Now that I could recognize some structures and sidechains, my problem is to put the segments inside of the density.
1-do you push and pull it manually after freezing the extremities? (it does not work well! not precise enough, and the all protein is moving)
2-Do you cut it in pieces and push it inside before to uncut? (it does not work well !)
3-CI on 0?
4-Do you freeze extremities then add a lot of bands in all directions, then wiggle? or rebuild? (it might work but it's very difficult since the front and back are not visible and put the segments in the blind)
5-Even with this in mind, it often happens that the structure length doesn't match. For example, my helix is longer or shorter than the related density. After many attempts, I don't succeed tu pout it "exactly" inside.
6-Big problem with the sidechains ! We have a backbone and we recognise a succession of sidechains in the cloud. But the position of the sidechain itself varies a lot. It's really not easy to put the backbone on the right place with sidechains going in wrong directions.
Thanks again for all your help ! Current results suggest that only 3-4 players (with > 17000 pts) are able to hand fold correctly on density puzzles ! That's not enough !
I use many cutpoints (maybe 40-50 for a 200 segment protein) to let me match the cloud with small pieces of backbone. If a small piece of backbone will not allow matching the sidechain positions, I will band those sidechains to their place in the cloud and rebuild (by hand) only that small piece of backbone until they match better (disable cut bands while rebuilding). Once I have matched as much as I can see, I use zero-length bands script to band all segments in place (band strength 10), set CI low (0.2 or lower), and shake/wiggle until score stabilizes. Then close cutpoints, wiggle some more, weaken bands, use DRW script on red areas. Then I run DRW for a long while (still at ci 0.2) with long sections (7, 8 or 9) to let it settle things better in the cloud. Then I look over the whole protein for places where I can improve the fit to the cloud. Then back and forth between scripts and hand-fitting until I am happy with the fit.
I saw the second video. It's like "lesson 2". Impressing technique ! Thanks also for the full explanation on cut points above.
If I find time, i'll try to "learn by doing" like you in the videos for this puzzle.
I think that this is the best way to learn, using the same puzzle and your video.
Looking forward for lesson 3 !
If you're watching the videos and need captioning, we're matching the transcript to our videos (because autocaptioning is so very terrible), and if you're interested in translating this to other languages, please send me a private message!
Curious to understand the contribution from the group AD to the final score that Susume has reached.
