in the BaTiO3-type structures it's common for the octahedra to be slightly tilted or elongated, in a ball-and-stick model this is hard to see, but become obvious if the polyhedra are drawn instead). This type of visualisation is really intended to give an overview of how a crystal 'fits together.' It also makes it easier to view subtle distortions (e.g. This is also a judgement call, but tends to minimize artifacts. I would however add the constraint that polyhedra are only drawn if all the atoms on the polyhedra's vertices are the same element. Regarding bond searching, there should be no additional bond searching required for the polyhedra. Provided the unit cell boundary is drawn, there should be no confusion caused by either choice. It's quite common to draw a few repeats of the unit cell too. Some visualisation tools will draw the extra atoms outside the unit cell if they are bonded to atoms within the unit cell. Some of the atoms in the open polyhedra are in the 'next crystal over', and so are not drawn, leading to the polyhedra having an open face. Specifically in this case it's an artifact of the crystal's periodic boundary conditions (or its infinite tiling in 3D space if you want to think of it that way). CrystalMaker is good, but a weird interface IMO and steeper learning. I'm not sure I have sufficient understanding of 3Dmol.js/JavaScript to implement this myself, but I'm happy to attempt it at a later date, or to help test this functionality. the good ol Balls&Sticks which can even draw partially transparent polyhedra.
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