DEVONthink Part 2 - My Preferences

Like many apps, the Preferences window can be opened by clicking CMD and , or by accessing through the menu bar. 

Let's start off on the General pane. 

Under Appearance, we have:  

- Alternating row colors in views. Unticking this simply toggles the colours of each alternate row in the file pane. I like to have this selected in order make it easier to view and identify multiple files. 

- Display number of items inside groups will show a number to the right of each group name. This number, as expected, relates to the number of items contained within the group!  I like keeping this selected because when I set up a Smart Group, which I'll come to later, I like to know that the rules I have setup work straight away and I haven't made a typing mistake anywhere. 

- Highlight Internet links in views does exactly what it says! If your file name is actually a Bookmark or link to a web page, then it will be highlighted as such. Untick this box and it will just look like any other regular file. 

- Mark duplicates and replicants in colour is very important for me. I will go into what duplicates and replicants are in a later screencast, however for now it is only necessary to know that if you wish to identify these, this is where you would toggle this setting.  

- Labels - this allows you to select the format type of the labels. Options are Classic (Mac OS), Modern (Mac OS X) and Dots (Mavericks)   

  The Interface section brings up some interesting options.  

- Hide “Groups and Tags” panel when inactive button will hide the floating Groups and Tags panel during periods of inactivity. The Groups and Tags panel is a nice little option for importing documents when in other applications.  

- Open contents after using “New with clipboard” will display the clipboard contents you have just pasted in a new window.  

- Always open groups in a new window will open a new DEVONthink Pro Office window when you double-click on a group name to open it’s contents. I leave this ticked as soon as I have finished with a window I am using, I always use + Q to close it anyway and this will always return me to my main view.  

- Retain View is not one I use. When the above option, Always open groups in a new window, is unchecked, this option keeps the actual view settings when you navigate the group structure instead of applying the group's individual settings.  

- Enable tabbed browsing allows you to open a tab whenever the key is pressed whilst opening a file. If it is unchecked then the documents are either opened in the same view, with their default application or in a new window. 

The Editing tab will give you the chance to change some of the DEVONthink editing options. A lot of these options are very self-explanatory however, as this is as detailed a guide as I can make it, I’ll cover the lot!  You will probably find yourself leaving a lot of these options de-selected as DEVONthink Pro Office is not primarily an editing tool, moreover a repository for files. However the ability to edit files inline is there so it’s good that these options are available. 

 - Display PDF attachments of rich texts will show any PDFs that have been attached to rich text documents.  I leave this de-selected. 

- Check spelling while typing/check grammar with spelling/correct spelling automatically - these I leave de-selected because I do not use DEVONthink Pro Office as an editor.  

- Smart Quotes - will change straight quotation marks for curly quotation marks. Again, this is de-selected for me. 

- Smart copy/paste - this will preserve the formatting of anything that is added to the clipboard within DEVONthink Pro Office. 

- Smart Links/Data Detectors/Smart dashes and Text Replacement - these are all standard options built into OS X so I leave all of these de-selected.  

- Rulers Units - You can change the unit of measurement on the built-in ruler. Options are centimetres, inches, points and picas. 

- Fonts - Default fonts can be selected for: Plain Text, Rich Text and Note as well as a Full Screen font. You can also select a background colour for full screen mode as well as a default width. 

- WikiLinks - You can select Automatic here if, when you type the name of a document that is contained within the DEVONthink Pro Office database, you would like a link to be created automatically.     This is essentially useful if you are planning on using a DEVONthink database to function as a fully fledged wiki for a team or organisation. You can change the behaviour of the WikiLink behaviour     here too. If you do not want it to link to groups, then this can be configured. You can also set it to only recognise meshed words (that is words that have a Capital letter contained within, such as     WikiLink). 

- Template - You can enter a template text here if you would like to create a link to a document that doesn’t exist yet. This notifies the end user that a document is currently in development for this     particular subject. 

- Summarization - You can tell DEVONthink to summarise based on either sentences or whole paragraphs. 

The Import folder defines how you can get information into your DEVONthink database. 

- Files - Here you will find a list of file types that DEVONthink will recognise automatically when they are     imported. 

