Adjust AlphaFold pLDDT coloring to better match EBI color scale.

[Tom Goddard]

From the ChimeraX mailing list:

​https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/NUGJGHGBG7ZNY3KGULOQWXLFXYRJ3VI6/

Hi Vladimir,

Looking closer at the ChimeraX pLDDT colors I see they are not quite what I thought. Here are the ChimeraX colors

​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/alphafold.html#colorConfidence

They are 100 dark blue, 90 light blue, 70 yellow, 50 orange, 0 red, and are linearly interpolated as I mentioned. The EBI discrete color ranges are

​https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/evaluating-alphafolds-predicted-structures-using-confidence-scores/plddt-understanding-local-confidence/

Dark blue 90-100, light blue 70-90, yellow 50-70, and orange 0-50.

So you see ChimeraX matches the colors from the high end of the EBI color ranges, not from the middle of the EBI ranges as I suggested in my previous message. So the ChimeraX coloring is going to appear skewed in general to look less confident than the EBI coloring. I think the ChimeraX coloring would give a better match if it used 95 dark blue, 80 light blue, 60 yellow, 25 orange, 0 red and linearly interpolated. In other words use the middle value of the EBI ranges combined with the EBI colors. I've made a ChimeraX bug suggesting this change.

Tom

[Tom Goddard]

One complexity of this is that the ChimeraX and EBI colors are actually not the same RGB colors so some testing would be important to see if the overall impression is the same with the proposed adjustment of pLDDT values for each color.