Everyone's gonna have a different natural progression of things for Early/Mid/Late game, and I can't speak for all players, but I'd imagine this is a good layout. Any script-heavy/script-only or hand-fold only players wanna weigh in, feel free.
Early game = Mainly hand folding, and choosing what kind of solution you wanna go for. Every puzzle is different and contextual, so for the Aflatoxin puzzle for example I'd be manually mutating residues to hydrogen bond or pack. With de novo freestyle (structure prediction) puzzles, early game is probably picking and choosing to keep/replace secondary structures and moving them into place. And as for monomer design puzzles, those early games are like de novos except you can do whatever you please to the residues. Shake, wiggle, mutate as needed. Script use is pretty limited, with the exception of quality of life scripts to do things like spot cysteines in some puzzles and band them together.
Mid game = Most of the big stuff is done, so it's time to do specific refinements. Maybe you want a specific residue to be somewhere, or perhaps you wanna re-do a secondary structure placement but not upend the whole thing. Still hand folding, but none of the from-scratch stuff. May include recipes, this area's a blurred line. The scripts/recipes that could be used here aren't really "slow churners", but really "one-off" utility recipes that do one pass and clean things up. These include single pass scripts like Blue Fuse or Fast Relax, or any of the previously mentioned quality of life scripts, like Bridge Wiggle to band cysteines together. Quickfix is another good one too. The whole point of this phase is to get the protein as best as possible by hand (more or less) in preparation for late game
Late game = Slow churner scripts. We're talking the works: TvdL's, Random Idealize, AFK3 (BounceWiggle), BandFuze, the list goes on. This is where you set up these scripts in their respective settings windows, tell it what not to mess with if applicable, and then set it and forget it. This is what we have people leaving their computer and game on for hours for: brute forcing more point refinements out of the existing structure. At this point, major edits are probably padlocked, or would get wiggled/mutate pass'd out. I'm less familiar with the metagame for this phase, but it's pretty easy to let a script do it's thing if it's simple enough to use. Don't forget a final Medium/High power wiggle once your scripts are all done to force ideality calculations for those last few partial points of score! Oh, and did I mention "multiboxing" is a thing? You can have a late game fold churning in one instance of the game while hand-folding another solution candidate in another instance of the game, assuming your computer can handle it and your game won't lag so much it becomes a PowerPoint Presentation.
What to use where is dependent on what you want to do with your solution. Mastering the controls is key to being able to do what you want in this game. I can't name everything off the top of my head worth knowing but if you bring something up like in the parenthesesed list you got there, I can prattle off what I know. There's a lot to teach here, and I shouldn't be the only one to teach it, but I can explain what I know in straightforward English hopefully.
Band strength: Sometimes, you really really want your band points to be at that specific distance you set, maybe to force a hydrogen bond, or whatever. Crank band strength up! In truth, scripts actually have the ability to set band strength beyond 1.50, but for whatever reason players can't do that. I guess with great power comes great responsibility. As for weaker bands, I'd only use them if wiggling or pulling with the bands active completely wrecks the entire setup in to something so mangled it's useless.
Band length: So it turns out the length units are in angstroms, if I remember what Sus' told me correctly. Hitting "use current" will give you the current length between the two band points, so you can crank it up or down as needed. Which should lead into a sometimes useful discovery: bands can push too! If something's too close, set band length farther than current, and the band will start to repel the points away. Vice versa if you want something even closer than default. Also important to remember: Hydrogen bonds will occur somewhere between 1.5 and 2.99 usually, if you're trying to use bands to help out. Check 'em out.
View modes: The view options are worth a post in their entirety.
- Toggle Settings
Toggling voids off is a good one, since they usually get in the way more than they honestly help (unless your score breakdown by mousing over + hitting tab with certain residues is suffering from packing. That reminds me: global score breakdown when? I don't have time to add up all the individual categories from the tab tooltip.).
Show backbone issues is something that's usually always on for me starting in mid-game: if there's a major problem, it becomes way easier to see.
Toggling bonds on and off can help ease the lag and also help you focus on the type of H-bonds you're seeking to form or monitor.
Show bondable atoms is a godsend. It opens up the sort of problem solving reflexes you get with jigsaw puzzles. Seeing the bondable atoms on the backbone/sidechain is a good way to figure out whether or not it's worth losing a few points to get an extra bond.
Showing constraints is usually a good idea, since they're exactly what they say on the tin.
Showing expected residue burials, isosurface, symmetric chains, outlines are usually not a thing I end up using. Symmetry puzzles haven't been around for me to play, the isosurface doesn't always work and lags like hell without really providing much, and outlines are personal preference.
Dark background. No eyebleed.
Turning off pulse while working can aid performance, but also having it on is useful to see where your script or wiggle is working.
X-ray tunnel for ligand can help you find your bearings if your ligand suddenly gets buried behind protein.
I personally play with hide/fade GUI off.
- Color coded for your chromatic convenience: In the Color menu there are a few worth noting.
EnzDes makes it easier to see ligands, like in the Aflatoxin puzzle, to get your bearings.
Hydro is useful for really getting used to pointing orange hydrophobics in and blue hydrophillics out since it colors the backbone blue/orange too. Great for helices!
Rainbow isn't only just pretty to look at, it's a natural progression of ROYGBIV from one end of the protein to the other, so you can find the middle and ends really quickly.
Finally, Score/Hydro+CPK is my go-to default: It looks just like standard Foldit with sidechains colored blue/orange and backbones colored based on score. CPK just makes it so that polar side chains have their polar H-bonding bits visible even when "Show bondable atoms" is turned off.
- View Protein Menu
Cartoon is the default, with cartoon ligand and cartoon thin shaking things up only slightly. The easiest model option to work with, and general purpose too.
Sphere, I've heard according to Susume, is useful to see whether or not a hydrophobic is exposed? It's pretty bulky and awkward.
Stick views, with or without hydrogens, are really nice for seeing how all the atoms are actually arranged. Organic chemists in the house?
Line views are like their cousin stick views. Except probably nigh on invisible since they're so thin. I guess it would lag less?
Trace Line/Tube I haven't really found much more useful than cartoon.
Wiggling individual segments: I tend to bust out selection interface to do this whenever I'm really getting into the nitty gritty specifics of a design. The most immediate example? The Aflatoxin puzzle. I'm trying for score attack, true, but I foresee a good science answer having a boatload of hydrogen bonds at the cost of some score. So, I'd mutate a new residue and try to pull it towards a donor/acceptor. One problem though: it is SUPER hard to get a sidechain exactly where you want it to go. Wiggle usually fixes the difference, but sometimes you don't wanna move the rest of the protein, you just wanna make that one segment find it's comfy spot. Selection interface, select, wiggle. Done.
