I am running ubuntu and have recently installed compiz config settings manager. I decided to enable desktop cube just cuz I could, but the cube ends up being displayed as a row of boxes. All the effects (reflection, disortion) are working but I want it to be a cube. How am I to do this. I've already toyed around with the number of windows.

Without screenshot how are we supposed to help you? Did you select No. of desktops -> 4 in General settings [ccsm]

I attached a .jpg of the screen when I initiate cube.

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Isn't there two ways to change the desktop with compiz?
I don't know, it's been a long time since I've used it.
I think I had to press Ctrl+Alt, hold it down, and then click on the desktop, somewhere, like if you were to drag an Icon and the cube would appear and start rotating in the way you're moving the mouse.

I think that's a "Desktop Wall", not the cube. You can have several effects set up with Compiz to do one task (for a lot of tasks), so for example to change desktop (or view all) you can see them as a wall, as a cube (or cylinder, depending on how you prefer to have it served) and so on. You can even have, depending on the case at hand, multiple such things enabled simultaneously and use them with different shortcuts (keys or mouse). So if you have enabled the cube and happen to see a wall, it doesn't mean the wall would be the "cube" -- you're just calling for the wall, not the cube.

You should familiarize yourself with the compizconfig settings and what you have enabled and what not. Disable those you don't use, enable those you do use, and if there are actions that are handled by multiple things, you're asked which thing you want to handle what, and answer accordingly.

Like mentioned, you would probably want something like 4 desktops for the cube. Two will show up a plane with two sides (obviously, sort of a "2-sided cube"), four resuls in a cube with four walls as desktops and two as logos (images), and so on. Tweak the settings and the cubic object turns into a cylinder with desktops surrounding it. So, open the configuration tool and read before you buy.

The shortcuts for using each Compiz thing are also presented in the appropriate configuration windows (don't just "enable" them, also see their settings), so if you don't know how to use the cube, see the key combinations there. Typically you hold ctrl and alt, then drag the desktop with your mouse to zoom out to the cube; with ctrl+alt+left/right/down you may end up using the wall or the cube, depending what choices you made when you enabled the things.

I figured it out. The button combination I was pressing was to unfold cube so it was displayed not unlike the desktop wall. I have to ctrl+alt+click to get the cube to be a cube.

Ctrl+alt+Left will rotate it left, right will rotate it right, down will show it as a wall like you saw.

And also like you said using the mouse while ctrl+alt will give you rotating capabilities. You can probably google all the commands, or go into the settings and go to configure to set up or view the current settings.

-Jessica-