Monday, June 17, 2013

Logos Bible Software Personal Books - PDF Conversion Revisited

This is a brief addendum to the post below from Nov-12.

Since then, I have acquired Microsoft Office 2013. Except for using Outlook 2013 (which I like a lot) I really haven't done too much experimenting with 2013. One thing I have discovered is: Word 2013 can convert PDFs to Word .docx format, and it does a really good job, most of the time. By the way, if your workplace buys certain Enterprise Licenses from Microsoft, you can participate in the Microsoft Home Use Program. This cost an unbelievable $10 and gives you a legal license for MS Office Pro as long as you work there and they continue in the Enterprise License program. Check with the computer folks at work.

One really nice benefit of using Word 2013 to convert PDFs is that in many cases Word can convert the PDF active linked footnotes/endnotes to Word's active footnotes/endnotes. When this .docx file is compiled in the Logos Personal Book compiler, the resulting personal book will also have footnotes that popup the note when the superscript number in the text is mouse-overed. This is tremendous, since that is one of the big problems with many personal books: most of us just don't have time to manually convert footnotes prior to compiling in Logos, and as a result, many personal books don't have functional footnotes.

I have experimented with converting some PDFs. I converted a couple of commentaries in PDF form from, and the footnotes are retained perfectly (as far as I could tell by spot-checking). I converted a couple of issues of the journal Themelios (available in PDF form from The Gospel Coalition). In this case the footnotes also came through fine. One thing I did notice is that some compound graphics, that is, graphics that were in the original source (from which the PDF was made) in the form of several graphics "grouped" together to form a single picture, don't compile at all in Logos. Another annoyance with some PDFs is that when they're converted, you can wind up with a bunch of words, phrases, and sentences that were in the PDF as all-caps, but convert all mixed between upper and lower case. (Looks like those poison-pen letters from crime movies.) This happened with Themelios. Conclusion:  if you want a Themelios issue, pony up the $2 and buy it from  Logos. [Edit 7/17/2016]: For the last couple of years, Logos and The Gospel Coalition provide the Logos edition of Themelios free when each issue is published.

A couple of caveats. One, the footnotes have to be linked, active footnotes in the PDF, or Word won't have any magical powers to make them active. It is possible that there are active footnotes that Word won't convert, but so far that hasn't been my experience. Two, a really large PDF might not even open. Word will report some vague error about not being able to open the file and stop. In this case, if you really need the document, you could probably split the PDF up into two or more files and make it work. There are a number of free PDF splitter programs; search for "PDF SAM (split and merge)".

One more issue: you might get a notice from Word that certain interactive features of the PDF won't be imported. I have run into this when converting PDFs from; I can't tell that anything is missing. I think the notice is referring to the links to the resident CCEL online Bibles.

To actually do a conversion, right-click on a PDF file in File Explorer (or Windows Explorer) and choose Open With, then Microsoft Word (assuming you have installed 2013). It takes longer to open than a regular Word .docx. When it has opened, simply save the file as a .docx.

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.


Sunday, November 27, 2011

The Finney Files - The Gospel According to the Heretic Pelagius

This begins a series of posts examining Charles Grandison Finney and his influence on modern American Evangelicalism. We start with the theology of the fifth century monk Pelagius because Finney is a vivid (relatively) modern example of a Pelagian. In this video, the gentlemen on the talk show White Horse Inn discuss Pelagius and his theology.

Thanks to WHI, and to Lane Chaplin for his work in making the video for the mp3.

Friday, November 25, 2011

Scripture Cookie O' the Week - Joshua 24:15

Joshua 24:15 (ESV)
15 And if it is evil in your eyes to serve the LORD, choose this day whom you will serve, whether the gods your fathers served in the region beyond the River, or the gods of the Amorites in whose land you dwell. But as for me and my house, we will serve the LORD.”

