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. >
