If you print a cylinder vertically or a cylindrical hole vertically they come out smaller than desired. Especially the holes. This is because PLA comes out like a liquid rubber band - like snot - it cools rapidly and shrinks and is stretchy and sticks to itself like snot. Combine these properties and it's like a liquid rubber band.
So as it gets laid down around a vertical cylindrical hole, it pulls inward and the diamter of the hole is typically 0.4mm smaller than desired. Because of this I usually add 0.4mm to 0.5mm to every vertical hole diameter (half that if radius) in CAD.
Solid cylinders are also smaller but not by as much if the outer layer goes on last because the inner layers help support. I'm not sure how much they shrink - maybe only 0.1mm.
Basically if you are printing a nut I would look at the diameter of the hole and scale up X and Y (but not Z) by the right amount to add 0.5mm. Or you can set horizontal expansion to -0.5. That shrinks the outside of the part and enlarges vertical holes.
If you are printing a screw I would probably leave it as is.
When you need really precise parts turn off acceleration control and jerk control and set all the printing speeds the same (anytime you speed up or slow down you get some under or over extrusion) and set the print speeds pretty low - maybe 25mm/sec if you want a perfect part. Patience is rewarded.
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ctbeke 133
There is a relatively new setting called "slicing tolerance", maybe you could give that a try? It's in the experimental category. There's also some details about it in this post: https://ultimaker.com/en/blog/52266-whats-new-in-ultimaker-cura-31.
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