Native Guide folding -- just don't get it

Started by jheadlee

jheadlee Lv 1

I've made it through all the tutorials, but I will admit some I "finished" without knowing much about what I was doing. One of those was solving puzzles with native guides. Try as I might, I just can't figure out how to make the puzzle "match" the guide – or even come close. Perhaps it is because I can't really decipher the guide and puzzle separately to make good comparisons, or perhaps it is something else. I did find Tlaloc's guide, with a good section, but perhaps I just didn't understand it. If that is the guide to go to, then I'll restudy and try again. Has anyone else had this problem, and how have you solved it? I'd really like to start really trying to do some human-intervention on these puzzles and not just relying on scripts, but I'm just pulling and rubber banding with no comprehension right now. Even with that, I really enjoy foldit – but I'd like to enjoy it and maybe do something good at the same time :-)

Thanks all!

Tlaloc Lv 1

I made a recipe named 'Bands for Native'. Each time you run it, it will add a new band on the next segment.

View the options, turn on "Show Outline," set the background color to white, and view stubs on the sidechains, view the guide, and set color relative to guide. Turn all the other view options off.

Press the 'align to guide' button once. Don't ever do it again or you will need to start over. Also, I've seen it lose the alignment to guide when I save the protein, exit foldit, and come back…possibly a bug in foldit.

Hover the mouse over the sidechain of the new band…the corresponding sidechain on the guide will appear. Pull he band to the first "knuckle" of the sidechain of the guide. You will need to rotate the image by 90 degrees several times to position it in 3D, since you are working in 2D. You may find that holding down the 'alt' key helps keep the band from snapping to the actual protein.

You can tell when you have the band positioned correctly when the spherical end encases the knuckle that it corresponds to. When positioned correctly, Wiggle All to get the sidechain to be positioned right. If you accidentally delete the band, press Ctrl-Z to get it back.

Each time you run the recipe, it will create the 'next' band on the next segment of the protein. The recipe uses a note to keep track of what the 'current' segment is.

Bug: The recipe currently does not handle segments without sidechains correctly–it positions the band on an atom on the backbone, and not the right one. Delete those bands and move on to the next segment.

It will take time proportional to the number of segments in the protein to position them all. You can save time by only putting bands on the ends of helixes and sheets (I usually do them on the loops on either end–use the slider to select the segment, hover over the protein and press tab to find the segment numbers). Proteins with more than 100 segments take a frustrating amount of time.

Since you won't be exact on your position, you will need to disable the bands and let the protein find its natural shape occasionally. You may find rebuilding helpful, too. Try the 'Tlaloc Rebuilder' script to rebuild.

This should be enough to get you within 100 points of the best possible score. After that you are on your own to find the last possible points.