Jan<div><br></div><div>Currently, PHENIX doesn't put the LINK records in the output PDB. There are arguments for and against so maybe that will change.</div><div><br></div><div>Nigel<br><br><div class="gmail_quote">On Sun, Nov 4, 2012 at 6:35 PM, Jan van Agthoven <span dir="ltr"><<a href="mailto:janccp4@gmail.com" target="_blank">janccp4@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Nigel ,<br>
Thanks for our help. It worked nicely. However, how do you make the<br>
covalent links appear in the pdb file?<br>
Thanks,<br>
Jan<br>
2012/11/2, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>>:<br>
<div class="HOEnZb"><div class="h5">> Jan<br>
><br>
> You can create the required file using<br>
><br>
> phenix.ligand_linking model.pdb<br>
><br>
> The one or two output files should be passed to phenix.refine.<br>
><br>
> Don't hesitate to contact me if this is unclear or you encounter more<br>
> problems.<br>
><br>
> Nigel<br>
><br>
> NB. Any files sent to me will be held in strictest confidence.<br>
><br>
><br>
> On Fri, Nov 2, 2012 at 1:53 PM, Jan van Agthoven <<a href="mailto:janccp4@gmail.com">janccp4@gmail.com</a>> wrote:<br>
><br>
>> 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'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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>><br>
><br>
><br>
><br>
> --<br>
> Nigel W. Moriarty<br>
> Building 64R0246B, Physical Biosciences Division<br>
> Lawrence Berkeley National Laboratory<br>
> Berkeley, CA 94720-8235<br>
> Phone : <a href="tel:510-486-5709" value="+15104865709">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
> Fax : <a href="tel:510-486-5909" value="+15104865909">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><br>
><br>
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</div></div></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>
</div>