machinelves
commented
10 years ago Using a 3D approach will cause people to design according to the global shape more than the chemical base pair composition. This is great and will open up new insights in how RNA behaves and is constructed. However, the underlying base chemistry is still critical path in design.
The easiest way to instantly assess base pair composition is still in the 2D view. Also, there are key factors like even distribution of base pair orientation that are easier to assess from a bird's eye 2D view.
I would like to see the option even in thumbnail view to have 2D toggle.
And as for the 3D view, we can either have a toggle, or better yet be able to see both at the same time, either through a popup window like with dot plot: http://prntscr.com/4b7m7a
Or, better yet, using the PiP split screen mode used for switches: http://prntscr.com/4b7loz
I will very much like a 2D view of the puzzle, like ingame Eterna. Where I can see the base sequence and the puzzle elements. RNA still behaves like we know it in 2D. I can’t grasp that info nearly as quickly from the 3D puzzle structure. I can click on bases to get information, but it only give me the information in bits. I lack the fast 2D overview. And internal loops, multiloops and length of helices is also faster grasping from 2D than 3D.
From what I understand, generally RNA folds up in stable 2D structure, before it starts making 3D tertiary interactions. So 2D RNA folding rules are very important to 3D folding and I wish us to have the benefit of using what we are already great at.