[phenixbb] refining sugars

Engin Ozkan eozkan at stanford.edu
Thu Oct 1 08:22:07 PDT 2009

Dear Jose and Tirumala,

If you read inside the file this command shows you: 
phenix.where_mon_lib_list_cif, you can see

BETA1-4  .        DEL-HO4  pyranose .        DEL-O1   pyranose

which will tell you that in the BETA1-4 link description, the first 
residue selection has the pyranose that loses its HO4 hydrogen, and the 
second residue selection has the pyranose that loses the O1 oxygen.

  BETA1-4  1 O4      2 C1        single       1.439    0.020

Also here, you can see that the first residue has the O4, and the second 
has C1 that are making the beta 1-4 linkage. Or at least I find it out 
that way. You may need further linkages and correct N-linked sugar names 
that phenix provides cif files for (such as L-fucose and D-mannose, 
which is apparently commonly misnamed in the pdb).


On 10/1/09 4:04 AM, Jose M Casasnovas wrote:
> Dear Ralf.
> I just solved the problem with the sugar refinement. Somehow the way 
> the BETA1-4 cif defines the link is in the reverse order to the 
> NAG-ASN cif link (at least to way I was used to do it).
> In the NAG-ASN cif, residue_selection_1 in the phenix.refine input 
> must be the NAG and residue_selection_2 the ASN, such as I was used to 
> do in CNS.
> However, the BETA1-4 cifs follows the opposite way: 
> residue_selection_1 must be the first sugar residue (linked through 
> O4) and residue_selection_2 the second sugar (linked through the C1), 
> which is the most distant residue to the Asn.
> Thanks so much for your help and to all who sent comments and suggestions.
> Jose M Casasnovas
> -- 
> Centro Nacional de Biotecnología (lab. B16)
> CSIC, Campus UAM
> Darwin 3
> 28049 Madrid
> Spain
> Ph. 34 915854917(8)
> Fax. 34 915854506
> email: jcasasnovas at cnb.csic.es
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Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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