[chimerax-users] Loading AlphaFold output

[Elaine Meng]

Right, and you can even omit the "range" part because the color-value mapping is included in the palette, as described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring>

color bfactor palette alphafold

You could use a different palette in the color command, if you like.

In case you didn't know already: ChimeraX also searches/fetches from the AlphaFold Database of already-made models and applies this coloring.  Just an alternative if you were going to that database, downloading files yourself, then opening them in ChimeraX.  The search/fetch can be done with either the AlphaFold tool or the alphafold command.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html>

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


> On Feb 10, 2022, at 3:34 AM, Tristan Croll via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Daniel,
> 
> The pLDDT scores are saved in the B-factor column in the PDB files returned by AlphaFold. If you open them, you should be able to do "color bfactor palette alphafold range 0,100".
> 
> Best,
> 
> Tristan
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Daniel Trejo Banos via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> Sent: 10 February 2022 10:46
> To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: [chimerax-users] Loading AlphaFold output
>  
> Hello everyone,
> 
> I have the results from some AlphaFold runs, is there a way to open them with ChimeraX, so I can see the plDDT, without needing to run Alphafold from within ChimeraX?
> 
> Thank you and best regards