Sorry Agnieszka, I guess you already had this solution in your earlier message, I just failed to see it! I can only hope that others on this list might benefit from my additional explanation of how to get discrete-ish coloring. Elaine
On May 15, 2024, at 11:22 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Agnieszka, You can achieve basically the same as the discrete coloring with the "palette" option by putting each of the colors twice, at each end of their ranges. There might be a tiny difference right at the boundaries but should not be discernable. I understand if you want them to look the same as the original, I was just trying to explain the difference.
Also, I thought the orange and light blue were the same but now I can see they're a bit different in the AlphaFold database coloring. If the colors blue, lightskyblue, yellow, and darkorange are similar enough to the database coloring, then you could use this palette:
palette 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
So "alphafold fetch ldlr_human" gives this
<af1.png> and then "color bfactor palette 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue" gives this, much more like what you wanted: <af2.png> You could also use the exact hex codes for the AlphaFold database coloring, if you know them, instead of these color names.
I hope this helps, Elaine
On May 15, 2024, at 9:46 AM, Agnieszka Obarska via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.
<PastedGraphic-3.tiff>
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> 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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