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 http://phenix-online.org/download/cci_apps/ Pavel. 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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