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Since every single time I start Mathematica, my first action is aligning the windows properly (Notebook on the left for $2/3$ of the screen, help on the right for the other $1/3$), I was wondering whether this could be done automatically. This is what it looks like:

enter image description here

How could I make Mathematica to use these window positions and sizes by default?

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On Windows I use "Tile Windows Tall" from the Window menu. I don't know if it's available on Linux. –  Szabolcs Feb 11 '12 at 23:18
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You can do this by setting (SetOptions) the WindowSize option on all Notebooks[] but the documentation one for window size, WindowMargins for window positions. Get the usable screen size (sans Gnome panel) with ScreenRectangle /. Options[$FrontEnd, ScreenRectangle]. Sorry, no time for a proper answer, but you should be able to work out the details going from here. –  Szabolcs Feb 11 '12 at 23:29
    
I cannot seem to position the "Documentation Center" even if I directly edit System/Guides/Mathematica.nb so it seems the position of that is controlled elsewhere. –  Mr.Wizard Feb 11 '12 at 23:53

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up vote 12 down vote accepted

The help window position can be set to be remembered from the Options Inspector: open it, select Global preferences, go to Global Options -> Dialog Settings -> Help Viewer Settings and set Enabled to True.

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Confirmed to work. It does not work after positioning only the Documentation Center page, but after position another window, that one also comes up in the new location. –  Mr.Wizard Feb 12 '12 at 4:03
    
Thank you, that's very helpful already. All that's left is now doing this for a new notebook as well. Would there be some way of having some autorun commands for each new nb created? –  David Feb 12 '12 at 6:46
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Unfortunately it is not possible to set a global default size and position for each new notebook that is created. So the 1/3 screen for the help browser is possible but not the 2/3 screen for the notebook. –  Mike Honeychurch Feb 12 '12 at 11:44
    
@David I don't know. I tried to change things like DefaultNotebook in the past but could not get it to work. I would very much like to know, too, for the same reason as you. –  acl Feb 12 '12 at 13:38
    
@acl I actually asked Tech Support about this a week or so ago after I couldn't figure out how to answer a question re: default size and positioning of notebooks. They advised it is not possible to globally set default size and position for new notebooks. (whereas you can for various dialogs as above) –  Mike Honeychurch Feb 12 '12 at 23:59

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