First you will need a texture that you want to make a alpha channel for, I am using this one that I made for my Quake3 level. So lets select the black part by using the magic wand. Press the shift key and hold as you left click with the wand on all black areas. I used RGB mode tolerance of 0 in the tools control. Now that is done easy huh.
Lets invert the selection.
Also easy huh. Now we need to save this to the alpha channel. Then this comes up. You can name the channel anything I used alpha1. Now that was also easy huh.