[phenixbb] refining sugars

Engin Ozkan eozkan at stanford.edu
Wed Sep 30 09:02:51 PDT 2009

You don't need to create cif files; phenix has them. NAG is definitely 
there, and you can have two NAGs linked by any biologically-relevant 
glycosidic bond you want. You need to define the links, however. I think 
posting the cif_link.params may get you more help.


On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote:
> Hi,
> My question is related to the 'refining sugars in phenix' questions
> that have been appearing on the bb for the last two days.
> I am trying to refine my NAGs and somehow phenix is ignoring the sugars
> in my structure. Neither it is making a bond between my ASN and NAG nor
> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly,
> though.
> I am using in version 1.4.125 still. Is this the problem ? Does
> upgrading to any of the later build will help ?
> Tirumal
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Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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