A walkthrough on how to create a custom peptide model in Avogadro.
Select the “Build” menu.
Bring up the peptide builder window. You can select amino acids to insert into the new peptide.
As you click on particular amino acids, they will be added to the sequence on the right. The peptide will build up as a sequence, starting from the N terminus. Of course you can also type the residues directly or paste from an online database.
You can pick the secondary structure
Click to insert the sequence into the main window. The new oligopeptide will be selected automatically, and the manipulate tool will allow you to translate and rotate the chain into the position you want.
You may wish to re-center the view, since the new peptide may be large.