FAQ Saving favourite colours
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Part of the MyPaint FAQ.
How can I save some colors I use often between sessions?
As of 1.1.1-alpha, you can bookmark the colour you want to the palette window.
For earlier versions, you can use the scratchpad feature, that is saved independently of the image you're working on. The scratchpad is essentially a mini canvas. You can add your preferred colors to it using any brush and then save it. You can later reopen it for use with other images. (Note: Sometimes the scratchpad is accidentally overwritten. Be sure to back up the "scratchpads" folder in your ".mypaint" periodically.)