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Cloud Sync



May I use Dropbox or equivalent to sync libraries?

No. We strongly advise against using file sync services like Dropbox (iCloud Drive, Googe Drive, OneDrive, Box, etc.) for Bookends libraries. If you use the library on more than one machine it's easy to get "collisions" that can prevent file synchronization and even cause corruption (this is probably the primary cause of damaged libraries that we see). Use Bookends cloud sync instead. It's much faster, more robust, and can serve as a backup mechanism if the library file itself becomes damaged.

Note that attachments (e.g. PDFs) should be synced with services like Dropbox. The corruption problem only applies to libraries (databases).

Why isn't scanning/inserting a citation in a Word document working?

Bookends exchanges information with Word via AppleEvents. There is a bug in Word that sometimes causes it to stop responding to the "paste" AppleEvent, and after a scan or Copy Citation Word comes to the front but the document's text is unchanged (although selected), and no bibliography was added. The immediate solution is to perform a Paste (Command-V) yourself.

The longer term solution is to either relaunch Word (which sometimes works) or reboot your Mac (which usually works). If those don't help, reinstalling Word seems to fix this issue.

Another possibility is that "Proofreading Scan" was checked in the scan dialog. Proofreading scans help you manage temporary citations, they do not replace temporary citations with final citations, and will not generate a bibliography. The User Guide has more information about Proofreading Scans.

If none of these solve the problem and the document contains numerous images, please see this discussion of how to deal with very large Word documents.

When I scan a Word document I get a run-time error '5', what does it mean?

This is a Word error message, not Bookends. One possible source of this error is file-access restrictions enforced by macOS, in which case giving Bookends Full Disk Access in System Settings → Privacy may fix it. In some cases, the “Bookends Access to Control Microsoft Word” dialog appears briefly but disappears before you can click on it, which appears to be a bug in macOS. If this occurs, the solution is to hover the mouse cursor over the location of the OK button and click quickly when it appears after you initiate a scan (it can be done). If all else fails, rebooting the Mac can take sometimes takes care of it, and if not reinstalling Word can be effective.

Why do some graphics disappear after scanning a Word document?

There is a problem with some versions of Word that causes TIFF images to disappear after scanning with Bookends. The solution is to save the images in another format (e.g. PNG or JPG) and use them to replace the TIFFs. The PNG or JPG images will be retained after scanning.

What can I do if my very large Word document has problems when scanned?

Documents are passed back and forth between Bookends and Word via the clipboard. Word has trouble copying styled text when files become very large, and if the file exceeds a certain size it will fail. This is almost always due to embedded images in the file.

Solution: Assuming the file has images, you should try File → Reduce File Size (in Word). Alternatively, you can save the images as smaller .jpg or .gif files and then add them to the Word document. Another method is to copy the images from the Word file, paste them in to TextEdit, copy them from TextEdit, and paste them back into Word. It is unlikely that you will ever notice any change in the quality of the images.

In the unlikely event that this does not work, you can save the file as RTF and scan it from within Bookends. Bookends will always scan a Word document saved as an RTF file, regardless of its size. Word RTF files can be rescanned and/or unscanned.

Another option is to remove some or all of the figures until the document can be scanned, then place the figures back in the scanned document.

OpenAlex doesn't recognize my ORCID ID, returns incorrect information, or otherwise misbehaves. What should I do?

The OpenAlex database is constantly growing and being updated. It may not contain your valid ORCID ID, may not resolve your name correctly, may return incomplete information, etc. The good news is that OpenAlex.org wants feedback and will try to fix problems brought to their attention. If you encounter such issues, first go to orcid.org and make sure your ORCID ID is registered and has publicly available content. If it is correct, see if the ORCID ID has been indexed by Crossref.org by searching its metadata here. Once verified and with this information, contact OpenAlex.org via their Help page and report the problem.

Google Scholar searches and/or importing stopped working, what do I do?

