Lab puzzlemaker function broken

I was trying to beam Pi’s 2 state switch puzzle to the puzzlemaker from the lab. I wanted the dot bracket from both structures. Earlier just a single beam to the puzzlemaker would have achieved this.

Here is what I did:

Here is what happened:

Notice that I get only one of the dot brackets. State 1 is just a bunch of dots.

Omei found a work around for getting the dot brackets for both states. I have added images:

  1. Beam to puzzle maker.

  1. Even though the molecule appears to be bound, it isn’t. Use the molecule binding tool to cement it in place.

  1. Switch to Natural mode

  1. Use the “Add base” tool to add base in state 2 at the 3’ end and then delete it with the “Remove base” tool. Puzzle maker should fill in the new structure.

Eli: This need to be done with the game buttons and not in the dot bracket. I found it easier to add in the 5’ end of the state 2, so that is what I did. Then I removed the base again with the Ø button. Notice that the state 2 has become stable.

  1. Repeat add/delete for state 1.

Now there are dot brackets for both states.

Amybarish and DigitalEmbrace have earlier called out this problem with missing dot brackets for lab beam.

Those are the secondary structures for the labs used as a template when making them. So not broken in this case. We just don’t save the native fold secondary structures anywhere last I heard.