I'm modeling a reaction inside the mordenite lattice and can't seem to get the atoms to match automatically. Between reactant and product, the zeolite framework barely changes - only the organic reactants inside the pore change significantly. Using autofind matches only 14 atoms. There are 310 atoms in the unit cell, so matching manually is out of the question. It seems like the extended network of bonding in the zeolite is throwing off the matching algorithm, but it would be nice if the algorithm could fall back on a matching scheme based on position or even atom name. Attached are the two structures