puzzle picture
1667: "Too Much Density!" Freestyle puzzle
Status: Closed

Summary

Name: 1667: "Too Much Density!" Freestyle puzzle
Status: Closed
Created: 04/25/2019
Points: 100
Expired: 05/06/2019 - 07:00
Difficulty: Expert
Description: This Electron Density puzzle is different than anything we've ever posted before! The extended chain is 187 residues long, but we are giving you a lot more density than that. You'll need to find where to fit this chain in the giant blob of density. (The "Trim Density" tool will be your friend)
Categories: Electron Density, Overall, Prediction

Top Groups

RankGroupScorePoints
1Go Science22,257100
2Beta Folders20,38773
3Anthropic Dreams20,34952
4Gargleblasters20,24436
5Russian team20,07524

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
1fiendish_ghoul 79 7  22,033100
2Batz 70 94 Go Science21,53397
3Bruno Kestemont 3 4 Go Science21,10494
4Galaxie 1 2 Anthropic Dreams20,34391
5johnmitch 79 9  20,33188


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Comments

jeff101's picture
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Secondary Structure

It looks like this puzzle starts with an extended chain with all residues having loop as their secondary structure.
If there is a reliable secondary structure prediction for this puzzle, please post it here.

Thanks!

Joined: 09/24/2012
Groups: Go Science
sequence

lrpalstfiflllitggvypllttvlgqwwfpwqangsliregdtvrgsaligqnftgngyfhgrpsat
aempynpqasggsnlavsnpeldkliaarvaalraanpdasasvpvelvtasasgldnnitpq
aaawqiprvakarnlsveqltqliakysqqplvkyigqpvvnivelnlaldklde

Joined: 09/24/2012
Groups: Go Science
PSIPRED pred

LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLEEEEELLEEEEEEELLLLLLLL
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHLLLLLLLLLHHHHHLL
LLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHH

but there are not so many helices in the cloud ...

Joined: 03/30/2013
Groups: Go Science
Why so much? Thirsty for more info.

What do you mean by "a lot more density"? I would love to know more. Does what we are given correspond to more than 1 asymmetric unit?
What do we expect to find there? 2 monomers, 3 monomers, another different peptide? Where does this density come from? X-ray diffraction, cryo-EM?
Resolution? I think some stuff like that would help us know what we are looking at. Thanks

jeff101's picture
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More questions about "a lot more density":

Is it possible that a section of the protein, say segments 1-30,
appears in the displayed ED cloud more than once? Could the
ED cloud be showing more than one conformation of the protein
simultaneously? Could the ED cloud be showing the average
of a distribution of conformations so that some regions of the
cloud look fatter than others? Is some part of the ED cloud
from proteins, ligands, or solvent molecules distinct from the
187-segment amino acid sequence you've given us? Should
we expect one continuous copy of our 187-segment chain to
be in the ED cloud, or should we expect one or more partial
copies of the chain to appear? Several partial copies would
seem to have multiple NH2 and COO termini, which would
be confusing.

Is this ED puzzle different from previous ones because usually
you trim the extra density before posting the puzzle, but here you
give us a very raw un-trimmed ED cloud? Is there some other key
difference between this ED puzzle and previous ones? Should we
expect unusually large Density subscores when we Tab on residues
in this puzzle?

Is the ED cloud here from a crystal or from a sample in solution?
At what temperature was the ED data taken?

When we use the Trim Density tool, do we just alter the appearance
of the ED cloud, or do we directly affect the scoring as well?

The pages below might be helpful:
https://foldit.fandom.com/wiki/Electron_Density_Puzzles
https://foldit.fandom.com/wiki/Electron_density_(tool)
https://fold.it/portal/node/995580 (Electron Density Trim)

Thanks!

toshiue's picture
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1667 secondaries: RaptorX, bruno's PsiPred, Psipred, Jpred4

RaptorX LLHHHHHHHHHHHHHHLHHHHHHHHHHHHHLLLLLLLLEEEELLEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLLLHHLLLLLLLLLLLLHHHHHLLHHHHHHHHLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHHHHLLLLL 187
bruno psipred LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLEEEEELLEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHH 180
PsiPred LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLEEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLHHHHHHHHHHHHLLL 187
Jpred4 LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLEEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLHHHHHHHHHHHHLLL 187

toshiue's picture
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Phyx's 1727 evo share secondary @ 17870

one other secondary currently in play...

phyx17870 LLLLEELLLLLLLLLLLHHHHHHHHHHLLLLLLLLLLLLEELLLLLLLLL
HHHHHHHHHHHHHLLLLLLLLLLLLLLHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
LLLLLLLLLLLLLLLLHHHHELLLLHHHHHHHLLLLLLLLLLLHHHLLHHHHHLLLLELLLLLLLLLLLLLLL 187

Batz's picture
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5MRW

The structure is actually known: look at PDB entry 5MRW
But it does not seem easy to build...

Joined: 03/30/2013
Groups: Go Science
5MRW chain C

To add on to Batz' observation:

5MRW has peptide chains A thru L

Specifically, we have been given chain C of 5MRW.

Batz's picture
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I actually took Chain K :D

I actually took Chain K :D

Joined: 09/24/2012
Groups: Go Science
More time needed

For my computer, density cloud is toooo slooow (video card limitation I suppose). Almost impossible to play (hand fold). More time would be needed.

horowsah's picture
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density questions

Just wanted to address a few questions from above- this density comes from cryo-EM. In EM, the resolution is typically low (in this case, around 4 angstrom resolution), and often it's of a multi-protein complex. One major challenge is figuring out which parts of the density correspond to which of the proteins in the multi-protein complex, or even which parts of the density might be noise. So having "spare" density like this is a hard but important scientific puzzle that microscopists frequently encounter.

jeff101's picture
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How do microscopists do it?

Apparently in previous puzzles, the Foldit team trimmed the density so it only contained the protein of interest. In practice, how do microscopists & the Foldit team know which parts to trim and which parts to keep?

Susume's picture
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I'd like to buy a sidechain....

I have found at least ten helices in the cloud (you can mark them with one dot, two dots, three dots etc to number them so you can tell them apart), but it's fairly impossible to tell which ones to use because the resolution on the sidechains is so poor. Without visible aromatics to use as landmarks, placing the protein is pretty much guesswork. Is it possible to recalculate the cloud from the data in a way that favors sidechains more?

frood66's picture
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oops1 I accidentally down

oops1 I accidentally down voted - sorry Sus.

Truth is - the definition is rather too low for an extremely mind boggling puzzle.....
there are some aromatic markers (but they are oft in areas of loop)
The majority of the cloud is of no use since this cloud contains more than one chain.
Once the superfluous are removed - that helps a bit. But I would still like to see an eraser to remove these - they are are pointless
As for completing the puzzle? I know some of it (and have it) Will I bother to try to complete? - prob not. Too much is loop and too much is disordered (invisible)

bkoep's picture
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Interesting idea

Unfortunately, I don't think there's any direct way to emphasize the density of sidechains. Cryo-EM only tells us where electrons are concentrated—it doesn't distinguish between electrons on sidechain atoms vs. electrons on backbone atoms.

We could think about calculating something called a difference map, using the player's solution. This means we would calculate a theoretical electron density cloud from the player's model, then subtract the theoretical cloud from the EM cloud. The result would be a "difference cloud" that highlights regions of density that are not occupied by the model.

For example, in a case like this one, where you can pick out helices but can't see the sidechains: the player might build the helices out of GLY and then compute a difference map. In the difference map, the theoretical density of the GLY helix would "cancel-out" the EM density along the helix backbone, and the density for the (missing) sidechains would be relatively more intense.

This wouldn't improve the "quality" of density at the sidechains, but it might be useful for visualizing weak sidechain density.

Susume's picture
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Yes please!

I would love to be given this ED again with designable residues (let us pick all glycine for example) so we could design into the backbone only (or add just a few sidechains if we see a good spot). Would you consider offering us such a puzzle, and then trying out the subtraction method to see if it helps to make sidechains visible in the density? It could go in the experimental category.

Joined: 09/24/2012
Groups: Go Science
Would it be possible "on the fly" ?

That would be great if the player could do it 'on the fly':

-give me a PSIPRED prediction

-let me "mutate" everything to GLY

-using that I can move pieces of helices and sheets in the cloud in order to construct my sidechain highlights.

-then I use a new foldit tool to re-calculate the density cloud (with more weight to what I identified to be sidechains)

-then I "mutate" everything back to the protein sequence

-and I find-tune the cloud position

(otherwise, you ask us a first round with PSIPRED and sequence information, but all-GLY and an extra-weight for ED bonus, then you give us a second round with the real sequence in protein)

LociOiling's picture
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PDBs

There are three PDBs that match:

* 5MRW, chains C, G, K; offset 0
* 6HRA, chain C, offset 3
* 6HRB, chain C, offset 3

For 6HRA and 6HRB, the "offset 3" means segment 1 in Foldit is segment 4 in the PDB model.

Both 6HRA and 6HRB show a complex of four proteins.

5MRW has the same four proteins, give or take a few segments, but they're repeated three times. So it's kind of a trimer of tetramers, with 12 protein chains overall.

5MRW has 4,335 segments, where 6HRB has only 1,458.

I'm guessing the density contains all or part of the four proteins.

frood66's picture
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just as a reminder to foldit

It has been 'de rigour' for puzzle pages to give the sequence for some time - so what has happened?

It has also been requested (and followed by FC) to state the definition (Angstrom) on ED puzzles.

I (and others) find it very curious that huge ED is posted - and neither 'usual' info has been given.

Just saying! :)

frood66's picture
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To be clear

All vets know that trim density is of little value in early game.

If players cannot get past early game - then it becomes doubly useless. It is generally only of value in mid/late game and only then with reasonable definition (which this puzzle does not have)

We all know this - strange that the setters do not. :(

Come on guys - give us something to work with! Or are U just using us as lab rats?

Joined: 05/19/2009
Groups: Contenders
The point

What exactly is the point of these puzzles if people lookup the structure and from all the info deduce which protein it is and how it should look like ? Wasn't the idea that we would train ourselves to recognize features and map those to a model that fits reality without prior knowledge ?

jeff101's picture
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It depends on if one cares more about points or the science...

I for one have not yet looked at the pdb files or my team's
shares for this puzzle. I am trying to do this puzzle as if its
results are unknown (and perhaps they are unknown, perhaps
this is a new structure for the same sequence, but maybe this
one is when bound to a new drug, for example). I am using the
PsiPred secondary structure listed above and relying a lot on
recipes so far. I had a solo rank 17 when last I checked, and
I have some more ideas to pursue regarding this puzzle.

Nevertheless, I haven't yet found a good starting position
(a terminal end or a recognizable sequence of residues in the
middle of the protein chain). My best solutions so far sort of
follow one chain over here and another chain over there. There
are many places where my solutions clearly jump from one chain
to another. I am still hopeful I can make more progress on this
puzzle. If nothing else, it is good practice. If we can do this
type of puzzle, it opens the door for more puzzles like this,
and the scientists won't have to spend as much time
processing their data before giving it to us to solve.

Finally, if this is a new structure for an old sequence,
scientists in the real world would certainly look at the pdb
files for the old structures. They would use whatever data
they could find to get insight into how this new structure
folds.

frood66's picture
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I agree BP - but that is the

I agree BP - but that is the way this place has gone.

With regard to this puzzle - the definition is too poor to do much else.....

But - on this occasion the native is mostly not gonna score well (other than density) which brings us back to whether it's all worth it.

So the game is being hoist by the petard of the setters.

It's a shame.

It would all make more sense if the cloud definition was better - imho.

Joined: 05/19/2017
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Cloud Control

Hey folks, your favorite young streamer's back with some preliminary comments and it's...not fantastic to say the least.

I actually had a lot of fun with the last couple ED puzzles because my strategy would be to get a lock on a region with a sequence of "landmark sidechains" (namely the ones with benzene rings) and proceed to attach them one at a time from there. Quite therapeutic once I got "into the zone" and got a steady flow going.

But then I got to this one. For those keeping up with my livestreams you probably saw last Friday that I wasn't able to get a lock on any portion of the cloud for a couple reasons. Firstly was discovering how Trim Density actually works.

What I *expected* it to do was cut away a portion of the cloud based on the slider from the point of reference of the camera. That probably sounded wordy, so I'll provide an example: If I looked at the cloud from afar, slid the slider to 75% and hit okay, I'd expect the 25% closest to the camera to cut away, exposing the layer underneath.

How it actually works is that it cuts away all of the cloud except for any bits that are close to the physical protein that you're manipulating, the distance threshold obviously being modified by the slider. So for those like me wondering why the entire thing disappears when you hit OK, this is why. Now I tried using it the proper way once I discovered what was wrong...but honestly with how it worked I didn't feel like it was useful. I'd have to spend time folding up a protein into a rough chunk of what I wanted to focus in on, resize it, re-fold it into the residues that I wanted to test for "landmark" status, rinse repeat. That's way too much effort for trying to insert a residue like a literal puzzle piece to see if it fits the metaphorical "hole" that's obscured by the rest of the holes (i.e., the rest of the cloud.)

Electron density puzzles are otherwise simple to me conceptually: find the patterns in the cloud, match them with what you have, and align accordingly. What strikes me as the main difficulty here is the workspace. Threshold manipulation was enough for me to scope out the landmark residues on the outside for me to align the rest, but once you layer in the shell of extraneous cloud, it's not impossible to do the same strategy, but it's much too time consuming to hold my attention in its current state.

