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Is it possible to disable evdev's EmulateWheel option when using specific programs? In my use case, I would like to be able to interact with the Acme text editor and with some VMs using my Thinkpad's middle-trackpoint-button as just an ordinary middle button rather than an "EmulateWheelButton".

It would be less convenient, but acceptable, if there were a simple command to turn emulation on and off, so that I could bind this command to a hotkey so I can toggle it manually.

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You can modify the properties of input devices with the xinput command. See Make mouse movements scroll when the middle button is held down for a detailed explanation. You'll want something like

xinput --set-prop 'Thinkpad Trackpoint' 'Evdev Wheel Emulation' 0

where Thinkpad Trackpoint is the name of the device found in the output of xinput list, and the final value is 0 to turn off and 1 to turn on.

These options cannot be changed based on the active program. A few advanced window managers allow you to run arbitrary program on a focus switch. A few advanced window managers (mostly the same, I expect) would let you program something like EmulateWheel which would only occur on certain windows. I'd expect Fvwm, Sawfish, Awesome and Xmonad to cope (with a nontrivial but not insurmountable amount of coding), and not many more.