Thursday, November 22, 2012

Logos Bible Software: On Converting Kindle & PDF

Important Update:  The information below hasn't been edited for this update.

  1. Mobi Pocket Creator is no longer available. But Word 2013 & > does a great job on PDFs.
  2. More recent updates to Calibre allow direct conversion to .docx format.


Below are the procedures I use to convert Kindle files and PDF files into Word docx files for compiling into Logos Personal Books.

It should be noted that these instructions are presented to help you in format-shifting eBooks that you have bought (or obtained free in a free offer), thus enabling you to use them in your other devices or software. It is not intended to help in removing DRM so that you can give your friends free copies of copyrighted material or to participate in other nefarious activities.

Using Calibre to convert Kindle books:

1.       Calibre is one of 3 programs I use at various stages of converting various formats. It’s here: .
a.       It can convert Kindle (even with DRM), epub, etc, to RTF, HTML, etc.
b.      It can also convert PDFs, but I don’t like the results. It does other things so well, it could be that I haven’t taken the time to learn configurations, etc. I use another program for PDFs (see below).
2.       The sequence I used for converting is: Kindle-->HTML.Z (an odd format I had never seen before; a compressed HTML)-->HTML (using a program called 7-Zip (see below)-->open in web browser, select all and copy-->paste in Word (2007 or 2010).
a.       I do all of these gymnastics because I have found that these steps do the best job in preserving some headings and it preserves pictures (not all converting sequences do).
3.       You’ll need a plug-in for converting Kindle books.
a.       You can find it here:
b.      Instructions can be seen here:  I also have brief instructions for this immediately below.
c.       To install it, in Calibre choose Preferences, Change Calibre behavior (don’t choose Get Plugins), at the bottom-left of the dialog click Plugins.
d.      Click the button “Load plugin from file”
e.      The zip file that you need direct access to is “”, which is several levels down inside the folder Calibre Plugins.
f.        Navigate to where you saved the zip file, “” and open it (the zip file itself; you don’t have to unzip it first).
g.       Click through the warning about viruses.
h.      You should get a confirmation dialog.
i.         Click Apply.
4.       In Calibre, choose Add books, Add books from a single directory, navigate to where your Kindle for PC content is stored (prob. My Kindle Content) and Open.
a.       Tricky part: the file names can be cryptic. Sometimes you can tell which one is the book you want if it’s the most recent file you’ve added; just sort in the Calibre Open dialog. If not, open the book up in Kindle for PC and navigate to somewhere and close the book. When you try to open in Calibre, sort by date and see the most recent dated file; it will probably be an index file or something with a name like the actual book file (the actual book file will have an extension of .mobi, .azw, .prc, etc). Books from some sources, like, do have the actual name in the file name.
5.       After it’s imported into Calibre, right-click the book name and choose Convert books, Convert individually.
a.       In the top-right corner, choose Output format “HTML.Z” and click OK.
b.      It goes pretty fast.
6.       The resulting HTML.Z file will be in My Documents/Calibre Library and then by author.
a.       I think you can open up that file straight in a browser, but if I remember correctly, the headings and other stuff don’t look as good.
b.      So, you need to use a program to convert the HTML.Z file. 7-Zip can be found here:
c.       BTW, all of these conversion programs are free.
d.      Install and open 7-zip and navigate to the Calibre Library folder and open the folder for the book.
e.      Click on the HTML.Z file, click the Extract button and the confirmation dialog.
7.       In Windows Explorer, navigate to the Calibre Library.
a.       Find the author folder and the book folder.
b.      Inside the book folder, 7-zip has created another folder.
c.       In that is a file “cover.jpg”, which is nice to use in Logos for a cover.
d.      You’ll also see an HTML file. Double-click it and it opens in your default browser.
e.      In the browser, do Ctrl+A and Ctrl+C
f.        Open Word and choose Ctrl+V.
8.       A nice thing about this procedure is: it preserves pictures; not all conversion procedures do.
a.       It also (generally and usually) preserves the original book’s headings. Word and Logos usually recognizes these and uses them for TOC entries. Sometimes Logos doesn’t; it’s a dice roll.
b.      The existing TOC that was in the Kindle book isn’t live in Word, so I usually cut it out of the text.
c.       If the text doesn’t have preserved headings, you can apply Heading styles in Word, which Logos uses for TOC entries. Find and Replace in Word can automate this to the extent that there are common format attributes in the parts you want as headings.
d.      You can create a TOC in Word, which usually gives a pretty good mock-up of how Logos will create the TOC.
e.      Using this method, the TOC in Logos won’t be in the body of the text, but will be in the left side contents pane (open by clicking the double arrow at the left of the locator bar).
9.       The Cliff notes for creating a Personal Book in Logos are below, but more extensive (and better instructions can be found in the Logos Help system in the program and at the user-maintained Wiki on Logos’ website, here: and here is a selection of Wiki articles dealing with Personal Books:
a.       In Logos, choose Tools, Personal Books.
b.      Click Add Book.
c.       Enter the title, author (Logos doesn’t parse for sorting, so use last, first)
d.      Choose Type and enter any other elements you need.
e.      Click Change under the cover area and choose the cover picture. (Note: GIFs aren’t recognized by Logos.)
f.        Click Add file to load the Word doc.
g.       Click Build book.
h.      When it’s done you can look at the log file. Sometimes there are warnings about milestones that need to be addressed, but the warnings about fonts and stuff like that don’t really matter if the document looks good to you.
i.         Logos will open the new resource in a tab in one of the open panes and will re-index so your new resource will show up in searches, etc.

