Rules of thumb for Rook positioning?

You can use them to pin , capture etc but before that create a situation through which you can get them out on open files such as castling to bring one out and pinning a piece to the queen /king with the other so you can mobilize it or other pieces

I like to line them up on the King or Queen sometimes, and then clear the file in front for a nice capture.

Good question. It's one of the things I still struggle with from time to time. There are some general principles that are often mentioned:
- Rooks are best on open or half open files.
- Files that (you expect) will open works as well.
- Rooks are well placed on the same file as the opponent's King or Queen
- Rooks can be very strong on the 2nd/7th rank (on the opponent's side), usually later in the game
- Doubling the Rooks on open files can be strong too.
These guidelines can be challenging to follow in practice, because it's not always clear which files will open up later in the game. That will vary for each position and is dependent on opening, potential pawns breaks, etc.
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