Papers 3: still disappointing

I was very optimistic about the most recent build of Papers 3. The company announced some change in file management (which I could not quite understand but decided that any change would be for the better). I have also found a way to search within the Papers3 package file (another post coming). So I finally decided to give it a full try by importing my Papers2 library and starting to write with help of Papers3. So far I am sorry to report significant disappointment and regret. The version is still too buggy. In particular, it consistently fails to rename files in accordance with the publication’s data and it also fails to display correct titles of publications in the list. In addition I spent some 30 minutes trying to add eight authors to a book chapter (the app kept erasing all data). Frustrating.


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About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He also coordinates MESPOM, a Masters course operated by six Universities.
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61 Responses to Papers 3: still disappointing

  1. Chan Cheah says:

    Completely agree. It has continually crashed, and for some inexplicable reason the scrolling of PDFs is choppy. I expect this from Acrobat, but disappointed to see it in a native Mac OS application!


    • Aariq says:

      Sometimes really choppy PDFs can be fixed by opening them in preview, saving them as a new file, and then re-importing to Papers. This usually happens when PDFs have very large file sizes and doing this opening and saving seems to shrink the file size considerably for some reason.


  2. Sotirios says:

    I have the same problem with my copy of papers, in addition, when I copy my library from one computer to another, some “metadatas” change back to the original incorrect values. It is frustrating, but I have reported the bugs to the developers!


  3. Ben says:

    Adding authors in Papers 3 is annoying, as there seems to be no way to do this without clicking the checkboxes (checkcircles?) that appear. When I’m already typing, I would be so much quicker to just hit Enter to select the topmost author in the list, or Tab down to the author I want.


  4. M says:

    Aleh, thanks for this post and reinforcing my saddening opinion about Papers 3. I am still with Papers 2, and I think that I will completely move on from Papers.
    I fail to understand what’s going on with the guys from Mekentosj. The fail with Papers 3 is not their only problem, but also their customer support. Four years ago I contacted their support, and got a very nice reply. Two years ago they replied with a generic reply in such a way that it was obvious that they haven’t even read my email. Two months ago, after reporting a serious bug that messed up my library, I have not even received a reply. The deterioration is obvious, and this is the first time in five years that I am thinking about finding an alternative. Papers 3 just made me feel they are on the wrong path: they are trying to sell a buggy software with no new major features (except a facelift), and presenting features available Papers 2 as new features is really insulting (just check their youtube video).

    Liked by 1 person

  5. Joe says:

    I installed the demo to see how I liked it and to be honest I don’t even like the interface changes. There is so much space used by padding, that on a 13″ MacBook you get much less information on the screen at once than Papers2. All the horror stories about stability scare me a lot too. I think a lot of development companies got a little obsessed by iOS development and ‘the cloud’ and have started ruining their programs just to follow this trend. I still find Papers2 perfect for my needs but I’d be really interested to hear about alternatives if you investigate any.


  6. J says:

    I, too, am disappointed in Papers 3. I admit this very reluctantly, because I find the iPad syncing immensely useful, and I still think the search and collections interface is done better than anywhere else. However, I simply no longer trust it to reliably perform basic functionality when I need it the most. It’s sad because I think they really have contributed to the overall betterment of citation management interfaces. But without a core of stability and reliability, everything else is moot. (And I recognize this is difficult to do- very few of the citation managers I’ve tried have felt “solid” to me).

    Reluctant as I am to waste time reorganizing my library, I would be very interested if any commenters here are happy with alternative solutions. It may be time for me to go back to basics for a few years.


  7. Dellu says:

    I am glad I stick with Sente. Its ipad app has been extremely elegant and the desktop version is also getting good updates…never crashed on my mac. The Magic Manuscript feature of Papers was seducing me a lot.


  8. Joe says:

    I’m still flabbergasted that Papers3 is a paid upgrade rather than an internal alpha/concept. I tried out the demo of Papers3 and in my opinion even the interface changes are bad. There’s too much padding and so on my 13″ MacBook screen I get a lot less information on the screen than in Papers2. Then with all the stability issues and the lack of easy access to the files, it’s a real mess. I think many developers currently are too obsessed by iOS style design and adding ‘cloud’ capabilities, to the detriment of their desktop programs. I for one, will not be paying for this ‘upgrade’ and I hope Mekentosj will wake up and design the desktop software they are certainly capable of.


