Hi,

I was preparing a figure and we opened the same AF2 structure both in chimerax and pymol, and colored according to pLDDT. We expected something quite similar, but some of the residues were not colored the same (left chimerax, middle official AF2 coloring, right pymol)

image.pngimage.pngimage.png

These are the corresponding CA atoms from the file, there are several that are above 70.
ATOM      2  CA  MET B   1      26.541 -48.983 -34.346  1.00 49.18           C  
ATOM     10  CA  ALA B   2      23.562 -47.870 -36.454  1.00 60.35           C  
ATOM     15  CA  ASP B   3      25.250 -49.497 -39.528  1.00 68.46           C  
ATOM     23  CA  ALA B   4      25.752 -52.804 -37.641  1.00 69.86           C  
ATOM     28  CA  TRP B   5      22.024 -53.025 -36.747  1.00 68.46           C  
ATOM     42  CA  GLU B   6      21.036 -52.590 -40.351  1.00 71.02           C  
ATOM     51  CA  GLU B   7      23.249 -55.575 -41.294  1.00 76.21           C  
ATOM     60  CA  ILE B   8      21.578 -57.739 -38.645  1.00 74.81           C  
ATOM     68  CA  ARG B   9      18.177 -56.653 -39.803  1.00 70.07           C  
ATOM     79  CA  ARG B  10      19.226 -57.507 -43.334  1.00 74.00           C  
ATOM     90  CA  LEU B  11      20.598 -60.932 -42.264  1.00 74.36           C  
ATOM     98  CA  ALA B  12      17.459 -61.553 -40.194  1.00 69.47           C  
ATOM    103  CA  ALA B  13      15.384 -60.625 -43.205  1.00 69.30           C  
ATOM    108  CA  ASP B  14      17.563 -62.981 -45.430  1.00 70.53           C  
ATOM    116  CA  PHE B  15      17.273 -65.769 -42.888  1.00 71.78           C  
ATOM    127  CA  GLN B  16      13.568 -65.190 -42.812  1.00 64.74           C  
ATOM    136  CA  ARG B  17      13.352 -65.300 -46.586  1.00 65.36           C  
ATOM    147  CA  ALA B  18      15.491 -68.455 -46.645  1.00 64.05           C  
ATOM    152  CA  GLN B  19      13.261 -70.000 -44.028  1.00 60.46           C  
ATOM    161  CA  PHE B  20      10.117 -69.389 -46.168  1.00 62.26           C  
ATOM    172  CA  ALA B  21      11.642 -70.083 -49.654  1.00 56.65           C  
ATOM    177  CA  GLU B  22      11.244 -73.693 -49.767  1.00 53.68           C  
ATOM    186  CA  ALA B  23       7.622 -74.493 -50.250  1.00 56.47           C

After looking at again the docs, I understood that chimerax has a different coloring
image.png
AFDB
image.png

Can you maybe change this? Most people are probably used to the database's coloring, and could interpret it wrong (like me... It drove me crazy when showing somebody else, why the plddt-s do not match to what I have shown before, just in a figure by chimerax).
I understand that in the documentation the colorbar is according to the coloring that chimerax does, but it would be better if it was according to the standard.

Thank you so much!

Kind regards,
Julia Varga