I recently decided to teach myself guitar with different websites and dvds. I am having a problem with the pick. When I do chord change exercises I can strum them and they sound good with just my thumb. As soon as I use the pick they sound not so hot. It also seems that I can make the chord changes more smoothly when I just use my thumb and fingers. Kind of odd I think. My timing gets thrown off when I use the pick, mostly becasue it sounds bad and I focus on that instead.

Why is this?

How do I overcome it?

Is it that I'm not actually doing chord changes correctly and it is easier to notice with a pick.
It's just technique, try and not hit the strings so hard with the pick, or if your really more cofortable with it, just use your fingers. There are plenty of great guitarist who never even looked at a pick.
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I would reccommend learning with a pick, but its certainly not necessary. Playing with one will make rock and metal play easier (in the most part) but using your fingers is a great technique. I nearly always fingerpick my acoustic, it is very rare for me to use a plectrum in that sense.
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I started by fingerpicking and didn't even think of using a pick until at least 2 years later. I had never felt comfortable with a pick, and I had always used my thumbnail and pointer finger, but there were a lot of songs that I couldn't keep up with. The move to a pick was rocky at first, but I got over it, and now I love picking.

There are some situations where you are going to have to either fingerpick or use a pick. Don't feel pressured to use a pick, but you should at least work on picking so that you feel comfortable doing it.
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Maybe try a thumbpick? combines the best of both
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try a lighter pick
and try to pick with a small angle, it helps to reduce the string noise
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I prefer a pick to fingers, it gets better sound out of chords (especially on electric) and I play with a very stiff pick, you are probably holding the pick too tight and it is really mashing on the strings so if you don't have perfect chords (which if your a beginner you dont) and you hit the strings hard with a pick it will have a lot of strings either muted or they will buzz badly, just keep workin at it, but i would definately suggest to learn both ways (finger and pick)... god knows i have been playing for awhile now and i cant strum with my fingers to save my life, but dust in the wind is second nature..... keep practicin, all the time, every day, you will get the hang of it
It's not a problem to be doing it with your thumb, honestly.
I have been for a while and i can still change chords just as fast.
Sometimes it just sounds better when its strummed softer with your thumb than with a pick.
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