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The presentation is amazing! However, the game wouldn't register the jump button half the time, leading to some frustrating moments where the character didn't jump as supposed to. I see 2 things that may cause this issue:

1) You are checking for input on FixedUpdate(). That's really bad, you should be always checking for inputs every single frame. Use Update() instead. Here:

Update(){

  bool Jump = Input.GetButtonDown("space");

  if (Jump == true) {

    bool HasJumped = true;

  }

}

FixedUpdate() {

  if (HasJumped == true) {

    // Insert physics calculations here.

    HasJumped = false;

  }

}

2) You check for an OnCollisionEnter/Stay/Exit instead of an OnTriggerEnter/Stay/Exit. The problem with this is that OnCollisionEnter isn't reliable for checking states. On your prefab or gameObject for the brain place a trigger collider on top that takes up some space and is set as a Trigger. Now use OnTriggerEnter/Stay/Exit to use it.

OnTriggerEnter (Collider other) {

  if (other.gameObject.tag == "Brain") {

     bool TouchingBrain = true;  

  }

}

(+1)

Thanks for the tips!