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
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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