Use the secondary fire only against the stronger enemies, such as bullsquids and vortigaunts. Even though it’s obtained quite early, it can easily kill many enemies from the game houndeyes, vortigaunts, bullsquids, barnacles and headcrabs being the easiest targets. Shotgun is by far one fo the most useful weapons in the game.
It wouldn’t work very well for the Vortigaunts though, for that you’ll need a shotgun (see the next section). If necessary, you can use them against houndeyes and bullsquids as well. As I mentioned in the last section, pistols can be used to terminate headcrabs from a safe distance.