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I have connected fan (5V, 0.2A) to raspberry pi 3 on pins 2 and 4. When I turn on raspberry, fan doesn't work. Does fan should start with turning on raspberry? Or I have to setup some configuration to get fan working?
According to the official pin diagram, pin 2 and 4 are both 5v.
Try to connect with pin 2 (5v) and pin 6 (ground).
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