[phenixbb] Fucose alpha linkage

[Timothy Springer]

Hi, I have just added alpha1-3 and alpha1-6 fucoses to NAG. The Fucose in the monomer library has O1 in the alpha position, which is axial. However, after refinement, the fucose moves so it is linked beta in the equatorial position.  I believe the alpha and beta linkages for Fucose may be reversed in Phenix.  Please advise. 

The links are below.






   apply_cif_link {
     data_link = "ALPHA1-3"
     residue_selection_1 = "chain A and resname NAG and resid 3821"
     residue_selection_2 = "chain A and resname FUC and resid 3824"
   }
   apply_cif_link {
     data_link = "ALPHA1-6"
     residue_selection_1 = "chain A and resname NAG and resid 3821"
     residue_selection_2 = "chain A and resname FUC and resid 3823"
   }


With my best regards,
Tim

Timothy A. Springer, Ph.D.                                    
Latham Family Professor of Biological Chemistry and Molecular Pharmacology                                     
Harvard Medical School                   http://idi.harvard.edu/springer 
Immune Disease Institute                 springer at idi.harvard.edu        
Program in Cellular and Molecular Medicine, Dept. Medicine
Div. Hematology                                 Children's Hospital Boston
3 Blackfan Circle, Rm 3103              phone:  617-713-8200                
Boston MA 02115                               fax:        617-713-8232                










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