I thought it would be good to start a thread with some basic tips for people to use in playing the game. It is certainly much more enjoyable when you have a feel for what you are doing. I don't really scientifically know what I'm doing. But I've been studying Rosetta for a long time. And spiralling those native sturctures around trying to see patterns from one protein to the next. And I seem to be scoring well, so I thought I would share some about things that seem to be working for me. I hope others will do the same and post their ideas here. Some combination of all of them will ultimately be a better approach.
In fact, let's make it a standing rule that if you take the top score when a puzzle is closed, you have to post a tip to this thread.
I'll add some tips once the paragraph spacing problems on these msg boards are fixed.
Firstly the sidechains are always colored and the backbone that they are attached to is gray. There are two views of the sidechains. The view is controlled from the File pop-up, then select "view options". There is a score view, where coloration depicts how "happy" a sidechain is with his position in the protein. And there is the hydrophobic view.
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I always start a puzzle basically by pulling it apart, and then
displaying it in the hydrophobic view. This depicts sidechains with two
different preferences. The hydrophobic sidechains are colored green. These prefer (i.e. score better) when pointing inward towards the greenish voids. The blue ones are hydrophilic. These prefer to point towards the outside, which is presumed to be basically surrounded by water (hence the blue). The suffix -phobic indicates an aversion to something, in this case water, and -philic indicates an attraction.
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So, the more blue you get on the outside, and the more green you get on the inside, the better your score will grow. And you will also notice rotational forces as you very gradually drag the backbone, or even just click down on it and do not move the mouse. If you carefully note the surrounding sidechains, you will see the rotation that is occuring is generally drawing more blue sidechains outward, and more green inward. Since both are generally on the backbone near each other, it is sometimes difficult to see the results of these forces, because they may be cancelling each-other out, or may be surpassed by other forces like a collision, or near collision.
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You will also want to consider hydrophobia carefully when selecting which portion of the backbone to drag. If you intend to pull it inward, then best to grab a green segment. If you intend to pull it outward, then best to grab a blue. This is because the point you grab basically is an anchor point where the rest of the backbone is flexing to accomodate. So as you grab a blue segment and pull outward, you tend to slightly rotate the neighboring segments in that direction as well (pulling a green around to point more directly inward at the same time hopefully).
Have you ever been starting a drag or doing a WiggleBB and suddenly had the whole protein flip flop around like a fish on land? For brief moments there is more red on the screen then gray? This is not a bug! Think of all these residues and sidechains as tiny magnets. And what happens when you get a bunch of magnets together? They suddenly snap into position. Often in a way you did not intend.
This tends to occur when you attempt to drag at or near what I call an anchor point. This is part of why I pull apart the puzzle when I start. Pull it out in to a more-or-less straight horizontal line. Now grab the backbone about a third of the way in from the left, and lift it upward. Do you see the anchor? The point after which your drag had no effect? Go ahead, really pull it hard! Now do the same on the right. Actually, it has only twisting effects, but you can't lift that specific residue (segment in the backbone).
This anchor point gives you something to push against when tweeking your model. It can help you make coils flex out or compress more tightly together. But if you happen to click within about 2 residues on either side of the anchor you have a lot of leverage against the rest of the backbone. So, depending on how things are folded up, sometimes you push segments of the backbone right through each other.
If you click and hold on the residues at and near the anchor, you can see some pretty interesting effects when the protein has been straightened out. It will start to coil in a mannar that it finds natural. Try to follow and foster this natural coil and your model will tend to be more stable and score better.
Sometimes the radical movement is simply due to stresses in your structure that you cannot see. If you hold a drag click on other residues in the protein (those further from the anchor), it tends to relieve stresses in the structure. Even though you don't move the mouse to do a drag, the structure (often) moves. If you have made a major swing of an arm of the protein, you will want to do this click and hold at several points around the pivot. This will help balance out the stresses along that portion of the backbone, and thus avoid the sudden movements during the wiggle backbone.
Doing a Wiggle-all before a WiggleBB can also help relieve stresses.
Also, if you have collisions (indicated by red) in your model, these are high stress points. I find it is generally best to relieve those stresses yourself with the hold of the drag click rather then to let the wBB straighten them out.
