Hi Khawar,

Your structure has pLLDT values near 70. The color scale used by Google and EBI has pLDDT 50-70 "Low confidence" yellow and pLDDT 70-90 "High confidence" cyan as documented here

https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/evaluating-alphafolds-predicted-structures-using-confidence-scores/pae-a-measure-of-global-confidence-in-alphafold-predictions/

The trouble is if your pLDDT values are slightly above 70 then the structure looks blue (high confidence), and if they are slightly below 70 it looks yellow (low confidence). That makes this discrete coloring misleading. That is why ChimeraX uses a continuous coloring, so you get a better idea of the actual pLDDT confidence scores. Your structure is one of these borderline cases and coloring it all in shades of blue is misleading and ChimeraX coloring is giving you a less misleading picture of the scores, they are somewhere between low and high confidence. The ChimeraX pLDDT coloring is continuously interpolated with 70 (midway between low and high) being yellow. See the "alphafold" palette in the ChimeraX docs

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/palettes.html

100

Tom

On Sep 2, 2024, at 9:45 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Dr. Khawar Sohail Siddiqui,
Please see this previous discussion thread (several messages) about how the coloring in ChimeraX is different:

<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/POWSVJQITEEIXUMM2TPVFINYPV7FD3T5/#POWSVJQITEEIXUMM2TPVFINYPV7FD3T5>

See especially Tom's explanation, which is about the 5th message in that thread
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/NZD4NHYFVXFNME2LDJTL6X5CL4V635HL/>

...and the tiff attachment in the first message, which I believe shows an image of the command needed to get the same coloring:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/POWSVJQITEEIXUMM2TPVFINYPV7FD3T5/attachment/4/PastedGraphic-1.tiff>

Regards,
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 Sep 1, 2024, at 6:27 PM, Khawar Siddiqui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Tom and ChimeraX team
I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence).

Thanks again for the help.
sohail
Dr Khawar Sohail Siddiqui,<image.png>
<image.png><Outlook-wfck3dy1.jpg>hoo.com

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