Step 3: Building a peptide chain

As another example, we will build a small peptide chain.

From the 'Amino Acids' submenu select the 'AA Backbone' and place it in the drawing area. 

There appears a subunit (or actually two) of a basic peptide chain. Notice that one of the atoms is selected, namely the terminal nitrogen. This atom is, again, the 'replacing' atom. In order to extend the peptide backbone, you now have to choose the right atom to be replaced. The obvious choice is the (non double-bonded) terminal oxygen.

Press space bar, which sets the focus on the last used structure. 
Double click on the terminal oxygen.
You may want to choose 'Reset View' from the view menu.

You can now replace the hydrogens on the backbone by amino acid side groups of your choice. These can be found in the 'Amino Acid/AA Side Groups' submenu.