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Do More With PDF in Skim for Mac

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Difficulty:BeginnerLength:LongLanguages:

There are plenty of ways to view PDFs on a Mac. Apple’s built-in Preview application is phenomenal because, apart from reading, you can annotate PDF files to highlight areas that need change, complete PDF forms, sign PDF documents and even add or re-order pages from another document. If you can perform your day to day tasks with Preview easily, then you hardly ever need to look for an alternative.

Academics needs are different. If you are a student or a professor then you have to concentrate on note taking, reading scientific journals and bibliography management at same time. 

Reading a journal is probably the toughest part because you have to record and answer many questions. You have to highlight the goal of the paper, record findings and methodology, and simultaneously take notes on discussion and conclusion. The PDF application should assist you in solving these problems.

In this tutorial I’ll show you: 

  1. Reasons for using Skim to read and annotate documents
  2. Various types of annotation tools in Skim and when should you use it
  3. Tagging in Skim
  4. Integrating Skim with other applications such as BibDesk and GoodReader for iPad
  5. Exporting the notes and annotations in various methods

Reasons for Using Skim

Focus on Reading

Reading and assimilating points from paper takes time and it’s easy to lose focus. The primary goal of any PDF application is to give you a good reading experience. It should let you customize the default settings for window layout and PDF display when you open a new file; it should allow you to read documents in full screen and temporarily highlight the line of text to maintain focus and easily find back what you were reading.

Skim lets you customize the default settings of the layout whether you want to read in normal or full screen mode. You can open new PDFs either Maximized or just Fit around the PDF. The side panes have the size of the last window shown and although by default only table of contents pane is visible you can hide them, toggle the Contents Pane button in the toolbar. Now it is possible to see only the main reading screen, after all you just want to read.

To tweak the view settings while reading, choose PDF > Use Current View Settings as Default to select your own preferred settings. The new PDF files will be opened with those settings including Single/Facing pages, Continuous, Book Mode, Page Breaks, Media/Crop Box, and Zoom factor

If you want to reset the current view settings, press the Normal button in the General preferences. In Full Screen mode you can choose different view settings, but remember they are only applicable for this mode.

Various PDF display options in Skim If you just want to focus on reading you can toggle both the contents pane and notes pane
Various PDF display options in Skim. If you just want to focus on reading you can toggle both the contents pane and notes pane

To help you concentrate on the reading, Skim includes a reading bar. Choose View > Show Reading Bar. To move the reading bar to the next (previous) line, hold down the Option key and press Down or Up Arrow key and similarly for the next (previous) page, hold down the Option key and press the Right or Left Arrow key

To resize reading bar, hold down the Shift key and drag the reading bar with mouse to another line.

Reading Bar is a great feature to help you focus on the document To resize the reading bar hold down the Shift key and drag the bar with mouse
Reading Bar is a great feature to help you focus on the document. To resize the reading bar hold down the Shift key and drag the bar with mouse

Skim the PDF

A book may contain both information and insights that would be valuable to you if you could dig them out, but there are two problems. 

  1. you do not know whether you want to read the book. You do not know whether it deserves an analytical reading.
  2. you have only a limited time to find this out.

In this case, what you must do is skim the book. Then you will know at least what the author’s main contention is, and what kind of book the author has written.

  1. Scan the title page and preface.
  2. Study the table of contents, bibliography and indices.
  3. Read a paragraph or two in sequence/without sequence.

Skim’s contents pane works pretty much like Preview’s Drawer, you can either view thumbnails of each page or table of contents (if it is present). In either mode you can at least skim title page and preface. 

Skim also lists the page numbers along with chapter’s name and if you hover the mouse over the pane it will display a quick preview of the content. You can adjust the width and height of preview tip through Terminal, explained later on.

Tooltip preview of chapters in content pane of skim In the top you can notice a search field and a toggle to preview either thumbnail or table of content
Tooltip preview of chapters in content pane of skim. In the top you can notice a search field and a toggle to preview either thumbnail or table of content

As usual, every PDF application has a search box to do a quick search but Skim goes one step further. It not only highlights the search term on the relevant pages but also encircle it with animated (not shown in screenshot) yellow box for few seconds. This will allow you to maintain focus while you’re skimming the book. 

Separate search results allows you to see results separately from page to page. In this case the relevant word or phrase is bolded. 

