As part of work with BJPS, I've made pectin builder - accessing through the web or using the Python scripts (tar.gz or browse svn). Accepts a simple 1D sequence string (G or E's) and builds a 3D PDB file.
These are just simple scripts that use Sweet II to do all the real work - cool stuff over in Germany.
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I read about it some days ago in another blog and the main things that you mention here are very similar
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