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It depends on your board. I'm hearing that some some firmware versions of the stock board will always run the fan at full speed once the hot end reaches a certain temperature. Try sending a 'M106 S1' to your printer and heat up the hot end. If the fan stays off then good. In that case you woulduse the radial fan on the fan header on the board and run the hot end cooling fan right off the power supply. Add 'M106 S1' to your starting GCODE. Then just have your slicer turn the part cooling fan on / off if necessary. If the printer turns the fan back on then unfortunately you'll just need to wire the radial fan to a switch and manually turn it on/off as needed.