Hi Toru,

What are you trying to do? If you want your structure coloured by pLDDT and your PAE in a green-white palette, you can just right-click on the PAE window and select "Color plot green". Your structure can be coloured in the typical pLDDT colours either by using the "Color pLDDT" button or the command you used.

I actually prefer the rainbow colour scheme for PAE over the AF3 white-green one (I think I suggested it to the developer back in the day). It makes differences in PAE much easier to recognise, so I'd recommend getting used to it — but to each their own.

Greetings

Jan

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------ Original Message ------

From: "Nakamura, Toru via ChimeraX-users" <chimerax-users@cgl.ucsf.edu>

To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>

Sent: 29/05/2026 13:32:32

Subject: [chimerax-users] displaying pLDDT in same color as Alphafold server?

Hello,

I am not sure if this is the right place to ask, but I have tried and failed Chimera to display what resembles the AlphaFold server, and it seems that it is using a long color scheme.

I typed “color factor #1 palette alphafold, but it does nothing, and the predicted aligned error & what is displayed is probably a different color scheme?

What am I missing here?

Thank you for your help!

Toru

====================================
Toru M. Nakamura, Ph.D.
Professor of Biochemistry & Molecular Genetics
~~~~~~~~~~~~~~~~~~~~~~~~~~
University of Illinois at Chicago
College of Medicine
Dept. of Biochem. & Mol. Genet.
900 S. Ashland Ave.
MBRB Room 2202, MC669
Chicago IL 60607, USA
~~~~~~~~~~~~~~~~~~~~~~~~~~
E-MAIL: nakamut@uic.edu
Lab: https://nakamura.lab.uic.edu/