color bfactor by alphafold palette
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
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>
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
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>
Hi Agnieszka, 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. Tom
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 <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>
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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>
Hi Tom, Thanks! One could argue what is more informative but since it is called alphafold palette we blindly expected it to agree with AF colouring scheme. So we thought that yellow means LOW score (below 70) while it is not the case, 80 (HIGH score) can be still yellow. It looks especially weird for AlphaFold3 models, where you have more scores 70-90, rather than 90-100, and regions of HIGH score according to AF, and it is blue on their server, are yellow in ChimeraX. See another example below. We will of course switch to AlphaFold coloring now but I just wanted to let you know. Cheers, Agnieszka
On 15. May 2024, at 18:52, Tom Goddard <goddard@sonic.net> wrote:
Hi Agnieszka,
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.
Tom
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 <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>
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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 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: 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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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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Hi Agnieszka, I don't think the AlphaFold pLDDT coloring is used at all in the original AlphaFold paper. I'm not sure if the EBI AlphaFold Database made it up. Here is an EBI AlphaFold database web page describing it https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/e... Their ranges are blue "Very high (pLDDT > 90", cyan "High (90 > pLDDT > 70)", yellow orange "Low (70 > pLDDT > 50)", orange red "Very low (pLDDT < 50)".  This is somewhat coarse as it goes directly from "high" confidence above 70 to "low" confidence below 70. It seems they think 70 is medium confidence, that is yellow in ChimeraX. The 80 value which you might call medium-high is a greenish color in ChimeraX, not yellow. Here is the ChimeraX pLDDT colors as rendered by ChimeraX  So ChimeraX gives a greenish color for the medium high 80 value and yellow ("caution") for the 70 value. Of course you can use the EBI AlphaFold database coloring that makes 70-90 all light blue and show their scale that names it "High confidence", even though <70 is also considered "Low confidence" on the same scale. It all depends on what you want to convey in your publication figure. If you want to be optimistic and suggest the AlphaFold model is more confident, then make pLDDT in the 70s light blue. But in ChimeraX I decided to add more shades so you can really see that 70 is medium (yellow) and 80 is medium high (green), and 90-100 is high (light blue to blue). Tom
On May 15, 2024, at 11:02 AM, Agnieszka Obarska <Agnieszka.Obarska-Kosinska@biophys.mpg.de> wrote:
Hi Tom,
Thanks! One could argue what is more informative but since it is called alphafold palette we blindly expected it to agree with AF colouring scheme. So we thought that yellow means LOW score (below 70) while it is not the case, 80 (HIGH score) can be still yellow. It looks especially weird for AlphaFold3 models, where you have more scores 70-90, rather than 90-100, and regions of HIGH score according to AF, and it is blue on their server, are yellow in ChimeraX. See another example below. We will of course switch to AlphaFold coloring now but I just wanted to let you know.
Cheers, Agnieszka
<PastedGraphic-4.tiff>
On 15. May 2024, at 18:52, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Agnieszka,
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.
Tom
On May 15, 2024, at 9:21 AM, Agnieszka Obarska via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto: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 <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>
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They did this database in collaboration with Deepmind so they probably agreed on the coloring and the interpretation of the scores. Deepmind people also use this coloring scheme in their AlphaFold 3 server and tutorials: https://www.youtube.com/watch?v=UqeQfRDA8Yk <https://www.youtube.com/watch?v=UqeQfRDA8Yk> (e.g. min. 9) So I would expect that people think about AF pLDDT scores in these colors, where e.g. light blue(or cyan) means above 70. It is just a matter of consistency. Of course if you read carefully the alphafold palette in ChimeraX you can see that yellow is for 70, so you can expect -60-80 to be yellowish. If ChimeraX had come up with a completely different palette people would read and learn what each color means, but if it was meant to look like alphafold coloring scheme, but it is not exactly like it, it is misleading, at least to me. Cheers, Agnieszka
On 15. May 2024, at 20:42, Tom Goddard <goddard@sonic.net> wrote:
Hi Agnieszka,
I don't think the AlphaFold pLDDT coloring is used at all in the original AlphaFold paper. I'm not sure if the EBI AlphaFold Database made it up. Here is an EBI AlphaFold database web page describing it
https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/e... <https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/e...>
Their ranges are blue "Very high (pLDDT > 90", cyan "High (90 > pLDDT > 70)", yellow orange "Low (70 > pLDDT > 50)", orange red "Very low (pLDDT < 50)".
<AFDB_plddt_colors.png> This is somewhat coarse as it goes directly from "high" confidence above 70 to "low" confidence below 70. It seems they think 70 is medium confidence, that is yellow in ChimeraX. The 80 value which you might call medium-high is a greenish color in ChimeraX, not yellow. Here is the ChimeraX pLDDT colors as rendered by ChimeraX <chimerax_plddt_colors.png>
So ChimeraX gives a greenish color for the medium high 80 value and yellow ("caution") for the 70 value.
Of course you can use the EBI AlphaFold database coloring that makes 70-90 all light blue and show their scale that names it "High confidence", even though <70 is also considered "Low confidence" on the same scale. It all depends on what you want to convey in your publication figure. If you want to be optimistic and suggest the AlphaFold model is more confident, then make pLDDT in the 70s light blue. But in ChimeraX I decided to add more shades so you can really see that 70 is medium (yellow) and 80 is medium high (green), and 90-100 is high (light blue to blue).
