Electron Density (ED) Puzzles - More Ideas
|Opened on:||Thursday, May 2, 2019 - 17:25|
|Last modified:||Wednesday, May 15, 2019 - 00:23|
This post is to continue an older post: Electron Density (ED) Puzzles
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.