[phenixbb] Geometry problem with sugars refined in phenix
Tirumala Kumar Chowdary
Tirumala.Chowdary at tufts.edu
Thu Mar 18 09:56:36 PDT 2010
I have refined a structure with NAGs linked to ASNs at 3 places in my
structure. I used the right link definitions and the NAG definitions
are from Phenix library.
Phenix refined all the sugars right and made the right links between
the NAGs. However, while submitting, PDB found problem with the
geometry of NAGs linked to the ASN at two places.
This is the issue
-the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A
#1670 are on a plane and the C1 atom center is far off to be
tetrahedral. Please, verify the chirality of C1 and provide the correct
coordinates if necessary.-
Any ideas on how to fix the geometry of these sugars will be of great help.
Regularization and real space refine in Coot is not working or I don't
know how to do it. I am looking for alternative ways to fix this
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