[phenixbb] Creating dictionary restraints for a LINK

[Mario Sanches]

Hi Nigel,

"phenix.ligand_linking"  is not an option with my current installation
(PHENIX version dev-1021). I have "phenix.ligand_identification"  and "
phenix.ligandfit" .

Mari Sanches

On Mon, Apr 2, 2012 at 11:57 AM, Nigel Moriarty <nwmoriarty at 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 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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> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
>
>
>
> --
> 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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>



-- 
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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