TRY THIS:
ChimeraX Command line to match pLDDT of AF3:
color bfactor palette 
0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65C
BF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6


Dr Khawar Sohail Siddiqui,
hoo.com
From: Vladimir Saudek via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Thursday, September 11, 2025 4:11 PM
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] AlphaFold3 structures coloured in ChimeraX
 

Hello,

I am using ChimeraX 10.1 to display the results of AlphaFold3 predictions. I observe a large discrepancy between the colour coding of the quality of the structure (pIDDT) displayed at the output of the AF3 server and ChimeraX (I use the command color bfactor #1 palette AlphaFold, 1 being thenumbero of the structure to colour). ChimeraX's colouring indicates that the quality of the predicted structure is substantially lower then than that of theAF3 server. Is there any possibility to get ChimeraX to display the AF3 server colours? Below is an example, right AF3 output, left ChimedraX.

Best regards

Vladimir




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