How can I configure Emacs to run pdflatex rather than latex on a LaTeX file when I type C-c C-f (tex-file)?

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You can do this by setting latex-run-command; see the the emacs manual. Something like this in your .emacs should do it:

(setq latex-run-command "pdflatex")

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Thanks! That did the trick. – John D. Cook May 19 '10 at 13:45
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You can temporarily switch AucTeX to pdf mode with CTRLctp. To make this change permanent set

(TeX-PDF-mode t)

in your ~/.emacs file.

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