id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
7246	Make PAE plots work on trimmed AlphaFold structures	phil.cruz@…	Tom Goddard	"Currently predicted aligned error plots can only be shown with the full length AlphaFold model so that the model has the number of residues matching the PAE matrix size.  But AlphaFold models are often trimmed by deleting N and C-terminal residues to match an experimental structure sequence.  I'd like to be able to use PAE plots with AlphaFold models that have had residues deleted.

A good way to handle this might be to remove the rows and columns of the PAE matrix corresponding to the deleted residues.  ChimeraX knows the full sequence of an AlphaFold model (from PDB SEQRES records) even when residues are deleted, so it can figure out which residues have been deleted and remove those rows and columns from the matrix.  Since the residues are deleted, showing predicted errors to those residues is not too useful so removing them from the PAE plot seems sensible."	enhancement	closed	moderate		Structure Prediction		fixed		Elaine Meng				all	ChimeraX