you can use http://www.glycosciences.de/modeling/sweet2/doc/index.php to get a pdb file of your sugar
and after fitting in density and refinement use http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/ to check the stereochemistry this should identify if there is a refmac dictionary problem your sugar is a "Core Fucosylated And Bisected N-glycan (N-Link 2)" [see the sweet doc pages] you can make the IUPAC notation in plain ASCII a-D-Manp-(1-6)+ | | a-L-Fucp-(1-6)+ | | | b-D-GlcpNAc-(1-4)-Asn | | b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ | | | | | a-D-Manp-(1-3)+ and drop this into sweet and get an idealised torsion angle(d) pdb an o/p is www.ebi.ac.uk/~henrick/sug.pdb unfortunately the original pdb output is not exactly pdb you have to move the residue name column and the ASN is labelled as UNK the torsion angles are from the database http://www.glycosciences.de/modeling/glycomapsdb/ if you want to check your fitted conformation with what is expected (a lot more freedom than a ramachandran but basically the same type of plots) -- Kim HENRICK [EMAIL PROTECTED] ::telephone: +44 (0) 1223 494629
