Instead of using Rotamers, one can instead change the \chi angles (often called “torsions”) “by hand” (using “Edit Chi Angles” from the “Model/Fit/Refine” dialog). To edit a residue's \chi_1 press “1”: to edit \chi_2, “2”: \chi_3 “3” and \chi_4 “4”. Use left-mouse click and drag to change the \chi value. Use keyboard “0” 1 to go back to ordinary view mode at any time during the editing. Alternatively, one can use the “View Rotation Mode” or use the <Ctrl> key when moving the mouse in the graphics window. Use the Accept/Reject dialog when you have finished editing the \chi angles.
For non-standard residues, the clicked atom defines the base of the atom tree, which defines the “head” of the molecule (it's the “tail” (twigs/leaves) that wags). To emphasise, then: it matters on which atom you click!
By default torsions for hydrogen atoms are turned off. To turn them on:
(set-find-hydrogen-torsions 1)
To edit the rotatable bonds of a ligand using this tool, you will need to have read in the mmCIF dictionary beforehand.