Hi,
I previously made an alignment in Jalview, and I used a user-generated color scheme to match coloring in some structures. I was able to color the actual font, and I did not have the little boxes of color around the letters. However, now I don’t remember how to do this, and I can’t seem to find documentation for it. Does anyone know what I am talking about and how to do it?
Thanks!
Hi Kate - the option you are looking for is 'Colour Text'. You'll probably also want to disable the 'colour Boxes' option, so you can actually see the text against the background 
It's a bit worrying that you can't find the documentation for it - if you'd like to tell be where you looked I'll check to make sure I haven't deleted something from our online documentation index !
Hope that helps!
Jim Procter.
On 20/03/2012 05:17, Kate Mittendorf wrote:
I previously made an alignment in Jalview, and I used a user-generated color scheme to match coloring in some structures. I was able to color the actual font, and I did not have the little boxes of color around the letters. However, now I don't remember how to do this, and I can't seem to find documentation for it. Does anyone know what I am talking about and how to do it?