User Defined Colours
-Each of the residues may be assigned a new user defined colour.
-You may save this colour scheme and reuse it at a later time.
-The default user defined colour is the last user colour scheme which was defined.
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+
You may define any number of new colour schemes, each with a unique name.
+
+ Each of the residues in a new colour scheme may be assigned a new user defined
+ colour.
+
+ Click "Apply" or "OK" to set your new colours on the active
+ alignment window.
Click "Cancel" to undo your changes if you pressed the "Apply"
+ button.
+
+ If you save your colour scheme with a unique name the colour scheme name will
+ be added to the "Colour" menu on each new alignment window.
+
+ Any saved colour schemes will be automatically loaded the next time you use
+ Jalview.