007Bistromath Lv 1
I'll begin by discussing the simpler problem which inspired the ideas in the title. A note: I understand that "chirality" refers to specific things in chemistry, so I'm sorry if I'm using the word in a way that seems improper. I'm obviously no chemist.
It would be helpful if there were a tool, possibly some sub-option of rebuild, which attempts to switch the chirality of a helix. Oftentimes doing so is a more efficient and less disruptive way of dealing with hydrophobes than the large amount of rotation necessary to get an entire side of a helix to face the right way. The rebuild function will eventually do this on its own, however it usually takes a long time to get around to those options, and will usually try many more radical changes in position before that point. Obviously, like anything, this can likely be done with rubber bands, but this is a complex and laborious process which I've only ever gotten to work once.
This touches on a couple deeper problems with the game. The rebuild tool is often quite chaotic without an obsessive amount of preparation and management, but is often the only thing for significant structural changes since it is difficult to make the correct parts pliable enough to use wiggle or pull. Rubber bands are meant to be the answer to this issue, however it is often difficult to tell how any given band will actually affect the piece you're working on, and that's when you're attaching one piece to another and therefore don't have to worry about whether your endpoint is in the wrong place due to perspective.
It is obvious while watching the rebuild tool go that its solutions fall into categories. If players could choose and/or rule out categories to search in, the functionality of the rebuild tool would be greatly improved. The only thing I have any name for is that helices could be designated clockwise or counterclockwise, but an experienced player will recognize several common shapes of sheet and loop which could be named and catalogued for this feature as well. Being able to tell the engine "this structure is type X" would eliminate many of the difficulties with rebuild by encouraging sane results.
Wiggle is already an immensely useful tool, but it has some limitations that are difficult to overcome. When a structure becomes too stiff, rubber bands become necessary to progress any further, and these often have either little effect or undesired effects. Especially problematic is when a structure is in the right place and facing the right way, but one of its sidechains is stubbornly not. This is often the case with sheets; a small twist necessitates several rounds of rebuilding, often fruitless. The solution I would suggest is to give Note Mode some functionality for soloists. The wiggle function could take as parameters several preset note tags that could be placed on individual pieces. Try this one straight, that one bent, the other one pointing left, etc. For sheets and longer loops, this would also improve rebuild, I think.
Finally, I have a suggestion which would help both functions a great deal and is probably much easier to implement than either of the previous. Rubber bands provide us a way to pull things to a place, but we have no way to keep things out of one. To remedy this, let the player draw planes within the space which a structure cannot be moved past. This alone would serve as a very effective filter to rebuild's output and prevent or mitigate explosions caused by wiggling with a clash.
