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Exactly as dwanthy says, if you click on the plugin's icon you should see a menu list of items - one of them is Customize. Once you click that there is a list of calibre fields including your Custom Column. The first column in the table is 'Action' and its a drop down selection list that includes '' (blank/none), Create, and Delete. Select 'Create' - this tells the plugin to Create collections based on this calibre field. Save it, and then use the 'Preview Collections' to view what you will create before running 'Create Collections'. Of course, you need to put some information into your custom column (either by manually typing it, or using Import Collections to use the data on your Kindle).
I never liked having to use a drop-down to select none/Create/Delete and much preferred it when I only had a checkbox - but feature requests such as they are meant it was needed when people wanted to delete entries as well...
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