A couple of questions:
Firstly, how strictly do we need to avoid those listed sidechains? So far I haven't been able to find a solution that doesn't use at least one of those listed sidechains to bond to the end of the ligand. (but that doesn't mean I'll stop trying to find a solution!!)
Secondly, it seems likely that a higher score can be achieved by using some of those sidechains that are to be avoided. e.g., I can run a global mutate to increase my score but I know that it'll probably change a number of my sidechains to the ones that ought to be avoided. If I have a solution that doesn't score as well as my best scoring solution, but fulfils the requirements, how do I submit it?
Ooh, I just realised I'm using asparagine, not aspartate. :-) I've been trying to avoid glutamine and asparagine by mistake.
Still, I think it's a valid concern that a global mutate will raise the score but not abide by the requirements, which means our 'best' or 'most appropriate' solutions may not be our best scores.
You are correct. However, many of the automatic algorithms only know about the score, and don't take the conditions into account. It is true that there may better scoring solutions that don't meet the conditions. I think there has been a request for "restore best with conditions met", would that be useful?
That could be helpful, although it is still possible to meet the conditions of this puzzle while using the 'illegal' residues (I think), so even restoring to "best with conditions met" could still restore the puzzle to a solution with an arginine attached to the ligand end. Could it not?
I chatted with austinday in game and he said that you guys check over all of our progress, not just our final, highest-scoring solutions. If that's the case then I think my concerns are covered because you'll be able to find our potentially lower scoring solutions that have better residue combinations.
Does anyone find it at all disturbing that only 3 players are even able to find a solution that meets the requirements to even get a score?
Why bother working on it - if you're number 4 you get one point?
Brick: wait a minute...
Per Madde's comment at http://fold.it/portal/node/987447 , I'm afraid that we're talking about zero points here (so far, only 5 scores registered, and supposedly you need 10 for a puzzle to score at all)
This "zero point" problem is indeed a bug (I just replied to the feedback tracker about this, http://fold.it/portal/node/987447#comment-6669) and we will assign credit for these 2 puzzles retroactively.
We apologize for that, and we realize how difficult these 2 biotin design puzzles have been.
We are trying to think of ways to make them more fun, and not quite so hard, but it is a difficult problem that we are trying to solve.
In terms of points, though, we will make sure everyone who played the Hold It! puzzles (and groups) get credit for it, but it might take us a while so please be patient.
To make this puzzle more playable, yet still yield results could I suggest the following :
1) Increase the allowable angle tolerances on the bonds. I guess they are set at about 1 degree at present...increase them to about 4 or 5 degrees
2) Score the puzzle with a bonus for the accuracy of the bonds. For example score 9500 for the structure plus
1 bond within 1 degree = +1000 pts
1 bond within 2 degrees = +300 pts
That way you will get a lot more people on the scoreboard and we can still refine the bond angles using the green and red traingle thingy.
Yes, steveB, we are planning on implementing a bonus system similar to what you suggest. Also, I believe the angle tolerances on this puzzle are +/- 25 to 35 degrees depending on the particular angle.
...so here's the pic
One of the difficulties in playing this puzzle is that as you get the bond close to the desired angle, the programme automatically switches the alignment triangle over to another bond which is further out of line than the one you are working on. This, amongst other things, drives you mad.
Would it be possible to implement in the 'conditions' section a seperate line for each bond, along with a 'show' check box for each bond...and have the traingle alignment tool remain with the selected bond ?