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5.1 How do I set up a .emacs file properly?

See Init File in The GNU Emacs Manual.

In general, new Emacs users should not be provided with .emacs files, because this can cause confusing non-standard behavior. Then they send questions to the help-gnu-emacs mailing list asking why Emacs isn’t behaving as documented.

Emacs includes the Customize facility (see Using Customize). This allows users who are unfamiliar with Emacs Lisp to modify their .emacs files in a relatively straightforward way, using menus rather than Lisp code.

While Customize might indeed make it easier to configure Emacs, consider taking a bit of time to learn Emacs Lisp and modifying your .emacs directly. Simple configuration options are described rather completely in Init File in The GNU Emacs Manual, for users interested in performing frequently requested, basic tasks.

Sometimes users are unsure as to where their .emacs file should be found. Visiting the file as ~/.emacs from Emacs will find the correct file.