Indeed ChimeraX AlphaFold plddt coloring is a bit different from the AlphaFold database color scheme. For one ChimeraX uses 5 colors while AFDB uses 4 different colors. I agree to best match the overall appearance of AFDB the ChimeraX color scheme should probably put light blue at 80 instead of 90. I'm not sure why AFDB decided to apply single colors to large range of plddt limiting the nuances shown -- maybe it was easier to render in their web pages. At any rate it seems like a poor choice. So I'm not inclined to blindly try to match their color scheme (I made our ChimeraX color scheme). I think the ChimeraX color ranges give a much better indication of the scores including placing light blue at 90 and yellow at 70 so that you get good discrimination of values in the medium confidence region of 70-90.

Thanks for pointing out the slightly more yellow appearance of the ChimeraX plddt coloring. As you showed in your images you know how to make the less useful AFDB color scheme in ChimeraX if that is what you would like to include in your publications. I agree it is unfortunate that a single color scheme was not established at the start that best showed the plddt values. For publications I think a color key would be needed in any case to document what the colors mean rather than relying on uncertain conventions.

On May 15, 2024, at 9:21 AM, Agnieszka Obarska via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Elaine,

Yes, I agree that color by gradient is more informative but I think the gradient you have is not consistent with AlphaFold coloring.
When you think about AF coloring, yellow means below 70, so LOW according to AF, while in ChimeraX you can have 80 still yellowish, while it should be already light blue.
I think you would need to adjust the boundaries, such that at 70 it becomes blueish.
See image attached.

Best,
Agnieszka

<PastedGraphic-2.tiff>

On 15. May 2024, at 17:51, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Agnieska,
The coloring is the same at the boundaries (90,70, ...) but the difference is that the ChimeraX coloring is continuously shaded based on value whereas the one on the right just gives exactly the same color for the whole range (e.g. 50-70 is all yellow on the right, whereas in ChimeraX it is gradually shaded orange to yellow). The continuous shading gives more information on the exact value so that 49 is similar to 51 instead of a totally different color as on the right.
I hope this makes sense,
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 15, 2024, at 6:15 AM, Agnieszka Obarska via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I’ve just would like to let you know that we’ve noticed recently that alphafold palette in ChimeraX is not consistent with original AlphaFold coloring.
Please see the slide attached.
On the left there is a model colored by the “color bfactor pal alpha” command in ChimeraX
while on the right there is the same model colored according to AlphaFold coloring scheme.

Best,
Agnieszka

<PastedGraphic-1.tiff>

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