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Power off the STK500
Push the 'PROGRAM' button while powering up the STK500
Start AVR Studio and make sure there is a serial connection between the PC and the STK500 DSUB9 marked 'RS232 CTRL'
Start the program 'Avr Prog' located in the AVR Studio 'Tools' menu
Locate the firmware upgrade hex-file 'stk500.ebn' by pushing the 'Browse'-button in the 'Avr Prog Hex File'-window. The path for the 'stk500.ebn' for a normal AVR Studio installation is "C:\Program Files\Atmel\AVR Tools\STK500".
Push the 'Program'-button in the 'Avr Prog Flash'-window. A progress bar will now appear while showing additional information messages. Wait until the verify operation is finished.
Close the 'Avr Prog' program
Power off and on the STK500 PCB. The STK500 is now ready to be used with the new firmware.