Problem with Skim notes from Scrivener

This is probably a Skim problem rather than Scrivener, but I’ve only experienced it when using Scrivener and post it here in case others have had the same problem and might know how to solve it.

I have lots of PDF files saved within Scrivener databases. As recommended elsewhere on this Forum, I use Skim as my default PDF reader to make notes on the PDFs, using the “Open in External Editor” feature. Recently I’ve found that Skim can no longer open the notes I’d previously saved in the PDFs - it gives this error message: “Unable to Read Notes: Skim was not able to read the notes at [path]/[file].pdf. Failed to reassemble attribute value. Do you want to continue to open the PDF document anyway?” Clicking Yes opens the PDF but without any of the notes, thus losing access all my work…

Anyone else had this? Any ideas?

I’m using Scriv 1.11 and Skim 1.1.13, OSX 10.5.5


I found the problem via the Skim site. Skim stores its notes in something called extended attributes, rather than in the PDF file itself. Unfortunately these EAs get lost when files are copied in many circumstances. The Skim site says EAs are preserved when copying using drag&drop in the Finder, but this is definitely not the case when I copy from my iMac to my Powerbook. The EAs are also apparently lost by TimeMachine.

This means that annotated Skim files are incredibly fragile. You can keep the advantage of Skim notes rather than embedding them into the PDF if you “Save As” a PDF Bundle (which is preserved during copying & backup) but its a hassle to remember each time. It’s a shame because there are definite advantages in research to having the Skim notes functionality, e.g. being able to export all the highlighted parts of a PDF.