Looking at it, I think it’s safe to say that infobot seems to handle loop-heavy puzzles better than the other two do. As such, it still baffles me that it would have such a hard time with bulges.
So, I launched two test puzzles- ‘InfoRNA bulge test’ 1 & 2. Both feature series of same-sided bulges. The first is a series of two bonds, one bulge, two bonds, one internal loop, two bonds, one bulge, etc. The second is slightly more chaotic in design, but features longer strings of bonds, multiple bulges on the same string, and bulges after loop closures. All of the bulges, except for one on the second puzzle, are 1 NT and same-sided. Infobot failed both puzzles, Vienna failed one, and SSDbot passed both.
I created 123and4 bulge puzzle which took a puzzle the bots had all succeeded in (called ‘very easy’) and added all 4 bulges (I had to cut a few stacks shorter as I was hitting the 85 limit) but the bots all failed that puzzle
next attempt will be the same puzzle with the 4 bulge removed - if that succeeds I’ll add it back as a 1/2/3 bulge and I can keep iterating until I find the most complex version of that puzzle the bots can solve.
the bots all failed that too - so one more bulge removed - rinse repeat
A clever idea, sir.
As a further note, InfoRNA has recently caught up on trying to solve my (historical) Kyurem puzzles. There are 19 of them: 17 in the main series, a 2-2 loop test puzzle and a non-lab puzzle which combines Kyurem 9 and Kyurem 10.
InfoRNA managed to solve 1 and 2, but I never expected it to fail everything else (except the 2-2 loop test and Kyurem 9). Hence, I propose an InfoRNA-foiling structure: corners and multiloops placed close to each other.
Quite the observation, good sir, thank you. Personally, I think that it still has to do with the bulges, even though your puzzles feature rather large ones as opposed to the 1 nt bulges I’ve been playing with. You may be on to something with the multiloops, though. I hadn’t considered testing with those. Now that I think about it, having bulges in sequence with internal loops (particularly of the uneven variety) seems to also mess with infobot’s success level.
Actually, Edward’s recent puzzle series emphasizes that point, Freywa.
The question I have is, are the bots right and these puzzles are solvable in EteRNA but not in nature? How could one test *that* hypothesis?
That is a great question, JL. I will look forward to get the answer on that one.
It’s definitely a valid question, but I don’t think the bots are right. eteRNA exists, in part, because Vienna can’t solve for structures that do exist in nature.
To get the answer on that, we could throw in the puzzles in the beta lab and try solve them to our best knowledge. If nature likes our solutions, then the bots are wrong. And if nature does not sanction the puzzles, then the bots are right and the energy model wrong.
I’m game. I just need to find a simple enough 60 NT structure that at least beat infoBot.
I would like to take this moment to DECLARE SHENANIGANS. Eli Fisker’s ‘Two Bulges and a 1-2 loop’ puzzle defeated Infobot when it was ran in the player puzzle section. I copied and then utilized the same structure, but facing the opposite direction (bulges that were on the left are now on the right, etc), and Infobot solved it. What is this tomfoolery?!
Not only did infoRNA solve it, but it did so at a horrifically fast speed, something like .9 or .09 seconds.
I think I figured it out. Infobot only fails on puzzles where the bulges are on the left side of the watch hand, so to speak. In other words, when the bulges are set up so that the endloop of the RNA has a clockwise trajectory relative to the stem. Case and point: Eli Fisker’s ‘two bulges and a 1-2 loop’ player puzzle ( http://eterna.cmu.edu/eterna_page.php… ). Infobot and Vienna both failed, where SSD succeeded. I then took the structure and mirrored it to have a counter-clockwise or right-wise trajectory so that I could post it in the player project beta and not get told I was making a duplicate puzzle. That’s when something really crazy happened: Infobot solved the puzzle in .09 seconds. It was truly a confounding result- why would infobot fail one puzzle, but be able to solve that puzzle’s exact mirror?
It’s because Infobot has more trouble with bulges on the 5’ half of the fold than the 3’. I don’t know why, but this is supported in almost every simple bulge-using puzzle that infoBot has failed. Go on, look and see for yourself. I think we’ve found a much more specific ‘what’ to our question. The next order of business, I think, is determining the how and or why, if you all agree that we’ve pinned down what causes the failures.
Hi Paramodic!
Yes, there seem to be a difference on puzzles based on which way they are turned. I have reversed some of Brourd’s and mine version were easier to solve as a puzzle. Which proves that Brourd publishes the hardest version possible 
I have also reversed some of my own. Depending on it’s direction, it is easy to the bot or sometimes stumps it. Somehow direction seem to matter. I haven’t figured out the why. But I like what you are on to.
Just pick one of the small puzzle mentioned in this post, a lot of them are shorter.
Thank you, sir. What I’ve noticed is that as long as the curving arms follow a clockwise path, the bots have a much worse time trying to solve the puzzle. What I mean is that it’s not just some directions for some puzzles, but clockwise with puzzles containing 1 NT bulges.
right and left handedness looks to apply to the “rnassd” bot if you look at the puzzle “2 bulge turned other way” - though I suppose that might be random chance so I’m now trying 123 bulge - with 2&3 reversed