[phenixbb] FEM by using FoFc map

Pavel Afonine pafonine at lbl.gov
Mon Mar 18 09:42:33 PDT 2019

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).


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

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