Tools for ED puzzles - summary

Started by Rav3n_pl

bertro Lv 1

I would like to be able to:

  • hide all bands (on/off checkbox in the density window)
  • hide the protein and shift the mouse control focus to the density (maybe with a ctrl/alt key combination)

while looking at the density cloud.

Susume Lv 1

After hour of fighting with blind ED puzzle I decided to push out my frustration.
WE NEED MORE TOOLS to play denovo ED puzzles.

  1. anchor view port to any point, not only segment. I wish to look on ED in different angles and I cant just rotate it around. When I pull protein out center of rotation is moving too
  2. my old idea of alignment editor. It would be 1000% easier to draw shapes on ED how we see them then thread protein into that shape. I wish to draw helices, sheets, then add loops and thread protein into it.
  3. editable ED config sliders. I wish to use only alpha and threshold, rest can be hidden after I set colors/shapes I prefer. Less part of screen would be covered.
  4. Pin/lock in space tool. When we are sure about some fragment we want to lock it totally. any wiggle, banding or whatever should not move locked part.
  5. force free/no CI mode/move frozen/locked parts. When I pull one part it should move exactly in place I pull. when I want pull helice it shpudl stay intact only loops should bend. It should not jump aside or bounce back when hit another part. When I pull sheet it suppose to stay flat and straight, not bending in strange ways

marie_s Lv 1

I dont understand the score at all and I need usual relative scoring to play.
You should be allowed to play this puzzle as another puzzle and use the cloud as a guide without interference with the score.

Garnasha Lv 1

First off, I'm completely new, just finished the tutorials, tried the beginner puzzles for a bit, and then plunged into the advanced puzzles. So I'm probably not qualified to make suggestions, but I'd still like to try:

  1. my old idea of alignment editor. It would be 1000% easier to draw shapes on ED how we see them then »thread protein into that shape. I wish to draw helices, sheets, then add loops and thread protein into it.

Came here after trying to do a DeNovo to see if someone already suggested this, and happy to find there's non-newbies wanting the same thing. Though I think I sought a solution in a different direction for the same problem. The editor sounds really nice. My idea was two parts: "lift restrictions on alignment tool" and "structure tool on sequence".

"Lift restrictions": What I'd like is having the entire available database of proteins with known structure (possibly supplemented by one's own solutions to previous puzzles) available for partial threading, regardless of what puzzle you're on. Even if there's no obvious evolutionary link, 3-10 residue parts with identical sequence in different proteins might well have similar structure, if only because that happens to be a very low-energy configuration for that particular part-sequence.

"structure tool on sequence": A sequence-based (as the alignment tool, as opposed to the "shape-based" default view) structure editor might be nice. When you start with a DeNovo protein, there's exactly no data in the shape, and it takes a lot of panning to check for parts of the sequence which might be sheets or helices and designating them as such. And letters are probably easier to recognize than sidechains sticking out at all angles, with next to no CPU usage to render.
Actually, a lot of tools might benefit from an option to "aim" them using the sequence rather than the shape, as long as there's no spatial component to the user input (so, nudge and tweak are out, but lock, cut/connect, local wriggle and maybe rubber bands between two residues could work)

Garnasha Lv 1

Ehm, oops, looking back, that became a different suggestion than that of the OP. Related, but not the same. Trying to avoid duplicates, I went off-topic. Sorry.

Could everyone please ignore my earlier comment except where it concerns the OP's suggestion and could a mod maybe delete both this and that comment? I don't seem to be able to. Thank you.

karstenw Lv 1

we discussed this in chat. maybe a stack of aas and a move tool so we can place these "aa markers" whe we think they go in the ed. plus instead of draw as rav suggests. how about a stack of 1 segment long sticks we can use move tool and place in the ed to try and build a mock up of backbone.