Request: Structure Initialization Tool
|Opened on:||Monday, February 24, 2014 - 20:35|
|Last modified:||Tuesday, March 4, 2014 - 21:14|
Design is very difficult for both new and experienced players. Remember when Foldit was set up for the gamification of the folding problem. We had shake, wiggle, and a structure painter. We have a mutation wheel but also the M command can take care of that for us.
But design is more difficult. Or rather, we can design neat structures and make them score high in rosetta, but actual STABLE designs requires too much player knowledge. You've tried to guide us with the filters. But now we have the problem where we have to set the primary sequence for rebuild to make a helix. Before, if we could get a helix, the mutate tool would then find an appropriate sequence.
I'm sure the response to this will be to tweak the fragment library again. But that's the wrong solution.
How to make a helix (according to foldit tutorials):
1) Paint the helix structure in structure mode
3) There is no 3, because you're done.
This is what needs to happen, especially in design mode. All this stuff about MALAK and fragment libraries is technical stuff that new players don't necessarily know about, and shouldn't need to know about. If a player wants a helix, they should get a helix. Let rosetta worry about the stability.
Here's how the proposed tool should work. It can basically be a part of the rebuild tool, as it preserves most of the original behavior:
1) If the rebuild selection does not have a free end, rebuild as normal.
2) If the rebuild selection is mixed SS, rebuild as normal.
3) If the rebuild selection is all one SS, and is flanked by loops, and one of those loops has a free end (a cutpoint or terminal) then just set all the non-loop residues to their ideal angles (loop angles remain unchanged). Just set them. Not 3 at a time, no fragment library, no cis bonds. Just a helix/sheet. Prolines will clash, fine.
At this point the player can place the helix/sheet and ask the mutate tool to find a reasonable sequence, and work on healing the cut point. Maybe they succeed, maybe not, but a huge amount of frustration evaporates.