Your gaming ideas for our 3D RNA game

I think that you guys sits with a lot of the potential solutions on how to get our new 3D RNA game made better.

There must be some really cool game control systems for 3D video games, that we could borrow ideas from.

Like intuitive controls for rotation the RNA and special views. I’m not very familiar with this type of game. But I was thinking that many of you are. So if you think of some cool ideas for ways to get best possible visuals of the RNA, great ways for controlling the motif in relation to the big pieces of RNA or close up views.

If you have seen something in a game you like playing and you think it could help in here, then please do mention. Feel free to leave a screenshot as well.

The better ideas we get put up here, the cooler and more fun our new 3D game will be.

As Machinelves said: Intuitive controls would be great, using industry standard navigation commands.

So dear gamers, upload your gaming experience for science!


I’ve been thinking about what kind of schematic representation of the RNA might be best for solving the new “construct a 3D path” puzzle Vineet is creating. Yesterday, I was replacing a clothes drier vent, and it gave rise to the following idea.

First, here’s the type of flexible venting tube that served as an inspiration.

The idea was to represent each stem (helical segment) as a section of straight tubing, and each motif as a segment that has been bent in a way representative of that motif. The puzzle then becomes one of choosing from those pieces to build a duct between the desired end points (as well as the proper twist.) This doesn’t really change anything about the puzzle, but it might make it easier to bring one’s repertory of 3D experience to bear.

I’m not a great 3D modeler, but I did manage to put together some models in Second Life to try out various ideas. Here’s what I came up with.

For starters, I constructed a schematic representation of double stranded backbone, throwing away all the details about the nucleosides.

This is similar to the “smoothed backbone” option in Chimera.

Then I added a partially transparent cylinder, constructed so that the backbone lay on the surface of the cylinder.

An interesting thing to point out here is that in an RNA double helix, the plane roughly defined by paired nucleosides is not perpendicular to the central axis of the helix. In the image above, this shows up in the fact that at the top and bottom of the cylinder, one of the backbone strands extends beyond the end of the cylinder and the other strand falls short. I think this accounts for the fact that the current “hints” don’t work out quite like I expected them to. When I look at the hints, I expect them to show the direction a helical section will project. But I think the hints actually show the plane of the closing base pairs, which is in a somewhat different direction.

To make the direction of a helix extension clear, I added an arrow that follows the path of the center of the helix, and thus points in the direction a subsequent helical extension would take.

Finally, I added a “cap” to the cylinder.

The point where the pie shaped wedge cut out of the cap meets the outer surface of the cylinder is supposed to represent where the backbone (or its extension) meets the end of the cylinder. (The cut-out wedge thus represents what is called the helix’s major groove.) In this picture, it looks like I didn’t get the torsion angle of the cap quite right.

If I were more accomplished at 3D modeling, I would have built a model for a non-helical motif or two. But you can imagine them just as just bent versions of the above. A simple bulge or small loop could probably be represented accurately by a simple curve, i.e. the entire central axis would lie in a single plane. A larger loop would probably have to be modeled by a kink turn, where the entering and exiting end of the central axis didn’t stay in one plane.

An important point to note is that all the essential information needed to specify the path of the RNA segment is encoded in the end cap, which should be easily computed from the 3D information already encoded into the program. Calculating the “best” path for a central axis through a twisty-turny motif might be tricky (or maybe not; I just don’t know), but it really isn’t important. Any simple smooth spline between the entering and exiting cap vectors will suffice for supporting the physical intuition of the complete RNA as being equivalent to a flexible duct built out of pre-made pieces, where each section has a groove that has to line up with the next piece.

Here’s two pictures showing joining segments.

Again, it would make a better illustration if one of the segments was a curved motif, but I hope this conveys the idea.


Big thx, Omei!

I really like what you have been up to. More wormlike RNA - more visible and more alive. :slight_smile:

“When I look at the hints, I expect them to show the direction a helical section will project.”