  9. I switched to Sente after frustrations with papers 3. Sente has a vastly superior annotation system and I love Rob Trew’s script for exporting quotes and comments to devonthink. Also, you have the option of keeping your pdfs in a folder, rather than a bundle, with renaming options similar to what we had in papers 2. Dellu, I have found the posts on your blog (and others) helpful for getting my Sente workflow figured out – so thank you for those. One of these days I will put together a post about my workflow, as everyone ends up with something slightly different. Anyway, for those who feel lost in the wake of the papers 3 debacle, I would highly recommend looking into moving your libraries to Sente. Both the mac and and ipad versions are free up 250 mb or 100 references, so it’s worth looking into. Premium pricing is very reasonable, especially with the academic discount.


    • Paul says:

      Can Chris or someone elaborate on this: “you have the option of keeping your pdfs in a folder, rather than a bundle, with renaming options similar to what we had in papers 2″? Maybe the previous version could do this, but It looks to me that Sente’s new version does not allow one to (say) have the PDFs stored in a Dropbox folder. That’s what many of us started doing in Papers2, and it’s a prerequisite for me.


  10. Pingback: Papers 3: still disappointing » Thomas Carrington

  11. John Sullivan says:

    I’m an academic who uses a Mac, so I really like this blog and all of the great tips. Usually I just pick up tips, but here I might be able to pass one along. Folks who are disappointed with Papers 3 might investigate using Zotero for bibliographic citation management. It’s free, open source, and a great tool that integrates into most word processors (but, sadly, not Pages, though it can work with Scrivener with a workaround). The iPad app Papership connects to your Zotero database and has PDF annotation tools as well, similar to Sente. If you’re a Papers 3 refugee and you don’t mind using MS Word or Libreoffice as your word processor of choice, you could do a lot worse than Zotero and Papership for iPad.

    Liked by 1 person

  12. Aleh,
    You are a great voice for all frustaded users of papers3 users..

    They’re completely out of the normal curve of costumer support software. I’ve been following all their staff on twitter since November and it seems the company is out of control. Their CEO haven’t post a single word since the problems were shown at papers3.
    Their papersgenius in twitter seems to be trying to solve unsolvable problems alone. Their CFO, Mathias, seems to be involved in several other projects and Springer doesn’t seem to give a s*** for them. They also seem to be having serious difficulties hiring new personal too (marketing, c’mon… Hire new developers).
    In fact I have the impression that everyone abandoned the ship and there are some single passengers doing damage control, after realizing that this “from the ground up” rewrite was a terrible mistake. When compared with something like omni group and Ken Case, I feel (as a long time and loyal user) as a lonely survival on a sunk ship, without a captain!

    In fact, I think their business is compromised. Read iTunes reviews. They had more than 2k for the original papers app (with an overall good rating), and less than 150 reviews for the 3 version (mostly 1-2 stars, with terrible reviews). Their hole “social buzz” is terrible and irrelevant. Facebook page is nonsense. Twitter is as painful as a “Rocky” movie. Google + is empty.

    As a loyal user, I hoped, believed and insisted that they could fix this broken version. It is sad for long time users to recognize and accept that a wonderful app, that a lot of us have even emotional relationships with, is sinking. Most loyal users have invested their time and effort to build a complete and organized database. But in more then 5 months, they couldn’t manage to release a reliable version. This version is so compromised, that even basic functions, like opening a PDF emailed to you in an iPad is not possible (or at least is painful). Highlighting is as slow. Syncing is slow and painful. Magic citations got me in trouble at deadlines. Copying citekeys from iOS app is impossible. Trying to match a PDF is hard and time consuming. And the number of repeating crashes is brutal.
    I really tried a lot to use the app. I’m trying to use it since beta. But not being reliable is not an option for a science app. Not having a trusted costumer service is even worse…

    C’mon… We are at 2014…
    Nobody deserves another windows vista/sony vaio terrible experience. Apps like drafts, editorial, folding text, scrivener, slack, devinthink, textexpander, google drive and many more are a reality for academics! They just work! Even office for iPad is not so buggy!

