[phenixbb] FEM by using FoFc map
danilo.belviso at ic.cnr.it
Mon Mar 18 08:40:30 PDT 2019
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
Is the procedure and keywords correct to perform FEM calculation of
Fo-Fc? Do you have any suggestions?
Dr. Belviso Benny Danilo, PhD
Istituto di Cristallografia (IC)
Consiglio Nazionale delle Ricerche (CNR)
via Amendola 122/o, 70126 Bari - Italy
Tel ++39 080 5929273
Fax ++39 080 5929170
mail: danilo.belviso at ic.cnr.it
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