Re: [phenixbb] Refinement and glycosylation.

Jan I'd still interested in seeing the "wrong" geometry. Cheers Nigel On Wed, Dec 12, 2012 at 9:55 AM, Jan van Agthoven wrote:

Sorry Nigel! I think I got a little confused here. The question was about the configuration of the ASN-NAG link. But by modifying it with Coot it remains correct after refinement. So problem solved. Sorry for the inconvenience.

Sent from my iPodu

On Dec 10, 2012, at 2:38 PM, Nigel Moriarty wrote:

Jan

NAG is the beta form. NDG is the alpha form. You may have an incorrect geometry.

Are you asking how to link two carbohydrate units?

If you can send me the model.pdb I will take a look.

Cheers

Nigel

NB. Any files sent to me will be held in strictest confidence.

On Mon, Dec 10, 2012 at 7:41 AM, Jan van Agthoven wrote:

...

Hi everyone, I refined my structure using phenix.refine and used the following parameters to define the ASN-NAG link: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resseq x residue_selection_2 = chain A and resname ASN and resseq y }

However I would like the glycosylation to be Beta (NAG in Beta configuration). How can I define this in the parameter file? Thanks, _______________________________________________ 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

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_______________________________________________ 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