    I’m abandoning this ship for now, with a broken heart.
    I really won’t wait for a version 4 paid release, written “from the ground up” to fix all their self created bugs.
    Good luck for all users, but for now, I will invest my time in another ship, with a real and leading captain.

    Ps: I really hate when a wonderful app is rewritten “from the ground up”. Why!?!? Do you need my money? Charge me for a working and reliable version and I won’t hesitate to give you my money!


  13. Me_too says:

    My theory: the “tosj” part of mek-en-tosj was actually crucial for the success of version 1, but sadly as of v2 “mek” is by himself. Even before the current situation, v2 failed to add much value to the app, and the main strengths that set it apart from other options (even today) are those that were inherited from v1… (in my view; I have no inside info on any of this, but find it hard to believe that the brain(s) behind v1 are the same that created the “innovation” of v2 or v3)


  14. sab says:

    As others here, I have been dissatisfied with Papers 3. My library is now around 10K refs, including 3k pdfs. Of the alternatives I’ve tried recently, BibTeX (too much work), Sente (didn’t sync my pdf annotations with other apps, no detection of duplicates), Mendeley (doesn’t scan the document file types I use, Pages, plain text, Emacs org mode…), the one the stands out for features, customer support and practicality is Bookends. If there is a feature you want, the developer will probably add it or give you a reason why he won’t, or more likely, point out it is already available, and often do so within minutes of you asking.
    Bookends has consistently impressed me, so do give it a try.


  15. Pingback: Thinking about Switching from Papers 2 to Sente | ORGANIZING CREATIVITY

  16. rickla says:

    I felt from the very beginning that Papers had a bit of a form-over-function problem. But a few of the slick features were so incredibly impressive that with both versions 2 and 3 I paid for an upgrade and tried the app out for a while. Fortunately, for the last few years I’ve committed myself to Sente, and the annotation, sync, and sharing features are wonderful. I do very occasionally take a quick look at other options, and dab’s comments on Bookends are spot-on. And, as John Sullivan says, Zotero is also impressive. (Thanks for telling us about PaperShip, by the way.)

    One thing I find puzzling is the mindshare that Papers has. Whenever I hear an academic talk about a reference manager on a Mac-centric podcast, it nearly always seems to be Papers that they use. I guess not everyone is having the same experience we are.


  17. Martin says:

    The development and release of Papers 3 seems to be an object lesson in how *not* to go about things. A sensible flow might be: first, develop — second, fix bugs — third, release a beta of the software to a few people, etc … One gets the impression that they have done things backwards, or something like it. It is a shame — I like Papers 2, although it is not perfect. But this disaster makes me think that I had better find an alternative, because Papers 2 will eventually stop working, and it might be better to have another program integrated into my workflow before that happens.

    I’m tempted by Mendeley, but I haven’t yet tried it out properly. There is an app for iPhone which is good for me.

    Bookends is bullet-proof, and has been for years. It has a lot of tools for tweaking its database and so forth, but it is far and away the ugliest duckling of them all. Also, the tools for finding and downloading references are not particularly slick, in my view. On the plus side, support is exemplary. In my experience, it does the job, and does it well, and has some tools that others just don’t have. But it just takes longer to do certain things because the interface lacks thought and polish. For those who use Tinderbox, it is the only program that integrates with it seamlessly.

    Sente is quite pretty, but I feel it is a little flaky, and the support is not ideal if you run into problems. The ios app is iPad only, and I don’t have one — so that is a minus for me. There are good scripts for integrating with Devonthink, which is a plus. Synchronisation with the cloud now seems to be good — though it is not much use to me as I’m limited to an iPhone.

    At the moment I’m slightly tempted to use Sente for finding and downloading references, and then exporting them to Bookends to do the rest, but that is hardly ideal. It’s bizarre that such a basic tool for academic work as a bibliographic database should be so difficult to find. But I suppose I shouldn’t be surprised.


  18. Alain says:

    I must confess that I had been impressed by the videos describing the new Papers 3. I went out and bought both the desktop and the iPad versions at once, without too much googling around.

    Now, what a mistake that was. I agree with all negative comments here. I have experienced all of them and many others. My own bug list has well over 25 entries (since last Friday). Papers 3 is a disaster. Following their Twitter it’s clear there isn’t a bug-fix version in the works, or else surely they would be mentioning it.

