You can use
phenix.ligand_linking model.pdb
to get the linking files for linking the carbohydrate in refinement.
You should inspect the file/s.
If you have any trouble feel free to send me your model (directly).
Nigel
On Wed, Jul 4, 2012 at 12:28 PM, crystallogrphy
Hi,
I want to refine my structure including a sugar oligomer as the ligand in Phenix GUI.
I first put each subunit into the density and merge them together as the oligomer in Coot. Then I merged the oligomer coordinates to the protein file. Then I run phenix.elbow to get the cif file. Finally, I run phenix.refine. However, the oligomer units were pushed away from each other. I guess I need to modify the cif file to link the oligo units together. Does anyone know how I can I do it?
thanks!
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