User Defined Colours

You may define any number of new colour schemes, each with a unique name.
Each of the residues in a colour scheme may be assigned any chosen colour.
Select one or more residues, then select the desired colour.
Use Ctrl-click to select multiple residues, or click then Shift-click to select a block.
Note that the currently selected buttons are highlighted by a lighter text colour.

The Case Sensitive option allows you to choose distinct colours for upper and lower case residue codes.

The Colour All Lower Case option allows you to apply a selected colour to all lower case residues.

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.