> I was wondering if it was possible to use the peptide building tools with
> protected amino acids? I have several protein structures with
> benzyl-protected glutamic acid. Would it be possible to add new amino acids
> to the protein building tools?
At the moment, no but that's a good idea. On the other hand, in Avogadro 1.1,
it's fairly easy to add the benzyl groups to the side-chain. Select the
insertion point (either the hydrogen or the oxygen atom) go to Build -> Insert
-> Fragment and pick out benzene.
You should also be able to select multiple atoms and perform the insertion
across all of them at once.
Hope that helps,
-Geoff
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