By default, “Add Atom At Pointer” will pop-up a dialog from which
you can choose the atom type you wish to insert 1. Using
(set-pointer-atom-is-dummy 1) you can by-pass this dialog and
immediately create a dummy atom at the pointer position. Use an
argument of 0 to revert to using the atom type selection
pop-up on a button press.
The atoms are added to a new molecule called “Pointer Atoms”. They should be saved and merged with your coordinates outside of Coot.
[1] including sulfate or phosphate ions (in such a case, it is probably useful to do a “Rigid Body Fit Zone” on that new residue).