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I've got references that have math markup in their titles, and I'm having trouble getting bibtex to compile subscript output. For instance, a title including $\mathcal{A}_5$ comes out as though it were $\mathcal{A}\_5$. Anyone know how to fix this? What formatting would bibtex prefer?

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Your two things are the same. Please post an example of your BibTeX database. –  Joseph Wright Sep 26 '10 at 16:06
    
You seem to have made a typo in your question, because I would have thought that having $\mathcal{A}_5$ come out as $\mathcal{A}_5$ would be exactly what you want, since they are the same. –  Lev Bishop Sep 26 '10 at 16:12
    
Ack, there's supposed to be a backslash there, but the markup ate it. When I use that in a title, the bibtex output puts in a backslash, and compiles as A_5 visibly. –  Charles Siegel Sep 26 '10 at 17:24
    
When you put the code in backticks (`), markdown parses your question the way I think you intended it. –  Caramdir Sep 26 '10 at 17:38
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What are you using to write your bib files? I used to use jabref and that went crazy sometimes adding in extra pairs of braces and all kinds of stuff... –  Seamus Sep 27 '10 at 14:36
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2 Answers

I don't see your behavior.

\begin{filecontents*}{foo.bib}
@misc{foo,
        title = {Math $a_x$},
        author = {Not me},
}
\end{filecontents*}

\documentclass{article}
\begin{document}
\cite{foo}
\bibliography{foo}
\bibliographystyle{plain}
\end{document}

Compiling this with pdflatex, bibtex produces foo.bbl:

\begin{thebibliography}{1}

\bibitem{foo}
Not me.
\newblock Math $a_x$.

\end{thebibliography}

There is no added backslash.

Can you give a similar minimal example that exhibits the behavior you see?

The one thing I can think of to try without seeing your example is to surround your math material in braces {$a_x$} in the .bib.

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This is what I was thinking, too. B.t.w, you can embed auxiliary files in minimal examples with the filecontents environment. –  Will Robertson Sep 27 '10 at 8:37
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Define in the beginning of your LaTeX document:

\newcommand{\superscript}[1]{\ensuremath{^{\textrm{#1}}}} % superscript
\newcommand{\subscript}[1]{\ensuremath{_{\textrm{#1}}}}   % subscript

Then, as bibtex record you may define:

@article{Duce1995, title={Large CO\subscript{2} change}, author={Duce, J.K.}, journal={Environmental Science}, volume={10}, number={5}, pages={10--25}, year={1995} }

And then you can use this reference with {.}, \citet{.}. I prefer this approach because the usual math mode italicizes super- or subscripts.

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