@Rhiju
Do I understand you correct: That you would like to make a training puzzle and then let people solve it different ways, so they can get the fealing about what works or not – from the estimated score they get? That would be absolutely cool.
We could actually ask them to make christmas trees and cub scouts, to let them see for themselves that this is propably not be a good idea. That could give them the feeling of the experience we already have. And keep most of the christmas threes in the playpen.
The only problem is that some of the christmas trees actually score fine – it’s just that they don’t have the potential to become the winner, which you can’t see from the score alone. So you might wanna go for the binary ranking, if that is some sort of ranking for which puzzles are good compared to the christmas trees and cub scouts. Or present the puzzle score with a text, explaing why this puzzle which scores great might not be the winning bet.
I would love to help making a list of ‘inarguable’ but important lessons from the lab so far. I have made a list of what comes to my mind first. Then you guys can select which you believe in and want to use for this practice puzzle.
Partly arguable but important lessons from the lab so far
Don’t make the arms totally identical. That will highten the chance that the structure will try to form alternate structures as Alan.Robot says. So they will pair up with each other and thereby mispair.
Don’t make the arms too different. Make the arms in you design in the same ‘mood’ of colors. Not a design where one arm leave an impression of blue, the next red and third green. Arms with very different collors means not just imbalance in colors, but also an energetic imbalance. The winning designs so far have the energy nicely spread out in the design, an almost even energy distribution.
Don’t use blue nucleotides in a multiloops, they have an ugly habit of breaking up things. Because Mat says so and I have demonstrated that they raise the level of energy inside the multiloop dramatically in positive direction, compared to nucleotides of other colors and thereby creating an energy jump.
And as Alan.Robot sugested it’s important the new players understands dot plots. Would it be possible to teach this along with the lab puzzle? That a messy dot plot means that some things have to be done differently. That a clean dot plot does not count, if the design is leaning towards christmas three. Tell them though that they don’t have to make a totally clean dot plot at first try, as failure to do so, could scare them away. Probably only a few of us did that anyway.
While using only the strong GC-pair all over the design is not a good idea, you should instead use your GC-pairs where their strenght is needed most, mainly in the junctions – like where a stack meet a multiloop and more often than not, when a basepair is closing a loop.
Tendency in the lab for tetraloops, is that they should have same value of energy inside (in a design with 4 tetraloops they should either be identical or should have a twin somewhere with the same energy level inside. 2 x2 identical.
Turn the GC-pairs in the multiloops in the same direction, red nucleotides to the right, as to raise the negative level of energy inside, to avoid a potential energy gap between inside multiloop and the arms connected to it.
The higher negative energy inside a multiloop – the better, as long as it gets the energy level in it more in line with the energy level around it. Which means don’t put colored nucleotides in the loop ring, unless they are green and raise the negative level, or red and you can afford to loose a bit of negative energy. And there is a right and wrong side to do this. (viewable in the energy tool)
And if no one end up arguing with my theory about energy jumps as a cause of mispairing, you might wanna include something about not making too big energy gaps, that is in stacks and between stacks and multiloops.
Make versions of the puzzle with different features automatically turned on. (The players might not have turned them on themselves yet.) Like putting the advance energy view tool in action, when teaching about energy gaps.
I might return with more suggestions here, when they comes to mind.