Forcing a line down

hi,
I think I follow your description of the circuit, but if you show us how you have the res/LED/Transistor connected to the pin, with a simple diagram, that would help us.
 
A tiny BCR148 transistor has a built-in 47k resistor in series with its base. For it to saturate with a 0.1V loss then the input to the resistor must be at least 47V or the resistor value must be reduced to 4.3k or less when powered from 5V.
 

Sorry, I don't use Atmel processors - but they may well have an open-collector part?, they copied everything else from MicroChip

Auido Guru, your suggesting it's the transistor I'm using thats at fault and with my limited knowledge I can see why (however I originally thought it was due to limitations of the transistor) can you sugest a replacment?

Just use a normal NPN transistor, like a BC148, and add an external base feed resistor.
 
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