[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.
phenix.elbow --do-all model.pdb
will generate the link files along with restraints for non-standard
will also generate the link files as well as add hydrogens to you model.
On 5/12/09 11:22 AM, Katya Heldwein wrote:
> 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.
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
More information about the phenixbb