Hi Tim, There are lots of different approaches to looking at contacts (e.g. also see "contacts" and "interfaces" commands, or menu: Select... Contacts) but if you prefer "select zone," that's one way. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html> If you want to define the zone with more than one chain, simply specify more than one chain in the "select zone" command, e.g. select zone #1/A,B,D 3.6 #1 residues true see command-line atom specification <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> However, that will just define /A,B,D as one lump and only select parts of chain /C in the case of 4hhb (chains A-D). If you wanted the contacts of every chain with every other chain, it may require require using the command, or any of the other approaches mentioned above, multiple times. There are many ways to show the contact/interface residues using the approaches mentioned above, but if you already selected the zone, you can just show the atoms in that current selection, or do other stuff to it, e.g. show sel color sel magenta label sel However, I don't recall any way to plot a contact map, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/