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I have a problem concerning Amnesia: The Dark Descent bought in Humble Indie Bundle V. The game crashes when I hover over notes, and so does Ubuntu. After the crash I can only see the desktop background, and the only way out is a restart.

As I can't find anything concerning this particular problem, I try to follow the Frictional Games' troubleshooting guide. In G-1 it says:

Make sure Amnesia has full disk read/write permission in the directory it is installed.

How do I do it?

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Run gksu nautilus(Using Alt+F2). Navigate to the parent directory/directories of Amnesia's install location (usually /usr/games and /usr/share/games and right-click any directories that have to do with Amnesia, click properties, permissions, and check what the owning group is. Then, change the group to be a group you are in(your username is good), or add yourself to the owning group with useradd -Ggroupxyzusername(not recommended)

Edit: Do not run as root. Ignore first part of old answer.

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A game such as Amnesia should not be run as root. You should only run programs as root that need to perform administrative tasks or tasks that regular users cannot perform (for example, it may make sense to run nmap as root). In general, the solution to this problem is to get the permissions right so the user running the program can access the files. If systemwide executables installed through the package manager have to have write permissions for non-root users, that's a bug. But for directories, you can probably add the user to the group owner of the directory (if not root). –  Eliah Kagan Jun 15 '12 at 5:41
    
Ok. How did I overlook that? –  hexafraction Jun 15 '12 at 11:51
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Right-click the Folder → Properties → Permissions tab → set to "Read and Write" for every option.

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