I am working on Polyoxometalates (POMs) based metal organic framewoks (MOFs). I want to make some diagrams in which POMs are incorporated/encapsulated inside pores of MOFs.
If you have CrystalMaker software you can calculate the center of the selected pore and then place a dummy atom like Si from the "edit-structure" panel. Later you can increase the radius of this dummy atom to fill the pore.