Hi All;

I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix.

I used the

" phenix.ligand_linking pdb_file_name" commond

It creates

apply_link.def

and

data_link.cif

I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand.

Thanks for your help

Bashir

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Muhammad Bashir Khan, Ph.D.
Research Associate
Department of Biochemistry
Medical Science Bldg.
Lab 3-27
University of Alberta
Edmonton AB, T6G 2H7

Phone: 780-492-4577-
e-mail: mbk@ualberta.ca