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When I export a plot to a PDF with something like

Export["test.pdf", Plot[Sin[x], {x, 0, 2 Pi}], "PDF"]

I get a file in which the axes have been separated from the rest of the plot in some editors and viewers (e.g., OmniGraffle):

enter image description here

Why is this happening? Is there a way to prevent it?

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This is certainly platform related... Which Mathematica version and operating system are you using? (Well the OS one can guess... :) – sebhofer Jan 16 '13 at 21:34
@sebhofer: In some viewers it looks fine. Exporting to SVG is not an option. The whole reason for exporting to PDF is actually that it's the only way to end up with a decent SVG. Mathematica's SVG export omits size and font information. – raxacoricofallapatorius Jan 16 '13 at 21:39
@Szabolcs I don't know... I would trust most pdf viewers more than Mathematica's pdf export. – sebhofer Jan 16 '13 at 21:46
Did you send the PDF to the Omnigroup? They're a pretty responsive bunch and I wouldn't be surprised if you get an answer. – Cassini Jan 16 '13 at 22:32
I finally have time to look this up and post this. There's a very nice open source tool that can reprocess PDFs for you, but unfortunately it's a bit difficult to get the older version that still supports this functionality. Get Multivalent from here (not from the official site---latest version is no good), and follow the instructions here to reprocess the PDF. If you have Acrobat, it's simpler to try 'optimizing' the PDF using it first. – Szabolcs Jan 17 '13 at 2:23
up vote 2 down vote accepted

This looks like a bug in OmniGraffle, but you can avoid it (at least for display) by copy/pasting the PDF (from the Finder) rather than Opening it.

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It looks to me like that just embeds a PDF as a single monolithic, uneatable object. – raxacoricofallapatorius Jan 17 '13 at 14:15
Yes, that's true - it's uneditable (and uneatable, too)... I'll bet you an up/down vote it's an OmniGraffle bug though... :) – cormullion Jan 17 '13 at 15:03
I'd agree. This won't answer it for me though. I've got to open it in a different viewer, save it, and then open that in OmniGraffle, where I can edit it. I've sent the file to Omni. – raxacoricofallapatorius Jan 17 '13 at 15:25
Can you start the answer with "This looks like a bug in OmniGraffle, but you can avoid it (at least for display) by...". Then I'll accept. – raxacoricofallapatorius Jan 17 '13 at 21:50

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