The Rotamers tool logged a swapaa command when you did that, and that command does indeed do the same thing as the tool.  The critical command argument in this case is “criteria” followed by a comma-separated list of integers.  Criteria is documented to either be a string indicating how to “tie break” rotamers (density fit, clash score, # H-bonds, or highest prevalence) or an integer indicating that the Nth highest-prevalence rotamer should be used.  What isn’t documented is that it can also be a comma-separated list of integers, in which case the corresponding rotamers will be added as alt locs.  It probably didn’t get documented because it seemed to only be useful in the context of the tool, because there is no easy way of knowing how many rotamers there are for a particular residue-type / backbone-configuration combo.  Nonetheless, I guess it would be safe to just use the top two (or possibly three) rotamers outside the context of the tool.

We will be documenting this additional criteria mode.