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@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@cgl.ucsf.edu on behalf of Daniel Trejo Banos via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: 10 February 2022 10:46 To: chimerax-users@cgl.ucsf.edu chimerax-users@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