Brief video to show how the rebuild tool in Fold It! works.
http://fold.it
Here's a narrative to help those non-native English speakers that
will find it easier to translate.
"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 much 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 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!"
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Ohhhh, I didn't know that you could use that drag function with rebuild, cool! That's actually useful on a puzzle that I'm working on right now
Angelmass 2 years ago
That was useful. I had not even known that locking with rebuild was an option. Just a newbie with foldit.
MegF142857 2 years ago
i get it, i didn't know we were supposed to use rebuild in the puzzles, i was thinking it changed the puzzle.
sonofhendrix 3 years ago
Wow, great video, it was helpful to me even though I thought I already knew how to use the rebuild tool well. Nicely done.
btbenj 3 years ago