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I have a Macbook Air 6,2 which is equipped with a synaptics clickpad. I have managed to turn on middle click emulation when three fingers are pressed on the trackpad. This works but I noticed that when the middle click is recognized the mouse cursor is locked in place. However, I need to use a middle click drag operation to manipulate the views in Blender and Freecad, which I can not do because the mouse cursor is locked in place.

Is there anyway to configure the click pad so that it does not lock the cursor when a three finger emulated middle click is performed?

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I suggest you to switch to libinput then configure it via .conf file.

A pretty complete guide is here: https://wiki.archlinux.org/index.php/Libinput

If you can't switch it off, try this: https://wiki.archlinux.org/index.php/Touchpad_Synaptics