[phenixbb] FEM by using FoFc map
pafonine at lbl.gov
Mon Mar 18 09:42:33 PDT 2019
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?
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