Low-resolution tomography requires recording images every few degrees. As a consequence, the sample is often degraded after such a procedure. However the required input can be reduced drastically by using knowledge about the position and the number of atoms in each atomic column. This concept has been tested in the present investigation where HREM image simulation (MacTempas) together with exit wave reconstruction (FEI Trueimage) have been performed. A cubeoctahedral nanoparticle is used for the simulation with different compositions i.e., pure solid Ga and In-Ga particles. Six different zone axes ([111], [1 1 1], [001], [110], [ 1 10], [011]) have been used and the parameters of an aberration corrected microscope (200kV, Cs = 0 mm, resolution = 0.5Å). The discrete grid data were determined by constructing a channeling map from the reconstructed exit wave images. In this special case only three projections [001], [110], [110] were sufficient to find a unique volumetric reconstruction, illustrating the potential of the method. The other projections were used for checking the solution. The comparison between the projected potentials (simulated input) and the final result shows that discrete tomography reconstructs the exact position of all 309 atoms and the three-dimensional shape of the nanocrystal.