Pesky PDFs: preserving Word bookmarks

I recently uploaded my PhD thesis as a single PDF file. I wanted to make this electronic copy as accessible and usable as possible. For such a large document (250 pages plus), this meant including bookmarks so that cross-references and table of contents are ‘clickable’ – they take you directly to the referred-to section. It also means that the document can be viewed as a hierarchy of section and subsection headings in PDF viewers such as Adobe Reader. Creating basic PDFs is easy, Mac OS X has a built-in “Save as PDF” option within print menus and there is freeware such as Cute PDF available for Windows, but this only creates simple PDFs that are effectively the output to a printer and include no bookmark information. Creating navigable PDFs is possible (there are some useful guides here and here), but turned out to be a bit more of a minefield than I expected.

The PDF file format was developed by Adobe, so the obvious place to start was their Acrobat software for creating PDFs. I’d written my thesis in (the ubiquitous) Microsoft Word, and Acrobat adds functions to Word that allow you to create PDFs from Word documents and translate any Word bookmarks (such as table of contents, cross-references) into bookmarks in the PDF. Perfect (you’d think) but as the trial version of Acrobat is only available to download for Windows and I’ve recently moved to Mac, it wasn’t to be. So, what were the other options? Apple’s Pages application within iWork’09 can generate bookmarked PDFs and it can open Word documents but there is a snag. Word and Pages deal with paragraph spacings differently, the net result being the document pagination changes which is hugely problematic in an academic publication (such as a thesis) where page numbering needs to be consistent – how can you confidently reference page 32 if, in the PDF version, it actually becomes page 34? Of course I could’ve just written the whole thing in Pages, but hindsight is a wonderful thing..

This sent me back to Acrobat. The Mac option was out, so I instead installed a Acrobat 9 on a Windows laptop I have for work. This laptop also has Microsoft Office 2003 installed and between it and Acrobat I could happily generate bookmarked PDFs. But, alas, the solution wasn’t to be quite so simple. The first problem is that Word 2008 on Mac and Word 2003 on Windows don’t paginate the document exactly the same – infuriatingly the 2003/Windows version ends up ever so slightly longer. The second problem is that Acrobat can translate all internal links in Word documents into links in the PDF except those in footnotes (where they often appear). This meant having to manually edit the resulting PDF file in Acrobat to add in all the internal links in footnotes, a not insignificant task. And it also meant that this PDF then becomes the ‘definitive’ version of my thesis – any prints must come from this file not the original Word document opened either on Mac or Windows to prevent pagination discrepancies. Phew.

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