Refinement and glycosylation. - phenixbb - phenix-online.org

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Refinement and glycosylation.

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pathological case with soaking

Jan van Agthoven

10 Dec 2012 10 Dec '12

1:41 p.m.

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,

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Nigel Moriarty

10 Dec 10 Dec

5:38 p.m.

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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Jan van Agthoven

12 Dec 12 Dec

3:55 p.m.

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Nigel Moriarty

4:25 p.m.

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ 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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Jan van Agthoven
Nigel Moriarty