New discussion based on this post from @amehta :
Alignment in Jalview and Web Services - #4 by amehta
We have been trying to project the ConSurf colouring schemes based on scores onto the alignment generated in Jalview, but we have not been successful so far. We attempted to automate this with a Python script, but that did not work either. We then tried a manual approach by loading the ConSurf scores as features and using the “View” options to apply colouring based on the scores; however, this also does not seem to work. If anyone can please shed light on what we are doing wrong, I would be most grateful. Thank you!
The best route for visualising consurf scores would be to create a ‘Per sequence’ annotations file from the per-residue scores in the consurf results. Would you be OK sharing your python script and an example consurf output in this thread ? alternatively reach out to me directly via my Uod email/teams and I’ll post a solution back here after we’ve fixed up your python script 