Mari Sanches

On Mon, Apr 2, 2012 at 11:57 AM, Nigel Moriarty <nwmoriarty@lbl.gov> wrote:

Mario

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.

Nigel

On Mon, Apr 2, 2012 at 8:29 AM, Mario Sanches <mariosan@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@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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--
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