Hi Kim and Kevin,
Even then you can have chirality inversions during real-space refinement, which would destroy the SWEET input model from. There is no substitute for common sense (and validation) here. That said, Kevin, something to autobuild carbohydrates (given a sequence) would be awesome. I'd use it a lot. Just don't make a WMD (weapon of model destruction). Cheers, Robbie ---------------------------------------- > Date: Tue, 26 Jul 2011 11:06:03 +0100 > From: henr...@ebi.ac.uk > Subject: Re: [ccp4bb] Straw poll: polysaccharide building? > To: CCP4BB@JISCMAIL.AC.UK > > 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. > >> > >
