Hello Shawn, Looks like you are (1) missing the "restrict" keyword before the second group of atoms, and (2) using a nonexistent keyword "cutoff" which should instead be "distanceOnly." So instead it your command should be something like: contacts (#1/A | #1/B) restrict #1/C distanceOnly 4.0 saveFile contacts_ABC.txt The command and its options are described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> Also optionally you could put a whole pathname (including directory location) instead of just the filename if you want to put it somewhere other than your current working directory. One way to figure out commands is to start out using the GUI tool, which will generate the corresponding command and show it in the Log. Be aware that you have specified the whole chains which might include waters and stuff like that with the same chain IDs. If you wanted only protein atoms vs. nucleic acid atoms, and not waters, could be something like contacts protein restrict nucleic [...etc... other options] See specifiers such as "protein" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> 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 Sep 22, 2024, at 7:08 PM, Shawn Rumrill via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello ChimeraX Users,

I would like to analyze protein/nucleic acid complexes from the PDB by comparing the protein/nucleic acid chain interactions in each. Ideally I would like to know: • The number of interactions < 4.0 A that the nucleic acid makes with neighboring protein chains • If possible, output a list of those interactions to a text file • Even better, generate a 2D interaction map I tried contacts (#1/A | #1/B) #1/C cutoff 4.0 saveFile contacts_ABC.txt for the first bullet (with a few permutations when it didn't work), but received the error "expected a keyword."

Has anyone successfully determined something like this in ChimeraX?

Thanks for the input!

Shawn R Rutgers University

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