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What settings apply, Cura or Machine?

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I've never set flow other than 100% in cura but I just played with it now to find your answer.

There is no gcode to set flow so what Cura does is it just increases the "E" or extruder distances by the flow amount.

The flow value on the control panel will increase it even more! Or decrease it. So a flow on the panel of 100% is nominal but you can increase it or decrease it. For example if you print with 110% in cura and 91% on the panel you are now back to 100% flow (1.10 X 0.909 = 1.00).

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No - those are different. Fan speed can be set in cura and it puts fan speed gcodes in the gcode file that goes onto the SD card. You can open it in a text editor and see that.

When you go into TUNE and look at fan speed it shows you the current fan speed - you can change it. But as it goes through the gcode if it hits a fan speed command it will obey the gcode and change the fan speed at that moment.

Also your material settings on the UM2 series has a fan % that modifies the fan speed by that percent I believe - I'm not sure how that works as I always do 100% (PLA - really only ABS needs lower fan speeds).

Temperature is same as fan speed - there is a gcode or you can change it in the tune menu but if you used a plugin that modifies fan speed the gcode will change the fan speed back. Also by default the fan speed comes on slowly on each layer until it gets to 100% so if you turn fan to 100% on first layer it will probably go back to whatever gcode sets it to on the next layer.

diameter is usually set on the machine, not in cura - at least it does in "ultigcode" mode. When you tell cura your machine is UM2go it assumes you want "ultigcode" which doesn't specify filament diameter - instead that is set up on the um2 in filament properties. it should default to 2.85 which should work fine - I haven't touched that ever.

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