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BTT CAN Bus toolhead control board I'm going to use has three fan connectors. Two 2-pin ones, and one 4-pin. What is more valuable, to have tachometer and PWM control over the part cooling fan, or over the hotend radiator cooling fan? On one hand, better part cooling fan control can make better prints (is the 20% cooling"really a 20%?).On the other, being able to easily detect stall on a radiator cooling may be useless 99% of the time, and save my posterior this one time it's needed, by stopping heater when hotendfan fails. So I am lost here.

Most printers use only 2-pin fans so I guess it's not that big of a deal, and having either one on full control would be a progress, but I want to get the best of what I've got when I'm building it myself.

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I would use it for the hotend cooling, not part cooling. There is utterly no reason to need to know if 20% is "really 20%". If you're using sub-100% fan settings, the actual linearity of the percentage is irrelevant; you just need to find (experimentally) the power setting that achieves the results you want, and use that.

On the other hand, as you've noted, stall detection is highly valuable for the hotend cooling fan. It can protect you from potentially very serious damage to your printer, if not outright fire hazards.

If you would like to use both, though, you don't need a 4-pin fan connector. Any endstop/filament-runout-sensor/etc. connector can be repurposed for the fan tach. Just make sure you check the circuit diagrams and ensure they work the way you think they do before connecting anything.

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