    I have just installed Sente. It proved to be a much superior product within minutes.


  19. fred says:

    To be fair: for my own work-flow Papers still seems to be the best approach, and I don’t see it as a “form-over-function” issue. I guess it depends on the function you’re looking for. I never was looking to replace endnote (or Procite etc). For my use, it instead complements Endnote, and rather replaces a reliance on hardcopy articles organized in paper folders, or PDF versions in digital folders. Thus, the key features are: viewing and reading the PDF, being able to rapidly search them (full text), and organizing into folders (or with keywords) in a fast, reliable and flexible way. This was the heart of Papers v1 and fortunately persists to this day (despite an apparent prioritization of the developers for all sorts of other features). In the end, I don’t really use (or need) the “new” features of v2 and v3: citations, highlighting/annotations, Livfe, twitter, facebook, etc. I don’t even use the (improved?) Papers built-in literature search anymore, going back to basics with a Safari-based search approach (along with a bookmarklet), made fast(er) by use of customized Alfred’s searches.


    • Paul says:

      My view is similar to Fred’s in most respects. Since abandoning Papers and not yet being sold on any of the alternatives (Sente, Mendeley, etc.), I am gradually discovering that the Finder in Mavericks does much of what I need very nicely. I have my PDFs in a folder (shared with other devices and students via OwnCloud), search them with Spotlight, and view the results as Cover Flow. With LaunchBar in the mix, I can do essentially everything from the keyboard (e.g., open a PDF in Skim for reading and note taking). A custom search that is saved will give updated results as the PDF archive grows, etc. I am sure there are lots of tricks that could make this an even more powerful workflow. For example, how to get the most value out of Mavericks “Tags”?


      • fred says:

        One big issue with this approach for me is that I rely on the ability to organize individual PDFs into multiple collections (folders), and I don’t think that using aliases (etc) is a viable/convenient way to handle it.


  20. Hamish says:

    If you’re looking for full text document and citation management, you might also want to consider Flow ( It’s free, with 2GB of space and up to ten collaborators. I switched from Zotero in February after getting fed up with paying for storage, and now I’m nearly done with my thesis and glad I moved. There’s a Word plug-in already and I hear there are more on the way (the word is they develop agile, so they’re pretty responsive to feedback from users). Just another one to consider for Mac users…


  21. Paul says:

    I have been wondering about a general issue regarding PDF format that has great bearing on this topic: shouldn’t there be a convention that allows saving tagged-field bibliographic data within the PDF file?

    I am pretty sure something like this is available for cataloging images in photography. I have been using (what is now) Phase One’s Media Pro, and it has long had a function for saving “personal information such as annotations, catalog sets, and custom fields to original files”. My understand is that this info then becomes part of the image file’s metadata and therefore accessible to other applications. There’s even an option to make updating metadata embedding automatic.

    If we could do this with bibliographic data and PDFs, it would open up all sorts of possibilities for sharing or switching between reference management applications.


    • fred says:

      I am not sure about citation and other metadata, but I do make good use of the ability to store annotations within the PDF (rather than having Papers-specific notations). (i.e. even from within Papers I tend to open the PDF in Preview to apply highlighting and comments)


    • rickla says:

      I have a more general question regarding metadata in OS X. When looking through the search options in Spotlight, it’s clear that there’s a wealth of metadata available to the system. But the names of the search options rarely give a clue as to what metadata they’re referring to in which application, nor as to where you’re supposed to enter those metadata in the first place. Alex, it would be great if sometime you could tackle this subject in a new post. (Apologies if you already have, and I just haven’t noticed.)


  22. morrifeldman says:

    I’m also very disappointed in papers 3, after happily using papers 1 and 2. I’d like to revert back to papers 1 or 2, but unfortunately I’ve added many important references in my papers 3 library. Does anyone have advice for converting a papers 3 library back to papers 1 or 2?


  23. zooop says:

    When I did this, I selected the “new” references from Papers 3 and exported them to a Bibtex file.
    Then I used my old database in Pap2 and imported the bibtex file. Anyway, you have to be careful about the files you export with Pap3, because the application can corrupt some of the metadata.
    That’s why I re”matched” (and if necessary reedited) each of the reimported refs.
    It took me some hours but finally it is in a state I can work with again.


