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Z-clipping is a feature present in Doom, but only partially. It was fully implemented in Heretic. It consists on using the height and z-coordinates of a thing for allowing any other actor to pass above or below and, for a falling actor, to receive falling damage depending on the height and speed of the fall.
Doom features a limited z-clipping that is only designed for projectiles and for allowing certain things, like monsters, to be able to enter a sector depending on its ceiling height. Aside of that, a given thing's height or z-coordinates are ignored by the engine, causing all actors to be infinitely tall. As a result, a player may stand on a ledge of 640 floor height, and a blocking decoration or monster standing just in front, on a floor of height 0 will completely block the player from jumping, and in the case of monsters, these are able to perform their melee attack on the player successfully.
Z-clipping limitations may be observed most easily using floating monsters such as Cacodemons. While the monsters can control their height to throw projectiles, the limitation becomes apparent when the player attempts to run under or jump over a Cacodemon; this cannot be done, as the monster appears to be "pulled" toward the player's own height.
In Heretic and Hexen, however, this is different, as a player can normally stand above monsters or obstacles. This is used for example in E5M3 of Heretic where, to access a secret area, the player needs to jump down from a balcony to a row of barrels, and run along the barrels to pass through window too high to reach otherwise. But z-clipping was mostly implemented for allowing players to use the Wings of Wrath artifact without being blocked by monsters and items clearly below it.