Loop fix?

[alcor29]

How about making the "penalty" for bad loops MUCH bigger so scripts don't mess up the good loops we started with?

[HuubR]

This is certainly an interesting idea!  I would expect, though, that the amount of the penalty was not chosen at random.

Would it help to have a setting like "ideal loop importance", that you could set to a value ("much") greater than 1?  (Without increasing the +500 points in the ideal situation, of course ;-)

Having said that, I don't think it is the script that messes up a good loop.  The way I look at it (disclaimer: without having a background in biochemistry!), it is hydrogen bonds and hydrophobic interaction that act on the helices or sheets adjacent to the loop, and sometimes pull them in the wrong direction.  A higher penalty might stop a recipe in its tracks, but it will not change the tendency of that section of the protein to move in the "wrong" direction.

[jeff101]

I think it would also help to have the Ideal Loops filter penalty 
depend on the # of segments that are in non-ideal loops. This way
one non-ideal loop containing 14 segments would have a larger
penalty than one non-ideal loop containing 10 segments or two 
non-ideal loops each containing 3 segments. Having the penalty 
depend on the # of segments that are in non-ideal loops would 
help recipes fix non-ideal loops in a more gradual and incremental 
manner. 

Please see the comments below for more details:
https://fold.it/portal/node/2005262#comment-41271
https://fold.it/portal/node/2005262#comment-41273