ETERNA FAQ - By players for players

This is the ingame player FAQ. Ask a question or help answering them. Devs are more than welcome to answer questions too.

Over time the best answers and questions will end up in this cleaned up version of the ETERNA FAQ.

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Common question:

Q: How do I take a screenshot, when I’m stuck on a puzzle and needs help?

A: There is a symbol of a camera in the chat box, to the right side in the top. Click on the camera and say yes to post the picture in the chat.

Common question:

Q: Should I aim for highest or lowest free negative energy (kcal) in my lab design?

A: So what is the optimal kcal?

Free negative energy is needed for RNA to fold spontaneously, without adding of energy. Having just the right amount of free energy is the goal. That means not have too many GC-pairs or too many AU-pairs.

What is the optimal balance of AU and GC-pairs?

If you aim for lowest possible free energy, there will not be enough energy in the design to fold correct in nature. It will not have the power to stick together. A design with mostly AU pairs, means little free negative energy. The RNA will be too weak to stay in the structure you want it to form.

If you aim for the highest possible free negative energy, there is too much energy in the design for it to fold correct. A design can have so much free negative energy, that it get caught up in wrong folds. If you use too many GC-pairs, the design becomes like an energeticly black hole. Folds can’t leave bad folds and the puzzle gets stuck on itself.

You can also imagine it like this:

GC-pairs are like electromagnets
AU-pairs and GU-pairs are like regular magnets – that rejects each other.

If you use mostly GC-pairs, they are very likely to get stuck somewhere wrong and then they won’t let go again. Which means for the RNA to fold correct, will take like forever.

Watch the optimal % of GC-pairs in earlier winning lab puzzles, in a puzzletype that looks similar to the one you are working on.

(Thanks to Iroppy for mentioning gravitation when I was thinking mostly in electricity and magnetism related to all GC-designs.)

Here is the crewgenerated part of the ETERNA FAQ

Thanks to Mat for finding the link.

Common question:

Q: What is melting point?

A: In EteRNA, the melting temperature can be thought of as the temperature at which there would be enough energy to pull the structure apart from it folded structure to a linear form. (Matt Baumgartner)

For more information see Matt Baumgartner’s post.

Common question:

Q: What can the meltplot tool be used for?

A: The meltplot tool can be used to avoid making one of the lowest scorings of designs. It can be used to predict a low score.

For more information on how to use it, read my post on the topic.

Common question:

Q: What is Free Energy?

A: When you are playing the puzzles in EteRNA, there is a box in the top left corner which displays the [free] energy of the current molecule. What that is a measure of is the potential energy of the molecule. (Quote Matt Baumgartner)

For more information see Matt Baumgartner’s post.

Also see Ksteppe’s Understanding free energy - using legos.

Common question:

Q: Is there a list of hot keys?

A: Yes, here.

Common question:

Q: What is dot plot or pairing propability plots?

A: See Jee’s answer

For more about dot plot, see Lab guide for new players

Common question:

Q: What are the algorithm for EteRNA? What energy parameters and, energy model does it run on?

A: Link to paper is in this forum post

Thanks to Brourd for noticing the question and provide the answer.

Common question:

Q: How do I make a puzzle?

A: Here is a quick guide on How to use the puzzle maker.

Common question:

Q: How do I take a picture of a puzzles to send in a message, without publishing it in the chat?

A: Click the camera in the right top of the chat box once and wait.

Then this box appears

Choose the option, the underlined THIS

Then copy the link that appears together with the screenshot of your puzzle and save it somewhere.

Click no to posting the screenshot in chat.

Thanks to Starry for explaining this to me too, while answering to another player with this question.

Q: My chat window never completes loading, hence the camera symbol is not available. How can I make the chat work?

Hi boganis -

can you tell me which platform (windows/mac/linux), internet browser you are using and perhaps which version they are? It’ll help us debug the problem.

we are sorry about the trouble.

EteRNA team

Hi, Jeehyung, OS: Windows 7 Professional (ver. 6.1 build: 7600), browser: Google Chrome (ver. 16.0.912.75 m).
I suspect it is the setup of my corporate McAfee SW or possibly blocking of computer ports - and the way the chat is implemented that could be part of the problem :slight_smile:

However, I can’t be the only one accessing EteRNA on a corporate laptop (in my leisure time) - thus I suspect that there are others that can’t access the camera as well :slight_smile:

Q: Why do I need to alternate (zigzag) AU-pairs in strings?

A: Because it enhances the stability of the string. Here is a post about Why AU-pairs should alternate in strings.

I think we need a bit of jargon help. There is the jargon that players use, and the jargon that is used in literature.

Ideally, we should help players understand both. Can we make something that succinctly defines all of these terms? Can we provide lots of visual examples?

Hi Quasispecies!

Yes, you are quite right. Especially as we now move on to reading science papers, some term explanantion will be needed.

We need to identify the key terms we need to know to be able to work together on this babel like project.

I think my Eterna dictionary is only a temporary solution. The best would be if we could somehow get the key terms build into the WIKI, as it has a more intuitive structure than reading a dictionary. Other posibilities than the WIKI?

I’m thinking what about having some sort of list where we all can add words we don’t understand but need to understand and then help each other with the explanation. And when a good explanation gets in, move it to the WIKI. We will need eterna crew to do some of the explanation too. And the biology students in here too. :slight_smile:

Later when our discoveries get wider known, we will need to be able to make ourself understandable to the scientists.

Let me hear what the rest of you think. How can we solve this problem best possible?

Q: What is shape data and how do I read it?

A: Shape data is the chemical mapping of how the RNA bases are paired up after the RNA is synthesised. Yellow bases are the unpaired bases and blue base pairs are those that paired up. Click the yellow/blue picture of the design to see the shape data, when you are viewing the lab results. Shape data is a help when reading the results we get back from lab. For how to read the advanced shape data with continous colors, see this answer by Jee.

Q: Why do basepairs pair up?

A: The 3 basepairs AU, GU and GC each consists of one short base and one long base. The bases in a basepair is bound together by hydrogen bonds.

Hydrogen-bonds are typically weak attractions between two different molecules that holds those two molecules close together. (Definition For a hydrogen bond to form, bases need to have a certain distance to each other.

The short bases consists of a single ringed base (green C and blue U) and are called pyrimidines.

The long bases are double ringed and are called purines (yellow A and red G)

I found the picture on this page.

To remember I chose to take the first letters in the short and long bases and connect them to something that I think I can remember. If it works, it works. :slight_smile:

CUT - cut short

AG - A giant

Back to the pairing of bases. Picture that RNA folds up in helices like DNA. If you have two double ringed bases opposite each other, they will bump into each other and be too close to form proper hydrogen bonds. Two single rings would be too short to reach each other and thus not form bonds.

However a single ring and a double ring opposite each other have the perfect distance. It is the same in DNA, a short base opposite a longer base.

There is another reason that two long or short bases opposite each other won’t work, not thinking in the hydrogen bonds. The helix would be quite bumpy if basepairs of two short bases were next to a basepair of two long. It would screw with the biological machinery that have read and work along the line of basepairs in the helix of DNA.