To show multiple sets of AlphaFold predicted aligned error between different chains you can use the "replace false" option alphafold contacts /A to /B alphafold contacts /C to /D replace false Another way to do it is to give each set of contacts a different name alphafold contacts /A to /B name AB_PAE alphafold contacts /C to /D name CD_PAE These names will be the names of the models that contain the colored lines that show the PAE contacts. Those models are under the AlphaFold model. These options are descrtbed in the ChimeraX alphafold contacts documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contact... Tom 
On Apr 27, 2024, at 5:44 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I think
alphafold contacts /A,B to /C
There is probably a way to do other combinations like A to B and C to D but I don't have a computer to test this weekend.
Tom
On Apr 27, 2024, at 2:53 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Greetings,
Was wondering if it’s possible to simultaneously display PAE contact lines for more than two peptides? For example, all contacts between A and B AND B and C etc.
Couldn’t find anything on it and have already made the obvious attempts such as "alphafold contacts /A to /C AND /B to /C distance 6”
Thanks!
David
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