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 : [email protected] Web : CCI.LBL.gov