Like Skippy, I just don't see anything in the density clouds, no matter how hard I try. The existing tools are useless for me, so I turn the cloud visualization off and play them like De-novos. De-novos are challenging enough, but having to deal with the ED "tug" makes them even more so. So yes, I dread each one that comes around.
Having the ability to toggle the "tug" off and on would be a good place to start.
I agree with getting smaller and easier ones to start (EDs are very slow for computers when viewing the density).
Also with some tryptophan inside (these are AAs that we have chance to identify in the cloud).
With no gap if possible (parts that are not in any density cloud) for de novos.
Any puzzles that are already for a big part in the density cloud are ok.
My main problem is to find a (density) starting point for a de novo.
Simple structures at start (e.g. only helices or only sheets), no more that 2 levels above each other in 3D (e.g. something like the design puzzles).
Revisiting (with a picture of the solution as help) or old design solutions that we have to put in a cloud.
Personally I really like ED puzzles, they are my favorite.
But the really frustrating part is that I cant position the dots in the places where I want them.
That takes a lot of time.
I would really like to be able to put them inside the ED, not on the surface.
We really need a way to select one and move it around, just like we can with the protein parts.
Now we can do it a bit with foreground and background moving, but that is not really easy.
When we would be able to have a slice of the density and control the thickness and the placement of the ED slice, in combination with placement of dots in the middle of the slice things might be easier.
Maybe two sliders on the ED menu for front cutaway and back cutaway, rather than the clumsy key-mouse combos. Also move the trim to a slider on the ED menu that stays where you put it. The RGB sliders could move to a secondary menu as they are less often changed.
The threshold slider is much more useful since jflat adjusted its scale.
and definitely the second, partially folded proteins would be beneficial, the building from a straight chain while also minding ED is super time-consuming particularly when also not so great at using the tools. Working on smaller "revisit" puzzles is an excellent idea for ED practice and gathering more feedback.
My preference would be just to slice the ED cloud, because I would like to be able to see more of the protein itself. And being able to put the dots in the middle of the slice.
I really like ED puzzles, but rarely have the time to do them. What I think would really help would take a bit of doing but..
1) being able to control the color of sections
2) being able to show/hide sections easier
What I think would be very helpful is to be able to create basics 3d shapes (sphere and cylinder primarily) and to be able to stretch them in 3d space to define an area (semi transparent with node points to manipulate them on their axis, and arrows to move them along axis)
Then have a drop down list with all your defined areas (undefined area, sphere 1, sphere 2, cone 1, etc…)
For each if these areas you could :
Name the area
Show/hide ED data in the area
Change color of the ED data in that area
Show/hide the area boundary (once set it may obscure view)
Then all ED data not in a defined area would have the same options as well
I think this would give a tremendous amount of flexibility in manipulating data.
In addition players who are looking for more manageable planes could simply move cubes around and show/hide any area(s) they wish
The University of Michigan undergrads used a program called Coot to build a protein into an ED cloud. Maybe looking at the Coot interface for viewing the cloud would yield some useful ideas.
I wonder if part of the change was the drop in regular players. In the past there were often 130 players online when I was on, now it's 70-90.
Maybe the 40-60 players who liked ED (I like them!) have drifted away.