Tweaking ThingsEditTweaking can be a useful tool for many things. However, if not used correctly, it can have adverse effects on your protein.
The Tweaking tool consists of a set of matching curved and straight arrows oriented around center, along the direction of a protein's structural sheet or helix. Arrows point clockwise, counter-clockwise, towards the beginning and end of the protein. There is also, at each pair's mid-section a sphere that hovers above the intersection of the two arrows.
The arrows that form arcs around the midline of the structure cause that section to rotate clockwise or counterclockwise. The arrows that point to the beginning and end of the protein cause the section to attempt to flip 180º while moving along the backbone. The hovering sphere causes to section to straighten. Activate each of these by pointing to the graphic and holding down the mouse button.
Tweaking will not take place if there are too many forces blocking the attempted path of movement. Tweaking will also not take place if there are frozen sections adjacent to the structure you are working on. Tweaking will be hindered if there are other sections, bands or frozen portions nearby.
Tweaking is a useful tool for flattening bent sheets. To do this, first right-click the sheet that you want to straighten and click Tweak. Then, click and hold the pink dot above the arrows used for tweaking. This should straighten out the sheet. After that, try shaking at 0.1 Clashing Importance (CI) and wiggling at 1.00 (CI).
Tweaking can also be used to hide hydrophobics, orange sidechains when View:Color is set to Hydro, and bring hydrophilics, blue sidechains when View:Color is set to Hydro, to the surface. Right-click a helix or sheet and click Tweak. On a helix, use the arrows on either side to rotate the helix and try to get the sidechains facing inward. Then, shake at 0.1 clashing importance and wiggle at 1.00 clashing importance. On a sheet, use any of the arrows to flip the sheet and hide orange sidechains and then shake at 0.10 (CI), wiggle at 1.00 (CI).
Another good use of tweaking is to tighten and curl helices. Right-click a helix that isn't fully curled and click Tweak. Then, click the pink dot and hold it. This should make a more even spacing between the segments of the helix.
While tweaking can give you great points early on, sometimes it may give you trouble in the middle or end-game. For example, flipping a sheet can twist and mangle the surrounding loops, making them more difficult to rebuild later and lowering the segment score, which in turn, could also make LWS'ing less effective on those loops. This also happens at the loops directly around helices when they are tweaked to a lesser degree.
Sometimes, tweaking can have nasty results. For example, flattening a sheet often pushes the loops on either side of the sheet apart, which can cause the loops to run into other parts of the protein and create clashes. If you don't stabilize the tweak correctly (shake at 0.1 (CI), wiggle at 1.00 (CI)), the protein could explode. This could rip your sheets apart or mangle a helix.
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