Dummy ("Xx") atoms are treated a little different when used in structures. A dummy atom will not replace an existing atom when it is defined as the 'replacing atom'. Instead, the double-clicked atom will remain and will accept the bonds that the dummy atom had in the structure.
Build a methane molecule Replace the carbon atom by a nitrogen atom Select one of the hydrogens and replace it by a dummy atom Select the dummy atom and choose Edit → Set Origin Save the structure in (a subdirectory of) your $SCM_STRUCTURES directory
Now you can select the structure from the structures menu and directly use it.
Select your new structure from the structures menu Double-click on one of the hydrogens
Notice that the hydrogen atom is not removed and that the NH3 group is attached to it. Similar behavior has been demonstrated with the bidentate ligands, where the dummy atoms are also used.
