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2596: Electron Density Reconstruction 114

Closed since 11 months ago

Intermediate Overall Prediction Electron Density

Summary

Created
April 03, 2025
Expires
Max points
100
Description

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

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Comments

bravosk8erboy Lv 1

@beta_helix thanks for putting up with everyone's complaints. the biggest problem is that the trim system doesn't fuze well with everyone's current recipes. if this is the future we might want to start investing in fixing or adding additional lua functions to support the trim. as someone who has jumped in on the deep end of writing recipes with trim, most current recipes are not build for it as is (major code overhaul is expected to get them to cooperate.)
the segment index change is the biggest problem as is. if we had an additional function that could convert an untrimmed segment index to the new trimmed index (or return a zero if the segment isn't available) this would really help with the implementation.
https://fold.it/recipes/108963 here is my best example of how to do this in the current system but keeping it all straight is just to hard. if instead all we had to do was keep track of if the protein is trimmed and use "structure.AdjustSegmentIndex(int Segment Index)" most code could be retroactively updated quite quickly to implement the Trim tool.
in addition checking the best score can get lost and break some stuff using trim / untrim. a function that could do a quick score check of the untrimmed fold while still trimmed could be useful. something like "number current.GetUntrimmedScore()" would reduce a lot of implementation steps. (this would probably return a score to a protein that needs a number of significant fixes but that could be worked around with proper trim buffer)
there are other problems to but these ones really get in the way.
Keep up the Amazing work!!! I love the game! wish i could help more.

beta_helix Staff Lv 1

Thank you all… this is all helpful.
It seems that this puzzle has pushed the limits of the Trim Tool, which we definitely need to fix for future large puzzles!

zeroblue Lv 1

Same. For me the indexing hasn't been as much of a pain as the unexpected score changes. That said, it's great to be able to do this at all, and I really appreciate the chance to play a fun game and maybe even help out with a little science!

LociOiling Lv 1

This puzzle was puckered due to missing residues.

The recipe Pucker Picker 3.0 RC 1 detected these puckers:

Pucker Picker 3.0 RC1
2400: Electron Density Reconstruction 72
1  pucker found!
pucker 1 (ideality), segments 55-56 (protein), distance = 8.004, ideality = -26205.963, -26201.891

LociOiling Lv 1

This puzzle was puckered due to missing residues.

The recipe Pucker Picker 3.0 RC 1 detected these puckers:

Pucker Picker 3.0 RC1
2596: Electron Density Reconstruction 114
4  puckers found!
pucker 1 (ideality), segments 315-316 (protein), distance = 5.597, ideality = -12072.761, -12074.463
pucker 2 (ideality), segments 680-681 (protein), distance = 8.991, ideality = -16897.966, -16896.571
pucker 3 (ideality), segments 1045-1046 (protein), distance = 9.877, ideality = -49392.723, -49390.321
pucker 4 (ideality), segments 1410-1411 (protein), distance = 6.038, ideality = -7807.601, -7808.269