I think options should be provided to allow the following:
User-defined colours for the four bases. It’s quite hard for me to perceive the difference between green and blue, particularly when zoomed out.
Change the background colour. The current blue background probably doesn’t help matters: the human eye is quite short of blue receptors relative to red and green.
Eliminate eye candy. This would include bubbles and particularly the pulsing of the binding oligonucleotides.
1- I agree, especially in the new 2D structure data browser.
2- How about a white background so a B&W printout doesn’t waste blue ink?
3- Changing the settings in the puzzle should do most of that.
Very good ideas, I know that Eterna has continually worked to improve these things in the past.
Changing the puzzle settings: does that mean checking Low Performance Mode? That removes the bubbles (which actually aren’t that annoying) but does nothing about the pulsing sequences.
You are correct, I can’t find anything that stops the pulsating (telltale heart) oligo’s
I like the background myself, but it would be nice to have a white (or certainly paler) background for certain purposes [thinking printer friendly version here]. Also I agree that pulsing should probably not be included in low performance mode.
I don’t mind the colors of the bases either, though it would be nice to have additional highlighting features such as for Keto vs aMino bases for instance or puRine vs pYrimidine bases as this could prove useful for analysis or even for solving some of the harder, bulkier puzzles.
I propose one more thing, that there be a way (if at all possible) to indicate hydrogen bonding or other binding interactions between those bases which are boosting, such as in the case of G-A pairs. Maybe a line between these bases. It would work nicely as a feature that could be toggled on or off as in the case of Free Energy or Nucleotide Position in the sequence.