- Encoding - Select the method of encoding you wish to use for plain text files. If you are unsure, then choose Automatic to let DEVONthink select. 

- Other file types - This allows DEVONthink to import files of an unknown type.  

 - Titles - You can select how the filenames will be presented within the database. You can select to have a filename with extension, without extension or a localised display name instead. I have the filename without extension as, in my display options, I always have a column that tells me the file type in case I need to sort by filetype for any reason, so it seems silly viewing the file type as well. That’s what suits me in any case. 

- New notes - If you select this box, then you will automatically select and display the last note you have taken. 

- Destination - This is a setting that really does depend on your use case. You can choose the default location for new files that are imported via any method that is NOT manual. So it could be the DEVONthink Safari Bookmarklet, or a system service, DEVONagent Pro as examples. You can choose the Global Inbox (my preference), the Inbox of the the current database (if you have one database, this makes sense) or you can choose the inbox as and when the files are imported. 

On to the Sorter window, which only applies if you use the Sorter itself - so I guess here is a good opportunity to talk about the Sorter and how you use it!

The DEVONthink Sorter is a very useful way to import information from other applications, even if a database is not available. It can run independently of the main DEVONthink application.

When activated, a small tab appears in the left hand side of the monitor screen. This tab expands when clicked, almost like a drawer would. In fact, drawers are a really good analogy for how the Sorter works. You can liken the Sorter to a chest of drawers that you put information in to and, when DEVONthink opens, the information is emptied and filed into whichever database you have specified.  

We will go into the Sorter in more detail in another post when we talk about using various methods to import data, however the Preferences options for the Sorter are not large in number and are limited to the following:  

- Availability: start at login - This determines whether the Sorter is activated when a user logs in. I have this     ticked.  

- Visibility - Ticking this box will determine whether the Sorter tab is translucent or solid in colour.  I have     this unticked as I know the tab is there and if I need it, I keep it in the bottom left hand corner of the     desktop. 

- Take Note HotKey - You can set a key combination to automatically open the Sorter and type a note ready     filing. 

- Copy Selection HotKey - Similar to the Take Note shortcut. This is something I make a lot of use of as whichever application you are in, it will copy whatever is selected to the clipboard once the shortcut is invoked and paste it into the Global Inbox. Very handy. 

- Hide Application In: The last window gives you the ability to be able to hide the Sorter tab when certain applications are open.

And so we move on to the Media options and this is probably the first time I’ve actually been into them to see what is available! I love media however I do not use DEVONthink to organise them. By the developers own admission, DEVONthink is not designed to be a permanent repository for media.  

- Movies: Create thumbnails - This option allows you to create thumbnails if you want DEVONthink Pro     Office to create thumbnails for imported or indexed movie files. 

- Play: Automatically/Loop - You can play files automatically when you display them and play them in a loop     if you so prefer. You are also able to set the background colour for viewing movies in this section.  

- Images: Create thumbnails - Like movies, you can create thumbnails for imported or indexed images. 

- Images: Generate from actual image will ignore thumbnails embedded into the image files and let DEVONthink Pro Office generate the thumbnails from the actual image. Again, you can choose a background colour for viewing images here if you so wish. 

- PDF and PostScript documents: Create thumbnails - Shall I type this one out again? No, I don’t think I need to.  Yes, you can change the background colour as well. 

- Create Thumbnails - here you can set whether or not DEVONthink Pro Office is going to set thumbnails for any of the folioing file types: Web Archives, Formatted notes, Bookmarks or Other Files. 

Colors is a very simple tab to explain. You can set different colours for labels, as well as the label names

If Colors was simple to cover then Web makes up for that with lots of different options to choose from. The web preferences are quite easy to understand as they resemble to settings that you will find in most web browsers. As DEVONthink Pro Office has a built-in web browser, it’s important that it is configured the way that you, as an end-user, are comfortable with. 

- Web Content: You can enable lots of web elements here, namely plug-ins, Java and JavaScript. You can also block various elements too, again this is standard in relation to other popular web browsers. You can block pop-ups, zooming (to prevent web sites form automatically zooming windows to full size and block advertisements which will block common inline advertisements provided by some search engines. 

- Images: Display images when web page opens - You will check this option if you wish to display web pages with images. 

