1964: Unsolved Huge Cryo-EM Density: Beet Virus

Closed since almost 5 years ago

Summary

• Created: March 04, 2021
• Expires: March 18, 2021 at 18:00 UTC
• Max points: 100

Description

We are very excited about this puzzle, because our collaborators who provided us with the 4 structures from Foldit's 2019 cryo-EM paper have been unable to solve this cryo-EM structure.
This will not be easy, because the full density has 46 symmetric monomers and we can't cut out a single copy of density for you (since we don't know the structure). Instead, we've sliced off a quarter of the entire density, which our collaborators estimate should be ~10 monomers. So keep this in mind, as we are only providing you with a single monomeric chain to fold. More details and pictures in the puzzle comments!

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Comments

[CryoEMguy]

Hi Jeff,
here some more info :
(1) RNA is somewhere in the ED cloud (see my answer to another question below). About its shape : you have a phosphate-sugar backbone that will form some sort of "necklace", from which the bases will stick out (and most likely form short stacks). The bases look like large amino acids (roughly the size of a tyrosine).
(2) You can expect different types of interactions. The phosphate groups of the RNA (which,by the way, will be strong densities) can interact with positively charged amino acids like arginines or lysines. The bases may, in some cases, interact with hydrophobic amino acids : you can even have stacking of bases to aromatic residues such as phenylalanine.

[jeff101]

In Puzzle 1964, I have found the Trim Density tool useful.
It seems very sensitive about 1mm from the Far end, and
that is the range I've found to work best. Having this
slider report a number for its present setting (and perhaps 
giving a finer resolution of settings about 1mm from the 
Far end) would make this slider more useful.

[jeff101]

On this puzzle, I've put so many dots in the ED cloud
that they are no longer helpful. I want to delete some
but not all of them. Removing dots by hand is pretty
tedious right now. It seems like I have to Tab on a dot
and then move the mouse to click on a Trash Can icon
that appears. It would be better if a single button 
like Delete or Backspace instead of Tab could be 
pressed, and this would remove a dot.

Also, Puzzle 1964 has many of the same problems that
Puzzle 1667: "Too Much Density!" Freestyle puzzle 
(https://fold.it/portal/node/2007726) had, and
https://fold.it/portal/node/2007742 lists many ideas 
to improve ED puzzles based on problems with Puzzle 
1667. If ED puzzles are to become more frequent in 
Foldit, please implement some of the ideas in the 
above Feedback.

One quirky thing I should mention is that when I
added a label to a dot in the Selection Interface,
I had to Tab on this dot to see its label. Also,
Note Mode would show this label in the Original 
Interface but not in the Selection Interface.

[APPAAP]

I realised that the ED given is very close to 1/4 or just 1/4, may be on top or bottom there is no cut planes.
The monomer (protein given) can only be seen fully in the ED given in the middle (there are almost 12 monomers but not all are fully seen in the ED given) because at the ends there are at least two cut planes. The RNA is best seen from top and closer to the inside part than to outside part.
Although this seems simple, I find extremely difficult to align. My protein fold is completely out of phase with the ED given. I need to refold but may be is not good practice refold only to achieve a higher score. I must learn using the ED trim tool with simpler cases.

[frood66]

this puzzle flips out too often…..please can that be sorted?. is it that u guys are asking too much? or is it that we have machines too small for it?

maybe now would be a good time for us to be advised about minimum machine size….internet speed etc? it would save a lot of heartache.

just saying

[jeff101]

Seems like when I try to turn the ED on while a recipe is running, 
1964 crashes. Also, if I am doing shake & trying to add a band at 
the same time, I often get a crash. Sometimes when I add bands,
the response is slow, and if I move the mouse too soon, it moves
my band from where I wanted it to be. Many times the Foldit
window has said "not responding", and if I try to do another
action, it crashes. When I see the message, it seems better to
wait for the message to go away before trying my next action.

1964 has generally been well-behaved when running recipes
(if I keep the ED off or don't try to change the ED view
settings).