    • fred says:

      I did not do this with the v3 but previously I had the best luck between v2 and v1 using endnote xml export/import to do the above. (although I maybe did not try bibtx)


  24. After all I’ve read, I haven’t even tried to look at Papers 3. Im still sticking to Papers 2 until it breaks. Has anyone tried ReadCube?


    • jsay says:

      ReadCube is a very nice but miniature program. No (basic!) organization features make it unusable for now. But unlike Papers, its advanced features are promising and compelling. My eye is on it and I may switch to it when it is out of beta.


    • Koenraad says:

      If you have anything like a professional library (a few thousand records), ReadCube is rather useless. It spent DAYS trying to match my 5000-paper library (over a high-speed connection). It is very slow/unresponsive and has very few features. Anyone who needs referencing software on a daily basis will be disappointed by this app.


  25. Danny says:

    Reblogged this on Daniel Rod and commented:
    Really enjoy Professor Cherp’s blog on academic workflows on the mac. His article about Papers is correct. I’ve been using it for a while now and am on to looking at other alternatives. Readcube – when the new version is released – will be my first stop. This aside, read this blog for some great ideas!


  26. MK says:

    Is there someone who has experience with PaperShip for mac ?


  27. Steve Martin says:

    Great comments. I loved Notabene when I was in the Windows world, but their new 64 bit version (which boasted compatability with OSX through Wine) took too long to develop (and is currently in Beta 20). NB was terrific as a suite for researching, writing, and referencing specifically for academic writers. I miss it terribly, but love the Apple way too much to go back. My first foray into an alternative for referencing (Scrivener having captured my imagination for writing) was Papers 2. I thought it was a great piece of Software, and I bought both the Mac and the iOS version. When I heard about Papers 3 and saw the beautiful new interface I immediately upgraded everything, only to learn that the upgrade for Mac was a buggy beta and the iOS upgrade just crashed continually. Much of its hype seemed to be about integrating into social media, which doesn’t interest me. I kept working with it and adding to its database, and now have gone too far to go back to Papers 2. In frustration I bought Bookends, which not only reminds me of Ibidem (NB’s reference manager) but it has imported my Ibidem database (so far) without any problems. It’s not pretty. But it works (and the developer is as responsive as Steve Siebert and the NB team were. I’ll never go for form over function again.


  28. Patrick Wanner says:

    I am looking for an alternative to Papers and was wondering if anyone here is familiar with ReadCube? It seems to have quite nice functionality, however it has ties to the publishing industry (not unlike Papers or Mendeley I suppose), which can be both positive and negative. Where do you see the future of academic paper software going and which path would keep one’s options most open? Thank you!


  29. Pingback: Trying Sente instead of Papers. Two annoying setbacks. | Academic workflows on a Mac

  30. Malcolm says:

    I’m really frustrated with Papers, and I’ve been using it since 2011 with Papers “1”. I actually didn’t mind too much the changes in appearance, and I liked the dropbox integration. However, recently (using 3.0.24), I’ve been having frequent crashes and problems; sometimes the program even forgets my license. Today, I’m stuck with all my collections missing (yet the papers themselves still say they are part of those non-existent collections…), this at a time when I really need to use Papers for a writing two proposals. I’m forced to use “colors” to tag my papers since I don’t know when the next crash will occur.


    • Patrick Wanner says:

      I actually just recently had something similar happen to me – all my references lost the links to their respective PDFs and all collections disappeared. Data corruption in a reference management program is a no-go for me. I’ve switched my critical stuff over to Sente and will be migrating the rest in the weeks to come. So far the functionality and stability have been excellent. I do however miss Paper’s Magic Citations, but am otherwise not looking back.


      • MCO says:

        I have had the very same problem with the lost collections. I have also reported several Bugs to the Papers developers but despite having spent money on the iPad and Mac version I guess I am moving on now. It is just impossible to work with such a buggy software. Finding a reference manager that works seamlessly across Mac, Windows and iOS is the challenge for me. I guess I am going to try out Mendeley although I am going to miss the awesome magic citation feature but in the end I night something that I can rely on…


      • zooop says:

        This reply actually goes to MCO:
        I got my money back for the iPad version. App Store support was helpful.
        For the Mac version: Well, I came upgrading from Pap1 and I still can use my Version 3 license with Version 2


  31. C20 says:

    Thanks for the update. I’m a doctoral student using papers 2 and I was contemplating whether the upgrade to papers 3 would be worth it – obviously not! I’m sticking with it until I finish my thesis!!


