Tim
The glycosidic bonds in PHENIX are taken from the Monomer Lib so I
think that should be OK.
O1 can be in the axial or equatorial position depending on the ring
pucker but the O1 should always be on the opposite side of the ring
(if you imagine the ring is flattened) from the C6. It is the
chirality around the C1 atom that specifies the alpha/beta linkage.
Please send me the PDB file (off-line) so I can double-check that it
is correct. Just the three carbohydrate residues would be fine.
Cheers
Nigel
On Tue, Nov 29, 2011 at 3:13 PM, 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 [email protected] 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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