Group search results by page allows you to see results in group from chapter to chapter. The latter option is quite useful because then I can see the intensity/relevance of that word or phrase in a chapter.

Search field in Skim is powerful 1 You can toggle the display view either in separate or in group mode 2 Search field box 3 Text highlighted with yellow box
Search field in Skim is powerful. 1. You can toggle the display view either in separate or in group mode 2. Search field box 3. Text highlighted with yellow box

It is quite possible that the document has a table of data that you find yourself going back to repeatedly. 

Skim let's you take snapshot of that section and keep them on your screen for easy reference. To take a snapshot choose Tools > Text Tool, hold the Command key and select a region. A window will then pop up displaying the chosen region. 

Snapshots are kept for easy reference in the Notes pane. Keep in mind that snapshots are temporary and not saved with the document.

It is very easy to take snapshot of a window in Skim notice the snapshot window in note pane as well
It is very easy to take snapshot of a window in Skim, notice the snapshot window in note pane as well

Having the ability to look at two places in the same document at the same time without making a copy can help you to skim the document efficiently. 

So I can either read the paragraph in sequence or without any sequence it doesn’t matter, the fact is I can skim the book quickly. To split the PDF choose View > Show Split PDF.

Split PDF feature in Skim lets you skim documents quickly
Split PDF feature in Skim let's you skim documents quickly

Access and Retain Annotations and PDF

Once you have finished reading and annotating your paper, the job of the PDF application does not ends there. You should be able to access your annotations and retain them for future use.

Skim is a spotlight friendly application. The application stores its annotation in a separate file (with a .skim extension) that Spotlight happily indexes. 

This means annotations are not locked in a PDF application. You can export it as a .txt or .rtf file or let it get indexed by Spotlight or to make your annotations searchable.

Skim has an advanced bookmarking feature to link to specific saved PDFs and/or specific pages in PDFs. To add a bookmark, choose Bookmarks > Add Bookmark, and enter a name. 

If you want to save the bookmark only for the current session, choose Bookmark > Add Session Bookmark, and enter a name. Skim has a full fledged bookmarks manager that lets you create folders for sorting your bookmarks.

Bookmark management in Skim you can create multiple folders and separators too
Bookmark management in Skim, you can create multiple folders and separators too

The Skim Interface

Having huge number of options in menu and cluttered interface can create hindrance while reading and your PDF application should not waste your time in searching them. The Skim interface is simple and unlike other PDF readers you won’t find it convoluted. It has three panes:

  1. A Contents pane on the left with inbuilt search box
  2. A PDF pane in the middle
  3. A Notes pane on the right. This display each snip of text you’ve highlighted—one line per highlight. It also displays inner notes.

Across the top is a toolbar with a range of buttons, that you can customize (View > Customize Toolbar). You can toggle the toolbar on and off using Command-B.

Judging by the interface and the options in Preferences you may feel that there is not much left to do for advanced users. 

Skim has a few advanced preferences that are not accessible through user interface but you can set these from the command line in Terminal app. Type the defaults command with the appropriate arguments. The arguments is arranged in a logical way, with the angles replaced by the appropriate values.

defaults write net.sourceforge.skim-app.skim - <Key>  -<type> <value>

So if you want to disable preview tool tips on various tables, replace your value with boolean or an integer with it’s type as true or false and the Key as SKDisableTableToolTips

The developer has already made a detailed reference to hidden preference, just remember to shutdown Skim beforehand to avoid any complications.

Types of Annotation Tools

When annotations are created, they have a contextual relationship. The object they annotate being a piece of text, or any other object has some sort of link to the annotation. 

Because of this, you expect annotations to be relevant and give value to the document. Similarly the type of tools you want to use for annotating a document should have a clear message and purpose.

a. Textual annotations—helpful if you want to emphasize a particular concept; of important or forceful concepts. Skim makes it easy to modify the colors of highlighted, underlined and strikethrough text, choose View > Customize Toolbar and add Favorite Colors toolbar item. Hold down the Option key and drag a color from the Favorite Colors control and drop it on any note or highlight.

b. Vertical lines at the margin—helpful if you want to emphasize a statement already underlined or to point to a passage too long to be underlined. Skim makes it easy for you to add vertical lines, choose Tools > Note Type > Line.

c. Vector annotations—helpful if you want to record questions and perhaps answers for a passage; and to record the sequence of major points. Skim makes it easy for you to add various shapes such as circles, box and more, choose Tools > Note Type.

d. Text Note—helpful if you want to get reminded about the things that you need to do regarding the text that you read. Skim makes it easy for you to add text note, choose Notes > New Text Note.

e. Anchored Note—helpful if you want to record longer notes. You can assign a title and icon to it. Skim makes it easy for you to add anchored note, choose Notes > New Anchored Note.

