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A PDF Reader and Note-taker for OS X

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Skim FAQs

Skim FAQs

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Where are the notes and highlights stored?

Skim stores its notes and highlights in extended attributes (EAs). EAs are metadata that many file systems, such as HFS+, can associate with a file. So the notes are not stored in the PDF data itself. Since 1.5.9 also fillable form data is saved in the EAs.

Does copying a PDF file preserve the notes and highlights?

That depends how you copy and where you're copying to. The first requirement is that the file system you're copying to and from support EAs. This is true for HFS+ (used in Mac OSX). A second requirement is that the copying mechanism preserves the EAs. Copying through drag & drop in the Finder and using the command line 'cp' tool preserves EAs.

Are notes preserved when I send a PDF over email?

No, email loses the EAs and therefore the notes. You can use the menu items in the File menu to safely send a PDF with notes in archived form over email.

Are notes preserved when I sync PDF files using backup tools such as cvs, svn, etc?

That depends on the tool you are using. To preserve the Skim notes, the tool is required to preserve EAs. It is known that CVS, Subversion, Git, Dropbox, and Unison do not preserve EAs. On the other hand tools such as cp, rsync, tar, zip, gzip, and SuperDuper do preserve EAs (though some versions of these tools, s.a. gzip from Fink, may not do so). However Finder's Create Archive and the backup functions Apple's Disk Utility on higher versions of Tiger are buggy and lose the EAs. Also Apple's Migration Assistant seems to suffer from the same bug; this is relevant when you upgrade to Leopard. Check out this discussion about backup tools on Mac OSX or this follow-up test to find which backup tools will preserve EAs.

How can I backup a PDF or send it over email so that the notes are preserved?

To make sure that your notes are preserved when you backup the PDF or send it over email, you can do either of 4 things.

You can archive the PDF or wrap it in a disk image, and send the archive or disk image. Be careful, because not all archiving processes preserves EAs. For example Apple's 'Create Archive' from the contextual menu in Finder loses EAs, even though the zip tool (e.g. accessed through the BOM Archive Helper utility) can preserve them. Also tar+gzip preserves EAs, and tar+bzip2. Also, creating a disk image from a folder in Disk Utility on Tiger does not preserve EAs. However if you create a new blank disk image and drag the PDF into it, the EAs are preserved. Skim can help you create an archive (tar+gzip) or a safe disk image using the Save Archive... and Save Disk Image... menu items from the File menu.
Save a copy of the notes in a .skim file. Choose Export... from the File menu and select Skim Notes from the File Format popup button. Notes from a separate .skim file can later be added using the Read Notes... menu item from the File menu.
Save as a PDF bundle. Choose Save As... or Export... from the File menu and select PDF Bundle from the File Format popup button. A PDF bundle wraps the PDF file and the .skim file in a package. You can see the contents of the package using the Show Package Contents contextual menu item in the Finder. The notes can even be viewed on Windows using the embedded .fdf file (at least using Acrobat Pro, Acrobat Reader now refuses this).
You can also save a copy of the notes in a .fdf file, which could also be seen in Acrobat. Choose Export... from the File menu and select Notes as FDF from the File Format popup button. Be aware that saving notes in an .fdf file could lose some data, in particular formatting and images in anchored notes.
See How can I save the PDF so that notes are visible in other viewers, such as Preview and Acrobat. However, this way the notes will not be editable anymore.

Why are the notes not stored in the PDF?

Skim uses Apple's PDFKit framework as a PDF engine. In Tiger, PDFKit cannot save annotations to a PDF. It can save them as 'ordinary' PDF (as Preview and Skim's export as PDF With Embedded Notes do), but you will lose the ability to edit the notes. On Leopard, some notes can be embedded as editable annotations in the PDF, but this is rather buggy and some types of notes still cannot be saved without loss of data (compare Export as PDF With Embedded Notes). Moreover, in many cases it is nice not to change the PDF itself. In some cases, such as when the PDF is password-protected, this is not even possible. Another reason is that Adobe's PDF specifications do not allow a note such as Skim's Anchored Note, featuring rich text and an attached image. So saving notes in the PDF would always lead to data loss.

Why are page rotation / crop not saved?

