As far as I could see, the script library support calculating free energy given a fold and finding a the fold of the min free energy of an RNA sequence. The TB puzzles use more than 1 RNA sequence and I was wondering if the script can compute those and how to do that. The nupack server uses the a “+” to denote where another RNA sequence begins. I tried that but it doesn’t seem to work with the script library (I think it ignores everything different than a base letter).
I know the flash app uses & instead of +. But the library may not have been touched for years, before Eterna moved on to emphasizing switches.
You can do what I think you want eith LFP’s script http://www.eternagame.org/web/script/7005225/. This is something he did as a critical part of getting predicted foldings into the new data browser’s database.
Thanks, I’ll see what I can do with that. What about puzzle creator, is it possible to create custom puzzles that have more than 1 RNA?
No, puzzle creator is limited to FMN and MS2 ligands. (That’s all Eterna had until recently, and the puzzle creator hasn’t been updated.)