This post is to continue an older post: Electron Density (ED) Puzzles
(https://fold.it/portal/node/2001368).
In ED Puzzle 1667, I have added many dots to the ED cloud to help identify
landmarks within the cloud. Now I have so many dots and labels for dots
that it is confusing. Below are some ideas to make life easier:
(1) Let us show/hide dots, dot labels, bands, segment/residue/amino-acid
labels, and even dots of a certain color, all independently. Right now,
for example, sometimes I want to view just the dot labels, and other times
I want to view just the residue labels. When all the labels show at once,
it is confusing. I also like to use one dot color for backbones and another
sidechains. Sometimes it would help to view just the backbone dots, and
other times it would help to show no dots at all.
(2) Have more dot colors to choose from. On ED Puzzles like 1667, where
many short peptide chains are visible in the cloud but it isn't clear which
ones connect to each other, one could color one chain red, another blue,
and another green. With enough colors, many individual chains could be
visualized, and this would help decide where each protein section belongs
in the ED cloud.
(3) Allow rectangles and thick & thin cylinders in addition to dots. Rectangles
could stand for sheets in the cloud, thick cylinders for helices, and thin
cylinders for loops. The lengths of these rectangles and cylinders could vary.
They might be easier to manage than a bunch of dots. It would also help if
one could show/hide different colors and shapes independently.
(4) For the objects (dots, rectangles, & cylinders) described
in (1-3) above, have LUA commands to count how many objects
have been placed into the ED, read/set these objects' labels
colors shapes lengths widths & radii, show/hide certain objects,
and delete certain objects. Such commands would let us make a
wide variety of utility recipes for handling all these objects.
For example, if one were marking each sidechain in the ED cloud
with a green dot, it would be nice to have a recipe to quickly
count all the green dots placed so far. Does the total exceed
the number of segments in the protein? If so, that would be
good to know. Also, if one were using different colored dots
for each peptide chain in the ED cloud and suddenly realized
that the red and blue chains were part of the same longer
chain, one could use a utility recipe to quickly change all
the blue dots to red.
Maybe in addition to the dot system there could be a "paint" system. If it had to lock down the threshold slider I'd be okay with it, but ideally I'd like to paint certain parts of the cloud and add a dot label to ID non-viable backbones or discernable structures.
Just the addition of an extra colour (perhaps 2) would be good…..this has been asked for B4 of course.
I think all know my views on ED - I think they are great - a way for scientific results to be interpreted by players here in foldit.
But…….low definition is a massive handicap……Angstrom definition over 2.2 or so is not realistic for most players - certainly not for Newbs. This is counter productive imho.
Perhaps the opportunity to change the blobs to some other 3 dimensional figure would help - perhaps it would be easier for FC to do this - IDK.
But I still stand by my suggestion from years ago - we need the ability to erase areas of the cloud. Trim density does this perhaps - but it usually removes areas we still want to see….the same is true of the other viewing options.
That's my ha'pence worth
The complex ED cloud in Puzzle 1667 (https://fold.it/portal/node/2007726)
got me questioning many things. For example, in previous ED puzzles, it
seemed like the ED cloud always contained exactly one full copy of the
protein of interest. Nevertheless, Puzzle 1667's ED cloud seems to have
many extra things in it. Do we know our protein of interest has its full
chain folded as one continuous piece within the ED cloud? What if part of
our protein is folded up in the left half of the cloud and then exits the
cloud through the left side, re-enters the cloud on the right side, and
then finishes folding up in the right half of the cloud? If the scientists
don't pre-process the ED cloud data, how do we know our protein isn't
chopped up like this? How do the scientists know the protein isn't chopped
up like this?
To compensate for odd ED data like above, it might help to be able to
translate the ED cloud. If the cloud were a box, it would keep its length
width and height, but the center of the box could be moved around. If you
allowed translations along the length of the cloud but shorter than the
length of the cloud, the cloud's contents could jump from one side of the
cloud to the other, sort of like in the side-view boxes below, where A & C
are the terminals of the protein and B is the center of the protein.
