I've been flailing around with the Rebuild tools for days now on about a half-dozen proteins, and I have yet to actually gain any ground by doing so; most often the change results in the protein falling apart. Would somebody be willing to post some video showing use of the rebuild tools that actually results in score improvement?
I would like to save some rebuild, but when I stop rebuilding tool, I do end everytime with starting structure.
What is the trick?
From what i've seen the rebuild tool will only change a structure if the score increases… if it doesn't then it wont save what its testing.
There's not much trick to the rebuild tool. It either helps a ton, or not at all.
You turn it on. You can have rubber bands on it or not; if you do band a structure, the rebuilds will all tend to go in that direction.
Then you get up, get yourself a beer, take a bathroom break, change the music on the stereo, feed the cats, and come back.
With any luck, it will have found a new and higher-scoring structure.
If not, don't feel bad. It doesn't always work, and it seems to work best on the super-simple ones, like the Insulin Mutant we had a while back. There may or may not be heuristics you can use to find good targets for a rebuild, but I have not been able to identify any reliably. Chances are this is a skill we're all going to have to develop together.
The latest update actually moves the protein to the new location it tries even if it makes the score lower! interesting….
I whipped together a 2:46 video that shows usage of the rebuild tool. Audio is included with the video, but I thought perhaps a narrative would helpfule to those that have a hard time understanding English.
The narrative:
"Hey it's Feet1st here. I thought I'd make a little video to show you how to use the new "rebuild" tool. I'm working on the third CASP8 target, a very complex protein with a lot "going on". I want to rebuild this area here, this connector tube. What I'm going to do is lock out, by middle clicking (or you can hold the shift key and left click), a small portion of the backbone here. Then right click on it, and "rebuild".
…we have our wonderful music, and you sit back and relax…
27593 is the score I had when I stared the rebuild.
It's going to go through different combinations of this sequence of amino acids, and orientations they might typically take in a native protein. When it finds a combination that matches the beginning and end position, it will transition to that, and show you that shape.
…So, you've seen it shift a couple of times now. Those are combinations that fit this puzzle. And the score will go up or down, either way, depending on the goodness of that fit, and the resulting scores of the side chains, and the conflicts that might resolve, or might be introduced by the new shape.
…so typically what you are doing is you are going to rebuild, …oh I love the "rank down"… and just play back to your best score. That will be the configuration that probably resolved a conflict or worked best for you. ..so you can stop the rebuild, that will take you to the orientation it last found. And then you can "undo" back to the best score. Which may actually be in the middle of that rebuild score there, it found something better, but that's not shown on the chart.
…now if we did this without selecting specific amino acids, you'd end up with it trying to rebuild a very large area. It goes too far really, and gives it too many choices to consider. So that is why I put a lock out on specific segments, and just do that portion.
…now the other thing you can do with rebuild is you can lock out specific segment and you can actually put a "drag" on it. I try to not put more then one, otherwise I will get confused about which way it will go. But you put a drag on the backbone out to the desktop as you setup the rebuild… or actually during a rebuild as well, as long as you give it 3 or 4 residues here to work with… do you see how it shifted there? with (towards) the drag?? …and it will try to find three points that now match. The two endpoints, and the end, or knob area of that drag. SO, that's useful as well if you want to actually change the shape in a specific direction as you are using the rebuild tool.
I hope that helps you enjoy Fold It! And have a good time!"
Great video, the people wondering about rebuild should definitely watch it.
Very helpful video, thanks for posting that
I don't quite understand what rebuild does - when I tried it in the past, it would go thru the entire chain, flash an image that was 90% offset, and then go back to the same. Yesterday I got more dramatic results with glycolysis. Great orchestral music, btw =) So, when you do rebuild, do you want to let it continue until it finishes, or do you want to stop it in the middle, hoping to catch when it hits a high score?
Update: OK, I should have watched the youtube first - thanks, very helpful.