Dear Kim,
I asume that Kevin plans to build in electron density maps. As far as I
can see Sweet will produce a model unhindered by experimental data.
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Kim Henrick
Sent: Tuesday, July 26, 2011 11:44 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Straw poll: polysaccharide building?
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-Ga
lp-(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-Gl
cpNAc-(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.
>
|