FAQ
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Skim FAQs
Feel free to add answers here, or ask additional question on the Skim users list!
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.
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.
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, 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.
- 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. Notes from a separate .fdf file can later 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.
- 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 some types of notes still cannot (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. You can save the page rotation and crop by exporting With Embedded Notes.
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 With Embedded Notes from the File Format popup button. 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.
Can I save PDF documents with fillable forms?
Skim allows you to fill forms in PDF documents that have editable forms. However, these forms will not be saved during the normal saving process. You can export the PDF with the filled in forms as described in How can I save the PDF so that notes are visible in other viewers, such as Preview and Acrobat?. However beware, after saving in this way, the forms will not be editable anymore.
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.
How can I print PDFs with landscape pages?
You can print a PDF in landscape or portrait orientation. Choose "Page Setup" from the File menu. Then select the appropriate button. Skim should already automatically have chosen the best orientation based on the size of the first page.
You can also select to automatically rotate (and scale) the pages to fit the pages. this rotates each page separately, so it can be used to print PDFs with only some pages (such as large tables) in landscape orientation. For this, select Skim from the Settings popup button in the Page Setup sheet, and check "Auto Rotate Pages". In Skim 1.0.1 and later, this setting will stick between launches and for new documents.
Skim does not open my .fdf file
Some journals send PDF files with an .fdf extension. If you change the extension to .pdf, Skim will open these files. You can see if a file with extension .fdf is actually a PDF file by opening the file in a text editor (such as TextEdit). A PDF file should start with "%PDF-", while a FDF file should start with "%FDF-".
Time Machine Restore loses my Skim notes
The Restore function on Time Machine currently seems to have a bug where it sometimes loses extended attributes that Skim uses to store notes and highlights. However the Time Machine backup does keep these extended attributes. If you manually copy your PDFs from the Time Machine backup folder, your Skim notes will be restored. You may also want to keep .skim backups of your important notes.
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.
