C-Command Software Forum

Skim search

Hi Michael,

I am trying out Eagle and so far love it. (Coming from DevonThink camp.) I really love that EF supports Skim and searches Skim annotations. But I found that EF does not highlight search results in Skim notes files, the way it does for PDF files. Is this something that could be added to EF, and would you consider adding it?

Currently, if I have to zone in on where my search term appears in Skim notes, I do this: (1) search in EF, (2) open the PDF in Skim, (3) go to notes panel, and (4) search again.

If EF can highlight the searched term in Skim notes, then I would just have to do: (1) search in EF (2) look highlighted search result in Skim notes in EF’s file view.


Currently, EagleFiler does search the Skim notes, i.e. it will find PDF files that contain your search query in the annotations even if it doesn’t appear in the text of the PDF itself. However, you are right that the viewer doesn’t highlight the matching annotations. It’s definitely a feature I’d like to add. I haven’t yet looked into this enough to know whether it’s feasible.

My understanding is that Skim itself doesn’t highlight the matching text inside of annotations, or even show them in the list of hits when searching a PDF. It has a totally separate interface for listing and searching the annotations. Do you like having the annotations stuff separate?

Thanks for the quick response!

So I tested the notes search in Skim. You are correct, when searching the PDF Skim does not search in the notes. To search the notes from the PDF you need to search in the Notes search panel and Skim will show notes with the search term but will not show notes details or highlight searched term.

But when I open a Skim Notes file (not the PDF) through EagleFiler it opens only the notes and there is a search field. The search results show the notes with the searched term but will not highlight any notes. Also the Skim Notes file appears to be stored not as plaintext, so highlighting the search outside the Skim interface might be tricky.

Given that the Skim notes viewer has a search field, would it be possible to pass on the search term when opening Skim notes, just like EageFiler currently passes on search term to opened Skim PDF? This way I can pinpoint to an annotation with my search term by first searching in EagleFiler and then just opening the Skim notes. (I saw a thread where some people did not want the functionality of passing search term to PDF. I actually think this feature is great and very thoughtful. I like it and it works well with my workflow. So, thanks for adding that!)

Oh wait, the way EagleFiler opens Skim notes from search results what I just suggested above would not work. This is actually a little confusing behavior. So I have a PDF and an attached Skim notes file. In the file viewer, EagleFiler shows both the Skim notes file and the pdf. When I open the Skim notes file, EagleFiler opens just the notes (not the pdf) with Skim viewer. But when I open the same Skim notes file when it appears in a search result, EagleFiler will open the associated PDF instead of opening the notes file. Is this the intended functionality? I am happy to share more details about this to reproduce this.

If you are referring to a .skim file, that’s a custom file format. EagleFiler displays it using the Quick Look plug-in provided by Skim, which is why it doesn’t support highlighting. It’s possible that in the future EagleFiler could provide its own viewer for .skim files and then it would be able to implement highlighting.

Yes, what’s happening here is that EagleFiler tells Skim to open the .skim file. But Skim is written to interpret that as opening the adjacent PDF file.

Another option, depending on what you’re trying to do, is to use the PDF Bundle format in Skim. Then the PDF and notes will be kept together and treated as a single unit.

I see. Thanks for the clarification. I would greatly appreciate the search highlighting feature in .skim.

A little bit about my workflow (in case it’s useful): I use pdf annotates a lot and write comments with annotations. In my workflow often the thing I want to search is in my annotation comments, which don’t appear PDF. So these can’t be searched with most PDF viewers. Skim lets me search in annotations. I like that EagleFiler does search in the annotations, which makes things a lot easy for me already. But to quickly zone in on the exact search results/annotation, it takes another 2 operations. So the highlighting results in .skim would save that effort.

Understood, thanks.