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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 at 21:34
Oh and another thing... have you tried opening the pdf in another viewer? A possible workaround could be to export to some other vector forma (svg, ps,...) and try to convert from there. Also, there are 2 other ways to export plots: 1) "Save Graphic As..." from the context menu and 2) "Save Selection As..." from "Edit". It's always a delight to see the different graphics these 3 methods produce! – sebhofer Jan 16 at 21:36
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@Szabolcs I don't know... I would trust most pdf viewers more than Mathematica's pdf export. – sebhofer Jan 16 at 21:46
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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. – David Skulsky Jan 16 at 22:32
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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 at 2:23
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1 Answer

You can avoid this problem by copy/pasting the PDF (from the Finder) rather than Opening it. Here it is in OmniGraffle:

pic

Looks like a bug in OmniGraffle to me...

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It looks to me like that just embeds a PDF as a single monolithic, uneatable object. – raxacoricofallapatorius Jan 17 at 14:15
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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 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 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 at 21:50

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