<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>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.<br><br>Sent from my iPodu</div><div><br>On Dec 10, 2012, at 2:38 PM, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>> wrote:<br><br></div><blockquote type="cite"><div>Jan<div><br></div><div>NAG is the beta form. NDG is the alpha form. You may have an incorrect geometry.</div><div><br></div><div>Are you asking how to link two carbohydrate units?</div><div><br></div><div>If you can send me the model.pdb I will take a look.</div>
<div><br></div><div>Cheers</div><div><br></div><div>Nigel</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br><br><br><div class="gmail_quote">On Mon, Dec 10, 2012 at 7:41 AM, Jan van Agthoven <span dir="ltr"><<a href="mailto:janccp4@gmail.com" target="_blank">janccp4@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi everyone,<br>
I refined my structure using phenix.refine and used the following<br>
parameters to define the ASN-NAG link:<br>
refinement.pdb_interpretation.apply_cif_link {<br>
data_link = NAG-ASN<br>
residue_selection_1 = chain A and resname NAG and resseq x<br>
residue_selection_2 = chain A and resname ASN and resseq y<br>
}<br>
<br>
However I would like the glycosylation to be Beta (NAG in Beta configuration).<br>
How can I define this in the parameter file?<br>
Thanks,<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
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