I'm afraid you'll have to venture out the GUI and use the command-line version for this particular program. You'll need to source the appropriate setup file for your shell and run the command. If you have trouble setting up the command-line environment, contact me off-line. Cheers Nigel On Mon, Apr 2, 2012 at 9:09 AM, Mario Sanches wrote:

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

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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

Thanks to Nigel and Nat for their help. The link description did the trick. Mario Sanches On Mon, Apr 2, 2012 at 12:49 PM, Nathaniel Echols wrote:

On Mon, Apr 2, 2012 at 9:09 AM, Mario Sanches wrote:

...

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

It's not shown by default. Open the Preferences, go to the "General" section, and check "Enable alpha-test programs and features", then close and restart the GUI. The ligand linking program will be listed in the Refinement category.

-Nat _______________________________________________ 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