LED USING PWM FAN HEADER
Ok, it's an old thread, but this is topic has a good shelf life, so here we go. I'm thinking about doing something similar myself, with a 12V LED strip.
I'm guessing that the reason why PWM can't feed your LEDs directly, is because the PWM pin is only outputting the signal at TTL level (up to 5V).
What should work then, is to use an NPN transistor, e.g. a 2N2222. Connect the base (via a resistor) to the PWM pin. Connect the emitter to ground. Connect the LED(s) and current limiting resistor(s) between 12V and the collector.
If I'm not mistaken, this configuration should be able to give you some ~11.4V of ~25 kHz PWM goodness at up to ~800 mA.
In other words, enough voltage to drive three LEDs in series, and enough current to drive a bunch of them in parallel too. The brightness should now be proportional to the set fan speed, and not inverted. Because of the PWM control, the brightness should also be somewhat linear, instead of dropping off a cliff at lower "fan speeds".
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