Tom
On May 15, 2024, at 11:02 AM, Agnieszka Obarska <Agnieszka.Obarska-Kosinska@biophys.mpg.de> wrote:
Hi Tom,
Thanks! One could argue what is more informative but since it is called alphafold palette we blindly expected it to agree with AF colouring scheme. So we thought that yellow means LOW score (below 70) while it is not the case, 80 (HIGH score) can be still yellow. It looks especially weird for AlphaFold3 models, where you have more scores 70-90, rather than 90-100, and regions of HIGH score according to AF, and it is blue on their server, are yellow in ChimeraX. See another example below. We will of course switch to AlphaFold coloring now but I just wanted to let you know.
Cheers, Agnieszka
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On 15. May 2024, at 18:52, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Agnieszka,
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.
Tom
On May 15, 2024, at 9:21 AM, Agnieszka Obarska via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto: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
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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
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Here's the command with AF color hex codes from the AF3 server website color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff key true Now it's very close except I'm noticing that some small regions colored very high confidence by AF3 look just confident in Chimerax. Digging into it a bit, it seems the difference is that AF3 colors a residue by either the max bfactor of its atoms or maybe averages just the main-chain atoms. ChimeraX averages all atoms of a residue to color the cartoon, so a couple of C-delta atoms in the 80's is sometimes enough to bring the whole residue below 90. I'm guessing there's not way to match that AF behavior
Hi Julian, My understanding is that for the standard amino acid residues, namely the ones that can be shown as cartoon or ribbon segments, AF only assigns a single pLDDT value per residue. The output structure file has exactly the same pLDDT (bfactor) for each atom of that residue. Maybe it is different for AF3, but things like ligands don't have mainchain/sidechain, at least in ChimeraX. One way to take a look at this is to use color bfactor on all atoms, e.g. sticks, instead of the cartoon representation, or save a PDB file and look in the bfactor column. 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
On Nov 8, 2024, at 7:22 AM, julian--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Here's the command with AF color hex codes from the AF3 server website
color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff key true
Now it's very close except I'm noticing that some small regions colored very high confidence by AF3 look just confident in Chimerax. Digging into it a bit, it seems the difference is that AF3 colors a residue by either the max bfactor of its atoms or maybe averages just the main-chain atoms. ChimeraX averages all atoms of a residue to color the cartoon, so a couple of C-delta atoms in the 80's is sometimes enough to bring the whole residue below 90. I'm guessing there's not way to match that AF behavior
AF3 does populate bfactor for each atom. So at least for proteins, doing: delete sideonly color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff reproduces a cartoon that's displayed on the AF3 server exactly as far as I can see
In that case, you can do that (delete the sidechains) to get your desired coloring behavior! You can have an additional copy open for when you need the sidechain atoms for display or other analyses. Elaine
On Nov 8, 2024, at 7:50 AM, julian--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
AF3 does populate bfactor for each atom. So at least for proteins, doing:
delete sideonly color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff
reproduces a cartoon that's displayed on the AF3 server exactly as far as I can see _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Julian, AlphaFold 3 does assign different pLDDT values to each atom of standard residues. This is different from AlphaFold 2 where the exact same pLDDT values was assigned to every atom of a residue. I don't know what web site you are using to look at the pLDDT coloring and I don't know how that web site combines the pLDDT values for the atoms of a residue. You are correct that ChimeraX averages the pLDDT values of all atoms in the residue (backbone and side chain) when coloring ribbons by bfactor. As we discussed on this mailing list at length the AlphaFold coloring in discrete bands 50-70, 70-90 and 90-100 can create erratic and misleading coloring. if you have pLDDT values near 70 then you either get yellow, described as low confidence for slightly less than 70, or light blue described as high confidence for slightly more than 70. Kind of absurd to go from low to high confidence when values cross pLDDT 70. So ChimeraX instead smoothly interpolates colors for the pLDDT colors if you use "color bfactor palette alphafold". Unfortunately some researchers prefer to use the misleading discrete coloring. Tom
On Nov 8, 2024, at 7:22 AM, julian--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Here's the command with AF color hex codes from the AF3 server website
color bfactor palette 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff key true
Now it's very close except I'm noticing that some small regions colored very high confidence by AF3 look just confident in Chimerax. Digging into it a bit, it seems the difference is that AF3 colors a residue by either the max bfactor of its atoms or maybe averages just the main-chain atoms. ChimeraX averages all atoms of a residue to color the cartoon, so a couple of C-delta atoms in the 80's is sometimes enough to bring the whole residue below 90. I'm guessing there's not way to match that AF behavior _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
I agree it's not a great coloring scheme but the command can still be useful if someone wants to put an image side-by-side with a screenshot from AF server. Also, this made me realize how a few distal side-chain atoms can bring down a whole residue's confidence down in an averaged cartoon, where most users would probably care more about main-chain
participants (5)
-
Agnieszka Obarska -
Elaine Meng -
julian＠hms.harvard.edu -
Tom Goddard -
Xiaohua Hu