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, [cid:77069661-1c4a-498b-b269-a936e3f74d9a]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 [cid:part1.3xWabto1.xnDhu9y4@gmail.com][cid:part2.OY11MAlU.YesutBDI@gmail.com] This email and any files transmitted with it may contain confidential information. If you believe you have received this email or any of its contents in error, please notify me immediately by return email and destroy this email. Do not use, disseminate, forward, print or copy any contents of an email received in error.
