id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18769	Adjust AlphaFold pLDDT coloring to better match EBI color scale.	Tom Goddard	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
"	enhancement	assigned	moderate		Structure Prediction				Elaine Meng				all	ChimeraX