Marcelo Covalently bound ligands is an active area at the moment. It is possible using the latest CCI-Apps and the interface will improve in the near future. If you have a modified amino acid in the PDB which contains the rest of the protein and you have modified the residue name (or in the near future, you have non-standard atoms in the modified residue) you can run elbow.builder protein_modified_amino.pdb --do-all which will scan the PDB file for residues it does not recognise and generate a restraints library. You can then phenix.refine data.mtz protein_modified_amino.pdb elbow.XXX.all.cif to tell the refinement about the restrains for your modified amino acid. The refinement attempts to include the modified amino acid in the backbone based on the atom names (C, N, CA, O). You should check that this occurs and let me know in the event that it fails. I'm also working on a scheme were by you can have the modified amino acids in other formats. Nigel 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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