The developers have implemented yet another new feature players have been requesting, the ability to copy and paste the dot-bracket notation in lab puzzles. The option is accessed by right-clicking in the puzzle (control-click on Mac).
Players can copy while in either natural mode or target mode, and paste in target mode. Here is an example of pasting a dot-bracket structure from a PKB or PDB file for the pseudoknot puzzle. This functionality enables players to record the expected (previously validated) structure for each submission. These structures will be provided to the researchers for inclusion on the pseudoknot SHAPE data card and Eterna score calculation.
Another use of this new functionality will be when we enter a known pseudoknot sequence in round 1, and mutate to test whether the structure changes (how stable the pseudoknot remains). I entered my S2-KL1 pilot submission in the round 1 sandbox to test out how this will work. EternaFoldThreshknot is predicting a different kissing loop interaction than the one I want to test. I copied the dot-bracket from the natural mode into a text editor, changed the brackets to the expected pseudoknot, then pasted it into target mode.
Now as I mutate the target structure to test if slightly different sequences will retain the same pseudoknot, my expected (player-predicted) dot-bracket will be stored in the game database as the target structure for later delivery to the researchers and quick comparison to the SHAPE results.