[phenixbb] Carbohydrate refinement

Nigel W Moriarty NWMoriarty at lbl.gov
Tue May 12 11:30:05 PDT 2009


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


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 

Option 2.

phenix.ready_set model.pdb

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


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

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