    • Stan says:

      Same here – just bought papers 2 academic license, writing thesis & will probably take aleh’s approach in folders=projects, reference=tags, with hazel workflow and tag my pdf’s. That way I can stay platform independent – hope it works ;)


  32. Les R. Becker says:

    I’m wondering if anyone has experienced the following on Papers3 on IPAD when syncing?

    1. Database download and merge proceed uneventfully;
    2. Database upload progresses to about 50% and then app closes.




  33. L. Yew says:

    Aleh, thanks for a couple of excellent blog entries on Papers 3. I’ve relied on them to decide on whether or not to move from Sente (after having moved from EndNote) as it wasn’t serving me very well. In the end I opted for Papers 3 because I liked the way it was allows me to streamline author name and publication title management.

    The only issue — and this is the reason why I’ve been changing my reference management software — is the eccentric way Papers does its DropBox synchronization. I’ve become a three device academic, working across my Mac Pro in my office, my MacBook while on the go, and on my iPad (usually for reading), so synchronization has become a must. The problem with other reference managers is that you need to rely on their servers for this task. Being located in Asia, I’ve found the process slow, probably because of the trans-Pacific network latency. So DropBox seemed like a great way to go. When a reference is updated on my desktop, it updates the library on my local DropBox account. The DropBox app then automatically syncs with the remote servers, which means the next time I turn on my laptop, the app on that machine should pull the updates across instantly. When I open Papers on the laptop, it should access the changed files on its library on the local DropBox folder.

    If only it could have been that simple. Apparently, the developers of Papers have added one layer of complexity. Papers doesn’t work directly with the library located on the DropBox folder. There is a separate Papers 3 library located in the “~/Library/Application Support/Papers 3″. When you start Papers 3, it loads from this library, and if you’ve told it to sync with DropBox automatically, it will do so eventually. This process just takes ages, even on my late 2013 Mac Pro! I’m not sure what the reasons the developers have for this but it just seems like an absolutely superfluous process when the whole point is just let the Dropbox app do the syncing than to repeat the process.


  34. Ben says:

    Have to say I agree. Having been using Papers since v1 and told all my friends to use it I am now in the position of trying to write up my PhD with software that is becoming worse with every minor “upgrade”. I wish I had stuck with Papers 2. I will never be recommending the software to anyone again.


    • fred says:

      My take on this is that indeed it is quite worrisome to see the priorities of the Papers team in recent years. Still, I can’t say that any of the alternatives are any better yet, at least for my way of working. My approach (and advice) is to indeed stick with v2 as long as possible. It is *now* overall better than v1 (after a pretty horrible start, that pretty much parallels the current launch of v3… so we know what to expect for v4, next year??).

      Note that at least with version 1 and 2, they did update and support version 1 for some time after release of version 2, such that it at least it worked on the newer versions of OS X. I don’t know if it works on Mavericks to be honest. Hopefully they will make sure that version 2 remains functional for the time being (even under OS X 10.10…)

      It does however seem sensible to try to avoid lock-in as much as possible, for a possible future where one would want to (or be need to) a different software package via export as BibTex or Endnote XML. The main non-portable features seems to be the builtin annotation feature – so I generally try to annotate the PDFs directly, which will be portable.


  35. candicedemo says:

    Will mendeley be a good replacement? I am a graduate student pursuing a Ph.D degree… So so confused after all the articles and posts online about all these literature tools.. I will really appreciate if you can give me some advice.


  36. Pingback: Papers 3: considerable improvements, but still beta | Academic workflows on a Mac

  37. dawnrazor says:

    I’m a long time Sente user, but I’ve been thinking of moving over to Papers, as I really like the less cluttered interface. I bought Papers 2 (before P3 came out) and exported a test library from Sente. First of all, the export was a pain in the b*tt, as most PDFs wouldn’t come along. Then, I used Papers 2 for a scientific article, but had to abandon ship mid-paper, as Papers kept messing up references. I thought P2 was in beta-mode, and was waiting for it to mature. Sadly, it seems to have gone the other way. So I’m sticking with Sente…


  38. I agree with all the comments above. Papers 3 is a total disaster. I have been using Mendeley however, it has its own problems – still ages behind what should be in a modern reference management software.
    I have started using paperpile app ( which lives in the cloud like GMAIL, however, at work I use a desktop and it works well. You have to use google docs but you can download the references in endnote to use. The best feature is when you are searching PubMed it tells you which papers you already have in your library. I would like an Desktop app/iOS app for it.
    The bottomline is that in 2014 we don’t have a cutting edge reference management software out there that can do all that we want. Such a shame.


