[phenixbb] Refinement and glycosylation.

Nigel Moriarty nwmoriarty at lbl.gov
Wed Dec 12 10:25:08 PST 2012


Jan

I'd still interested in seeing the "wrong" geometry.

Cheers

Nigel

On Wed, Dec 12, 2012 at 9:55 AM, Jan van Agthoven <janccp4 at gmail.com> 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 <nwmoriarty at lbl.gov> 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 <janccp4 at gmail.com>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
>> phenixbb at phenix-online.org
>> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> 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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121212/0b18a2c3/attachment.htm>


More information about the phenixbb mailing list