At first everything is in the MM region. You can select the residues of your choice, and put them in the QM or MM region using the pull-down menu. You can also move individual atoms to either the QM or MM part using the check boxes next to the atoms. If you have a range of residues selected, and use the pull-down menu to move them to the QM region, ADFinput will try to make the proper cuts. Thus, the parts of the backbone connecting to the MM region will also be kept in the MM region.
Select a range of residues (for example, residue 7 through 10) Move them to the QM region using the pull-down menu
The atoms in the QM region will be visualized using larger spheres.
