Hi Haleh, You will need to spend some time experimenting with using different options and learning how atoms are described by name, residue number, and chain ID. You would need to decide: - whether you want to measure distances between all pairs of atoms or only use certain atoms, like only one atom per residue, such as the CA (alpha-carbon). Of course that would make the results simpler to view, but it may not be what you want. - whether you want all distances, or only the ones that are within some distance range All of the options are described in the help, e.g. if you click the Help button on the tool it will show the help for that tool. You can also view the copies of the help pages on our website, e.g. <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> Probably you will run several different calculations and save the results from each rather than trying to get all the measurements in the same single calculation. The tools actually run by creating commands, and the commands have all the same options as shown in the tools. Here are some example commands assuming you want all pairwise atomic distances <100 Angstroms between chains A and B and within chain A, example structure 1zik, and send results to the Log. open 1zik show contacts /A restrict /B distanceOnly 100 log true contacts /A restrict /A distanceOnly 100 log true There are lots of other options to the contacts command (like saving to a file instead of showing in the Log), please see the help shown with command "help contacts" or see the copy at our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> Then the Log shows a whole bunch of results like [...] /A GLU 22 OE1 /B VAL 23 CG1 5.238 /A HOH 65 O /B VAL 23 CG2 5.238 [...] meaning that chain A glutamine 22 atom OE1 distance to chain B valine 23 atom CG1 is 5.238 Angstroms, chain A water 65 atom O distance to chain B valine 23 atom CG2 is also 5.238 Angstroms, etc. If you don't want water included you could delete it first, or you could modify the command to be more specific, e.g. contacts (/A & protein) restrict (/B & protein) distanceOnly 100 log true ...or you could use only CA atoms for the measurements, e.g. contacts /A@CA restrict /B@CA distanceOnly 100 log true How to specify atoms in the command line also has a help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 5, 2023, at 10:03 AM, Haleh Shahbazi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am using ChimeraX under “version 1.6rc202304182023 (2023-04-18)” and contacting you regarding contacts and distances tools

I am working on analyzing biological assembly PDB files including two chains. Simply, I want to identify / calculate distance between residues within each chain and across two chains separately – In the other word, display interchain and intrachain residue distance.

To get that done, I’ve already explored “Distances” and “Contacts” tools under “Structure Analysis” but I have difficulty with identifying interchain residue distances and also understanding all those features / options provided.

Thanks in advance for your support!

Haleh