I was expecting that too and got confused about the motif ending up pointing in another direction. So I’m very glad you point out why this is happening.

I like that one can see direction of the RNA pieces. I also like that one tell can separate each motifs from each other.

I was kind of wishing to have an option for highlighting the motifs I have used. So if I click on one motif on the used list, then only this motif will glow in the puzzle itself.

But what you suggest is better, as one would not have to perform any unnecessary actions to get that information. As is we don’t have any means to tell the motifs apart.

This will help improve the feel of it being a puzzle - being able to tell the bricks apart. To see what a particular motif adds to the puzzle as a part and if the motif is actually helping getting the puzzle closer to a solve as a whole.

Foldit 3D interface

I have asked Mat to share some of his experience from Foldit and what he wish to see in our 3D game. He sent me this yesterday:

Here is a video that may give you a few ideas. I know its for DNA, but can still be reference idea for RNA. This is how I would like to view motifs:

Tutorial Puzzles.,Level 7-3 DNA Pairing

Image shots from the video:

One can move around the DNA piece with a big yellow ball cursor. Which reminds me. It is pretty easy seeing where the mouse is in Foldit, but it is harder in Eterna.

Mat afterwards told me that he had added the yellow ball/circle for the video make it easier to see.

I kind of liked it, though it doesn’t have to be this big. As Mat said: if it was an option, it would be fine.

Here is the palette from which to pick bases. It would be cool if such a wheel could be used to select motifs from, after which way they bent. With a sorting of different bends of helix and motifs, as this would make it more visual. I still very much like keeping shot cuts for it though and the motifs pick list.

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Using minimap to aim for the 3D RNA end point

I am building onto following idea of Mats:

“Making the RNA bigger will be easier for now, but an independent and isolated 3D preview of just the motif in game would be best.”

I was thinking about a compass like tool. Like a minimap, that is showing if RNA motifs we add, gets our structure closer towards the endpoint.

The point with this sort of view, is to get a much bigger image and working space, for seeing how the RNA and motif fits together. To get it easier to add motifs and see what one do there.

As Machinelves so neatly summed it up:
Like a minimap for the global molecule’s orientation & endpoints, with option for closeup in main view.

Not as much will need to be in the game interface at once. Just the point where to attach the motif and the motif itself. All the rest that is not really useful seeing, is gone. Especially if computers are better closing the end gap than humans anyway. Else when gap is close to be bridged, then it could be useful again to see both sides of the gap.

Here is a primitive image of the idea. First image shows how the RNA structure is moving too far away from the goal. Second showing that it hit target.

RNA compass

(Outline from chat, 16 Aug, 2014 with an added link)
Eli Fisker: And i also very much like that thing from the protein program, where one don’t have to see everything at once but simply get a closeup at the nearest structure.
Eli Fisker: That would be very useful for motif placement to see what one adds and how well it fits, without being bothered by the rest of the molecule.
But still one will need to somehow see where one is going in relation to the other end
machinelves: yes, i found it hard to move and navigate the larger molecule, that’s a good idea machinelves: hmm good point, on the needing to see endpoint
Eli Fisker: Yes, if not directly in the image - then at least on a small map, so one can see what direction one is aiming at.
Eli Fisker: That could make it simpler to show a close up, as not as much would need to be in the image and that could give more space for actually seeing real close what one is doing
machinelves: and mat’s point about preview of motif, good idea
Eli Fisker: I really like that idea too
Eli Fisker: That is what I’m building onto now
machinelves: interesting, like a minimap for the global molecule’s orientation & endpoints, with option for closeup in main view?
Eli Fisker: Exactly

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Give a choice of background color

Mat suggested following:

It would be good to have the option of choosing background color in eterna too.

I shot an image from one of Mat’s FoldIT video tutorials.

