I’d like give a big thumbs up to Nando for his Disco Blacklight bond editing capability and suggest a slight tweak:
In addition to Natural/MFE and Target modes, I’d like to see an “Unlocked” mode where even target bonds can be altered. That allows a freedom to experiment with bonds and see what “near-miss” folds might have as energies. It could be especially useful for switch and dimer modeling so that you could experiment with how a switch might unfold and re-fold in the presence of another molecule.
I tried playing with the dimers without the “Unlocked” target bonds and could not quite get the shapes I needed.
I think I had a past forum post discussing this sort of feature, but have not been able to dig it up as yet.
So as not to confuse new players, perhaps this mode could be added by a normally off configuration option under Advanced Settings. (Likewise for alternative energy models? Hint. Hint.)
Agreed on the “normally hidden” condition. This said, I see good and bad sides to that idea. The good one is that it would be computationally cheap, but the problem I see is that I doubt players would be be able to see much with it.
The alternative would be to expand the native mode with the capacity to display suboptimals. Drawback: computationally much more costly. Advantage: the structures returned by the engine may very well make more sense than whatever the players can come up with, or it may inform the players of unforeseen possibilities.
This still needs a little thinking I believe…
Agreed on the sub-optimals. I’ve long been looking for better ways to visualize them. I have a web tool that I’ve played with that does this via exposing secondary structures and estimated probabilities along with infor on a dot-plot. If you are interested in checking it out, send a PM and I will pass along the URL.
As for not seeing much with it, I find it helpful for exploration of near-miss foldings. I can do some of that in the Puzzle Maker by manually changing the secondary structure for monomers, but it is far more tedious than clicking to bases to make/break a bond - and it doesn’t work for dimers.