Using Hookmark with the Free Skim PDF Reader app: Deep Links!

Hookmark enables you to link PDF files to and from anything that is also linkable. Hookmark supports many PDF readers, including the excellent, free PDF reader Skim, available on

Hookmark treats PDFs similarly to other files, except you can create “deep links” that point to specific locations in a document.

Click on the link and Hookmark will open the PDF and scroll to the specific page and location to which it points!

Copy Link, Copy Markdown Link and Hook to Copied Link

By default, Hookmark’s Copy Link and Copy Markdown Link in Skim copies links of the form hook://file// which point to the entire PDF file. You can paste those links anywhere.

In addition, you can create deep links to specific locations in a PDF (i.e., a specific page number and place on that page.)

Creating Deep Links (to specific locations in a PDF file)

To create a deep PDF link, simply select some text and use Hookmark’s Copy Link. Hookmark will append the coordinates of the selection to the hook://file/ URL.

You can paste the link in:

  • Any document (for instance in Pages, Nisus Writer, or Microsoft Word); even in another PDF!
  • A “to-do” app (such as OmniFocus, Things or TaskPaper).
  • An email.
  • Any editable field (even Items in DEVONthink).
  • And just about anywhere else

Share deep links to PDFs with others!

Before Hookmark, there was no easy way to refer to shared PDFs in Dropbox or iCloud. Hookmark solves this problem. Use the Copy Link (or Copy Markdown Link) command on a PDF or a selection of a PDF, then paste the link into a document or email. Send it to anyone with access to the PDF: if they have Hookmark (even if they use its free Basic mode), the deep links will open at the exact location in the PDF.

That way, instead of manually scrolling to the location in a (potentially very long) PDF, all they need to do is click on the link.

Hookmark links to specific locations in PDF files that are shared with others will normally work as long as the recipient has Hookmark and Skim installed and a copy of the file that has the same unique name on the recipient’s Mac (if two files have the same name, Hookmark will try to disambiguate them based on their meta-information [not their content]).

Try it; you and your recipients will be amazed at the time (and communication) savings!

Default app for opening PDFs

In order to use Hookmark’s deep links to PDFs you currently need to ensure that the default app you have configured in macOS Finder to open “.pdf” files supports deep PDF links. See Choose an app to open a file on Mac.

Hookmark also supports deep PDF links with Curio using an alternative integration. In Curio, PDFs are not stand-alone files that you directly access with Finder. They are embedded in Curio documents.

Switching between PDF readers, and compatibility of deep PDF links

Hookmark’s deep PDF links are designed with the same standards-compliant principles and philosophy as Hookmark’s email links. (See Openness).

Where Hookmark’s email URLs (hook://email/<ID>) utilize RFC 5322 compliant email identifiers, Hookmark’s deep PDF URLs (hook://file//<...>p=<page-number>&s<starting-point>&e=<end-point>) use coordinate information defined in the PDF specifications.

This means you can switch from one PDF app to another — as long as the other app supports automated deep linking. You can copy a deep PDF link in one app (e.g. Skim) and open said deep links in another app (e.g. PDFpenPro).

Preventing deep links from being formed

If you’d rather get a link to the entire PDF, rather than a deep link, then prior to using the Copy Link or Copy Markdown Link command, simply clear the selection in Skim. You can do this by option-clicking in the margin of a PDF in Skim (or close and reopen the PDF file).

Hook to New > Skim

Hookmark does not currently support the creation of new PDFs. So there’s no Skim item in the Hook to New menu.

Searching for PDFs that you’ve bookmarked with Hookmark

To find PDF files you’ve linked with Hookmark, simply:

  1. Invoke Hookmark.
  2. Enter search mode (with ⌘F or a click of Hookmark’s search toolbar-button).
  3. Type ".pdf" and hit the Return key (for a more precise search: "pdf" url:"hook://file").

Your PDF bookmarks will show up in the search results. This is a very handy trick, so it’s a good idea to get into the habit of using Hookmark’s search feature.

Think of it this way: if something is important, you’ve likely bookmarked it with Hookmark (e.g., by copying a link to it). So use Hookmark to search for relevant information.

PDF coordinates

When Hookmark creates a deep PDF link, the URL contains coordinates in the PDF. Page-level precision of Hookmark’s links is interchangeable between compliant apps, meaning you can create a link in Skim and consume it in (say) PDFpenPro or (in Hookmark 2.3) Adobe Acrobat.

However, the within-page coordinates of Hookmark’s deep PDF links in Skim depend partly on the type of Skim tool you use when clicking in Skim (selected via Skim’s Tools menu), i.e., before you invoke Hookmark and use Hookmark’s Copy Link command

  1. If Skim’s tool is set to ‘Select Tool’, then the deep URL will contain the page number, and the x and y coordinates of the selection, like this: #p=4&x=60&y=213.
  2. If Skim’s tool is set to ‘Text Tool’, then the deep URL will contain the page number, and search coordinates (start and end) of the selection, like this: #p=4&x=0&y=0&s=2114&e=2271.

In either case, you get the page number, and some offset information. The page number is useful for any compliant PDF app. However, the search coordinates (returned by the Text Tool) can only be used by Skim.

That means that if you use the Text Tool before in process of creating a deep link, Hookmark will only take you to the correct location on the target page if you open that URL in Skim.

For completely interchangeable within-page precision of deep links from Skim, use the Select Tool.


This requires Hookmark 2.2 or later with integration scripts v. 158 or later.

Readdle’s PDF Expert

We’re sometimes asked about Readdle’s PDF Expert, so we mention here that as of this writing, PDF Expert for macOS is still not a linkable app as defined in What’s a Linkable App and Why Does Linkability Matter?.

See also Contacting Developers of Other Apps and Information for Developers.

See also…

Luc Beaudoin’s two Cognitive Productivity books explain in great detail how you can use the Skim PDF reader to boost your cognitive productivity.

Skim is also discussed and illustrated elsewhere on this website. To find out more: