Hi everybody!
We were going over the Foldit Survey puzzle results and turns out it has been pretty useful, especially looking at trends over time! If you didn’t get to put your thoughts in that way (and a bunch of you did, thank you very much), unfortunately that survey is closed.
We asked the survey takers, just like last year, what your favorite and least favorite puzzle categories were, provided you had to pick just one. It’s a tough choice.. or is it? What struck as immediately as interesting was not only did our respondents pick “electron density” for "least favorite" two years in a row, this year there was a huge jump in doing so, making it a runaway choice compared to the other categories.
Seriously, what’s up? That’s some pretty strong dislike, and I’m sure some of you probably feel the same way but didn’t get to the survey for whatever reason (don’t make that error over our demographic survey though). We want to know where the problems are with electron density puzzles, so we can address them as much as possible given our resources. We also want to know what's working for you on those. We have some theories and speculation what’s causing these numbers, but we don’t want to influence the discussion and so we’re opening this thread let you tell us your thoughts.
Please note that this discussion is restricted to electron density puzzles only. This is not a discussion about other puzzle types, bugs, or general game feedback/suggestions (and those will likely be removed, as well as anything not keeping in spirit of the community guidelines, obviously).
This is a good start for context to the discussion (and we have seen those links), thanks for digging them up. Which of these suggestions are your favorite?
https://fold.it/portal/node/993959#comment-32465
proposes a way to fix the "Align Protein to Density"
or "Center Protein on Density" button using 3 xyz
coordinates to translate the protein, 3 Euler angles
to rotate the protein, and an optimization algorithm
like the Nelder-Mead Simplex Direct Search Method
to vary the 3 xyz coordinates and the 3 Euler angles.
https://fold.it/portal/node/2002670#comment-33044
https://fold.it/portal/node/2001368#comment-31396
are about filling continuous parts of the ED with color,
like in a paint program, as if the ED were a mold and
we were squirting a colored liquid into it.
https://fold.it/portal/node/2001368#comment-32121
have options to show the calculated ED for the
present protein conformation so you could compare
the calculated ED with the given experimental ED.
https://fold.it/portal/node/2001368#comment-31397
https://fold.it/portal/node/2001368#comment-31401
let players fold the protein without the electron
density affecting its score. This could be by
confining the electron density to a few unit cells
and having the rest of space have zero electron
density. It could also be by letting players turn
on/off the electron density score as they fold.
http://fold.it/portal/node/993956
Rav3n_pl's "old idea of alignment editor. It would be
1000% easier to draw shapes on ED how we see them then
thread protein into that shape. I wish to draw helices,
sheets, then add loops and thread protein into it."
http://fold.it/portal/node/993956#comment-20594
having hoops (fixed points in space that the protein
must slide through in a particular order).
What I would wish for ED puzzles is more control of the viewing planes.
In particular being able to lock one axe (or have a wheel like tool keeping one axe fixed but ajustable) while playing with the mouse in that 2d plane.
Also better control of the Z-planes near and far (better cutoff)
These are still mysterious to me.
I can't seem to put the dots where I want them (always a "mile off") So some way of orienting the dot where you want it that is more precise as a marker would be one wish.
MAYBE a higher contrast puzzle color scheme that would show up better against the cloud… or highlight colors specifically for ED that show your higher ED scoring segments, not just aggregated scoring.
An in-game key to shapes to look for in the cloud similar to that diagram circulated during the contest.
I agree about improving navigation through slices of the cloud.
"Snap to cloud" — is that even a possibility? (like snap to grid in graphics programs) if you get close enough to a cloud shape.
Better control of the cloud alpha and threshold (1-100 "dials" or numeric entry)
Definitely fix the center/align. Would align puzzle to highest ED score aggregate be possible?
(ideas, I got 'em. Thanks for the official forum to post them!)
I think it would help to have some easier ED puzzles for people to practice on - the only ones we get are high-stakes puzzles, when struggling with the tools is most frustrating.
Maybe every third revisit puzzle could have an ED cloud added to it. Give us the protein partially folded (not straight chain) just like they are now, but have a cloud next to the protein to fit it into. The revisit proteins are generally solved, so the ED data ought to be available.
If you are going to make some of the suggested improvements to the ED tools, letting us try the changes out on a revisit and offer feedback would be better than introducing tool changes on a high-stakes puzzle.
I agree that all the tools suggested sound highly useful. That said, I still can not "see" alignment, no matter how much time Susume & Frood have spent trying to help me work them. I can't tell a backbone from a sidechain often, "see" the helices, etc. I have watched the black belt videos several times, but just can't get there.
Secondly, all the ED puzzle this year have been monster sized. I can't do anything monster sized, never mind a monster sized ED. I do not have the computer capacity to do it, nor the time & ability to sit for hours at a stretch to work these large puzzles
If this is the preferred tool, we need a "training program". Start with some small ones with really good resolution. Let us work several before moving on to bigger ones or ones where some or all of the protein can not be presented well. Maybe even keep those puzzles for those of us who have never been able to do an ED. My only decent score was to stick 4 helices into the cloud once. I was embarrassed to score a top 10 on that one. FoldIt should be too, as it showed that the scoring system outweighed a useful answer
Absent training that I can follow and use as a foundation, I will open these ED puzzles only to evo a team mates solution when it is competitive. I know the science may be going there, but the citizen part of citizen science may not be able to follow
Agree with Susume regarding practice puzzles, we get so few ED ones I forget how to use the tools and interpret the clouds.
The great thing about ED with decent resolution is certaintity. Also agree with smaler ones for practice.
The markers are useful but may be more useful to me if they were rods as I find them difficult to position in 3D space when I am marking big rings.
Practice puzzles with tryp and other hydro rings are easier to get a grip on because they are easier to see in the cloud.
I really like ED and would like to see more of them, certainly prefer a better resolution.
