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)+
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| a-L-Fucp-(1-6)+
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| b-D-GlcpNAc-(1-4)-Asn
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b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
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|
|
|
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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 [log in to unmask] ::telephone: +44 (0) 1223 494629
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