In multiple areas of molecular biology research, series of closely related atomic structures of biomacromolecules are routinely generated. In particular, rational structure-based drug design heavily relies on the structural analysis of experimentally determined complexes between the target protein and multiple designed ligands (small molecules or biologicals). Here, we introduce DDtrek, a system for alignment, evaluation, and presentation of such structural data. This system is implemented as a plugin for the highly popular molecular graphics software PyMOL. A special feature of DDtrek is visualization of the aligned ligand structures together with the corresponding experimental density maps obtained through X-ray crystallography or cryoelectron microscopy, providing for the assessment of atomic model reliability and partial disorder. DDtrek is a lightweight and user-friendly system that can be utilized by whole research teams. DDtrek is freely available for Windows, MacOS, and Linux from https://github.com/BiocrystLab/DDtrek.