Help with maintaining PID coloring in groups

Dear Jalview team,

Apologies for what is probably a trivial issue, but I’m struggling to highlight an alignment in Jalview the way I’d like.

I have a set of 8 proteins; my goal is to highlight the entire alignment by PID and then emphasize all the S and T residues (I have been going about this by creating groups of these residues and setting the group text color to red). However, every time I create a group, it loses the PID coloring from the alignment; when I reset the PID coloring, all of the groups appear dark blue (reflecting the similarity to the group) instead of reflecting the similarity to the consensus sequence. Is there a way to maintain the PID coloring while still selecting and coloring certain residues as groups? Or, is there another way to differentiate all the S and T residues without creating groups?

Thanks for your help!

No question is a trivial question!!

Are you aiming for this kind of effect as shown in my screenshot?

I first coloured the whole alignment by PID then made groups and within each group set the group text colour.

Right click the group then:

Selection->EditGroup->Group Colour->Text Colour

This seems to persist and not reset the PID colouring.

I’m running Jalview on (OSX Catalina) which is the current release version from

Incidentally, in exploring this option I did notice that there is no Custom Colouring option within a group. Not sure why that is, so should be a feature request!

I hope this helps?


P.S. for the screenshot I could colour the lines around groups the same as background so that they are not visible.

Just to add that if you wanted to highlight the background colour for each S/T you can do this by first doing a Find for S/T then Click “New Feature”. You can then colour the residue background. Sorry, I forgot this option when I answered above. Picture shows the result on a test alignment with PID colouring but S/T backgrounds in Red.

Please let us know here how you get on and if these suggestions help. Many thanks, Geoff.

Hi Geoff,

Thank you for your help! Your first screenshot is very close to what I’m hoping to achieve - the only thing is that it doesn’t look as though the PID highlighting is visible within each group (all backgrounds in the group are white). Is there a way to make and color the group but keep the highlighting? I’m wary of coloring each group by PID because then the highlighting is based on intra-group percent identity, not the column as a whole.

If this is not possible, I will probably end up using the Feature option in your second post; it’s very similar to my goal and would probably work fine!
Thanks again for your advice.

Glad it helps. Do you mean something like this?

I made the group then changed the text colour in the group, then applied PID. Unless you slelect “Apply Colour to All Groups” I think this is the correct behaviour. Jim Procter will be able to answer this more completely when he returns from holiday as he knows the implementation details and constraints in the code.

In the meantime, hopefully, this helps you get most of the way to what you want to show? For publication figures, we usually reach a point where output to SVG or PS then edit in Illustrator to finalise is neccessary.

Oh, the forerunner to Jalview was ALSCRIPT which allows you to tweak most things about boxing/shading/colouring/fonts/etc on alignments but is far less easy to use than Jalview (why we developed Jalview in the first place!) However, some people find it helpful and still use it. You can download it from

Finally, would you mind sharing who you are and where you work? It is nice to know who we are helping and also can help us build the case for continued funding for Jalview development. If you don’t want to do this on the public list, just email me. Many thanks, Geoff.