The "contacts" or "clashes" command gives all-by-all distances (and VDW overlaps) between two sets of atoms.  You can write all the info to a file or to a log.  It does not automatically only give you the shortest distance, but it sorts the output so that the shortest is first.

For example (these structures are nonphysically on top of each other, but work for illustrating the commands):

open 1zik

open 1gcn

contacts #1 restrict #2 distanceOnly 5 log true

...shows in the log all the pairwise distances between the two sets of atoms that are within 5 angstroms, with the shortest distance first.

  

See measurements:

<https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html>

Clashes or contacts command:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

For scripting, instead of "log" you could use "saveFile" to get an output file for each structure pair.  What you get in the Log or file looks like this:

I hope this helps,

Elaine

On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all, 
I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX?
Thanks a lot in advance, 
Best,
Matthias