Thank you Adel and Christoph! sym.add_site_family(lat, other_vectors=[v]) with v orthogonal to the translation symmetry vector places the lead in the way I expected. Still, there are one supercell's extra sites added in blue connecting the original central region and the lead (https://www.dropbox.com/s/3c1uioclcbsez4g/lattice2.pdf?dl=0). If I put disorder in the central region, I presume these added sites although in blue color will be the same as the lead Hamiltonian and thus do not have disorder? If so, I guess it might only very slightly affect the physics once the central region is not too small. And these extra sites are currently unavoidable?