On the AlphaFold3 models it is more striking. Many models are colored blue on AF3 server while they are yellow in ChimeraX. See image attached.
On 15. May 2024, at 18:21, Agnieszka Obarska <Agnieszka.Obarska-Kosinska@biophys.mpg.de> 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 <mailto: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 <mailto: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>