Converting PDFs:

There are a number of tools for converting PDFs, both freeware and cheapware. But many of them will either convert a PDF paragraph into a Word textbox, or will convert each line on the screen into a paragraph in Word, producing a zillion paragraphs, which I don’t think would do well when compiled in a Logos Personal Book. As I had mentioned earlier, I don’t really like the results of converting a PDF in Calibre. The tool I use for this is the (free) Mobipocket Creator. Mobi is the company that Amazon bought to get its foot in the ebook door. The program is found here:

This program’s main function is to convert various formats to a Mobi .prc file (which can be read by a Kindle). But what I use it for is to convert a PDF to HTML. One of the intermediate steps of creating the Kindle file creates an HTML file which can be pasted into Word. And just like when Calibre converts a Kindle to HTML.Z, this sequence preserves a lot of native formatting and pictures from the PDF.

Here are the steps:

1.       Open Mobipocket Creator
2.       From the Home page, under Import From Existing File, click Adobe PDF
3.       Browse to where the PDF is stored and open it
4.       Specify the Create publication folder or note the default that Creator shows
5.       Click the Import button
6.       When the importing is finished, we’re done with Creator
7.       In Windows Explorer, go to the publication folder and find the folder named after your PDF you imported.
8.       In that folder, open the HTML file
9.       In the browser, press Ctrl+A, Ctrl+C
10.   Open Word, and press Ctrl+V
11.   See the instructions above for the rest of the procedure.



  1. Here is a free ebook tool for you.

    You can easily convert your ebook from epub to pdf,epub to mobi, epub to kindle, etc.

    Free Online Converter / EPUB Converter

    It provides you with the best mobi to epub converting experience.

  2. Under "Using Calibre to convert Kindle books:" 3. a. The file attempted to give me a virus.

    1. Odd, I have been using this for about three years for that same purpose with no problems. I wonder if it was your virus checker giving a false positive? It does happen.

  3. Hello, Another alternative would be - It's a free conversion tool that enables users to transform pdf files to epub formats for a great readign experience. Maybe it's a good option for Calibre program. Thanks.

  4. Thanks for the help that you guys have provided above. I recently purchases a very expensive book on Kindle and naturally wanted to find a way to use it within Logos 5 (which I just discovered a few days ago). I'll try to covert a few books tonight. By the way, Logos software is great; I wish I had heard of it a long time ago.

  5. Very useful post, thank you!

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  6. I really appreciate this wonderful post that you have provided for us. I assure this would be beneficial for most of the people.

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  8. Hi, that was a great post. I love Calibre. I was wondering if you know what format Logos is and if it is possible to convert it to an eReader friendly format such as .epub or .mobi? Thanks in advance

    Not sure if I'll get the reply, but you could email me too. I'm very interested in finding out:
    davedanikinsella (at) hotmail (dot) com

    1. Hi Unknown:
      Logos does have a feature called "Send to Kindle" that was new in Version 6, which came out in Oct '15. It works with most of the books/resources Logos sells; sometimes permissions issues with the publisher prevent it. I haven't used it much, but from what I've seen, it does a very good job. I would not, however, work with any books that you make yourself with the Personal Books tool.

      Also, relatively serious Logos users can learn a huge amount from reading the forums at . One user in particular, M.J. Smith, provides very useful tip posts just about every day.

      I'll send this to your e-mail, also.

    2. Oh, and here's a link to the intro thread for the Send to Kindle feature:

  9. I can't seem to get Calibre conversion to preserve the endnotes from my kindle book. Any tips?

    1. Hi Benj:

      I don't think Calibre is capable of preserving end/footnote capability when converting Kindle books, at least I don't know of a way and I haven't read others who have discovered it. It certainly would be nice! (If you find out a way, please let me know.)

      I have, however developed a Word macro that might be able to convert those Calibre-converted Kindle end/footnotes. You can get this here:

      When this tool works, it is very cool. However, sometimes it doesn't, and I can't always determine why. It would be because Word doesn't find some aspect of the process as consistent as my initial inspection indicated. So sometimes you'll just have to know when you're licked and give up on that book.

      Some books can still be a lot of work, but always substantially less work that manually fixing the notes. The main thing is experiment and find out what your tolerance level is for the various amounts of difficulty different books will require to convert.

      Read the documentation sheet carefully, paying particular attention to creating the section breaks and being careful about the number of footnotes in each chapter/section. And save your document between each phase of the conversion. Make a safe copy of your converted .docx before you begin converting the footnotes, especially if you have done other format work on it.


  10. Wow! That is great info! Not only pdf to word but Kindle to preferred format. It seems to be interesting tool.

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