sounds to me like your getting yourself confused.
Read this
The control differences between Metroid Prime and, say, the average first-person shooter, become more apparent through the use of Samus's visor modes. Using the D-Pad, players can toggle two known visor styles -- combat and scan. When Samus is in Combat mode, she can lock onto enemies by pressing the L button, and then blast away while strafing around them (or even dodging by pressing the B button). Pressing L in certain areas will also trigger the character's grapple beam, which can be used to swing across chasms and other dangerous areas. It's possible to swing from beam spot to spot by merely pressing the L button -- a kind of Spider-Man meets space, for players. Using the analog stick, gamers can even look at Samus's grapple beam as she swings about, which of course is impressive.
To get a better idea download the image of the controller below. It shows what buttons do what.
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Threaded Mode
