Electron Density Discussion

Started by inkycatz

jeff101 Lv 1

To change the sidechain positions without using scripts,
try wiggle sidechains or shake. Wiggle sidechains
can be done at different wiggle powers and
can be done while varying the clashing importance.

Skippysk8s Lv 1

I still can't see anything. I think I might have scored worse on ED for crystallin than on de novo. If this is the wave of the future, I still need a lot more help with puzzles and tools. I'd prefer a small puzzle with no known reload from before. That way I can work at trying to find where to start threading the protein through
Skippy

Bruno Kestemont Lv 1

Then the same but with a full cloud but the tryptophan almost in the middle: "find the tryptophan by clicking shift + Q on the chain on the middle to see the shapes in the density cloud".

Then n° 3: "shift + Q on the chain then move it in the cloud and fint the tryptophan position

n°4: "now that you have the starting tryptophan, align the other 2-3 segments in the density by freezing the tryptophan and moving the other segments."

Susume Lv 1

Could you post a no-points puzzle with the published solution from 1152 as the starting position, and let us load our saved solutions from 1152, so we can load one as a guide to the other and see where we diverged? This would also let people see what a well-placed protein in a cloud looks like.

Note, the saved solutions loaded as guides would have to load in the right position in space relative to the cloud - there is a feedback about this not currently working: https://fold.it/portal/node/2002559

Susume Lv 1

Much as I would love to see an ED puzzle of the LGMD dysferlin protein, I hope you will postpone that until after you have given us at least 2-3 more small ED practice puzzles, like the recent revisit. That would help people get more used to ED and the ED tools, and can only improve the number and quality of solutions on a hard protein like LGMD.