I uses my thumb to mute and to play low E string this is becayse John Frusciante is also my role model too. However when i attain my guitar class, my teacher told me i should change the habit. He said it will affect my strength in pressing the chord and i will lose the muscle memories of the chords. So should i stop using John's method of using thumb to mute and play? Or should i continue to do so?

I have another problem that is John uses his thumb to play his electric but when playing acoustic, does he use his thumb? Thanks
With certain songs, it helps a lot, but it can affect your speed and stretching ability. Overall, though, I don't think it hurts your playing too much. Also, if you learned how to play using your thumb, and then changed, that would hurt your muscle memory a lot more than using it, I would think.
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Learn how to play both ways... full barre chords and fast runs are easier to play that way. There are some things you can't do without the thumb, but there are some things you can't you play with your thumb there. It doesn't matter if you prefer one over the other, its important to develop both.
Thats surprising that your guitar teacher said that. He must have been taught that when he was younger because really there is no reason not to. In the past year or so, Ive really developed using my thumb and its really nice to be able to use. I also find that with my thumb overtop the fretboard like that, that my fingers work better. I feel more in control of the fretboard. However, remember that full barre chords you wouldnt have your thumb up because you wont get any strength.
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justin, that was easily the most inspiring, helpful piece of advice anyone has ever given me in regards to my musical pursuits.

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There's nothing wrong with using your thumb I do it, not just because of Frusciante and Hendrix, both of whom I love, but I find it more comfortable then doing barre chords. I was taught barre chords first then started using my thumb. And yes john use's his thumb on acoustic watch live at Slane Castle watch Venice Queen.

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