<p>We are having the same problem. Sugars are not linked properly after
runing<br />
phenix.refine, whereas they are fine using CNS. Distance can be preserved, but
the bond angles are wrong.<br /> </p><p>I am using phenix-1.4-2.<br /><br></br>
<br />
Jose M Casasnovas<br />
</p><p></p><p>
Quoting Tirumala Kumar Chowdary <Tirumala.Chowdary@tufts.edu>:<br />
<br />
> Hi,<br />
><br />
> My question is related to the 'refining sugars in phenix' questions<br />
> that have been appearing on the bb for the last two days.<br />
><br />
> I am trying to refine my NAGs and somehow phenix is ignoring the sugars<br
/>
> in my structure. Neither it is making a bond between my ASN and NAG nor<br
/>
> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly,<br />
> though.<br />
><br />
> I am using in version 1.4.125 still. Is this the problem ? Does<br />
> upgrading to any of the later build will help ?<br />
><br />
><br />
> Tirumal<br />
><br />
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/>
><br />
<br />
<br />
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email: jcasasnovas@cnb.csic.es</p><br />