[phenixbb] covalently linked ligand

Nigel Moriarty nwmoriarty at lbl.gov
Tue Apr 14 16:45:40 PDT 2020


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 at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Tue, Apr 14, 2020 at 4:02 PM Muhammad Bashir Khan <mbk at 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 at ualberta.ca <cbrooks1 at ualberta.ca>
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