[Chimera-users] Structural alignment of a protein-ligand complex with other ligands only

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?