Hi Omei, I like your proposal 1 for the change to (not A). Not complaining, I think this is all really cool, but I just spent days not being able to distinguish (not A) from ©. The only reason I caught it was by carefully running back the mutation booster changes. This is what it looks like on my screen. #26 is (not A) and #27 is a ©. I think this is a needed change.
How to see the purple areas
Astromon brought up an excellent question:
“can we get a list of all purple area bases?”
The reason why it is interesting seeing the purple areas is that they regularly hold some kcal lowering options.
The thumbnail showing the purple areas is really tiny and most of our Ribosome challenge puzzles are large. So it has gotten rather hard seeing the purple bases. But it turns out there is a way.
LFP6: If you look at the RNA strand itself.
They have little “halos”
Gray and purple
Images by LFP6 With marker on
Without marker
But the purple hue don’t show up with the explosion factor on.
There still is a way to get to see the purple markers. As LFP6 said: “Temporarily unmarking them is probably the way to go at least for now”
However it takes installing a booster. Here is the one I use for this:
Mark Mutations (v0.7) (Eli’s copy)
I run the booster and say no to the option “repeatedly automark mods?”
Then the booster pulls off all the colored rings and only leave the the changed bases with black rings on.
Now here is what the 1.7 puzzle looks like with color markers off and visible purple halo’s.
For how to install a booster see AndrewKae’s intro.
I am posting this here as I seem to have failed to post it to chat. These sequences are for the POTW 1.12. The original un-mutated sequence is at the top, below are the solutions listed newest to oldest. I grayed out all bases which are shared between the original puzzle sequence and the player solutions (that is, gray bases=not mutated by the player). Colored bases are player-made mutations. These results were current as of 08-29-19. I have posted this in the hope that the pattern in player-made mutations will help in analysis. Please let me know if you have any questions.
I really like this, cynwulf! Do you have a script to do this? The reason I ask is that I have been thinking about doing a cluster analysis of the submissions, and it seems like this would be a great way to visualize which mutations are characteristic of the individual clusters.
Gerry, I just read this (again?), and it brought to mind a closely related question.
When one finds oneself in a Death Valley (regardless of whether it is a delta energy of a structural Death Valley), does this provide a good heuristic for the first step in getting out?
Beautiful, Cynwulf! It stands out clear that some bases seems to be obligate changes for solving.
I’ve always favored this kind of analysis, but ultimately no script was used; I did all of the editing by hand (took an hour or two) in Word 2016. If I had a fast way to generate this data I’d do so regularly.
Here is a variant on what Cywulf has done. In excel, so you just need to insert sequence. The second comparison shows pairs together.
I had to change my browser to 150% zoom to begin to see the color difference between the outer circles of those bases.
I’d be happy to do this for anyone - just send me list of sequences - or share excel file.
You could probably use a sequence alignment software for all of that, Omei. There are better programs out there (if you want to focus more on something like sequence alignment), but I’ve used UGENE and BioEdit for sequence annotation and viewing. There are very simplistic alignment software associated with these, if I recall correctly.
@Omei suggested that I post here about transferring a POTW solution into one of the labs. I noticed that the 1.13 POTW was a partial match to the 16Sp2Ribosome Pilot Challenge Warm-up. By inspection it seemed that bases 11-200 in the POTW were part of the target lab puzzle, so I copied my solution from the POTW and pasted it into a text editor. Next I truncated it to 200 bases (the last base I wanted), and then deleted the first 10 bases, leaving only the sequence of bases that I wanted to transfer. Since these were a contiguous substructure in the target puzzle, I could use the Smart Paste function in the _ Lightning menu _ of the lab tool to apply this whole sequence to the lab puzzle. (If it had not been one contiguous sequence, I would have had to do it in stages). Turning on the Soft Constraint Marker (also in the Lightning menu) I could see that the soft constraints for the lab differed slightly from those in the POTW and made one or two adjustments. The result was a sequence that matched the target structure of 16Sp2 in the area of concern. The rest of the 16Sp2 puzzle did not seem to have as many options for mods as per the soft constraints, so my conjecture is that at least some of the remaining “miss-folding” is possibly required for switching-action during the operation of the ribosome as it translates the mRNA into proteins.