+-----+ +-----+ +-----+ +-----+ +-----+
|A | | A| | A | | A | | A |
| B | <-> | B | <-> |B | <-> | B| <-> | B | <-> far left box
| C| | C | | C | | C | |C |
+-----+ +-----+ +-----+ +-----+ +-----+
^ ^ ^ ^ ^
| | | | |
v v v v v
+-----+ +-----+ +-----+ +-----+ +-----+
| B | | B | |B | | B| | B |
| C| <-> | C | <-> | C | <-> | C | <-> |C | <-> far left box
|A | | A| | A | | A | | A |
+-----+ +-----+ +-----+ +-----+ +-----+
^ ^ ^ ^ ^
| | | | |
v v v v v
+-----+ +-----+ +-----+ +-----+ +-----+
| C| | C | | C | | C | |C |
|A | <-> | A| <-> | A | <-> | A | <-> | A | <-> far left box
| B | | B | |B | | B| | B |
+-----+ +-----+ +-----+ +-----+ +-----+
^ ^ ^ ^ ^
| | | | |
v v v v v
top box top box top box top box top box
In Foldit, as one translates the ED cloud around, any ED dots should
translate as well. There could also be a button to translate the ED cloud
so that its center lines up with the center of the protein we are folding.
Letting us translate the ED cloud around would help us see how much
low-density space there is between each copy of the protein complex
in the ED cloud. Perhaps in some puzzles, there would be enough
low-density space that one could fold the protein in that space,
where the ED cloud would have little influence on the Foldit score.
Then, after achieving a good fold away from the influence of the
ED cloud, one could translate the folded protein into the hi-density
part of the ED cloud and try to find where it scores best there.
Suppose there was a box within which the ED cloud was visible.
Suppose we could move this box around on the screen so that
sometimes all of the hi-density parts of the cloud were
centered in the box and other times the hi-density parts
were split so there might be one chunk on the left side
of the box and another chunk on the right side of the box.
This mobile box would let us see some cross-sections through
the hi-density parts of the cloud. It would also help us
identify regions between the hi-density parts where we could
fold the protein with minimal interference from the ED cloud.
It would help if dots and other ED-marking objects would jump
from one side of the box to the other when their parts of the
ED cloud did the same. It would also help if large ED-marking
objects like cylinders and rectangles would split into parts if
they happened to cross a border of the box, thus, for example,
showing one part of a cylinder on one side of the box & another
part of the cylinder on the other side of the box.
It might help more if we could shrink or stretch the sides of
the box. Then, ED-marking objects outside the box would be
hidden, and if 2 or more copies of part of the ED cloud were
to appear in the box, the ED-marking objects within this part
of the ED cloud would also have 2 or more copies appear within
the box.
There could be one button to reset the sides of the box to
their original lengths and another button to move the center
of the box back to its original position. If the box is able
to rotate in addition to being able to translate, there could
be a button to restore the box's original orientation as well.
AS far as I understand it - all space in ED puzzles is tiled….so working outside the 'rendered' area is pointless.
I have rethought the idea of different shapes for the existing blobs - this will not work when zoomed out - all 'blobs' will ultimately look like a pixel (unless huge)
I agree with the argument for more colour options - bit this should be backed up with the option to switch off (not remove) those of chosen colour(s)
I still want an eraser. Trim and viewing options cannot do what that would achieve. Though the option to select segs prior to trimming might prove of some use in mid game.
The issue with ED will always be the start - find some handles to work with and a player has a chance.
The primary tools available should concentrate on this.
(5) It would also help to be able to select a large group
of ED-marking objects (dots, cylinders, rectangles) manually
and do the same operation (like hiding them or changing their
color) on them all at once.
(6) Having a LUA command to read an object's color can make
even colors that are hard to distinguish by eye useful. One
could select them based on their color and hide or show each
color independently. Also, black dots could help when the
background is white, and white dots could help when the
background is black.
(7) To make a cylinder or rectangle, one could select 2 dots
for its endpoints and then press a button.
(8) Being able to copy ED-marking objects from one solution
to another would be very helpful. If one copies these objects
from a teammate's solution, should the resulting solution be
an evo?
The dimensions (length width & height) of the box described
above could be set or read using LUA commands or a set of
sliders. Beside each slider could be the present numeric value
(like 80 Angstroms) for its dimension. Then we could use the
sides of the box as a reference on the screen to estimate
distances within the ED cloud or protein, for example. Each
slider could also have a mark showing where its original value
lies. Then if we reset the box to its original size, all the
sliders would line up with these original value marks.
