[phenixbb] covalently modified proteins

Pavel Afonine PAfonine at lbl.gov
Fri Mar 16 11:24:07 PDT 2007

Hi Marcelo,

another option to try (different from what Nigel explained) is:

1) You use eLBOW to generate a cif file for your ligand like:
% elbow.builder model.pdb --do-all
You will get a file like elbow.xxx.all.cif.

2) Then you run refinement as:
% phenix.refine model.pdb data.mtz elbow.xxx.all.cif params
where params is the file that defines the covalent bond between your 
macromolecule and ligand. An example of params file is (file params 
contains lines below):

refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain A and resname HEM and resid 154 and name FE
    atom_selection_2 = chain A and resname HIS and resid 93 and name NE2
    distance_ideal = 1.8
    sigma = 0.01

For more details see "Documentation"  at 


Marcelo Carlos Sousa wrote:
> I have followed with interest the discussions regarding refinement of  
> proteins with ligands. I wonder if Pavel or anybody else could  
> comment on the refinement of proteins with covalently attached  
> ligands. I am currently handling that in CNS as I know how to write  
> the patches. Is this possible in phenix? Coudl it be handled by  
> generating a "new amino acid" like say a Cys with beta mercapto  
> ethanol attached and then get the program to link this "new amino  
> acid" via normal peptide bonds with the rest of the protein? What  
> about a capped N-terminus? can we make the "new amino acid" say N- 
> acetyl-Gly and get the program to put this at the N-terminus?
> Any help is appreciated.
> Marcelo
> ____________________________________________
> Marcelo C. Sousa, Ph.D.
> Department of Chemistry and Biochemistry
> Cristol Chemistry Building. Room 100
> 215 UCB
> University of Colorado at Boulder
> Boulder, CO 80309
> Phone: (303) 735 4341
> Fax: (303) 492 5894
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