You can use Python in ChimeraX to find the shortest distance.  Here is some example code closest.py to do that.

https://rbvi.github.io/chimerax-recipes/closest/closest.html

If you open that Python code in ChimeraX it registers a command "closest"

open 7LUP
closest /A to /B maxDist 100

> Minimum distance 2.27 between /A LYS 45 NZ and /B ASP 522 OD1

  Tom


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
 
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