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2266: Electron Density Reconstruction 27

Closed since about 3 years ago

Novice Overall Prediction Electron Density

Summary

Created
February 07, 2023
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.

Sequence
MDETGKELVLVLYDYQEKSPREVTIKKGDILTLLNSTNKDWWKIEVNDRQGFVPAAYLKKLD

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    1. Go Science
    100 pts. 16,327
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  1. Avatar for kermyt 71. kermyt Lv 1 1 pt. 15,835
  2. Avatar for Randolph_M_Snyder 72. Randolph_M_Snyder Lv 1 1 pt. 15,812
  3. Avatar for djdamien 73. djdamien Lv 1 1 pt. 15,762
  4. Avatar for ZAMCF2020 74. ZAMCF2020 Lv 1 1 pt. 15,715
  5. Avatar for WuWTq 75. WuWTq Lv 1 1 pt. 15,619
  6. Avatar for spvincent 76. spvincent Lv 1 1 pt. 15,512
  7. Avatar for furi0us 77. furi0us Lv 1 1 pt. 15,406
  8. Avatar for edahay23 78. edahay23 Lv 1 1 pt. 15,112
  9. Avatar for greengrass 79. greengrass Lv 1 1 pt. 14,406
  10. Avatar for spark69! 80. spark69! Lv 1 1 pt. 14,385

Comments

grogar7 Lv 1

Tell us more about the little dot that identifies as residue #1 Glycine, and is not attached to the rest of the protein?

LociOiling Lv 1

Weird, a solution loaded at 2,292 after being saved at 15,893. The 2292 killed a version of DRemix that's been working a long time. Not sure what's wrong with this one.

LociOiling Lv 1

Shared with scientists, a second one saved on 15,893, which loads at 2,298. The damaged load also manages to break some fancy Lua code related to getting the density score for a section. Regular old DRemix doesn't have that problem.

LociOiling Lv 1

See more comments in #bugs-and-feedback. The damaged solutions end up with around -3,000 ideality in 4 segments, totalling up to a roughly 13,000 point loss.

LociOiling Lv 1

See also https://fold.it/forum/bugs/saved-solutions-for-puzzle-2266-lose-score

The sequence is a another mystery here. The sequence shown on this page is an exact match for PDB 1E6H.

The puzzle starts with G for glycine in segement 1. The puzzle shows segment 1 as just a small sphere, not a normal-looking segment at all.

The puzzle ended up with gaps between 1-2 and 31-32. So the alignment ends up looking like this:

mdetgkelvlvlydyqeksprevtikkgdiltllnstnkdwwkievndrqgfvpaaylkkld (1E6H)
    g elvlvlydyqeksprevtikkgdiltllns nkdwwkievndrqgfvpaaylkkld (puzzle 2262)
    1 234567890123456789012345678901 2345678901234567890123456
              1         2         3          4         5

The two gaps in the sequence seem to be the source of the problem with saved solutions.