Z6 | how to edit the original PDF in Z6 pdf viewer ?

Hi there,

First of all, thank you for the latest developments on the software, it has an amazing potentiel and that's what makes me want to stick with it in my workflow.

My workflow being : download articles and store them on my pc > read articles > annotate, highlights them and adjust metadata on iPad > export ann., hl., metadata to obsidian.

Maybe you can enlighten me on one thing I didn't find a way to manage correctly yet:

Is it possible to ''synchronize'' the annotate pdf inside Zotero with the original pdf stored on my pc. An option for this would be deeply appreciated. (Or at least a manual option to save pdf (with new annotations, highlights, metadata in zotero) over the original one). So I can open it with any other pdf app and I will see all the annotated and highlighted things.


  • Not sure what you mean by "pdf inside Zotero with the original pdf stored on my pc". Files in Zotero are on your computer. If you save from the web, you'll have a single file, and if you get a PDF from somewhere else (e.g., email), you would delete the original file after adding it to Zotero.

    Zotero 6 stores annotations in the database. If you want a copy of the file with the annotations embedded, you can export the file, but that's not normally something you would do unless you were sharing the file with someone who doesn't use Zotero.
  • edited April 1, 2022

    Thanks for the clarification. Indeed, I didn't noticed you could export pdf from zotero pdf reader.

    The thing is, I have a folder on my pc where all my pdfs are stored, and now when I place theses pdfs inside zotero, instantly it duplicate the pdf and store them inside zotero database.

    And from here, all modifications (metadata, annotations, highlights) I make inside zotero pdf reader only being stored inside zotero. This isn't what I need in my workflow. Its crucial to me that the original pdf (not the new one stored in the zotero databse) reflect these changes!

    So this is why I'm asking if there is a sort of synchronisation system possible, or batch process that I can use so the orginal pdf get the zotero's modifications ?

    Thank you!
  • @dstillman -- I think charles_c180 would be well served by linked files and store annotations in PDF. I think given this and similar scenarios, I'd advocate reconsidering https://github.com/zotero/zotero/commit/e0097df068299b759447b639dbb2e48df30b70e2
  • Store Annotations in PDF didn't turn on some automatic setting, though, which is what people looking for this — including @charles_c180, it sounds like — actually want, and which we're not going to implement, because of all the problems it creates that led us to design annotations the way we did. So then you're left with an option that has to be triggered manually after every change, which is tedious and dumb, for an end result that causes the same problems we were trying to avoid in the first place. The PDF reader stores annotations in the DB and provides various export options to guarantee data portability, and if someone wants annotations saved within the file they should use a PDF reader that works that way (which, of course, isn't all — choice is good!).
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