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 : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov

On Tue, Apr 14, 2020 at 4:02 PM Muhammad Bashir Khan <mbk@ualberta.ca> 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

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