Viewing molecular orbitals read from Molden files can be a problem in case the basis set elements are not in the same order as the atoms. This behavior is going to change in the next release of Molekel and a fix has already been committed. In the meantime if you need to visualize molecular orbitals read from Molden you could simply reorder the atoms in the Molden file in the same order as the basis set elements. E.g. In case the atoms are ordered like this: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 H 2 1 0.0000000000 0.0000000000 1.0856415283 H 3 1 0.0000000000 1.0343722180 -0.3297423077 H 4 1 -0.9307128069 -0.4512369987 -0.3298275233 C 5 6 1.2066572971 -0.7558134495 -0.5524694437 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 And the basis set is: [GTO] 1 0 ... 5 0 ... 2 0 ... 3 0 ... 4 0 ... 6 0 ... 7 0 ... 8 0 ... If you change to: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 C 2 6 1.2066572971 -0.7558134495 -0.5524694437 H 3 1 0.0000000000 0.0000000000 1.0856415283 H 4 1 0.0000000000 1.0343722180 -0.3297423077 H 5 1 -0.9307128069 -0.4512369987 -0.3298275233 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 ... [GTO] 1 0 ... 2 0 ... 3 0 ... 4 0 ... 5 0 ... 6 0 ... 7 0 ... 8 0 ... It should work.