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Main Controls
CTRL-Root is the 'base' of the character. All of the controls will follow along with this bone, unless dictated otherwise.
Note
Note that while moving CTRL-Root will visually move the entire character in Project Zomboid, it will not actually move the character's evaluated position. See the next section for how to properly do this.
In Project Zomboid, moving the 'Translation Data' means that your animation will perform in game movement. For instance, a walk animation will move the 'Translation Data' object forwards in front of the player, upon which the game will move them that much in the game.
Tip
Unless intended, it is best to make all interpolation on CTRL-TranslationData movement linear instead of Bezier.
Here is a simple animation that moves CTRL-TranslationData forward over 30 frames (1 second):
And here is how Project Zomboid reads that animation and turns it into game movement:
(Note that there is no player input, the animation is moving the player on its own)
CTRL-Pelvis is by default the 'core' of the character, and all of the other bones move alongside it. Extremely helpful when used along with inverse kinematics.
The main way to rotate the spine/torso is with CTRL-Chest, which looks like a green hyperbola near the shoulders/chest. Further adjustments can be made with the two 'CTRL-Spine' controls, but it is recommended only to use them when you really need to force a certain pose.
The 'CTRL-Dress' bones exist to help automatically move the dress to be in between the legs, no matter the current rotations and positions of the legs. If need be, the controls can be adjusted on top of the automatic placement.
The dress controls can be parented to the legs (default behavior), to the root (meaning they will no longer move with the legs), or to nothing.

You can animate small movements in the fingers with these controls. Note that the Project Zomboid model doesn't necessarily do hand rotations vary well, so don't go overboard.
The 'Prop' bones are what Project Zomboid uses to attach things like weapons and items to the character model's hands.
There are options to have the prop bones parented to the hands (default behavior), to the root, to nothing, or to optionally copy another object in the scene's location (see the look point section in Head Rotation for more details)
Note
The rig currently does not support automatically adding weapons and the like to the player's attachments. For those who are more Blender savvy, look up how to parent a model directly to a bone in the meantime if you must have this behavior.
CTRL-Backpack is used to move, as you may have guessed, the backpack. This is a fairly niche control, but can add some depth to more dynamic animations to make the backpack rustle around.