- Images: Animate images/Loop animation - These will be checked if you wish to run web graphics animations or run animated graphics in a loop. 

- Accept Cookies: You can decide whether or not you wish the DEVONthink Pro Office web browser to accept cookies or not. For those who are unaware, cookies are little text files filled with information that web pages store on your computer. They speed up the web browsing experience and are generally harmless, however you may wish to exercise control over what is being stored on your machine. Therefore you have the following options:

    - Always - this will accept all cookies

    - Never - this will..that’s right…NEVER accept any cookies!

    - Only from sites you navigate to - this will accept cookies, but only from sites that you consciously navigate to. It will not accept them from other sites, like ad trackers. 

    - Delete cookies on quit - this will delete all cookies that have been stored upon quitting DEVONthink Pro Office. 

- Fonts - At the bottom of this tab you can see options for setting the both the standard fonts and the fixed-width fonts for your browser windows. 

- Style Sheet - if you have experience with CSS, you can specify your own Cascading Style Sheet file to further modify the look and feel of your web browser, however this is only to be used by advanced users due to the adverse effects it can have on some pages. 

- Text Encoding - You can select your desired Text encoding for displaying web pages. I have this set at Automatic however you may wish to choose a more specific one for your own particular language group. 

DEVONthink Pro Office can be used as an RSS reader as well. It’s certainly an application of many hats! I don’t really use this capability myself, relying on a more dedicated third party reader, however I can see this would be useful if you have a particular project that is being run exclusively in DEVONthink Pro Office and you have RSS feeds related to it that you would like to collate in the same place as the remainder of your documentation. The preferences are as follows:

- Check for updates - You can elect to refresh the RSS feeds manually, after opening the database, every 5/15/30 minutes, every hour or every day. You can elect to Skip duplicates (definitely wise as many feeds have duplicate data) and you can also convert the RSS categories into tags, which is very handy for searching the database for specific subjects. 

- Remove articles - Here you can choose how often articles are removed. This is either manually or another pre-determined time. By default, unread articles will not be deleted however you can check a box to allow unread articles to expire also. 

- Feed Style Sheet - Like the web preferences earlier, you can elect to have a different CSS file to format your feed, however this setting is much safer than it’s web counterpart as there are only four different pre-defined sheets you can choose: Default.css, Leopard.css, Simple.css and Tiger.css

The following set of preferences is not something I have had the need to make use of. DEVONthink Pro Office features a built-in web server. You can share documents on your LAN (local area network) and over the Internet. This of course involves DEVONthink Pro Office being installed on an ‘always-on’ machine. 

This is a fantastic collaboration feature that we will cover in a later post but let’s quickly cover off the different configuration options now for future reference:

- Incoming Files - You can convert incoming images and PDF documents to searchable PDF’s. This increases the size of the files however this is strongly off-set by the convenience and productivity advantages this brings. The ability to be able to search all images and PDF’s is a mainstay of my paperless regime and I urge you to do the same. 

- Bonjour Name - This will be a distinct name that identifies your computer on the local network using Bonjour. Bonjour is a service that locates resources such as printers, other computers and the services those devices provide using multicast Domain Naming System records (mDNS) however that is a discussion for another time. And another book!

- Bonjour Domain/Port - These settings will configure the Bonjour domain and TCP/IP port number it uses. Generally you will leave these blank unless you really know how and why you are making the changes. 

- User/Password - This will help protect your database by ensuring that anyone that would like to search your database from a web browser has to enter credentials before they will be given access. 

- Start on Launch - As expected, this will automatically start DEVONthink Pro Office’s web server as soon as you launch DEVONthink Pro Office. 

Now the Email tab is something that DOES have a lot of relevance to me as I use DEVONthink Pro Office as a tool for archiving all of my mail.  


- Conversations: Import complete conversations - This will allow DEVONthink Pro Office to scan your Sent Messages folder and import sent messages that belong to the same conversation as another email message you are importing. This is selected for me. 

- Conversations: Group conversation threads - This will combine all messages belonging to a conversation thread into a group, making identifying conversations a lot easier. Again, I have this ticked. 

- Messages: Previously imported will become replicants - When this option is unchecked, as it is in my setup, DEVONthink Pro Office skips previously imported messages. 

