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Funny, in another post someone complains that his mouse cursor goes laggy in full screen while I seem to have the opposite effect. In full screen, the mouse goes super fast.

I think this is because the resolution is changed and the mouse cursor speed doesn't change accordingly in Linux (Mint 18 by the way).

Is there a way to make this game upscale to the native resolution instead of switching graphics mode?
Solved it!

When you enable 'quick alt-tab' in the options, the game just scales to the native resolution. For some reason, it keeps the taskbar, but it's still better.
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scippie75: Solved it!

When you enable 'quick alt-tab' in the options, the game just scales to the native resolution. For some reason, it keeps the taskbar, but it's still better.
This is not a bug in SpaceChem, but in SDL library that is used for rendering. The fix is to set SDL_MOUSE_RELATIVE to 0 environment variable like export SDL_MOUSE_RELATIVE=0'.

Source: https://wiki.openttd.org/FAQ_troubleshooting#My_mouse_is_not_sensitive_enough_.28SDL_.2F_Fullscreen.29
and more info https://www.linuxquestions.org/questions/linux-desktop-74/mouse-sensitivity-too-high-in-fullscreen-928988/

And again the quote of the OpenTTD wiki in case the link stop working.

My mouse is not sensitive enough (SDL / Fullscreen)

OpenTTD does nothing with the mouse sensitivity, SDL takes full control over the mouse. Some people might feel it is not doing a good job about this; but luckily you can change SDL's mouse setting. Please read the doc over at [1].

The necessary environment variable is SDL_VIDEO_X11_MOUSEACCEL.
I found that setting SDL_VIDEO_X11_MOUSEACCEL didn't work for me without setting SDL_MOUSE_RELATIVE=0 too.

So, for example:

$ SDL_MOUSE_RELATIVE=0 SDL_VIDEO_X11_MOUSEACCEL=6/1/0 openttd

There are other reports which suggest that

$ SDL_VIDEO_X11_DGAMOUSE=0

might work.