The allows the addition alternate (dual, triple etc.) conformations to the picked residue. By default, this provides a choice of rotamer (Section Rotamers). If there are not the correct main chain atoms a rotamer choice cannot be provided, and Coot falls back to providing intermediate atoms.
The default occupancy for new atoms is 0.5. This can be changed by using use slider on the rotamer selection window or by using the scripting function:
(set-add-alt-conf-new-atoms-occupancy 0.4)
The remaining occupancy of the atoms (after the new occupancy has been added) is split amongst the atoms that existed in the residue before the split. It is important therefore that the residues atoms have sane occupancies before adding an alternative conformation.
The default Split Type is to split the whole residue. If you want the default to be to split a residue after (and including) the CA, then add to your .coot file:
(set-add-alt-conf-split-type-number 0)