Types of TweakEditTweak is a tool that comes in two varieties: rotate and normalize. Both kinds of tweak are very new, having just been released on July 2, 2008. Accordingly, material in this entry is even more subject to change and/or doubt than most others. Advice on how to use tweak to the best effect would be welcome.
"We are trying out a new tweak action which currently allows two different kinds of tweaks: the much requested rotation, and idealization. You can start this through the Pull Mode's pie menu, when you have selected a sheet or helix bordered by loops (and the longer the loops, the better!). A little purple widget will pop up that allows you to manipulate the sheet or helix; you can mouse over it to see what each piece does. Click on a curved arrow to start it rotating, the further out sphere to start idealizing (which will straighten out your selection), or the closer in sphere to pause.
"Let us know what you think of these changes! If the tweak action is useful, we may add more moves to it.
Starting a Tweak SessionEdit
To use either variety of tweak, you must select a helix or a sheet at least three units long. This element must be bordered on either end by a loop at least three units long, or by the end of the protein. Right-click the sheet or helix, and a pie menu will open up.
Choose "tweak." The option "tweak" will not appear if the sheet or helix is currently unable to be tweaked based on the secondary structures assigned to it and its neighbors. If this is the case, you will see "tweak help" instead. Do what "tweak help" tells you, then continue.
It is possible to use Structure Mode to change elements so that they meet these criteria; tweak does not depend on the default structure, but only on the structure the protein currently has. Note however that if you change an amino acid to have a secondary structural designation that is not its optimal, tweak will give very poor results. Some intuitive sense of
When tweak is active, you will see a purple dot (used for straightening the sheet) and two purple curved arrows (used for rotating) on both sides of your sheet or helix. The dot is the straighten (normalize) function. The arrows will twist the element.
- Tweak almost never yields a gain in points on its own. It may do best when a player can see the shape a structure "ought" to have, and then tweak it into that structure, following this with a local and/or global wiggle to settle the new local structure into its overall place within a fold. This process may require multiple local wiggles within and around the tweaked structural element, sidechain manipulations, and other adjustments. It is in some ways a good test of the player's intuitive feel for structure.
- Tweak will also adjust the loop amino acids on either end of the element you are tweaking. This is why it needs at least three of them. Fewer than three of these amino acids would give too little flexibility. Including too many may cause changes in areas of the protein you would prefer to leave mostly untouched. Additionally, one useful tactic with tweak is to apply it to a helix or sheet with the aim of having an intended effect on the nearby loops: A tweak may cause these loops to straighten, or curl under, or expose hydrophilic sidechains while hiding hydrophobic ones.
- One frequently effective approach is to normalize a secondary structure, then lock it. Next, do a global wiggle. The disadvantage to this approach is that you may have over-normalized a structure that is supposed to be slightly crooked.
- Sometimes tweak generates strange or unpredictable results; for example, when you have a single helix and a protein otherwise nothing but loops, the two arrows will just cause the entire protein to rotate, with no change in score. You'll need to lock at least one amino to see useful results here. Additionally, a tweak carried too far can cause the entire structure of a protein to explode when the locks are released and the entire thing is wiggled.
Using Tweak in the end gameEdit
I've found the following technique very useful for generating extra points at the end of a puzzle.
1) Find a section of the protein that looks as if it could use a bit of attention; perhaps its twisted or otherwise looks a bit unsightly. Actually I'm not even sure if this is necessary: I've used this method successfully on other parts of the protein as well.
2) Using Structure Mode as necessary, convert a 3 amino acid sequence in the designated area to sheets. Make sure this sheet is bracketed by loops at each end. Then lock the sections beyond the loops so we have a sequence of amino acids that looks like this : Locked-Loop-Sheet-Sheet-Sheet-Loop-Locked.
3) Now go back into Pull Mode if necessary and invoke the Tweak Tool by Control-Clicking on the sheet and selecting Tweak from the pie menu. You've got 3 ways of using the tool; twist clockwise, twist anticlockwise and straighten (that's the dot separate from the rest of the controls). One and only one will have a chance of working: you'll likely have to try all three to see which one works.
4) Select the direction you're going to twist in and start pressing. The tweak tool works very fast and you'll have to be alert to stop the tweak after a fairly short time: otherwise the protein will get distorted beyond recognition. The shorter the better.
5) Press L to remove the locks and then W to start wiggling. Don't expect the score to return to its former value: it won't. In fact the score behaves quite oddly when you wiggle: it goes up very slowly for a bit and then jumps rapidly before settling down to its new value.
6) Do two or three random global nudges and wiggles. If you're in luck, the score will go past your previous high score. If not, press undo as necessary so as to return to step 4 and try straightening or tweaking in the opposite direction.