Hi Nigel,<div><br></div><div>"phenix.ligand_linking" is not an option with my current installation (PHENIX version dev-1021). I have "phenix.ligand_identification" and " phenix.ligandfit" . </div>
<div><br></div><div>Mari Sanches<br><br><div class="gmail_quote">On Mon, Apr 2, 2012 at 11:57 AM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mario<br>
<br>
You can use<br>
<br>
phenix.ligand_linking model.pdb<br>
<br>
to generate the links between ligands and residues. Don't forget to<br>
look in the .geo to ensure the links are made once you add the files<br>
to the phenix.refine input.<br>
<br>
Nigel<br>
<div><div class="h5"><br>
On Mon, Apr 2, 2012 at 8:29 AM, Mario Sanches <<a href="mailto:mariosan@gmail.com">mariosan@gmail.com</a>> wrote:<br>
> I have a question regarding link dictionary generation. Nigel helped me with<br>
> a molecule dictionary last week (thank you Nigel) so the molecule is<br>
> refining well now. This molecule is covalently bound to on of the residues.<br>
> I tried generating a dictionary that describes both the molecule and the<br>
> link but so far phenix.refine is ignoring it. Again, the molecule itself<br>
> refines very well but the link is not there. What is the best way to define<br>
> it?<br>
><br>
> Thank you very much.<br>
><br>
><br>
> --<br>
> Mario Sanches<br>
> Postdoctoral Researcher<br>
> Samuel Lunenfeld Research Institute<br>
> Mount Sinai Hospital<br>
> 600 University Ave<br>
> Toronto - Ontario<br>
> Canada<br>
> M5G 1X5<br>
> <a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
><br>
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<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
--<br>
Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : <a href="tel:510-486-5709" value="+15104865709">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
Fax : <a href="tel:510-486-5909" value="+15104865909">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>
Canada<br>M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
</div>