One of the strong points of EZ-Viz comes in transparency. Because of poor documentation and the need for command line interaction, novice PyMOL users will in most cases not be able to figure out how this feature works. Therefore, we set out to simplify this process with a series of clickable buttons and entry fields to be described in a later section. That aside, transparency is used in some of the presets, one of them being the hetero atoms.The purpose of this preset is to clearly display the presence of hetero atoms, commonly referred to as “ligands”, in the molecule. To do so, these atoms are shown in a sphere representation. Next, the ligand – molecule interactions are displayed by showing sticks in surrounding regions. Finally, the remainder of the molecule is made transparent, such that the ligands and surrounding sticks are clearly evident to the user.