JellyJump Lv 1
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TL:DR Mutate but only applied to the amino acid you clicked on
This exists in the Selection Interface (Main->Selection Interface). Click on the residue (or shift-click for multiple residues) you want to mutate to select them, and then use the Y/Mutate key/button to mutate just those residues to their best identities.
Alternatively, you can use the M key/button to mutate to particular identities. (This latter tool also exists in the Original Interface, where switching to Design Mode (hotkey 4) and clicking on a particular residue brings up a pie menu with particular residue identities.)
In original interface you can freeze the whole protein (including sidechains) and unfreeze the segment you are interested in, then run the mutate tool to change it to its best identity.