I've seen frood's eraser suggestion, and that could be a good remedy, and it's quite similar to a solution I had in my mind where one could cut out fragments like a surgeon to expose the cloud underneath. Controls have always been a bugbear with Foldit and if I were in the developer hotseat I'd be looking at other 3D modeling programs or sandbox games as a reference to improve the UI/UX shortcomings of Foldit.

I'm gonna separate this post so that it doesn't get too long, so check the replies.

Joined: 05/19/2017
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Gameplay Style and Puzzle Design

So another thing that is probably holding me back is that I prefer to approach from a gameplay-first, reference later perspective. As in: I don't look up the puzzle sequence on the PDB. All power to those who do, but for me, I have reasons.

I don't necessarily do this with other games. I've spent more hours in the Runescape, Minecraft, Terraria, and Warframe wikis than I care to admit. But with Foldit my personal justification (and emphasis on personal; people should have every right to play the way they want) is that with Foldit, I should ideally be relying on the patterns I see given the game data in front of me to play, to an extent. It's also worth noting in those other games that the core gameplay loop is engaging and satisfying enough for me to justify looking at pages of words and documentation to get the most out of my time there, whereas in Foldit, I'd feel like I'm missing the point if I go to look at references. Not to discount the collaborative nature of the game, of course, but this is how I get myself to practice improvement.

So, for example:
- In Prediction puzzles like Unsolved DNFs, I'll make little changes to the pre-set PSIPRED secondary structures and work with those for as long as possible to put together my rough draft fold
- In Design puzzles I often do not consult the PDB for inspiration on what I should make; I simply kitbash together building blocks at my leisure in the hopes that it creates something pleasing and roll with it. I follow the rules of the game of course, but otherwise my designs are rather random!
- In Revisiting puzzles the only hints I allow myself are the proper disulfide bridges when applicable. I otherwise again work from what I'm given.

So for this puzzle, I tried to employ my strategy for finding the landmark residues outlined in my previous post, and had difficulty. This was the one time I actually broke tradition and ran PSIPRED on the puzzle sequence (which I had to use the print protein recipe for) just to try and find an extra clue. During stream you could see me try to no avail to align the predicted secondary structures.

This brings me to the puzzle design. Foldit's honestly the hardest to do, because you're pitting the difficulty of actual science with the entertainment value of a game. I really don't want to go looking stuff up only to find that having the knowledge didn't really help my gameplay experience to much (or compromised the sort of "point" of the game to come up with predictions *ex nihilo*.)

Given the current state of the controls, the difficulty of the puzzle, and the time investment needed to come up with a solution, this puzzle is poorly designed from a gameplay perspective. From a science perspective, I actually think that it's ideally designed! But as with a vast majority if not all scientific studies: High internal validity usually means lower external validity. Bridging the analogy here: This puzzle has rock solid integrity in terms of scientific practices and theoretical application (I love the idea of this being the hardcore standard of bringing the game close to what actual microscopists have to deal with), but as a difficult puzzle for a video game it's pretty much restricted to any savant who has the time, energy, and force of will to take on these challenges willingly. And that, I assure you, is a minority for any video game.

Joined: 05/19/2017
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The Threshold Slider and UI/UX

Mind you this is coming from an end-user perspective, but is it just me or is half of the threshold slider useless? Legit, the entire left side of the slider results in too noisy of a cloud to use.

I feel like that entire left side of the slider can just be cut out and the other half expanded to the original scale so that we could have finer control of what we want to see.

Even better, add numerical input boxes to all sliders.

If anything this puzzle is just another reminder of how much we take for granted when it comes to UI/UX polish. Sometimes nobody thinks to add a feature until someone brings it up, and that's why playtesting/feedback response is so important in games. Of course, I'm not going to ask the impossible; developer resources and working time are finite, and the last thing I want is someone to crunch in order to make our lives as players marginally better. But, as I have heard from accessibility advocates in gaming, if Accessibility/Quality of Life features is/are planned out from the get-go or sooner rather than later, everyone benefits (see the "Curb Cut" effect for a deeper justification).

