In coming up with these specific colors, the player dev team had two primary considerations:
- The colors should be distinguishable, and
- The colors should be suggestive, e.g. mixing yellow (A) and red (G) points makes orange (A or G).
Another thought I have is that we might treat 2-base choices (the middle line in the image above) systematically different than the 3-base combinations (the last line). With this third consideration added to the first two, I constructed this set of colors.
Here I have attempted to distinguish between the 2-base and 3-base choices by making the former brighter and the latter darker.
Working in the player dev group on this, we found that it can be hard to judge any specific suggestion for an improvement without seeing it in the context of the other colors. To address that, I have created these two charts as Google "drawings" and made them readable/copyable by anyone with the URL. The URLs for these are https://docs.google.com/drawings/d/1qXcEVka68nH1sTUNc9gVnLokeQ-F4OqP5idZSvAqat8/edit and https://docs.google.com/drawings/d/1FBL1MEWYen6V_7orInubudy9tXi5Rs9SsI8NFbJCNU0/edit. So if you have some specific suggestions for one or more colors to change, make a copy of one of these, make the changes and post the new picture here. If you have used any of Google's other document types, I think you'll quickly figure out how to change a color. If not, you can always ask here.
Also, there have been numerous good ideas on how we could convey the constraints better than just colored marks. For right now, we're concentrating on the color marks because we can do that with Eternascript, as opposed to adding new capabilities into the game. Changes to the game code are possible, but they are subject to the constraints of longer-term planning in a way that Eternascript code isn't. So keep up those thoughts, even if we can't implement them right away.
Locked bases - Some bases that are involved in tertiary bonding with other subunits and proteins are locked in order to prevent modifications that could damage ribosome functionality.
Purple regions (in the small red box upper left) - The energy models don't really know how to predict what bases pair up in these loops. Don't worry about misfolds in these areas.
Base mutation constraints (multicolored rings) - Known species variations based on the degree of base conservation among gammaproteobacteria, which is the phylogenetic class that includes E coli. By comparing the e. Coli rRNA to its closest relatives, we have identified mutations that may be less likely to disrupt the ribosome.
One more note, be sure to click on the red box indicating misfolds in the target secondary structure so that misfolds are highlighted in red on the puzzle. Then put the puzzle into natural mode and look for stems marked in red. These are the misfolds that need to be forced apart, so try to find a mutation that a) satisfies the constraints (which you can tell by sight once you get some practice reading the colors), b) reduces the energy delta significantly (not just a few tenths) and c) causes the puzzle to significantly change its folding.I wrote this explanation for the ribosome designs we were creating (and will be creating) but thought I would share in case it helps clarify what is going on in the weekly challenge puzzles.
Where Delta Death Valley is a design with suboptimal Delta low that you can't get out of by just adding new mutations.
When deciding which sequence to choose among a list of current low Delta sequences, I avoid sequences where there are no IUPAC mutable NT's within the red mis-folding areas. Instead I pick a low Delta sequence with a large number of IUPAC mutable NT's.
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
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.
Quick Start Guide to Using Scripted Tools in Eterna