Hi Danilo, FEM is a sort of highly 'massaged' 2mFo-DFc map, so it is not a difference map. Ligand fit just fits the ligand; I'm guessing you need to run some refinement so that the ligand optimally fits the map (coordinates, occupancy, ADPs). Pavel On 3/18/19 08:40, Danilo Belviso wrote:
Dear all,
I am interested in fitting a ligand in the case of a structure where water molecules have been already placed. I know that this is not the standard procedure, but these water molecules are quite sure. To do this, I used ligand fit procedure with command "lig_map_type = *fo-fc_difference_map fobs_map pre_calculated_map_coeffs" command. At the end, the procedure provides ligands with low CC (0.4-0.55).
So, I would try ligand fitting by using FEM of Fo-Fc. The rationale is that FEM of Fo-Fc could help (likely) ligand fitting, by consider the presence of water molecules at the same time (Fo-Fc should be 0 where water molecules are placed). Maybe nothing will change, but I would try.
I calculated FEM by using
phenix.fem start_FEM.pdb start_FEM.mtz input.xray_data.label='FOFCWT'
and also by using
phenix.fem start_FEM.pdb start_FEM.mtz maps.map_coefficients_label='FOFCWT PHFOFCWT' file_name_prefix='FEM_map'
where start_FEM.pdb and start_FEM.mtz are the pdb and mtz resulting from the refinement with water.
However, by checking the the fem maps by coot, I notice that fem is completely different from Fo-Fc and it is not the expected feature-enanched Fo-Fc.
Is the procedure and keywords correct to perform FEM calculation of Fo-Fc? Do you have any suggestions?
Thanks
Danilo