Viewing chemical mapping results in OpenKnot projects

Viewing the results of the chemical mapping experiments is an important step in the Eterna player iterative design process. Just because a submission received a high OpenKnot score does not mean that it folded as predicted in the puzzle. The actual structure can be quite different. In many cases, it’s fine to simply copy the sequence and paste into a new round for repeat testing. But if you want to modify the design, you’ll want to work with the highest confidence pseudoknot structure.

To view the results for your designs, go to the lab project page and click Review.
Enter puzzle

Sort by Synthesis Score to see your top designs, if desired. I find sorting by score helps me organize information for study. Click heading twice for descending sort.

Enter a few letters of your player name in the Designer search box.

I decided to further search for C. difficile scan submissions. Click on the first design in the list to view the info card. Click on See Result.

When the result loads, which can take a few minutes, click the Estimate Mode button to see how the sequence folds according to the chemical mapping data processing by the research team. Browse results by clicking Next or Previous.

At this point, you can click on View/Copy design to see your original design in the puzzle, but whenever I do that while working in these large datasets, my computer’s 8GB RAM gets overwhelmed and nothing loads any further. What I do instead is open a second tab and follow the same process, but click View/Copy design instead of See Results. That way I have two tabs open for switching back and forth. (My computer overheats frequently while doing this, but it never freezes up.)

Three of the stems folded as predicted but the others did not. I might re-submit this sequence as is to be tested again, but I’d also like to eliminate the misfold with the GG in the locked region at the beginning to see how that changes how the neck folds. I can do this by adding CC or UCC or CCC at bases 27-29 to tie up the GGG. I’ll probably shift the design sequence three bases towards the 3’ end and insert CCA at bases 27-29 to leave at least one unpaired base between the stems. (I don’t have any proof that is necessary, it’s just my gut instinct.) I might try submitting with UCC at bases 27-29 as well.

I like to collect the screenshots and sequences in a google doc when designing for a new round, such as this one I created for some of my round 1 submissions, to help cut out the portion of the sequence I want to paste in the new round.