  39. Paper is my favorite Reference Management Software. But, it takes 5 steps to move a paper to a more specific collection. For some reason (1) moving it via drag-and-drop unfiles it, (2) unchecking the parent collection (in the info panel) also removes the paper from all child collections, and (3) you can’t see which papers are in the general collection without going through each paper one-by-one.

    Unfortunately, Papers support said this is the “expected behavior.”

    Here’s a screencast of the problem:

    Are you all experiencing the same behavior? Am I the only one that incrementally files papers?


    • Aleh Cherp says:

      Thank you for sharing the video. I have not experienced this behavior because I don’t usually move by dragging. I use the right sidebar instead, click on the plus sign and choose the collection I want. This produces an accurate behavior. Moreover, if a paper belongs to a child collection it seems to show in the parent collection as well.


      • Hi Aleh,
        When looking at the sidebar, it is possible for a paper to be in “hand” and “thumb” or just “thumb.” However, if the paper is in both “hand” and “thumb,” and you use the sidebar to remove “hand,” then it will remove “thumb” also. The only way to get a paper that is filed in both to be filed only in “hand” is to un-file it completely, and then re-add it only to “thumb.”


    • Fred says:


      I think that part of what you see is indeed ‘intended behavior’, but that you’ve also highlighted some real bugs. E.g. the moving to a more specific (sub)folder issue that unfiles them altogether clearly is not by design (at ~0:35 in video), but I think there are one or two other bugs in the filing operations, in particular using the mouse.

      However, I also want to mention that some of the other behavior does reflect a real feature of papers, which is that by design all articles in a sub-folder are also part of the higher (parent) folder. To leverage this your collections should reflect a hierarchy where this makes sense. (i.e. papers on thumbs should also be papers about hands). I actually really like this feature and miss it in other programs. But it does result in some complexities that are not directly apparent. E.g. you are not allowed to have a paper only in the subfolder. What this means is that if you have papers on thumbs that are not in a “hand” context, then you should probably not be filing it in a sub-collection of “hand”.

      Nonetheless, I very much agree that this could/should be more transparent. (perhaps a KB article at the least?)

      Regarding the bugs: did you share this video with them? In my experience they sometimes glance at the report and then assume that you’re simply confused by the designed features. You may have to really spell it out to explain what is going wrong, and I would think that your video is pretty clear.


      • Hi Fred,
        I agree that it can be useful to see all “hand” papers (recursively).

        However, it is also useful to be able to see *only* “hand” papers. If I have one paper that is about biology in general, then even though I marked it as “biology in general,” there is no way to find it.

        I agree this was the intended behavior (so I filed it as a feature request), but I think the lack of option is a real usability problem. Imagine if the unix command “ls /” showed the millions of files on your computer, and there was no other way to find the handful of top level files!

        I filed the other ones (moving un-files, un-starring un-files) as bugs, but I believe they also said that is the intended behavior.


  40. Alex says:

    I’ve enjoyed using Papers for many years now and it has served me well. But Papers3 has been a thorn in my side. In Papers2, the PDFs were accessible in the file system and were indexed by Spotlight, so I didn’t have to be in Papers to access a file or to search for it. But now, Spotlight never sees my Papers3 database. I used to index in Devonthink too, but I’m not even going to try that anymore. And I’ve found that tagging PDFs stored in Papers2 with the Mavericks tags is a no-go as well. The only thing keeping me with Papers3 now is the magic manuscript feature. If somebody else can do that but not have the idiosyncracies of Papers, I’m sold.


    • Koenraad says:

      I have gone back to Papers 2. Your Papers 3 license is also valid for Papers 2, and Papers 2 can still be downloaded. But keep in mind that this will eventually stop working.


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