We often hear people in the quest for Biblical evidence of autonomous human free will quote Joshua 24:15, although they usually just quote a single clause of it:  “Choose this day whom you will serve…” However, when this passage is quoted in this way, the entire context is missed. Even a cursory glance at the whole verse (above) points this out. The choice given is between two evils: the gods that Terah (and presumably Abram, before he was called) worshiped in Ur and the gods of the Amorites. Let’s look at the whole of Chapter 24.

Joshua 24 is a typical covenant renewal passage. Yahweh, through Joshua, recounts to the judges, elders, and other leaders what He has done for the people of Israel, His deliverance of them from bondage and what He is providing for them in the Promised Land. He begins noting that Abraham worshipped other gods prior to his call. Note the language used here “Then I took your father Abraham from beyond the River…” Interestingly God didn’t say “I offered to Abraham”, or “I negotiated with Abraham”, no, “I took Abraham…”

Joshua then, in Verse 14, issues a command “Now therefore fear the LORD and serve him in sincerity and in faithfulness. Put away the gods that your fathers served beyond the River and in Egypt, and serve the LORD.” This is a command; not the first volley in a debate or an offer of negotiation, but a command. In Verse 15, Joshua provides a choice, but it is a choice between two evils: “And if it is evil in your eyes to serve the LORD ,choose this day whom you will serve, whether the gods your fathers served in the region beyond the River, or the gods of the Amorites in whose land you dwell.”

It’s worth noting here that those who follow Reformed Theology (or Calvinism) don’t deny that men have wills; the issue is how free the will is. Since the Fall, Biblical history and our own experience confirm that fallen (that is, unbelieving or natural) men have always had a choice of the evil they prefer. Here, Joshua is giving them a choice between two evils, if they don’t follow the command to serve the LORD.

The leaders of Israel respond by affirming that they will serve the LORD. Joshua then says something curious in Verse 19: “You are not able to serve the LORD, for he is a holy God. He is a jealous God; he will not forgive your transgressions or your sins. If you forsake the LORD and serve foreign gods, then he will turn and do you harm and consume you, after having done you good.” Commentators have various explanations for this statement. Some take it as a warning; others say Joshua is pointing out that Israel is not able to faithfully follow Yahweh under their own power; others assume it is a prophecy from Joshua of the ultimate outcome of all but a remnant of Israel. I tend to think it is a combination of the latter two ideas:  Israel is unable to be faithful without faith granted by God and most of them will not be granted this faith.

In any case, this passage does not confer an autonomous free will to anyone.

Sunday, September 18, 2011

Quotes 'O the Week

"¿Por qué no te callas?"
("Why don't you just shut-up?")

King Juan Carlos of Spain to the Odious Hugo Chávez during the 2007 Ibero-American Summit.

KJC is probably untrustworthy like all the other socialists, but these words are immortal.


"This is in more senses than one a remarkable book. It is to a degree very unusual an original work; it is the product of the author's own mind. The principles which he holds, have indeed been held by others; and the conclusions at which he arrives had been reached before; but still it is abundantly evident that all the principles here advanced are adopted by the writer, not on authority, but on conviction, and that the conclusions presented have all been wrought out by himself and for himself. The work is therefore in a high degree logical. It is as hard to read as Euclid. Nothing can be omitted; nothing passed over slightly. The unhappy reader once committed to a perusal is obliged to go on, sentence by sentence, through the long concatenation. There is not one resting-place; not one lapse into amplification, or declamation, from beginning to the close. It is like one of those spiral staircases, which lead to the top of some high tower, without a landing from the base to the summit; which if a man has once ascended, he resolves never to do the like again."

Charles Hodge in a review of Charles Finney's Lectures on Systematic Theology.

"Free will I have often heard of, but I have never seen it. I have always met with will, and plenty of it, but it has either been led captive by sin or held in the blessed bonds of grace."

