I'm a developer of a Blender addon, which is called "Atomic Blender PDB/XYZ". The addon imports/exports atomic structures described in PDB and XYZ files into the form of balls (atoms) and sticks (bonds). A related panel helps to easily modify the atomic structures.
- I/O of PDB and XYZ files
- Corresponding panel for manipulating atomic structures
Furthermore, I wrote an addon which creates atom nanoparticles/clusters.
See here: Link