After trying every publicly available RNA software listed in Wikipedia I noticed that only EteRNA and NUPACK share the assumption that NT’s are evenly spaced. All the others had places where the loop NT’s were compressed and places where they were stretched out. So it is a complete waste of time to compare EteRNA dot plots to anything other than NUPACK, because the other packages make such completely different assumptions about loop NT spacing that they are totally incompatible.
I found one amazing site that would give you a thumbnail grid of the 20 lowest energy configurations for a given RNA sequence, and would even give you a movie of how the RNA would curl on itself as it was being made NT by NT. But not a single one of the 20 states given ever corresponded to either of the 2 states in EteRNA, because of the dramatically different assumptions about loop NT spacing.
So if it turns out that loops NT’s are not evenly spaced, how is the EteRNA user interface going to cope?
2D representation has nothing to do with reality anyway. Why focus on completely irrelevant software design choices ? Whether loops look compressed or not on a pseudo-map (which is what 2D rendering is, at best), if the pairs are the same, then it is the exact same secundary structure.
Now if we’re talking esthetics, my preference goes to EteRNA hands down. I find this 2D rendering much more elegant and appealing than any other I’ve seen so far. But it’s neither more, nor less realistic than other 2D graphical representations.
By phase I meant phase angle, I was thinking of a segment of a helical strand as being like a photon with a particular polarity. In actual 3D a loop is a helix and a stack is a double helix, right? So the bond between the loop and the stack is the place where the stack and the loop connect such that the single helical strand of the loop works its way back into the double helix of a stack. I’m assuming that the angle of the two strand segments on either side of a stack is an issue in stack bonding, needing to be at or close to 180 degrees opposite each other. And I am also assuming that both ends of a single loop at the end of a stack need to line up with the angle of orientation of the two ending NT’s of the stack that the loop connects to.
That’s a question I’m keenly interested in, but it was a bit non-sequitur to your reply (apologies for posting under the influence). A more relevant question to your reply is, are the compression and expansion of loop NT’s in other software packages the result of casting 3D to 2D? I don’t think so, or I would expect to see something like the epicycles of early astronomy. But there is no apparent regular pattern of oscillation between expansion and compression that would characterize a helical depiction compressed to 2D. I think it is some other factor entirely that is being represented by the expansion and compression of loop NT’s in these other software packages.
“Whether loops look compressed or not on a pseudo-map (which is what 2D rendering is, at best), if the pairs are the same , then it is the exact same secundary structure.”
The base pairs are not the same in any of the other packages except NUPACK. The expansion and compression of loop NT’s completely throws off the spacing such that nothing in these other packages corresponds to either state in EteRNA and NUPACK. As an example I gave CFold, which generates a thumbnail grid of the 20 lowest energy configurations, none of which ever correspond to either of the 2 states in EteRNA. Changing the spacing of loops completely alters which base pairs line up with each other in stacks.
Ok, now I understand what you meant, and yes, you are correct that strings will adopt a helical (eventually double in case of pairings) conformation, if they stack on each other. If they don’t stack, which does happen too, the backbone is quite flexible, and may present some impressive turns and kinks.
As for the compression/expansion, I’m unsure what details in the algorithms make those softwares represent unpaired strands in that way. Personally, I find those 2D representations confusing, and I just don’t like them.
If you’re interested in seeing realistic representations of folded RNA, I’d suggest trying to view some sequences in 3D. For instance, you could look up 1EHT or 1O15 (those are the “consensus” sequence for a theophylline aptamer) on the PDB website, and use the online Jmol viewer.
Those 3D images are hard to take in all at once, especially since you can’t color it by base. The first thing I noticed is that the stack pairs are not side-by-side, they are mostly staggered like a zipper or interlocking gears. That would seem to me to throw the whole EteRNA 2D simulations completely.
The 2nd thing I noticed is that the aptamer is extremely bunched together with partial bonds between them. Some have all three bonds like a stack base, but not all to one other base, the bonds are to two or more other bases in the loop.
Does Jalview 2.6.1 allow for coloring the image by NT? It seems like it does, but the documentation is rather sparse on the issue. If you could color it by base it would make it SO much easier to digest visually.
I finally got my new laptop and followed your tutorial, but when I load the PDB file it starts out as a jumble of overlapping structures, presumably different states of the RNA, so how do you select one state out of the jumble of states?