Google Scholar uses a proprietary algorithm to detect activity coming from Web robots. If it suspects you are a robot, searching and downloading metadata will be suspended. Note that the suspension is time-limited (approximately 24 hr). However, you can have your privileges restored more quickly if you take the following steps. If you are using Bookends Online Search, a reCAPTCHA will usually appear in the lower pane when you try to search Google Scholar. Once you have answered the questions correctly your search privileges should be restored. Restoration of importing privileges may take longer (up to 24 hr). If you don't see a reCAPTCHA in the lower pane, i.e. searches fail silently, on the same machine go to Google Scholar in a standalone browser and identify yourself as human.

I'm getting a "-39" error when opening a library. What does it mean?

A "-39" error means that macOS security features are blocking Bookends from opening or updating a library. The solution is to go to System Settings → Privacy and give Bookends Full Disk Access. If that doesn't resolve the problem, try moving the library to a new location in the Finder, such as the Desktop, and open it from there.

Where is my reference library on the hard drive?

When you create a new library, it is given a name and saved to disk using the standard Save dialog. The default location is in your user Library folder

~/Library/Application Support/Bookends/

Remember that you can access your Library folder by holding down the Option key and selecting the Go menu in the Finder.

Note that you can always see the full path to your reference library by pressing the Command key and clicking on the file proxy icon in the library window title bar.

You can also get to the Bookends folder via the Bookends Help menu: Show Bookends Folder in Finder

Where is the User Guide? Where are the tutorials?

The User Guide, tutorials (PDF and video), and Release Notes are available from the Bookends Help menu.

Can I scan Word files that have EndNote citations?

Usually. Follow these steps:

  1. The key is to make sure that the EndNote record number in the citation matches the Bookends unique ID for that reference. To do this, export your EndNote library as XML. Import this into a fresh Bookends library and the EndNote record numbers will now be Bookends unique ID numbers.

  2. Open your document in Microsoft Word and use the EndNote unformat command if the citations were entered with Cite While You Write. All citations should now be visible in their temporary form (for example, surrounded by curly brackets).

  3. Scan the document with Bookends (make sure that the citation delimiters, such as curly brackets, as set in Bookends Settings are the same as those used by EndNote).

An alternative if you use references from PubMed is to create temporary citations as Author, Date, PMID (an option introduced in Bookend 13.2). Such temporary citations will be recognized by both Bookends and EndNote.

How do I import references from other reference management apps?

You can export and then import references, often with links to PDFs intact, from applications such as EndNote, Papers, Sente, Zotero, and Mendeley. Here are specific instructions.

Bookends isn’t working properly. What do I do?

Damage to your Bookends library can have unpredictable results. If you are having problems that cannot be reproduced in a fresh Bookends library, it is likely that this is the cause. In this case, the first thing you should do is to rebuild the library (File → Library Maintenance → Rebuild). If the problem persists, try to repair your database (File → Library Maintenance → Repair). If the problem has still not been resolved, contact us for technical support.

How do I merge two libraries?

There are two ways to do this: (1) Mark all your references, use File → Export References (Hits) to export them as a "Bookends" file, and then import this file into the destination library, or (2) drag the references from one library window and drop them on another. If you think there may be duplicate references, after the merge choose the menu item Refs → Remove Duplicates.

Why are text styles (i.e. italics, bold) not showing in my formatted references?

Check Settings → Scan & Bib or Biblio → Bibliography and make sure the output is set to Styled Text. If it is, then check the bibliography font you are using (the default is in Settings), and the font used in a reference that is not displaying styled text. Not all fonts have an italic face (Lucida Grande, for example), and in that case only plain text will be output.

Bookends doesn't have the format I need. Where can I get it?

