id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6730	Make AlphaFold PAE plot coloring work even when residues deleted	Tom Goddard	Tom Goddard	"If residues of an AlphaFold structure are deleted then the PAE plot cannot be used to color domains.  It gives an error saying the number of residues does not match.

One idea to fix this is to make AlphaFold model remember the original residue indexes so that even if residues get deleted we can still use the PAE plots. I could add a residue attribute ""alphafold_residue_index"" when the alphafold command trims a structure. But this would not fix the case when the user opens an AlphaFold model directly and deletes some residues. Still may be worth handling the trim case."	enhancement	assigned	moderate		Structure Prediction								all	ChimeraX