The game does not recognize unstabilities in the higher order knots, beyond the first order pseudoknot. I have reported on the issue here:
Bug in the higher order pseudoknots
I think if we are to fully investigate higher order pseudoknots, the interface will need to say if they are not solved.
As discussed in the linked post, the issue here is not that instability in higher order pseudoknots is unrecognized, but that the requirement is just that any pseudoknot is present (regardless of target structure) - if you have one stable first-order pseudoknot and one instable first-order pseudoknot, that constraint would still pass.
I believe the desired behavior here would be a mechanism to indicate whether the natural mode does not match the target mode, even if it is not “required”. Happy to discuss further if you feel this is insufficient for your use case!
@LFP6, yes, I think the check you propose, on if natural mode match target, will fix the problem.
Because the base pairs in the second, third and above pseudoknot will need to be base pairs, for natural mode to be identical with the target mode.