The red and blue results are showing us how close (or far) we are to obtaining the correction solution. The blue shows residues which are protected or “basepaired” and the reds show the ones that are exposed or “unpaired”. In the perfect scenario, we would expect to see that where there are basepairs, the residues are blue, and where there are loops and bulges, they would be red.
Bumping this question because I’m still a bit confused.
First off, I assume that red has been changed to yellow since the question was written, so hopefully I’m talking about the same thing.
Mostly my question has to do with how in a certain basepair one of the two nucleotides can be yellow and one blue – does that mean that one of them is interacting with another section (in 3d)?
also, what does gray mean?
Ding - yellow always has been yellow. Perhaps you were talking about different thing?
Can you explain where you saw red and blue?
In the title to this question - “what do the red and blue results mean?” Maybe the original question wasn’t actually asking what I thought it was?