You can create your own formats by selecting one in the Formats Manager that is similar to the one you want and clicking on the Add button (use Biblio → Create Format Catalog to see examples of all the formats shipped with Bookends). Create an appropriate name for the new format and make whatever changes are necessary. Alternatively, you can ask other Bookends users if they have created such a format and will share it on the Bookends User Forum. If you have altered a format we supply and want to revert to the original, you can move the edited format out of the Custom Formats folder and Bookends will use the version distributed with Bookends.

Cloud Sync

What is the difference between Bookends cloud sync v1 and v2?

The original Bookends cloud sync (v1) used Apple's CloudKit JS APIs, which give web apps access to iCloud. Bookends 14 introduced sync v2, which uses native CloudKit. The major advantage is that v2 uses your macOS iCloud account to access your data, meaning that there is no need to log in separately for Bookends cloud sync. Another advantage is that you will be able to share libraries with others.

How do I upgrade a library to sync v2?

Bookends 14 offers to do this for you automatically when you open a library that was synced in Bookends 13 or earlier. If you decline, the library will continue to use sync v1 (when opened in Bookends 13) and Bookends 14 will temporarily suspend syncing for that library.

Will I be able to sync databases using v1 and those using v2?

Yes, you can link and sync to the same cloud library using v1 and v2. The only limitation is that new or modified reference links synced with v2 will not be visible to libraries synced with v1, and vice versa.

What are the advantages vs. the disadvantages of upgrading my library to sync v2?

There are no disadvantages. However, if you used an Apple ID other than your system Apple ID for sync v1, you will have to re-upload the library. To do this

  1. Run Bookends 13 and use the cloud icon to Unlink the library

  2. If you plan to migrate this library to sync v2 on all your Macs, remove the library from the cloud .

  3. Quit Bookends 13.

  4. Run Bookends 14 or later and upload the library to the cloud.

The main advantage is that v2 uses your macOS account to interact with iCloud. This means that there is no longer any need to log into iCloud with your credentials. Native CloudKit also makes it possible to share libraries with others.

Can I downgrade from v2 to v1?

Yes, if you downgrade to Bookends 13. In this case, you would install Bookends 13 and download your library from the cloud. Libraries synced with v2 can still can be opened by Bookends 13. If you do, you will receive a warning that the library has been synced with a newer version of Bookends. You should unlink and then resync it with the existing library in the cloud.

Why am I frequently asked to re-sign in to iCloud with my Apple ID?

Note: this issue can only occur with sync v1. If you are using Bookends 14 or later (i.e., sync v2) you are logged in using your Apple ID, entered in the iCloud tab in System Settings.

Cloud sync v1 requires that you log in with your Apple ID. The re-sign in dialog put up by Apple no longer offers the option to stay signed in. If you are asked to re-sign in frequently (e.g. every day or two), do not click "Continue with Password". Instead, click the Cancel button at the window's top right or "Use a different Apple ID”. A new sign in window with the "Keep me signed in" option will appear.


Can I install Bookends on both my desktop and laptop computers with one license?

Probably. Licenses are per user, not per computer. That means if you are the only person using a license you can install it on more than one computer for your own use. Note that you can not run Bookends on more than one computer simultaneously (a single user has no need for this). If more than one person is using Bookends, you need one license for each person.

I bought Bookends on the Mac App Store. I no longer see it there, how do I get it?

As of version 13, Bookends is no longer for sale on the Mac App Store. You can pay to upgrade to Bookends 13, which is available on our web site. If you don't want to upgrade you can still download Bookends 12.8.4 by clicking the Purchased tab in the Mac App Store app.

I own Bookends—where can I find my registration (serial) number?

Your registration number was provided in the email you received when you bought Bookends. If you bought Bookends 13 or later from Sonny Software or the Bookends/Mellel bundle, the email was sent from fastspring.com. If you bought Bookends 12 or earlier from Sonny Software, the email was sent from sales@sonnysoftware.com. If you bought from the Mac App Store you have no registration number. If you can't find the fulfillment email, contact Sales with the name and address you used when you made the purchase and we'll look it up for you