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BandOntoSphere1.0 recipe:

One recipe I've been using for ED puzzles is called BandOntoSphere1.0
(https://fold.it/portal/recipe/102961). I made it to keep the protein inside
a sphere centered on the center of the ED cloud. Before running this recipe,
I identify a point in space roughly at the center of the ED cloud and make a
band from a segment of the protein to this point in space. This band is called
the hub band. Then, when I run the recipe, it makes a bunch of bands from
evenly-spaced segments of the protein to the center of the ED cloud based
on the hub band. I set keephub to 0 to remove the hub band before the recipe
finishes. For Puzzle 1667, I have found that setting the band length to 36 and
the band strength to 0.1 work well. Otherwise, I use the default settings.

If the band strength is large, BandOntoSphere1.0 forces the protein to lie on a
thin spherical shell with radius equal to the band length setting. With lower
band strength, the thickness of the spherical shell increases. Setting the
band strength to 0.1 lets the protein fill a good portion of the sphere.

This recipe would work better if Foldit had LUA commands for one-way bands,
in particular, the type that keeps the band length shorter than a specified value
(https://fold.it/portal/node/996372#comment-27202). This kind of band
would be enabled when the band length is above a certain value and
disabled when the band length is below a certain value.

frood66's picture
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clarity of ED

I think a trick has been missed here.

If this puzzle had been set with better definition (this one is real poor) I think many would have embraced and enjoyed the challenge.

But it has not.

Net result - few can even be bothered.

I'm a true exponent for ED - but this is not set up to enthuse.

Suggestion for FC - if U R going to create a huge puzzle with much cloud that is extraneous - at least
allow for a level of definition that does not cause despair.

It's bad enough that the memory usage is massive - but to not even throw a bone to yr dogs is daft.

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Thanks for all your comments!

Thank you all for your candid and specific feedback about this puzzle.

With the success of the previous group of cryo-EM puzzles, we are trying to figure out how to present future puzzles where the density has not been successfully trimmed by a microscopist.

Clearly, this will require several new Foldit tools in order for this to be feasible... so thank you very much for pointing those out! Some of these will take a lot more time to implement (such as the ED eraser tool), but some tools should be easier to add to the game (such as adding numerical input boxes to all sliders and LUA commands for one-way bands).

We realize this particular protein exists in the PDB, but there is no other way for us to post such puzzles... unless there was a specific CASP for cryo-EM structures (which would be awesome because all of you would do so well!).

Thank you for your patience on this one, we won't post another similar puzzle like this until we come up with a better way.

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thanks for those comments :)

thanks for those comments :)

jeff101's picture
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Do backbone CO groups make ED cloud features?

In my efforts to identify amino acids in this puzzle's ED cloud,
I asked myself if CO groups on the backbone make any features
(like little spikes or bumps) in the ED cloud. I don't recall
seeing such features in previous ED puzzles, but sidechain CO
groups certainly give features in the ED cloud. In the image at
https://fold.it/portal/node/2001386 sidechain oxygens seem to
act like sidechain carbons within the ED cloud. I also think the
COO group at the COO terminal of a protein chain shows up in the
ED cloud, looking like an extra valine or threonine sidechain there.

So, do backbone CO groups give features in the ED cloud?
If so, what do they look like? If not, why not?

Thanks!

horowsah's picture
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re: Do backbone CO groups make ED cloud features?

The answer is that they do, if you have high enough resolution data to see them stick out (usually need about 2.8 angstrom resolution data or better for that to happen). In this puzzle, the data isn't good enough, which is usually the case with electron microscopy-derived density. This is one of the things that makes building into these maps a challenge.

Joined: 09/24/2012
Groups: Go Science
Poor (top scoring) results. What if unsolved protein?

If it has been an unsolved puzzle, I guess no player had found anything.

I tried during hours without being able to even find a starting position. Then I/we moved to a visual copy of the 5MRW, yet the result is poor.

I evolved the top solution and I'm ranked 3 for another solution + I shared to scientists 5 more high scoring solutions: it's obvious that none of them are even close to a realistic structure (the 5MRW solved one). Sidechains out of the cloud, one protein helix jumping through 2 "cloud helices" etc.

What would have helped us (in a case of unsolved protein)?

-some PSIPRED or other SS prediction
-partial solving of the other chains would have been on great help (in order to be able to erase other parts of the protein, or to be told to accept unburied helices - I would never have accepted this unburied helix starting seg 1 as a right solution without seeing it in the 5MRW)
-the erase tool (in my old&slow computer case, no erasing means no possibility to hand fold)
-contact map or any other help
-any tool or model that would help us to find the aromatics in the cloud (I like the GLY idea above)

bertro's picture
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Side-by-side comparison of W and Y relative to resolution

I wonder if some Side-by-side comparison of W and Y (and some other maybe) relative to resolution would be useful to us in visualizing cloud shape for said resolution?

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