I haven’t really got to grips properly with Skim - downloaded it mainly due to the points being made on this forum, about it’s searchable Notes option - and related integration with DTP.
I do however find the “split Pdf view” very useful, especially when reviewing a PDF that has endnotes, as opposed to footnotes. Being able to split between the main text, and the endotes, saves plenty of scrolling back and forth.
Having said all of the above - I mostly do my reviewing/reading/editing in DTP. Today, I opened an article in DTP, and made it fullscreen. I started reviewing as per usual, and when the scrolling annoyed we, I opened it with Skim - did the split - and it occurred to me, that I had never checked to what extent any highlighting in Skim, was transferred to DTP.
So I highlighted the first sentence in Skim - saved it - went back to DTP (might have closed and re-opened it?) – and was pleased to see that the highlight had shown up in DTP.
Then the penny dropped. I have custom-colour highlight options in DTP, that mean a particular thing in the context of my reviewing my research pdf’s. AFAIK - I cannot replicate this in Skim?
Furthermore - and somewhat more concerning - it now appears as if my editing options on the associated file in DTP are no longer enabled?
In other words - I cannot continue highlighting within that specific pdf within DTP - nor can I annotate/place notes?
Am I correct in that my selecting to “open in Skim”, has DTP treat the pdf as now being ‘editable by outside application’ only? Is there any way to override this? Hope so…
Skim does not use the same methods for annotating files that DEVONthink, Preview, Acrobat or most other applications uses. When you use Skim’s annotation features, it is the only application that can access them for editing – though, as you’ve seen, other applications such as DEVONthink or Finder can view them. The trade off, then, is that you get access to Skim’s powerful set of annotation features, but you’re in a sense “locked-in” to using Skim.
I have found that on some PDFs it is possible to mix Skim and DEVONthink annotations – but that usually leads to a horrible mess where I’ve mangled the PDF beyond repair.
While DEVONthink has a fixed set of 7 highlight colors in its palette, Skim’s highlight colors are set once in Skim > Preferences > Notes > Highlight and that setting can be over-ridden for each highlighted selection using the OS X color picker – select the highlight and use the contextual menu.
There is an entry on the Skim project wiki that might be helpful – unfortunately it looks out of date.
But to confirm - once a DTP pdf is opened via Skim - then that’s it as far as DTP is concerned - no further in-house DTP editing on that particular pdf? No way to “undo” that?
If you annotate PDFs in DEVONthink you can only edit those annotations with DEVONthink or the apps that use the same annotation methods – Preview, Acrobat, PDFPen, and so on. You could add an annotation note with DEVONthink and then edit that in Preview, for example.
You can open the PDF in Skim, and Skim will display your annotations. But the annotations cannot be edited in Skim. If you want to change this, you use Skim > File > Convert Notes…, which will make all of the existing annotations into Skim annotations. From that point, you’re committed to Skim. The situation is now flipped. You can edit annotations in Skim, but only view them in DEVONthink and its friends.
If you’re not sure, just duplicate the PDF in DEVONthink before flipping it over to Skim annotations. That’s klugey, but safe.
Thanks Korm - I never realised that going with Skim, would forever close down editing rights on those PDF’s in DTP!
I am so relieved that I found this out now - rather than much later down the line… I actually don’t mind the DTP editing options - sure, could be a bit more feature-rich - but having it all in-house is appealing… I’ve already removed Skim as the default app - don’t want to forget about this again later on, and go through the same exercise…
As for the searchable notes - useful, no doubt - but managing with the annotated RTF just fine. Only started playing around with the wikilinks feature this afternoon - and almost blew my own mind when I dragged a pdf into a annotated RTF, and saw the “scrollable-pdf” end result! Wow! Live and learn!
And the work-around for my split-pdf-view issue - open said pdf in Preview on my 2nd screen, scroll to footnotes - continue working on my main screen, where I need to. Kicking myself that I’ve now lost editing rights in DTP on my current PDF - really wish I hadn’t opened it in Skim now, but so be it.
You cannot revert this file’s Skim annotations back to DEVONthink-editable annotations. But you can export a copy where DEVONthink can edit the annotations if you use these settings in Skim > File > Export:
Just to close this loop - and at risk of stating the obvious - did as Korm suggested, and simply exported/saved the file where it was (i.e. within the DTP database folder - I do not index) - was asked if I wanted to rewrite - YES - and back in DTP, could edit again.
As mentioned above - this might be problematic if you have made many annotational/editing changes in both DTP and Skim, since the two styles of annotation etc. might not play together nicely, but if (like me) it was merely one or two minor changes, then this works a treat.
If you export and overwrite a file directly inside the database’s internal folders you run the risk of “missing” or orphaned files. Do Verify & Repair to be sure there’s no damage.
Exporting into the database package is different than doing “open with” and then saving.
