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Procedure to calibrate Z-home / limit. Repetier Host. (no replies)

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I've just built my first 3d printer, an prusa I3. And everything is working, I guess, but I have some problems with the procedure to find the zero position for the Z-axis.
I have a limit switch at the lowest position.

When I send the Home-command the nozzle crash into the heatbed before it finds the limit. Then you might ask, why set the z-limit switch below the heatbed?!
well, that because the Z-axis still gets a zero-position above the heatbed. Even though the nozzle is pushing the heatbed down, maybe half a mm, the distance between the nozzle and heatbed is still at least 0.5 - 1 mm ABOVE when done.

So, i guess there is some calibration/configuration that has to be done here. Can someone help me in the right direction?

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