[phenixbb] covalently linked ligand

Muhammad Bashir Khan mbk at ualberta.ca
Tue Apr 14 15:59:31 PDT 2020

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

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

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 at ualberta.ca <cbrooks1 at ualberta.ca>
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