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
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. Engin 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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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
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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phenix.refine doesn't automatically link the sugars. You need to define the links manually via apply_cif_link as described in the phenix.refine documentation. Ralf
participants (4)
-
Engin Ozkan -
Jose M Casasnovas -
Ralf W. Grosse-Kunstleve -
Tirumala Kumar Chowdary