[phenixbb] Carbohydrate refinement

[Nigel W Moriarty]

Katya

You can find the details of the mechanism for linking residues here

http://phenix-online.org/documentation/refinement.htm#anch78

You can create your own file or use the tools available in PHENIX.

Option 1.

phenix.elbow --do-all model.pdb

will generate the link files along with restraints for non-standard 
residues.

Option 2.

phenix.ready_set model.pdb

will also generate the link files as well as add hydrogens to you model.

Nigel

On 5/12/09 11:22 AM, Katya Heldwein wrote:
> Hi,
>
> I have several N-linked sugars in my structure. Some are modeled as 
> single NAGs and others, as NAG-NAG chains.
>
> How do I specify Asn-NAG and NAG-NAG linkages for phenix refinement? 
> Currently, when I try to refine the model, NAGs move away from Asn and 
> from each other.
>
> Katya
>
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov