Electron Density Discussion

Started by inkycatz

jeff101 Lv 1

I think ED puzzles are important and wish I were better at them.
The last few I have done very poorly on as a soloist.
It seems the best I can do is evo my teammates' ED solutions.

Bruno Kestemont Lv 1

I agree with Steven if I understood him wel.

My problem is eliminated all "noise" views when working on a small part, trying to fit it into the density.

Shift+q and slices are ok but it still gives too much to view.

I would like to be able to focus only on a "sphere" or "cylinder" around where I'm working on, but independent spheres for protein and density.

For example, seeing a large portion of the protein, but limiting the cloud only to a small sphere around the segments I'm working on.

Then also beeing able to "freeze" or "glue" a portion into a density (no possible move in the cloud for this part). It's frustrating fitting well a portion in the density then seeing it moving away on first wiggle all (and adding a lot of bands in space takes time).

Other Idea: "band to density" that would always link a segment to the same density position (not to neutral space).

inkycatz Lv 1

These are the results from players who filled out the puzzle survey. Not everyone who is active is inclined to fill out the survey (being an optional thing).

Fun fact: More people filled out the puzzle survey than last year's puzzle survey.

frood66 Lv 1

I like ED puzzles - I believe them to be a great opportunity for players to build on existing science. I also accept that , for many, it can be very difficult to see things even after careful viewing selection. I feel sure that in many cases this comes down to practice and clear instruction. Eyesight is also an issue - I rarely work for more than 20 mins at a go. (I principally use handwork)

I do, however, have one proviso: The resolution needs to be reasonable. If I cannot spot an aromatic when it's in the core, I don't bother to continue. When I have to ask if a side chain is methionine or Tyrosine I know that I am wasting my time (but that's me)

I agree with many comments above - particularly with Susume's re better tutorials and sliders. I think it would be better to have the depth of field tools on a nice small window of it's own. I rarely change the other 'main' viewing sliders once I've set them up. It is very annoying when any slider resets to default.

I do not like the fact that the ED cloud covers all space - this appears pointless to me at a number of levels.

The one thing I would love to see is an eraser for the rendered cloud area. In many (but not all) posted puzzles, parts of adjacent molecules are inside the working (rendered) area - I want to be able to remove these at an early stage. The ability to create one's own edited cloud as a template that can be recalled at anytime would be great! To be clear - I am not suggesting permanent erasing of the cloud data. I can see probs with this re threshold setting - but if any 'template cloud' created was reloaded with the 'original' setting - would that not work? Taken further, this ability could answer many of the viewing issues raised above.

inkycatz Lv 1

We know that ED puzzles are hard/not fun/etc. to work with, and that's part of the reason we've started this thread! The feedback so far has been very useful for helping us sort though the issues, and several recurring themes bring out the most important suggestions from players to help decide and prioritize improvements. Not being a coder myself, I can't speak to the feasibility of certain suggestions, or the timeline in which they could be implemented, but do be assured the team is watching this thread diligently!

Bruno Kestemont Lv 1

Batz said this in PM to our group and bkoep when we discussed the way we achieved the result of the paper. I think it's interesting for this threat (and sure Batz would agree that I quote this). May be other high level density players share this opinion:

"In order to improve the results of Electron Density Puzzles, I would like to point out some issues with Foldit, since I recently observed several things during the last puzzle.

1) Especially aromatic residues like Histidines do not really fit well within the density. Are there enough rotamers available for these residues in Foldit? Because it seems that other rotamers are preferred even though I tweaked the residue in its right place. After wiggling and shaking the aromatic ring was always offset again…

2) How much is the weight of the density in the scoring function? I noticed especially for Arginines and Lysines, that they do not like to be in their densities but rather form hydrogen bonds with other residues or the backbone. Therefore, it seems that the scoring term for hydrogen bonding is higher weighted than the term for the ED.

2b) Which belongs to the previous point. It's water molecules. Electron densities at that resolution always show water molecules within or next to the protein. This is another reason why in Foldit residues like Arginines do rather form hydrogen bonds with e.g. Glutamates although in reality a water molecule is in between these two residues.

3) At the end a really good thing, the Remix Tool! Especially for loops, I could much better sample several conformations and see which ones fit better into the density. It is much more suitable than the rebuild tool, it always shows the score and it is really fast. This makes it a perfect tool for these puzzles.

Now for those who use scripts, did you notice some similar problems, that residues do not fit quite well into their densities?"

Bruno Kestemont Lv 1

This is very true:

"Editing of nearly complete structures could form a base of easier Foldit puzzles for new players, allowing players to practice their model-building skills before moving to more difficult de novo model-building puzzles. To further improve the capability for Foldit players to aid crystallographers, ongoing development will make it possible for the players to add or remove residues with insufficient electron density, and have these changes accurately reflected in the Foldit score"

Anfinsen_slept_here Lv 1

I find navigating thru the density frustrating. I would like to have better control over the slab width, and maybe some way to navigate along the z axis. I believe this has been mentioned by other people too.

My second desire would be some different way of treating fragments in the scoring. If I can fit 10 residues here and 10 residues there, and maybe 15 somewhere else, and I don't yet know how to make loops to connect them, I am likely to have a global score of -999999. This is also frustrating.

frood66 Lv 1

Much about ED puzzles is due to lack of 'easy' practice.

I suggest some ED puzzles on short proteins - perhaps 60 segs or so. Start with high resolution - and I do mean high. These would be rather like QTTN puzzles - but using an ED cloud instead.

I'm pretty confident that many players would be turned on to this over a little time. I believe that the mystery has to be removed - this appeals to me and others as a simple, straightforward way to achieve this