Electron Density (ED) Puzzles

Started by jeff101

jeff101 Lv 1

Below are some questions about Electron Density (ED) Puzzles, based on Puzzle 1152:

(1) If you press Tab on a segment to show its Segment Information, does the ED only contribute via the "Density" subscore? Does the ED ever contribute via "Other", "Reference", or any other subscore?

(2) On Puzzle 1152, I have seen the "Density" subscore be nonzero, sometimes positive and sometimes negative, even when the protein is far away from the ED cloud. Is the exact same ED cloud tiled repeatedly through 3D space but only shown for one small region of 3D space? What do negative "Density" subscores mean?

(3) When you press the "Center Protein on Density" button, the overall score you get depends on the "Threshold" setting. Does the overall score depend on any of the other settings in the Electron Density Window (see the image on the left below)?

(4) I would like to play around with the settings in the Electron Density Window while a Recipe is running, but I worry that I will press the wrong thing, change how my protein is scored, and so mess up what the Recipe is doing. Is "Center Protein on Density" the only thing in the Electron Density Window that will directly alter the overall protein score? If I vary things like the "Threshold" but never press "Center Protein on Density", am I only affecting how the ED cloud is displayed? Can selecting "None" as opposed to "Solid" or "Wireframe" affect the overall protein score?

(5) Is it possible to list values for "Red", "Green", "Blue", "Alpha", and especially "Threshold" in the Electron Density Window like you already list for the "Clashing Importance" in the Behavior Window? This way, we could easily tell each other what settings we find work best. Right now, we have to say things like "Threshold to far left", "Threshold at the center", or "Threshold over the m in mouse". It would be easier if we could say something like "Threshold=0.05" instead.

(6) http://foldit.wikia.com/wiki/Electron_Density_Puzzles is helpful. Are there other places you would recommend for help with ED Puzzles? I think many players have trouble seeing things within the ED cloud. It would be nice if there was one place that described every item in the Electron Density Window, explaining things like "Alpha" and "Backface Culling", for example.

Thanks!

Susume Lv 1

Personally, I recommend never using Center Protein on Density. It is essentially a random move of the protein in space. I have never seen it make the density match better. It does not look at the current position and try to improve on it. I took a protein well-matched to the density (overall density score 3735) and clicked Center Protein on Density, and it moved the protein about 90 degrees and reduced its overall density score to 90 points. The one thing it is useful for is if you have not made any progress matching the density and are having trouble finding the cloud.

It is safe to use the None/Solid/Wireframe etc., Backface Culling, Red/Green/Blue, Alpha, Threshold, and shift-Q controls during a script - they will not alter the score. I tested all of them during wiggle and none of them changed the outcome.

LociOiling Lv 1

I find the density cloud has a tendency to disappear suddenly when I try to rotate it.

Trying to view the density, I move the protein far away. Then I use "Focus on Density" from the Electron Density dialog. When I try to rotate the density in any direction, it quickly fades and then disappears. Often it seems to just disappear.

It would be nice if there was a mode where you could move the density as you would the protein. It would seem like "Focus on Density" could select this mode, and then a new "Focus on Protein" would switch back to normal mode. As it is, it seems like there's some mystery center point relative to the protein that causes the disappearing density issue.

Just in general, it seems like a "drone mode" would be a nice option. In other words, treat the protein and the density as floating motionless in space, and have the "camera" fly around them. The foldit model seems to hold the camera still and move the protein around. There's always a center point, which becomes an issue when things are spread out. An option to show the center point would also help in this regard.

My next step is to make a compact ball of the protein and move it just a little to the side of the density.

LociOiling Lv 1

Even with a reasonably compact protein off to one side of the density, the density tends to disappear when you rotate.

The best solution I've found so far is to switch to the "Line" view with the EnzDes or CPK coloring, still with an extended chain. Then "Center Protein on Density" from the Electron Density panel and maybe "Focus on Density" if needed.

These settings minimize the visual distraction of looking at the protein, and let you rotate the density without having it disappear.

Susume Lv 1

To return from focus on density to focus on protein, type Q.

I always place the extended chain in the cloud to examine the cloud at the beginning. This lets me use shift-Q to zoom in on portions of the cloud and to see the interior. Place the extended chain in or near the portion you want to examine, hover mouse over backbone, and hit shift-Q. To examine another area, shift the extended chain to or near that area and do it again. I never attempt to see into the cloud without having some protein in it to anchor the focus to.

LociOiling Lv 1

Hotkeys and shortcuts for electron density in case I forget again.

Thanks Susume for mentioning shift-q. When you hover on a segment, shift-q limits the density display to things in the same plane that segment. Hitting shift-q again (or just plain q) restores the full view of the density.

Shift-q does not seem to be present in the foldit help (under Menu->Help).

The near and far visibility can also be helpful.

The shortcut ctrl-shift-click-drag changes the far distance cutoff. So if you hold ctrl+shift, then click somewhere and drag the pointer downward, you'll see the more distant parts of the protein fade and disappear. If you ctrl+shift then click and drag the pointer upward, the distant parts reappear.

The shortcut alt-shift-click-drag changes the fog or haze. If you hold alt+shift, then click and drag downward, the more distant parts of the protein grow hazy. Dragging the pointer upward cuts through the haze. Unlike the far distance cutoff, the distant parts don't disappear, they just get dimmer.

The fog shortcut doesn't seem to be present in the foldit help (under Menu->Help).

The short ctrl-alt-click-drag changes the near distance cutoff. If you hold ctrl+alt, then click and drag the pointer upward, you'll see the near parts of the protein fade and disappear. Dragging the pointer downward brings the near parts back into view. Note that the direction of dragging seems to be reversed relative to the two far view shortcuts, but perhaps there is some higher-order symmetry at work here.

The "q" shortcut seems reset the visibility and fog options, in addition to clearing shift-q and potentially moving the protein back to front and center.

And of course the shift-e shortcut toggles the Electron Density panel.

jeff101 Lv 1

Since the results of "Center Protein on Density"
seem to depend on the setting of "Threshold",
perhaps the following would give better results:

(1) Set "Threshold" to the far left,
then press "Center Protein on Density"
until the score stops changing.

(2) Set "Threshold" to the center,
then press "Center Protein on Density"
until the score stops changing.

(3) Do the same thing for
several other "Threshold" settings.

(4) At the end, use the Undo Graph or
Restore Recent, Credit, or Very Best
to get the best possible score.

I'd imagine there is a sweet spot for the
"Threshold" that gives the best results.

If we had LUA commands to read and set the Threshold
(for example, density.GetThreshold and density.SetThreshold) and
press the "Center Protein on Density" button (density.CenterProtein),
we could make Recipes to do the above procedure automatically.