id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17701	AF3 pLDDT score not displaced correctly in ChimeraX	Lukas.Bauer@…	Tom Goddard	"{{{
Hi,

I am experiencing a wired error:

For some reason the pLDDT score displayed on the AF3 server is not the same as if I downloaded the structure and displaced it in ChimeraX, by the command:

color bfactor palette 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

Same goes for  ""color bfactor palette alphafold""

For some reason the backbone does not have the same score, however some atoms of the side chains have the “correct” score.


I don’t understand how that can be, shouldn’t the pLDDT score cover the backbone?

I wrote the AF3 DeepMind team and I was told the issue would be on the ChimeraX side, which I have a hard time to believe… I only experienced this issue with AF3 predictions, where a residue was modified by PTM…

Would you have any idea to fix this issue?

Thanks a lot.

Best regards,

Lukas
}}}

[attachment:""fold_2025_05_06_1_20_p42858_hd_human_s16p_p63261_actg_human_model_0.cif""]

[attachment:""ChimeraX_pLDDT.png""]

[attachment:""AF3_server_Screenshot.png""]
"	defect	closed	normal		Structure Prediction		not a bug		Elaine Meng				all	ChimeraX