When you make annotations in a PDF document, they get listed in the Notes pane. Once you start highlighting your document the notes pane can get filled up quite easily. 

That’s obvious, but Skim provides you an option to filter the notes easily, just click on the respective column you want to filter and select them according to color, page number, date and more.

You can even label your annotation in the Notes pane, to do this double-click the note and add your text. Just remember that labeling the annotation does not change the content of what you highlighted. It simply makes it easier to identify the highlight for review and study purposes.

Filter pane in Skim lets you filter the notes in various ways Notice that you can also see the highlight color type of annotation tool used and page number
Filter pane in Skim let's you filter the notes in various ways. Notice that you can also see the highlight color, type of annotation tool used and page number

Tagging in Skim

Tagging has many benefits because it can help you to summarize, understand, assess, and remember what you read. It let’s you capitalize the information in depth. For example—if you are reading a paper then within few clicks you could list out it’s important concepts and findings.

Skim creates an editable note object for each snip you’ve highlighted in the Notes pane and in order to make the highlight function as a tag, prefix the annotation with a label. The label could either be a Term, Goal of the Paper, Findings, Criticism, Agreement or Disagreement or anything which you decide more suitable for a research paper.

Skim’s Notes pane has a filter that enables you to list only notes that match your typing. If you want to find all the snips of the text you criticize, enter criticism in the search field. 

When you double-click on an entry in the Note pane, Skim scrolls the document to display the note and snips of text associated with that entry. So you can quickly focus on the information you’re listed in.

Of course, you don’t want to type in long snips or big terms while reading. That would interfere with your comprehension and focus. I would highly recommend you to use TextExpander for this purpose, just define an abbreviation for each tag you commonly use.

Exporting PDF Notes and Annotations

One of the most useful features in Skim is the ability to export notes and annotations, but they do it in multiple ways. Notes and highlights, you add to a PDF document, are not saved in the PDF but are added to the file as extended attributes (hidden information attached to the PDF file on disk). 

Although these extended attributes are searchable through Spotlight, it can get lost while archiving the PDF file or sending it over email.

As a Separate File

you can save the notes to a separate .skim file for backup, or send them by email. To save the notes as a separate file, choose File > Export and select Skim Notes from the file format popup. You can also save notes added in Skim to a RTF or TXT file. 

As a Bundle

You can save the PDF and the notes wrapped in a bundle, with file extension (.pdfd). To save the PDF and notes as a bundle, choose File > Save as and select PDF bundle from the file format popup. A pdf bundle contains the unmodified PDF file and files containing the notes. You can see those files in the Finder using the Show Package Contents contextual menu item.

As Embedded Notes 

Skim also allows you to save a copy of your PDF file as notes in the PDF data i.e embedded notes. 

Technically this allows you to see the annotations and notes in different PDF viewers. To save a copy of the PDF with notes included, choose File > Export, select PDF from the file format popup and choose With Embedded Notes.

If you are planning to view your PDFs and annotations in another application, such as Preview or iPad PDF reader’s then export that PDF from Skim with their notes embedded. 

If you want to review notes, store data in a portable format or hand them to your teacher as a part of research project then export and save your annotations separately in a Text, RTF, RTFD, or FDF file format and if you want to send PDF with all the annotations over email then save the PDF and notes as a bundle, so they are kept together when exported.

