Color PAE plots using domain colors

[Tom Goddard]

Gerard suggests coloring PAE plots using the domain colors, I guess just the diagonal block so you could easily see the domain interaction strengths and visually compare to the structure coloring.

Begin forwarded message:

From: Gerard Kleywegt
Subject: Re: [PDBe #580574] ChimeraX dropping support for old Linux distributions
Date: April 26, 2022 at 7:33:42 AM PDT
To: Tom Goddard

Hi Tom,

I like the video! I wonder if it would be helpful to have an option to apply the domain colourign after Tristan's algorithm to the PAE plot as well (e.g., as -togglable- squares coloured in the same way as each domain on top of the PAE plot). When you have more than 2 or 3 domains this will make it easier to see which pairs or subgroups of domains have low or high PAEs between them.

...

Best wishes,

--Gerard

[Tom Goddard]

Done.

Added AlphaFold PAE plot context menu entries "Color plot from structure" and "Color plot default". The color from structure takes the ribbon colors of the residues and colors plot points where both residues (x-axis and y-axis) have the same color to match that residue color. If the two residues have different colors then it leaves the plot point with the default dark green coloring.

[Tom Goddard]

Example of PAE plot with structure colors.

[Tom Goddard]

I attached an example of a PAE plot with structure colors.

Elaine can put these two new context menu entries in the documentation.

[Tom Goddard]

I made the off-diagonal color black instead of green to avoid confusion with green colored domains in the structure. I've attached another example image.

[Tom Goddard]

Plot color with black off-diagonal