Engin I have been improving the glycosylation linking in Phenix and noted the lack of chirality and just plane wrong torsions. Here is my current thinking about NAG-ASN. I have added torsions to the BETA1-4 etc in recent nightly builds and will be working on torsions soon. I shall keep you informed. Cheers Nigel On Wed, Aug 28, 2013 at 5:00 PM, Engin Özkan wrote:

Dear Nigel,

Can I please vote in favor of having torsion and chirality restraints added to the monomer library for NAG-ASN links? BETA1-4, etc. have them, why not NAG-ASN? Something like CNS has for the equivalent B1N in "carbohydrate.top". This would really help those of us cursed with glycosylation, and would make our unfortunate lives wee bit easier.

Cheers, Engin

P.S. You may want to resend your post; I didn't receive your attachment.

On 8/28/13 6:54 PM, Nigel Moriarty wrote:

Fengyun

Supply this file to phenix.refine to retain the chiral. I have been debating adding this to the GeoStd so if it works I'd like to see the result and maybe add it.

Cheers

Nigel

On Wed, Aug 28, 2013 at 4:18 PM, wrote:

...

Hi everyone,

I am refining a glycoprotein model, and I have applied NAG-ASN link to the ASN. But the beta-conformation of NAG could not be retained after refinement for some sites. I read the cif file and find that there are only angle definitions for NAG-ASN. The dihedral and charility information are missing. Is there a way that I could retain the charility of C1 of NAG?

Thank you! Fengyun

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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