- Messages: Use alternate view - This allows you to click links or copy text in the Quick Look preview. 

- Message Content: Fallback text encoding: By default, when DEVONthink Pro Office decodes an email message it will use the messages encoding information. When there is no encoding information to hand, DEVONthink Pro Office will use the encoding that is set within this menu. 

- Message Content: Download remote images in HTML messages: I leave this unchecked as a security setting as it is a way for people to track whether or not you have accessed a message, spammers especially. 

- Message Content: Encryption: DEVONthink Pro Office can decrypt secure messages as they are filed which is a requirement for using the AI-based functions of DEVONthink Pro Office, such as Classify or See Also 

Font and Colors - There are options here for selecting the fixed-width font for plain text messages and marking quoted text in specific colours. It should be noted these do not take effect whilst the message is in QuickLook mode. QuickLook mode is for documents that DEVONthink Pro Office cannot render natively. 

You can also select which labels you would like to assign to messages that have been flagged or marked as high priority. 

OCR is a vital component of the paperless ecosystem. Optical Character Recognition ensures that the contents of your file, whether image, PDF or text, is searchable from within the database. The files are larger than the original as an additional text layer is contained over the top of the original file (this cannot of course be seen). Therefore when you look at the the file type of an OCR’d document in DEVONthink Pro Office, you will see it is PDF+Text. 

This preferences section will help determine how the OCR is applied. 

Incoming Scans: You can elect here whether or not OCR is going to be applied to to PDFs that have been sent from known scanning software. I have this selected. 

Original Document: You can move the original document to Trash once OCR has been applied. I keep this selected as it would be very easy for my databases to fill up with large files quickly if I didn’t.  

Searchable PDF: You can add your own metadata to files as they are scanned in by ticking this box. You can use this to enter your own preferred document name, author and keywords. I have this unchecked as my workflow tends to mean I scan a lot of files in batches and I don’t want this dialog box appearing every time I scan a document. 

Resolution and Quality: These two options can be used to control the dpi resolution and picture quality of the PDF created by the OCR process. I go for 150 dpi and 75% quality to try and ensure a good quality of output without maximising the file size. 

Recognition: You can control the accuracy of the text recognition against the speed of the processing. The faster the processing, the less accurate some of the text recognition may be. I have had no problems with this being set as Automatic.  

  Finally, you can choose the language that will be used within the OCR process. You can select both primary and secondary languages. Mine is at the default however I could choose a further two secondary languages if I so wished, bringing it up to it’s maximum of four.  


DEVONthink Pro Office gives you the opportunity to keep multiple copies of your database synchronised in multiple locations. Options for this are found on the Sync tab.  


On the left, you can see the Databases column. This gives a list of databases that are able to be synchronised with another location. On the far right, you can select a location by clicking the + button. 

I have selected a Dropbox location as my Sync however you can choose any of the other options as per your needs. Clicking the - button can remove any you have configured. You can also have multiple destinations here, you are not limited to one sync location per database. 

In the centre pane you specify the schedule you would like syncing to adhere to. Myself, I like to sync once an hour and upon the closing of the application. I know this gives me a clean exit when I finish for the day and I don’t have to worry about data somehow being corrupted - that’s just a piece of mind issue for me really. 

If you click the Incoming Connections button you can define whether other DEVONthink users on your network can synchronise with your instance of DEVONthink Pro Office. You’ll have to specify a port number that will be used for access. 

The Backup tab needs some clarifying. This is very important so please please pay attention. This does NOT determine how the whole database is backed up. If you want to backup the database in it’s entirety, then you will need to use Time Machine or some other third party software. The built-in backup functionality within DEVONthink backs up the database index on a regular basis. It will take a copy of important database files and move them into a new Backup folder. You can decide on an Hourly, Daily, Weekly or Monthly backup (lr never if that’s what you would like!) and also how many backup files will be retained. 

You can still create a manual backup anytime you wish by using Tools > Backup & Optimize.  

The last tab is for Updates and you can simply decide how often you would like DEVONthink Pro Office to check whether there are software updates available for download and install.  I have this set to Daily.  

And so that brings us to the end of the Preferences section - quite a lot there to get on with. Now, we are going to move into the detail of how to use the application in full.