[phenixbb] ask refinement question including an aligo as the ligand

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 5 08:02:54 PDT 2012

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).


On Wed, Jul 4, 2012 at 12:28 PM, crystallogrphy <qunwan1 at gmail.com> wrote:
> 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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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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