[phenixbb] a question on NAG-ASN cif file

[Nigel Moriarty]

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 <eozkan at stanford.edu> 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, <fn1 at rice.edu> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
>
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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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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