[jeff101]

I think for Puzzle 1964's helical protein/RNA complex,
you could break up the overall structure into many 
identically-shaped pieces, a bit like pie pieces in 
the board game Trivial Pursuit. The tops and bottoms 
of these pieces would be slightly-slanted so that if
you made a long enough ring of them, they would not
form a perfect circle. Instead, there would be almost
circular layers one on top of another, forming an 
overall helical shape. Each of these pieces would 
contain all the segments for a complete protein 
monomer, but it might be segments 1-30 for one 
monomer, segments 31-120 for a second monomer, and 
segments 121-188 for a third monomer, for example.

It would be neat if we could see the ED for just 
one of these pieces, and if our protein crossed 
through any of the boundaries for this piece, it
would get chopped off at that boundary. The rest
of the protein would continue through the correct
point on another part of the piece's boundaries, 
and it would continue within the same piece of 
the ED. This way, if our protein straddled several
of the repeats within the overall structure, we
could easily check that it wasn't overlapping 
with another copy of itself. Perhaps the Foldit
score could account for interactions of proteins 
with other copies of themselves and help prevent
them from overlapping with each other.

Having a small chunk of the ED like above would 
make it easier to spot features within the ED
and mark them with dots.

https://fold.it/portal/node/2007742#comment-38508
discusses similar things for a simpler complex
that has box-shaped repeats, more like the 
typical unit cell discussed in chemistry.

Finally, if you can break up the experimental 
ED into many repeat units, maybe you can average 
the ED from many of these different repeat units 
to give an ideal repeat unit's ED with better 
signal to noise.

[frood66]

I have long asked for the ability to erase parts/volumes of the ED that I do not want to see.

sure…we have trim to density, radius and a multitude of viewing options. But the truth is…the more we put in the cloud, the harder it gets to look at what we want to.

how about a selection option….where only the selected segments count….all others disappear along with any ED associated with them.

Is this worth a punt?

anything to avoid headaches and sore eyes imao

[Formula350]

The need for a numerical value on the Trim slider would be helpful.
Also, that it be explained somewhere (or maybe it is, these days) on how that Trim tool works. Not so much in the overall function, but that there are factors and quirks (it seems).

For example, that when using the Trim menu, it will always reset the slider to its full amount. Therefore, if you Trim, do stuff, and open the Trim menu again… if you just click OK, it removes your Trimmed amount. If you slide it down some, but to a value that was not as low as what you used before, when you click OK that will add some density back!
So, even if there's a number value included… either the slider needs to actively remember what your slider was previously set at, or you need to have it at least display the previous value that was used, so we have that as a reference.
(For months I had thought the Trim tool's slider worked in an "Additive" way, where by sliding it down 3 notches, then coming back and sliding it down 3 more notches, resulted in a total Trimming of ""6"". That's usually how software has worked in my experience, where a slider that resets conveys a sense of "Ok, your previous value is now the new baseline (max slider value), how much change would you like to do this time". Wasn't until I needed to reset the cloud and just decided to try it at Max Slider, did I realize that's how to reset it lol Also that I had been not trimming my density how I had wanted to, that entire time!)

The other thing is that the Protein's shape apparently is what the Trim tool is working off of… Which I only found out in this puzzle :S
I wanted to try and trim out juuust a single Monomer's density, and hadn't yet folded the protein, so I Centered Protein on Density and ran the Trim, expecting it to sort of work like a combination of Radius and Threshold (admittedly, I don't know why I expected that it'd work that way… lol), yet I was left with a tinny little cylinder of Density around my toothpick protein. Doh! :P
</br>

At any rate, all three of Jeff's suggestions (though the Density Notes might just be a bug) above get a thumbs-up from me!

[beta_helix]

Thank you for these examples, as we can hopefully now reproduce these crashes on our end.

We realize a puzzle with density this big is pushing the limits of what Foldit and your computers can handle, but that doesn't mean it should be crashing this badly.

Now that we have your steps to reproduce it, we're looking into a solution and hope to resolve these crashes soon.
Thanks for you patience!