I have to detect the presence of a ligand in many PDB files.

So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand.

Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ?

In general, can Chimera superimpose ligands in 2 PDB files ?

Thank you