Feature: Skeleton Display

[vineetsk1]

As I mentioned in dev chat, I'd like to see a less cluttered "skeleton" mode of display that only shows the backbone and a bar across the end of each motif/helix. It might make it easier to judge the rough orientation than when the display is cluttered with all of the atoms and bonds. It also could serve as a way to show multiple motifs (as skeletons) for a selection/choice aid.

• jandersonlee

[machinelves]

Multiple view options would help us visualize the structure.

=> I would like this to extend to thumbnails in motif box as well. *And Mat suggested that we have a popup view of individual motif thumbnail images, which would help evaluate them from the motif library prior to selection. Currently, we basically have to place motif to see what it looks like.

With 3D being this project, and 2D being the previous bubbles approach, consider 1D as just the sequence AGGCTCGAGA... etc. So I see the sequence as being the starting instance for interpreting any view of the molecule into an alternate render, whether 2D or some flavor of 3D.

I see 2D as something qualitatively different from all the 3D views, so it's my preference to handle that view slightly differently as described in: https://github.com/vineetsk1/EteRNA-3D-Public/issues/9

And as for 3D views, the current options are beautiful and it would be great to keep them, and just add view toggles for the following:

1. toylike mode ( as described below in Eli's post - will make it easier for kids... and big kids too! )
2. skeleton mode ( as described above, like http://prntscr.com/4b6x7c )
3. space filling mode ( like http://prntscr.com/4ae9pz )
4. cartoon / spheres per base ( like http://prntscr.com/4b6yja or the following but without the white sphere backbone: http://prntscr.com/4b6yog )

Display Overlays ( for any view option, like in 2D view http://prntscr.com/4b72e3 )

1. nucleotide numbers overlay ( http://prntscr.com/4b73gi )
2. nucleotide letters overlay ( http://prntscr.com/4b73v9 )
3. free energy overlay ( http://prntscr.com/4b74dt )

[machinelves]

About Toy View, from Eli Fisker:

Lego like building blocks

First a big thanks for all the hard work you developers put into finding our way towards the 3D age.

I have a hard time seeing what goes on in the new 3D RNA puzzles. So now I will be dreaming a bit aloud.

I would like to see the motif, like a brick and get a feel for its size and what way it actually bends. I don’t get as much feel for bends from the motifs in the box, despite them being more structural accurate. (I’m not saying to remove structure as an option, just proposing to get more options on how to view them)

These bricks, looks are like I could just grab them. I can almost feel them in my hands.

I want a brick like feel to the pieces. Like when I solve a puzzle with my hands. I want the visual feedback be of a feel as it was like something I just grab. Something toylike. Bricks I can put together so I can better see if they will fit. On the grabbing experience, here is an example in a video that Mat shared with me:

I want it to be easier to tell the RNA jigsaws apart from each other. I find it hard to know which motifs to pick, as I can only see the skeletal of a brick but not its contours.

Here I do get some sense of what the structure fills. The skeletal is still visible through. I think this is protein structure determined from X-ray images.

I think what I particular like about this is that I can see the local picture where as the background fades. Everything I don’t need to use for attachment of the motif, fades away in the background.

Though this is in the very accurate business, I also very much like the far simpler view of Chimera. Chimera simulate RNA folding in 3D and has some very slick viewing options. I can see the bends and the RNA design as a whole in no time. I can immediately read of the sequence.

It is easy to see what base is connected where. It is simplified here. I think a viewing style like this could work well.

But it also has the option to see base positioning.

I would likely prefer having the backbone a single different color from the bases, like grey or something. Chimera is very adjustable when it comes to that.

Images copied from Omei’s Intro to Chimera

Or like Nando so beautiful shows in his blog post on SCOR

I think what I wish for is both very simplified view, (like what Meechl and Redspah suggested) but still with the option of a very accurate view.