selected my ligands by using atom selection feature under the
map options(and in the omit map method I put refine). What map type I should give in the map types
input to get the F0-Fc maps. Currently I may getting a map
that look like my 2F0-Fc map that I got after my refinement.
Also, I have no waters in my model.
Can we define areas (boxes) around the ligand to generate
omit map of that particular region to get output maps with densities
like Fo-Fc maps.
So many thanks in advance.
Regards
Manoj