Moving from Papers to Bookends (update)

“My opinions may have changed, but not the fact that I am right.”
Ashleigh Brilliant

My posting about wanting to move from Papers to a different citation manager got a couple of interesting responses. Some voices for Sente, and strong support for Bookends.

The problem with Sente

At the time, I thought about moving to Sente, but after trying it out I buried that idea. The problem is syncing the literature to my iPhone/iPad. Sente uses cloud storage and transferring the papers and books (PDFs) takes ages. Work literature is about 1.3 GB (a couple of full book scans and the like) and while the premium account can accommodate up to 20 GB, it takes ages to sync (and I do have an extremely fast Internet connection here). Not only because I do not want to openly “share” the literature, I think I prefer a more direct syncing option. Papers 2 and Bookends provide it (via WiFi, which I can control).

Bookends as an interesting Option

I did only a quick test of bookends (have yet to buy the full version), but it looks like it would work. Of course, you should have a look at the settings — I tried to import a couple of PDFs from DEVONthink and did not notice that it moves the PDFs, not copies them. And DEVONthink did not inform me that the file is no longer available, only when I clicked on it. Another argument for redundancy.

Regarding switching from Papers to Bookends, Luísa did forward me an eMail asking the developer for advice. Apparently, a more direct import is planned. But until this is implemented, the advice was:

Export from Papers as EndNote XML and import that. I think Papers 2 also has a direct Export To Bookends under the File menu.

All you should need to do is move the pdfs to the Bookends default attachment folder OR point the default folder (in Bookends preferences) to where Paper stores them.

The Bookends demo is fully functional, so you can try all this before you buy.

Looks like a good customer support. And as long as you can export your data from Bookends as well (imagine what would happen if the company folds or the developer dies), it is my current favorite for the next citation manager.

For the next few months I’m continuing using Papers 2, however.


  1. Jon, the developer of Bookends, provides legendary support. I’ve used Bookends for years, and he has never taken more than a few hours to respond to any query I’ve had or plea for help. He reads the user forum pretty much every day and puts a lot of effort into helping his users.

    Sente, on the other hand, has abysmal support. I’d guess that at least half of the questions posed by users on their forums are never answered at all. I used it for half a year and gave up.

    Bookends is also very, very flexible with formatting your data. You can get very creative with the formats, because you can output text in addition to all the various reference fields.

  2. Hi Daniel.
    On the problem of PDFs moving from the original source (in your case, DEVONthink) to Bookends, I think the answer to that is on pages 95-96 of Bookends User Guide (accessible from the Help menu on the app). There is stated that “By default, attached files are opened in the application that created them” (p.95) and when you want to attach a file to a reference you must choose on the dialog box if you want to move or to copy to the “Attachment Folder” (p.96). I hope this helps, the “magic move” happened to me too. 🙂

  3. Hi, since you’ve written about using reference managers in scrivener before (how I found your website today actually), and I’m trying to choose a citation manager to work with scrivener (not impressed with endnote), how do these two reference managers integrate with scrivener?

  4. Hi Daniel,

    Few months have passed :). Are you still using Papers2 or have moved to Bookends? Following your workflow -thanks a lot for sharing-, I kinda use Papers2 for citation purposes only while writing in Scrivener. Did you find that Bookends have similar -and as simple to use- feature?

  5. Hoi Alfi,

    I’m still using Papers 2, leaving my current job soon and still have a paper to write, so this is a bad time to change.

    All the best


  6. W.r.t. getting your content from Papers to Bookends, I’ve written a “Papers to Bookends” script which exports all publications selected in your Papers 3 library to Bookends:

    The script will also transfer the publication’s primary PDF (if there’s any) and can also transfer the publication’s rating, color label, flagged status, language, edition, citekey, and “papers://…” link.

    The PDF file’s annotations can be also transferred if you follow the steps given in the “Known Issues” section of the README.

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