I'm looking for free (as in freedom) software for Linux that allows me to visualize simple crystal lattices and produce images such as this:
Good features would be the ability to easily choose colors, add labels, select how many unit cells to show and add custom geometry like in the picture (faces). I should be able to create the structure from scratch in the software or using a well-documented non-proprietary file format. It shouldn't be too tied down to actual chemistry: I should be able to create "quasi-atoms", e.g. as stand-ins for molecules or whole classes of atoms.