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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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Understand. Small circles usually have very sort traces. Either the gear box backslash or firmware is not able to react to it.
For full step set MS1, 2 and 3 pin on electronics to open and recalculate firmware. You will get around 41 microsteps per mm in X and Y axis. Than upload it again.