The Behavior menu (aka Behavior Options) is a small, but very important menu, which contains quite powerful options in it. Familiarizing one's self with their abilities is critical to being able to manipulate a protein and bend it to your will!
These Importance sliders are what define how Foldit will behave in certain instances. Changing the value for these will enable your tools, and therefore recipes, to accomplish certain feats they would otherwise be unlikely to do when left to their default values. Their defaults correspond to the how proteins behave in real life, and therefore you will want to be sure that if you are changing them while folding, to run the primary tools (wiggle, shake, mutate) a few times with them set them back to their default value. This way your protein will more closely resemble the shape that it would have in real life, which makes it a crucial step before sharing your designs with the Scientists, as otherwise it will be unlikely to fold in the Wet Lab.
Clashing Importance, aka "CI", is the primary Importance slider, changing the weighting for the Clashing subscores. This impacts how close atoms are allowed to be to each other. These atoms, like people, prefer a certain amount of "personal space". When another atom gets too close, as you may have noticed, th
e Clashing Indicator (the red spikey ball) will show up and dance around, informing you that these atoms are closer than they would like to be. If you were to Wiggle, then your protein would push apart --or in extreme cases with lots of clashing it may 'explode' in that situation, which we say due to the violent way the protein flings apart to clear itself of the clashes-- all in an effort to give the atoms their desired "personal space".
Setting the CI to something lower than 1.0 will change the weighting for the Clashing subscore. What that means is, if you were to perform that same Wiggle, the protein will push apart much less. It also means that when performing a Shake or a Mutate, the position or sidechain will ignore some of the Clashing when performing the action, which can allow for position choices or larger sidechains that if set at 1.00 Foldit otherwise wouldn't have permitted.It is important to realize that since the atoms are allowed to be 'closer' to each other than usual, that if Wiggled, the protein will become more "compacted". Often times, this can be benefitial to the player since that will assist in the prevention of Voids, which is somethign we try to prevent, or eliminate.
Sidechain H-Bonds Importance is the importance value that relates to the Sidechaing-to-Sidechain and Sidechain-to-Backbone Hydrogenn Bonds (aka HBonds/H-Bonds). When its value is INCREASED ab
ove the default value (1.00), the sidechains seek out the closest atom it can make an HBond to. Any HBonds that are already created will in turn be prioritized over other subscores, which can make those bonds stronger. By DECREASING the value, this lowers the priority and can cause everything to shift more easily, but that can then break the HBonds.
What this results in, is when the this importance is Increased, it can lead to "compression" of the protein. Whereas when Decreased, can cause a "relaxing" effect, which is the opposite of what happens when lowering the Clashing Importance value.
Backbone H-Bonds Importance is the importance specifically for the Backbone-to-Backbone HBonds. The most common instances for this to impact would be in Helix and Sheet structures; however, it will
also impact and random loop-to-loop bonds as well, since all of these are still "Backbone" realted. Beyond that difference, the Sidechain information contained above is otherwise still applicable and the protein will behave similarly based on the values used.
[Based on Formula350's experience, this slider's impact on protein behavior is not very noticeable during Wiggling. This may prove more useful during Rebuild or Remix usage instead.]
TEMPORARY TEXT BELOW! I figure scattered info for now is better than no info, until I can get it formatted together... These are mostly messages I've shared in Veteran chat or are paraphrased/quoted from Josh (UI Dev; responsible for adding these new options) -- Formula350
Direct quote from rmoretti (Rosetta Dev) that I relayed to others: "Sidechain slider will change both the Sidechain-Sidechain HBond weights as well as the Sidechain_Backbone hbond weights. The Backbone slider adjusts only the Backbone-Backbone weights (both the alpha-helical short range and the beta+loop long-range ones)."
Note: For those reading and are less technically-inclined with software stuff... by "Weights" he means the "Importance". So the value of "1.0" is default, and the game will behave as you've come to expect. Setting it _lower_ than 1.0 will be of lower-priority, and in turn cause HBonds to be more susceptible to being broken. And then _higher_ than 1.0 (max 3.0) will increase the priority of HBonds, resulting in more chances of making HBonds. (which is howit'll be helpful with HBNetworking)
The code from Clashing Importance was used to make these (and the additional upcoming sliders; hover that Recipe checkbox to see the others that'll eventually come out), so any tool that changing the CI will impact, is going to be similarly impacted by these new sliders. However, the "strength" of some of these Importance Sliders will not behave as extremely as with CI changes. So setting it to 0.0 or 3.0 isn't going to cause your protein to behave erratically.
1.0 is "normal". Anything higher-than 1.0 equates to "increasing its importance", meaning Foldit will favor those over other subscores, meaning it will go out of its way to establish, keep or make them stronger. Less-than 1.0 means it does not consider it as important and will break bonds more easily in favor of improving other scores.
Just like the Clashing Importance. Setting it lower than 1.0 means Foldit will not worry as much about creating clashes.
THe major difference between these different Importances (clashing vs hbonds) is that we're used to a lower CI causing things to compress. Whereas now with these HBond importances, setting it HIGHER will compress your protein (albeit rather gently/minimally).
Josh's reply to Boots on the Forums:
"The new behavior options are simply there to be additional tools for you. Similar to clashing importance, you might find that lowering or raising a subscore's importance may help you get into a better fold. I think some of our scientists said that the hbond subscore importances might be helpful for forming hbond networks or making bonds with a binder target. Ultimately, this is just more power for you to shape the protein as you'd like!
In terms of what tools to use them with, they work exactly like Clashing Importance, so they should affect whichever tools CI affects.
Technically speaking, what all of these sliders do is change the score function used by tools, making tools believe they are making an improvement by weighting the importance of certain subscores differently. However, the Score displayed at the top always uses the unmodified score function, so you will never get an increased score directly by modifying slider values.
So far in my experience, the best way to use them is to crank them up when trying to form hbonds, then you can bring them back down to 1 when your hbonds have formed. The backbone hbond slider might also be useful as a slider for how much you care about your secondary structures keeping all of their backbone-backbone bonds. And the sidechain slider is probably useful when trying to make more bonds to a target for binder puzzles.
Hope this helps! Good luck with experimenting with them and let us know what you find!"