User Defined Colour Schemes

  1. Load a sequence alignment PF03460 from the PFAM seed database. Ensure that the Colour $\Rightarrow$ None is selected. Select the alignment menu option Colour $\Rightarrow$ User Defined. A dialog window will open.

  2. Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.

  3. Insert a name for the colourscheme in the appropriate field and click Save Scheme. You will be prompted for a file name in which to save the colour scheme. The dialog window can now be closed.

  4. The new colour scheme appears in the list of colour schemes in the Colour menu and can be selected in future Jalview sessions.

For more information on this topic go to section 3.1 of the Jalview manual.
 This exercise can be viewed in the Colouring protein residues in an alignment video.