Charles Spurgeon

Tuesday, September 6, 2011

Scripture Cookie ‘O the Week – Jesus Wept; But He Didn’t in Matthew 23:37

Matthew 23:37 (ESV)

37 “O Jerusalem, Jerusalem, the city that kills the prophets and stones those who are sent to it! How often would I have gathered your children together as a hen gathers her brood under her wings, and you would not!” (emphasis added)

How many times have you heard this verse repeated thus:

“O Jerusalem, Jerusalem, the city that kills the prophets and stones those who are sent to it! How often would I have gathered you together as a hen gathers her brood under her wings, and you would not!”

I’ve heard it a zillion times; frequently from people who have a specific theological ax to grind and sometimes, from men whose theology doesn’t lead them to it, but human tradition has so engrained itself that they don’t realize they’re misquoting Jesus.

The immediate issue, of course, is the omission of the phrase “your children” and substituting “you.” What’s the difference, you might ask? It’s a big difference. In the first place, every single word in the Bible is important, or it wouldn’t be there. That doesn’t mean it is necessarily bad to paraphrase Scripture in casual conversation, but when the paraphrase presents a different meaning, it is. Secondly, the exclamation “Jerusalem, Jerusalem” is what is known as a metonymy, which is figure of speech that references a thing or things by using the name of something closely associated with it. You might be familiar with its modern use when newscasters use “Washington” as a metonym for the Federal government or “Moscow” for the Russian government.

Now, the big question here is, “What is Jerusalem a metonym for?” The answer to that depends on the context of the larger passage. Matthew 23:37 comes at the end of an entire chapter where Jesus severely chastises the Scribes and Pharisees, who were the de facto leaders of the Jews in Jerusalem. He points out their pomposity, their love of adoration and attention, calls their mothers vipers, and calls them “sons of hell.” Take a few minutes and read the entire chapter. Note particularly Verse 13:

Matthew 23:13 (ESV)
13 “But woe to you, scribes and Pharisees, hypocrites! For you shut the kingdom of heaven in people’s faces. For you neither enter yourselves nor allow those who would enter to go in.”

This verse is important to see as a bookend to Verse 37.

Here’s where the theological axes begin to grind. Critics of Reformed Theology (or Calvinism) believe Verse 37 refutes the Calvinist doctrine of Irresistible Grace and proves that people have an inviolate free will. Irresistible Grace means that God is sovereign and can overcome all resistance when He wills, particularly in the regeneration of a sinner. (See the link above for a more complete definition.) They would quote the verse with the “you” substituted for “your children” and say “See, God’s will can be resisted because Jesus is lamenting that He wanted to save all of the Jews in Jerusalem, but all of the Jews would not allow it.”

But, when Jesus says “your children”, He is speaking specifically to the Scribes and Pharisees and saying that they would not allow the people under their spiritual authority to be gathered. Remember Verse 13? It’s saying essentially the same thing. Now, this doesn’t mean that Jesus is saying they have power to prevent Him from His saving work; He is holding them responsible for trying. Keep in mind that this is a passage of severe chastisement and judgment, probably the most severe in all of Scripture.

But wait…there’s more. Those misquoting Jesus typically also add that He is weeping. However, the text nowhere mentions that. The somewhat parallel passage at Luke 13:34 also does not mention any weeping, as it also is a passage of judgment. There is a passage in Luke where Jesus does weep; it’s in Luke 19:41, which occurs just after the triumphal entry into Jerusalem (which is paralleled in Matthew 21, but with no weeping), and He prophesies the destruction of the city in 70 A.D.

So, why the reference to weeping? It is an attempt to use emotion to gain a theological point, pure and simple. As I mentioned earlier, I’ve heard Reformed pastors and teachers make the same misquoting, but not in the context of refuting Calvinism. Why do they do it? I can only guess that they’ve heard it misquoted so many times in their lives that it is ingrained in their tradition.

What are our lessons here?
  1.           Read the Bible carefully
  2.           Quote passages in context
  3.           Recognize and challenge your traditions when reading the Bible
  4.           As James White says:  “A man who does not recognize his tradition is a slave to that tradition.”
  5.           Emontions aren't the best bases for Bible interpretation.
  6.          The text says what it says what is says.