We describe a multiresolution solver for the all-electron local density approximation Kohn-Sham equations for general polyatomic molecules. The resulting solutions are obtained to a user-specified precision and the computational cost of applying all operators scales linearly with the number of parameters. The construction and use of separated forms for operators (here, the Green’s functions for the Poisson and bound-state Helmholtz equations) enable practical computation in three and higher dimensions. Initial applications include the alkali-earth atoms down to strontium and the water and benzene molecules.