Creating dictionary restraints for a LINK
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
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
_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
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
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
_______________________________________________ phenixbb mailing list [email protected] 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 : [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
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
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
_______________________________________________ phenixbb mailing list [email protected] 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 : [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
_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Apr 2, 2012 at 9:09 AM, Mario Sanches
"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
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
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
participants (3)
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Mario Sanches
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Nathaniel Echols
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Nigel Moriarty