arising from C.-C. Chen et al. , 74–77 (2013)10.1038/nature12009 At first sight, the achievement of determining atom positions in three dimensions appears spectacular1. Chen and colleagues1 apply a form of tomographic reconstruction to a tilt series of annular dark field (ADF) images of crystalline particles with defects, where the original data has a filter applied to reduce noise. However, the filtering imposes periodicities and significantly downgrades resolution, and the condition of signal linearity—a requirement for tomography—has not been met. We consider that their procedure gives an illusion of locating atom positions accurately. There is a Reply to this Brief Communication Arising by Miao, J. et al. Nature503,http://dx.doi.org/10.1038/nature12661(2013) .