Various export options in Skim choose the one accordingly for your needs
Various export options in Skim, choose the one accordingly for your needs

Scripting With Skim

Skim has an extensive support for scripting, such as Applescript, shell scripts (sh, perl, python, ruby and more), applications and Automator workflows. You can organize scripts into submenus by adding them to subfolders. To add a script menu to skim, create a folder in

~ Library/Application Support/Skim/Scripts (you may have to create those directories if they do not exist)

The scripts appear in the Scripts on the right side of the menu bar whenever Skim is the active application. You may have to enable the Scripts menu in the System Preferences

There are some great scripts out there to automate note processing. I personally find them very useful and if you have an elaborate annotation setup, these can prove to be a real time saver. Let me give you some examples:

  1. Join Highlights—This script will join all highlights of the same type that are on the same    page into a single highlight note. That means all the highlights done in a particular page will be joined together, similarly for underlined, strikethrough or other note type.
  2. Set Color of Notes—Set the colors of all notes of selected types to a chosen color. Helpful if you have read and annotated a huge book.
  3. Synchronize Folder Bookmark—Keeps a folder bookmark synchronized with the contents of a folder on a disk. Helpful if you depend on bookmarks a lot and keeps your papers in one place without fear of losing it.

If you want to make your own script, there is an entire applescript wiki section, just make sure to check out the Skim scripting dictionary in Applescript Editor.

With this script I can join highlight underline or strikeout notes hold command key if you want to select all of them
With this script, I can join highlight, underline or strikeout notes, hold command key if you want to select all of them

Integration With Various Applications

Skimmer

Skimmer—Workflows are one of the key features in Alfred. They provide a way for you to extend Alfred to perform the tasks you need more efficiently. 

 Whether you’re just looking to add a few hotkeys or you’re an advanced coder, workflows can be molded to your needs to be as simple or complex as you want. One such useful workflow is Skimmer, it bundles a number of helpful scripts for use with the PDF viewer Skim.

Download the workflow from Packal workflow repository and install it. Alfred will show you a preview of the name and description of the workflow and details, if available. Click the Import button to add the workflow to the sidebar on the left. The developer has made some documentation on how to use this workflow, just go through the steps before you start using it.

This script provides three major benefits to my workflow:

  1. It export all the PDF annotations to Evernote or Markdown with live hyperlinks back to the exact PDF page for the annotation, that means my sources are cross-linked within the annotation itself and I don’t have to entirely depend on bibliography management software to read a cited paper or worst folder hierarchy of the hard drive to find the file.
  2. It translate certain highlight colors into labels. That means you can devise your own scheme for classifying what you read. For example—yellow highlight for Summary, Pink highlight for Technique, Blue highlight for Quotable text, Red highlight for Disagreement and so on.
  3. It extract data and search Google Scholar from the currently viewed OCR’d PDF.

GoodReader

Goodreader—a popular PDF reader for iPad and like every other PDF readers it follows the adobe annotation protocols. By default, Skim saves all of your annotations as a separate file and not within the PDF itself. 

Though this file is searchable through Spotlight, your annotations are not visible if you viewing that same document in other PDF viewers like Goodreader.

In order to save your annotations to a PDF file, you must export the PDF. Choose File > Export from the menu bar and under file format, open the drop-down menu and select PDF. This will present you with three options Default, Without Notes, With embedded Notes. Click the With embedded Notes option and save your PDF. If you open this PDF in Goodreader, you can see all your annotations.

If you want to save annotated PDF notes as a plain text from Preview, choose File > Convert Notes from the menu bar. Skim will then convert all the highlight and notes to Skim notes. Now simply go to export and choose Notes as Text from the file format popup.

BibDesk

BibDesk—a piece of software meant for bibliography management focused on the BibTex format. It automatically store files to a given location and shows the bibliographic information in a nice overview. 

It lets you search in journal repositories such as PubMed, Web of Science and Google Scholar as well as download the paper in PDF format. BibDesk allows you to view and search notes that were added using Skim.

To view the Skim notes added to a linked PDF file, choose Publication > Show Notes for Linked file. A separate window will then open to reveal all the highlights and notes you added to the PDF document. To search for Skim notes of linked files, type the text in the search field of toolbar and choose Skim Notes from the search buttons.

Conclusion

Skim is indeed a powerful PDF reader and note taker for Mac. It has all the benefits at its disposable for the academics and for the most part reading and annotating documents is all you need. 

If you are more towards advanced stuff then you can integrate Skim with Applescript, customize interface with Terminal and develop a workflow with BibDesk and iPad PDF readers.

Developing a workflow with Skim is not easy but if you have any trouble in getting started with the application or have any unique method you want to share, let me know in the comments below.



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