Q:

Is doing squats using a rack with rails defeating the purpose?

I moved recently and the gym here doesnt have a free standing squat rack. Instead it has one of these racks with rails
http://cdn2.hubspot.net/hub/354582/file-499385451-jpg/images/Equipment/About_-_Equipment.Smith_Machine.jpg?t=1400007711933
I can feel my legs/glutes working but clearly it is not the same. The rails restrict the range of motion so I dont feel the full body workout Im used to. The muscles that would normally attempt to stabilize and hold the bar are not activated.
I have been doing squats mostly since it has helped strengthen supporting muscles and helped me deal with lower back pain.
I'm not sure if I should continue using it. Any thoughts?

A:

Unlike CCCV, I would not summarily dismiss using the Smith Machine with the assumption that one does not work as hard while using the machine.  Granted, there is a restricted range of motion, but, that does not totally remove any potential benefits from using this machine.  And, while I'm not trying to imply you should substitute machine squats for free standing squats, I am saying that machine squats can provide an effective leg work out.  
In a 2009 study, A comparison of free weight squat to Smith machine squat using electromyography, researchers measured the activity of several muscles during the study: tibialis anterior, gastrocnemius, vastus medialis, vastus lateralis, biceps femoris, lumbar erector spinae, and rectus abdominus.  

“Electromyographic activity was significantly higher by 34, 26, and 49
  in the gastrocnemius, biceps femoris, and vastus medialis,
  respectively, during the free weight squat compared to the Smith
  machine squat (p < 0.05). There were no significant differences
  between free weight and Smith machine squat for any of the other
  muscles; however, the EMG averaged over all muscles during the free
  weight squat was 43% higher when compared to the Smith machine squat
  (p < 0.05). The free weight squat may be more beneficial than the
  Smith machine squat for individuals who are looking to strengthen
  plantar flexors, knee flexors, and knee extensors. “

(my emphasis)
While the free squat is arguably the better movement, the study results do not imply that there is no benefit to performing machine squats. It simply says that for some muscles, free squats are better.  
Machines do have a place in training, but, are often dismissed based solely on perpetuated opinions.  Rather than dismissing a machine outright, I would suggest using them on those occasions when a piece of equipment is not available, you don't have a spotter, or, simply to switch things up to keep the training fresh.
As for the different feel to machine squats, there are many variations of the squat (eg. split squat) that can be performed to provide an effective workout.  And, if you're dealing with lower back pain, machine squats can provide a sense of security because the movement is restricted and there's less likelihood that you'll injure yourself further.

