[phenixbb] Geometry problem with sugars refined in phenix

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Mar 18 10:07:12 PDT 2010


Can you send me the PDB file, the link definitions you used and the .geo 
file from the final refinement.  Please send it directly to me and it 
will be keep in he strictest confidence.


On 3/18/10 9:56 AM, Tirumala Kumar Chowdary wrote:
> Hi,
> 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 problem.
> Thank You
> Tirumal
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909     Web   : CCI.LBL.gov

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