[chimerax-users] AlphaFold colouring of models predicted outside of ChimeraX

[Elaine Meng]

Hi James,
I don't have such a structure handy but I believe so, assuming that the confidence values are written to the bfactor field of the resulting PDB file.  In that case you can use command:

color bfactor palette alphafold

...as mentioned here (and there is also an example command for drawing a color key if you want that too)
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring>

...or if you have other models open and you only wanted to apply this coloring to a specific one, say #1:

color bfactor #1 palette alphafold

See also "color bfactor"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#bfactor>
...and palette options
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 10, 2022, at 2:13 PM, James Hodgkinson-Bean via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi
> Recently I’ve been performing batch AlphaFold predictions on colab. I was wondering if it’s possible to apply the confidence colour pallete to these structures in chimera if they have not been predicted in ChimeraX directly?
> Thanks, 
> James.