Hi Elaine,

Thank you for the link. It makes a lot of sense now. I came across a similar page on how to make it more like the Alphafold server, but you sent me an explanation of why the Chimera coloring differs so much, especially Alphafold3.

Again, thank you so much! (It may be helpful to explain this in the help section, as the Chimera help page actually gave me the impression that it should look somewhat the same as the alphafold server.  (I suppose Alphafold 3 is actually worse?)

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/

On May 29, 2026, at 12:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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Maybe the question is because of the differences in the coloring at the AlphaFold server website versus in ChimeraX.  There is a long discussion of that here:

<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/AQTRFQ2NXL4IOI5W5CFPA4CFRE4TARWY/>

... to summarize, the coloring in ChimeraX is chosen to make the user more aware of the continuous value rather than putting them into categories with stark boundaries where the value just above the color change is not really that different from the value just below the color change.  However, you can make the coloring the same by using the "palette" option in the coloring command and specifying all of the color/value pair boundaries.  See the command in the attached TIFF that was provided by Agnieska Obarska in that discussion:


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Sorry cannot cut and paste, but you can see in the image what to type.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco





> On May 29, 2026, at 4:55 AM, Jan Gebauer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> 
> 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 
> 
> <blyqkncw.png><0zdmper0.png>
> 
> 
> -- 
> Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann
> Institut für Biochemie | University of Cologne
> Zuelpicher Str. 47 | 50674 Cologne | Germany
> 📞 +49 (221) 470 90616 (neu!) 📠Fax: +49 (221 470 5066)
> 📧 jan.gebauer@uni-koeln.de 🌐http://px.uni-koeln.de/ 💎Visit the Cologne Crystallisation facility (C2f) !🌐http://c2f.uni-koeln.de/
> 
> 
> ------ 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
>> 
>> 
>> <Screenshot 2026-05-29 at 6.30.14 AM.png><Screenshot 2026-05-29 at 6.30.45 AM.png>
>> 
>> ====================================
>> 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/
>> 
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