Hi Markus, I had a brief look at the structure fragment that you had included in your mail, and I don't think that you really observe these two conformations. Stereochemistry of the A conformation looks fine, but the sugar in the alternate B conformation is not an NAG but an NDG (i.e. it has an alpha-linkage, not a beta-linkage). In N-glycans, however, the GlcNAc residues are always in beta anomeric conformation in nature. Therefore I recommend to exclude the alternate B conformation (atoms 139-152) from your structure. By the way, the ring shapes of the sugars look twisted, maybe that is a result of the produced overlap in the coordinates?
Best regards, Thomas