Here is a side by side view of Eterna and Foldit.…

In Foldit one can choose color of background. Here are a few of the alternative views:

Dark background…

With contours…

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Makes perfect sense to me omei and I like your thoughts. Should work nicely

Here’s a suggestion/request that is pretty mundane, but it would have a huge impact on anyone who approaches the problem by starting with a rough approximation and then seeking to refine it. Here’s an example:

Suppose I have created a rough solution that looks like this:

Although it is not easy to see it from this snapshot, it is clear from the 3D interface that the solution would be improved by adding a second helical section at the very beginning. Intuitively, I would like to be able to (say) right click on the first item (either in the list or the 3D model) and get choices for adding/replacing/deleting a piece.

As it stands now, I have to write down my sequence, undo it down to one item, add the extra helix section and then re-type the rest of the sequence.


Thank you both!!! This wheel is exactly what I was talking about, for organizing mutative options.

And on the motif closeup view, yes exactly, we need to see clearly what the motif is. And I could see having different view types, like this fold it one here, and even the simplified chimera-like one, or with simply colored balls instead of actual nucleotide chemical structure, since that extra info gets a bit busy-looking and distracting when judging overall base composition. But for troubleshooting and learning, I like to be able to see full detail. Just also have the option for simple view.

this idea would be helpful for like you say seeing up close more easily, and also I wonder if it would be less processor intensive, since we’d only render a smaller portion of detail. My computer overheats just with 2D flash…

I see a possible opportunity to combine this idea with Omei’s air duct tube idea above, so I’ll make a comment there explaining what I see.

Either way, some way to collapse or focus on the part of the puzzle working on + having a global minimap to maintain awareness of orientation & endpoints would be a great feature!

Omei!! Beautiful inspired ideas & mockups. I love how quickly you can mockup 3D stuff in the opensim platform. real time imagination. :smiley:

I am wondering, I might be misunderstanding your original idea, but the collapsible air duct idea, I think could be combined with Eli’s idea below to focus on one part of the molecule at a time in conjunction with a minimap.

Like, in your mockup with two green discs, the space between those nodes could be collapsed with a + / - icon, such that you can leave only the parts you wish to focus on as rendered. This would defeat the purpose of understanding the global shape, which would have to be seen in minimap or full view.

But, it would allow focus on multiple segments of your choosing, and allow the collapsing / management of the large amount if info in a big molecule.

I don’t know though, whether my interpretation of it would be useful enough to be worth building, since it would likely be more dev time than just an up close cameo of one segment. just a thought!

I would love to see as many alternate view options as possible!!! it helps so much to get another view of a puzzle to see it in other colors and outlines. This would be great.

totally agreed - real time editing of already placed pieces is a must. This is partly why I gave up trying to solve the puzzles, because the likelihood of guessing the solution not only in general, but -in sequence- is just too tedious. I want to play! hence the toy box idea.

When we play to imagine solutions, we should easily be able to make changes and swap out motifs, or snip them out or insert some in between. Foldit does have some of these editing tools, and it took them a while to add each as a feature to the interface.

So I understand it is just a matter of dev time. But absolutely, it is a high priority request to edit motifs & main molecule in place.

I did mention the idea of inserting a motif in the middle of a sequence in chat one day and one of the devs , I forget, said it would be programming intensive and lengthy. But I must say, out of most of the ideas to improve 3D usability and the chance of success to solve the puzzle it would perhaps be the inserting option. With better prediction of the center axis and direction points from both ends as a very close second.

Interesting that it would be considered difficult to do. I can see how making a smooth animated transition from the original to the final might be relatively hard, depending on what tool set they are using. But a really simple minded approach of programmatically undoing to the point of change, making the change, and then redoing the rest should be pretty darn easy. That’s not slick, but it would get the job done.

I don’t know anything about programming but perhaps he misunderstood my thought. Not sure.

i don’t know how it’s built either. i think one dev may have mentioned that the motifs are stored as separate entities in the whole sequence and that in theory they can still be edited separately after placement in the main molecule, as well as calling up individual motif info after placement. but that it is not currently set up to do this. but at least it sounds like the framework would support it.