I am trying to align a ligand to a protein fragment using their pdb files. The two do not have the same number of atoms, neither do they have the same number of atoms of the same type. Sequence-based alignment is not successful in pymol or chimera, as the ligand does not have amino acids in. Are there any pure structure-based alignment packages/online tools that are able to achieve some success in this case?
Thank you and looking forward to your input.