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Occluding the window will also produce either blank or incorrect images.
If you already have a Python script, say before you create a figure and it will use an offscreen window for the rendering.
It is recommended to install software from Repositories, in order to keep your system secure and updated.
In some cases this is not possible (some Java applications or software with custom installers).
However, you can use the command line if you prefer. You can find these applications using Ubuntu Unity Dash (see image) or from the applications menu in other Ubuntu flavors.
If you want Ubuntu to setup software other than open source officially supported, then check "Install third-party software for graphics and Wi-Fi hardware, Flash, MP3 and other media" during installation procedure.
However, you can do it later, but it is recommended to be done during installation.
Doing this allows one to view X3D files without a network connection.
To view Mayavi visualizations on the notebook one should first do: The X3D data is embedded in the notebook and can be shared but if the scenes have a lot of polygons, these files can be large.