Closed since about 2 years ago
Novice Overall Prediction Electron DensityThe 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. In addition two of the same protein chains, this one has DNA! As a result, not all recipes will work as usual.
AA Edit sees this puzzle as alternating chains of protein and DNA.
Both protein chains are "Homeobox protein Meis1". (Chain C is missing the first residue.)
PDB 5BNG seems to be a good match.
Here's what AA Edit finds:
A: fpkvatnimrawlfqhlthpypseeqkkqlaqdtgltilqvnnwfinarrrivqpmidqs
B: ttagctgtcatgacagctaacg
C: pkvatnimrawlfqhlthpypseeqkkqlaqdtgltilqvnnwfinarrrivqpmidqs
D: gattagctgtcatgacagctaa
As noted in veteran chat, the puzzle starts with bad ideality in the DNA. DNA segments 80 and 81 have ideality scores of around -100,000 each.
As the puzzle comments suggest, many tools don't work on DNA. Their tool icons will be dimmed when DNA segments are selected. Rebuild is in this category, along with idealize backbone and idealize secondary structure. So these tools aren't going to help with the less-than-ideal parts of the DNA.
The remix icon is undimmed if you select three contiguous DNA segments, but then Foldit crashes if you click it. That seems like an oversight.
Wiggle does work on DNA, and you can also drag the DNA to a new position. Using bands is another way to change the shape of DNA.
Remix and rebuild work on the protein parts. If you're using the standard TvdL recipes (such Tvdl enhanced DRW 3.1.1 or TvdL DRemixW 3.1.2), you can first select the protein, then click on "(Re)select where to work on", then "Work only on selected". Selecting the protein is easy if it's all set to loop, as it is at the start of the puzzle. Just double-click on one chain to select it, then hold control and double-click on the other change. Now you're ready to remix or rebuild using the classic recipes.
Although the rebuild icon is dimmed when you select DNA, the rebuild Lua work just fine.
So with Tvdl enhanced DRW 3.1.1, you can select DNA, then tick "Work only on selected", and it won't crash, and in fact will find points. I suppose this means you can just go wild and rebuild everything, DNA and protein, without restriction.
On the other hand, TvdL RemixW crashes if it encounters DNA. I opened a bug report, "puzzle 2406 seems to allow remixing DNA, but then it crashes".
Seems like 5BNG is a good fit. Here's the view in Jmol.
Also, Bletchley Park reports that you open a cutpoint in the DNA, but then you can't close it. https://fold.it/forum/bugs/puzzle-2406-allows-cuts-in-dna-that-cannot-be-closed-anymore
And alcor29 reports that idealizing DNA causes a crash.
The recipe Get Cuts closes cuts in DNA, even though you can't close them by hand.
