Adding to Loci Oiling's wish list (with a huge YES YES YES to the cut-related ones and simpler yeses to the others):
For bands, I would like a better sense of what existing bands "do": some sort of GetBandEndpoints() that returns the endpoints or GetBandDirection() that gives the direction info for bands-in-space. (Maybe a contained GetBandInfo() that returns all the info in one place - length and strength) And if there's a disabled band already between two endpoints, I'd still like to be able to put one of my own there.
For distance measuring, I'd like to be able to have a GetDistance function that works on atoms, such as "endpoints" of amino acid sidechains.
I don't know if this is a short question, though….
Ordinary wiggle and banding actions generally manage to cause sheets to appear "naturally" (as far as our processes are natural), but helices don't do so - if there's a stretch of aas that ought to become a helix, no amount of ordinary actions seem to cause helixing to happen spontaneously. But in real life proteins, helices really do exist.
What's going on, what's the reason? What kinds of actions would encourage "helixing up" to occur?
If you did not catch my post on puzzle 968 comments, I really felt like I did not not get to work it the right way. I am relatively new. Yet, I knew I started with a sub-optimal structure. I was still using mid-game scripts when the game closed. I managed a 13th solo rank in spite of this, but feel like I never got to do something that would be useful to CASP or to science in any way.
While I am aware that Fold-it does not control CASP timing, I found this to be very disappointing. I self limited the number of puzzles I did, but still couldn't do what I would like.
Perhaps there is a way to manage puzzle load that would allow us to feel good about something besides just points.
