To summarize for users, the ChimeraX alphafold coloring to show pLDDT values is continuously shaded, whereas the coloring shown at the AlphaFold database is similar but discontinuous, and differences may be evident. The reasoning behind the ChimeraX alphafold coloring palette is that it may be more informative about the specific values. However, it may be confusing that it looks similar, yet not the same, as the AlphaFold database pLDDT coloring. A few months ago, Abnieszka Obarska (thank you!) helpfully provided a command to match the coloring shown at the AlphaFold database. Since it was in an image, however, it is not convenient for cut and paste, so I have copied it here: color bfactor palette 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 Although I did not check if the color hex codes exactly match the AlphaFold database colors, I tried it on a couple of examples at least to my eye, it reproduced the coloring of structures shown at the database. I hope this helps, 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