Superpose is a feature that positions multiple structures on top of one another, based on a specified region of sequence that is shared among the different structures.
The Superpose feature is useful for aligning and comparing multiple structures in the Structure Viewer especially after running an Action that alters the protein backbone such as Relax Design.
1.) Once you have run your Action, the structures that you would like to superpose must be made visible in the Structure Viewer. To make structures visible select 
for each structure.
2.) Click 
to open the Sequence Viewer. Select a region of sequence that spans across all the structures’ sequences as demonstrated in the example below.
Note: For the selected region each structure must have the exactly the same sequence in that region in order to superpose the structures by atom. Each structure must also have the same number of positions selected in order to superpose by backbone.
3.) Once you’ve made your selection, press 
on the top of the Structure Viewer as shown in the example image above. Depending on which of the criteria described in step two are fulfilled, you will see the option to superpose by ‘Selected atoms’ or by ‘Selected backbone atoms’.