I agree that Thought Types would be an easy way to accomplish this. I wanted to explain the steps in a bit more detail, just in case you haven't used the selection box much.. You can hit Ctrl and click on each Thought you wish to move to Selection box. Alternatively, to move a group of Child Thoughts to selection box at once, hold Ctrl and click on the Child gate. Then, as rogerwalk mentioned, right click in the selection box and choose to set the Thought Type. Before you do any of this, you create the Thought Types from with the Properties and Attachments tab. Click: Type - New - Color
It would be very helpful if the PB developers added a "Set Color" menu option for Thoughts. Then we could use the menu to set the color for selected Thoughts in one click (the same way we can set tags or types).
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