Sonny Software

I have a large PDF, which is a book with about 400 pages and takes about 280 MB. It is generated by photo-scanning the paper version.

Now, when I put some annotations in the PDF and click anywhere in the reference list pane (the top middle pane), Bookends hangs.

I suspect this happens because Bookends tries to save the PDF with the annotations. I think clicking outside the PDF view pane signals the intention to exit the current PDF, so Bookends tries to save the changes made in the PDF so far. However, saving a large file takes time, so the program hangs.

I am trying to migrate from Sente, where I did not have this problem. Sente, like Skim, stores annotations as a separate metadata file, so annotating does not change the PDF itself. Storing annotations as a separate metadata file outside the PDF is also very convenient when I want to send the PDF to collaborators. I tend to put lots of annotations in papers and books that I read, but when I send those papers and books to collaborators I want to send clean PDFs without annotations that contain my thoughts. (In case I want to share my annotations with collaborators, Sente and Skim also allow us to embed the annotations in PDFs, like Bookends does by default.)

Is there a possibility to fix this issue? This almost prevents me from using Bookends as an alternative of Sente, but I need to leave Sente finally because it does not work properly in the newest macOS Mojave.

When you say Bookends "hangs", what do you mean? Is it unresponsive for 5-10 seconds while the PDF is saved (expected), or do you need to force-quit to regain control?

Saving annotation in the PDF itself is far better than in the database, IMO, for many reasons. One is that the annotations are now part of the "record", and can be seen in any other PDFKit-compatible PDF reader (which is pretty much all of them). Another, perhaps the most important, is portability. That is, if you decided to stop using Bookends for whatever reason your annotations would be lost. Just look at Sente for an example (or Papers, for that matter) -- embedding the annotations is clumsy at best, requiring an export and, AFAICT, working one PDF at a time. I consider saving annotations with the PDF as a major advantage.

As for sharing PDFs without the annotations, Bookends lets you strip them out when emailing (Preferences -> Internet tab -> E-mailing PDFs -> Remove annotations when sending), or when exporting (the PDF Action menu -> Export PDF -> With/without annotations).

Jon
Sonny Software