Schopper was appointed professor at the University of Karlsruhe in 1961 and director of the newly established Institutes for Experimental Nuclear Physics of TH Karlsruhe and the Karlsruhe Nuclear Research Centre. In order to continue his research on electron scattering he set up a group to carry out one of the first experiments at DESY. He also created a group at CERN to investigate neutron scattering at high energies at the Proton Synchrotron (PS) and Intersecting Storage Rings (ISR). These experiments where then continued at the Institute for High Energy Physics (IHEP) in Serpukhov, Russia. The group made important contributions to the study of neutron-proton and neutron-nuclei scattering cross sections. For this purpose, the first hadron calorimeter was developed and optimised by Monte Carlo simulations. Another group at Karlsruhe developed the first superconducting high frequency cavities in Europe, a technology which was transferred to CERN for particle separators and later for particle acceleration at LEP.