Wiggle is a tool that comes in two varieties: Global wiggle and local wiggle. Both of them will move the backbone slightly, in random directions. Local wiggle is confined to a small area of the protein, which can be further limited by placing local locks on adjacent amino acids. Global wiggle will move the entire backbone, although it will not change the shape of any locked structures. (Locked structures may move, however.)
To global wiggle, just hit "w." To local wiggle, right-click a local section and choose "wiggle."
In itself, the amount that a wiggle will move the backbone is not visible to the naked eye. However, the wiggle may cause some instability in the overall structure, causing it to move visibly to a new configuration. When this happens, the score may go up or down.
Besides their differences in scope, global and local wiggles appear to have different properties as well. For example, a local wiggle of a low-scoring area may result in radical changes to that area, even in changes that approximate a rebuild. These changes however will not be observed if the player undoes the local wiggle and chooses a global wiggle instead. It is unclear why this should be so.
Wiggles also appear to affect different structures differently. Little is known about the mechanics of these differences, but they have been verified experimentally as well.
Wiggle is also used in conjunction with rubber bands; this combination will cause the banded element and those attached to it to be pulled in the direction of the rubber band. A local wiggle is also frequently a good idea for an area that has just been rebuilt.
A few points related to wriggling that may be useful: needless to say your mileage may vary.
1) In the early stages of the game it seems quite useful to pause global wiggle occasionally, shake the sidechains, and then resume the wiggle. This seems to give the sidechains the opportunity to change configuration along with the backbone. A suitable score to insert this shake into the wiggle seems to be about 150 points below the current maximum. Often you will see the score increase by a few points, which is a promising sign that the subsequent wiggle will produce a new high score. Paradoxically, too great a score increase from this shake is a bad omen.
2) Local_Wiggle_Strategy. SirenBrian's page on this is pretty comprehensive but there are some small tweaks which seem to work for me. First, I like to use relative score colouring, all loops, and no sidechains showing: this makes visualization easier. Secondly it seems most effective to put the locks on the 'elbows' and red areas: often these are one and the same thing. Thirdly, if you get an improvement in an area you can try reducing (as well as increasing) the size of the affected segment: further improvements are possible this way but somehow it seems more natural to increase the segment size rather than reduce it. Finally, after doing this rather tedious (or peaceful, depending on your personality type) operation, unlock everything and try some global wiggles. It's surprising how often local enhancements 'free up' the structure and permit improvements at the global level. SirenBrian's already makes this point but I think it needs to be emphasized.
3) After doing a nudge followed by a global wiggle, you'll often find that the end result, slightly disappointingly, is a score slightly lower than your starting point. At this point, don't be in too much of a hurry to restore your best solution and start again. Instead, try nudging in a different direction (as the force directs you) and wiggle again. Repeat a couple more times and often you'll see an improvement on the original score.