Bruno Kestemont Lv 1
Amazing that the ED cloud only exist for 2 out of the 4 monomers
2596: Electron Density Reconstruction 114
Closed since 11 months ago
Intermediate Overall Prediction Electron DensitySummary
- Created
- April 03, 2025
- Expires
- Max points
- 100
The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. This puzzle is large, so we highly recommend using the Trim tool. It's also unusual that the four proteins are separated in space. As a result, this puzzle will be open for two weeks.
- Sequence
- MPFGNTHNKFKLNYKPEEEYPDLSKHNNHMAKVLTLELYKKLRDKETPSGFTVDDVIQTGVDNPGHPFIMTVGCVAGDEESYEVFKELFDPIISDRHGGYKPTDKHKTDLNHENLKGGDDLDPNYVLSSRVRTGRSIKGYTLPPHCSRGERRAVEKLSVEALNSLTGEFKGKYYPLKSMTEKEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKSFLVWVNEEDHLRVISMEKGGNMKEVFRRFCVGLQKIEEIFKKAGHPFMWNQHLGYVLTCPSNLGTGLRGGVHVKLAHLSKHPKFEEILTRLRLQKRGTGGVDTAAVGSVFDVSNADRLGSSEVEQVQLVVDGVKLMVEMEKKLEKGQSIDDMIPAQK
Top groups
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1. Contenders100 pts. 140,112 -
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Comments
LociOiling Lv 1
This puzzle has been extended to two weeks, due to the large size, 1,460 segments.
As the comments indicate, there are four copies of the protein, and they are far apart. As a result, you'll need to zoom out to see all four copies. The "Home" and "q" hotkeys won't give a good view of all four copies.
The protein in this puzzle is a match for PDB 1I0E.
There are supposed to be four identical chains of 365 residues, but there are missing residues. As a result, Foldit tools like AA Edit 2.1 think there are eight chains.
The PDB file indicates the missing residues are the same for each copy of the protein. The missing residues are identified as A 323 to A 331 using PDB numbering.
In Foldit, the segments on either side of the gap are connected to each other. The result is that the two segments start with very negative ideality scores.
Segments 315 and 316 are example. The segment information window for 315 shows it corresponds to "PDB #: A 322". Then 316 shows "PDB #: A332". Both 315 and 316 have ideality scores around -12,000.
Segments 315 and 316 are in the first chain, chain A. The same gap occurs for the other three copies of the protein. The complete list of gaps is:
315-316, 680-681, 1045-1046, 1410-1411
SelectoPro v1.3 can select the problem segments using the list above. The resulting selection can then be wiggled on high wiggle power to improve the ideality score. This isn't a substitute for the nine residues. More realistically, there'd be a break between 315 and 316 and the other gap segments. In effect, there really would be eight chains. In other words, segment 315 would not be connected to segment 316, segment 680 would not be joined to segment 681, and so on for the other two chains.
LociOiling Lv 1
One note on using SelectoPro v1.3 is that the chains it identify can change as things move.
At first, SelectoPro sees one chain A that ends at segment 315 and another chain B which starts at segment 316. These segments get stuck with filling in the nine segments that were supposed to appear between them.
If you succeed in getting 315 and 316 closer together, SelectoPro will now think they are both part of chain A.
You may eventually get to the point where SelectoPro will see only four chains.
Determining where chains begin and end is tricky, since Foldit doesn't provide all the info needed. So recipes can look at the distance between segments. There's a narrow range of distances possible under normal conditions. Anything over a certain distance indicates the start of a new change.
For the tortured segments which bridge the gaps in 2596, the distance based logic doesn't work, so there are eight chains at the start instead of four. There are also eight very unhappy segments. As mentioned above, it would be much better if there were actually eight chains….
WBarme1234 Lv 1
With four copys so far away, it would be better to give us only 1 group at all.
With four copys so far away, they only stress our home systems and our time at lot!
bravosk8erboy Lv 1
I agree with WBarme1234. It would be logical that we do them individually. Some people might have higher score for individual protein but lower overall score. since they don't interact it doesn't make much since to score them together. additionally my computer is running like a potato on this one. idk if its a weird glitch but when I untrim some of my segments scores are dropping to -1500 score in ideality when they were around 0 while trimmed.
beta_helix Staff Lv 1
Comment from horowsah — from Discord @12:25 PM
So yes to everyone- this is a weird weird puzzle. The reason for it is a very strange choice by the original crystallographers on the symmetry of the crystal that I'm not convinced was right. That's what leads to symmetric copies distant to each other. So in theory, once one is solved, so should others, but that's not how it was set up originally
https://discord.com/channels/676550660694605825/702953756177989683/1360289705710715145
Floddi Lv 1
Eventhough it might be intended this way by the crystallographers it seems to be unpractical for many foldit players.
My computer isn't a potato but it still lacks the power to wiggle or shake without lagging. Even on minimalist settings.
With the 2 missing electron density clouds it's also a guess how to fold these.
And most importantly: the best solution isn't the best solution for every protein but an average.
It's also impossible (or at least i don't know how) to select one protein easily to make it better and then doing the next.
Overall, this puzzle seems to fail using the full potential of foldit let alone work with foldit properly.
beta_helix Staff Lv 1
Thank you for the feedback, @Floddi.
Have you been able to use the Trim Tool, and does it help break down the puzzle into manageable chunks?
zeroblue Lv 1
@beta_helix I've tried using the trim tool, but when I exit out of the trim mode, the protein isn't the same as it was in the trim view. For example, the ideality scores can change a lot. I end up doing so much clean up afterwards it isn't really worth it to use the trim tool.
beta_helix Staff Lv 1
Thank you very much for the feedback, @zeroblue!