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I recently bought a TFT module driven by SSD1963 I have experience on t6963 and ks0108 and by a quick look it seems ok to make a MCU interface to ATMega128. What is confusing to me is the difference between the supply voltage of SSD1963 = 3.3volts and micro bus voltage =5 volts. Should I reduce all voltages on the micro-controller's pins from 5 v to 3.3v?

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If possible, I'd recommend to use 3V3 for the entire circuit; the ATMega is perfectly capable to operate at 3v3. But if you can't for some reason (if you already have a board that depends on 5v to work, or whatever), use the staple for level shifting, the TXB0108. Since it has just 8 lines you'll have to use probably 3 of them (for 18-bit rgb and other signals). TI has a version of this IC with more lines, but is BGA only, which is generally impractical for prototypes.

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You can do it by several way,

  1. using of your MCU(in this case ATMega128) by 3 or 3.3 volts
  2. using of Voltage divider

and another way that i can't recall...

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    \$\begingroup\$ Voltage divider is not a good idea in general for anything high speed. The RC constant will make fast signals very slow. \$\endgroup\$ – Gustavo Litovsky Oct 1 '13 at 22:24

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