Star Trek Online Wiki
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Fundamentally joystick setup works much the same as Keybinds except with different inputs. Thus you can bind joystick functions to anything you can bind keyboard keys to(to include console commands). The trick is figuring out what names to use in the bind file. Also you need to access the joystick configuration menu and check to make sure all of the buttons are mapped to game controls.

name used in bind name used in joystick setup
AB Button0 (trigger)
LStick Button1
XB Button2
YB Button3
LB Button4
RB Button5
LeftTrigger Button6
RightTrigger Button7
Select Button8
Start Button9
RStick Button11

Here is a sample set of binds:

/bind AB "FirePhasers"
/bind XB "throttletoggle"
/bind LB "throttleadjust .25"
/bind YB "throttleadjust -.25"

If you want to verify how your joystick buttons are mapped you can open the file "Star Trek Online\Live\controller.cfg". The left column of the file is the name you would need to use for binding.

You will probably end up creating the setup on one character, then using the commands for saving and loading the binds on your other characters.

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