I've been working on the Electron Density Puzzle 1588 tonight.
One goal was to put purple dots in the cloud where I thought
the sidechains were and red dots in the cloud where I thought
the backbone was. It seemed like if I tabbed on a part of the
cloud, it put a purple dot there. If I wanted a red dot, it
seemed like I had to right-click on a purple dot and then
select red for its color. Is it possible to click something to
change the default dot color to red so that the next series of
tabs will make red dots instead of purple ones? Then I could
pick a default color, tab to make a series of dots with that
color, then pick a different default color, then tab to make
a series of dots with this new color. If this isn't possible
now, can you change the interface so it will work in the
future?
I asked in Chat about the above, and Loci requested yellow
as a dot color option as well. Then we could pick among
red, yellow, green, blue, and purple for our dots' colors.
Another question I had was if there was a page on the
Foldit website or in its wiki showing examples of how
different sidechains looked in the electron density
cloud in actual Foldit puzzles. The images at
https://fold.it/portal/node/2001386 are useful, but I
think more sample images from within actual Foldit
puzzles would help.
Would someone able to recognize the different
sidechains post images of each one rendered several
different ways (Solid, Wireframe, Isocontours, and
Grid)? If there is variation from puzzle to puzzle
or even within the same puzzle, would someone post
additional images to help players learn to recognize
the different shapes?
Thanks for reading!
Another idea for puzzles like 1588 with multiple starting
structures would be to let players copy all the dots & notes
they build in the electron density cloud from one starting
structure or saved solution to another.
I'd also like a way to keep the density note dots around when doing a reset.
yes please - keep those density notes on reset
it depends on the level of definition - but, using wire frame mode (my personal favourite) I don't believe I could improve on the images u mention.
How about the proline? I would expect the backbone to bend
at each proline, but the image cited above doesn't really
show the backbone. Can you actually see proline-induced
bends in Foldit's electron density cloud?
on 2nd inspection - it would, perhaps be better if the images u refer to showed the backbone also. I also see yr point re proline. But, in truth, prolines are quite easy to recognise - not so much by the backbone bend but more by the side chain 'blob' being large and close/part of the backbone cloud. Ultimately, the most important thing is the definition - the higher the better. This puzzle does not have the highest definition we have seen - but it is good enough. In any event, the viewing settings are paramount. again, this puzzle's default required no changes for me - but it is very much a personal thing.
Another thing I'm curious about is what are good
Density subscores for each type of amino acid?
For example, if you tab on Methionine 23 in
Puzzle 1588 and it gives a Density subscore
of 18.6, is that a good result for Methionine?
Is 7.8 a good result for Lysine 2?
Is 15.8 a good result for Threonine 4?
Is 5.6 a good result for Glycine 13?
Is 10.4 a good result for Alanine 22?
Is 18.6 a good result for Methionine 23?
Is 18.5 a good result for Tyrosine 24?
Is 13.3 a good result for Asparagine 25?
Is 20.2 a good result for Glutamate 27?
Is 5.8 a good result for Glutamine 48?
Is 13.8 a good result for Arginine 51?
Is 11.1 a good result for Valine 58?
Is 19.1 a good result for Aspartate 67?
Is 10.2 a good result for Isoleucine 77?
Is 16.4 a good result for Proline 170?
Is 15.7 a good result for Leucine 177?
Is 13.1 a good result for Serine 188?
Is 7.3 a good result for Tryptophan 197?
Is 15.3 a good result for Phenyalanine 212?
What are good results for Cysteine & Histidine?
What does a negative Density subscore mean?
Is a negative Density subscore undesirable?
Are there known maximum possible Density
subscores for each amino acid that would
be the same for every puzzle?
Is there a recipe out there that lists each
segment's amino acid and its Density subscore?
I'd be curious what ranges are typical for each
amino acid.
print protein 2.8 includes some density analysis, and at least lets you compare the amino acids in a particular pose. There's cut-and-paste report that shows the mean density score by amino acid, along with the best and worst densities identified by segment number.
With persistence, you could accumulate the results across puzzles, but I haven't tried that.
