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The following minimal code using the chemnum package was designed to replace TMP1, TMP2 and TMP3 in an eps file made by ChemDraw by numbers:

\documentclass{article}
\usepackage{graphicx}
\usepackage[runs=2]{auto-pst-pdf}
\usepackage{chemnum}

\newenvironment{scheme}{}{}

\begin{document}

\begin{scheme}
    \cmpdref{ref:nucleophile1}
    \cmpdref{ref:nucleophile2}
    \cmpdref{ref:nucleophile3}
    \includegraphics[scale=0.6]{aziridineopening}
\end{scheme}

\end{document}

A copy of the eps file can be found here. Is this problem due to my eps file or my code?

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Welcome to TeX.sx! Perhaps consider picking a more memorable user name that user1281358 :-) For me, your example works as expected: could you add \listfiles to your input and edit the file list you get into the question? –  Joseph Wright Mar 25 '12 at 10:44
2  
Also a chemistry comment about the scheme. Your arrow is coming from 1, but in the text you indicate that 1 is added after some initial step. Unless you use two separate equivalents of 1, that is misleading. –  Joseph Wright Mar 25 '12 at 10:55
    
The log file can be found here. I don't have a lot of experience with latex, so I looked over this one at first: Package etexcmds Info: Could not find \expanded. Could this be of any importance? By the way the schema was taken literally from a peer-reviewed article. –  ErwinL Mar 25 '12 at 11:17
    
I see you are running on Windows, and that the log claims that the auxiliary compilations have failed. Could you try using \usepackage[crop=off]{auto-pst-pdf} and see if that helps? pdfcrop is not always successful on Windows, at least for me. –  Joseph Wright Mar 25 '12 at 11:24
    
Oh: I added \usepackage{epstopdf} to make it work. –  ErwinL Mar 25 '12 at 11:26

1 Answer 1

(Summarising my comments into an answer.)

The most common issue when using auto-pst-pdf is a failure of the conversion after the LaTeX run. Here, in the log we find

Package auto-pst-pdf Warning: 
    Creation of minimum-pics.pdf failed.
This warning occured on input line 124.

As the file compiles without errors with pdfLaTeX, the most likely explanation is that pdfcrop is failing to rung: this is the final step of the conversion process. In particular, pdfcrop will not work 'out of the box' on Windows. Thus a solution may well be to use

\usepackage[crop=off]{auto-pst-pdf}
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