I recently took off the front wheel off of my mountain bike, and have been having considerably difficulty getting the front wheel on the right spot such that the wheel doesn't rub against the brake when I'm riding. I know there is clearance possible, because if I pull the quick release on my wheel and turn the wheel, it spins just fine. What can I do to align the brake properly?
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Assuming you mean that the disk caliper pads are rubbing on the rotor when the lever is not being used/squeezed:
1) The fixed/non-moving pad/side in the caliper on my brakes are adjusted with an allen key from that outer side of the caliper. If it has been a while this bolt could require some effort to get moving. On my brakes there is a detent such that I back off the bolt one click at a time and see how the clearance is.
2) The moving pad/side in the caliper is adjusted by cable tension in the usual way, i.e. with the barrel adjuster at the lever or the pinch bolt at the caliper.
@Arbalest has the correct answer for one specific problem with brakes with just one cylinder, If that is not it, the best way would be to reset the caliper alignment. I am not expert, theres heaps of information on how to do it - the owners manual is a good start - it's not hard, but a novice may need a couple of goes at it to get it spot on.
Essentially, loosen the bolts holding the caliper enough so it moves, but is not loose. Pump the brakes gently a couple of times with the wheel spinning (in normal direction). Then while applying the brakes "firmly but not hard" (i.e. enough to hold the caliper in place), slowly tighten the bolts, alternating between them 1/2 turn at a time (so it tightens evenly on each side).
I've had this problem with more than one bike, and risk factors for that are:
The problem is that, due to the very tight distance between the disk and the pads, a minimal amount of "shape changing" creates rub and noise. This shape changing might occur between opening and closing the quick release, or because of more aggressive twisting forces while cornering on difficult terrain.
Usually, a little rubbing is not a real problem, but much more of a nuisance, and even very small rubs can cause an unpleasant noise.
One possible solution, and one that works for me when I'm in an "I need silence" mood, is to catch the front wheel of the bike in a corner, or even against a wall or a tree or a fence, and TWIST THE HANDLEBARS. If you do this gently, you'll notice that the fork twists (a tiny bit of course) enough to make the disk reposition itself inside the caliper, also showing the direction you should apply a greater force to reposition the disk/caliper "permanently", and this is enough to solve the problem, but only if the rubbing is minimal (otherwise it is necessary to properly adjust the brake).
Of course I am not suggesting to twist anything in a way that would cause damage, but I think some setups are so prone to misalignments that the same poison should cure the disease, and that's it.
Also, of course this problem has a WAY smaller chance to happen with non-quick-release. 20mm thru-axle hubs/forks.
Hope this helps!
Tip of the day for how to adjust brakes so they dont rub when tightened:
Use shims on either side of the disk!
Here's how to do it:
Make sure your beer can strip is really clean (use soapy water and properly rinse) so you don't contaminate the pads or disk.
I've got Avid Juicy brakes and I had huge problems with getting them properly aligned so they didn't make little squealing sounds whenever I was riding (they never really rubbed) and this made it so much more pleasant!