Feet1st,
This is an amazing tip! I'm learning a lot. I can't wait to put your technique in action. Btw, have you played with the pivot tool? It allows you to change the pivot point for a drag. (We're thinkig of folding user-defined pivot points into the general drag tool… what do you think?)
Adrien
Once you are satisfied with your model, and feel you have aligned the hydrophobic and hydrophilic sidechains as best as you can, you can pull more points out of your model (and more voids out of it) if you do a lot of tweeking.
Watch your score closely and if it drops, then use the "undo" function to get back to the point where you started. Now drag, very slightly, a portion of the protein, try to pick a portion near the exterior. Push or pull it. Now do a wiggle back bone action. If you gain more then one
point, try the same thing on the same portion of the backbone again. Do this around many points of your structure. Do this as you click and hold to relieve tensions. Sometimes you have to click several portions of the protein before each wiggle to make any progress on the points.
You will see that generally the wiggle backbone puts things back where they were... so why does it score better? I believe it is because the scoring system is so accurate, that it detects the very minute differences in how the resulting structure is formed. Your drag and the wiggle caused a slight difference in rotation, and this brought a greater attraction between your hydrophobic sidechains, and so it scores better.
Are you saying allowing several hinges to be created?
I'm not sure why... but the neat thing about the existing pivot test tool is that the sidechains seem to flex, and you can get the sidechains to align nicely. Just like the anchor point I referred to.
For example, open puzzle 18 to it's initial state (if you have saved a puzzle, you can open puzzle 18, save a copy of what you've got, then tell the game to switch to puzzle 18, and it will restart you at the initial state.
Go to the hydrophobic view. Then go to the end with the ring that's curled around. Select the test Pivot tool. Now inward from the ring there are 4 blues in a row. Right click on the first green after that (it's residue 69 if you click it in the drag view). Now pull on that ring and uncurl that end. Did you see all the sidechains in the whole puzzle move? I don't know what that's about, but other then the anchor and the pivot tool, I don't know if any other way to do that. They seem to be in a permanent wiggle state or something. They will actually bend out of your way if you drag something up near a sidechain.
...now, click on the residue we placed the pivot point in and hold it down (we're in the pivot tool now). Hold it for 5 or 10 seconds, don't move the mouse at all. Did you see that whole end of the backbone flex around?? Now... ready for something cool?? Click on the next segment inward, away from the ring end, and hold THAT down for 20 or 30 seconds! Once it stops moving much, move to the next segment inward and hold a click on that.
What seems to happen is that the backbone balances out all the stresses and pulls all the hydrophobic sidechains to one side and the hydrophilic to the other... just as you would want. And from there you can go about doing your folding.
I don't know of any other way to get what is often such an exact alignment on all the sidechains. And I suspect that is a good measure of why many folks are having trouble getting higher scores.
Oh my God! P18 just came unhinged! The double ring is no longer an anchor. I've not seen that happen before. It seems the pin tool, even is nothing is pinned, releases the normal anchor. When I went back to drag, now it is anchored again.
As you are tweeking, it is often a real timesaver if you can see where things are heading and move them further in that direction. After you've done several tweeking moves, and completed a wiggle, bring up the "undo" menu and click on the prior peak in your score. As you do so, notice which direction things are moving. Now you can move to the right and click to return to where you were. Again notice the areas of the structure that are moving. Perhaps these areas will bring you more points quickly with further tweeking.
If you can't clearly see the changes that the wiggles achieved, you might want to rotate the protein around to another viewing angle and again undo and redo the change to get a feel for which direction is improving your score.
Why are you so committed to the model you have? You may have already squeezed, tweeked, and extracted all of the possible points from it. ...but it is possible that a more radically different model would do better. Look for hydrophobic (or -philic) sidechains that are out of place. These are clues to you that a better model exists. But you may not be able to reach it without some radical changes. So, if you find yourself not making any progress on points, save a copy of your model, and pull it apart and see if you can make another one that better fits things together.
Picture a mouse in a maze. He may be very very close to the exit, and have a very high score. But it is possible that the only way for him to actually get out is to backtrack and try another path. Picture your protein as a long string that has been folded onto itself. The order of the folds can dramatically change the fit. And in order to find out, you have to unfold it, swing things around and try another alignment.
