The ChimeraX "alphafold contacts" command should work with Boltz predictions. It works fine for me (image below). Do you get an error message? Maybe you don't have the PAE output. Can you show the PAE plot in ChimeraX?

On Apr 21, 2026, at 11:06 AM, Nathan Davis via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster.

Thank you!
Nathan
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