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I am using Prusa HE3D Xi3. While printing after 5 or 6 layers it misses the step on x and y axis.

Can anybody explain what is the reason?

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    $\begingroup$ What research have you done? There are several questions on this site about skipped steps, could you perhaps explain why those answers do not address your question? $\endgroup$ – Tom van der Zanden Jul 29 '16 at 12:43
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There's a possibility that your power supply lags after a while, the quality of power supplies on cheaper 3D printers are sometimes an issue.

There's also a possible that the stepper motor drivers aren't putting out enough power. This can be adjusted by turning the trimmer on the driver, check the printer documentation for instructions on how to do that.

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