reading/highlighting/annotating on iPad

I use Scrivener’s import and documents/convert functions all the time to turn webpages, PDFs, Word docs, and other documents in diverse formats into text I can read, highlight, and annotate. How can I read, highlight, and annotate such diverse file types on my iPad and open them in Scrivener with highlighting and annotation? – another Scrivener lover.


I use iBooks for annotating ePub files, and GoodReader for PDF files (I could also use PDF Expert or iAnnotate for this).

When done, I mail all the highlights/notes to my address as a message/text file, and copy the annotated PDF files back to my Mac (they can be read by both Apple Preview and Adobe Reader, so they should also be accesible from Scrivener).


Hi Paulo,
I have the same question. Thank you for sharing your workflow, but it sort of seems like a lot.

Is there an easier way to work with the PDFs that are stored within my Scrivener projects? I use PDF Expert, regularly. Can these two talk to each other? Or can I access the PDFs in my project from PDF Expert?


I’m not entirely sure how PDF Expert works to download, annotate, and then upload the file. This suggestion depends on being able to overwrite the file at the original location rather than needing to upload a separate copy after annotating. My understanding from what I’ve read is that you can just sync Dropbox items with PDF Expert, so I think this will work fine, but you’ll be in a better place to judge! :slight_smile:

Rather than importing the PDFs into your Scrivener projects, just keep them somewhere they’ll be accessible from PDF Reader and your project both, e.g. a Dropbox folder, and use the project references or Import as Alias to link to the PDF from Scrivener. Then you can make whatever edits to the PDF file you want via external apps, and as long as you overwrite the original with your saves, you’ll see them all when you open the PDF from Scrivener.

MM - you are my answer queen!

I am in the middle of organizing, then I will give this a try.

I do wonder, though, once I import to Scrivener, don’t my PDFs just stay static? I guess maybe I could use a better explanation of that process.

I have all of my research PDFs in Scrivener. I import them from my Dropbox. I use the same folder to sync my PDF expert, but I have never seen an update in my Scrivener research. In PDF expert, I do need to save my “annotated copy” which does not override the original PDF. Is that why it does not show up? The Dropbox folder where both items are is being watched by Scrivener.

Thank you for your patience and lightening fast responses. I love Scrivener and recommend it to all of my PhD friends. If it held hands with Mendeley I would be in heaven!!

There are basically two methods for accessing research in Scrivener: import it or link to it. If you import (using File > Import > Files… or dragging into the binder), a copy of the document is saved in the Scrivener project. At that point then it is disassociated from the original, which still exists in the original location on your drive. Thus it sounds like now, you’ve imported PDFs from Dropbox so you have a copy of them in the project and then are updating the originals via PDF Expert; the changes aren’t affecting the copy in Scrivener, since it’s not connected in any way to the originas still in Dropbox. You can choose from within Scrivener to open a PDF in an external app, so you can make edits to it using another program on your computer and save those changes to they update the file within the Scrivener project, but this isn’t going to help out with the iOS case.

The other method is to just link to the research file from Scrivener. For PDFs, this still allows you to view the linked file in Scrivener’s editor, but it keeps the file outside of the project package–you can store it wherever you want and easily access it from other programs without having to go through Scrivener. Typically you’d just add links to the Project (or Document) References in the inspector, but the Import > Research Files as Aliases… option will let you essentially put the link straight in the binder, so the PDF appears as its own document in the binder list and acts in general just like an imported item–exception being of course that it is just an alias pointing at the external file, so if you move or delete the original file, it will no longer appear in Scrivener, either.

Which method is better depends on your needs–if you move the project a lot from one machine to another, importing your research will ensure that it travels with the project and remains accessible. If you have a ton of large files you need to reference, storing them outside of the project and linking will keep the project itself more lightweight (meaning faster and smaller backups). And of course you can do either in any project, so there’s plenty of flexibility.

