[phenixbb] Sugar refine in phenix

Nigel Moriarty nwmoriarty at lbl.gov
Fri Nov 2 14:06:03 PDT 2012


You can create the required file using

phenix.ligand_linking model.pdb

The one or two output files should be passed to phenix.refine.

Don't hesitate to contact me if this is unclear or you encounter more


NB. Any files sent to me will be held in strictest confidence.

On Fri, Nov 2, 2012 at 1:53 PM, Jan van Agthoven <janccp4 at gmail.com> wrote:

> Hi everyone,
> This is a basic question. I would like to refine the sugar ends of my
> protein. The sugar polymers are made of NAG and BMA and whenever I use
> phenix.ready_set and subsequently phenix.refine it results in a
> structure of disconnnected sugar monomers. Indeed the cif file
> generated by
> phenix.ready_set does'nt give any geometry constraints for connecting
> the monomers. How do create a cif file that tells phenix.refine how to
> refine the sugars?
> Thanks,
> Jan
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> phenixbb at phenix-online.org
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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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