Open Vienna. You could end up using it a lot, so you might want it in the bookmarks of your search engine.
You get the RNA sequence for the a design, by clicking on this copy page symbol in the tool section in Eterna.
You paste the RNA sequence in this field in Vienna.
Then click this bottom
What to use the numbers for.
The MFE structure number should be high, as it means your design is more likely to fold correct.
Ding said that ensemble diversity should be below 0,5. She also said that entropy should be under 0,3. These are good tested rules.
However lately we have had designs with triloops in them. In those design entropy and ensemble diversity will be higher. That is also the case, to a lesser degree, in designs with asymmetry. But remember - low is good.
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How to read graphics.
Notice this section under Grapichal output. Move the dot from base-pair probabilities to positional entropy. This will give you a better view on where there might be weeknesses in your design. A red colored design means that your design is good or that it is a christmas tree - which is bad. An all red design is rare, so just try to turn cold colors in to warmer colors. (Without using too much GC-pairs when designing) Vienna is your chance to get an idea about where you need to change things.
Here is a picture of the entropy of a design. This one will not do good. It has 5 spikes with high entropy. You need as few spikes as possible and you need them low. The numbers from 0-100 represents nucleotides in the design. You can use this to see where in your design entropy is bad.
If you want to know more about Vienna RNA fold and especially about how and why it works, you should check Alan.robot’s introduction to Vienna. This quick guide is just an easier version of his page about how to use vienna.