[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
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

Phone: 780-492-4577-
e-mail: mbk at ualberta.ca <cbrooks1 at ualberta.ca>
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