Hi Vivian, I don't know what information you are looking at, it seems a mixture of Chimera and ChimeraX. Make sure you are looking at the help for ChimeraX only, since the commands and options are frequently different between the two programs. It sounds like you were able to run the Contacts graphical interface, which would show in the Log the successful command, and you can click the link on the command name to see the full help page, or view the same thing on our website here. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> In ChimeraX, there is no "findclash" command. The command is "contacts" or "clashes" as shown in the help link above; the command does not have an "atoms" keyword, nor does it have a "distanceCutoff" option (instead it is "distanceOnly" and you would only use that if you want to ignore the different VDW radii of different atom types). Are you trying to find all the contacts inside of /C,D collectively, or only the ones between /C and /D? I'm guessing it is the second one. In that case maybe something like the following, although you may want additional options: contacts /C restrict /D reveal true log true If you really want to see all the contacts inside of /C,D collectively, something like: contacts /C,D reveal true log true Please see the help page for all the options and what they mean. 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 Oct 10, 2025, at 10:38 AM, wwvivian.wang--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, this is my first time using ChimeraX-1.10.1 and I ran into a little bit of trouble with syntax errors in this version.\ I opened a pdb file that contains two chains of proteins that I'm interested in - Chain A and B. I then renamed and coloured them to Chain C and D for clarity. In the Contacts window, I made the following changes: Find pairs of atoms with: ✅ VDW overlap ≥ –0.4 Å Limit by selection: ✅ with at least one end selected Ignore interactions between atoms 4 or fewer bonds apart: ✅ Ignore interactions between residues <5 apart: ✅ Include intermodel: ✅ Include intramodel: ❌ (uncheck it) Include intramolecule: ❌ (uncheck it) Ignore hidden models: ✅ Display as pseudobonds: ✅ (keep green, radius 0.075, dashes 6) Write info to: Log ✅ Then click Apply

I then selected the atomic model #1 (Chain C+D) and deselected surface models #1.1 (Chain C) and #1.2 (Chain D) and ran the Contacts Command: "contacts atoms #1/C #1/D makePseudobonds true distanceCutoff 4.0 log true" but the software returns "Expected a keyword" argument and highlighted "distanceCutoff 4.0 log true" in red.

Alternatively, I also tried "findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true" but again it fails to output contact coordinates between the two chains and returns the following: "Unknown command: findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true".

I would appreciate your help in resolving this error for me.

Thanks, Vivian