id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6902	Improve AlphaFold PAE plot appearance	jan.gebauer@…	Tom Goddard	"Jan suggests AlphaFold PAE plots can have axis labels, chain dividing lines, multicolor palette and color key.  See the attached image for an example.

Begin forwarded message:

From: ""Jan Gebauer""
Subject: Re[2]: [chimerax-users] Identifying residues based on PAE plot?
Date: May 6, 2022 at 4:12:21 AM PDT
To: ""Tom Goddard""

Hi Tom,

thanks your your quick response and even quick implementation. I am already using the newest daily and really love the function. Just so that you get an idea: I constantly look at multimers where only parts (the interface) are probably predicted correctly. I have to identify them on the sequence basis to compare it between various predictions. 
I would be also very helpful if the various selection in the sequence could be printed to the log file. Currently, I select the interface are in the PAE plot and than have to redraw the selection to get the sequence stretch. If you tool would display it's selection syntax for the chains in the log would be great. Like

Selected from PE
#1/B:481-697
#1/C:1-161

As you suggested lines for the differen chains would be helpfull - to better identify the interface.
Here your PAE and a (none-interactive) display of roughly the same complex by one of our local scripts:

Your PAE plot


Our favoured internal visualisation (non interactive however 👎)

(see attached image)

Best
Jan
"	enhancement	closed	moderate		Structure Prediction		fixed		Elaine Meng				all	ChimeraX