Struggle with my Workflow (Macbook, iPad, DT 3, LiquidText, Papers)


I read several threads about good workflows but still struggle with my setup.
I’m using DT 3 as my central storage for all documents I work with. I’m using DT 3 on my Mac and DTG on my iPad. Until recently I used Zotero together with DT. The best way here was to index an external directory with DT so that my annotations appear in DT and in Zotero. I switched to Papers now, but this does not affect my problems.
The sync between DT 3 and DTG is not working as it should if I don’t import the PDFs into DT. With the external files my annotations will not be save. Sometimes the iPad wins, sometimes the Mac. I never know if the sync worked and the annotations made it into the pdf on the other platform. I know this would work if I would import the pdfs into DT. But this would destroy the sync with my literature database (and the citation I copy from there into Scrivener).
Even worse is the fact the LiquidText (great for annotions) copies the pdf into an internal database too. This results into an additional copy of my pdf. Worst case: three versions in DT, LiquidText and Papers.

Any idea how to optimise this workflow?

Thanks a lot,

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I store all my data in DT
I mostly rely on the DT editors, but will use external editors for extended features

Can you explain your requirements for LiquidText and Papers?

I use LiquidText for the annotations and sticky notes in the pdf file. Annotations in DT are fine, but the added area for comments I get with LiquidText is missing.
With Papers (or Zotero) I manage my bibliography and the citations when writing a paper. I need the annotations made in outhers app there too.

As far as I know, you will not get past the need to think about working in LiquidText (and its competitor MarginNote) in its own, self-contained sphere. These two apps are ideal for manipulating the ideas that you form in them or outside them. Do not expect to have any other app recognize your handy-work inside them, certainly not as the standard for PDF annotations.

You do not say where and how you do the annotating. Only in LiquidText? Or in LiquidText and DevonThink and DevonThink To Go and Papers/macOS and Papers/iPadOS? Can you clarify this part of the workflow in better detail.


A good discussion here:

PhD workflow setup - help!

@DrJJWMac I do most of my annotations in LiquidText (LT) but sometimes also in DT or DTTG (this may be caused by my incomplete workflow). It would be OK to transport the “in-text” standard Adobe-style annotations of LT into DT and leave the comments/notes outside of the text area in LT. I’m looking for some kind of “data portability” (nice article:

Even the sync between LT on the iPad and LT on my Mac doesn’t work (and I rarely use LT on the Mac).

For example I often get papers where parts were rotated 90° - this is no problem in DT, but nothing you could solve in LT - so I have to switch back to DT and do the rest of my annotation work there. Not what I intended to do but no option to stay in LT.

I use LT (and DT/DTTG currently) to add annotations. I use Papers (or Zotero) to extracted them from the PDF and move them into Scrivener.

By the way: I do store all my files on a cloud server so iPad and Mac can access the files.

LT promises to save the annotations back to the original PDF but this feature doesn’t work in reality.

@Silva thanks!

P.S.: LiquidText (LT) has an “Auto-Send” feature → “automatically send annotations on your PDFs back to their source files”. This would help but doesn’t work reliable. Seems that the link between the external file and the LT internal representation gets lost and I found no way to edit the connection again.
DevonThink also has some sync problems with the index files. I have to refresh the folder manually most of the time on my Mac to see the current list of files. And it always takes some time until DTTG reflects the changes visible in DT

Reading between the lines in your comments, I might believe that your first problems are that

  • LiquidText is unreliable at syncing with itself between platforms (iOS and macOS)
  • LiquidText is unreliable at sharing out annotations to other apps or importing in annotations from other apps (sidebar: my experience many years ago was that LiquidText would not respect annotations from PDFExpert and would not export annotations except in flattened form)

The issues you have to connect LiquidText to DevonThink could be related to the second problem above. Also, from my experiences, all PDF annotation apps are still working out how best to be able to sync PDF annotations among themselves. Some apps are openly pro-active about doing this (e.g. DevonThink and Bookends), some appear to be interested in fixing any problems but are quiet about their plans to do so (PDFExpert), and some apps seem to leave you to figure out the problems on your own (Highlights and perhaps LiquidText).

To cap off your post, I suggest that your frustrations have two parts … You expect all these apps to work perfectly with each other – and they do not – and you jump between apps to annotate – because one or the other in this set of apps fails to handle the annotations in a way that you want/need. You cannot control the first problem. You could try to fix the second problem by limiting your wants/needs down to one app for doing annotations, with the hope that sharing out those annotations to all other apps works in the ways that you want/need.

The issues with syncing between DevonThink macOS and DevonThink To Go iOS might be worthy of a separate thread if one has not already been started.



Thats interesting you are using LiquidText in your workflow - I have sent my protests to them, as the file is “captive” and not accessible to the operating system directly.

I did a lot of beta testing for them, and have taken the application to the limit. But then I found I couldn’t use those features practically with projects. Inside relevant folders on my choosing. It’s a shame, because its a really good application… (bit of a ferrari in a garage, but without a garage door key…)

I simply would like to edit LT file and save in iCloud - but that’s IMPOSSIBLE.

Why do they do this? My opinion is that they are building in a handicap ready to offer a PAID syncing service between devices. If true, this seems totally unethical to me — to remove base level functionality like saving a file.., only to offer a paid workaround.

My replacement for LT (and mind maps) is DT…

(1) LT can get a bit slow - and require lots of mousing, meandering, scrolling, clicking … to get relevant info---- Whereas a search on DT gets me to that doc nexus faster. Along with associated doc context.
(2) LT has a huge number of visuals - at some point this distracts the thinking process. I’ve seen this effect with larger maps. If you see too much of the background, it distracts------DT is not visually distracting. I use the magnification on the Mac (hold down control and slide forward with two fingers on trackpad), which is the equivalent of concentrating.
(3) LT will not work conveniently with other applications - eg I once tried to drop an LT file within DT, but I knew I couldn’t use it ( I think this illogical action was my subconscious, wishing for this option…) For those not aware of the problem, this is what happens. The file opens up, and it generates a copy within the LT space (not accessible to the OS, and further duplicating content it already has). If you update anything, it stays inside LT. You can export, but after all the steps and fiddle, was this all worth it to save a file. My conclusion. No----- So far DT works with everything else in its environment- that’s important!
(4) LT does update the pdfs, but this is buggy. And messy. I can’t really rely on it ---- DT, I can, so far :slight_smile:

Conclusion - Remove LT… until they unlock it to the OS. It’s more problems than it is worth at the moment.

With respect to references I use “Bookends” and Google Scholar.

My workflow thoughts?

Use Macbook, iPad, DT 3, Bookends, Google Scholar, Ulysses