Researchers often have a new sequence they want to model or use as a starting point for future design work. We have a quick and simple method for doing this
1.) Load the protein into CAD
Use the 
as usual. Include or exclude any additional molecules in the file that you want to appear in the final structure. Click 
.
2.) Click the structure and Choose Design from Actions
3.) Select the Mutations
Remove the wild type positions from the mutation table and only select the new point mutations that you want. Only 1 repeat is needed.
4.) Click 
to run
This will rapidly create a single structure with just your specific position changes. Since Design keeps the backbone stable during modeling, it do the mutation followed by Repack. You will probably want to do some rounds of Relax in order to allow the structure to makes conformational changes to adapt to the mutations.