How to change city borders in a custom map?

Go to the "Paint" tab in Worldbuilder. There's a check-box / drop-down for Culture Borders. Select that check-box, use the drop-down for that check-box to select which player you want to "paint" borders for, and select tiles or tile-groups that should be assigned to the culural borders of player_X.

Note that there are also a "brush-shape" and "brush-size" drop-down menus to select the number and 'shape' of tiles that are selected with each mouse-click.

edit: there are also some things in Worldbuilder that are only effective after you make player selections within the Scenario Properties tab. I'm not sure Culture Borders will work if you have not already assigned all the civs your map is going to use.
 
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