We report a resonant x-ray diffraction study of the magnetoresistant perovskite Pr0.6Ca0.4MnO3. We discuss the spectra measured above and below the semiconductor-insulator transition temperature with aid of a detailed formal analysis of the energy and polarization dependences of the structure factors and ab initio calculations of the spectra. In the low temperature insulating phase, we find that inequivalent Mn atoms order in a CE-type pattern and that the crystallographic structure of La0.5Ca0.5MnO3, (Radaelli et al., Phys. Rev. B 55, 3015 (1997)) can also describe this system in fine details. Instead, the alternative structure proposed for the so-called Zener polaron model (Daoud-Aladine et al., Phys. Rev. Lett. 89, 097205 (2002)) is ruled out by crystallographic and spectroscopic evidences. Our analysis supports a model involving orbital ordering. However, we confirm that there is no direct evidence of charge disproportionation in the Mn K-edge resonant spectra. Therefore, we consider a CE-type model in which there are two Mn sublattices, each with partial eg occupancy. One sublattice consists of Mn atoms with the 3x 2 − r 2 or 3y 2 − r 2 orbitals partially occupied in a alternating pattern, the other sublattice with the x 2 − y 2 orbital partially occupied.