[phenixbb] FEM by using FoFc map

Danilo Belviso danilo.belviso at ic.cnr.it
Mon Mar 18 08:40:30 PDT 2019

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?



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
web: users.ba.cnr.it/ic/crisdb00

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