In your case, to access the research files directly from PDF Expert, linking to them or importing them as an alias in Scrivener should let you edit the files on Dropbox and then see the changes in Scrivener next time you open the project. The key here is that you need to ensure the file path for the PDF remains the same, hence the need to overwrite the original–if you have Scrivener linked to FileA.pdf and then edit that on PDF Expert and save a new copy, FileA1.pdf, Scrivener is still looking at the original and won’t see any of your edited work. If you can’t sync the changes in place via PDF Expert, you may need to do a little more finagling after editing to replace the originals with the edited versions, e.g. delete ~\Dropbox\FileA and then rename ~\Dropbox\FileA1 to become ~\Dropbox\FileA.


I’m still organizing my workflow, so please consider this as just my personal habit, not a general suggestion for everybody.

What I do is keeping a safety copy of the original PDF, and moving a copy of it (maybe with a slightly different name, for example with the “(annotated)” suffix) to Dropbox.

When syncronizing with Dropbox, GoodReader dowloads this (annotated) PDF file to the iPad. I work on it, then synchronize again, and the (annotated) PDF is again at my Mac.

From there, I move the (annotated) PDF file to either Scrivener or DevonThink. I usually prefer this latter, because the annotated file becomes part of my general archive of research materials.

From GoodReader I also mail myself the extracted annotations and highlights, that go into my Scrivener project (and in DevonThink, next to the annotated referring PDF file).

I guess this workflow can also happen with PDF Expert, but I have never tried.


I’ve never used PDF Expert, so can’t comment on it. However, I do use GoodReader (as mentioned by Paolo) and it is possible to automate almost the entire sync process.

First, I use Cubby: GoodReader can sync with WedDav folders and Cubby folders use WebDav (sounds complicated but, in essence, all it really means is a cloud folder is given an internet address). This means that any changes made in GoodReader can be synced back to the Cubby folder by pressing the “sync” button in GoodReader. This is the only manual part of the process, once it is out of GoodReader, everything else is automated. On your Mac you can, as MimeticMouton suggested, link to the original file from within Scrivener instead of importing it. This then means that all the annotations made in GoodReader will show up in Scrivener.

I believe that GoodReader can also sync with DropBox, so you could set that up to achieve a similar result. The benefit of Cubby is that, unlike DropBox, any folder on your hard-drive can be made into a “cubby” and that folder will be synced online. So, for example, I have personal folders, work folders, study folders, teaching folders, reading folders, etc, all synced via Cubby, but all in their original locations on my computer. Makes it much easier to keep track of things and keep everything neatly organised.

I’m having an issue here in that when I create an alias to a PDF in Dropbox, then edit that PDF on my iPad, the link from Scrivener goes to the original but now deleted version in Dropbox (they’re hidden, but they are there) rather than to the newer updated version, even though the latter has the original file name.

Does anyone have any idea how that might be overcome? I’m not sure why Scrivener’s alias would follow the deleted file’s name change.

Hope that makes sense!

Seems this one has dropped into the too hard basket?

Technical question then: are the alias created inside Scrivener (when importing as aliases) actually aliases in the system sense as opposed to symbolic links? Perhaps this is where the problem lies, as the alias points to the original file, rather than the file name and location. So even when the file name changes at the Dropbox end (i.e. it adds its deleted file string), the alias persists with pointing to that file, not the new annotated version?

That may well be the issue. The files inside Scrivener are the same as Finder aliases, so they work in exactly the same way - you would need to modify the original file rather than replace it, I believe.

All the best,

So the answer is to use a less sophisticated service than Dropbox.

I just created a account – works much the same as Dropbox but the free account doesn’t save versions. I put my research files in a folder within the Box syncing folder on my Mac and add them to Scrivener as aliases. I access the documents on the iPad via iAnnotate (which can access Annotations made on the iPad, once synced back from iAnnotate, are then reflected in the version which is visible in Scrivener.

Problem solved!