Use/offer official AlphaFold color palette

[419434238@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
In alphafold2 or alphafold3 official website, there are four different color to show the plDDT score, as following: 
Very high (plDDT > 90) 
Confident (90 > plDDT > 70) 
Low (70 > plDDT > 50) 
Very low (plDDT < 50) 
  
  
But in chimeraX, there are five different color to show the plDDT score, which resulted in a different color output compared to alphafold2 or alphafold3 official website. 
  
It is about:   toolsàstructure predictionàalphafold error plot 
The command is:  color bfactor palette alphafold 
  
  
So I think that It would be better if alphafold palette in chimeraX was changed to be the same as what is displayed on the official website. 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open F:\chrome_download\AF-Q8W3K0-F1-model_v4.pdb format pdb

AF-Q8W3K0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for probable disease resistance protein
AT1G58602 (Q8W3K0) [more info...]  
  
Chain information for AF-Q8W3K0-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | probable disease resistance protein AT1G58602 | DRL9_ARATH 1-1138  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> F:\\\chrome_download\\\AF-Q8W3K0-F1-predicted_aligned_error_v4.json

> color bfactor #1 palette alphafold

9258 atoms, 1138 residues, atom bfactor range 23.3 to 98.2  

> set bgColor white




OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: TIMI
Model: RedmiBook Pro 15
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,952,647,680
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz
OSLanguage: zh-CN

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File attachment: 屏幕截图 2024-07-20 233927.png

屏幕截图 2024-07-20 233927.png​

[419434238@…]

Added by email2trac

[Eric Pettersen]

Reported by Weiwei Rao

[Tom Goddard]

This was discussed on the ChimeraX mailing list in May 2024

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

The standard AlphaFold color scheme goes from "low confidence" at 69 to "confident" at 71 producing absurd results where a small difference in pLDDT scores produces a totally different appearance (yellow vs blue). ChimeraX instead uses a continuous coloring so it does not produce misleading depictions. We will not be promoting the bad AlphaFold coloring scheme in ChimeraX. It is unfortunate that Google and EBI chose that poor color scheme.