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If I move the mouse curser to the top left or the top of Atril, the document position scrolls up. Also sidewards movements are possible.

I observed this behaviour for a while (even before Ubuntu 16.10), and it caused me so much pain, that now I start this question here.

If I move my mouse outside of the Atril window (e.g.) to write the contents of the pdf by keyboard into an other field or copy paste something, my view on the pdf changes.

How can I change that behaviour of Atril?

I am using Ubuntu Mate 16.10

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It is probably because you pressed auto scroll button. Green triangle icon in Edit Toolbar and later you saved Current settings as default. Press it again to stop and save new current settings as default

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