Editing PDFs Opened Through Zotero


I am new to Zotero and have a simple problem that doesn't seem resolvable through the preferences panel. I am currently using the Zotero application on my Mac. Right now, I am in the process of organizing my data, so have several folders organizing various topics, etc. I am currently working on tagging, but also have the habit of opening PDFs through this interface and making highlights, leaving text reminders, etc. The problem I'm experiencing is that this then creates an "edited" version of the original PDF that then needs to be 'saved as.' This issue is really not okay, because as you can imagine it's causing things to be re-saved in the wrong places, creating redundancies, etc. Is there any way to turn this function off, so that when I open a PDF through double-clicking on it in Zotero, it doesn't need to save-as an edited version?

Help please and thank you so much. Also, if you would recommend a Zotero tutorial that may cover work-flow in Zotero desktop application, that would be greatly appreciated as well :)))
  • Which pdf reader?
  • Make sure you're using Zotero 5. Zotero 4 stored the Zotero data directory within the Application Support directory, and in recent macOS versions Preview started to require resaving outside of that directory. Zotero 5 automatically migrates the data directory to a "Zotero" directory at the root of your home directory, and you'll be able to edit PDFs normally.
  • Thanks, @dstillman, you are correct. I just downloaded 5.0 and am running it.

    New question: If I open a PDF directly from Zotero 5.0 and say highlight a word.... this modification is saved and visible if I close the PDF and reopen it through Zotero. However, the modification is not saved to the original file outside of Zotero. How can I make these modifications sync to the original file as well?
  • If you add a PDF to Zotero as a stored file, there's no longer a connection to the original file, and you would generally then delete the original file.

    If you don't want to do that, you would want to add it as a linked file instead.
  • @dstillman I see. Thank you. I guess that explains it for now.

    Is there an online tutorial that you would recommend? I don't want to lose any data and don't feel that I fully understand how Zotero works.
  • For a basic introduction:

    For best practices on getting stuff into your library, see:

    (Specifically, you should use the Add to Zotero button in your browser most of the time.)
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