The daily build of today (Oct 2nd, 2013) provides a new behavior. So far, when you opened an RNA molecule stored in a FASTA file, Assemble2 computed and displayed a single 2D prediction. Now, it opens a new lateral panel named “2D folds”, gathering all the 2D predictions computed with Contrafold and RNAfold, along with a random sample of 20 suboptimal structures computed with RNAsubopt.
You can select a 2D prediction by clicking on the “eye” icon in its upper left corner. Using these icons, you can easily switch between the different folds.
Now, if you assign qualitative or quantitative data to the secondary structure selected, these data will also be automatically assigned to all the 2D predictions displayed within the panel “2D folds”.
This means that you can more easily find the 2D prediction that fits the best with your experimental data. IMHO, that should be useful!!
One more thing: once a 2D structure selected, open the lateral panel named “Secondary Structure”, right-click on the 2D node. You will see that you can now “Display base pairing probabilities”. These probabilities are computed from all the 2D predictions displayed in the panel “2D folds”.