Hi there!
I recently downloaded thesis because I’m interested in using it to write my dissertation. I’ve been googling a lot and searching forums but for now, I haven’t been able to find a comprehensive workflow to use a reference manager (I use bookends) along with scrivener and then exporting it to PDF or word.
I would appreciate your help. Thanks.
What is thesis? -----extra character to make 20
I don’t know how my phone changed scrivener to thesis. Maybe it was a typo from myself, thanks for pointing it out.
I’m a Bookends—and obviously Scrivener—user too. My workflow does not expand over both apps alone but over all my apps (and platforms) handling text. Bookends always lurks in the background, so to speak.
For example, my information manager is DEVONthink. I keep everything in it that has not yet become a Scrivener project. And even after that—it is great for fetching things like webpages, both manually and automatically, and then I drag the stuff into Scrivener. The references are Bookends citations.
I’m using Bookends also in note taking apps like 1Writer and Drafts—they allow me to instantly write on mobile devices.
Especially Drafts is highly customizable. For example, I have created an action that displays a list of the recent and upcoming paper books I am reading. I can pick from that list and add a page number. Both gets added as a Footnote to the quote I wrote, dictated, or scanned from the book.
Mostly all of these notes are kept in DEVONthink, sometimes I send them directly to Scrivener. Please note that both notes apps use Markdown. But because Scrivener can import Markdown quite well by Import And Split including proper footnotes—unlike RTF!—in that is not at all a problem. Actually that is one of the reasons I switched to Markdown in DEVONthink too.
I have a section dedicated to Bookends references in my clipboard manager Paste too.
For all of this I do not use permanent citations but temporary ones like {Kaufman, 2021, #297372}. Because I don’t know which format I will have to or want to use in the actual text my citations might become a part of.
You were certainly told which format to use for your dissertation, like MLA or Chicago, but to make your workflow future proof I’d strongly recommend you to use temporary citations too.
And now, finally, to Scrivener: When Bookends on the Mac is running you can cite from its database in every writing app by hitting CMD three times (or is it two? I’m not at my Mac for a while).
I found it more convenient to set Scrivener as the dedicated word processor in Bookends’ settings. Then you can call B from S to the foreground by hitting CMD-y , pick a citation, and send it to S, now back in the foreground, by hitting it again. (If I remember correctly, from a certain version on CMD-y in Scrivener is used as a shortcut for something else but of course you can remap that in the OS settings.)
On the restricted iOS/iPadOS I either copy a reference directly from Bookends To Go or from the Bookends section in Paste.
That was about how to get Bookends citations into texts. Now to the final step:
Sadly, Bookends cannot work in Scrivener directly. It has to process Scrivener’s compiled output which has to have a format Bookends can handle like RTF.
But since you mentioned Word: Bookends can install a plug-in in Word which replaces the temporary citations by the final ones and generates a bibliography at the end of the document.
CMD+Y is the toggle that takes you back and forth between Scrivener and Bookends. But just as you have to set Scrivener as your word processor in Bookends preferences. You have to set Bookends as your citation/bibliography manager in Scrivener. Only then will CMD+Y work as described above.
One thing that was not mentioned is that Jon over at Bookends offers fantastic support. Often he responds within an hour even on weekends. That has been my recent experience with him.
Whoever invented auto-correct should go to hello. 
Hi, thanks for answering.
I also use DevonThink as my personal knowledge manager, I take notes and keep all my journal articles there; it is a wonderful tool.
Then you can call B from S to the foreground by hitting CMD-y , pick a citation, and send it to S , now back in the foreground, by hitting it again
How did you set the format of your citation? Or what do you recommend? When I do that, I get this format:
[@Article{Savini2019,author = {Savini, Lara and Candeloro, Luca and Perticara, Samuel and Conte, Annamaria}, title = {EpiExploreR: A Shiny Web Application for the Analysis of Animal Disease Data}, journal = {Microorgan]
Is this format useful or should I change it?
And now, finally, to Scrivener : When Bookends on the Mac is running you can cite from its database in every writing app by hitting CMD three times (or is it two? I’m not at my Mac for a while).
For me, I have to press control twice while on Scrivener and I get a popup to look for a specific reference, and it gets inserted with the format I wrote before.
Sadly, Bookends cannot work in Scrivener directly. It has to process Scrivener’s compiled output which has to have a format Bookends can handle like RTF.
I’m planning to export it as a .rtf and import it to mellel to make the final touches there.
That is the temporary citation that BookEnds places into Scrivener or whatever program you have designated as your word processor. I believe it also supports Mellel, Nisus, and perhaps some others. Their website will tell you what they support.
After you have exported your Scrivener project to RTF and opened it in your Word Processor of choice, I currently use MS Word 2019. Bookends installs a script into MS Word. You choose “Scan document”
It will then convert the temporary citations into whatever style you have chosen in Bookends, and there are abundant choices like Chicago, MLA, APA, and hundreds of other specialty styles used by different publications. Or, you can create your own custom style. You are also asked if you want to generate a bibliography according to the style you have chosen. You can also customize you bibliography format if you like.
If you want to submit your work to a publication that uses a different style then choose that style in Bookends, unscan in your word processor to return to the temporary citations then rescan to get the new style.
There are some real power users of Bookends and other citation managers on this forum like nontroppo and lunk who could give you a lot more ideas about best practices.
This old discussion about citation managers gives a lot of information that is still relevant today.
I have a Keyboard Maestro macro that gives me these choices automatically when I type scriv:
When the palette comes up, I type
. for .scriv
e for Scrivener
i for scrivenings
x for .scrivx
Interesting. So you have assigned the same “Typed String” “scriv” to all 4 macros in KM? But then you could just type “scriv + any letter” to get the word you want directly 
Exactly. It saves me a lot of time.
Not sure I understand you. You could set that up.
scriv. = .scriv
scrive = Scrivener
scrivi = scrivenings
scrivx = scrivx
What’s the palette for?
My method does the same thing as your method, with the same amount of effort to use … all but the last, which leaves out the . in .scriv.
… And I like to see options, so I don’t have to memorize them.
Ok, many ways lead to Rome
Thanks for all the advice and sharing that post. Yeah, I managed to currently use bookends with scrivener inserting the temporary citations (not the bibtex format I posted) which I’m going to export to a rtf and then just polish it with mellel.
That looks great, unfortunately I need to learn how to use Keyboard Maestro first, which I will with the Macsparky guide.
If you try that, the conflict palette comes up, which is what my setup does.
Right, I see what you mean. It’s 4 macros either way, and activation works the same either way. I get the conflict palette because all of them have the same trigger – and you don’t get the palette – but it doesn’t matter. If I type scrive, I get Scrivener, same as you. Et cetera. With a little work, it could be one macro, but I don’t bother with the logic code for that.
