I’m wondering whether I can reassign the shortcut that’s currently being used for searching inside the database, cmd+opt+f. I have manually reassigned it to Full Screen, but when I hit the shortcut, my cursor goes to the search bar.
You’d go to System Preferences > Keyboard > Application Shortcuts. Click the “+” sign and add DEVONthink as an application (browse the app list). The “Menu Title” you want to assign the shortcut to is “In Database…”, because the full menu entry is Edit > Find > In Database…. To type the ellipses, press command-;
The shortcut you assign to this menu entry for DEVONthink will override the default.
Thank you for the consideration korm, but after changing the shortcut of this command, and having it listed in the menu, it doesn’t override the original shortcut. The shortcut I put in does call up the command of focusing my cursor to the search bar, but so does cmd+opt+f. It seems that shortcut is hardcoded into the program.
Sorry, but, actually, overriding in the manner described does work. You probably have some other conflict in the shortcuts in your configuration (either in DEVONthink or a global shortcut).
I looked through my list and I don’t see any conflicts. Have you personally tried to change the shortcut for this specific command? Other commands can be overridden, but this one in particular is stubborn, at least for me. Cmd+opt+f always puts the focus of the cursor back in the search database bar and so does cmd+shift+f, which is what I personally assigned to the command.
I’ve been able to change the shortcut for every other app’s full screen command, just not this one. And I double checked the full screen command in DevonThink and know that the command name is Window for DevonThink and the menu reflects the shortcut (cmd+opt+f) that I assigned to it.
I have tested this for you and it worked. Don’t know what else to say.
Korm, I initially appreciated your consideration. Now I don’t know whether you’re here to help or just here to mock and be derisive, just like how your attitude reflected in your private message.
Look. Evidently, on your machine, the shortcut overrode the default command. But on mine the specific shortcut doesn’t override the default. If I change the shortcut for ‘Window’ to shift+cmd+opt+f the command works. But when I change it to the shortcut I want, it works once, but then goes back to the default command of focusing the cursor to the search bar.
Now either you can help or you can’t. If you can, I’d be immensely grateful. If you can’t then there’s no need for your immature antics anymore. It’s not professional, and it doesn’t behoove a support forum, especially for an app like DEVONThink.
Sorry if my ironic answer offended you. That’s not the intent. I am not a staff member – just a volunteer looking to be helpful. I’ve explained how the keyboard shortcut process works. I’ve tested it (as I always do whenever I write a reply here or anywhere) before I posted my answer, using your description of your circumstances. That it doesn’t work for you is unfortunate, but that’s all – just unfortunate. As I said before, there’s probably some unseen conflict among all the keyboard shortcuts on your machine. That might also be unfortunate, but that’s the way things work out sometimes.
I just tried this morning to duplicate what the OP wants to do and I have to say that I’m experiencing the same behavior. I don’t know what the conflict is, and I don’t plan on looking further to see what it is, but I do see it also. Normally I wouldn’t suggest giving up so quickly but I do have to ask the OP-why not stick with command-control-f to switch to fullscreen mode? Most apps have standardized on this shortcut to go in/out of fullscreen mode, so it would seem that the simple solution is stay with that shortcut.
There is a tricky aspect of setting application shortcuts in System Preferences, which is dealing with menu names that contain ellipses, such as the “In Database…” item that the OP wants to assign a keystroke to. The reliable method to type ellipses in that System Preferences dialog is to press Option-; (that is, Option together with semicolon). This was supposed to have been fixed in Mountain Lion (so that pressing three periods would also work), but really wasn’t fixed reliably.
I can report again that the shortcut I created for “In Database…” yesterday has gone through several reboots, etc., and is still working reliably. With that, I will never respond to this thread again. 
I did enter the new shortcut’s menu name using option-; to create an ellipse, and the new shortcut does work-same as what the OP reported. However, command-option-f continues to work also to put the cursor in the find in database field of the toolbar. In other words, both shortcuts do the same thing when the new shortcut should replace the app’s default shortcut.
For anyone interested, this is set in symbol and text substitutions, from the System Preferences for Language & Text, under the Text tab.
I haven’t given up. I believe that this is no longer an issue with DT and more of an issue with the OS.
With regards to the question of why I didn’t stick to the default shortcut: I just find that keystroke awkward where I have to use my right hand to hit the F-key that is normally used with the left, and I find hitting the cmd+alt key easier to hit than cmd+ctrl. Just a personal preference.