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For me it works with homologous but very different structures with no problem. Just run the script provided for non-identical PDBs, and not theseus3d direct. You need to also install muscle for that, which is also easy. Tassos On 21 Jul 2007, at 17:57, Donnie Berkholz wrote: > Anastassis Perrakis wrote: >> I really like THESEUS these days >> >> http://www.theseus3d.org/ >> >> Really neat work, easy to install and to use and kind of unique in >> the >> ML idea. > > I would be a lot more likely to use it if it was a bit more > flexible in > its input. I tried it once and it seemed to require identical lists of > atoms, even as far as requiring multiple conformations and the same > waters in both PDBs. > > Thanks, > Donnie >