[phenixbb] Creating dictionary restraints for a LINK

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 2 08:57:10 PDT 2012


You can use

phenix.ligand_linking model.pdb

to generate the links between ligands and residues. Don't forget to
look in the .geo to ensure the links are made once you add the files
to the phenix.refine input.


On Mon, Apr 2, 2012 at 8:29 AM, Mario Sanches <mariosan at gmail.com> wrote:
> I have a question regarding link dictionary generation. Nigel helped me with
> a molecule dictionary last week (thank you Nigel) so the molecule is
> refining well now. This molecule is covalently bound to on of the residues.
> I tried generating a dictionary that describes both the molecule and the
> link but so far phenix.refine is ignoring it. Again, the molecule itself
> refines very well but the link is not there. What is the best way to define
> it?
> Thank you very much.
> --
> Mario Sanches
> Postdoctoral Researcher
> Samuel Lunenfeld Research Institute
> Mount Sinai Hospital
> 600 University Ave
> Toronto - Ontario
> Canada
> M5G 1X5
> http://ca.linkedin.com/in/mariosanches
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
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

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