Yes but it is easier to take the sweet model for the required sequence and fit that to density rather than do it residue by residue which will lead to glycan structures unknown to the source
kim > 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Kim Henrick > Sent: Tuesday, July 26, 2011 11:44 AM > To: CCP4BB@JISCMAIL.AC.UK > 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. >> >
