Branching of amylopectin and amylose

General Discussion
1

I’m doing some science teaching stuff, where i have to explain some of the properties of starch. I would like to use avogadro to show the branching of larger amylopectin- and amylosemolecules. Are there any smart way to achieve this? I’ve tried Build->insert fragment, but I can’t seem to find the relevant elements. I’ve also tried to import the relevant molecules from Import->Fetch by chemical name, but it seems I can only get a rather simple form of amylopectin by doing this.

Thanks in advance =)

1 Like
2

Oligosaccharides are hard. I’ve been looking for good tools to create 3D structures for them for a while. (Hoping something will get into Avo v2)

A search turned up:
https://www.biotopics.co.uk/jsmol/amylose.html
https://www.biotopics.co.uk/jsmol/amylopectin.html

Looking through those webpages, it looks like you can get the PDB files to download:
https://www.biotopics.co.uk/jsmol/molecules/amyloseplus.mol
https://www.biotopics.co.uk/jsmol/molecules/amylopectin84.pdb

If you look into the source, you’ll see JavaScript that calls load molecules/amylose.mol etc. for molecules on that page.

It’s definitely on my radar to get glycan / saccharide building into future versions.