why not use
http://glycosciences.de/modeling/sweet2/doc/index.php
which works perfectly
and would save the duplication of effort
cut & paste
#---
a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+
|
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
| |
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+
|
|
a-L-Fucp-(1-3)+
a-D-Manp-(1-6)+
|
|
b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+
| a-L-Fucp-(1-6)+
|
|
b-D-Galp-(1-4)+
|
b-D-GlcpNAc-(1-4)-Asn
|
|
|
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
|
|
|
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
|
|
|
|
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-4)+
|
|
|
|
a-L-Fucp-(1-3)+
a-D-Manp-(1-3)+
|
a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+
and click and your o/p is as attached
apart from the poor excuse for a pdb file
it has the model with glycosidic torsion angles as expected
as in glycomapsdb
> Straw poll:
>
> Are you interested in software to autobuild polysaccarides?
>
> Kevin
>
> p.s. I expect I'll have to spend at least a year working on the problem
> before before I spell polysaccharide consistently.
>
|