Jan<div><br></div><div>You can create the required file using</div><div><br></div><div>phenix.ligand_linking model.pdb<br><br>The one or two output files should be passed to phenix.refine.</div><div><br></div><div>Don&#39;t hesitate to contact me if this is unclear or you encounter more problems.<br>

<br>Nigel<br><br>NB. Any files sent to me will be held in strictest confidence.<br><br><br><div class="gmail_quote">On Fri, Nov 2, 2012 at 1:53 PM, Jan van Agthoven <span dir="ltr">&lt;<a href="mailto:janccp4@gmail.com" target="_blank">janccp4@gmail.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi everyone,<br>
This is a basic question. I would like to refine the sugar ends of my<br>
protein. The sugar polymers are made of NAG and BMA and whenever I use<br>
phenix.ready_set and subsequently phenix.refine it results in a<br>
structure of disconnnected sugar monomers. Indeed the cif file<br>
generated by<br>
phenix.ready_set does&#39;nt give any geometry constraints for connecting<br>
the monomers. How do create a cif file that tells phenix.refine how to<br>
refine the sugars?<br>
Thanks,<br>
Jan<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709     Email : NWMoriarty@LBL.gov<br>

Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a><br>
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