Rule:
"A sheet-sheet connection with 2-3 loops must turn left"
Fig1a Left rule sheet-sheet23
I obtained this by
1) cut the loop
2) align the sheets for bonds, wiggle, uncut
3) mutate loops to glycine
4) adjusting with Rama map in selection interface (both glycines must be in green or yellow)
5) shake, wiggle (if rama not ok, undo)
4) filter on for ideal loop (shows red bowls)
5) freeze unless ends of sheets
6) rebuilds, shake, wiggle until Filter AND Rama ok for the 4 residues
Correct me if I'm wrong. From Fig 1d, it seems that the direction of the last sidechain from the first sheet is not important (even if it's up, we are still turning left in the figure above). Then my "First rule" of "both to the same direction" would be erroneous. :P
In this figure you have the sheet sidechains closest to the loop pointing away from you - and the loop turns left - this is correct. If the closest sheet sidechains were pointing toward us, the loop would have to turn right - it just means you are looking at the left-turning loop from the other side (I think of this as viewing from the "back").
If you placed your sheets so the closest sidechains faced away (so you are viewing from the "front") and the loop turned right, it would break the ideal design rule, and an ideal loop would be unlikely to form. The easiest way to fix this is to add one segment to each sheet next to the loop (between n and n+1, and between n+2 and n+3). Then the NEW sheet sidechains would face toward us, and the right-turning loop could be made ideal (really left turning, but you are now viewing from the back).
Another way to fix the above problem would be to steal one seg from each sheet and make it loop - then the new closest sheet sidechains would be facing toward us (the ones facing away have been changed to loop), and the 4-seg loop would turn right. If you turn the protein so the new closest sheet sidechains face away (to view from the front), you can see it is "really" a left-turning loop. There is one 4-seg ideal loop that passes the filter, and it turns left. It is red-red-red-green, so you would have to make the 4th loop seg glycine (so it can be green), set the first 3 loop segs to helix (remember red on the rama map is helix), and try rebuilding or remixing or rama map dragging until the loop turns to red-red-red-green - then it will be ideal.
According to the ideal design rules, a 4-seg loop can also turn right (when viewed from the front), but the devs have not yet given us a right-turning 4-seg ideal loop, so it would not pass the filter.
Woooow Awesome, thnks for the video, I'm absolutely new to this (just finished the tutorials) and this series of Black Belt videos seem too cool, gonna watch them all. Thnks for the links
https://fold.it/portal/node/996236 has links to more Black Belt Folding videos.
The Rebuild tool is suspected of causing isolated cases of problematic backbones. It's now recommended Rebuild not be used to create ideal loops. Remix is still recommended for ideal loops.
red red green doesn't mean anything to me. I don't know how to mutate to that. Hopefully the blueprint tool will solve this problem.
As of puzzle 1294 (Oct 2016) the Ideal SS tool in the game curls the helixes at a slightly different angle than it used to, such that the helix lengths given in the ideal design papers are correct in foldit as well. The reason I kept needing different length helices than the scientists used was because the Ideal SS tool was curling them a little different than what the scientists started from.