This is for the same reason that notes and highlights are not saved in the PDF. The page rotation and page crop are contained in the PDF data, so if Skim would save this, it was forced to save the modified PDF. This would lead to a loss of editable notes and highlight and would lose the Table of Contents.

Only if you export the PDF With Embedded Notes, the page rotation and crop will be saved in the modified PDF data.

How can I save the PDF so that notes are visible in other viewers, such as Preview and Acrobat?

Save a copy of the file with the notes included in the PDF. Choose Export... from the File menu and select PDF from the File Format popup button and select the With Embedded Notes option. Notes and highlights are now visible in other viewers, such as Preview and Acrobat Reader. Alternatively, you can Print to a file. Go to the print dialog window (command+P) and choose Print to PDF. However with both techniques, you won't be able to edit the notes and highlights in the exported copy.

Starting with Skim 0.9, you can also save a copy of the notes in a .fdf file, which can also be read by Acrobat. Choose Export... from the File menu and select Notes as FDF from the File Format popup button. Notes from a separate .fdf file, possibly saved from Acrobat Pro, can be added using the Read Notes... menu item from the File menu. Be aware that saving notes in an .fdf file could lose some data, in particular formatting and images in anchored notes.

How can I select text in columns?

You can select text inside a rectangle by holding the Option key while selecting. When you select text without the Option key held down, columned text will be selected over the full width of a page, ignoring the columns. This is the way Apple's PDFKit works, and we cannot change this behavior.

To highlight columned text you can add the highlights in sections. Using Option-select, you can select a rectangular block and add a highlight for it. Next, you can select a partial line before or after the block and add a highlight. You can then join these highlights to a single highlight by selecting the highlights while holding down the Shift key. In the Text Tool Mode, you can also select another highlight after selecting text to extend the highlight.

Update: in Mac OSX 10.6 text selection will respect columns.

Some fonts are missing or replaced

Sometimes characters in some fonts are missing, or are displayed in another font. In particular on Leopard this seems to happen often. The result is likely a corrupted font cache, which could be fixed by resetting your font caches. There are several third party utilities to help you with this, but you can also try fixing it as follows. Open Terminal.app, type "atsutil databases -removeUser" (without the quotes) and hit Enter. If you also want to reset the font caches for the system, you should replace "-removeUser" with "-remove". You need to log out and/or reboot after doing this. See also this post. For Tiger, see this post.

I can't get the icon preview for PDF files in Finder

This is not really Skim's responsibility, but rather the System's, because Skim does not handle QuickLook for PDF files. The problem can arise due to bugs in Finder. When you choose Skim as the default app to open a file, Finder will automatically set the file icon to Skim's PDF file icon. This is a bug, because Finder should use this icon anyway when Skim is used for this file. Moreover, when a file has a custom file icon set, this will prevent Finder from showing the icon preview. I also consider this a bug, because a custom icon is not an icon preview but an icon. Luckily, you can easily fix this bug. Select the file in Finder, choose File > Get Info..., select the custom icon in the Info window, and hit Delete.

Can Skim support image notes?

No, this is not possible, as Apple's PDFKit does not support notes based on embedded images.

I cannot select text

If you cannot select text in a PDF while you are using the Text tool mode, you probably have a scanned PDF. Such a PDF simply does not contain text, instead it contains bitmap images of the pages. Without text information, it is not possible to select. It is possible to add a text layer using third-party OCR software, however Skim can not do this itself currently.

Format for Dash Pattern in Lines -> Line and Border Style

This field is expecting a series of space-separated numbers, representing the length in points of the dashes and spaces between the dashes to draw the lines. The dash lengths are rotated repeatedly.

Skim won't launch

After (re)installing an older version of Skim, sometimes the system refuses to open Skim, instead showing the message "“Skim” can’t be opened because Apple cannot check it for malicious software." When this happens, go to your the Security & Privacy in your System Preferences, and in the General tab make sure you "Allow apps downloaded from:" "App store and identified developers." Then, navigate in Finder to Skim.app, probably in your Applications folder, and Open Skim from the contextual menu in the finder UI, and Accept the opening of Skim. After this, you should be able to launch Skim normally.

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