We are having the same problem.  Sugars are not linked properly after runing
phenix.refine, whereas they are fine using CNS.  Distance can be preserved, but the bond angles are wrong.

I am using phenix-1.4-2.



  Jose M Casasnovas

Quoting Tirumala Kumar Chowdary <Tirumala.Chowdary@tufts.edu>:

> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>


--
Centro Nacional de Biotecnología (lab. B16)
CSIC, Campus UAM
Darwin 3
28049 Madrid
Spain
Ph.  34 915854917(8)
Fax. 34 915854506
email: jcasasnovas@cnb.csic.es