Re: [phenixbb] Creating dictionary restraints for a LINK

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 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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- 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