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I just read a post that mentioned the use of keyboard shortcuts in the manual alignments tool. When I run the tool only one window opens, the GUI to edit the alignments. I can't seem to find any settings where this other window would be enabled/disabled. And using the keyboard over the mouse to delete multiple misaligned faces would be super handy. Any thoughts on why I'm not getting the "third window?"
Either I read incorrectly, or this will be embarrassing operator error.
I'm not sure I understand what you mean by the 3rd window. Keyboard shortcuts are shown in [] (square brackets) in either the tooltips or right click menu where they are available.
My word is final
Here's an example of the post(s) I'm referring to: viewtopic.php?t=427
He states there's a dedicated window with keyboard shortcuts. But I think you've answered my question anyway. I was hoping for a way to delete multiple alignments quickly when manually checking them. When a source kicks out <20K alignments I often choose to delete the problem children rather than fix 'em. 
Not a biggy.
Thanks again for the outstanding tool.
Ah, yeah. That was the old (much less fully featured) manual tool.
As it stands, the manual tool is better for fixing/tweaking rather than large-scale data removal. It's best to try to clean things up as much as possible in your OS'es file manager and clean the alignments file prior to launching the manual tool.
My word is final
