Closed since about 5 years ago
Advanced Overall Prediction Electron DensityThis protein is part of a large protein complex with multiple subunits, which was recently solved by cryo-electron microscopy (cryo-EM) at 4.2A resolution. Unfortunately, the solved structure could really use some work so we are hoping you can improve the structure. One end of the unfolded chain is close to its correct position in the electron density, but the rest of the chain is completely extended and will need to be refolded to fit in the density cloud. Keep in mind that this will not be easy, as 4.2A resolution results in a challenging electron density cloud to work with! The starting structure includes several locked protein fragments in the electron density cloud. These are additional proteins that are also present, and are expected to make interactions with the final folded structure. Good luck!
***More details about the native structure in the puzzle comments***
<pre>Thanks for all your answers so far about
this puzzle.
Are there certain N-terminal atoms in this
puzzle's starting structure that are very
close to their desired positions in the
ED Cloud? Perhaps we could use zero-length
bands from these atoms to space to keep
these atoms in their starting positions.
If so, which N-terminal atoms would you
fix in place with respect to the ED Cloud?
Thanks again!</pre></code>
It's been seven years since I've done an ED puzzle, so I don't know how they've evolved. Please forgive any ignorance.
The puzzle supposedly has locked fragments inside the density cloud. When I moved my design inside the cloud, my designed structure stayed pretty much the same, but the fragments exploded in all directions and landed a full monitor screen away from the cloud. How is that possible, if they are locked?
Also, just rotating my design along an axis, while nowhere near the cloud, dropped my score by thousands of points. How is that possible, when nothing was done to my design's structure, and it was too far from the density cloud to matter?
but hopefully this view helps: https://i.imgur.com/lwSb2lK.png
Again, keep in mind this could be incorrect… especially since the ends of a protein chain tend to flop all over the place! But it's at least probably in that general area.
<pre>In addition to the ED Cloud you can see,
many of these puzzles have invisible clouds
nearby. It is like a periodic lattice of
ED Clouds in all directions with some empty
space between them. If a segment of your
protein is in the empty space, it gets a
zero or negative Density subscore. If a
segment of your protein is in an ED Cloud
(either the visible one or one of the many
invisible clouds), it gets a positive
Density subscore.
It is possible to have your protein be
straddling more than one ED Cloud. Then
you will have some regions with zero or
negative density (between the clouds)
and others with positive density (within
a cloud).
Below is a Feedback with a diagram of a
periodic lattice of ED Clouds.
https://fold.it/portal/node/2007742#comment-38544
I have written many other Feedbacks about
ED Puzzles, some as listed below:
https://fold.it/portal/feedback/all?filter0=electron+density+jeff101</pre></code>
Indeed, this is the case with the ED cloud in Foldit (as well as in many other density programs)
The only workaround would be for us to pad the map with a buffer of zero density, but this would sadly increase the size of the map in memory… which we obviously don't want to do! (as demonstrated by your feedback: https://fold.it/portal/node/2011161#comment-44012, we don't want to increase that even more!)
Boots, your second question is answered above, but we are stumped by your first question.
Has anyone else run into this bug?
Boots, do you have a screenshot or scientist save of this explosion?
Thanks!
https://fold.it/portal/node/2011169/show_players
Or are you and alcor29 referring to something else?
I was just looking into the issue the Boots reported.
In mine, segments 5-9 are now a long distance outside the cloud.
Uploaded for scientists as "segments 5-9 ejected".
Not sure how to fix it, I guess I can band them back to where they started.
In my opinion, Foldit team should give an SS prediction for this kind of difficult puzzle. This would help us to find an approximate match in the density, refining later on.
<pre>Say a player puts some of 1952's protein fragments
in a visible ED cloud and other fragments in an
identical but invisible ED cloud. Both ED clouds
contain the same pockets A-D. Say fragments
a-d belong in ED cloud pockets A-D respectively,
but the player puts fragments a-c in pockets
A-C in one ED cloud and fragment d in pocket
A in the other ED cloud. Being in distinct
but identical ED clouds, fragments a & d would
be too far apart to clash with each other, but
they might both fit very well into pocket A.
This would give good density subscores for
all of the fragments, but it would neglect
the score penalty for putting both fragments
a & d into ED cloud pocket A, a pocket just
large enough to hold either fragment a or d
but not both fragments a & d simultaneously.
Maybe the scenario above can explain why
Boots' exploded protein scored so well in
Puzzle 1952.</pre></code>
