Re: [phenixbb] covalently linked ligand

Bashir Can you explain what you mean by "not see"? What were you expecting to "see" that told you that phenix.refine had applied a restraint between your ligand and the protein? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Apr 14, 2020 at 4:02 PM Muhammad Bashir Khan wrote:

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

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