There is not a command to select all residues within a specified distance of some residue in another chain. The "interfaces" command in ChimeraX shows a graph of which chains contact which other chains and clicking on that graph shows a menu with an entry "Select All Contact Residues". Unfortunately it does not have an equivalent command and does not let you specify a distance cutoff. Below is an image where I opened PDB 9hux (command "open 9hux"), pressed the Interfaces button on the Molecule Display toolbar (or equivalently command "interfaces #1"), then used the menu entry.

Also there is no way to show a PAE plot of just interface residues. Such a plot would still show PAE values between residues belonging to different interfaces since it shows an all residue against all residue heatmap. Maybe you'd be interested in showing PAE contacts at interfaces (again command only handles one pair of chains at a time).

Usually one looks at molecule interfaces one at a time so that is what the ChimeraX commands are geared towards. I'm not sure what the use case is for handling all interfaces in one command, maybe you could clarify that.

On Jan 14, 2026, at 7:49 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I am analyzing a complex made with Alphafold with 7 protein subunits and am trying to find all the interchain contacts.
The zone command is useful
select zone #1/A 3.6 #1 residues true,
but how can I make it find all interchain contacts at once, rather than one chain at a time?
What is a command to display sidechains of all residues in the zone?
I really like the PAE plot that ChimeraX makes from alphafold predictions. Could I make a similar plot of the contact residues made with the zone command?

- Tim
Timothy A. Springer, Ph.D.
Latham Family Professor, Harvard Medical School and Boston Children's Hospital
Founder, Institute for Protein Innovation
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