I find that as I get the model more and more compact, that using the drag tool then wiggling the backbone makes the score drop. Some times locking the side chains using the lock all action before using the drag tool keeps the side chains from being pushed out of alignment by the drag and improves your score. Try it the next time you get stuck and anything you do drops your score, it may help, or not.
greens in, blues out, drag->shake all->wiggle backbone->rinse->repeat 
Hey folders,
Here's a little insight I got into the wiggle backbone tool. If you click wiggle BB and everything blows apart, don't worry! It just means that there's something bad with your protein and wiggle BB is overreacting trying to correct it. Here's the trick:
Repeatedly undo (control-z on windows or command-z on mac) to before the wiggle and redo (shift-control-z on windows or shift-command-z on mac) to after the wiggle until you can figure out exactly where your protien blew apart. That should tell you where your problem is. Fix that problem (moving the sidechain, or gently dragging the backbone), and then try wiggle BB again.
Repeat this process until wiggle BB is well behaved. :)
When you have a loosely folded starting structure (i.e. no pre-formed beta sheets, a bunch of helices tangled together) I often find it helpful to set up a network of rubber bands and pull, hopefully "snapping" the protein into an approximately correct conformation, then do the usual wiggle & shake combo to get things packed down. It worked out pretty well on puzzle 21 for getting the bizarrely-ordered beta strands into place.
- Chris
If you've tried a number of things and can't seem to see a higher score, try changing your perspective. Zoom in, or out. Rotate the structure around and view it from the other side. Change your viewing options to show (or don't show) voids.
…now that you've changed your perspective, go back and undo/redo your last few moves and see what effects they had from this perspective. You will often find that there were side effects occuring that you weren't able to see previously.
If you keep pushing the backbone inward and the wiggle backbone keeps moving it back out, and bringing your score back to where you started… stop doing that! Try pulling it outward once. Then try pulling it up, then down. Each time doing the wiggle backbone to see where it puts it back and how it settles in to it's surroundings.
If you keep dragging the same portion of the backbone to make your moves… try grabbing the opposite side of one of the nearby residues. If you were pulling inward, try moving a nearby residue, and pushing instead. This sometimes gives you some rotation of the entire coil you are working with, and pulls it around in to a better position then was possible from the one that seemed so obvious to you that you were using it over and over.
If doing so happens to prove difficult to get the motion you were attempting… perhaps that is a clue that what you are picturing is not how the protein will behave.
When I was first learning to drive "a stick" (manual transmission vehicle), I would practice by driving down (and back up) our country driveway using ONLY the clutch, no gas pedal.
I think some people may be jumping into the Fold it! driver's seat and "flooring it". Try a gentler, slower touch. When you do so, you will see movements and reactions you did not expect, these are clues to some of the forces within your model.
Hugothehermit and I are working together to bring you videos to illustrait some of the tips of the day. Sometimes a picture is worth a thousand words. Through the videos, you can also get a feel for how others use the tools in the game to achieve the scores they get.
This first video illustraits the importance of understanding the hydrophobic and hydrophilic sidechains. In the version of the game captured in this video, the hydrophboic sidechains are shown as green. These want to be away from all of the water molecules that surround the protein, and so you will want to arrange them to point inwards into the center of the protein. The blue are hydrophilic. They like the water, and will tend to be pulled around to point outward in the form of the protein found in nature.
In the current version of the game, you click the checkbox to glow hydrophobic sidechains, and they are presented as glowing yellow for the hydrophobic, and glowing blue for hydrophilic rather then the green and blue coloring shown in the video. Either way, it's easy to remember, blue LIKES water and you will score better if you find ways to get them to point outward.
Hugo created the video, and I'm hosting it on my website here:
http://www.violetoaks.com/hugovideo/start.swf.htm
It is 22MB. Just let the whole thing download, then click the play button.
In just 131 seconds Hugo shows you how to get a score that would put you at 7th place on top scorers list!
Hugo shows you how to get a great score! ...but forgot to turn on his microphone. So, what you hear in this video is actually his brain as it solves the problem.
Note how the protein folds fairly easily in the directions he's pulling it. This is due to the properties of the hydrophobic sidechains. If you are finding it difficult to pull, it is likely because you are trying to pull it in a direction that is not natural for this series of amino acids.
Also note how he rotates the protein around and pulls from a different direction to get the action he's looking for.
Hugo used a tool called CamStudio
to capture his screen and produce a swf file that many people can view in their browser without any additional plug-ins.
If you would like me to host a video for you, you can send me a PM here on the game website, or on Rosetta. On the game website, you identify my user ID (feet1st), on Rosetta, they use the user ID number (44890). I will send you back instructions on how to upload videos up to 150MB.
This was a test, I can downscale and add audio to it, though I'm not sure that a puzzle 17 is really useful?
RosettaMod also needs a mention as he tested my first video capture, and we talked about it, though he never said if my Australian accent was understandable :)
Adrien also told me that the video capture was (paraphrasing) recorded in a higher resolution the down-sized to 640*480 (I'm relying on my bad memory here take with a grain of salt)
RosettaMod also metioned a different video capture programme (without going through my e-mails I can't tell you it's name) that may be better. Also that the flash file could be played in quicktime.
I havn't played Foldit for a while as RL is getting in the way, and for the forseeable future this will continue.
All files, video, audio etc… I release as Copyleft, GPL, or GFDL, what ever you prefer.
Lend me your ears for about 2 min. and I'll "show" you something that seems to help score higher with most any puzzle.
"Undo" back to your best score.
Write down your current best score.
Begin wiggle backbone.
leave it wiggling…
Now, drag a very short little band out from a piece of backbone (drag a right click) to the background and leave it for a moment. Direction doesn't matter so much. But make it almost as short as you can.
Now draw another band on the opposite end of the thing and pull the band in opposite direction of the first. Again, very short length.
Now stop wiggle, "clear bands" and wiggle until the score halts again.
If you can nail the x's and delete the bands as you go, you can keep wiggling for VERY long periods of time. It tracks your best score at any point during that period so any future "restore best" will find your intermediate high during the whole wiggle.
I call it "full adrenalin RUSH".
It's much like drag, drag, drag, wiggle… drag, drag, drag, wiggle… all in one ball of wax.
It basically causes the wiggle to fight with itself and explore hundreds of combinations in that whole area of the structure shape. ONE of those stands a good chance of being better then where you were before.
You will find cases where one little band doesn't cause anything to move… but your score drops. Then you clear it and score returns. This is a reflection of how the stress on that point of the protein was reducing the score. These invisible stresses are what you are improving upon (reducing) as your score improves.
You will find cases where it seems to wiggle higher and higher until it reaches your previous high (or very close), then it flips the whole thing around or shifts it over and drops the score down again… I call 'em "landslides". They seem to occur because you had a tight structure ("local minima") at that previous high. The protein doesn't distort from that point very much when pulled… just try the same process again from different angles at different points on the backbone.
Large proteins, such as CASP Practice 4-2 just need a little nudge, then clear the band and let it settle.
…now go back to drag, drag, wiggle. Lock, drag, drag, wiggle…shake. Then come back to adrenalin rush.