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

[N.R. Jena]

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?