On May 8, 2015, at 15:12, Rob MacLeod wrote:

> Hi,
> 
> I have used Skim off and on for some years, just updated to the new version, 
> and appreciate a great deal of what the program offers.  I drift back to 
> Preview at times but then get frustrated again with each new version and 
> return to Skim for a while.  This relationship is a little like serial 
> monogamy and I am trying to figure out why I cannot commit to Skim as my 
> lifelong partner (-: 
> 
> The main reason I leave Skim is the clumsy file management it requires and so 
> I thought I would bring this up, perhaps as a topic long since discussed and 
> put to bed.  So please point me at the answers, if they exist somewhere on 
> this list or the help pages.  
> 
> The clumsy part, of course, is the need to export the file each time I wish 
> to save a version I can read with another pdf reader or send to another 
> person.  I use pdf markup for all my grading, much of the markup of papers 
> and grants I collaborate on, and most anything else students or colleagues 
> send to me for comment.  So I guess I am a power user or at least a committed 
> user of pdf markup tools.  I have to share the results of those edits with 
> others and most others do not use Skim--and I am not likely to change this 
> behavior.  As a result of need to share, I need to save conventional pdf 
> files with the markup embedded and visible.  Skim makes this harder to do 
> that I would like and I wonder why the Skim designers figured their 
> convention was useful.  Why take a portable document format and make is 
> non-portable?
> 
> I try to be very careful about my workflow, saving the file each time through 
> the export path, then ignoring the complaints from SKim when I close the 
> file.  But I have slipped up and I have lost edits and I have sent out 
> strangely unmarked files to my students.  I really should not have to worry 
> about this.  Why is the default not to save files with embedded markup?  Can 
> I change the default somehow to make it save standard pdf files?
> 
> Thanks in advance for any guidance and counseling I might need to get over my 
> hump with Skim and finally make it the tool I use all the time.
> 
> Best
> 
> Rob
> 
> 
> 
> Rob MacLeod, PhD
> Professor of Bioengineering and Internal Medicine
> University of Utah
> Scientific Computing and Imaging (SCI) Institute
> Comprehensive Arrhythmia Research and MAnagement (CARMA)
> Cardiovascular Research and Training Institute (CVRT)
> 72 South Central Campus Drive
> Salt Lake City, Utah 84112
> Email: macl...@sci.utah.edu
> URL: www.sci.utah.edu/~macleod
> 



Yes, this has been discussed to death on this list before. Though I don't have 
the links ready. There is also a discussion of it on the Wiki. (And there is 
also no way this will change, so don't try.)

The original reason for this is that when we started with Skim PDFKit did not 
allow saving notes to the PDF. So partly this is about backward compatibility. 
However this is by no means the only reason. There are many reasons to have 
this. It has the notes as a separate layer, so you also still have the original 
unedited PDF. Also, you can view the notes separately. Most of all, PDFKit's 
saving is too often really bad, it can lose you PDF data (partly because PDFKit 
only supports older versions of PDF), or it can save it inefficiently, and it 
often messes up the notes. Also, when it is password protected, PDFKit can not 
simply save it, unlike Skim. Moreover, saving and reason in Skim is because of 
this a lot faster. And then there is backward compatibility with files saved by 
Skim.

Christiaan

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