When I'm playing my bass I rest my thumb on the back of the neck and use it to apply extra pressure for a don't break my fretting fingers(duh, everyone does that)
My problem is that when doing that my thumb hyper-extends(bends backwards) as a result of me being double jointed. This tends to cause a lot of discomfort in longer songs, or more technical songs.
Does anyone else have this problem? Is there a different way to hold the neck to avoid this?
Maybe you should rest your thumb and put it around the neck when you feel discomfort. Also try stretching your thumb and try not to apply too much pressure.
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Stretching beforehand is a good start. But it also sounds like you're applying too much pressure.
How high is the action on your bass? If you have to press to hard with your fingers, your thumb will follow suit to help out and that's causing you trouble. It might be a good idea to take your bass somewhere and have it professionally set up. Get that action as low as possible, and you won't have to press as hard...and your thumb will stop hurting too. If you're having trouble with a few longer or technical songs, a 3 hour gig will kill you!!